BtaINT0042299 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019081 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr22:51868503-51868909:+
Coord C1 exon
chr22:51868503-51868649
Coord A exon
chr22:51868650-51868736
Coord C2 exon
chr22:51868737-51868909
Length
87 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
GCTGCTGGACCACTCCTTAGGGC
3' ss Score
3.25
Exon sequences
Seq C1 exon
GCACAGCCGTGGTTACAGCCCACAGATACCTGCTGGCACCAGATGCGCCTGGACGCCGCCGGCATGTGCCGGGGGTGATGGTTCTCCTGGTGGATGAGCCCTTGAGAGGTGACATCTTCAACTCTATCCGTGAGGCCCAGGCTGCTG
Seq A exon
GTGAGGACCAGGGCTGGTGGGAATGGGACCTGGGAGCAGCCTTGGCCCCGGCAGGGTCATCATGCAGGCTGCTGGACCACTCCTTAG
Seq C2 exon
GGCTCAGAGTGATGATGCTGGGGCTGGCGGGAGCTGACCCAGAGCAGCTGCGTCGCTTGGTGCCTGGCATGGACCCTTCCCAGACCTTCTTCGCTGTGGATGATGGTCTGAGCTTGGAGCGGGCCGTCAGTAGTCTGGCAGCAGCCCTGTGTCAGACAGCCTTGACCACGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019081:ENSBTAT00000025418:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.448
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(27.8=100)
A:
NA
C2:
PF0009223=VWA=PD(25.6=77.6)
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:
ATGAGCCCTTGAGAGGTGACA
R:
GCTCAGACCATCATCCACAGC
Band lengths:
167-254
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]