Zkscan3 zinc finger with KRAB and SCAN domains 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Zkscan3provided by MGI
Official Full Name: zinc finger with KRAB and SCAN domains 3provided by MGI
Primary source: MGI:MGI:1919989
See related: Ensembl:ENSMUSG00000021327 AllianceGenome:MGI:1919989
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
Also known as: Skz1; Zf47; Zfp-47; Zfp306; Zfp307; mszf35; 2810435N07Rik
Summary: Predicted to enable several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and identical protein binding activity. Predicted to be involved in lysosome organization; negative regulation of metabolic process; and regulation of DNA-templated transcription. Predicted to be located in cytoplasm and nucleoplasm. Is expressed in several structures, including central nervous system; early conceptus; genitourinary system; and retina nuclear layer. Orthologous to human ZKSCAN3 (zinc finger with KRAB and SCAN domains 3) and ZKSCAN4 (zinc finger with KRAB and SCAN domains 4). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 18.0), limb E14.5 (RPKM 16.1) and 28 other tissues See more
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Genomic context

Location:: 13 A3.1; 13 7.78 cM

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	13	NC_000079.7 (21571174..21586942, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	13	NC_000079.6 (21387004..21402755, complement)

Chromosome 13 - NC_000079.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

ALKBH5 suppresses autophagic flux via N6-methyladenosine demethylation of ZKSCAN3 mRNA in acute pancreatitis.
Title: ALKBH5 suppresses autophagic flux via N6-methyladenosine demethylation of ZKSCAN3 mRNA in acute pancreatitis.
Effect of Lacking ZKSCAN3 on Autophagy, Lysosomal Biogenesis and Senescence.
Title: Effect of Lacking ZKSCAN3 on Autophagy, Lysosomal Biogenesis and Senescence.
Cardiomyocyte ZKSCAN3 regulates remodeling following pressure-overload.
Title: Cardiomyocyte ZKSCAN3 regulates remodeling following pressure-overload.
The kidney-expressed transcription factor ZKSCAN3 is dispensable for autophagy transcriptional regulation and AKI progression in mouse.
Title: The kidney-expressed transcription factor ZKSCAN3 is dispensable for autophagy transcriptional regulation and AKI progression in mouse.
Zkscan3 affects erythroblast development by regulating the transcriptional activity of GATA1 and KLF1 in mice.
Title: Zkscan3 affects erythroblast development by regulating the transcriptional activity of GATA1 and KLF1 in mice.
Deacetylation of ZKSCAN3 by SIRT1 induces autophagy and protects SN4741 cells against MPP(+)-induced oxidative stress.
Title: Deacetylation of ZKSCAN3 by SIRT1 induces autophagy and protects SN4741 cells against MPP(+)-induced oxidative stress.
ZKSCAN3 in severe bacterial lung infection and sepsis-induced immunosuppression.
Title: ZKSCAN3 in severe bacterial lung infection and sepsis-induced immunosuppression.
a mouse model lacking Zkscan3 expression, is reported.
Title: The role of ZKSCAN3 in the transcriptional regulation of autophagy.
ZKSCAN3 regulates the expression of several genes favoring tumor progression including integrin beta 4 and VEGF
Title: Unbiased screening for transcriptional targets of ZKSCAN3 identifies integrin beta 4 and vascular endothelial growth factor as downstream targets.

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Variation

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Alleles

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

Endonuclease-mediated (3) 1 citation
Gene trapped (1)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH124729 (e-PCR)
- UniSTS:161551

AI132359 (e-PCR)
- UniSTS:160274

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	ISS Inferred from Sequence or Structural Similarity more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology 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 identical protein binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in autophagy	IEA Inferred from Electronic Annotation more info
involved_in lysosome organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of autophagy	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cellular senescence	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: zinc finger protein with KRAB and SCAN domains 3

Names: SCAN-KRAB-zinc finger gene 1; SCAN-KRAB-zinc finger protein; zinc finger protein 306; zinc finger protein 307; zinc finger protein 47 homolog

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_001145778.2 → NP_001139250.1 zinc finger protein with KRAB and SCAN domains 3 isoform a

See identical proteins and their annotated locations for NP_001139250.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 both encode the same isoform (a).

