RnoINT0040387 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117715020-117715308:+
Coord C1 exon
chr8:117715020-117715073
Coord A exon
chr8:117715074-117715239
Coord C2 exon
chr8:117715240-117715308
Length
166 bp
Sequences
Splice sites
5' ss Seq
AAGGTGATC
5' ss Score
4.41
3' ss Seq
CCATGGTTTTGGACTTACAGGTG
3' ss Score
7.44
Exon sequences
Seq C1 exon
GGCAGAGATGGCCATCCCGGCCTTCCTGGACCACCTGGCCCTCCTGGCCCCAAG
Seq A exon
GTGATCACCCAGCCTGTGACCAGTGATGATACTACCCTGAGATTGGGCCCCAGAAACCCCATGTAGTATCTTCAACCCCATACGTTTATGTGATCCTGGAACCTGACCTCTTCCCTTCACACCTATATGACAGACTCATTTTCCCTCCATGGTTTTGGACTTACAG
Seq C2 exon
GTGGCCATTGAAGAGCTAGGTCCTGGACCCGCTAGAGAACAAGGACCTCCTGGACTCAAGGGTGCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:75
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=FE(27.4=100)
A:
NA
C2:
PF0139113=Collagen=PD(1.6=4.3),PF0139113=Collagen=PU(24.2=69.6)
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:
GCAGAGATGGCCATCCCG
R:
CTTAGCACCCTTGAGTCCAGG
Band lengths:
122-288
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]