BtaINT0042347 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019081 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr22:51878263-51878549:+
Coord C1 exon
chr22:51878263-51878298
Coord A exon
chr22:51878299-51878426
Coord C2 exon
chr22:51878427-51878549
Length
128 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
TGACCCTGCATGTCACCCAGACA
3' ss Score
4.95
Exon sequences
Seq C1 exon
AATGCAGAGCGGTTGCTGGAAAATATTGGCATCAAG
Seq A exon
GTAGGTTGATGGGGGCTGGACACAGGGGCCGCGGGGAGCCCCACGGGACACGTAATGCCCCCAGGGCTGGCCAGGGCATGGGTGGCTGCAGCCTTGGCCTTCCTCTTCTGACCCTGCATGTCACCCAG
Seq C2 exon
ACATCTGCCCTGAGGGAGATCGTGGAGACCTGGGAAGAAAGCTCTGGTGGCTTCCTGCCCACGCCTGAACGGCGTCGCGGCCCCAAGGGGGACCCAGGCGAGCGGGGCCCCCCAGGCAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019081:ENSBTAT00000025418:71
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(0.1=0.0)
A:
NA
C2:
PF0139113=Collagen=PU(26.6=41.5)
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:
GCGGTTGCTGGAAAATATTGGC
R:
GTTCAGGCGTGGGCAGGAA
Band lengths:
98-226
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]