GgaINT0022907 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9078314-9078599:+
Coord C1 exon
chr12:9078314-9078358
Coord A exon
chr12:9078359-9078527
Coord C2 exon
chr12:9078528-9078599
Length
169 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
TGACCATGCTGTGCCCACAGGCA
3' ss Score
9.97
Exon sequences
Seq C1 exon
GGCAGAGATGGCTTGCCAGGCCCCCCAGGGCCCCCAGGGCCCAAG
Seq A exon
GTAGGTGGTGGATGCTGCTGGGGAATGTCCCCAGGAGGTGCCAGCAGATGCCTCCAGGGATGGGTGTTCATGTCTGGTCCCCTGGCACGGGGGCTTGGGAAGGATTGTGCCACGGGGGGACCTCTCTGGGGTCCCCTGGATGCCAGTCCTGACCATGCTGTGCCCACAG
Seq C2 exon
GCAGACGCAATGGAGGGCAGCCTGATGGGCTTCCCAGGCGAGCGCGGTCCCCCCGGACTTAAGGGAGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:73
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(20.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(2.9=8.3),PF0139113=Collagen=PU(27.0=70.8)
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:
CAGAGATGGCTTGCCAGGC
R:
TTCACTCCCTTAAGTCCGGGG
Band lengths:
114-283
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]