BtaINT0042284 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019081 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr22:51863164-51864076:+
Coord C1 exon
chr22:51863164-51863292
Coord A exon
chr22:51863293-51863932
Coord C2 exon
chr22:51863933-51864076
Length
640 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGG
5' ss Score
7.13
3' ss Seq
TGTCCTACCTTCTCTCATAGGGG
3' ss Score
10.03
Exon sequences
Seq C1 exon
GTCCAGAGCTGCCCGTGGGCCCCGTCACAGCCCTCCAGGCCACCGAGCTGCCTGGGCAGCGTGTGCGAGTGTCCTGGAGCCCAGTTCCCGGCGCCACCGAGTATCGCATCACTGTGCGCAGCGCCCAGG
Seq A exon
GTGAGGAAGACACCGCCAGACTGTGCTGACCCTGAAGTTCCAGCCCTCGGGGTCTGACTGCACTCTTACTGCATCCCTTTCCACTCCTGGGGCTCTACCGCCTCCTCCTGTCTCCTTGTCCATCCATCTCCCAAGAAGGCCCCGAAGCCACACCTGTCACAGGGCCTGTCTTACCCCTGTCCTGCCCCTGCCTAGCTCTGCACCTGGATCTGTCTCCACTCCTCACCCCACATCCCTGACCGTGGCTTTCATCTTCTCCACAACCACGAGCTCAACCCCTGCCCTTCTATAAGCTTAGCTGGGACCACTGTCCTCCCCTGCCCCCGTCCAGTACCGACCCGACATCATTATTAATGACCTGTCAGCTCACATTGCCATCCACCAACTTCTGACATCCTGCATCTTATGTCCCTGTCTGCTCCCTCCCATCACTATCGCCATTCATCACAGGCCTGTTTTTCCTGTGTCGCTGACCCTCGACTCCTTTTATCCCCTGTCCTTACATCTCACCCTTTTCTGTCCCACATCCCATCCCTCACTGACCCTTTTCGCCCTGTATCTCTGTCCATCACTGACCGCCTTTGTCCCCCGCCCCCATCCCTCACTGACCCCTGCCTGCCTGTCCTACCTTCTCTCATAG
Seq C2 exon
GGGTTGAGCGGAGCCTGGTGCTTCCTGGGAGTCAGACGGCCTTTGACTTGGATGACGTCCGGGCTGGGCTCAGCTACACAGTGCGGGTGTCAGCGCGAGTAGGCGGCCGGGAGGGCGCTGCCAGCATCCTCACTGTCCGCCGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019081:ENSBTAT00000025418:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.273 A=NA C2=0.163
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(46.8=84.1)
A:
NA
C2:
PF0004116=fn3=PD(51.9=83.7)
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:
GTCCAGAGCTGCCCGTGG
R:
GGCGGACAGTGAGGATGCT
Band lengths:
270-910
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]