Source sequence(s)

AI132359, AK028902, AK031286, BX001068

Consensus CDS

CCDS26274.1

UniProtKB/Swiss-Prot

Q3V3Z2, Q8CD81, Q91VW9, Q9ESY5

UniProtKB/TrEMBL

A0A0R4J1L3

Related

ENSMUSP00000068424.9, ENSMUST00000070785.16

Conserved Domains (6) summary

smart00431
Location:47 → 159

SCAN; leucine rich region

COG5048
Location:367 → 514

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:371 → 391

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:507 → 529

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:328 → 350

zf-H2C2_2; Zinc-finger double domain

cl02581
Location:213 → 267

KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
NM_001368182.1 → NP_001355111.1 zinc finger protein with KRAB and SCAN domains 3 isoform b

Status: VALIDATED

Source sequence(s)

AI132359, AK028902, BX001068, CK627138

Consensus CDS

CCDS88419.1

UniProtKB/TrEMBL

A0A286YD32

Related

ENSMUSP00000153241.2, ENSMUST00000223831.2
NM_023685.5 → NP_076174.3 zinc finger protein with KRAB and SCAN domains 3 isoform a

See identical proteins and their annotated locations for NP_076174.3

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses a different splice site in the 5' UTR, compared to variant 1. Variants 1 and 2 both encode the same isoform (a).

Source sequence(s)

AI132359, AK028902, BX001068

Consensus CDS

CCDS26274.1

UniProtKB/Swiss-Prot

Q3V3Z2, Q8CD81, Q91VW9, Q9ESY5

UniProtKB/TrEMBL

A0A0R4J1L3

Related

ENSMUSP00000112135.4, ENSMUST00000116434.11

Conserved Domains (6) summary

smart00431
Location:47 → 159

SCAN; leucine rich region

COG5048
Location:367 → 514

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:371 → 391

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:507 → 529

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:328 → 350

zf-H2C2_2; Zinc-finger double domain

cl02581
Location:213 → 267

KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

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_000079.7 Reference GRCm39 C57BL/6J

Range

21571174..21586942 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006516790.5 → XP_006516853.1 zinc finger protein with KRAB and SCAN domains 3 isoform X1

See identical proteins and their annotated locations for XP_006516853.1

UniProtKB/Swiss-Prot

Q3V3Z2, Q8CD81, Q91VW9, Q9ESY5

UniProtKB/TrEMBL

A0A0R4J1L3

Conserved Domains (6) summary

smart00431
Location:47 → 159

SCAN; leucine rich region

COG5048
Location:367 → 514

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:371 → 391

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:507 → 529

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:328 → 350

zf-H2C2_2; Zinc-finger double domain

cl02581
Location:213 → 267

KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
XM_006516789.5 → XP_006516852.1 zinc finger protein with KRAB and SCAN domains 3 isoform X1

See identical proteins and their annotated locations for XP_006516852.1

UniProtKB/Swiss-Prot

Q3V3Z2, Q8CD81, Q91VW9, Q9ESY5

UniProtKB/TrEMBL

A0A0R4J1L3

Conserved Domains (6) summary

smart00431
Location:47 → 159

SCAN; leucine rich region

COG5048
Location:367 → 514

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:371 → 391

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:507 → 529

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:328 → 350

zf-H2C2_2; Zinc-finger double domain

cl02581
Location:213 → 267

KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
XM_006516792.4 → XP_006516855.1 zinc finger protein with KRAB and SCAN domains 3 isoform X2

UniProtKB/TrEMBL

Q9CSC5

Conserved Domains (4) summary

COG5048
Location:113 → 260

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:117 → 137

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:253 → 275

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:74 → 96

zf-H2C2_2; Zinc-finger double domain
XM_036158185.1 → XP_036014078.1 zinc finger protein with KRAB and SCAN domains 3 isoform X3

UniProtKB/TrEMBL

D3YTV4, Q5RJ53

Conserved Domains (2) summary

smart00431
Location:47 → 159

SCAN; leucine rich region

cl02581
Location:213 → 251

KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
XM_036158186.1 → XP_036014079.1 zinc finger protein with KRAB and SCAN domains 3 isoform X3

UniProtKB/TrEMBL

D3YTV4, Q5RJ53

Related

ENSMUSP00000112134.2, ENSMUST00000116433.2

Conserved Domains (2) summary

smart00431
Location:47 → 159

SCAN; leucine rich region

cl02581
Location:213 → 251

KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
XM_036158187.1 → XP_036014080.1 zinc finger protein with KRAB and SCAN domains 3 isoform X3

UniProtKB/TrEMBL

D3YTV4, Q5RJ53

Related

ENSMUSP00000112862.2, ENSMUST00000117721.8

Conserved Domains (2) summary

smart00431
Location:47 → 159

SCAN; leucine rich region

cl02581
Location:213 → 251

KRAB_A-box; KRAB (Kruppel-associated box) domain -A box