GgaINT0022863 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9068412-9068753:+
Coord C1 exon
chr12:9068412-9068540
Coord A exon
chr12:9068541-9068606
Coord C2 exon
chr12:9068607-9068753
Length
66 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
CACCTCTCTGTCCCCACCAGGTG
3' ss Score
10.33
Exon sequences
Seq C1 exon
CGGAGGCGGCCCCGGTGCCCCCTGTTAGCAACTTCCAGGTGATGGAGGCCTCAGAGCATCGCCTGCGCCTCGTGTGGGTGCCAGTATCTGGCAGCAGCGGGTACCGCCTGGTCTGGCGCCCAGCTGAGG
Seq A exon
GTGAGTGTGCCCAAGCCTTGTGTCTCCATGCCAACCCCTGGCCACTCACCTCTCTGTCCCCACCAG
Seq C2 exon
GTGGTCCCCAGCGCAGCCAGCAGCTTCCAGCCACCGCCAACTCCTATGACCTGGGAGGGCTGGAGCCGGGCCGGCGCTACCACATCAGCATCACCAGCATGGTGGGCAGCCGGGAGAGCGCTCCAGTCACCGTCACTACTGCCACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.295 A=NA C2=0.600
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(46.8=84.1)
A:
NA
C2:
PF0004116=fn3=PD(51.9=82.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCTGTTAGCAACTTCCAGG
R:
TCCCAGGTCATAGGAGTTGGC
Band lengths:
167-233
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]