RnoINT0039316 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176505900-176506580:+
Coord C1 exon
chr3:176505900-176506023
Coord A exon
chr3:176506024-176506443
Coord C2 exon
chr3:176506444-176506580
Length
420 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
GGCCTTGTTGTGTCTTGCAGCTG
3' ss Score
10.38
Exon sequences
Seq C1 exon
GTACATGTAGGACGGCCTGAGGTAGTGCTGGACGATCTGGAGCCTGGCCAGGACTATGAGGTTTCAGTGCAGAGCCTTCGTGGACCAGAGGCCAGTGAGGCCCGGAACATCCATGCCAGGACCC
Seq A exon
GTGAGTATTGGTTCAGACGGTCCAGTGTTCTCAACCGTACTAATGCTGTGACCCTTTAATACAGTTCTCATATTGTGGTGACCCCCCCCAACCACGAAATTATTCTCATCACTAATCCATAACTGTGATTTTGCTACTGTTAGGAATTGTAATGAGTATCTATGATTTGGGATGATTTTAGGTGACCCCTATGAAAGGATCATTTGATTCCCAAAGGGTTTGGGACCCACATGTTGAGAATCTCTGACACAGCAGTTACCCTGTTCTGTTCTGTTCTGTTCTGTTCTCTAGCTTGCTCTAGGGTAGGAGATCACAGATAACTCTAGATGACCCATATGCCCTCAGGCTCAGTGCTTCCTACCCTTTCCTCAGTCGCAAGGGTAGGGGTGGCAGCTCCTGAGGCCTTGTTGTGTCTTGCAG
Seq C2 exon
CTGTCCCGGGGCCCCCAAGACACCTGAGTTTCTCAGATGTGCGCTACAACTCAACCTGTGTGTCCTGGGAAGCCCAGAGGCCTGTGCGCCTGGTCAAGGTCAGCTACGTCTCTAGCGATGGCAGCCACTCTGGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.833 A=NA C2=0.217
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(41.2=78.6)
A:
NA
C2:
PF0004116=fn3=PU(53.8=91.3)
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:
TACATGTAGGACGGCCTGAGG
R:
AGAGTGGCTGCCATCGCTAG
Band lengths:
254-674
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]