GgaINT0022930 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9082885-9083035:+
Coord C1 exon
chr12:9082885-9082929
Coord A exon
chr12:9082930-9082999
Coord C2 exon
chr12:9083000-9083035
Length
70 bp
Sequences
Splice sites
5' ss Seq
ATGGTACGT
5' ss Score
9.89
3' ss Seq
CTTTCTCCTCTTTCCCACAGGGC
3' ss Score
13.54
Exon sequences
Seq C1 exon
GGTGAAGATGGGCGCCCAGGGCTGGCAGGTGACCGCGGGCCAATG
Seq A exon
GTACGTACCACTCAGCTCGCCACCCCATCAGCTGGCCCTCCCCCAAGCAGCTTTCTCCTCTTTCCCACAG
Seq C2 exon
GGCTTGCCTGGGAACCGAGGAGAGCGTGGGGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:96
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(23.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.6=100)
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:
CAGGGCTGGCAGGTGACC
R:
CTTGTCCCCACGCTCTCCTC
Band lengths:
65-135
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]