Human Gene NEDD9 (ENST00000379446.10_10) from GENCODE V47lift37
  Description: neural precursor cell expressed, developmentally down-regulated 9, transcript variant 1 (from RefSeq NM_006403.4)
Gencode Transcript: ENST00000379446.10_10
Gencode Gene: ENSG00000111859.17_14
Transcript (Including UTRs)
   Position: hg19 chr6:11,183,531-11,232,901 Size: 49,371 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr6:11,185,395-11,232,748 Size: 47,354 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:11,183,531-11,232,901)mRNA (may differ from genome)Protein (834 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CASL_HUMAN
DESCRIPTION: RecName: Full=Enhancer of filamentation 1; Short=hEF1; AltName: Full=CRK-associated substrate-related protein; Short=CAS-L; Short=CasL; AltName: Full=Cas scaffolding protein family member 2; AltName: Full=Neural precursor cell expressed developmentally down-regulated protein 9; Short=NEDD-9; AltName: Full=Renal carcinoma antigen NY-REN-12; AltName: Full=p105; Contains: RecName: Full=Enhancer of filamentation 1 p55;
FUNCTION: Docking protein which plays a central coordinating role for tyrosine-kinase-based signaling related to cell adhesion. May function in transmitting growth control signals between focal adhesions at the cell periphery and the mitotic spindle in response to adhesion or growth factor signals initiating cell proliferation. May play an important role in integrin beta-1 or B cell antigen receptor (BCR) mediated signaling in B- and T-cells. Integrin beta-1 stimulation leads to recruitment of various proteins including CRK, NCK and SHPTP2 to the tyrosine phosphorylated form.
SUBUNIT: Interacts with BCAR3 and SH2D3C (By similarity). Homodimer. Can heterodimerize with HLH proteins ID2, E12, E47 and also with p130cas. Forms complexes in vivo with related adhesion focal tyrosine kinase (RAFTK), adapter protein CRKL and LYN kinase. Interacts with MICAL and TXNL4/DIM1.
SUBCELLULAR LOCATION: Cytoplasm, cell cortex. Nucleus. Golgi apparatus. Cell projection, lamellipodium. Cytoplasm. Cell junction, focal adhesion. Note=Localizes to both the cell nucleus and the cell periphery and is differently localized in fibroblasts and epithelial cells. In fibroblasts is predominantly nuclear and in some cells is present in the Golgi apparatus. In epithelial cells localized predominantly in the cell periphery with particular concentration in lamellipodia but is also found in the nucleus. Isoforms p105 and p115 are predominantly cytoplasmic and associate with focal adhesions while p55 associates with mitotic spindle.
SUBCELLULAR LOCATION: Enhancer of filamentation 1 p55: Cytoplasm, cytoskeleton, spindle.
TISSUE SPECIFICITY: Widely expressed. Higher levels detected in kidney, lung, and placenta. Also detected in T-cells, B-cells and diverse cell lines. The protein has been detected in lymphocytes, in diverse cell lines, and in lung tissues.
INDUCTION: Activated upon induction of cell growth.
DOMAIN: Contains a central domain containing multiple potential SH2-binding sites and a C-terminal domain containing a divergent helix-loop-helix (HLH) motif. The SH2-binding sites putatively bind CRK, NCK and ABL SH2 domains. The HLH motif confers specific interaction with the HLH proteins ID2, E12 and E47. It is absolutely required for the induction of pseudohyphal growth in yeast and mediates homodimerization and heterodimerization with p130cas.
DOMAIN: The SH3 domain interacts with two proline-rich regions of PTK2/FAK1.
PTM: Cell cycle-regulated processing produces four isoforms: p115, p105, p65, and p55. Isoform p115 arises from p105 phosphorylation and appears later in the cell cycle. Isoform p55 arises from p105 as a result of cleavage at a caspase cleavage-related site and it appears specifically at mitosis. The p65 isoform is poorly detected.
PTM: PTK2/FAK1 phosphorylates the protein at the YDYVHL motif (conserved among all cas proteins). The SRC family kinases (FYN, SRC, LCK and CRK) are recruited to the phosphorylated sites and can phosphorylate other tyrosine residues. Ligation of either integrin beta-1 or B-cell antigen receptor on tonsillar B-cells and B-cell lines promotes tyrosine phosphorylation and both integrin and BCR-mediated tyrosine phosphorylation requires an intact actin network. In fibroblasts transformation with oncogene v-ABL results in an increase in tyrosine phosphorylation. Transiently phosphorylated following CD3 cross-linking and this phosphorylated form binds to CRK and C3G. A mutant lacking the SH3 domain is phosphorylated upon CD3 cross-linking but not upon integrin beta-1 cross-linking. Tyrosine phosphorylation occurs upon stimulation of the G-protein coupled C1a calcitonin receptor. Calcitonin-stimulated tyrosine phosphorylation is mediated by calcium- and protein kinase C-dependent mechanisms and requires the integrity of the actin cytoskeleton. Phosphorylation at Ser- 369 induces proteasomal degradation.
SIMILARITY: Belongs to the CAS family.
SIMILARITY: Contains 1 SH3 domain.

