BtaINT0042265 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019081 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr22:51884338-51884530:+
Coord C1 exon
chr22:51884338-51884373
Coord A exon
chr22:51884374-51884473
Coord C2 exon
chr22:51884474-51884530
Length
100 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
ACTTCCCCCTGTCCACTCAGGGC
3' ss Score
9.99
Exon sequences
Seq C1 exon
GGTGACGCTGGTGCCTCAGGACTGAAGGGTGACAAG
Seq A exon
GTGAGTGTGGGCACGGGAGAGGGCAGGGCTCAGGGGGCACGGGGGAGGGCAGGGGGTTCAGGGTGCTCCTCACTCCTCTGACTTCCCCCTGTCCACTCAG
Seq C2 exon
GGCGACTCAGCTGTGATTTTGGGGCCTCCGGGGCCACGGGGTGCCAAGGGGGACTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019081:ENSBTAT00000025418:100
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(18.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(6.7=21.1),PF0139113=Collagen=PU(20.7=63.2)
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:
GTGACGCTGGTGCCTCAG
R:
GAGTCCCCCTTGGCACCC
Band lengths:
91-191
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]