RnoINT0040392 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117697236-117697579:+
Coord C1 exon
chr8:117697236-117697352
Coord A exon
chr8:117697353-117697432
Coord C2 exon
chr8:117697433-117697579
Length
80 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
CCCTCTGTGTCCCTACACAGGTG
3' ss Score
12.06
Exon sequences
Seq C1 exon
CTGCCAAGGAAGGGCTAGAGCTGAGCGTCCAGAACATCACATCCCACAGCCTCCTGGTGGCCTGGAGGAGGGTACCAGGTGCTAATGGCTACCGCGTAACATGGCGGGACCTCAGTG
Seq A exon
GTAAGTGAGAGGCGTGGACTGACAAAATTATCGATTCCTGCCTCTACAAGGCCCACTGAACCCTCTGTGTCCCTACACAG
Seq C2 exon
GTGGGGGGGCACAGCAGCAGGACCTGAGCCCTGGGCAGGGGTCAGTGTTTTTAGATCACTTGAAGCCTGGCACGGACTATGAGGTGACTGTGAGCGCCCTATTTGGCCGCAGCGTGGGGCCTGCTGCTTCTCTGACTACCCGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.150 A=NA C2=0.300
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(44.2=85.0)
A:
NA
C2:
PF0004116=fn3=PD(54.5=84.0)
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:
AATGGCTACCGCGTAACATGG
R:
GTAGTCAGAGAAGCAGCAGGC
Band lengths:
173-253
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]