RnoINT0040297 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117694605-117695350:+
Coord C1 exon
chr8:117694605-117694692
Coord A exon
chr8:117694693-117695169
Coord C2 exon
chr8:117695170-117695350
Length
477 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGC
5' ss Score
6.32
3' ss Seq
ATCTCTCCTCCTTGCTTCAGTGA
3' ss Score
8.18
Exon sequences
Seq C1 exon
ATGAGGCTGCGGCTCCTGGTCGCTGCGCTCTGCACTGCCGAGATCCTGGTGGGGGCGCCCGGAGTGTGGGCCCAGCCCAGAGATAGAG
Seq A exon
GTGGGCATCTTCCGGGGCTCGGCACCCTGTCACCTATGCAACTACTCAAACTTTATCCCTGACATCTTTCCACCGAGGATTTCTCCAAACTCTTCATGGATTCTTCCTAAACTCCTTGAATTCTACTCTGTGTTCCCCAAATTGCCTCCTACCCCATAGCACTCCAATTCTAGCTCCCTAGATGCACGCTGAATCCTCCGTCCTATCAGCAACAGTCTCTGCAAGCTGATCTCAGCCCTGGAGCTACACCCCTGCTTGCAGCTTATTCTCCCCCAAGGTGCTCCAGCCCTCCCTTGAGAAGCTCTGTTCCCAGGCCCACTGTGGTTTCCTCCAACACTGGCAGAAATACGCCTACCTGGGCTCCGTTTGCATAGGAAGACAAGCCTATTGTCCTCCTAGTCCCCAAGTCCCTGGGGACCTCAGTGTCTAGAGGACCTGTATTCCCTAAAAGGTCATGATCTCTCCTCCTTGCTTCAG
Seq C2 exon
TGACCTGCACCCGCCTTTATGCTGCTGACATTGTGTTCTTGATTGACGGCTCCTCGTCCATTGGCCGCAGCAACTTTCGAGAAGTGCGGGGATTCCTGGAGGGGCTGGTGCTGCCTTTCTCAGGAGCAGCCAATGCACAGGGCGTCCGATTTGCAACAGTGCAGTACAGTGATGATCCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=PU(29.3=83.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTGCACTGCCGAGATCCT
R:
TGTGGATCATCACTGTACTGCAC
Band lengths:
242-719
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]