RnoINT0040337 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117696066-117696405:+
Coord C1 exon
chr8:117696066-117696225
Coord A exon
chr8:117696226-117696311
Coord C2 exon
chr8:117696312-117696405
Length
86 bp
Sequences
Splice sites
5' ss Seq
AAGGTGTTC
5' ss Score
1.14
3' ss Seq
GGTCTTGGCACCTATCCCAGGTC
3' ss Score
3.9
Exon sequences
Seq C1 exon
GACAGAATTTGGTCTGGATACACTTGGCTCTGGGGGTGACACCATTCGTGCCATCCGGGAGCTCAGCTATAAGGGTGGTAACACTCGAACGGGGGCTGCTCTTCTCCACGTTTCCGACCGGGTCTTCCTGCCTCATCTAACACGTCCTGGCATCCCCAAG
Seq A exon
GTGTTCCCTAAACCTACCATGCCTCCAAATGTGACCCCAAAATAAATGTCCGAAACATCCCTGACTGGTCTTGGCACCTATCCCAG
Seq C2 exon
GTCTGTATCCTGATCACAGATGGGAAATCCCAGGACTTAGTGGACACAGCTGCCCAAAAACTGAAGAGGCAGGGGGTCAAGCTGTTTGCCGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(30.5=100)
A:
NA
C2:
PF0009223=VWA=FE(17.8=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:
CGGGAGCTCAGCTATAAGGGT
R:
TCAGTTTTTGGGCAGCTGTGT
Band lengths:
169-255
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]