BtaINT0042315 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019081 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr22:51871319-51871509:+
Coord C1 exon
chr22:51871319-51871378
Coord A exon
chr22:51871379-51871473
Coord C2 exon
chr22:51871474-51871509
Length
95 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
AATCTCTGAACCCCTTTCAGGGC
3' ss Score
7.76
Exon sequences
Seq C1 exon
GGTGACTGTGAAGATGGAGCCCCGGGCCTCCCAGGACAACCCGGAATTCCGGGTGAGCGG
Seq A exon
GTGAGTGTGGTGGGCAAGGCCCCAGCCCTCAGCCTCAGCCATCAACCCTCTACTCCATCCTTATTACCAAACCCAAATCTCTGAACCCCTTTCAG
Seq C2 exon
GGCCTTCGGGGACTTCCTGGAGATGCTGGCCCCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019081:ENSBTAT00000025418:40
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(5.4=15.0),PF0139113=Collagen=FE(29.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(17.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGACTGTGAAGATGGAGCCC
R:
TTTGGGGCCAGCATCTCCAG
Band lengths:
95-190
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]