U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Deaf1 DEAF1, transcription factor [ Mus musculus (house mouse) ]

    Gene ID: 54006, updated on 27-Nov-2024

    Summary

    Official Symbol
    Deaf1provided by MGI
    Official Full Name
    DEAF1, transcription factorprovided by MGI
    Primary source
    MGI:MGI:1858496
    See related
    Ensembl:ENSMUSG00000058886 AllianceGenome:MGI:1858496
    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
    NUDR; C230009B13Rik
    Summary
    Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including behavioral fear response; chordate embryonic development; and visual learning. Acts upstream of or within regulation of transcription by RNA polymerase II. Located in cytoplasm and nucleus. Part of RNA polymerase II transcription regulator complex. Is expressed in several structures, including bone; early conceptus; reproductive system; sensory organ; and urinary system. Human ortholog(s) of this gene implicated in Vulto-van Silfout-de Vries syndrome. Orthologous to human DEAF1 (DEAF1 transcription factor). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in CNS E14 (RPKM 6.3), ovary adult (RPKM 5.5) and 28 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Deaf1 in Genome Data Viewer
    Location:
    7 F5; 7 86.61 cM
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (140877089..140918758, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (141297176..141338869, complement)

    Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_20485 Neighboring gene secretin Neighboring gene dopamine receptor D4 Neighboring gene STARR-seq mESC enhancer starr_20486 Neighboring gene predicted gene, 53347 Neighboring gene STARR-positive B cell enhancer ABC_E4985 Neighboring gene transmembrane protein 80 Neighboring gene EPS8-like 2 Neighboring gene RIKEN cDNA B230206H07 gene Neighboring gene STARR-seq mESC enhancer starr_20489 Neighboring gene predicted gene, 25725

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (4)  1 citation

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    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 transcription regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of RNA polymerase II transcription regulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in fibrillar center ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    deformed epidermal autoregulatory factor 1 homolog
    Names
    nuclear DEAF-1-related transcriptional regulator
    suppressin

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001282072.1NP_001269001.1  deformed epidermal autoregulatory factor 1 homolog isoform 2

      See identical proteins and their annotated locations for NP_001269001.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate 5' structure, and thus differs in the 5' UTR and 5' coding region, compared to variant 1. These differences cause translation initiation at an alternate AUG and result in an isoform (c) with a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AI604909, AK144333, CD353366, CJ045430
      Conserved Domains (1) summary
      pfam01753
      Location:250286
      zf-MYND; MYND finger
    2. NM_001282073.1NP_001269002.1  deformed epidermal autoregulatory factor 1 homolog isoform 3

      See identical proteins and their annotated locations for NP_001269002.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) represents use of an alternate promoter, differs in the 5' UTR, and has multiple differences in the coding region, compared to variant 1. The resulting protein (isoform 3) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AA269946, AC163434, AI430175, AI604909, BY051636, CF538574, CJ281229, W53084
      UniProtKB/TrEMBL
      Q80V49
      Conserved Domains (1) summary
      smart00258
      Location:116188
      SAND; SAND domain
    3. NM_001282076.1NP_001269005.1  deformed epidermal autoregulatory factor 1 homolog isoform 4

      See identical proteins and their annotated locations for NP_001269005.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and has multiple differences in the coding region, compared to variant 1. The resulting protein (isoform 4) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC163434
      Conserved Domains (1) summary
      pfam01753
      Location:249285
      zf-MYND; MYND finger
    4. NM_016874.3NP_058570.1  deformed epidermal autoregulatory factor 1 homolog isoform 1

      See identical proteins and their annotated locations for NP_058570.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AI604909, AK146546, CJ045430
      Consensus CDS
      CCDS40185.1
      UniProtKB/Swiss-Prot
      C7SHZ9, Q3UJA4, Q9Z1T5
      UniProtKB/TrEMBL
      A0A1B0GRZ5
      Related
      ENSMUSP00000079395.8, ENSMUST00000080553.9
      Conserved Domains (2) summary
      pfam01342
      Location:199273
      SAND; SAND domain
      pfam01753
      Location:505541
      zf-MYND; MYND finger

    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

    1. NC_000073.7 Reference GRCm39 C57BL/6J

      Range
      140877089..140918758 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030242789.2XP_030098649.1  deformed epidermal autoregulatory factor 1 homolog isoform X5

