GgaINT0022940 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9084442-9084660:+
Coord C1 exon
chr12:9084442-9084504
Coord A exon
chr12:9084505-9084597
Coord C2 exon
chr12:9084598-9084660
Length
93 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGG
5' ss Score
8.76
3' ss Seq
CTGCGCCTTCCTCTCCACAGGGT
3' ss Score
12.77
Exon sequences
Seq C1 exon
GGAGAGCTGGGGTTGTCGGGAGCACCCGGCGTCCCCGGGAAGGAGGGGCTCATGGGACCCAAG
Seq A exon
GTAGGGCAATGGGAGGCTGTGCTGAGACCTCAGGAATGGCCCCTCAGGACTGCTCCCCCCAAACTCCTGCTGCCTGCGCCTTCCTCTCCACAG
Seq C2 exon
GGTGACCGCGGCTTCGATGGGCAGCAGGGAGCCAAAGGAGACCAGGGGGAGAAGGGAGACCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:106
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(20.4=100),PF0139113=Collagen=PU(21.2=66.7)
A:
NA
C2:
PF0139113=Collagen=FE(20.4=100),PF0139113=Collagen=FE(30.3=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:
GAGCTGGGGTTGTCGGGAG
R:
TCTCCCTTCTCCCCCTGGTC
Band lengths:
119-212
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]