Human Gene NSRP1 (ENST00000247026.10_11) from GENCODE V47lift37
  Description: nuclear speckle splicing regulatory protein 1, transcript variant 1 (from RefSeq NM_032141.4)
Gencode Transcript: ENST00000247026.10_11
Gencode Gene: ENSG00000126653.18_15
Transcript (Including UTRs)
   Position: hg19 chr17:28,443,834-28,513,493 Size: 69,660 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr17:28,443,862-28,512,692 Size: 68,831 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:28,443,834-28,513,493)mRNA (may differ from genome)Protein (558 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NSRP1_HUMAN
DESCRIPTION: RecName: Full=Nuclear speckle splicing regulatory protein 1; AltName: Full=Coiled-coil domain-containing protein 55; AltName: Full=Nuclear speckle-related protein 70; Short=NSrp70;
FUNCTION: RNA-binding protein that mediates pre-mRNA alternative splicing regulation.
SUBUNIT: Interacts (via C-terminus) with SRSF1. Interacts (via C- terminus) with SRSF2.
SUBCELLULAR LOCATION: Nucleus. Nucleus speckle. Note=Colocalizes with splicing factors SRSF1 and SRSF2 in speckles.
TISSUE SPECIFICITY: Expressed in dendritic cells, T-cells, B-cells and natural killer cells. Expressed in secondary lymphoid organs such as spleen and mesenteric, axillary and brachial lymph nodes.
INDUCTION: Up-regulated in motile T-cells.
SIMILARITY: Belongs to the NSRP1 family.

-  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

+  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: 13.42 RPKM in Testis
Total median expression: 441.44 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -5.2028-0.186 Picture PostScript Text
3' UTR -197.20801-0.246 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
IPR018612 - DUF2040

Pfam Domains:
PF09745 - Coiled-coil domain-containing protein 55 (DUF2040)

ModBase Predicted Comparative 3D Structure on Q9H0G5
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 orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

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

Biological Process:
GO:0000381 regulation of alternative mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0032502 developmental process

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016607 nuclear speck
GO:1990904 ribonucleoprotein complex


-  Descriptions from all associated GenBank mRNAs
  AK297102 - Homo sapiens cDNA FLJ50801 complete cds, highly similar to Coiled-coil domain-containing protein 55.
AL136806 - Homo sapiens mRNA; cDNA DKFZp434K1421 (from clone DKFZp434K1421).
BC062425 - Homo sapiens coiled-coil domain containing 55, mRNA (cDNA clone IMAGE:6654717).
AK094552 - Homo sapiens cDNA FLJ37233 fis, clone BRAMY2002072.
AK313963 - Homo sapiens cDNA, FLJ94609.
BC105044 - Homo sapiens coiled-coil domain containing 55, mRNA (cDNA clone MGC:132704 IMAGE:8144047), complete cds.
BC105046 - Homo sapiens coiled-coil domain containing 55, transcript variant 1, mRNA (cDNA clone MGC:132706 IMAGE:8144049), complete cds.
BC143417 - Homo sapiens cDNA clone IMAGE:9051925, containing frame-shift errors.
BC143539 - Homo sapiens coiled-coil domain containing 55, mRNA (cDNA clone IMAGE:9052050), partial cds.
BC040118 - Homo sapiens coiled-coil domain containing 55, mRNA (cDNA clone MGC:48714 IMAGE:5176197), complete cds.
AF161358 - Homo sapiens HSPC095 mRNA, partial cds.
BC016313 - Homo sapiens coiled-coil domain containing 55, mRNA (cDNA clone IMAGE:4099763), partial cds.
AB462988 - Synthetic construct DNA, clone: pF1KB8663, Homo sapiens CCDC55 gene for coiled-coil domain containing 55, without stop codon, in Flexi system.
AM392705 - Synthetic construct Homo sapiens clone IMAGE:100001704 for hypothetical protein (CCDC55 gene).
AM392719 - Synthetic construct Homo sapiens clone IMAGE:100001707 for hypothetical protein (CCDC55 gene).
CR533555 - Homo sapiens full open reading frame cDNA clone RZPDo834E0521D for gene DKFZP434K1421, hypothetical protein DKFZp434K1421; complete cds, incl. stopcodon.
DQ588592 - Homo sapiens piRNA piR-55704, complete sequence.
JD123052 - Sequence 104076 from Patent EP1572962.
JD184277 - Sequence 165301 from Patent EP1572962.
JD508687 - Sequence 489711 from Patent EP1572962.
JD338224 - Sequence 319248 from Patent EP1572962.
JD465042 - Sequence 446066 from Patent EP1572962.
JD179311 - Sequence 160335 from Patent EP1572962.
JD291654 - Sequence 272678 from Patent EP1572962.
JD197316 - Sequence 178340 from Patent EP1572962.
JD075244 - Sequence 56268 from Patent EP1572962.
JD112036 - Sequence 93060 from Patent EP1572962.
JD089240 - Sequence 70264 from Patent EP1572962.
JD119488 - Sequence 100512 from Patent EP1572962.
JD243301 - Sequence 224325 from Patent EP1572962.
JD500554 - Sequence 481578 from Patent EP1572962.
JD199398 - Sequence 180422 from Patent EP1572962.
JD532998 - Sequence 514022 from Patent EP1572962.
JD250931 - Sequence 231955 from Patent EP1572962.
JD380248 - Sequence 361272 from Patent EP1572962.
JD298960 - Sequence 279984 from Patent EP1572962.
JD502224 - Sequence 483248 from Patent EP1572962.
BC046116 - Homo sapiens coiled-coil domain containing 55, mRNA (cDNA clone IMAGE:3913258).

-  Other Names for This Gene
  Alternate Gene Symbols: CCDC55, ENST00000247026.1, ENST00000247026.2, ENST00000247026.3, ENST00000247026.4, ENST00000247026.5, ENST00000247026.6, ENST00000247026.7, ENST00000247026.8, ENST00000247026.9, NM_032141, NSRP1_HUMAN, NSRP70, Q6FI71, Q9H0G5, uc317euy.1, uc317euy.2
UCSC ID: ENST00000247026.10_11
RefSeq Accession: NM_032141.4
Protein: Q9H0G5 (aka NSRP1_HUMAN)

-  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.