Celf3 CUGBP, Elav-like family member 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Celf3provided by RGD
Official Full Name: CUGBP, Elav-like family member 3provided by RGD
Primary source: RGD:1563168
See related: Ensembl:ENSRNOG00000020875 AllianceGenome:RGD:1563168
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: Tnrc4; RGD1563168
Summary: Predicted to enable 7SK snRNA binding activity and mRNA binding activity. Predicted to be involved in mRNA splice site selection; positive regulation of mRNA splicing, via spliceosome; and regulation of alternative mRNA splicing, via spliceosome. Predicted to act upstream of or within several processes, including flagellated sperm motility; ncRNA transcription; and nuclear body organization. Predicted to be located in nuclear body. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasm and nucleus. Orthologous to human CELF3 (CUGBP Elav-like family member 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Brain (RPKM 32.8), Adrenal (RPKM 20.3) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q34

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (184805078..184819189)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (182116034..182130163)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (195716373..195732872)

Chromosome 2 - NC_086020.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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 7SK snRNA binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in RNA splicing	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within flagellated sperm motility	ISO Inferred from Sequence Orthology more info
involved_in mRNA splice site recognition	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within nuclear body organization	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in regulation of alternative mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of alternative mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within spermatogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in nuclear body	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
part_of ribonucleoprotein complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: CUGBP Elav-like family member 3

Names: CUG-BP- and ETR-3-like factor 3; trinucleotide repeat containing 4

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_001109190.2 → NP_001102660.1 CUGBP Elav-like family member 3

See identical proteins and their annotated locations for NP_001102660.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/TrEMBL

A6K2R6

Conserved Domains (4) summary

PRK12323
Location:214 → 351

PRK12323; DNA polymerase III subunit gamma/tau

cd12639
Location:384 → 462

RRM3_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

cd12632
Location:2 → 88

RRM1_CELF3_4_5_6; RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

cd12635
Location:94 → 174

RRM2_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

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_086020.1 Reference GRCr8

Range

184805078..184819189

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063282393.1 → XP_063138463.1 CUGBP Elav-like family member 3 isoform X21

UniProtKB/TrEMBL

D4A916
XM_063282398.1 → XP_063138468.1 CUGBP Elav-like family member 3 isoform X25
XM_063282388.1 → XP_063138458.1 CUGBP Elav-like family member 3 isoform X19

UniProtKB/TrEMBL

D4A916
XM_063282399.1 → XP_063138469.1 CUGBP Elav-like family member 3 isoform X26
XM_063282390.1 → XP_063138460.1 CUGBP Elav-like family member 3 isoform X20

UniProtKB/TrEMBL

D4A916
XM_008761322.4 → XP_008759544.1 CUGBP Elav-like family member 3 isoform X1

See identical proteins and their annotated locations for XP_008759544.1

UniProtKB/TrEMBL

A0A8I6AGJ7

Related

ENSRNOP00000092441.1

Conserved Domains (4) summary

TIGR01645
Location:8 → 491

half-pint; poly-U binding splicing factor, half-pint family

cd12639
Location:412 → 490

RRM3_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

cd12632
Location:2 → 88

RRM1_CELF3_4_5_6; RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

cd12635
Location:94 → 174

RRM2_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
XM_006232904.5 → XP_006232966.1 CUGBP Elav-like family member 3 isoform X8

See identical proteins and their annotated locations for XP_006232966.1

UniProtKB/TrEMBL

D4A916

Conserved Domains (4) summary

TIGR01628
Location:21 → 225

PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family

PRK14951
Location:174 → 300

PRK14951; DNA polymerase III subunits gamma and tau; Provisional

cd12639
Location:336 → 414

RRM3_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

cd12635
Location:18 → 98

RRM2_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
XM_063282394.1 → XP_063138464.1 CUGBP Elav-like family member 3 isoform X22

UniProtKB/TrEMBL

D4A916
XM_039102932.2 → XP_038958860.1 CUGBP Elav-like family member 3 isoform X9

