BtaINT0041050 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010050 | COL16A1
Description
collagen, type XVI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2193]
Coordinates
chr2:122588046-122588344:+
Coord C1 exon
chr2:122588046-122588099
Coord A exon
chr2:122588100-122588311
Coord C2 exon
chr2:122588312-122588344
Length
212 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGT
5' ss Score
8.37
3' ss Seq
CTCGTGTCTGTCTCTTTCAGGGA
3' ss Score
12.55
Exon sequences
Seq C1 exon
GGGGTGCCCGGGCACAACGGTTTGCCAGGACAGCCCGGGCTAACTGCAGAACTG
Seq A exon
GTAGGTACTGGCCAGATCTCATTGCCCGCCGCCTCCCCCACTCTTCTCGGGGCTGAGTTTGCCACGCCAGCACCCTTAGCCTCAGTGGGGGTCCCTCTTCCCTCCCTCTTCCCAGGCTGGGAGAAGCCTGGATGCCATGTGGCTTCCCAAGGCTTCACCTGGTGCCCTAAGTCCCCATACCCCTTCTGAGCCCTCGTGTCTGTCTCTTTCAG
Seq C2 exon
GGATCCTTGCCCATTGAACAGCACCTCCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010050:ENSBTAT00000038016:42
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=0.545
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(28.8=100)
A:
NA
C2:
PF0139113=Collagen=PD(1.7=9.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]