RnoINT0040348 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117696312-117696661:+
Coord C1 exon
chr8:117696312-117696405
Coord A exon
chr8:117696406-117696499
Coord C2 exon
chr8:117696500-117696661
Length
94 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGA
5' ss Score
6.04
3' ss Seq
CTGTATGGACACCACTTCAGGAA
3' ss Score
3.62
Exon sequences
Seq C1 exon
GTCTGTATCCTGATCACAGATGGGAAATCCCAGGACTTAGTGGACACAGCTGCCCAAAAACTGAAGAGGCAGGGGGTCAAGCTGTTTGCCGTGG
Seq A exon
GTGAGAACCAAGTTGAGGTGGGGAGGGGTCTCTTGGAGTGGGGACCGTGCAGAGAATGTGTAAACAACTGAGCCCTGTATGGACACCACTTCAG
Seq C2 exon
GAATCAAGAACGCCGATCCTGAGGAACTGAAGCGCATCGCCTCACAGCCAACCAGCGATTTCTTCTTCTTTGTCAATGACTTCAGCATCTTGAGGACCCTGTTGCCCCTCATTTCCCGGAGGGTGTGCACCACGGCTGGTGGTGTGCCTGTGACCCTGCCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:4
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=0.182
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(17.8=100)
A:
NA
C2:
PF0009223=VWA=PD(21.3=67.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACTTAGTGGACACAGCTGCC
R:
GGCAACAGGGTCCTCAAGATG
Band lengths:
167-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]