Human Gene CRLF3 (ENST00000324238.7) from GENCODE V44
  Description: Homo sapiens cytokine receptor like factor 3 (CRLF3), transcript variant 1, mRNA. (from RefSeq NM_015986)
RefSeq Summary (NM_015986): This gene encodes a cytokine receptor-like factor that may negatively regulate cell cycle progression at the G0/G1 phase. Studies of the related rat protein suggest that it may regulate neuronal morphology and synaptic vesicle biogenesis. This gene is one of several genes located in the neurofibromatosis type I tumor suppressor region on the q arm of chromosome 17, a region that is subject to microdeletions, duplications, chromosomal breaks and rearrangements. Alternative splicing of this gene results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 2 and 5. [provided by RefSeq, Aug 2012].
Gencode Transcript: ENST00000324238.7
Gencode Gene: ENSG00000176390.12
Transcript (Including UTRs)
   Position: hg38 chr17:30,782,684-30,824,692 Size: 42,009 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg38 chr17:30,784,187-30,824,651 Size: 40,465 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:30,782,684-30,824,692)mRNA (may differ from genome)Protein (442 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CRLF3_HUMAN
DESCRIPTION: RecName: Full=Cytokine receptor-like factor 3; AltName: Full=Cytokine receptor-like molecule 9; Short=CREME-9; AltName: Full=Cytokine receptor-related protein 4; AltName: Full=Type I cytokine receptor-like factor p48;
TISSUE SPECIFICITY: Expressed in skin and squamous cell carcinoma (SCC) and in lesion actinic keratosis (AK).
SIMILARITY: Belongs to the cytokine receptor-like factor 3 family.
SIMILARITY: Contains 1 fibronectin type-III domain.

-  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           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 11.01 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 166.13 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 -14.3041-0.349 Picture PostScript Text
3' UTR -354.601503-0.236 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
IPR003961 - Fibronectin_type3
IPR013783 - Ig-like_fold

ModBase Predicted Comparative 3D Structure on Q8IUI8
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
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGI Ensembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0042802 identical protein binding

Biological Process:
GO:0000082 G1/S transition of mitotic cell cycle
GO:0030308 negative regulation of cell growth
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0046427 positive regulation of JAK-STAT cascade
GO:0071158 positive regulation of cell cycle arrest

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane


-  Descriptions from all associated GenBank mRNAs
  AF046059 - Homo sapiens cytokine receptor related protein 4 (CYTOR4) mRNA, complete cds.
LF384775 - JP 2014500723-A/192278: Polycomb-Associated Non-Coding RNAs.
MA620352 - JP 2018138019-A/192278: Polycomb-Associated Non-Coding RNAs.
BC023567 - Homo sapiens cytokine receptor-like factor 3, mRNA (cDNA clone MGC:20661 IMAGE:4309046), complete cds.
AF120151 - Homo sapiens cytokine receptor-like molecule 9 (CREME9) mRNA, complete cds.
AK296238 - Homo sapiens cDNA FLJ53011 complete cds, highly similar to Homo sapiens cytokine receptor-like factor 3 (CRLF3), mRNA.
DQ298450 - Homo sapiens type I cytokine receptor like factor (p48) mRNA, complete cds.
DQ892276 - Synthetic construct clone IMAGE:100004906; FLH184786.01X; RZPDo839B11146D cytokine receptor-like factor 3 (CRLF3) gene, encodes complete protein.
AK313315 - Homo sapiens cDNA, FLJ93830, highly similar to Homo sapiens cytokine receptor-like factor 3 (CRLF3), mRNA.
HQ447715 - Synthetic construct Homo sapiens clone IMAGE:100071046; CCSB012521_01 cytokine receptor-like factor 3 (CRLF3) gene, encodes complete protein.
CU692798 - Synthetic construct Homo sapiens gateway clone IMAGE:100021993 5' read CRLF3 mRNA.
LF326947 - JP 2014500723-A/134450: Polycomb-Associated Non-Coding RNAs.
MA562524 - JP 2018138019-A/134450: Polycomb-Associated Non-Coding RNAs.
JD261461 - Sequence 242485 from Patent EP1572962.
JD510261 - Sequence 491285 from Patent EP1572962.
JD534692 - Sequence 515716 from Patent EP1572962.
JD549511 - Sequence 530535 from Patent EP1572962.
JD411314 - Sequence 392338 from Patent EP1572962.
JD420418 - Sequence 401442 from Patent EP1572962.
JD151021 - Sequence 132045 from Patent EP1572962.
JD109478 - Sequence 90502 from Patent EP1572962.
JD516022 - Sequence 497046 from Patent EP1572962.
JD057607 - Sequence 38631 from Patent EP1572962.
JD441661 - Sequence 422685 from Patent EP1572962.
JD250270 - Sequence 231294 from Patent EP1572962.
JD356905 - Sequence 337929 from Patent EP1572962.
JD502997 - Sequence 484021 from Patent EP1572962.
JD359868 - Sequence 340892 from Patent EP1572962.
JD066983 - Sequence 48007 from Patent EP1572962.
JD507881 - Sequence 488905 from Patent EP1572962.
LF326948 - JP 2014500723-A/134451: Polycomb-Associated Non-Coding RNAs.
MA562525 - JP 2018138019-A/134451: Polycomb-Associated Non-Coding RNAs.
LF326949 - JP 2014500723-A/134452: Polycomb-Associated Non-Coding RNAs.
MA562526 - JP 2018138019-A/134452: Polycomb-Associated Non-Coding RNAs.
LF326950 - JP 2014500723-A/134453: Polycomb-Associated Non-Coding RNAs.
MA562527 - JP 2018138019-A/134453: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NJF3, B2R8C3, CREME9, CRLF3_HUMAN, CYTOR4, ENST00000324238.1, ENST00000324238.2, ENST00000324238.3, ENST00000324238.4, ENST00000324238.5, ENST00000324238.6, NM_015986, P48, Q2MLY7, Q8IUI8, Q9UNI3, Q9Y6M8, uc002hfr.1, uc002hfr.2, uc002hfr.3, uc002hfr.4, uc002hfr.5, uc002hfr.6
UCSC ID: ENST00000324238.7
RefSeq Accession: NM_015986
Protein: Q8IUI8 (aka CRLF3_HUMAN)
CCDS: CCDS32607.1

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