RnoINT0040346 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117706604-117706808:+
Coord C1 exon
chr8:117706604-117706657
Coord A exon
chr8:117706658-117706745
Coord C2 exon
chr8:117706746-117706808
Length
88 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGG
5' ss Score
9.35
3' ss Seq
GTTTGTTTACTTCTTTCAAGGGG
3' ss Score
6.26
Exon sequences
Seq C1 exon
GGTCCCCCAGGACCAGGCACTGGTGCCAGTGAGCAAGGCAGCCCTGGACTTCCG
Seq A exon
GTGAGGGGGCCTTGAGGTACTGCTGGAGCAGTGGCTGGGTGCTGGCCTTCCTAGTTTTTTGCTTATGAGTTTGTTTACTTCTTTCAAG
Seq C2 exon
GGGCTTCCTGGAAGCCCTGGACCCCAAGGCCCACCTGGTCGAACTGGAGAGAAGGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:38
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(8.5=27.8),PF0139113=Collagen=FE(30.4=100),PF0139113=Collagen=PU(9.3=44.4)
A:
NA
C2:
PF0139113=Collagen=FE(35.7=100),PF0139113=Collagen=FE(23.3=100)
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:
CTGGTGCCAGTGAGCAAGG
R:
TTCTCCCTTCTCTCCAGTTCGA
Band lengths:
95-183
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]