GgaINT0022937 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9083970-9084179:+
Coord C1 exon
chr12:9083970-9084050
Coord A exon
chr12:9084051-9084125
Coord C2 exon
chr12:9084126-9084179
Length
75 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
GACTCTCTTTGTCCCTGCAGGGT
3' ss Score
11.66
Exon sequences
Seq C1 exon
GGCTTGCCTGGCCGGGATGGCATTGCTGGAGCACGAGGAGAGAAGGGGGACATAGGGCCGCTGGGCTTGCGTGGCCCCAAG
Seq A exon
GTGGGTCATCCCCTGCGCTCCGTGGCCAGGACACGTGCTGGCTTTGCGGGGCTCTGACTCTCTTTGTCCCTGCAG
Seq C2 exon
GGTGAACGGGGCATGAAAGGAGCCTGTGGCCTCGATGGAGACAAGGGTGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:103
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(28.9=100),PF0139113=Collagen=PU(15.3=55.6)
A:
NA
C2:
PF0139113=Collagen=FE(18.9=100),PF0139113=Collagen=FE(17.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGGATGGCATTGCTGGAG
R:
TCACCCTTGTCTCCATCGAGG
Band lengths:
119-194
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]