Tfcp2l1 transcription factor CP2-like 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Tfcp2l1provided by RGD
Official Full Name: transcription factor CP2-like 1provided by RGD
Primary source: RGD:1305456
See related: Ensembl:ENSRNOG00000002414 AllianceGenome:RGD:1305456
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Tcfcp2l1
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including determination of adult lifespan; epithelial cell maturation; and negative regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm and membrane. Predicted to be active in nucleus. Orthologous to human TFCP2L1 (transcription factor CP2 like 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Kidney (RPKM 368.0), Adrenal (RPKM 39.4) and 2 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13q11

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (32286643..32346671)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (29733813..29793870)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (34610689..34671617)

Chromosome 13 - NC_086031.1 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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Markers

D13Rat59 (e-PCR), detects polymorphism
- UniSTS:226576

AU027291 (e-PCR)
- UniSTS:113450

PMC304100P4 (e-PCR)
- UniSTS:272529

Gene Ontology Provided by RGD

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

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cytoplasm organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within determination of adult lifespan	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within epithelial cell maturation	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
acts_upstream_of_or_within positive regulation of growth	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within salivary gland development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in membrane	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: transcription factor CP2-like protein 1

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_001107170.1 → NP_001100640.1 transcription factor CP2-like protein 1

See identical proteins and their annotated locations for NP_001100640.1

Status: PROVISIONAL

Source sequence(s)

CH474028

UniProtKB/TrEMBL

A6K7W1, D3ZHA6

Related

ENSRNOP00000003280.4, ENSRNOT00000003280.8

Conserved Domains (2) summary

cd09590
Location:310 → 376

SAM_LBP9; SAM domain of LBP9 transcriptional factors

pfam04516
Location:34 → 237

CP2; CP2 transcription factor

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_086031.1 Reference GRCr8

Range

32286643..32346671

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039090683.1 → XP_038946611.1 transcription factor CP2-like protein 1 isoform X1

Conserved Domains (1) summary

cl15755
Location:126 → 192

SAM_superfamily; SAM (Sterile alpha motif )