RnoINT0040333 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117703928-117704334:+
Coord C1 exon
chr8:117703928-117704074
Coord A exon
chr8:117704075-117704161
Coord C2 exon
chr8:117704162-117704334
Length
87 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
ATTGCTGGATCTCTTCCTAGGGC
3' ss Score
7.68
Exon sequences
Seq C1 exon
GCACAGCCGTGACCACAGCTCACAGATACCTCTTAGCACCCAATGCTCCCGGTCGCCGTCGGCAAGTGCCAGGCGTGATGGTACTGTTAGTGGATGAACCTCTGAGAGAAGACATATTGAGCCCCATTCGTGAGGCCCAGGCTTCTG
Seq A exon
GTGAGCTGTAGGACTGATGGGGTAGGGCCTTGGGAATCAGGGTGACCCCGGTGAGGTTGTCATGTAGATTGCTGGATCTCTTCCTAG
Seq C2 exon
GGCTCAAGGTGATGATGCTGGGTCTGGTGGGAGCTGACCCAGAGCAGCTGCGCCTCTTGGCACCAGGCATGGACCCCATCCAGACCTTCTTTGCTGTGGATAATGGCTTAGACTTGGACCGAGCAGGCAGTGATCTGGCTGTAGCCCTATGTCAGGCAGCTGTGGCCATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.040 A=NA C2=0.103
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(27.8=100)
A:
NA
C2:
PF0009223=VWA=PD(25.6=77.6)
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:
CGTGACCACAGCTCACAGATAC
R:
CACCAGACCCAGCATCATCAC
Band lengths:
169-256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]