BtaINT0042360 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019081 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr22:51880719-51880891:+
Coord C1 exon
chr22:51880719-51880751
Coord A exon
chr22:51880752-51880828
Coord C2 exon
chr22:51880829-51880891
Length
77 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
TCAACTCCCGCTTCCTCCAGGGC
3' ss Score
9.57
Exon sequences
Seq C1 exon
GGGGAGCCCGGAGAGACAGGACCACCAGGACGG
Seq A exon
GTGAGTGGCCCAGCCCATGGGGAAGTCACAGGGAGCTGGGCGGGGTTGGCACTGCCCTCAACTCCCGCTTCCTCCAG
Seq C2 exon
GGCCTGCCTGGACCTACTGGAGCCGTGGGACTTCCCGGGCCCCCTGGCCCTTCAGGCCTGGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019081:ENSBTAT00000025418:83
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=FE(16.4=100),PF0139113=Collagen=FE(13.9=100)
A:
NA
C2:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(27.8=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:
GAGCCCGGAGAGACAGGAC
R:
GAAGTCCCACGGCTCCAGTAG
Band lengths:
64-141
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]