Human Gene SP140L (uc010fxm.1)
  Description: Homo sapiens SP140 nuclear body protein-like (SP140L), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr2:231,191,894-231,268,445 Size: 76,552 Total Exon Count: 19 Strand: +
Coding Region
   Position: hg19 chr2:231,191,985-231,267,611 Size: 75,627 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:231,191,894-231,268,445)mRNA (may differ from genome)Protein (580 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
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H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedUniProtKBBioGrid CRISPR DB

-  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;

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SP140L
CDC HuGE Published Literature: SP140L
Positive Disease Associations: Platelet Count
Related Studies:
  1. Platelet Count
    , , . [PubMed 0]

-  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: 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 -38.9091-0.427 Picture PostScript Text
3' UTR -258.89834-0.310 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

SCOP Domains:
47370 - Bromodomain
63763 - SAND domain-like
57903 - FYVE/PHD zinc finger

ModBase Predicted Comparative 3D Structure on Q9H930
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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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  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.
JD251145 - Sequence 232169 from Patent EP1572962.
JD156344 - Sequence 137368 from Patent EP1572962.
JD334115 - Sequence 315139 from Patent EP1572962.
JD255430 - Sequence 236454 from Patent EP1572962.
JD255431 - Sequence 236455 from Patent EP1572962.
JD540388 - Sequence 521412 from Patent EP1572962.
JD474538 - Sequence 455562 from Patent EP1572962.
JD263647 - Sequence 244671 from Patent EP1572962.
JD260278 - Sequence 241302 from Patent EP1572962.
JD260279 - Sequence 241303 from Patent EP1572962.
JD074289 - Sequence 55313 from Patent EP1572962.
JD316820 - Sequence 297844 from Patent EP1572962.
JD296525 - Sequence 277549 from Patent EP1572962.
JD346240 - Sequence 327264 from Patent EP1572962.
JD365858 - Sequence 346882 from Patent EP1572962.
JD533872 - Sequence 514896 from Patent EP1572962.
JD069985 - Sequence 51009 from Patent EP1572962.
JD397304 - Sequence 378328 from Patent EP1572962.
JD415262 - Sequence 396286 from Patent EP1572962.
JD345744 - Sequence 326768 from Patent EP1572962.
JD508794 - Sequence 489818 from Patent EP1572962.
JD482435 - Sequence 463459 from Patent EP1572962.
JD427090 - Sequence 408114 from Patent EP1572962.
JD254720 - Sequence 235744 from Patent EP1572962.
JD264631 - Sequence 245655 from Patent EP1572962.
JD560694 - Sequence 541718 from Patent EP1572962.
JD438217 - Sequence 419241 from Patent EP1572962.
JD433802 - Sequence 414826 from Patent EP1572962.
JD553476 - Sequence 534500 from Patent EP1572962.
JD287491 - Sequence 268515 from Patent EP1572962.
JD363101 - Sequence 344125 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: LY10L_HUMAN, NM_138402, NP_612411, Q2M375, Q4ZG65, Q9BSP3, Q9H930
UCSC ID: uc010fxm.1
RefSeq Accession: NM_138402
Protein: Q9H930 (aka LY10L_HUMAN)
CCDS: CCDS46538.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_138402.4
exon count: 19CDS single in 3' UTR: no RNA size: 2668
ORF size: 1743CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3686.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.