GgaINT0022903 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9077413-9077697:+
Coord C1 exon
chr12:9077413-9077448
Coord A exon
chr12:9077449-9077565
Coord C2 exon
chr12:9077566-9077697
Length
117 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
GCCTCTTTCCTCCCTTCCAGATC
3' ss Score
13.52
Exon sequences
Seq C1 exon
AACATCGAACGTAGCCTGGAAGCCCTCGGCATCAAG
Seq A exon
GTATGGGGTGGGCATGGGGATGGGGCCGGGTGGTGGTGAGAGACCAGAGGGATGTGGGATGGGGCACTGGGACTGGAGTGCGTGACTGCTGATCGCTGCCTCTTTCCTCCCTTCCAG
Seq C2 exon
ATCTCATCTCTGAAGGAGCTGACGGGTGCCTATGATGGGAGCTCGGACTCCTTTCTGCCCGTGTCCGAACGGCTGCGGGGGCAGAAGGGCAGCCGGGGGGAGCCAGGGGAGAGGGGTCCCCCAGGCCGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:69
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=PD(0.1=0.0)
A:
NA
C2:
PF0139113=Collagen=PU(30.2=43.2)
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:
CATCGAACGTAGCCTGGAAGC
R:
GGGACCCCTCTCCCCTGG
Band lengths:
154-271
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]