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

Gene ID: 54006, updated on 8-Feb-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; genitourinary system; nervous system; and sensory organ. 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, Apr 2022]
Expression
Ubiquitous expression in CNS E14 (RPKM 6.3), ovary adult (RPKM 5.5) and 28 other tissues See more
Orthologs
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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)
  • Targeted (4)  1 citation
  • Endonuclease-mediated (2) 

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 
Process Evidence Code Pubs
involved_in behavioral fear response IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in embryonic skeletal system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within nervous system development IEA
Inferred from Electronic Annotation
more info
 
involved_in neural tube closure IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of DNA-templated transcription 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 mammary gland epithelial cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of mammary gland epithelial cell proliferation 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
 
acts_upstream_of_or_within regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in visual learning IMP
Inferred from Mutant Phenotype
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 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)

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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_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