RnoINT0039329 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176515536-176516363:+
Coord C1 exon
chr3:176515536-176515613
Coord A exon
chr3:176515614-176516276
Coord C2 exon
chr3:176516277-176516363
Length
663 bp
Sequences
Splice sites
5' ss Seq
TTGGTAGGT
5' ss Score
7.03
3' ss Seq
AATGATCTCTTTTCTTCCAGAGG
3' ss Score
9.11
Exon sequences
Seq C1 exon
TTCCAGCTCCAGATGTTGCAGATCATGTGCAGCGATACGTGGGCGGACAAGGACAGGTGCTGCGAGCTTCCTGCATTG
Seq A exon
GTAGGTGGTGGCAAAAAGGCCCTAGACACTGTCCCTTGGCCCCGTGGGAATGCCACTAAGGCTCTGTAACACAGAGTCCGGGGTAGATGGCCTGTCCTGATCCACTATGCTGAGAGAGACGAAAGCAGGCTTTCTGAATGAGGTATCCAGGGGTCTGATAGGAAAGTCCCACAGGCTTTGGGGGAAGGCCAAGCAACGTCATCTGTTGTTATTATAGCTACCATGTACTGGAACATCCAATTTCCATCAGTGACACCTATGTGTCAGGTAGAAGTCCCTGGTCAGCCCTAGAGAGCAGCTTCTCTATAGGCCCAGGTGGAGGCTCATTCAGGGAGGCTGTGGGACCCTGCTAGGCCTGCTGGGGACTTGGGAGCTTTCCTCACTAGTCCACTGGGATCCCATACTGAGCGGACATGCTAGGAGCCTGGAAGAAGAGTGAGAAAAAGGAGATACCATCATGCCATGGGGTTCATGTGAGTGTCTAGGAAGGGCACCTGAGCCTGCTGCATACACAGGTCCTGGCAGCCCTCACTCCGACCTACCCTACCTCTGGTGATGACCCCAGAGGTCTCCTGGAGTCAGGTGTCCTTTGGCCATGCCGAGTCTTAAATCAGATGAGATCCAGTTAGTGGTTCACTAAGCAAATGATCTCTTTTCTTCCAG
Seq C2 exon
AGGGATGGAGAGACATGCCCGGCCTTCCCTTTAGCCTGTACCTACTCATCTGAGACCCCTGGGCCACCAGGGCCCCAAGGCCCTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.038 A=NA C2=0.655
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(18.6=37.9)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]