RnoINT0040383 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117714247-117714517:+
Coord C1 exon
chr8:117714247-117714282
Coord A exon
chr8:117714283-117714394
Coord C2 exon
chr8:117714395-117714517
Length
112 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
CTGCCCCTCACGCTCCTCAGGTG
3' ss Score
9.23
Exon sequences
Seq C1 exon
AATGCGGAGCGGTTCCTGGAAACTGCTGGCATCAAG
Seq A exon
GTAGGTTGTTGAGAAGCTGATGTAGGATCCAGTGGGGCCCTGTGAGACAAGCAGTGTCCACAGGGCCCTGTGGATGAGCACTTACAGGCCTGCTGCCCCTCACGCTCCTCAG
Seq C2 exon
GTGTCAGCCCTGCGGGAGATTGTGGACACCTGGGGTGAGAGTTCTGGCAGCTTCCTGCTGGTGCCTGAGCGGAGACAAGGTCCCAAGGGGGACCCTGGTGACCCAGGCCCTCCAGGCAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:71
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=PD(0.1=0.0)
A:
NA
C2:
PF0139113=Collagen=PU(26.6=41.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGCGGTTCCTGGAAACTG
R:
CTGGAGGGCCTGGGTCAC
Band lengths:
146-258
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]