Special

RnoEX0005781 @ rn6

Exon Skipping

Gene
Description
aggrecan [Source:RGD Symbol;Acc:68358]
Coordinates
chr1:140808277-140821498:+
Coord C1 exon
chr1:140808277-140811747
Coord A exon
chr1:140818264-140818377
Coord C2 exon
chr1:140821340-140821498
Length
114 bp
Sequences
Splice sites
3' ss Seq
TGGCCCTTGGTTTCTTGCAGACA
3' ss Score
8.98
5' ss Seq
TCGGTACGG
5' ss Score
8.77
Exon sequences
Seq C1 exon
TGCTGCCCCTGAGGCCAGCAGTCAATTGTCTGAGTTCCCAGATCTGCATGGAATCACCTCTGCCTCCCGTGAAACAGATCTGGAGATGACAACCCCAGGCACGGAGGTGAGCAGCAACCCATGGACCTTTCAGGAAGGCACCAGGGAGGGATCCGCTGCTCCAGAAGTGAGTGGAGAATCTAGCACTACCTCCGACATAGATGCAGGCACTTCAGGTGTGCCTTTTGCCACGCCCATGACTTCTGGAGACAGGACTGAAATCAGTGGAGAATGGTCTGATCATACCTCAGAGGTGAATGTTACCGTCAGCACCACCGTCCCAGAGTCCAGGTGGGCCCAGTCTACCCAGCACCCTACAGAGACACTTCAAGAAATCGGATCCCCAAATCCCTCATACTCAGGAGAAGAGACCCAAACAGCAGAAACAGCCAAGTCCCTGACAGACACCCCTACCCTTGCTTCTCCAGAAGGGTCAGGAGAAACAGAGTCAACCGCTGCAG
Seq A exon
ACATTGATGAGTGCCTCTCAAGCCCTTGTCTGAATGGAGCCACCTGCGTGGATGCCTTGGACACTTTCACATGCTTATGCCTTCCGAGCTACAGAGGGGACCTGTGTGAGATCG
Seq C2 exon
ACCAGGAGCAATGTGAGGAGGGGTGGACCAAGTTCCAGGGCCACTGTTATCGCCACTTTCCCGACCGCGAGACCTGGGTGGATGCAGAGAGACGGTGTCGGGAGCAGCAGTCACATCTGAGCAGCATCGTCACCCCTGAGGAACAGGAGTTCGTCAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028992_CASSETTE1
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact

Alternative protein isoforms (Ref)

No structure available
Features
Disorder rate (Iupred):
  C1=0.962 A=0.000 C2=0.250
Domain overlap (PFAM):

C1:
NO
A:
PF0000822=EGF=WD(100=79.5)
C2:
PF0005916=Lectin_C=PU(30.2=59.3)


Main Inclusion Isoform:


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
ALTERNATIVE
Chicken
(galGal3)
ALTERNATIVE
Zebrafish
(danRer10)
ALTERNATIVE
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATGTTACCGTCAGCACCACC
R:
CGATAACAGTGGCCCTGGAAC
Band lengths:
257-371
Functional annotations
There are 1 annotated functions for this event
PMID: 14722076
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]