RnoINT0040323 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117700307-117700887:+
Coord C1 exon
chr8:117700307-117700450
Coord A exon
chr8:117700451-117700761
Coord C2 exon
chr8:117700762-117700887
Length
311 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
TCCCTTGCCTTCGTCCCTAGCTC
3' ss Score
10.22
Exon sequences
Seq C1 exon
GTCCAGAGAAATCTCAATTGGTTTCTGGGGACGCCACGGTGGCTGAAATAGATGGACTGGAGCCAGACACAGAGTATATAGTGCGTGTGAGAACCCATGTAGCCGGTGTGGATGGAGCCCCGGCCTCTGTGGTTGTGAGGACTG
Seq A exon
GTGAGTGGATCCTGCCTTGGCTGACCCAGGCCGCTGTGTATCTCTGATTGTTGCACCTGCTCATTCCAGTGCTACTCAGTAACCTTCCTGTCCAGACTGAACCACCCCTGGCCACTGAGTGTCCATTCGTGTTTCTGACCTTGGCCATACAACACCCCCGGCCGAAACACTAACCTCCTCCCCTTAAAGTTCCCTCCACTGACCCAGCCACACTAACCTTCCCTAGCCTTCATTACCCACGCCTGTCTTGCCCCCCTTGTCTCTGCTGGATACCCAGTGACCCCTCACTCTTCCCTTGCCTTCGTCCCTAG
Seq C2 exon
CTCCTGAGCCTGTAGGCAGTGTGTCAAAACTGCAAATCCTTAATGCTTCCAGTGATGTTCTCCGCGTCACTTGGGTGGGAGTCCCTGGAGCCACATCCTATAGACTGGCTTGGGGACGTAGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.429 A=NA C2=0.093
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(51.9=83.7)
A:
NA
C2:
PF0004116=fn3=PU(46.8=86.0)
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:
GTCCAGAGAAATCTCAATTGGTTTCT
R:
CTTCACTACGTCCCCAAGCCA
Band lengths:
270-581
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]