Aire autoimmune regulator [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Aireprovided by MGI
Official Full Name: autoimmune regulatorprovided by MGI
Primary source: MGI:MGI:1338803
See related: Ensembl:ENSMUSG00000000731 AllianceGenome:MGI:1338803
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary: Enables identical protein binding activity. Involved in immune system development; positive regulation of chemokine production; and regulation of thymocyte migration. Acts upstream of or within humoral immune response; negative thymic T cell selection; and positive regulation of transcription by RNA polymerase II. Located in cytoplasm; germ cell nucleus; and nuclear body. Is expressed in several structures, including alimentary system; genitourinary system; hemolymphoid system; nervous system; and sensory organ. Used to study Guillain-Barre syndrome; Sjogren's syndrome; and autoimmune polyendocrine syndrome type 1. Human ortholog(s) of this gene implicated in autoimmune polyendocrine syndrome and autoimmune polyendocrine syndrome type 1. Orthologous to human AIRE (autoimmune regulator). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in thymus adult (RPKM 20.4), spleen adult (RPKM 1.4) and 1 other tissue See more
Orthologs: human all
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Genomic context

Location:: 10 C1; 10 39.72 cM

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	10	NC_000076.7 (77865856..77879444, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	10	NC_000076.6 (78030022..78043610, complement)

Chromosome 10 - NC_000076.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Aire mediates tolerance to insulin through thymic trimming of high-affinity T cell clones.
Title: Aire mediates tolerance to insulin through thymic trimming of high-affinity T cell clones.
AIRE relies on Z-DNA to flag gene targets for thymic T cell tolerization.
Title: AIRE relies on Z-DNA to flag gene targets for thymic T cell tolerization.
Tracking the role of Aire in immune tolerance to the eye with a TCR transgenic mouse model.
Title: Tracking the role of Aire in immune tolerance to the eye with a TCR transgenic mouse model.
A partial form of AIRE deficiency underlies a mild form of autoimmune polyendocrine syndrome type 1.
Title: A partial form of AIRE deficiency underlies a mild form of autoimmune polyendocrine syndrome type 1.
Autoimmune regulator (Aire) deficiency results in reduced memory CD8[+] T cells after Listeria monocytogenes infection in a murine model.
Title: Autoimmune regulator (Aire) deficiency results in reduced memory CD8(+) T cells after Listeria monocytogenes infection in a murine model.
Aire drives steroid hormone biosynthesis by medullary thymic epithelial cells.
Title: Aire drives steroid hormone biosynthesis by medullary thymic epithelial cells.
Cutting Edge: Aire Is a Coactivator of the Vitamin D Receptor.
Title: Cutting Edge: Aire Is a Coactivator of the Vitamin D Receptor.
AIRE Deficiency Leads to the Development of Alopecia Areata-Like Lesions in Mice.
Title: AIRE Deficiency Leads to the Development of Alopecia Areata‒Like Lesions in Mice.
CTLA-4 on thymic epithelial cells complements Aire for T cell central tolerance.
Title: CTLA-4 on thymic epithelial cells complements Aire for T cell central tolerance.
PD-1 cooperates with AIRE-mediated tolerance to prevent lethal autoimmune disease.
Title: PD-1 cooperates with AIRE-mediated tolerance to prevent lethal autoimmune disease.

Submit: New GeneRIF Correction See all GeneRIFs (161)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (4) 1 citation
Targeted (17) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Aire (e-PCR), detects polymorphism
- UniSTS:141058

Aire (e-PCR), detects polymorphism
- UniSTS:530812

Aire (e-PCR), detects polymorphism
- UniSTS:228479

NoName (e-PCR)
- UniSTS:489115

Aire (e-PCR), detects polymorphism
- UniSTS:536516

Aire (e-PCR), detects polymorphism
- UniSTS:548051

Aire (e-PCR), detects polymorphism
- UniSTS:259036

D10Jhu43 (e-PCR), detects polymorphism
- UniSTS:158699

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	ISO Inferred from Sequence Orthology more info
enables histone binding	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables translation regulator activity	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in central tolerance induction to self antigen	IBA Inferred from Biological aspect of Ancestor more info
involved_in central tolerance induction to self antigen	ISO Inferred from Sequence Orthology more info
involved_in central tolerance induction to self antigen	ISS Inferred from Sequence or Structural Similarity more info
involved_in humoral immune response	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within humoral immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative thymic T cell selection	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative thymic T cell selection	IGI Inferred from Genetic Interaction more info	PubMed
involved_in peripheral T cell tolerance induction	IBA Inferred from Biological aspect of Ancestor more info
involved_in peripheral T cell tolerance induction	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of chemokine production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of thymocyte migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of thymocyte migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of translation	IEA Inferred from Electronic Annotation more info
involved_in thymus epithelium morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in thymus epithelium morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in female germ cell nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in intracellular anatomical structure	IDA Inferred from Direct Assay more info	PubMed
located_in male germ cell nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear body	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: autoimmune regulator

