RnoINT0104833 @ rn6
Intron Retention
Gene
ENSRNOG00000042407 | Obp2a
Description
odorant binding protein 2A [Source:RGD Symbol;Acc:1588212]
Coordinates
chr3:2910083-2910833:+
Coord C1 exon
chr3:2910083-2910173
Coord A exon
chr3:2910174-2910699
Coord C2 exon
chr3:2910700-2910833
Length
526 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGG
5' ss Score
4.17
3' ss Seq
GACAGCTTCGTCTCCTGCAGTAC
3' ss Score
6.19
Exon sequences
Seq C1 exon
GGAGATGAAGAGCCTGCTCCTTACCGTCCTGCTACTGGAGCTGGTGGCTGTCCTAAAGGCTCAGGAACTCCTATTAGATGACCAGGAGGAT
Seq A exon
GTGAGGACGGAGGGACAATGGGTGGTGGTTGGAGATGGCCTGCCCCTGCTTGACGCTGGTAGATTTATGTTAAGGTGAAGGATATCTTCTTGAAGGTTGAGTTTGACTCCATACTTCATCTCAGCAGTTGGATCAAGGGTAGAAGATAGGGGTCCTCCTGAAAACATGGGTCCTCCTAAGACCTGAGACAGAACAGAAAACCAGGTTTGGGTGAAGAATCCTTGTTCAAGTAACACCCAGAGCTAGAACATTGAGAGCAGGACATCCGGGGCAGAGGAGCCATCCAGTGCCCTCTTTGAGGGGCAGACATCAAAGAATACATACACTGAGCTCGGGGAAGACACTTCTGCCATCAGGGGATTGGGCAGCCCAAGTGCTGGTATCTCTTTATTGACCGCAGGTCTTGGAACACGTGGGGTTAGCTCACCTGAGTGGCTACACCCTGGGCTCTGCAGAGTCTATTCAGGAGCTAGCCTGGGGTAGACTTGGGAAGACCTGGGTGTGCTGACAGCTTCGTCTCCTGCAG
Seq C2 exon
TACTCTGGGACCTGGTACCCGAAGGCAATGGTACACAATGGGAGCCTACCCCATTGCAAGCTACCCACTAGGGTTTTCCCTGTGAAAGTGATAGCTCTGGAAGACGGAGACTTGGAGGCCACAGTTACAGTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000042407:ENSRNOT00000064745:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0006118=Lipocalin=PU(30.9=95.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal4)
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:
GGAGATGAAGAGCCTGCTCCT
R:
AGACTGTAACTGTGGCCTCCA
Band lengths:
224-750
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]