RnoINT0039341 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176524684-176526018:+
Coord C1 exon
chr3:176524684-176524761
Coord A exon
chr3:176524762-176525788
Coord C2 exon
chr3:176525789-176526018
Length
1027 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAT
5' ss Score
6.6
3' ss Seq
GCCTACTCTTCTCTCTCCAGGAC
3' ss Score
12.02
Exon sequences
Seq C1 exon
GTGAGCCTGTGGCTATCAGCCACACAAGCAAACCTGTACTGCAGGAGGTGCAGACCCCAGAGCCCCTGGAGTGAACAG
Seq A exon
GTGAATCTCTGTCATTGTGCCAGCCATGGGGCAAGAAGGAAGGATAGCTGGAGGGGAGATCTGCATGGGCCGAACAGCAAGAGAGTGGGAGAGGGCGCTGTCTCCATCTGAGAAGAGTGGGGTAGAGCTGGTGCTTGTGAAGCTGGTTGTCCTGCAGACCCTGGTTGGGCCTGCGAGTATGAGGAGACACAGGGTGGAGGAGAGGTTTGAGCTGCAGGAGTGTGGGTGCTCACGGATCCTGGGAGGGGGTGCTTACAGAGACTGGACCTCAGGGGTGCATTCCGGTGAGCACCCGGCCAGGTGAGAGCACCCGAGGCCTGAGACAGAGCACTATGGAGGTTCTGAGTTGGTGGACAGAGTGCAGCACCAGATGACCTCTTCCCTATCTCAGGATGTGCTGAGCAAGCTTCCTGTGTACAAACCTGCCTGAGGAGGTGTTTCTAGGTGCAAGTGTGGGGTAGGGTACCACGAACACAGGTGGGGTGTGAGCACAGATAAACTCAGGTGAGCTCTGTGAACACAAGCACAGGTGAGCACAGGTGGCACAGGTGGGTTTAAGTGACACAAGTGGGCACAGGTGAGCACAGTTAAGCACAGGTGGGACAGATGGATTTATATGGCACAGGTGGCATAGGTGGCACAGGTGAGCACCGGTGGGTTCATATGACACAGACGGCGGCACAGGTGGGTGAAACAGTATTGCTCTCAAGTACATGATGGAGCTGGAGGCATACCGGGGCAGACTCAGCAGGCACAGAGGCTCAGGGGTGTGCGTGACAGAAAGTGAGTGGCAGGAGTAGAGAGCTACCTATGGACAAGCTAGAGTCCTGCATTGAGTGCAACCCTATAACTGCTCCTGAGACCAGAGAACAACTCAAGGTTCTGCTCTGTTTCCTGTCACAAGAGCTGGGGTGTGGAGACCTCAGCTTCTTTCACCACACAGGGGAAGCCTGAGCTCAGTGTGTGAGGAGGTTGGGCCGCCGTCTCCTAGACTGCAGTCCAGCAGTGCCTACTCTTCTCTCTCCAG
Seq C2 exon
GACCTTCCCTCTGCCACTTCAACTCGCCCCGTCCTTCCCCAGCACCATCATCCATAATTTTGTCTCAACACTGAGAGCAACTGTGCTCTGCAGGGGCAGAGAAGGAAACCCAAAGGAAGACCCTGAAGTGGCAGGAGTCGGAAGGGAGGAGGGTGGGGCTCCTCCTCAAGCCCCTTCTTTATAGCATTTCCAGGTTCAGATAAACTTGTGCTAGCTCATCAGCCTCTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:36
Average complexity
IR
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=NA
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCAGCCACACAAGCAAACCT
R:
CACAGAGGCTGATGAGCTAGC
Band lengths:
294-1321
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]