DreINT0049554 @ danRer10
Intron Retention
Gene
ENSDARG00000069093 | col2a1a
Description
collagen, type II, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-980526-192]
Coordinates
chr8:21174423-21174703:+
Coord C1 exon
chr8:21174423-21174521
Coord A exon
chr8:21174522-21174649
Coord C2 exon
chr8:21174650-21174703
Length
128 bp
Sequences
Splice sites
5' ss Seq
TCTGTACGT
5' ss Score
4.47
3' ss Seq
ACTCTGCTGTATTTATACAGGGA
3' ss Score
7.56
Exon sequences
Seq C1 exon
GGTGCTTCTGGCATTGCTGGTGCTCCTGGTTTCCCAGGACCACGTGGTCCACCAGGACCTCAGGGAGCCACTGGACCTCTTGGGCCTAAAGGACAATCT
Seq A exon
GTACGTGAAGATGTCTTGAACATGTTCTCAGTGTCTCCCAGACATCGATTAGTAATTTTATACAGTTGATCCGGAGTGAAGATTAGTTTGCCATCATACTAATTGAAAACTCTGCTGTATTTATACAG
Seq C2 exon
GGAGACCCTGGTATCCCAGGATTCAAAGGCGAGGCTGGACCCAAGGGAGAGCGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069093:ENSDART00000100234:21
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(17.9=42.4),PF0139113=Collagen=FE(34.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.5=100),PF0139113=Collagen=PU(6.6=27.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTCTGGCATTGCTGGTGCTC
R:
CTCTCCCTTGGGTCCAGCC
Band lengths:
146-274
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]