RnoINT0039313 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176503975-176504680:+
Coord C1 exon
chr3:176503975-176504144
Coord A exon
chr3:176504145-176504550
Coord C2 exon
chr3:176504551-176504680
Length
406 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
GATGGGGTTTTCCTGCTCAGGTG
3' ss Score
7.66
Exon sequences
Seq C1 exon
TCAAACCAGCGGCGGGTACTCGGATCCTGGACCCTCTCCCCACGCCCACCAGACTGACCCTGACCCACGTCACCTCATCCAGTATCCACCTGTCTTGGACTCCGGCCTTATACCCACCCCTCAAGTATCTAATTGTATGGCAGCCTTCTAGGGGTGGTGCCCCCAAGGAG
Seq A exon
GTAAGAGGAGGGGATCCCCTGATTCAGCTTCTGCTAAGACCATCCTTGGGAGTTGGGGCAGCTGGCAGGACTCAACCAGCATGGTTCAGGTGGGTTCCGCTGAGCTGTGCAGAAGGAGGGCCTATAGATGAGTAAGTCTGCATGAGAGAAGAGATCCAGGGTGGTGCTGGGAATGGGTAGCTACACATGGATGTACCCATCAGACTGGGTCAGAGTGTGGAGTGCCGGGCCATGACTGCAGACACCAGACTGGTTTTGATGACATGTTGCTAGATAAGTGGATGGTTTTACAGTCTCACCTGCCTCCATGGTGCCTGGTGTTGCTCCACGTGGGGACCTAACCTCCCAGGATGGTAGTACCATGTCTCCCAAGTCTACACCCTGTTGATGGGGTTTTCCTGCTCAG
Seq C2 exon
GTGGTGGTGGAGGGGCCTGTCTCATCCATGGAGCTTGGAAACCTGACCTCCAACACAGAATACTCGGTCTCTGTGCTTCCTGTCTACGAGAGTGGGGTTGGCAAGAGTCTGCAAGGACGGGCAACCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.123 A=NA C2=0.341
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(53.8=75.4)
A:
NA
C2:
PF0004116=fn3=PD(43.8=79.5)
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:
CAAACCAGCGGCGGGTAC
R:
CTGTGGTTGCCCGTCCTTG
Band lengths:
299-705
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]