Nfya nuclear transcription factor Y subunit alpha [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Nfyaprovided by RGD
Official Full Name: nuclear transcription factor Y subunit alphaprovided by RGD
Primary source: RGD:70976
See related: EnsemblRapid:ENSRNOG00000012702 AllianceGenome:RGD:70976
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: CBF-A; CBF-B
Summary: Enables transcription coregulator binding activity. Predicted to be involved in positive regulation of DNA-templated transcription and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II. Part of CCAAT-binding activity factor complex. Orthologous to human NFYA (nuclear transcription factor Y subunit alpha). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Spleen (RPKM 81.3), Thymus (RPKM 70.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 9q12

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	9	NC_086027.1 (20085067..20111521)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	9	NC_051344.1 (12587437..12613911)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	9	NC_005108.4 (14551752..14577002)

Chromosome 9 - NC_086027.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A novel mechanism involving coordinated regulation of nuclear levels and acetylation of NF-YA and Bcl6 activates RGS4 transcription.
Title: A novel mechanism involving coordinated regulation of nuclear levels and acetylation of NF-YA and Bcl6 activates RGS4 transcription.
c-Jun and E1A regulate basal transcription of bsp in osteosarcoma cells by recruiting the NF-Y transcriptional complex to the ICE box in a mechanism that is independent of p300/CBP and P/CAF HAT activities
Title: Recruitment of nuclear factor Y to the inverted CCAAT element (ICE) by c-Jun and E1A stimulates basal transcription of the bone sialoprotein gene in osteosarcoma cells.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH94866 (e-PCR)
- UniSTS:120112

RH94867 (e-PCR)
- UniSTS:120113

RH132381 (e-PCR)
- UniSTS:215664

RH132935 (e-PCR)
- UniSTS:216218

RH136693 (e-PCR)
- UniSTS:218782

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
contributes_to RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
contributes_to transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription coregulator binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
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 transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in rhythmic process	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase II	IC Inferred by Curator more info	PubMed

Component	Evidence Code	Pubs
part_of CCAAT-binding factor complex	IBA Inferred from Biological aspect of Ancestor more info
part_of CCAAT-binding factor complex	IDA Inferred from Direct Assay more info	PubMed
part_of CCAAT-binding factor complex	IEA Inferred from Electronic Annotation more info
part_of CCAAT-binding factor complex	ISO Inferred from Sequence Orthology more info
part_of RNA polymerase II transcription regulator complex	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of protein-DNA complex	IEA Inferred from Electronic Annotation more info
part_of protein-DNA complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: nuclear transcription factor Y subunit alpha

Names: CAAT box DNA-binding protein subunit A; CCAAT-binding transcription factor subunit A; CCAAT-binding transcription factor subunit B; nuclear transcription factor Y subunit A; nuclear transcription factor-Y alpha

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_001413345.1 → NP_001400274.1 nuclear transcription factor Y subunit alpha isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

UniProtKB/TrEMBL

A0A8L2Q8B5

Related

ENSRNOP00000112249.1, ENSRNOT00000125437.1
NM_001413346.1 → NP_001400275.1 nuclear transcription factor Y subunit alpha isoform 3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

UniProtKB/TrEMBL

A0A0G2KB97, A0A8L2Q8B5

Related

ENSRNOP00000075707.2, ENSRNOT00000091532.3
NM_012865.3 → NP_036997.1 nuclear transcription factor Y subunit alpha isoform 2

See identical proteins and their annotated locations for NP_036997.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

UniProtKB/Swiss-Prot

P18576

UniProtKB/TrEMBL

A0A8L2Q8B5

Conserved Domains (1) summary

pfam02045
Location:257 → 312

CBFB_NFYA; CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086027.1 Reference GRCr8

Range

20085067..20111521

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006244411.5 → XP_006244473.1 nuclear transcription factor Y subunit alpha isoform X2

See identical proteins and their annotated locations for XP_006244473.1

UniProtKB/TrEMBL

A0A8L2Q8B5

Conserved Domains (1) summary

pfam02045
Location:262 → 317

CBFB_NFYA; CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B
XM_063266815.1 → XP_063122885.1 nuclear transcription factor Y subunit alpha isoform X5

UniProtKB/TrEMBL

A0A8L2Q8B5
XM_006244410.3 → XP_006244472.1 nuclear transcription factor Y subunit alpha isoform X1

See identical proteins and their annotated locations for XP_006244472.1

UniProtKB/TrEMBL

A0A8I5Y9Y4, A0A8L2Q8B5

Related

ENSRNOP00000078156.1, ENSRNOT00000115817.2

Conserved Domains (1) summary

pfam02045
Location:262 → 317

CBFB_NFYA; CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B
XM_063266814.1 → XP_063122884.1 nuclear transcription factor Y subunit alpha isoform X4

UniProtKB/TrEMBL

A0A8L2Q8B5, A6JIF1
XM_006244412.5 → XP_006244474.1 nuclear transcription factor Y subunit alpha isoform X3

UniProtKB/TrEMBL

A0A8L2Q8B5

Conserved Domains (1) summary

pfam02045
Location:261 → 316

CBFB_NFYA; CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B
XM_063266816.1 → XP_063122886.1 nuclear transcription factor Y subunit alpha isoform X6

UniProtKB/TrEMBL

A0A8L2Q8B5
XM_017596305.3 → XP_017451794.1 nuclear transcription factor Y subunit alpha isoform X7

UniProtKB/TrEMBL

A0A8L2Q8B5, A6JIF2

Conserved Domains (1) summary

pfam02045
Location:228 → 283

CBFB_NFYA; CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B