      UniProtKB/TrEMBL
      Q8BUW3
      Conserved Domains (2) summary
      smart00258
      Location:116188
      SAND; SAND domain
      pfam01753
      Location:419455
      zf-MYND; MYND finger
    2. XM_006536206.4XP_006536269.1  deformed epidermal autoregulatory factor 1 homolog isoform X2

      UniProtKB/TrEMBL
      A0A1B0GRZ5
      Conserved Domains (1) summary
      smart00258
      Location:202274
      SAND; SAND domain
    3. XM_030242786.1XP_030098646.1  deformed epidermal autoregulatory factor 1 homolog isoform X6

      UniProtKB/TrEMBL
      Q8BUW3
      Conserved Domains (2) summary
      smart00258
      Location:116188
      SAND; SAND domain
      pfam01753
      Location:418454
      zf-MYND; MYND finger
    4. XM_017322368.3XP_017177857.1  deformed epidermal autoregulatory factor 1 homolog isoform X1

      UniProtKB/TrEMBL
      A0A1B0GRZ5
      Related
      ENSMUSP00000147728.2, ENSMUST00000211537.2
      Conserved Domains (2) summary
      smart00258
      Location:202274
      SAND; SAND domain
      pfam01753
      Location:504540
      zf-MYND; MYND finger
    5. XM_006536213.1XP_006536276.1  deformed epidermal autoregulatory factor 1 homolog isoform X10

      See identical proteins and their annotated locations for XP_006536276.1

      Conserved Domains (1) summary
      pfam01753
      Location:249285
      zf-MYND; MYND finger
    6. XM_030242784.2XP_030098644.1  deformed epidermal autoregulatory factor 1 homolog isoform X5

      UniProtKB/TrEMBL
      Q8BUW3
      Conserved Domains (2) summary
      smart00258
      Location:116188
      SAND; SAND domain
      pfam01753
      Location:419455
      zf-MYND; MYND finger
    7. XM_030242787.2XP_030098647.1  deformed epidermal autoregulatory factor 1 homolog isoform X7

      UniProtKB/TrEMBL
      Q80V49
      Conserved Domains (1) summary
      smart00258
      Location:116188
      SAND; SAND domain
    8. XM_017322370.3XP_017177859.1  deformed epidermal autoregulatory factor 1 homolog isoform X10

      Conserved Domains (1) summary
      pfam01753
      Location:249285
      zf-MYND; MYND finger
    9. XM_030242791.2XP_030098651.1  deformed epidermal autoregulatory factor 1 homolog isoform X9

      Conserved Domains (1) summary
      pfam01753
      Location:250286
      zf-MYND; MYND finger
    10. XM_030242785.2XP_030098645.1  deformed epidermal autoregulatory factor 1 homolog isoform X6

      UniProtKB/TrEMBL
      Q8BUW3
      Conserved Domains (2) summary
      smart00258
      Location:116188
      SAND; SAND domain
      pfam01753
      Location:418454
      zf-MYND; MYND finger
    11. XM_036153248.1XP_036009141.1  deformed epidermal autoregulatory factor 1 homolog isoform X3

      UniProtKB/TrEMBL
      A0A1B0GRZ5
      Conserved Domains (1) summary
      pfam01342
      Location:201273
      SAND; SAND domain
    12. XM_006536207.4XP_006536270.1  deformed epidermal autoregulatory factor 1 homolog isoform X4

      UniProtKB/TrEMBL
      A0A1B0GRZ5
      Conserved Domains (1) summary
      smart00258
      Location:202274
      SAND; SAND domain
    13. XM_030242788.2XP_030098648.1  deformed epidermal autoregulatory factor 1 homolog isoform X8

      UniProtKB/TrEMBL
      Q3TYJ5, Q8BUW3
      Conserved Domains (1) summary
      smart00258
      Location:116188
      SAND; SAND domain
    14. XM_006536211.4XP_006536274.1  deformed epidermal autoregulatory factor 1 homolog isoform X8

      See identical proteins and their annotated locations for XP_006536274.1

      UniProtKB/TrEMBL
      Q3TYJ5, Q8BUW3
      Conserved Domains (1) summary
      smart00258
      Location:116188
      SAND; SAND domain

    RNA

    1. XR_004934151.1 RNA Sequence

    2. XR_389957.4 RNA Sequence

    3. XR_004934152.1 RNA Sequence