RnoINT0040321 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117699390-117700172:+
Coord C1 exon
chr8:117699390-117699533
Coord A exon
chr8:117699534-117700052
Coord C2 exon
chr8:117700053-117700172
Length
519 bp
Sequences
Splice sites
5' ss Seq
CTGGTCAGA
5' ss Score
3.96
3' ss Seq
CCCGTTATCTCCCTCTCCAGATC
3' ss Score
11.56
Exon sequences
Seq C1 exon
GTCCAGAGTCCAGTCAGACGCTGGCCCCAGACTCTACTGTCACAGACATCCTGGGGCTGCAGCCTGGAACCTCTTATCAAGTGGCTGTGTCAGCCCTTCGAGGGAGAGAAGAGGGGCCCCCTGTGGTCATCGTGGCTCGAACTG
Seq A exon
GTCAGAGCCTGACCCAGTCTCCTGGCTCTTTACCTCCCGGCCCCCTTAGACTTCTGTGGTGCCCTCAGTGGTGCACACTACTTCCACCTTGAGTCCCAGTCCACCGCATCCCTACTCTCGGGCCTTCCCCTTCGCGGTCACTTGTCTCTCCCATGGCTCCCTCTATCTGACTCTTATTTCTGCTACTCGTCCCTCAGAGCCTACCACTTCCTCCTCCTCCTCTTCCTCCTCTTCATTTGTTGGACACAACTCTCCTCTTGGACCTTTACTTTGTCATTTGCCTGATGTCCTCATGGTCCCCTAATGCTTCCACGGACCCCTCTCTGTCAGACCTCATCCTTCCGATCGCTGCTACCTGACAGCTAAGTTTCCTACTGTGCCTTCTGTAGAACCCCTCACTGCCCTTTGGTGAGGTCCCTGCCTCCTATAAACCTCAAAGTCTTCCCTTGCCAAACAGTTGCCCATCTTCTCCTGTCAGACCTGCCTACTTTACCAGACTCCCGTTATCTCCCTCTCCAG
Seq C2 exon
ATCCACTGGGCCCAGTGAGGAGAGTCCACTTGACTCAGGCTGGTAGCTCATCTGTCAGCATTACCTGGACTGGGGTTCCTGGCGCCACCGGATACAGGGTTTCCTGGCACTCAGGCCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.551 A=NA C2=0.293
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(53.2=83.7)
A:
NA
C2:
PF0004116=fn3=PU(46.8=90.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCAGAGTCCAGTCAGACGC
R:
CTGAGTGCCAGGAAACCCT
Band lengths:
257-776
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]