BtaINT0041032 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010050 | COL16A1
Description
collagen, type XVI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr2:122573528-122573706:+
Coord C1 exon
chr2:122573528-122573563
Coord A exon
chr2:122573564-122573661
Coord C2 exon
chr2:122573662-122573706
Length
98 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
3' ss Seq
CGTGGCTTCTTATCACACAGGGG
3' ss Score
8.05
Exon sequences
Seq C1 exon
GGTAATTTCGGGGAGGTAGGGCCAGCCGGCAATCCG
Seq A exon
GTAAGTGAGCTTTGGATGCCAATAGCTCGAGGGAGCAGGACGAGGTGGGAGTGGCCCAGGCAGATGCAGGGCATCACACGTGGCTTCTTATCACACAG
Seq C2 exon
GGGCCGCCAGGGCCTGCGGGACCCACAGGCATCAAAGGGGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010050:ENSBTAT00000038016:26
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=FE(15.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(20.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAATTTCGGGGAGGTAGGGCC
R:
CTTCTCCCCTTTGATGCCTGT
Band lengths:
79-177
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]