Names: APECED protein homolog; autoimmune polyendocrinopathy candidiasis ectodermal dystrophy protein homolog; autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy); autoimmune regulator AIRE1a

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001271549.1 → NP_001258478.1 autoimmune regulator isoform 2

See identical proteins and their annotated locations for NP_001258478.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame acceptor splice site in the coding region compared to variant 1. PubMed ID 10550218 supports this variant and calls it Aire 1b. It encodes isoform 2 which is shorter than isoform 1 by one amino acid.

Source sequence(s)

AF128115, AJ243821, AK153690

Consensus CDS

CCDS70053.1

UniProtKB/TrEMBL

Q3ZB65

Related

ENSMUSP00000019257.9, ENSMUST00000019257.15

Conserved Domains (4) summary

smart00258
Location:198 → 264

SAND; SAND domain

cd15539
Location:299 → 341

PHD1_AIRE; PHD finger 1 found in autoimmune regulator (AIRE)

cd15540
Location:432 → 474

PHD2_AIRE; PHD finger 2 found in autoimmune regulator (AIRE)

pfam03172
Location:17 → 103

Sp100; Sp100 domain
NM_001271550.1 → NP_001258479.1 autoimmune regulator isoform 3

See identical proteins and their annotated locations for NP_001258479.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate in-frame donor splice site in the coding region compared to variant 1. PubMed ID 10550218 supports this variant and calls it Aire 1c. It encodes isoform 3 which is shorter than isoform 1 by four amino acids.

Source sequence(s)

AF128116, AJ243821, AK153690

Consensus CDS

CCDS70060.1

UniProtKB/Swiss-Prot

Q9Z0E3

Related

ENSMUSP00000120150.2, ENSMUST00000145975.8

Conserved Domains (4) summary

smart00258
Location:198 → 264

SAND; SAND domain

cd15539
Location:296 → 338

PHD1_AIRE; PHD finger 1 found in autoimmune regulator (AIRE)

cd15540
Location:429 → 471

PHD2_AIRE; PHD finger 2 found in autoimmune regulator (AIRE)

pfam03172
Location:17 → 103

Sp100; Sp100 domain
NM_001271551.1 → NP_001258480.1 autoimmune regulator isoform 4

See identical proteins and their annotated locations for NP_001258480.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) uses two alternate in-frame splice sites in the coding region compared to variant 1. PubMed ID 10550218 supports this variant and calls it Aire 1d. It encodes isoform 4 which is shorter than isoform 1.

Source sequence(s)

AF128117, AJ243821, AK153690

Consensus CDS

CCDS70058.1

UniProtKB/Swiss-Prot

Q9Z0E3

Related

ENSMUSP00000122659.2, ENSMUST00000130972.8

Conserved Domains (4) summary

smart00258
Location:198 → 264

SAND; SAND domain

cd15539
Location:295 → 337

PHD1_AIRE; PHD finger 1 found in autoimmune regulator (AIRE)

cd15540
Location:428 → 470

PHD2_AIRE; PHD finger 2 found in autoimmune regulator (AIRE)

pfam03172
Location:17 → 103

Sp100; Sp100 domain
NM_001271552.1 → NP_001258481.1 autoimmune regulator isoform 5

See identical proteins and their annotated locations for NP_001258481.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) lacks an alternate in-frame exon in the coding region compared to variant 1. PubMed ID 10550218 supports this variant and calls it Aire 2a. It encodes isoform 5 which is shorter than isoform 1.

