RnoINT0081605 @ rn6
Intron Retention
Gene
ENSRNOG00000059492 | LOC100365363
Description
vomeronasal 1 receptor, F4-like [Source:RGD Symbol;Acc:2319215]
Coordinates
chr1:60884761-60885663:+
Coord C1 exon
chr1:60884761-60884993
Coord A exon
chr1:60884994-60885534
Coord C2 exon
chr1:60885535-60885663
Length
541 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGG
5' ss Score
9.08
3' ss Seq
GTTACTGTCTTTGTAAACAGGAA
3' ss Score
9.06
Exon sequences
Seq C1 exon
GGTTTATTTTCTTTAAATTAGTTCATCCTTTTGATTTTTCACTTGTGTCACCTCTGTGTAAAGCTCTTAAATGTCCACATGGTAAAATGTGTTTGTTCCCTTTTAGGGACAGTTGACATTCAGTGATGTGGCCATAGAGTTCTCTCAAGAGGAATGGGACTGCCTAGACCATGCACAGAGGGCTTTGCACAGGGATGTCATGTTGGAGAACTACAGCAACCTGGTCTCCCTGG
Seq A exon
GTAAGGATGGCTTTCTTTGTAACTTTCCATTTTCCTTCTGTGCCTTTGGGGATCCATGTAACTATTCTACCTTTCTCCTATTCCTTCTTTCTTCCCTCCCTTCCTTCATTGGGAATAAAACTTAAGACTTTCATACAAGCAAGCGTTCTACCACTGGGCTGTGCTCCAGGCCCTTATGATAGATTTTTTGGCCTTTTAATTTATTTTTTTTTTATTTTGAGTTGTATAGTCTAGTAGCCTTGAACTTACAGTCTGCTTGCCTCACACTGGAATTATAAGCATTTGCCACCATGCATGACTCTTGGCACCTAGGCATGTGTTTAAAGTATCTAATTCCTTGCTTTCTTTCCCTGAGCTTTTGAGTCAGTACTTCTTTGTAGATAACTAGTTTCTGTCCATTAAGTTCCCAGAGGGAGGCATTCATGATAAGTTTGTGAAGTATTTTTCTAGATTTATATGTAACATGTTCTGTCCTCACTTTATCACAGTATGGAATTTCTATAACATCCTCAGTTCCTGATGTTACTGTCTTTGTAAACAG
Seq C2 exon
GAATGACACTTCAAAGTCTGAATGCTGTGTCTAAGTTGGAACAAAACAAAGGACCCTGGACCGTGGAGAGTGAGGCAATAATAACCAGAAAATCAAATGTACAGGAATATGCCATAGCTATGAATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000059492:ENSRNOT00000088689:1
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:
PF0135222=KRAB=WD(100=100.0)
A:
NA
C2:
PF0135222=KRAB=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTTCATCCTTTTGATTTTTCACTTG
R:
TGCATTCATAGCTATGGCATATTCCT
Band lengths:
342-883
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]