DreINT0050566 @ danRer10
Intron Retention
Gene
ENSDARG00000037845 | col9a3
Description
collagen, type IX, alpha 3 [Source:ZFIN;Acc:ZDB-GENE-030131-9799]
Coordinates
chr23:489956-490686:-
Coord C1 exon
chr23:490615-490686
Coord A exon
chr23:489992-490614
Coord C2 exon
chr23:489956-489991
Length
623 bp
Sequences
Splice sites
5' ss Seq
CGGGTCAGT
5' ss Score
6.55
3' ss Seq
TGTGTGTGTGTGTGTCTTAGGGA
3' ss Score
11.05
Exon sequences
Seq C1 exon
GGTGTGAAAGGAGCTTTGGGAGATCCAGGTCTGCCTGGTCCAACTGGAATCAGAGGCGGGTTTGGAGAGCGG
Seq A exon
GTCAGTCATGCACAATAATCTCTCTCAGTAATTGTGTTTGTTTGTTTCTAGACTTTATTTACCCCTAAGCAGGACGTTTTTTGTATTTCAATATAGTGTGATGCAGTAAAGAATTTAAAAACAGTCAGAATTATTCACCCTCCTGGGAATCTCCTTTCCAGATATTTCCCAGATGCTGTTTCTCAGATTGAGGAGTTGTTCACAGTGTTTCCTCTAATGTTTGTCTTCTGGAGAAAGTCTTATTTGTTTAATTTGTGCTAGAATAAAGGCTGTTTTTAATAGTTTTTAACCCATTTTGAGGTCAATCTTATTAGCCACTTCAGCAATACTAGTGTTGGATTATACCCAGTAGGGTAAGCTAAATGATCCAGTTTTTGCTTTGACATATTTTTTCTCTAACCCCATTGTCAGATTATTTAACTTGTTTTCAGGAGAAACTCACTTCATTTTGACTCATTTTTTCTGAAAACACACAATATATTTATTACTTGTCTAGAAAATGCTTCTTGATTTAAGAGTTTGTAGATATTTGGACTAGAAGCACGACTCTGAGTAATTGCACATGTTTAACTCTCTCTCTCTCTCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCTTAG
Seq C2 exon
GGACCAGGTGGAGCTGGAGGACCTAAAGGAGACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000037845:ENSDART00000055139:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(26.7=83.3),PF0139113=Collagen=PU(31.7=83.3)
A:
NA
C2:
PF0139113=Collagen=FE(14.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]