RnoINT0040099 @ rn6
Intron Retention
Gene
ENSRNOG00000020525 | Col5a3
Description
collagen type V alpha 3 chain [Source:RGD Symbol;Acc:70922]
Coordinates
chr8:21800793-21801382:-
Coord C1 exon
chr8:21801293-21801382
Coord A exon
chr8:21800847-21801292
Coord C2 exon
chr8:21800793-21800846
Length
446 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
TTGGTCATTTCTTCCCCCAGGGA
3' ss Score
9.85
Exon sequences
Seq C1 exon
GGTGAGCTAGGACCCCTGGGGTCCCTCGGAAAGGAGGGGCCACCTGGGCCCATGGGCTTCCCTGGCCCACAAGGAGCCCCCGGAGACCCA
Seq A exon
GTGAGTATCTTTGGAGAGTCCACTGGAGTGTGGGGCTGTTGGGGGCTCTTCAAGATCGGGCATGGTGACAGCAGACAGGAGAAGGGCCTGGGTAGAGAGTAGTTAGTGGTGGCCAGTGGGAGAGGTCAGAAGGTGGAGAGGCTTGCTGCTGAGCCTGGTAACTGAGTTCAATCCCCAGGACCTACATGATAGGAGAGAACTAACTCTTGCTAGTTGTCCTCTCACCTTGACATGTATGCTGTGGGAGGTGTGAGCACACACACACACACACACACACAAACACACACACACCAAGACATGGTAGTGGCAGAGACCTGGAGTGGCCAGATCTACAGAACTCAGGGATCATCTTCAGATAGGGCTAGGGATGGTGAGAGTCCCCAAAAGTGAAGGCAAATCCTTGGGGGTCCTTGGGAGATTTTCTGATTGGTCATTTCTTCCCCCAG
Seq C2 exon
GGACCCATTGGTTTGAAGGGTGACAAGGGTCCCCCGGGCCCTCTTGGGGCAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020525:ENSRNOT00000027897:40
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(37.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(22.1=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]