Special

HsaEX0001787 @ hg19

Exon Skipping

Gene
Description
aggrecan [Source:HGNC Symbol;Acc:319]
Coordinates
chr15:89399751-89414771:+
Coord C1 exon
chr15:89399751-89402648
Coord A exon
chr15:89403557-89403670
Coord C2 exon
chr15:89414613-89414771
Length
114 bp
Sequences
Splice sites
3' ss Seq
CTCTCCCCTGGGGGTTGCAGCCC
3' ss Score
4.93
5' ss Seq
TAGGTAAGG
5' ss Score
9.31
Exon sequences
Seq C1 exon
CGGGGCATCTGCCGCCCCTGAGGCCAGCAGAGAAGATTCTGGGTCCCCTGATCTGAGTGAAACCACCTCTGCATTCCACGAAGCTAACCTTGAGAGATCCTCTGGCCTAGGAGTGAGCGGCAGCACTTTGACATTTCAAGAAGGCGAGGCGTCCGCTGCCCCAGAAGTGAGTGGAGAATCCACCACCACCAGTGATGTGGGGACAGAGGCACCAGGCTTGCCTTCAGCCACTCCCACGGCTTCTGGAGACAGGACTGAAATCAGCGGAGACCTGTCTGGTCACACCTCGCAGCTGGGCGTTGTCATCAGCACCAGCATCCCAGAGTCTGAGTGGACCCAGCAGACCCAGCGCCCTGCAGAGACGCATCTAGAAATTGAGTCCTCAAGCCTCCTGTACTCAGGAGAAGAGACTCACACAGTCGAAACAGCCACCTCCCCAACAGATGCTTCCATCCCAGCTTCTCCGGAATGGAAACGTGAATCAGAATCAACTGCTGCAG
Seq A exon
CCCCCGCCAGGTCCTGTGCAGAGGAGCCCTGTGGAGCTGGGACCTGCAAGGAGACAGAGGGACACGTCATATGCCTGTGCCCCCCTGGCTACACTGGCGAGCACTGTAACATAG
Seq C2 exon
ACCAGGAGGTATGTGAGGAGGGCTGGAACAAGTACCAGGGCCACTGTTACCGCCACTTCCCGGACCGCGAGACCTGGGTGGATGCTGAGCGCCGGTGTCGGGAGCAGCAGTCACACCTGAGCAGCATCGTCACCCCCGAGGAGCAGGAGTTTGTCAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000157766_MULTIEX1-1/2=C1-C2
Average complexity
C1
Mappability confidence:
100%=100=100%
Protein Impact

Alternative protein isoforms (Ref)

No structure available
Features
Disorder rate (Iupred):
  C1=0.954 A=0.179 C2=0.244
Domain overlap (PFAM):

C1:
NO
A:
PF0000822=EGF=WD(100=78.9),PF0000822=EGF=PU(5.3=5.3)
C2:
PF0005916=Lectin_C=PU(30.2=59.3)


Main Inclusion Isoform:


Main Skipping Isoform:


Other Inclusion Isoforms:


Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
ALTERNATIVE
Chicken
(galGal3)
ALTERNATIVE
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGTCATCAGCACCAGCATCC
R:
CAGTGGCCCTGGTACTTGTTC
Band lengths:
247-361
Functional annotations
There are 1 annotated functions for this event
PMID: 14722076
This event
The proteoglycans aggrecan, versican, neurocan, and brevican bind hyaluronan through their N-terminal G1 domains, and other extracellular matrix proteins through the C-type lectin repeat in their C-terminal G3 domains. Here the authors identify tenascin-C as a ligand for the lectins of all these proteoglycans and map the binding site on the tenascin molecule to fibronectin type III repeats, which corresponds to the proteoglycan lectin-binding site on tenascin-R. In the G3 domain, the C-type lectin is flanked by two epidermal growth factor (EGF) repeats and a complement regulatory protein-like motif. In aggrecan, the EGF repeats are subject to alternative splicing (each repeat is encoded by a cassette exon: EGF-like 1 is encoded by HsaEX0001787, and EGF-like 2 is encoded by HsaEX0001788). To investigate if these flanking modules affect the C-type lectin ligand interactions, the authors produced recombinant proteins corresponding to aggrecan G3 splice variants. The G3 variant proteins containing the C-type lectin showed different affinities for various ligands, including tenascin-C, tenascin-R, fibulin-1, and fibulin-2. The presence of an EGF motif enhanced the affinity of interaction, and in particular the splice variant containing both EGF motifs had significantly higher affinity for ligands, such as tenascin-R and fibulin-2.


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

  • The Cancer Genome Atlas (TCGA)
  • Genotype-Tissue Expression Project (GTEx)
  • Autistic and control brains
  • Pre-implantation embryo development