BtaINT0042352 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019081 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr22:51879269-51879456:+
Coord C1 exon
chr22:51879269-51879337
Coord A exon
chr22:51879338-51879411
Coord C2 exon
chr22:51879412-51879456
Length
74 bp
Sequences
Splice sites
5' ss Seq
AAGGTCCGT
5' ss Score
6.16
3' ss Seq
GTGACATGTCATTCCCACAGGGG
3' ss Score
9.28
Exon sequences
Seq C1 exon
GTGGCCGTGGACGAGCCAGGTTCTGGGCTCTCTAGAGAACAAGGACCCCCTGGATTCAAGGGTGCTAAG
Seq A exon
GTCCGTGTGCGGGCTCAGCCTGGGGGCCACCCCTGCTGTGGCACCAGGGCCTGGGTGACATGTCATTCCCACAG
Seq C2 exon
GGGGATCCAGGCAGTGATGGCGACCGAGGCCCCAAAGGAGACAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019081:ENSBTAT00000025418:76
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(10.3=30.4),PF0139113=Collagen=PU(23.5=69.6)
A:
NA
C2:
PF0139113=Collagen=FE(20.6=100)
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:
TGGACGAGCCAGGTTCTG
R:
CCTGTCTCCTTTGGGGCCTC
Band lengths:
107-181
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]