DreINT0049570 @ danRer10
Intron Retention
Gene
ENSDARG00000069093 | col2a1a
Description
collagen, type II, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-980526-192]
Coordinates
chr8:21177730-21177937:+
Coord C1 exon
chr8:21177730-21177783
Coord A exon
chr8:21177784-21177883
Coord C2 exon
chr8:21177884-21177937
Length
100 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAT
5' ss Score
7.87
3' ss Seq
CTTTTATCTTTTTCTCACAGGGT
3' ss Score
10.95
Exon sequences
Seq C1 exon
GGTTTGACTGGTCCAATTGGCCCACCTGGTCCTTCTGGTCCCAATGGCGCAAAG
Seq A exon
GTACATGCCTCATCCTTCATGTGGTCTTTTCCCAATGGTTGATAGTTGTAGTTGAAATTATTTGAGCAGATTGTTTAATTCTTTTATCTTTTTCTCACAG
Seq C2 exon
GGTGAAACTGGTCCTATTGGTTCAATTGGTGCTCCTGGTGCTCGTGGTGCCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069093:ENSDART00000100234:36
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(24.6=88.9),PF0139113=Collagen=PU(20.0=77.8)
A:
NA
C2:
PF0139113=Collagen=PD(5.6=22.2),PF0139113=Collagen=FE(22.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTGACTGGTCCAATTGGCCC
R:
CACGAGCACCAGGAGCAC
Band lengths:
98-198
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]