-  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
  • D013749 Tetrachlorodibenzodioxin
  • C023514 2,6-dinitrotoluene
  • D001564 Benzo(a)pyrene
  • D014212 Tretinoin
  • C028474 1,4-bis(2-(3,5-dichloropyridyloxy))benzene
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone
  • C063002 2,3-dimethoxy-1,4-naphthoquinone
  • C016403 2,4-dinitrotoluene
  • C548651 2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester
          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: 33.22 RPKM in Lung
Total median expression: 359.71 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 -47.60153-0.311 Picture PostScript Text
3' UTR -468.701864-0.251 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
IPR021901 - CAS_DUF3513
IPR014928 - Serine_rich
IPR001452 - SH3_domain

Pfam Domains:
PF00018 - SH3 domain
PF07653 - Variant SH3 domain
PF08824 - Serine rich protein interaction domain
PF12026 - Crk-Associated Substrate C-terminal domain
PF14604 - Variant SH3 domain

SCOP Domains:
47655 - STAT
50044 - SH3-domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2L81 - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q14511
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    
 RGDEnsembl   
      
      

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

Biological Process:
GO:0007010 cytoskeleton organization
GO:0007049 cell cycle
GO:0007155 cell adhesion
GO:0007165 signal transduction
GO:0007229 integrin-mediated signaling pathway
GO:0040008 regulation of growth
GO:0051017 actin filament bundle assembly
GO:0051301 cell division

Cellular Component:
GO:0000922 spindle pole
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005819 spindle
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0005938 cell cortex
GO:0030027 lamellipodium
GO:0030054 cell junction
GO:0042995 cell projection


-  Descriptions from all associated GenBank mRNAs
  BX648041 - Homo sapiens mRNA; cDNA DKFZp686G08168 (from clone DKFZp686G08168).
AK292682 - Homo sapiens cDNA FLJ75094 complete cds, highly similar to Homo sapiens neural precursor cell expressed, developmentally down-regulated 9 (NEDD9), transcript variant 1, mRNA.
BC040207 - Homo sapiens neural precursor cell expressed, developmentally down-regulated 9, mRNA (cDNA clone MGC:41852 IMAGE:4820745), complete cds.
AJ420493 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1681585.
L43821 - Homo sapiens enhancer of filamentation (HEF1) mRNA, complete cds.
JD542451 - Sequence 523475 from Patent EP1572962.
JD497629 - Sequence 478653 from Patent EP1572962.
JD241112 - Sequence 222136 from Patent EP1572962.
JD551684 - Sequence 532708 from Patent EP1572962.
JD214530 - Sequence 195554 from Patent EP1572962.
JD353666 - Sequence 334690 from Patent EP1572962.
JD148971 - Sequence 129995 from Patent EP1572962.
JD172628 - Sequence 153652 from Patent EP1572962.
JD302873 - Sequence 283897 from Patent EP1572962.
U64317 - Human Crk-associated substrate related protein Cas-L mRNA, complete cds.
DQ891725 - Synthetic construct clone IMAGE:100004355; FLH179440.01X; RZPDo839G07130D neural precursor cell expressed, developmentally down-regulated 9 (NEDD9) gene, encodes complete protein.
DQ894902 - Synthetic construct Homo sapiens clone IMAGE:100009362; FLH179436.01L; RZPDo839G07129D neural precursor cell expressed, developmentally down-regulated 9 (NEDD9) gene, encodes complete protein.
AB528553 - Synthetic construct DNA, clone: pF1KB5797, Homo sapiens NEDD9 gene for neural precursor cell expressed, developmentally down-regulated 9, without stop codon, in Flexi system.
GQ497714 - Homo sapiens large regulator RNA B2 gene, complete sequence.
AY166681 - Homo sapiens non-small cell lung carcinoma noncoding RNA, partial sequence.
BC020686 - Homo sapiens neural precursor cell expressed, developmentally down-regulated 9, mRNA (cDNA clone IMAGE:4717875), complete cds.
BC050740 - Homo sapiens neural precursor cell expressed, developmentally down-regulated 9, mRNA (cDNA clone IMAGE:6193276), containing frame-shift errors.
EU832607 - Synthetic construct Homo sapiens clone HAIB:100067636; DKFZo004H1130 neural precursor cell expressed, developmentally down-regulated 9 protein (NEDD9) gene, encodes complete protein.
EU832525 - Synthetic construct Homo sapiens clone HAIB:100067554; DKFZo008H1129 neural precursor cell expressed, developmentally down-regulated 9 protein (NEDD9) gene, encodes complete protein.
CU676642 - Synthetic construct Homo sapiens gateway clone IMAGE:100022996 5' read NEDD9 mRNA.
KJ897235 - Synthetic construct Homo sapiens clone ccsbBroadEn_06629 NEDD9 gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K9G7, A8MSJ9, CASL , CASL_HUMAN, ENST00000379446.1, ENST00000379446.2, ENST00000379446.3, ENST00000379446.4, ENST00000379446.5, ENST00000379446.6, ENST00000379446.7, ENST00000379446.8, ENST00000379446.9, G5E9Y9, NEDD9 , NM_006403, Q14511, Q5T9R4, Q5XKI0, uc318ozd.1, uc318ozd.2
UCSC ID: ENST00000379446.10_10
RefSeq Accession: NM_006403.4
Protein: Q14511 (aka CASL_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.