RnoINT0040318 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117698085-117699078:+
Coord C1 exon
chr8:117698085-117698213
Coord A exon
chr8:117698214-117698934
Coord C2 exon
chr8:117698935-117699078
Length
721 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
CCCACCCTGCCTTTCCTTAGGGG
3' ss Score
9.95
Exon sequences
Seq C1 exon
GGCTAGAGCAGCTGGTGGGCCCGGTGATGAATTTACAAGCCACAGAACTACCTGGGCAGCGGCTGCGAGTGTCTTGGAACCCAGTCCTCGGTGCCACCGAGTACCGTTTCACTGTACGCACCCCCCAGG
Seq A exon
GTAAGGCAGAAGCAGCGAGAAAAGTTCCCCCAGACCGAAGTCCCAGCCTGCAGTTCCCTCCCACTCTGGCTGGGTTCCCACACCCTCCTTCGTCTTTGTGGCCATCTACATCCTGAGAACTGTCAACCCCAGAACAGCCTCAGGGTCTCTCTTTCCTCTCCTCTACCTCAGCTCTTCAGTTGTGGTTCGCCCTTCTCTACTGCCACAAGCTCTGTGGACCACAATCCTGCTGTCCTTCTCTAGGGAGAAGAGGGCCCCCCTGTGGTCACTGTGGCTCAAACTAGTCAGAGCCTGTCTCTGTCTCTTGGTCCTTTCTTTGCCTGAGCGCCTGCCCCTTCAGTCTCTTGCATTCCCACTGCCTTCCCACTAAGATTCCTCTAATACTGACCTCTCGCCTCACCCAACGCTCACCCATCATCCTGTGTCAATGTCTATCTGAGGCTTGCCAACTTGCGTCACTGTCTCAGACTCTCATCTTGCTATGTCCTAAGCCCTGTCTGTCATCCAGCGTCCCCATCACTGGTGACTCCTGTTATTCCGTGCTACCACCGTGGACCCCTTACCCCTGCATCGTTTTCTCTTACTGTTCTCCTCTCTCACTGCCCCTCCCCGTCCAATCTCCCCATCTCCCATGATGTCTGGTGTCCTTGCCTATCGCTGACTGCTGTCCTAGATCCCTGTGTGGTACTCACCCCTGCCTGCCCACCCTGCCTTTCCTTAG
Seq C2 exon
GGGTCGAGCGGACTTTGTTGCTTCCTGGGAGTCAGACAACCTTTGACTTAGATGATGTTCGAGCCGGGATTAGCTACACAGTGCGAGTGTCTGCTCGAGTGGGCACTCATGAGGGTGATGCCAGCACCCTCACCATCCACAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:12
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=0.184
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(46.8=84.1)
A:
NA
C2:
PF0004116=fn3=PD(51.9=83.7)
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:
CTAGAGCAGCTGGTGGGCC
R:
CTCTGTGGATGGTGAGGGTGC
Band lengths:
271-992
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]