GgaINT0022848 @ galGal4
Intron Retention
Gene
ENSGALG00000005811 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr12:9065206-9065560:+
Coord C1 exon
chr12:9065206-9065299
Coord A exon
chr12:9065300-9065401
Coord C2 exon
chr12:9065402-9065560
Length
102 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGC
5' ss Score
7.23
3' ss Seq
ACCATTCCTGTCCCCTTCAGGAA
3' ss Score
11.34
Exon sequences
Seq C1 exon
ATCTGCATCCTCATTACGGATGGCAAGTCCCAGGATGATGCTGAACAGCCGGCGCTGAGACTGAAGAGCCTGGGCATCAAGGTCTTTGCTGTGG
Seq A exon
GTGAGCATATCTGTGGTGTGCCCATTGGTATCCATACCCCTGAGTAATGGACTCCCCCAGGAGCTGGGTTCTGCCCTCACCCACCATTCCTGTCCCCTTCAG
Seq C2 exon
GAATCAAGAACGCCGACCGTCAGGAGCTGATCCGCGTGGCCTCACTGCCTACTGACTCCTTCTTCTTCTATGTGGGTGACTTCAAGCTACTGGGGACGTTGGTGCCGCTGATGACACGCAGGGTGTGCACAAGCTCAGGGGGCACTCTACGTACCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005811:ENSGALT00000009331:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.185
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(17.8=100)
A:
NA
C2:
PF0009223=VWA=PD(21.3=68.5)
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:
GCATCCTCATTACGGATGGCA
R:
GTACGTAGAGTGCCCCCTGAG
Band lengths:
244-346
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]