Source sequence(s)

AF128118, AJ243821, AK153690

Consensus CDS

CCDS70055.1

UniProtKB/TrEMBL

Q3ZB71

Related

ENSMUSP00000117094.2, ENSMUST00000154374.2

Conserved Domains (4) summary

cd15539
Location:300 → 342

PHD1_AIRE; PHD finger 1 found in autoimmune regulator (AIRE)

cd15540
Location:374 → 416

PHD2_AIRE; PHD finger 2 found in autoimmune regulator (AIRE)

pfam03172
Location:17 → 103

Sp100; Sp100 domain

cl02536
Location:198 → 264

SAND; SAND domain
NM_001271553.1 → NP_001258482.1 autoimmune regulator isoform 6

See identical proteins and their annotated locations for NP_001258482.1

Status: VALIDATED

Description

Transcript Variant: This variant (6) lacks an alternate in-frame exon and uses an alternate in-frame acceptor splice site in the coding region compared to variant 1. PubMed ID 10550218 supports this variant and calls it Aire 2b. It encodes isoform 6 which is shorter than isoform 1.

Source sequence(s)

AF128119, AJ243821, AK153690

Consensus CDS

CCDS70052.1

UniProtKB/Swiss-Prot

Q9Z0E3

Related

ENSMUSP00000101035.3, ENSMUST00000105396.9

Conserved Domains (4) summary

cd15539
Location:299 → 341

PHD1_AIRE; PHD finger 1 found in autoimmune regulator (AIRE)

cd15540
Location:373 → 415

PHD2_AIRE; PHD finger 2 found in autoimmune regulator (AIRE)

pfam03172
Location:17 → 103

Sp100; Sp100 domain

cl02536
Location:198 → 264

SAND; SAND domain
NM_001271554.1 → NP_001258483.1 autoimmune regulator isoform 7

See identical proteins and their annotated locations for NP_001258483.1

Status: VALIDATED

Description

Transcript Variant: This variant (7) lacks an alternate in-frame exon and uses an alternate in-frame donor splice site in the coding region compared to variant 1. PubMed ID 10550218 supports this variant and calls it Aire 2c. It encodes isoform 7 which is shorter than isoform 1.

Source sequence(s)

AF128120, AJ243821, AK153690

UniProtKB/Swiss-Prot

Q9Z0E3

Conserved Domains (4) summary

cd15539
Location:296 → 338

PHD1_AIRE; PHD finger 1 found in autoimmune regulator (AIRE)

cd15540
Location:370 → 412

PHD2_AIRE; PHD finger 2 found in autoimmune regulator (AIRE)

pfam03172
Location:17 → 103

Sp100; Sp100 domain

cl02536
Location:198 → 264

SAND; SAND domain
NM_001271555.1 → NP_001258484.1 autoimmune regulator isoform 8

See identical proteins and their annotated locations for NP_001258484.1

Status: VALIDATED

Description

Transcript Variant: This variant (8) lacks an alternate in-frame exon and uses two alternate in-frame splice sites in the coding region compared to variant 1. PubMed ID 10550218 supports this variant and calls it Aire 2d. It encodes isoform 8 which is shorter than isoform 1.

Source sequence(s)

AF128121, AJ243821, AK153690

Consensus CDS

CCDS70057.1

UniProtKB/Swiss-Prot

Q9Z0E3

Related

ENSMUSP00000122190.2, ENSMUST00000155021.8

Conserved Domains (4) summary

cd15539
Location:295 → 337

PHD1_AIRE; PHD finger 1 found in autoimmune regulator (AIRE)

cd15540
Location:369 → 411

PHD2_AIRE; PHD finger 2 found in autoimmune regulator (AIRE)

pfam03172
Location:17 → 103

Sp100; Sp100 domain

cl02536
Location:198 → 264

SAND; SAND domain
NM_001271556.1 → NP_001258485.1 autoimmune regulator isoform 9

See identical proteins and their annotated locations for NP_001258485.1

Status: VALIDATED

Description

Transcript Variant: This variant (9) lacks two alternate exons in the coding region, which results in a translational frameshift, compared to variant 1. PubMed ID 10550218 supports this variant and calls it Aire 3a. The resulting protein (isoform 9) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AF128122, AJ243821, AK153690

Consensus CDS

CCDS70054.1

UniProtKB/Swiss-Prot

Q9Z0E3

Related

ENSMUSP00000101034.3, ENSMUST00000105395.9

Conserved Domains (4) summary

cd15539
Location:300 → 342

PHD1_AIRE; PHD finger 1 found in autoimmune regulator (AIRE)

pfam03172
Location:17 → 103

Sp100; Sp100 domain

cl02536
Location:198 → 264

SAND; SAND domain

cl02608
Location:320 → 395

BAH; BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in ...
NM_001271557.1 → NP_001258486.1 autoimmune regulator isoform 10

