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

Gene ID: 29508, updated on 4-Jan-2025

Summary

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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, Jan 2025]
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

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See Nfya in Genome Data Viewer
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_086027.1Genomic Context describing neighboring genes Neighboring gene translocator protein 2 Neighboring gene apolipoprotein B mRNA editing enzyme catalytic subunit 2 Neighboring gene O-acyl-ADP-ribose deacylase 1 Neighboring gene triggering receptor expressed on myeloid cells-like 1 Neighboring gene triggering receptor expressed on myeloid cells 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Biochemical analysis of the B subunit of the heteromeric CCAAT-binding factor. A DNA-binding domain and a subunit interaction domain are specified by two separate segments. Maity SN, et al. J Biol Chem, 1992 Apr 25. PMID 1569083
  2. The B subunit of a rat heteromeric CCAAT-binding transcription factor shows a striking sequence identity with the yeast Hap2 transcription factor. Maity SN, et al. Proc Natl Acad Sci U S A, 1990 Jul. PMID 2196566, Free PMC Article
  3. The short isoform of NF-YA belongs to the embryonic stem cell transcription factor circuitry. Dolfini D, et al. Stem Cells, 2012 Nov. PMID 22969033
  4. Recombinant rat CBF-C, the third subunit of CBF/NFY, allows formation of a protein-DNA complex with CBF-A and CBF-B and with yeast HAP2 and HAP3. Sinha S, et al. Proc Natl Acad Sci U S A, 1995 Feb 28. PMID 7878029, Free PMC Article
  5. Co-evolution from yeast to mouse: cDNA cloning of the two NF-Y (CP-1/CBF) subunits. Hooft van Huijsduijnen R, et al. EMBO J, 1990 Oct. PMID 1698608, Free PMC Article

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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)

  1. 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

  2. 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

  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

  1. NC_086027.1 Reference GRCr8

    Range
    20085067..20111521
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. XM_063266815.1 → XP_063122885.1  nuclear transcription factor Y subunit alpha isoform X5

    UniProtKB/TrEMBL
    A0A8L2Q8B5

  3. 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

  4. XM_063266814.1 → XP_063122884.1  nuclear transcription factor Y subunit alpha isoform X4

    UniProtKB/TrEMBL
    A0A8L2Q8B5, A6JIF1

  5. 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

  6. XM_063266816.1 → XP_063122886.1  nuclear transcription factor Y subunit alpha isoform X6

    UniProtKB/TrEMBL
    A0A8L2Q8B5

  7. 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
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P18576.1 GenPept UniProtKB/Swiss-Prot:P18576

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