RnoINT0040361 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117709282-117709497:+
Coord C1 exon
chr8:117709282-117709362
Coord A exon
chr8:117709363-117709461
Coord C2 exon
chr8:117709462-117709497
Length
99 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGA
5' ss Score
2.75
3' ss Seq
CTGACCCTCATGTCTCACAGGGT
3' ss Score
8.99
Exon sequences
Seq C1 exon
GGTGACTCAGGGCCTCCTGGAGAGAAGGGAGAACCTGGGCGACCTGGTTCCCCAGGACCTGTTGGCCCTCGAGGAAGAGAT
Seq A exon
GTGAGAGGCTGGATCTGGGGCTGTCTTGGGGAATGGGAGTATGGGTGTTTGGATGTATCAGTGGGGGTGAGGACTAAGACTGACCCTCATGTCTCACAG
Seq C2 exon
GGTGAAGCTGGAGAGAAAGGTGACGAGGGTGCCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:51
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(31.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(13.1=100)
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:
GGTGACTCAGGGCCTCCT
R:
ACCCTCGTCACCTTTCTCTCC
Band lengths:
111-210
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]