Human Gene INTS11 (ENST00000411962.5_4) from GENCODE V47lift37
  Description: Nucleus (from UniProt C9IYS7)
Gencode Transcript: ENST00000411962.5_4
Gencode Gene: ENSG00000127054.22_11
Transcript (Including UTRs)
   Position: hg19 chr1:1,246,981-1,260,053 Size: 13,073 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr1:1,247,239-1,259,988 Size: 12,750 Coding Exon Count: 15 

Page IndexSequence and LinksPrimersGene AllelesRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:1,246,981-1,260,053)mRNA (may differ from genome)Protein (502 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblExonPrimerGeneCardsMGIPubMedUniProtKB
Wikipedia

-  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


+  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: 52.46 RPKM in Brain - Cerebellum
Total median expression: 1300.32 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 -27.9065-0.429 Picture PostScript Text
3' UTR -97.20258-0.377 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
IPR022712 - Beta_Casp
IPR011108 - RMMBL

Pfam Domains:
PF07521 - Zn-dependent metallo-hydrolase RNA specificity domain
PF10996 - Beta-Casp domain
PF16661 - Metallo-beta-lactamase superfamily domain

SCOP Domains:
56281 - Metallo-hydrolase/oxidoreductase

ModBase Predicted Comparative 3D Structure on C9IYS7
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 orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0005654 nucleoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK000549 - Homo sapiens cDNA FLJ20542 fis, clone KAT11395.
BC000675 - Homo sapiens cleavage and polyadenylation specific factor 3-like, mRNA (cDNA clone IMAGE:3349422), partial cds.
AL136813 - Homo sapiens mRNA; cDNA DKFZp434A1923 (from clone DKFZp434A1923).
BC007978 - Homo sapiens cleavage and polyadenylation specific factor 3-like, mRNA (cDNA clone MGC:14999 IMAGE:3836956), complete cds.
BC042444 - Homo sapiens cleavage and polyadenylation specific factor 3-like, mRNA (cDNA clone IMAGE:5167769), containing frame-shift errors.
AK058018 - Homo sapiens cDNA FLJ25289 fis, clone STM07125.
BC013904 - Homo sapiens cleavage and polyadenylation specific factor 3-like, mRNA (cDNA clone IMAGE:3619747), partial cds.
BC047576 - Homo sapiens cDNA clone IMAGE:4814349, containing frame-shift errors.
BC008041 - Homo sapiens cleavage and polyadenylation specific factor 3-like, mRNA (cDNA clone MGC:15050 IMAGE:3831587), complete cds.
BC020199 - Homo sapiens cleavage and polyadenylation specific factor 3-like, mRNA (cDNA clone MGC:31782 IMAGE:4642543), complete cds.
AK123641 - Homo sapiens cDNA FLJ41647 fis, clone FEBRA2024136.
AK056652 - Homo sapiens cDNA FLJ32090 fis, clone OCBBF2000719, highly similar to Homo sapiens cleavage and polyadenylation specific factor 3-like, transcript variant 1, mRNA.
AK092190 - Homo sapiens cDNA FLJ34871 fis, clone NT2NE2014758.
AK021939 - Homo sapiens cDNA FLJ11877 fis, clone HEMBA1007087, weakly similar to CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 100 KD SUBUNIT.
AK023356 - Homo sapiens cDNA FLJ13294 fis, clone OVARC1001232, weakly similar to CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR, 100 KD SUBUNIT.
JD483432 - Sequence 464456 from Patent EP1572962.
KF274554 - Homo sapiens minisatellite 33.15 tagged transcript pAKT-42 sequence.
AK291387 - Homo sapiens cDNA FLJ77752 complete cds.
JD187606 - Sequence 168630 from Patent EP1572962.
JD157172 - Sequence 138196 from Patent EP1572962.
JD546574 - Sequence 527598 from Patent EP1572962.
CR533557 - Homo sapiens full open reading frame cDNA clone RZPDo834G0521D for gene FLJ20542, hypothetical protein FLJ20542; complete cds, incl. stopcodon.
AK297350 - Homo sapiens cDNA FLJ55759 complete cds, highly similar to Homo sapiens cleavage and polyadenylation specific factor 3-like, transcript variant 1, mRNA.
KJ904787 - Synthetic construct Homo sapiens clone ccsbBroadEn_14181 CPSF3L gene, encodes complete protein.
KJ902732 - Synthetic construct Homo sapiens clone ccsbBroadEn_12126 CPSF3L gene, encodes complete protein.
AB463529 - Synthetic construct DNA, clone: pF1KB8303, Homo sapiens CPSF3L gene for cleavage and polyadenylation specific factor 3-like, without stop codon, in Flexi system.
AM393218 - Synthetic construct Homo sapiens clone IMAGE:100001720 for hypothetical protein (CPSF3L gene).
JD172802 - Sequence 153826 from Patent EP1572962.
JD381154 - Sequence 362178 from Patent EP1572962.
JD470340 - Sequence 451364 from Patent EP1572962.
JD543682 - Sequence 524706 from Patent EP1572962.
JD065356 - Sequence 46380 from Patent EP1572962.
JD360810 - Sequence 341834 from Patent EP1572962.
JD395250 - Sequence 376274 from Patent EP1572962.
JD438063 - Sequence 419087 from Patent EP1572962.
JD270293 - Sequence 251317 from Patent EP1572962.
JD511727 - Sequence 492751 from Patent EP1572962.
JD057185 - Sequence 38209 from Patent EP1572962.
AK027767 - Homo sapiens cDNA FLJ14861 fis, clone PLACE1001729.
AK022675 - Homo sapiens cDNA FLJ12613 fis, clone NT2RM4001594.

-  Other Names for This Gene
  Alternate Gene Symbols: AK058018, C9IYS7, C9IYS7_HUMAN, CPSF3L , ENST00000411962.1, ENST00000411962.2, ENST00000411962.3, ENST00000411962.4, hCG_20422 , INTS11 , uc319iaa.1
UCSC ID: ENST00000411962.5_4
RefSeq Accession: NM_001256460.2
Protein: C9IYS7

-  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.