RnoINT0133044 @ rn6
Intron Retention
Gene
ENSRNOG00000004033 | Sema6a
Description
semaphorin 6A [Source:RGD Symbol;Acc:1305493]
Coordinates
chr18:41366075-41366741:-
Coord C1 exon
chr18:41366565-41366741
Coord A exon
chr18:41366216-41366564
Coord C2 exon
chr18:41366075-41366215
Length
349 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
CTCCTACCTCATCAAACTAGGTG
3' ss Score
7.59
Exon sequences
Seq C1 exon
ATACCGCCTGACCAAAATTGCAGTAGACAACACTGCTGGGCCATATGAGAATCACACTGTGGTTTTCCTGGGATCAGAAAAGGGAATCATCTTGAAGTTCTTGGCCAGGATAGGAAGCAGTGGTTTCCTAAATGGCAGCCTTTTCCTGGAGGAGATGAATGTTTACAACCCAGAAAA
Seq A exon
GTGAGTGGAACGTTGGGTCCTTTCTTGCTAATTATTTGTCATTCTACTGAGACCTTTTACATTCATGGGAAATTACAGAAGACAAGTGTGATCACACCATTTCTAAAAAATACTGAGCATATTAAAAAAACATTGTTTTTTTTTCCATGCCAATAATGTATGTTCCTATAGCTGCTCATGTAGGGTGTCCACATAAGTTCTGTAAAGTTTCAGTTATATCAGATCATGAAGTCAGCATGTCAGTCCAGATAAGGGTGAATGAGTCCAGTGGGGTACAAGGGTGGTGGCAGGAGAAAGAAAATTGTTCTTAAGAATCTACTAATGGTCTCCTCCTACCTCATCAAACTAG
Seq C2 exon
GTGCAGCTATGATGGTGTAGAAGACAAAAGGATCATGGGTATGCAGCTCGACAAAGCAAGTGGTTCACTTTATGTTGCATTCTCTACTTGTGTGATAAAGGTGCCTCTTGGCCGCTGTGAGCGACATGGGAAGTGTAAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004033:ENSRNOT00000005446:12
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(13.5=100)
A:
NA
C2:
PF0140314=Sema=PD(3.4=31.2),PF0143720=PSI=PU(13.6=18.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATACCGCCTGACCAAAATTGCA
R:
TTTTTACACTTCCCATGTCGCTCA
Band lengths:
318-667
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]