RnoINT0040364 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117709970-117710303:+
Coord C1 exon
chr8:117709970-117710041
Coord A exon
chr8:117710042-117710258
Coord C2 exon
chr8:117710259-117710303
Length
217 bp
Sequences
Splice sites
5' ss Seq
AATGTGAGT
5' ss Score
7.8
3' ss Seq
GACTCCCTGGCCTTCTGCAGGGC
3' ss Score
7.59
Exon sequences
Seq C1 exon
GGGGCACCTGGGCCCCGGGGGCCTGTGGGTGAGAAGGGGAATGAGGGGGATCCTGGAGAAGATGGCCGGAAT
Seq A exon
GTGAGTCTTAACTTCTGGCCCCTCACCCTTGACTTCAGCCCCAACTCATCCATCCAGTTCCCACCTCATCCTCTCAGGGATCACCCCACAGTCCTCACCTCCCTTCTCTCTTCTGTGAGAACTCCCCAAAGGCCAGCAGGACCCCATAGCCCTCATGGCACTTCTAAACATCTCCCCAATTGTTGACCACCTTGAGTGACTCCCTGGCCTTCTGCAG
Seq C2 exon
GGCACCCCTGGACCATCTGGACCCAAGGGTGACCGTGGGGAGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:54
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(3.6=12.5),PF0139113=Collagen=FE(38.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(23.3=100)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]