DreINT0050571 @ danRer10
Intron Retention
Gene
ENSDARG00000037845 | col9a3
Description
collagen, type IX, alpha 3 [Source:ZFIN;Acc:ZDB-GENE-030131-9799]
Coordinates
chr23:485800-486692:-
Coord C1 exon
chr23:486638-486692
Coord A exon
chr23:485983-486637
Coord C2 exon
chr23:485800-485982
Length
655 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGA
5' ss Score
6.56
3' ss Seq
GCGGTTTATGTTGTCCACAGATC
3' ss Score
10.22
Exon sequences
Seq C1 exon
GGCAAGCTGGCGAGTGAGCAGCACATCAGGGAACTGTGTGGATCAATGATTGATG
Seq A exon
GTATGAGCTGAGTTACACTCTTACACTGTAAAAAACATTAGCTGACTTTACTTTAAATAAGAGAGTAAACGTGTTGCCTTATCATTATTAAAGGTCCATTCTTTTCAGGTTTTAGTAATAGTATGTTAATCTGAAGAACATTTGTAGATATAAACCTGATATAAACATGTAAAGCTTGCAGTTTGTCACTTCCGCCTAAATGGATCAATGATTTTTTTCTCATCACTTCATACTTCAGTTACTCAGATCTTCTGACCAATCAAATGCTCTCTAGTATCAGACATGCCCCGCCCCCTTCATCTCATTGGTTGTTCATTTGATGTCCTTGAGCTAAACCACTCTCACTGGCAAAGTTTGAAGAAAAGCTAAATGCTATTGGCTGCTTTTTGTTAAAAGGGGGAGGAGTTACTCTATGTCCCGCCCCCTCTCTTCATTTTTCAATTAAGATTACATCAAATAAAAACATGCACATTTCAAAGCACTTCACAGGACTATAAGTAAACAAACAGCATAATTATTAAAGTTAAGTTAATGGATTTACTGACTTATTTTAAAGTAAGATCAACTTATTGATTTTAAGGCAACGGGTTTTTCATAGTAAAGTAGCTAATCATTTATTTGAGGAGGTTCCTGAAGCGGTTTATGTTGTCCACAG
Seq C2 exon
ATCAGATAGCTCAGCTTGCCGCTAACCTGAGAAGACCTCTGGCTCCTGGGGCTGTGGGACGCCCTGGACCCCCTGGACCTCCTGGAGAGCAAGGAGAAGTGGGATCTATTGGCCACCCTGGATCCCTGGGCCCACCAGGATATAGAGGACTGCCTGGAGATCTGGGTGATCCTGGTCCTAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000037845:ENSDART00000055139:29
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(7.6=26.3)
A:
NA
C2:
PF0139113=Collagen=PU(73.4=75.8)
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:
GGCAAGCTGGCGAGTGAG
R:
CTCTAGGACCAGGATCACCCA
Band lengths:
238-893
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]