RnoINT0040334 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117704162-117704461:+
Coord C1 exon
chr8:117704162-117704334
Coord A exon
chr8:117704335-117704425
Coord C2 exon
chr8:117704426-117704461
Length
91 bp
Sequences
Splice sites
5' ss Seq
CAGGTTTGG
5' ss Score
5.63
3' ss Seq
AGAATCTTCTTTCTCCACAGCCA
3' ss Score
8.84
Exon sequences
Seq C1 exon
GGCTCAAGGTGATGATGCTGGGTCTGGTGGGAGCTGACCCAGAGCAGCTGCGCCTCTTGGCACCAGGCATGGACCCCATCCAGACCTTCTTTGCTGTGGATAATGGCTTAGACTTGGACCGAGCAGGCAGTGATCTGGCTGTAGCCCTATGTCAGGCAGCTGTGGCCATACAG
Seq A exon
GTTTGGAGAAAGCCTTTGGGGACTGGTAGTAGAGAGGGGCCTTAGGGTTCTTTTAGAACTTCCCGGTTTCAAGAATCTTCTTTCTCCACAG
Seq C2 exon
CCACAACTAGAGCCTTGTGCTGTGCCCTGTCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.103 A=NA C2=0.750
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(25.6=77.6)
A:
NA
C2:
PF0139113=Collagen=PU(6.7=33.3)
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:
GATGATGCTGGGTCTGGTGG
R:
GCACAAGGCTCTAGTTGTGG
Band lengths:
183-274
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]