Human Gene CRNKL1 (ENST00000536226.2_8) from GENCODE V47lift37
  Description: crooked neck pre-mRNA splicing factor 1, transcript variant 5 (from RefSeq NM_001278628.2)
Gencode Transcript: ENST00000536226.2_8
Gencode Gene: ENSG00000101343.15_11
Transcript (Including UTRs)
   Position: hg19 chr20:20,015,012-20,033,110 Size: 18,099 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr20:20,016,839-20,032,986 Size: 16,148 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:20,015,012-20,033,110)mRNA (may differ from genome)Protein (687 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CRNL1_HUMAN
DESCRIPTION: RecName: Full=Crooked neck-like protein 1; AltName: Full=Crooked neck homolog; Short=hCrn;
FUNCTION: Involved in pre-mRNA splicing process.
SUBUNIT: Identified in the spliceosome C complex. Present in a spliceosome complex assembled in vitro containing CRNKL1, HPRP8BP and SNRPB2. Isoform 2 seems to be predominant in the spliceosome complex.
SUBCELLULAR LOCATION: Nucleus speckle. Cytoplasm. Note=Colocalizes with core spliceosomal snRNP proteins. Also diffusely expressed in cytoplasm.
TISSUE SPECIFICITY: Widely expressed. Highly expressed in testis. Not expressed in brain and lung.
SIMILARITY: Belongs to the crooked-neck family.
SIMILARITY: Contains 17 HAT repeats.
SEQUENCE CAUTION: Sequence=BAB14303.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB14485.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 10.50 RPKM in Testis
Total median expression: 304.13 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -38.60124-0.311 Picture PostScript Text
3' UTR -436.301827-0.239 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003107 - HAT
IPR013026 - TPR-contain_dom
IPR011990 - TPR-like_helical

Pfam Domains:
PF02184 - HAT (Half-A-TPR) repeat
PF05843 - Suppressor of forked protein (Suf)

SCOP Domains:
81901 - HCP-like
48439 - Protein prenylyltransferase
48452 - TPR-like
89009 - GAT-like domain
144059 - ImpE-like

ModBase Predicted Comparative 3D Structure on Q9BZJ0
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details   Gene Details
Gene SorterGene Sorter   Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0000245 spliceosomal complex assembly
GO:0000398 mRNA splicing, via spliceosome
GO:0006396 RNA processing
GO:0006397 mRNA processing
GO:0008380 RNA splicing

Cellular Component:
GO:0000974 Prp19 complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0016607 nuclear speck
GO:0071007 U2-type catalytic step 2 spliceosome
GO:0071010 prespliceosome
GO:0071011 precatalytic spliceosome
GO:0071012 catalytic step 1 spliceosome
GO:0071013 catalytic step 2 spliceosome
GO:0071014 post-mRNA release spliceosomal complex


-  Descriptions from all associated GenBank mRNAs
  AL832435 - Homo sapiens mRNA; cDNA DKFZp762M013 (from clone DKFZp762M013).
JD038267 - Sequence 19291 from Patent EP1572962.
JD502673 - Sequence 483697 from Patent EP1572962.
JD513454 - Sequence 494478 from Patent EP1572962.
BC144222 - Homo sapiens cDNA clone IMAGE:9052742, containing frame-shift errors.
JD493936 - Sequence 474960 from Patent EP1572962.
JD225012 - Sequence 206036 from Patent EP1572962.
AK022908 - Homo sapiens cDNA FLJ12846 fis, clone NT2RP2003308, moderately similar to CROOKED NECK PROTEIN.
AF255443 - Homo sapiens CGI-201 protein mRNA, complete cds, alternatively spliced.
AF318303 - Homo sapiens CGI-201 protein, type II mRNA, alternatively spliced, complete cds.
AF318304 - Homo sapiens CGI-201 protein, type III mRNA, alternatively spliced, complete cds.
AF318305 - Homo sapiens CGI-201 protein, type IV mRNA, alternatively spliced, complete cds.
JD562903 - Sequence 543927 from Patent EP1572962.
JD062073 - Sequence 43097 from Patent EP1572962.
JD181656 - Sequence 162680 from Patent EP1572962.
JD172053 - Sequence 153077 from Patent EP1572962.
JD502369 - Sequence 483393 from Patent EP1572962.
JD379393 - Sequence 360417 from Patent EP1572962.
JD203132 - Sequence 184156 from Patent EP1572962.
AK023246 - Homo sapiens cDNA FLJ13184 fis, clone NT2RP3004206, moderately similar to CROOKED NECK PROTEIN.
AK026342 - Homo sapiens cDNA: FLJ22689 fis, clone HSI11092, highly similar to AF255443 Homo sapiens CGI-201 protein mRNA.
JD288223 - Sequence 269247 from Patent EP1572962.
JD528931 - Sequence 509955 from Patent EP1572962.
JD515614 - Sequence 496638 from Patent EP1572962.
AK023728 - Homo sapiens cDNA FLJ13666 fis, clone PLACE1011664, moderately similar to CROOKED NECK PROTEIN.
JD509001 - Sequence 490025 from Patent EP1572962.
JD378982 - Sequence 360006 from Patent EP1572962.
AK292799 - Homo sapiens cDNA FLJ76100 complete cds.
JD266991 - Sequence 248015 from Patent EP1572962.
AF111802 - Homo sapiens MSTP021 (MST021) mRNA, complete cds.
JD380377 - Sequence 361401 from Patent EP1572962.
AF318302 - Homo sapiens CGI-201 protein, short form mRNA, complete cds.
AB016840 - Homo sapiens crn mRNA, complete cds.
LF207046 - JP 2014500723-A/14549: Polycomb-Associated Non-Coding RNAs.
BC156789 - Synthetic construct Homo sapiens clone IMAGE:100062303, MGC:190238 crooked neck pre-mRNA splicing factor-like 1 (Drosophila) (CRNKL1) mRNA, encodes complete protein.
LF360514 - JP 2014500723-A/168017: Polycomb-Associated Non-Coding RNAs.
LF360515 - JP 2014500723-A/168018: Polycomb-Associated Non-Coding RNAs.
LF360516 - JP 2014500723-A/168019: Polycomb-Associated Non-Coding RNAs.
LF360517 - JP 2014500723-A/168020: Polycomb-Associated Non-Coding RNAs.
LF360518 - JP 2014500723-A/168021: Polycomb-Associated Non-Coding RNAs.
MA442623 - JP 2018138019-A/14549: Polycomb-Associated Non-Coding RNAs.
MA596091 - JP 2018138019-A/168017: Polycomb-Associated Non-Coding RNAs.
MA596092 - JP 2018138019-A/168018: Polycomb-Associated Non-Coding RNAs.
MA596093 - JP 2018138019-A/168019: Polycomb-Associated Non-Coding RNAs.
MA596094 - JP 2018138019-A/168020: Polycomb-Associated Non-Coding RNAs.
MA596095 - JP 2018138019-A/168021: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9BZJ0 (Reactome details) participates in the following event(s):

R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A8K9T4, CGI-201, CRN, CRNL1_HUMAN, ENST00000536226.1, MSTP021, NM_001278628, Q5JY64, Q8WYI5, Q9BZI9, Q9BZJ0, Q9BZJ1, Q9BZJ2, Q9GZW7, Q9H8F8, Q9NQH5, Q9NYD8, uc324opu.1, uc324opu.2
UCSC ID: ENST00000536226.2_8
RefSeq Accession: NM_001278628.2
Protein: Q9BZJ0 (aka CRNL1_HUMAN or CRN1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.