Deaf1 DEAF1 transcription factor [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Deaf1provided by RGD
Official Full Name: DEAF1 transcription factorprovided by RGD
Primary source: RGD:620671
See related: Ensembl:ENSRNOG00000017960 AllianceGenome:RGD:620671
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: NUDR
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 positive regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm; fibrillar center; and nucleoplasm. Predicted to be part of RNA polymerase II transcription regulator complex. Predicted to be active in nucleus. 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: Biased expression in Kidney (RPKM 49.1), Spleen (RPKM 46.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q41

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (205831428..205865106, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (196401857..196435541, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (214283787..214317466, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

In pregnancy stress, prefrontal cortex Deaf1 levels were reduced in rats.
Title: Stress-induced alterations in 5-HT1A receptor transcriptional modulators NUDR and Freud-1.
chronic social defeat stress downregulates the 5-HT1A receptor mRNA but does not significantly alter the levels of Freud-1 and NUDR in PFC; this stress paradigm could offer a useful rodent model for depression and other stress related disorders
Title: Chronic social defeat downregulates the 5-HT1A receptor but not Freud-1 or NUDR in the rat prefrontal cortex.
results point to the importance of understanding the mechanism for the differential regulation of 5-HT1AR, Freud-1 and NUDR in the prefrontal cortex as a basis for understanding the related effects of chronic stress and stress-related disorders
Title: Differential regulation of the serotonin 1 A transcriptional modulators five prime repressor element under dual repression-1 and nuclear-deformed epidermal autoregulatory factor by chronic stress.

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General gene information

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Markers

RH130094 (e-PCR)
- UniSTS:213382

BF390771 (e-PCR)
- UniSTS:249552

Gene Ontology Provided by RGD

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	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation 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

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

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in fibrillar center	IEA Inferred from Electronic Annotation more info
located_in fibrillar center	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
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: deformed epidermal autoregulatory factor 1 homolog

Names: DEAF-1 related transcriptional regulator (NUDR); 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)

NM_031801.2 → NP_113989.2 deformed epidermal autoregulatory factor 1 homolog

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

A6HXT9, F1LQ17

Related

ENSRNOP00000046656.3, ENSRNOT00000048817.4

Conserved Domains (2) summary

pfam01342
Location:198 → 272

SAND; SAND domain

pfam01753
Location:504 → 540

zf-MYND; MYND finger

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_086019.1 Reference GRCr8

Range

205831428..205865106 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063275606.1 → XP_063131676.1 deformed epidermal autoregulatory factor 1 homolog isoform X5

UniProtKB/TrEMBL

A6HXT9
XM_063275596.1 → XP_063131666.1 deformed epidermal autoregulatory factor 1 homolog isoform X3

UniProtKB/TrEMBL

A6HXT9
XM_008760013.4 → XP_008758235.1 deformed epidermal autoregulatory factor 1 homolog isoform X4

UniProtKB/TrEMBL

A6HXT9

Conserved Domains (1) summary

pfam01342
Location:203 → 277

SAND; SAND domain
XM_008760012.4 → XP_008758234.1 deformed epidermal autoregulatory factor 1 homolog isoform X2

UniProtKB/TrEMBL

A6HXT9

Conserved Domains (2) summary

pfam01342
Location:203 → 277

SAND; SAND domain

pfam01753
Location:508 → 544

zf-MYND; MYND finger
XM_008760011.4 → XP_008758233.1 deformed epidermal autoregulatory factor 1 homolog isoform X1

UniProtKB/TrEMBL

A6HXT9

Conserved Domains (2) summary

pfam01342
Location:203 → 277

SAND; SAND domain

pfam01753
Location:509 → 545

zf-MYND; MYND finger
XM_006230582.5 → XP_006230644.1 deformed epidermal autoregulatory factor 1 homolog isoform X7

UniProtKB/TrEMBL

A0A8I5ZRK7

Related

ENSRNOP00000081039.1

Conserved Domains (2) summary

pfam01342
Location:113 → 187

SAND; SAND domain

pfam01753
Location:419 → 455

zf-MYND; MYND finger
XM_006230583.5 → XP_006230645.1 deformed epidermal autoregulatory factor 1 homolog isoform X9

UniProtKB/TrEMBL

A0A8I5ZRK7, A0A8I6A6A4

Related

ENSRNOP00000086677.1

Conserved Domains (1) summary

pfam01342
Location:113 → 187

SAND; SAND domain
XM_063275622.1 → XP_063131692.1 deformed epidermal autoregulatory factor 1 homolog isoform X8

UniProtKB/TrEMBL

A0A8I5ZRK7
XM_008760014.4 → XP_008758236.1 deformed epidermal autoregulatory factor 1 homolog isoform X6

UniProtKB/TrEMBL

A0A8I5ZRK7

Conserved Domains (2) summary

pfam01342
Location:118 → 192

SAND; SAND domain

pfam01753
Location:424 → 460

zf-MYND; MYND finger
XM_063275626.1 → XP_063131696.1 deformed epidermal autoregulatory factor 1 homolog isoform X10