RnoINT0039314 @ rn6
Intron Retention
Gene
ENSRNOG00000010326 | Col20a1
Description
collagen type XX alpha 1 chain [Source:RGD Symbol;Acc:1563901]
Coordinates
chr3:176504551-176505814:+
Coord C1 exon
chr3:176504551-176504680
Coord A exon
chr3:176504681-176505668
Coord C2 exon
chr3:176505669-176505814
Length
988 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
GATGATCACCCCCTCCTCAGCAC
3' ss Score
5.05
Exon sequences
Seq C1 exon
GTGGTGGTGGAGGGGCCTGTCTCATCCATGGAGCTTGGAAACCTGACCTCCAACACAGAATACTCGGTCTCTGTGCTTCCTGTCTACGAGAGTGGGGTTGGCAAGAGTCTGCAAGGACGGGCAACCACAG
Seq A exon
GTAAAAAGGTGACCTTCGTGTAGTCCTGCCCTTTGGGGATATAGTACCAGCATATGTGACTACAGACAGCTCTGGGTCTGAAGGATTCCCACGAGCCACAAGAGGCTTGGGATCAAGCCTCTCTGACCCATGTCCTCTTTTGAACACAGTGGCATCACACCAGGGCTCAATACTGCTGATGCTATGATGTCCTAAGGCACCCTTCCTGTCTGGTGACAGGACATGGTCGAGGCCACTGGCTCTCAGCCTGCTGCTGGACCTACAATGATTTCTGGTTAATAGCCCCACTGAGATAGGGCTCATGCACCCACACTCACCCACTTACAGAGGAGATCTGTTAGCGTATTCAAGGCTTTGCCGGTTGTGGTAGCACACACCTTTAATCCCAGCATTAGAGGGGCAGGTGAATCTCCGTGAGTTCAGGGCCAGCTTTGTCTACACAGCCAGTTCCAGGACAACCAGGGTTAGAAAGAGGGAACCATTTCTCAAAAGATAGAAACCTGAACAAACAAACAAGTAGGAAGAACAATATATAAAGAGAAGTTTACACCAAGATCATATTCATTCCCCAAAGGAAACTGCACATTTCACTGACAGCTTCACCCAGCCCTTACAACCTCGGCTCTGCTCTTTGCCTCTGATCTGCCTCTTCTGGTCATTCATAGAGACACCTCCGTGAAGTATGTGAGGGTTTGTGTGTGTGAACCTGGATACTACATCCCTTACCACGTCTGTAGCAAATTGCCTTAGGCCAGCGGGGTGACCTGGCTCCCCCAGAATTGTTAGCCGAAAATACAGCCCGCTGACATTTGAGACACATGTGACCTAGAATCCTGTACTCTGATTGGTGGTCGCTTACCTGGCTGTCTTTACAACCCTACCTACTCAAAGCCTCGTCACTGGAAAAGGGGCTCTGTTGCTCACGTATATGAGTTCTGCATGTGCCACAATCCCCCTGAGATTCTCCCGATGATCACCCCCTCCTCAG
Seq C2 exon
CACCCCTGCCTCCACCTGGGCCACTGACCCTAGCTGCGGTGACACCCAGAACTCTCCACCTTACCTGGCAGCCCTCTGCTGGGGCCACTCAATACTTGGTACAGTACTTGCTGGCTGCCTCCACTGGGGAGGAACAAAAGAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010326:ENSRNOT00000040270:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.341 A=NA C2=0.347
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(43.8=79.5)
A:
NA
C2:
PF0004116=fn3=PU(56.2=91.8)
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:
GTGGAGGGGCCTGTCTCATC
R:
CTCTCTCTTTTGTTCCTCCCCA
Band lengths:
270-1258
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]