RnoINT0104836 @ rn6
Intron Retention
Gene
ENSRNOG00000042407 | Obp2a
Description
odorant binding protein 2A [Source:RGD Symbol;Acc:1588212]
Coordinates
chr3:2911522-2912288:+
Coord C1 exon
chr3:2911522-2911632
Coord A exon
chr3:2911633-2912186
Coord C2 exon
chr3:2912187-2912288
Length
554 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGG
5' ss Score
6.74
3' ss Seq
CCTGCCCCACCTCCTCACAGGGA
3' ss Score
9.84
Exon sequences
Seq C1 exon
TTCATGGCAAGAAGACTGTTCATGTGGAAAAGACATCAGTGGAGGGGCACTACATTTTCTACTGCGAAGGACTGCACAACGGGAAGTCGTTTGGGATGGGAAAACTCATGG
Seq A exon
GTGAGGTTCCACAGAGGACCCATGTCCTGTCCCTGGTCTCTGTTTCTGGTAGCCATGAGAAAGGCATGCGACATGCCTGGTACTGGTGCTGGACCCAGCCAGGACGTGGCCCAGGAAATGTGTGAGGTCCAAAGTGAAAAATAGGGAAAACTGGGTTAGGAATGGGGTTTGTGTGGCCTCTGGAGGCCTGAACACTCAGGAGAGGGTCCCATACCTGGAAGCAGCCAATACCACTCCCAGGCTCTCAGTCAAGAGTCACATGAACTTAAAAGGACATGTCTTGGTAGGGGACATTTTATTGTAGGTAGGAATCCTCCAGGGCAAGGAGCAGCCTCATGGCCTTGAGATTCAGGGGTCCGATAGGACTGTGTAGGCCCCGCAAGCCTGCTTGGGTCTGAGGATCAGTCGGTGTCTGTGGACGTCTACACACTGAACTTCCTTGTCTACCGCCAGGGTCCTCGCTGACTCCTGTGCTGGTTTGCACCTCTATCTTGTGTCTCTGGCGCTCTGCAGAGCTGAGTACCACCCCTCAAACCTGCCCCACCTCCTCACAG
Seq C2 exon
GGAGAAACCCTGAGGAAAACCCGGAGGCTATGGAAGAATTTAAGAAATTCATACAGCGCATGGAACTCCAAGAGGAAAACATGTTTGTGCCAGAGATCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000042407:ENSRNOT00000064745:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.158 A=NA C2=0.314
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=FE(26.6=100)
A:
NA
C2:
PF0006118=Lipocalin=FE(24.5=100)
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:
GGCAAGAAGACTGTTCATGTGGA
R:
TCTGATCTCTGGCACAAACATGT
Band lengths:
207-761
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]