DreINT0049023 @ danRer10
Intron Retention
Gene
ENSDARG00000012422 | col11a2
Description
collagen, type XI, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-000208-23]
Coordinates
chr19:7266391-7267129:-
Coord C1 exon
chr19:7267076-7267129
Coord A exon
chr19:7266671-7267075
Coord C2 exon
chr19:7266391-7266670
Length
405 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
GAATTCTGCTTTTGTTTTAGGGT
3' ss Score
10.2
Exon sequences
Seq C1 exon
GGTGGGGCTGGTCCTAAAGGAGAAAAGGGTGTACAAGGACCACCAGGACCACCT
Seq A exon
GTGAGTTGAAAATGAACACCACAACATTATGTTATAAATTAGTATTAAACATAATAATTCATGCTTTATAGTATTTCAGTTAAAATAACAAATTATTGATTTATTTTATTATAGTGCTTCATGTAAGATGATGTTTAGTTGTTTACTCGAGGTTTGATTATTTGTTTGTTTCTGAAAGTCAGTTTTTAGTTCCGTCACTCAATGACATTGCATATGTTGTTAAAGACTAGAAGGGATGATTTAGTCAAGAAGCTATTTGTAGTCTGACTTGCTTATTTTCCATGACATAATCTCACACTATTGAAATATTTTTGAGATGAACATTAAAAACAAACACTATAATTAACACTTTGAAACAGAGTTCCTGCATCTTTTAAATGCATCTGAATTCTGCTTTTGTTTTAG
Seq C2 exon
GGTCCCCCTGGTGATGTCATCCAGCCGCTGCCCATTCAGATCCCCAAGAAGTCCAAGCGCTCCATCGACGCCAGTAAGATTCTGTCTGAGGCTGACGCTGAGGCTGCCGACACCACTGGCTCTGAGTTCCTGACTGGTAATGAAGGAATGGAGGAGATCTTCGGCTCACTTAATTCCCTGCGCCAGGAGATCGAGAGCATGCGCTTCCCATTGGGCACAAAGGAGAGCCCCGGCCGCACCTGCCAGGATCTCCATCTCAGCCAACCAGATCTGAAAGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012422:ENSDART00000104799:60
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=0.809
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(28.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(13.3=8.5),PF0141013=COLFI=PU(12.7=28.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGGGGCTGGTCCTAAAGG
R:
CGTCTTTCAGATCTGGTTGGCT
Band lengths:
334-739
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]