Crnkl1 crooked neck pre-mRNA splicing factor 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Crnkl1provided by RGD
Full Name: crooked neck pre-mRNA splicing factor 1provided by RGD
Primary source: RGD:620507
See related: Ensembl:ENSRNOG00000010587 AllianceGenome:RGD:620507
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: Crn
Summary: Predicted to enable RNA binding activity. Involved in cellular response to brain-derived neurotrophic factor stimulus; cellular response to leukemia inhibitory factor; and cerebral cortex development. Predicted to be located in nucleus. Predicted to be part of Prp19 complex; U2-type catalytic step 2 spliceosome; and post-mRNA release spliceosomal complex. Human ortholog(s) of this gene implicated in basal cell carcinoma. Orthologous to human CRNKL1 (crooked neck pre-mRNA splicing factor 1). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: 3q41

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (153764718..153807973, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (133338593..133354329, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (18349226..18351540, complement)

Chromosome 3 - NC_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

General gene information

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Markers

AU022874 (e-PCR)
- UniSTS:207419

RH141585 (e-PCR)
- UniSTS:223579

UniSTS:479086 (e-PCR)
- UniSTS:479086

Crnkl1 (e-PCR), detects polymorphism
- UniSTS:479086

RH143622 (e-PCR)
- UniSTS:232868

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in cellular response to brain-derived neurotrophic factor stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to leukemia inhibitory factor	IEP Inferred from Expression Pattern more info	PubMed
involved_in cerebral cortex development	IEP Inferred from Expression Pattern more info	PubMed
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	IEA Inferred from Electronic Annotation more info
involved_in mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in mRNA splicing, via spliceosome	ISS Inferred from Sequence or Structural Similarity more info
involved_in spliceosomal complex assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in spliceosomal complex assembly	ISO Inferred from Sequence Orthology more info
involved_in spliceosomal complex assembly	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of Prp19 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of U2-type catalytic step 2 spliceosome	IBA Inferred from Biological aspect of Ancestor more info
part_of U2-type catalytic step 2 spliceosome	ISO Inferred from Sequence Orthology more info
part_of U2-type catalytic step 2 spliceosome	ISS Inferred from Sequence or Structural Similarity more info
part_of catalytic step 2 spliceosome	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
part_of post-mRNA release spliceosomal complex	IBA Inferred from Biological aspect of Ancestor more info
part_of spliceosomal complex	ISO Inferred from Sequence Orthology more info
part_of spliceosomal complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: crooked neck-like protein 1

Names: Crn, crooked neck-like 1; crooked neck homolog; crooked neck pre-mRNA splicing factor-like 1; crooked neck-like 1 protein-like; crooked neck-like protein 1-like

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_053797.2 → NP_446249.1 crooked neck-like protein 1

See identical proteins and their annotated locations for NP_446249.1

Status: VALIDATED

Source sequence(s)

BC085718

UniProtKB/Swiss-Prot

P63155

UniProtKB/TrEMBL

A0A0G2K5Q2, A6H999

Related

ENSRNOP00000014632.6, ENSRNOT00000014632.8

Conserved Domains (4) summary

pfam02184
Location:196 → 227

HAT; HAT (Half-A-TPR) repeat

COG5107
Location:130 → 525

RNA14; Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]

sd00006
Location:84 → 109

TPR; TPR repeat [structural motif]

cl26712
Location:64 → 195

U3_assoc_6; U3 small nucleolar RNA-associated protein 6