RnoINT0039322 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176508890-176510054:+
Coord C1 exon
chr3:176508890-176509019
Coord A exon
chr3:176509020-176510015
Coord C2 exon
chr3:176510016-176510054
Length
996 bp
Sequences
Splice sites
5' ss Seq
CAGGTTAGT
5' ss Score
8.02
3' ss Seq
GACCTTCCATATCCTCTCAGCAG
3' ss Score
5.37
Exon sequences
Seq C1 exon
ATCTCTGTACCAGGCACCAGGAGCCATGTTGTACTTCGTGATCTGATGTCTGCCGCCAAGTACAGGGTCCTGGTCTCAGCTGTCTATGGAGCAGGGGAGAGCATGGCAGTGTCTGCCACATACCGCACAG
Seq A exon
GTTAGTGGACACCAATGCCGTAGCTCTTTCTAAATACCAAGCCCAAGCCAGACTCGGTCCAGCTAGATGCTAGACCTAGTCAGAGTTCAAAACTGGTCAGACCCCAGAGTAGGCTAGATACTAGATTCAGTGAGACCTCATAGCCAGTGAGGCCCCAGAAACAGTGGCACCCCAGAGCTGGTGAGACCTCAGAAGCCACTGAGACCTCATAGCCAGTGAGGCACCAGAGCCAGTGAGGTCCCAGGCACAACATAGAAGGTAGAGGCTGTGGACAGCGGGGTACCCAAAGCAAATAGAAAAAGCTGGATTAGAGTAACTGTGGGATGCCTAGAAAATATGGAGAGTTCTGCCAAGAAGAGACCTGCCCTTGATGCCACAGGACATGAGCAGGTAGGTCTCTGGTGGCCTGGTGTCCTCCAACCCACAAGGCCAAGCTCAGCTGGGAGACACAGCTGCTCAGAGCATAGGACCTTCAGAGGCTGTGAAGCCCACTACCTCAGCCGTAGTGCCCCCTTCGGGGTCATCCACTTATAATCCAAACGCTTATCACAGTTAGTCCCTCACTGCTCAGTGGATGCCACCATGCCTGGAGCCCTGACTGTGACGTCATCTGCCTTGTACTGGCCACAGGATCAGCCTGTACCGCCACCTCAAGGCCTATGCTGTTTCCAGTCATCTCCCTGACCCTACCATCTGGTGCCTGGGAGTCATTTGGAGCCCATAATGTCTTTAGGCAGAGTCCCCAGTGGAACCTTGGGTTTTGGCCTGAGGTGTGCAGGGTAAGCAGTGGCATCCGCTTGCTCAGTGTGACCCAGGATGACAGTGAGGAATGGAGACAACAGGGTTGGTGTAACGAAGGGGGGCAGGTAGAGCAGACGCCTACTTGAGCCTAGGTCCACCTGTGCTCACCAGAGGCCCGACATTGCCCATGAAGTGGTCCTTCTGGTAGTCGGGCTAGCTTTGCTGTGACTCACCGGACCTTCCATATCCTCTCAG
Seq C2 exon
CAGCCTGCCCAGCCCTGCACCCGGACAGTTCCCTCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.034 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(43.2=79.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
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]