BtaINT0042311 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019081 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr22:51870856-51871018:+
Coord C1 exon
chr22:51870856-51870882
Coord A exon
chr22:51870883-51870964
Coord C2 exon
chr22:51870965-51871018
Length
82 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
GACCTGCTGTTCCTTCCCAGGGC
3' ss Score
10.18
Exon sequences
Seq C1 exon
GGTGAGAAAGGCGATCGTGGGGAGCAG
Seq A exon
GTAAGCAAGGGGCACGTTAGGCTGGGGGTGGCATGGAACCTGATTGCCCCTGGCCATCCTCCGACCTGCTGTTCCTTCCCAG
Seq C2 exon
GGCCCCCCTGGACCAGGTGACGGCACTGCTGCTCTGGGCGAGCCTGGGCTGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019081:ENSBTAT00000025418:37
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(12.9=100),PF0139113=Collagen=FE(14.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(12.9=44.4),PF0139113=Collagen=FE(30.4=100),PF0139113=Collagen=PU(10.9=38.9)
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:
GTGAGAAAGGCGATCGTGGG
R:
CTCGCCCAGAGCAGCAGT
Band lengths:
68-150
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]