Human Gene SPATC1L (ENST00000291672.6) from GENCODE V44
  Description: Homo sapiens spermatogenesis and centriole associated 1 like (SPATC1L), transcript variant 1, mRNA. (from RefSeq NM_001142854)
Gencode Transcript: ENST00000291672.6
Gencode Gene: ENSG00000160284.15
Transcript (Including UTRs)
   Position: hg38 chr21:46,161,160-46,184,459 Size: 23,300 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg38 chr21:46,161,379-46,182,816 Size: 21,438 Coding Exon Count: 4 

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 (chr21:46,161,160-46,184,459)mRNA (may differ from genome)Protein (340 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CU056_HUMAN
DESCRIPTION: RecName: Full=Uncharacterized protein C21orf56;
MISCELLANEOUS: Highly variable expression among individuals is associated with differential sensitivity to the DNA alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), decreased expression being associated with increased sensitivity.
SEQUENCE CAUTION: Sequence=BAA95497.1; Type=Erroneous gene model prediction;

-  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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 31.50 RPKM in Testis
Total median expression: 242.96 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 -442.001062-0.416 Picture PostScript Text
3' UTR -84.50219-0.386 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
IPR026176 - Spatc1/UPF_C21orf56

ModBase Predicted Comparative 3D Structure on Q9H0A9
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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function
GO:0005515 protein binding

Biological Process:
GO:0008150 biological_process

Cellular Component:
GO:0005575 cellular_component
GO:0005813 centrosome


-  Descriptions from all associated GenBank mRNAs
  AL136871 - Homo sapiens mRNA; cDNA DKFZp434N0650 (from clone DKFZp434N0650).
BC084577 - Homo sapiens chromosome 21 open reading frame 56, mRNA (cDNA clone MGC:99490 IMAGE:6646538), complete cds.
BC065570 - Homo sapiens chromosome 21 open reading frame 56, mRNA (cDNA clone MGC:74537 IMAGE:6171749), complete cds.
BC009497 - Homo sapiens chromosome 21 open reading frame 56, mRNA (cDNA clone MGC:16456 IMAGE:3949357), complete cds.
AK304535 - Homo sapiens cDNA FLJ61082 complete cds.
JD187173 - Sequence 168197 from Patent EP1572962.
CR533451 - Homo sapiens full open reading frame cDNA clone RZPDo834A0117D for gene C21orf56, chromosome 21 open reading frame 56; complete cds, incl. stopcodon.
BC093804 - Homo sapiens chromosome 21 open reading frame 56, mRNA (cDNA clone MGC:120839 IMAGE:7939649), complete cds.
BC112293 - Homo sapiens chromosome 21 open reading frame 56, mRNA (cDNA clone MGC:138498 IMAGE:8327761), complete cds.
KJ894949 - Synthetic construct Homo sapiens clone ccsbBroadEn_04343 C21orf56 gene, encodes complete protein.
HQ258090 - Synthetic construct Homo sapiens clone IMAGE:100072399 chromosome 21 open reading frame 56 (C21orf56), transcript variant 2 (C21orf56) gene, encodes complete protein.
AB528086 - Synthetic construct DNA, clone: pF1KE0414, Homo sapiens C21orf56 gene for chromosome 21 open reading frame 56, without stop codon, in Flexi system.
AM393702 - Synthetic construct Homo sapiens clone IMAGE:100001863 for hypothetical protein (C21orf56 gene).
AM393719 - Synthetic construct Homo sapiens clone IMAGE:100001859 for hypothetical protein (C21orf56 gene).
AK309847 - Homo sapiens cDNA, FLJ99888.
JD137646 - Sequence 118670 from Patent EP1572962.
JD052089 - Sequence 33113 from Patent EP1572962.
JD099524 - Sequence 80548 from Patent EP1572962.
JD550405 - Sequence 531429 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B4E323, C21orf56, CU056_HUMAN, ENST00000291672.1, ENST00000291672.2, ENST00000291672.3, ENST00000291672.4, ENST00000291672.5, NM_001142854, Q52LS9, Q6FIH5, Q6P0L3, Q9H0A9, Q9NSE5, uc011afu.1, uc011afu.2, uc011afu.3, uc011afu.4
UCSC ID: ENST00000291672.6
RefSeq Accession: NM_001142854
Protein: Q9H0A9 (aka CU056_HUMAN or CU56_HUMAN)
CCDS: CCDS46653.1

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