GgaINT1010133 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9068189-9068540:+
Coord C1 exon
chr12:9068189-9068335
Coord A exon
chr12:9068336-9068411
Coord C2 exon
chr12:9068412-9068540
Length
76 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGC
5' ss Score
3.59
3' ss Seq
GTCTGCCCATATCCCCACAGCGG
3' ss Score
9.35
Exon sequences
Seq C1 exon
GGGGCTCGGAGAGGAGCCAGCATGTTCCTGGCCACATCAGCTCCTTCGACATCCCCGACCTGGAGGGAGGTGTCTCCTACACTGTGAAGGTCACAGCACTCATAGGCAACCATGAAGGCAACCCCGTGTCCATCATCGTCACCACCC
Seq A exon
GTGAGCGTGGGGCTAGGGGACAGCACACGGGGGGGGGTGGGCATCTATGTCCTAATGTCTGCCCATATCCCCACAG
Seq C2 exon
CGGAGGCGGCCCCGGTGCCCCCTGTTAGCAACTTCCAGGTGATGGAGGCCTCAGAGCATCGCCTGCGCCTCGTGTGGGTGCCAGTATCTGGCAGCAGCGGGTACCGCCTGGTCTGGCGCCCAGCTGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.400 A=NA C2=0.295
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(51.9=82.0)
A:
NA
C2:
PF0004116=fn3=PU(46.8=84.1)
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:
CATCAGCTCCTTCGACATCCC
R:
GATGCTCTGAGGCCTCCATCA
Band lengths:
173-249
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]