Human Gene SP140L (ENST00000458341.1) from GENCODE V38
  Description: Event=Alternative splicing; Named isoforms=4; Name=4; IsoId=Q9H930-4; Sequence=Displayed; Name=1; IsoId=Q9H930-1; Sequence=VSP_040889; Name=2; IsoId=Q9H930-2; Sequence=VSP_031833; Note=No experimental confirmation available; Name=3; IsoId=Q9H930-3; Sequence=VSP_031830, VSP_031831, VSP_031832; Note=No experimental confirmation available; (from UniProt Q9H930)
Gencode Transcript: ENST00000458341.1
Gencode Gene: ENSG00000185404.17
Transcript (Including UTRs)
   Position: hg38 chr2:230,342,070-230,372,744 Size: 30,675 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg38 chr2:230,357,959-230,371,665 Size: 13,707 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Methods
Data last updated at UCSC: 2021-09-27 09:51:20

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:230,342,070-230,372,744)mRNA (may differ from genome)Protein (129 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblExonPrimerGeneCardsHGNCHPRD
LynxMGIneXtProtPubMedUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: LY10L_HUMAN
DESCRIPTION: RecName: Full=Nuclear body protein SP140-like protein;
SIMILARITY: Contains 1 bromo domain.
SIMILARITY: Contains 1 HSR domain.
SIMILARITY: Contains 1 PHD-type zinc finger.
SIMILARITY: Contains 1 SAND domain.
SEQUENCE CAUTION: Sequence=AAX88869.1; Type=Erroneous gene model prediction; Sequence=BAB14413.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 15.94 RPKM in Spleen
Total median expression: 162.79 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 -76.40258-0.296 Picture PostScript Text
3' UTR -311.101079-0.288 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
IPR001487 - Bromodomain
IPR000770 - SAND_dom
IPR010919 - SAND_dom-like
IPR004865 - Sp100
IPR019786 - Zinc_finger_PHD-type_CS
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00439 - Bromodomain
PF00628 - PHD-finger
PF01342 - SAND domain
PF03172 - HSR domain

ModBase Predicted Comparative 3D Structure on Q9H930
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:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0046872 metal ion binding

Biological Process:
GO:0006357 regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus
GO:0016604 nuclear body


-  Descriptions from all associated GenBank mRNAs
  AK301267 - Homo sapiens cDNA FLJ60913 complete cds, highly similar to Nuclear body protein SP140.
KF419365 - Homo sapiens SP140L-1 protein (SP140L) mRNA, complete cds, alternatively spliced.
KF419366 - Homo sapiens SP140L-2 protein (SP140L) mRNA, complete cds, alternatively spliced.
KF419367 - Homo sapiens SP140L-3 protein (SP140L) mRNA, complete cds, alternatively spliced.
BC004921 - Homo sapiens SP140 nuclear body protein-like, mRNA (cDNA clone IMAGE:3546703), complete cds.
JD440694 - Sequence 421718 from Patent EP1572962.
AK023116 - Homo sapiens cDNA FLJ13054 fis, clone NT2RP3001527, highly similar to Human Sp140 protein (Sp140) mRNA.
JD189943 - Sequence 170967 from Patent EP1572962.
BC105007 - Homo sapiens cDNA clone IMAGE:8144010.
BC143624 - Homo sapiens cDNA clone IMAGE:9052137.
JD481349 - Sequence 462373 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BC004921, LY10L_HUMAN, Q2M375, Q4ZG65, Q9BSP3, Q9H930, uc010fxn.1, uc010fxn.2, uc010fxn.3
UCSC ID: ENST00000458341.1
RefSeq Accession: NM_001352894
Protein: Q9H930 (aka LY10L_HUMAN)

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