UniProtKB/TrEMBL

D4A916

Related

ENSRNOP00000028324.7

Conserved Domains (4) summary

TIGR01628
Location:30 → 224

PABP-1234; polyadenylate binding protein, human types 1, 2, 3, 4 family

PRK14951
Location:173 → 299

PRK14951; DNA polymerase III subunits gamma and tau; Provisional

cd12639
Location:335 → 413

RRM3_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

cd12635
Location:17 → 97

RRM2_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
XM_063282401.1 → XP_063138471.1 CUGBP Elav-like family member 3 isoform X27
XM_063282380.1 → XP_063138450.1 CUGBP Elav-like family member 3 isoform X11

UniProtKB/TrEMBL

D4A916
XM_063282395.1 → XP_063138465.1 CUGBP Elav-like family member 3 isoform X23

UniProtKB/TrEMBL

D4A916
XM_063282383.1 → XP_063138453.1 CUGBP Elav-like family member 3 isoform X14
XM_063282384.1 → XP_063138454.1 CUGBP Elav-like family member 3 isoform X15
XM_063282387.1 → XP_063138457.1 CUGBP Elav-like family member 3 isoform X18
XM_063282386.1 → XP_063138456.1 CUGBP Elav-like family member 3 isoform X17
XM_063282376.1 → XP_063138446.1 CUGBP Elav-like family member 3 isoform X3
XM_039102915.2 → XP_038958843.1 CUGBP Elav-like family member 3 isoform X5
XM_063282377.1 → XP_063138447.1 CUGBP Elav-like family member 3 isoform X6
XM_063282381.1 → XP_063138451.1 CUGBP Elav-like family member 3 isoform X12
XM_006232898.5 → XP_006232960.1 CUGBP Elav-like family member 3 isoform X2

Conserved Domains (4) summary

TIGR01645
Location:8 → 490

half-pint; poly-U binding splicing factor, half-pint family

cd12639
Location:411 → 489

RRM3_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

cd12632
Location:2 → 88

RRM1_CELF3_4_5_6; RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

cd12635
Location:93 → 173

RRM2_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
XM_006232900.5 → XP_006232962.1 CUGBP Elav-like family member 3 isoform X4

Conserved Domains (4) summary

PRK12323
Location:213 → 350

PRK12323; DNA polymerase III subunit gamma/tau

cd12639
Location:383 → 461

RRM3_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

cd12632
Location:2 → 88

RRM1_CELF3_4_5_6; RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

cd12635
Location:93 → 173

RRM2_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
XM_063282378.1 → XP_063138448.1 CUGBP Elav-like family member 3 isoform X7
XM_063282382.1 → XP_063138452.1 CUGBP Elav-like family member 3 isoform X13
XM_063282385.1 → XP_063138455.1 CUGBP Elav-like family member 3 isoform X16
XM_006232908.5 → XP_006232970.1 CUGBP Elav-like family member 3 isoform X10

See identical proteins and their annotated locations for XP_006232970.1

Conserved Domains (3) summary

cd12639
Location:334 → 412

RRM3_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

cd12632
Location:2 → 88

RRM1_CELF3_4_5_6; RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

cd12635
Location:94 → 174

RRM2_CELF3_4_5_6; RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins
XM_063282379.1 → XP_063138449.1 CUGBP Elav-like family member 3 isoform X8

UniProtKB/TrEMBL

D4A916
XM_063282389.1 → XP_063138459.1 CUGBP Elav-like family member 3 isoform X19

UniProtKB/TrEMBL

D4A916
XM_063282392.1 → XP_063138462.1 CUGBP Elav-like family member 3 isoform X21

UniProtKB/TrEMBL

D4A916
XM_063282397.1 → XP_063138467.1 CUGBP Elav-like family member 3 isoform X25
XM_063282391.1 → XP_063138461.1 CUGBP Elav-like family member 3 isoform X20

UniProtKB/TrEMBL

D4A916
XM_063282396.1 → XP_063138466.1 CUGBP Elav-like family member 3 isoform X24