Spdef SAM pointed domain containing ets transcription factor [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Spdefprovided by RGD
Official Full Name: SAM pointed domain containing ets transcription factorprovided by RGD
Primary source: RGD:1594842
See related: Ensembl:ENSRNOG00000000491 AllianceGenome:RGD:1594842
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
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Predicted to be involved in cell differentiation; positive regulation of apoptotic process; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including columnar/cuboidal epithelial cell differentiation; positive regulation of cell fate commitment; and regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Orthologous to human SPDEF (SAM pointed domain containing ETS transcription factor). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 8.9), Testes (RPKM 4.9) and 6 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 20p12

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (5773236..5787685, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (5771440..5785893, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (7292823..7308053, complement)

Chromosome 20 - NC_086038.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of cell fate commitment	ISO Inferred from Sequence Orthology more info
acts_upstream_of epithelial cell fate commitment	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within glandular epithelial cell development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within intestinal epithelial cell development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lung goblet cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of cell fate commitment	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of cell fate commitment	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	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 transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
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: SAM pointed domain-containing Ets transcription factor

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_001109530.2 → NP_001103000.1 SAM pointed domain-containing Ets transcription factor

See identical proteins and their annotated locations for NP_001103000.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000020

UniProtKB/TrEMBL

A0A0G2K6F0, B2RYE0, F7EQE7

Related

ENSRNOP00000000583.4, ENSRNOT00000000583.6

Conserved Domains (2) summary

cd08532
Location:124 → 204

SAM_PNT-PDEF-like; Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor

pfam00178
Location:241 → 322

Ets; Ets-domain