BtaINT0042278 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019081 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr22:51887552-51887825:+
Coord C1 exon
chr22:51887552-51887605
Coord A exon
chr22:51887606-51887776
Coord C2 exon
chr22:51887777-51887825
Length
171 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
TTGTGGTCTTGGGCTCCTAGGAG
3' ss Score
6.45
Exon sequences
Seq C1 exon
GGGCGACCAGGCCCCGCGGGGCCCCGTGGTGAAAAGGGAGAAGCTGCGCTGACG
Seq A exon
GTGAGTGTGTGTGGGGCAGGGGGGCGGGGTGGTGCCCTGCCTCCTTCTCCCGACCCCTTGGACCCTGGGCCCTGACTCTGCACTGTTCCTCCACGATCCCTGCATCACGTACCCTTTGTCCTTCCGTGACCCATGGGTTCCTTCATGACCCTTGTGGTCTTGGGCTCCTAG
Seq C2 exon
GAGGATGACATTCGGGGCCTTGTGCGTCAGGAGATGAGTCAACATTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019081:ENSBTAT00000025418:112
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=0.706
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(25.8=100)
A:
NA
C2:
PF0139113=Collagen=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCGTGGTGAAAAGGGAGAA
R:
CGCAATGTTGACTCATCTCCTGA
Band lengths:
82-253
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]