RnoINT0039346 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176502705-176503757:+
Coord C1 exon
chr3:176502705-176502869
Coord A exon
chr3:176502870-176503604
Coord C2 exon
chr3:176503605-176503757
Length
735 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGC
5' ss Score
7.23
3' ss Seq
TGCACACTTCCCCAAAGCAGGTG
3' ss Score
5
Exon sequences
Seq C1 exon
GCCTTGCCCTAACCCATGTGCTGGGGCAGAACCTGAAGCCAGCAGCAGGTGTCCGTCCAGAGGCAGCCAAAGTGTTGATTCTGGTGACAGACGGCAAGTCTCAGGATGATGTGCGCACAGCTGCCAGAGTCCTTAAGGACCAGGACATTGATGTCTTCACTGTGG
Seq A exon
GTGAGCCCACACAGTGCCTGGGCCCCGGGTTGGGATGGCTGTGGCTGGGGTGGGCTCTGGGTCACAGACACATCTTTACTCTGGCTTTACCATCTCTGCTAAAAAGCTTGGGTCCATTATAACTGCTGCCCTGCAACTTCCACACCCATAGGGCCCAGAGGTTGAGTGCTGCTCCATAGAGGTTCATGGCTACCCCTTGTAACAGCATCTGCAAAATCTATCCCTGCCTCCTCCCCTGCTGTGACACTCCCCAACTTCCTGCCCCCCTCCGACTCACAATGCAAGTGACCCTCATACTGGTCCCCTGCCTGGCACCTGCTGTCATACCTGACAGCTCTTCCCCTGCCCCATTTGCTCCTCAAGCAAGGACTGTTCCGAGTGGTCTCTGGGACGTCGACCACATTGGTTGCACTGTTTGATGGGAAGGAAACTCTAAGTGTAGGGAGTGTTCTAGGATCTCCTCTCTCCCAGGAGCCCCCTCTCTTATGGGTGGGTATCTGACACCAGCATCCACATAGCCTGGCCCACTTCTCAGAGCTCCCAGGGCTAAGCACACTGGCCTCCCCTGCCCCATTCCTATGCTCCACCGAGACCCCGTGGAATCTAGGACATATGTCTTCAGTGTGTGCCCTCCCCCACGCTGGGAACTCTGTTAGGTCCCTCCCCTGTGGTCTTGTCTGTAAATAGAATGAGAGTTCTCAGAGTGGCTTGTTGGTGCACACTTCCCCAAAGCAG
Seq C2 exon
GTGTGAAGAATGTCGACGAGGCCGAGCTGAAGCTCCTGGCATCCCAGCCGCTGGACATCACTGTCCACAACGTGCTGGACTTCCCTCAGCTGACCACCTTAGCCCCTCTGCTCAGCCGTCTTATTTGCCAAAAAATTCAGGGCAGAGGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.018 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(31.8=100)
A:
NA
C2:
PF0009223=VWA=PD(21.4=71.2)
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:
CCTTGCCCTAACCCATGTGC
R:
TGGCAAATAAGACGGCTGAGC
Band lengths:
294-1029
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]