RnoINT0040339 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117704778-117705414:+
Coord C1 exon
chr8:117704778-117704840
Coord A exon
chr8:117704841-117705342
Coord C2 exon
chr8:117705343-117705414
Length
502 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
TGACCTCTCTGTCTCTTTAGGGC
3' ss Score
12.85
Exon sequences
Seq C1 exon
GGCAGGACCGGTGCTCCAGGCCCACAAGGTGCTCCCGGAAGTACCCAAGCAAAAGGCGAGAGG
Seq A exon
GTGAGTGTGGAACTCATTGACTGTCACTAGTGGGTGCTCCCACTAGTCTTCCTGGAGGGTGTAGGGCAAAAGGAAGAAGTAGAGTTAGAGCTGGGCATGGTGGTGCCCACCTGTAACCCTAGCGCCCAAGAAGCAGAAGCAGGATGAGACACAACTCTTAGGCTAACCTAGATCATACAGCTAGACCCTGTCTCAATAAATAATAAATCAATAAAGACCCATGGAATGTTCCTAGAGGCATGAGTGAAGATTTTAAAGCACACCAGGTTTGGGGGAGGTTCAGGAATGGACAGAAAGGGCTTTGAGATCCCCTGGAGAGGCTGGCCTCTTGCTGGCATTAGATCCATTCAGCTGACAGAGCTGCGTCTCTGCCCTACCACTCGGCTCTGGTAACACTTGGGAGCCTGTGGGGTTGGAGCCACGGTGGATGGTGTGGAGCTCTTTATGTAAGCTGGGACACTGGGGAAGGATCTTTTCTGCTCTGACCTCTCTGTCTCTTTAG
Seq C2 exon
GGCTTTCCTGGCCCAGAAGGCCCTCCAGGCAGTCCTGGCCTACCTGGTGTTCCTGGGTCTCCTGGCGTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:31
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(33.3=100),PF0139113=Collagen=PU(8.1=23.8)
A:
NA
C2:
PF0139113=Collagen=PD(15.0=37.5),PF0139113=Collagen=FE(37.1=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:
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]