GgaINT0022944 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9085275-9085535:+
Coord C1 exon
chr12:9085275-9085328
Coord A exon
chr12:9085329-9085486
Coord C2 exon
chr12:9085487-9085535
Length
158 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGG
5' ss Score
10.38
3' ss Seq
TTTGCTCCACCGCTGGGCAGGAG
3' ss Score
4.96
Exon sequences
Seq C1 exon
GGCAGTCCTGGTGCTGAGGGTCTCCGTGGGGAGAAGGGGGATCCGGGCATGACG
Seq A exon
GTAAGGGGCTGTCAGCATGGGGCCGGCACGTGGGAAGGGGCACTGCATCCATCCCACTGCTGCTGATGGAGCATAGCCCACCTCCGGACTCTGCTCTGAACCTGGGGAAAGCTTTTTCCTATCTCTAATGGTGCATTCTTTGCTCCACCGCTGGGCAG
Seq C2 exon
GAGGAGGAGATCCGCGCCTTCGTCAGGCAGGAGATGAGCCAGCACTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:110
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(26.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(3.1=11.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCTGGTGCTGAGGGTCTC
R:
ACAGTGCTGGCTCATCTCCT
Band lengths:
98-256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]