Crnkl1 crooked neck pre-mRNA splicing factor 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Crnkl1provided by MGI
Official Full Name: crooked neck pre-mRNA splicing factor 1provided by MGI
Primary source: MGI:MGI:1914127
See related: Ensembl:ENSMUSG00000001767 AllianceGenome:MGI:1914127
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: crn; 1200013P10Rik; 5730590A01Rik
Summary: Predicted to enable RNA binding activity. Predicted to be involved in spliceosomal complex assembly. 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. Is expressed in several structures, including central nervous system and sensory organ. 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, Nov 2024]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 12.8), liver E14 (RPKM 8.1) and 24 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 G1; 2 71.28 cM

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (145759402..145776620, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (145917482..145934700, complement)

Chromosome 2 - NC_000068.8 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH126853 (e-PCR)
- UniSTS:207418

AU022874 (e-PCR)
- UniSTS:207419

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

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

RH143622 (e-PCR)
- UniSTS:232868

Gene Ontology Provided by MGI

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 mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info	PubMed
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	PubMed
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

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_025820.3 → NP_080096.1 crooked neck-like protein 1

See identical proteins and their annotated locations for NP_080096.1

Status: PROVISIONAL

Source sequence(s)

AL672100

Consensus CDS

CCDS16828.1

UniProtKB/Swiss-Prot

P63154, Q542E8, Q9CQC1

Related

ENSMUSP00000001818.5, ENSMUST00000001818.5

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