BtaINT0042325 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019081 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr22:51861476-51861970:+
Coord C1 exon
chr22:51861476-51861637
Coord A exon
chr22:51861638-51861809
Coord C2 exon
chr22:51861810-51861970
Length
172 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
CTGACTGCCCCCTTCCCCAGCCG
3' ss Score
8.38
Exon sequences
Seq C1 exon
GCATCAAGAATGCCGACCCCGAGGAGCTGAAGCGAATTGCCTCACAGCCGACTAGCGATTTCTTCTTCTTCGTCAATGACTTCAGCATCTTGAGGACGCTCCTGCCTCTGGTTTCCCGGAGGGTGTGCACAACTGCGGGTGGTGTGCCCGTGACCCTGCCCC
Seq A exon
GTGAGTTCCCGCTCACTCTGGGTACCCTGACCTGAACCCCGGCCCAAACCCCAACGTGGCCATGCCAATTCCATCCCGTGTGCTCCTAACCTTTGACCCTGGTGCTGACCCTGCACCCTTAGTGCTGACCCCTGATTCTCTTGCCTGGTTGCCTGACTGCCCCCTTCCCCAG
Seq C2 exon
CCGACGACTCGACCTCTGGTCCACGAGACCTGCTGCTTGAGCCAGGCAGTCAGTCCTTGAGAGTCCAGTGGACAGCGGCCAGTGGCCCCGTGACTGGCTACAAGGTCCAGTACGCACCCCTGACAGGGCTGGGACAGCCATTGCCAAGCGAGCTGCGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019081:ENSBTAT00000025418:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.164 A=NA C2=0.296
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(20.8=65.5)
A:
NA
C2:
PF0004116=fn3=PU(56.5=88.9)
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:
AATTGCCTCACAGCCGACTAG
R:
GTGCGTACTGGACCTTGTAGC
Band lengths:
245-417
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]