RnoINT0039344 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176501631-176502379:+
Coord C1 exon
chr3:176501631-176501789
Coord A exon
chr3:176501790-176502259
Coord C2 exon
chr3:176502260-176502379
Length
470 bp
Sequences
Splice sites
5' ss Seq
TAGGTGGGT
5' ss Score
5.56
3' ss Seq
CAACCAAAGTCCACCCCTAGGTC
3' ss Score
2.96
Exon sequences
Seq C1 exon
ATGACCCCCAGTTCCAGTGCACACCCCCAACACCTGCTGACATAATCTTCCTGGTGGATGGGTCCTGGAGCATCGGCCACAACAACTTTCAGCAGGTGAAAGACTTCCTGGCTAGCATCATCACACACTTTGCAATAGGACCAGATAAAGTCCAAGTAG
Seq A exon
GTGGGTACCATCTCCTTTGCCCTGCCCTTGTGTGTGGGGGGTGGGGAGGATTGGACTTCTTGAGTTCTTGCCAGCAGAAGGGTGCTGCTCTCAGGAAAGGATAGTGACTGCCTCAGCCTCTCAAGATTAAGAAACCTGGCTGAAACCTGCTTGGCTGGGTCAGGTCCATAACTCACTTTGTGAGTCAGGGCTGTTGTTATGGTCTGCAGGAATGGCTAGCTTCCGATTAGTCCCTCTGATGATATCTCTGTGCAAGCCTTGGGCCCTGAAAATGTGTCATTTCCTGGGAGTGGGACTCCCAGAGGCCGTACTCAGAGCAGGGGATTCTGTGGATCTGGTTTTCAAAGCTGAGCCTTGGCATTGAGGATACAGTAGCACAGCACTTGCCTAGCATGCTTGCCCCCAGCGATGCAAAAAAGAAAGACCCCTTCCCCTAAAACCTCAACCTAGCAACCAAAGTCCACCCCTAG
Seq C2 exon
GTCTGACTCAGTACAGTGGAGACCCCCAGACCGAGTGGGACCTGAACTCCTTCCACACCAAGGAGCAAGTGCTAGCAGCAGTACACCACCTCCACTACAAAGGAGGAAACACGTTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.111 A=NA C2=0.098
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(23.1=74.1)
A:
NA
C2:
PF0009223=VWA=FE(23.1=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:
ATGACCCCCAGTTCCAGTGC
R:
TGTGAACGTGTTTCCTCCTTTGT
Band lengths:
278-748
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]