RnoINT0039320 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176508052-176508733:+
Coord C1 exon
chr3:176508052-176508184
Coord A exon
chr3:176508185-176508584
Coord C2 exon
chr3:176508585-176508733
Length
400 bp
Sequences
Splice sites
5' ss Seq
CCTGTAGGT
5' ss Score
3.22
3' ss Seq
TATTGCCTGTGCCTGGATAGCTG
3' ss Score
6.58
Exon sequences
Seq C1 exon
ATCTCTGTCCCAGGGACCCTTGGCACAGCCATCTTGCCTGGTCTGATGAAGCATGTGGAATATGAGATCACCATCCTTGCCTACTATAGGGACGGCACTCGCAGCGACCCCGTGTCCCTCCGCTACACCCCCT
Seq A exon
GTAGGTGGTCTATCACCTACATTCAGACAGTCTTGGGACAGGAGCAGGACAGAGGGGACTCAGGCCTTCCTTGGTCCACATATACTCTCAGGACATCATATTCTCAGACTCAAGTCAAGCAGGCTACCTGAGTCCCTGAGACTCTGGGCTGGACCATTGTATCTGAGCCCACAAGGGGAACAGATCTTGGGGTGGCTAAGTCCAAATTCCCCAGCTGGGTGACACAGCTTCTATGCAAGACCTCCTAGGAGTATTGGGGAACTCAGCAGGGGCATTGTGTAGAGTCAGGCAGGTCAGGGGCCTAAGACATGGTGCAAGGCCACCTGGCTAGCTGGCCTTCTGGCTGTGGGTACCTCCAGTCTGGAAAGCATTGAATTCCATATTGCCTGTGCCTGGATAG
Seq C2 exon
CTGCAGCAAACAGGAGCCCCCCATCCAGCCTGGCCTTGTCCTCGGAGACCCCCAACAGCCTGCAGGTCAGCTGGGCACCACCAAGTGGCCATGTCCTCCATTACCGGCTCAACTACACACTGGCCTCAGGCTCTGGACCAGAGAAATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.156 A=NA C2=0.230
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(43.9=80.0)
A:
NA
C2:
PF0004116=fn3=PU(54.3=88.0)
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:
CCAGGGACCCTTGGCACAG
R:
TCTGGTCCAGAGCCTGAGG
Band lengths:
266-666
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]