DreINT0050573 @ danRer10
Intron Retention
Gene
ENSDARG00000037845 | col9a3
Description
collagen, type IX, alpha 3 [Source:ZFIN;Acc:ZDB-GENE-030131-9799]
Coordinates
chr23:485371-485982:-
Coord C1 exon
chr23:485800-485982
Coord A exon
chr23:485449-485799
Coord C2 exon
chr23:485371-485448
Length
351 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
ATATACTGTTCATTCTGCAGGGG
3' ss Score
8.47
Exon sequences
Seq C1 exon
ATCAGATAGCTCAGCTTGCCGCTAACCTGAGAAGACCTCTGGCTCCTGGGGCTGTGGGACGCCCTGGACCCCCTGGACCTCCTGGAGAGCAAGGAGAAGTGGGATCTATTGGCCACCCTGGATCCCTGGGCCCACCAGGATATAGAGGACTGCCTGGAGATCTGGGTGATCCTGGTCCTAGAG
Seq A exon
GTGAGAAGACGACCACATTGTGTTGTTATTAGTTGTGTTTCCAGTGAAAACAGCTGATCATTGTTAGTTTACATCAGCTCATTAAATTATACAATCATACAGCTTCTGATGTTATTAGTGTACTTTAACTGTGGAAATGAGGTCAGATTGAGCAGATTGTTAGTTTGTGTTAATGATGTTGATAATGAAAAGAGCGCCAAGGTGACTCTGCAAGATTTATTGTCAGATCTACCAATTCTATACACTTTATTTCTTTAAAAATAATCGGTATTAACTTTATGAAACTTGGAACAACTTGAAATCCTTACAGTAATTATTAATAACTGTATATATATACTGTTCATTCTGCAG
Seq C2 exon
GGGACGTCGGTGAGGCAGGTGATAAGGGGCCGATTGGTAAAGCAGTTGAAGGGCCCACTGGAGACCAGGGTGACCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000037845:ENSDART00000055139:30
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=PU(73.4=75.8)
A:
NA
C2:
PF0139113=Collagen=PD(25.0=59.3),PF0139113=Collagen=PU(25.4=63.0)
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:
ATCAGATAGCTCAGCTTGCCG
R:
GTGGTCACCCTGGTCTCCA
Band lengths:
260-611
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]