GgaINT0022932 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9083118-9083288:+
Coord C1 exon
chr12:9083118-9083153
Coord A exon
chr12:9083154-9083231
Coord C2 exon
chr12:9083232-9083288
Length
78 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
CACCTCTCTCCTGCATGCAGGGT
3' ss Score
8.37
Exon sequences
Seq C1 exon
GGAGACGTCGGGGCCGTGGGGCCCAAAGGAGACAAG
Seq A exon
GTGAGACCCCAGGGCTGGGGGGGGAGGGTGGCAGTGCTGTCCCCCCCCGGCTCACACCCACCTCTCTCCTGCATGCAG
Seq C2 exon
GGTGATACCGTTGTGGTGGAGGGGCCTGCTGGGGCGAGAGGCAGCAAGGGGGAGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:98
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(18.6=100)
A:
NA
C2:
PF0139113=Collagen=PD(5.1=15.8),PF0139113=Collagen=PU(21.7=68.4)
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:
TGGGGCCCAAAGGAGACAAG
R:
TCCCCCTTGCTGCCTCTC
Band lengths:
73-151
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]