RnoINT0133091 @ rn6
Intron Retention
Gene
ENSRNOG00000004812 | Sema6d
Description
semaphorin 6D [Source:RGD Symbol;Acc:1310910]
Coordinates
chr3:116948675-116949987:+
Coord C1 exon
chr3:116948675-116948848
Coord A exon
chr3:116948849-116949846
Coord C2 exon
chr3:116949847-116949987
Length
998 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
AAAATGTAACCACCAAATAGGTG
3' ss Score
2.65
Exon sequences
Seq C1 exon
GTACAGGCTGACAGCCATCGAAGTGGACCGTTCGGCAGGGCCGTACCAAAACTACACAGTCATCTTTGTTGGCTCTGAGGCCGGCGTGGTGCTTAAAGTTTTGGCAAAGACCAGTCCTTTCTCTTTGAACGACAGTGTATTACTCGAAGAGATCGAAGCTTATAACCCAGCCAA
Seq A exon
GTAAGTATGTTTTGGGAGAACGCTCTTTAGCCCTGCTCAAAAAAATGATGGGTGTCTAGCTTATCTGGCCATTTTTCTTTCAGACTCCTGAATTAGCGATTTTTTTTACATGTTCCATTTGGGTTTTATTTCTTCGTTTATTATTTACCTCCCCCATAGAAGTGCTTTTCAGGATTGTTTGTTTTCCTAAGCCCACTGGGGCCAGGAGGGCGAACAGCTGATGAGTTTAAAAATAAGGCACCCCTCCTTCCTTTCTCACCTGTGAAAACGAGAACATTTTAGCACCGTCTTACCTTGCAGATCTATTTCGGGATGCTGCATGTGGCACAGTTGGTCGTAAGCATGCGCACAGAGAATATTCTCAGAGTTCAGCAAGAGAGTGTGGACGGTTAAAACACATAAGGAGTGAGCGAGGGACGTTGAATACAGGAGACACCCAGAGTCCTCTAGCATGGGAGGATTTAAATGCGTTAGAATGCCATCCTCCTCCTCTCCTAGAATCGAACCAGTCCTTCACAGCCGCAACCCCATTCGAAAGCAATTTTTTTTAAAAAGACCCTTTGTCCAGCTGGAAATGTAACCAGCTACACAAAACCATAGCGCTATATCCCACAATTATAATTTCTCAAATTATAATTTGTTTTGGTTGAGCCGCCAAATTGCACCTCTTACATCGTTGGTGCAGGCTTGACTTCAGTGTATGTCTTCAAAATGTAACCACCAAATAGGTGCAGCGCCGAGAGTGAGGAGGACAGGAAGGTCGTCTCGTTACAGCTGGACAGGGATCACCCGCAACCCCATTCGAAAGCAATTTTTTTTAAAAAGACCCTTTGTCCAGCTGGAAATGTAACCAGCTACACAAAACCATAGCGCTATATCCCACAATTATAATTTCTCAAATTATAATTTGTTTTGGTTGAGCCGCCAAATTGCACCTCTTACATCGTTGGTGCAGGCTTGACTTCAGTGTATGTCTTCAAAATGTAACCACCAAATAG
Seq C2 exon
GTGCAGCGCCGAGAGTGAGGAGGACAGGAAGGTCGTCTCGTTACAGCTGGACAGGGATCACCATGCTTTATACGTGGCCTTCTCCAGCTGCGTGGTCCGCATCCCCCTCAGCCGCTGTGAGCGCTATGGCTCCTGTAAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004812:ENSRNOT00000066101:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(14.4=100)
A:
NA
C2:
PF0140314=Sema=PD(1.5=12.5),PF0143720=PSI=PU(11.8=18.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGACAGCCATCGAAGTGGAC
R:
TTACAGGAGCCATAGCGCTCA
Band lengths:
305-1303
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]