RnoINT0040408 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117719312-117719653:+
Coord C1 exon
chr8:117719312-117719419
Coord A exon
chr8:117719420-117719581
Coord C2 exon
chr8:117719582-117719653
Length
162 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGA
5' ss Score
9.84
3' ss Seq
CTTGCCCCATTTTTCTGTAGGGT
3' ss Score
10.13
Exon sequences
Seq C1 exon
GGAGACTTGGGCCCCCCTGGTGCCCCCGGTGCTCCTGGTATTGTTGGATTTCCTGGTCAGCCAGGACCTCGAGGAGAGACGGGCCAGCCAGGGCCTGTTGGAGAGCGG
Seq A exon
GTAAGAAGGCTGGGGAGAGCACTGGGCACCAGGACCTCTAAATTTGGTTAACAGGTGGGGAGGAAGGGACTGGACACCTTCCTTGGTGGTACCCAGCCTTGAGAGGAAGAGAAGGATGCTTCCCAAGTCACTCCCTACCTCCCTTGCCCCATTTTTCTGTAG
Seq C2 exon
GGTCTGGCAGGCCCTCCAGGGAGAGAAGGTGCCCCAGGTCCCTTGGGACCACCTGGACCACCGGGGTCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:94
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(60.3=100),PF0139113=Collagen=PU(28.3=47.2)
A:
NA
C2:
PF0139113=Collagen=PD(8.6=20.8),PF0139113=Collagen=FE(38.3=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:
CGGTGCTCCTGGTATTGTTGG
R:
CCGGTGGTCCAGGTGGTC
Band lengths:
146-308
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]