Human Gene HNRPLL (uc021vgc.1) Description and Page Index
  Description: Homo sapiens heterogeneous nuclear ribonucleoprotein L-like (HNRPLL), transcript variant 1, mRNA.
RefSeq Summary (NM_138394): HNRNPLL is a master regulator of activation-induced alternative splicing in T cells. In particular, it alters splicing of CD45 (PTPRC; MIM 151460), a tyrosine phosphatase essential for T-cell development and activation (Oberdoerffer et al., 2008 [PubMed 18669861]).[supplied by OMIM, Aug 2008].
Transcript (Including UTRs)
   Position: hg19 chr2:38,790,328-38,830,178 Size: 39,851 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr2:38,791,324-38,829,768 Size: 38,445 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:38,790,328-38,830,178)mRNA (may differ from genome)Protein (542 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaBioGPSCGAP
EnsemblEntrez GeneExonPrimerGeneCardsGeneNetworkH-INV
HGNCHPRDLynxMGIneXtProtOMIM
PubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: HNRLL_HUMAN
DESCRIPTION: RecName: Full=Heterogeneous nuclear ribonucleoprotein L-like; Short=hnRNPLL; AltName: Full=Stromal RNA-regulating factor;
FUNCTION: RNA-binding protein that functions as regulator of alternative splicing for multiple target mRNAs, including PTPRC/CD45 and STAT5A. Required for alternative splicing of PTPRC.
SUBUNIT: Interacts with HNRNPL.
TISSUE SPECIFICITY: Widely expressed. Detected in bone marrow stroma cells, skeletal muscle, heart, placenta, pancreas, kidney and lung.
INDUCTION: Up-regulated in stimulated T-cells.
SIMILARITY: Contains 3 RRM (RNA recognition motif) domains.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): HNRPLL
CDC HuGE Published Literature: HNRPLL
Positive Disease Associations: Respiratory Function Tests
Related Studies:
  1. Respiratory Function Tests
    Jemma B Wilk et al. BMC medical genetics 2007, Framingham Heart Study genome-wide association: results for pulmonary function measures., BMC medical genetics. [PubMed 17903307]
    GSTO2 and IL6R are credible candidate genes for association to pulmonary function identified by GWA. These and other observed associations warrant replication studies. This resource of GWA results for pulmonary function measures is publicly available at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?id=phs000007 webcite.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 14.28 RPKM in Testis
Total median expression: 315.56 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 -222.60410-0.543 Picture PostScript Text
3' UTR -224.31996-0.225 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
IPR006536 - HnRNP-L_PTB
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF13893 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on Q8WVV9
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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding

Biological Process:
GO:0006397 mRNA processing
GO:0033120 positive regulation of RNA splicing

Cellular Component:
GO:0005634 nucleus
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  AY236963 - Homo sapiens stromal RNA regulating factor mRNA, complete cds, alternatively spliced.
AL512692 - Homo sapiens mRNA; cDNA DKFZp667I103 (from clone DKFZp667I103).
AK000155 - Homo sapiens cDNA FLJ20148 fis, clone COL08032, highly similar to ROL_HUMAN HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN L.
AK291462 - Homo sapiens cDNA FLJ77557 complete cds, highly similar to Homo sapiens heterogeneous nuclear ribonucleoprotein L-like (HNRPLL), mRNA.
AY236962 - Homo sapiens stromal RNA regulating factor mRNA, complete cds; alternatively spliced.
BC017480 - Homo sapiens heterogeneous nuclear ribonucleoprotein L-like, mRNA (cDNA clone MGC:15775 IMAGE:3502860), complete cds.
AK292259 - Homo sapiens cDNA FLJ77927 complete cds.
KU178839 - Homo sapiens heterogeneous nuclear ribonucleoprotein L-like isoform 1 (HNRPLL) mRNA, partial cds.
KU178840 - Homo sapiens heterogeneous nuclear ribonucleoprotein L-like isoform 2 (HNRPLL) mRNA, partial cds, alternatively spliced.
KU178841 - Homo sapiens heterogeneous nuclear ribonucleoprotein L-like isoform 3 (HNRPLL) mRNA, complete cds, alternatively spliced.
JD553407 - Sequence 534431 from Patent EP1572962.
JD063519 - Sequence 44543 from Patent EP1572962.
JD090775 - Sequence 71799 from Patent EP1572962.
DQ575677 - Homo sapiens piRNA piR-43789, complete sequence.
BC008217 - Homo sapiens heterogeneous nuclear ribonucleoprotein L-like, mRNA (cDNA clone MGC:5437 IMAGE:3449607), complete cds.
KJ903589 - Synthetic construct Homo sapiens clone ccsbBroadEn_12983 HNRPLL gene, encodes complete protein.
CU675994 - Synthetic construct Homo sapiens gateway clone IMAGE:100019827 5' read HNRPLL mRNA.

-  Other Names for This Gene
  Alternate Gene Symbols: BLOCK24, HNRLL_HUMAN, NM_138394, NP_612403, Q53T80, Q5JB51, Q659B9, Q8IVH5, Q8IVH6, Q8WVV9, Q96HR5, SRRF
UCSC ID: uc021vgc.1
RefSeq Accession: NM_138394
Protein: Q8WVV9 (aka HNRLL_HUMAN)
CCDS: CCDS1796.2, CCDS46261.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_138394.3
exon count: 13CDS single in 3' UTR: no RNA size: 3053
ORF size: 1629CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3421.50frame shift in genome: no % Coverage: 99.41
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 436# strange splices: 1
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.