See identical proteins and their annotated locations for NP_001258486.1

Status: VALIDATED

Description

Transcript Variant: This variant (10) uses an alternate in-frame acceptor splice site and lacks two alternate exons in the coding region, which results in a translational frameshift, compared to variant 1. PubMed ID 10550218 supports this variant and calls it Aire 3b. The resulting protein (isoform 10) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AF128123, AJ243821, AK153690

Consensus CDS

CCDS70051.1

UniProtKB/Swiss-Prot

Q9Z0E3

Related

ENSMUSP00000115162.2, ENSMUST00000156417.8

Conserved Domains (4) summary

cd15539
Location:299 → 341

PHD1_AIRE; PHD finger 1 found in autoimmune regulator (AIRE)

pfam03172
Location:17 → 103

Sp100; Sp100 domain

cl02536
Location:198 → 264

SAND; SAND domain

cl02608
Location:319 → 394

BAH; BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in ...
NM_001271558.1 → NP_001258487.1 autoimmune regulator isoform 11

See identical proteins and their annotated locations for NP_001258487.1

Status: VALIDATED

Description

Transcript Variant: This variant (11) uses an alternate in-frame donor splice site and lacks two alternate exons in the coding region, which results in a translational frameshift, compared to variant 1. PubMed ID 10550218 supports this variant and calls it Aire 3c. The resulting protein (isoform 11) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AF128124, AJ243821, AK153690

Consensus CDS

CCDS70059.1

UniProtKB/Swiss-Prot

Q9Z0E3

Related

ENSMUSP00000118317.2, ENSMUST00000148469.8

Conserved Domains (4) summary

cd15539
Location:296 → 338

PHD1_AIRE; PHD finger 1 found in autoimmune regulator (AIRE)

pfam03172
Location:17 → 103

Sp100; Sp100 domain

cl02536
Location:198 → 264

SAND; SAND domain

cl02608
Location:316 → 391

BAH; BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in ...
NM_001271559.1 → NP_001258488.1 autoimmune regulator isoform 12

See identical proteins and their annotated locations for NP_001258488.1

Status: VALIDATED

Description

Transcript Variant: This variant (12) uses two alternate in-frame splice sites and lacks two alternate exons in the coding region, which results in a translational frameshift, compared to variant 1. PubMed ID 10550218 supports this variant and calls it Aire 3d. The resulting protein (isoform 12) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AF128125, AJ243821, AK153690

Consensus CDS

CCDS70056.1

UniProtKB/Swiss-Prot

Q9Z0E3

Related

ENSMUSP00000121477.2, ENSMUST00000140636.8

Conserved Domains (4) summary

cd15539
Location:295 → 337

PHD1_AIRE; PHD finger 1 found in autoimmune regulator (AIRE)

pfam03172
Location:17 → 103

Sp100; Sp100 domain

cl02536
Location:198 → 264

SAND; SAND domain

cl02608
Location:315 → 390

BAH; BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in ...
NM_009646.2 → NP_033776.1 autoimmune regulator isoform 1

See identical proteins and their annotated locations for NP_033776.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AF079536, AJ243821, AK153690

Consensus CDS

CCDS23961.1

UniProtKB/Swiss-Prot

Q9JLW0, Q9JLW1, Q9JLW2, Q9JLW3, Q9JLW4, Q9JLW5, Q9JLW6, Q9JLW7, Q9JLW8, Q9JLW9, Q9JLX0, Q9Z0E3

UniProtKB/TrEMBL

B2MVU6

Related

ENSMUSP00000114904.2, ENSMUST00000128241.8

Conserved Domains (4) summary

smart00258
Location:198 → 264

SAND; SAND domain

cd15539
Location:300 → 342

PHD1_AIRE; PHD finger 1 found in autoimmune regulator (AIRE)

cd15540
Location:433 → 475

PHD2_AIRE; PHD finger 2 found in autoimmune regulator (AIRE)

pfam03172
Location:17 → 103

Sp100; Sp100 domain

RNA

NR_073358.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (13) uses an alternate acceptor splice site in an internal exon and contains an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC153507

Related

ENSMUST00000143735.8

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000076.7 Reference GRCm39 C57BL/6J

Range

77865856..77879444 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011243277.1 → XP_011241579.1 autoimmune regulator isoform X1

Conserved Domains (2) summary

cd15539
Location:24 → 66

PHD1_AIRE; PHD finger 1 found in autoimmune regulator (AIRE)

cd15540
Location:157 → 199

PHD2_AIRE; PHD finger 2 found in autoimmune regulator (AIRE)