RnoINT0133045 @ rn6
Intron Retention
Gene
ENSRNOG00000004033 | Sema6a
Description
semaphorin 6A [Source:RGD Symbol;Acc:1305493]
Coordinates
chr18:41365903-41366215:-
Coord C1 exon
chr18:41366075-41366215
Coord A exon
chr18:41365984-41366074
Coord C2 exon
chr18:41365903-41365983
Length
91 bp
Sequences
Splice sites
5' ss Seq
AAAGTATGT
5' ss Score
6.93
3' ss Seq
CAGTCCTCCTTCTCCTACAGAAC
3' ss Score
9.22
Exon sequences
Seq C1 exon
GTGCAGCTATGATGGTGTAGAAGACAAAAGGATCATGGGTATGCAGCTCGACAAAGCAAGTGGTTCACTTTATGTTGCATTCTCTACTTGTGTGATAAAGGTGCCTCTTGGCCGCTGTGAGCGACATGGGAAGTGTAAAAA
Seq A exon
GTATGTAATTTTTTTGGCCTTGCTGACAATTCAAAAATCGTTAGTACTTCGAAAGCAACCTGGTTAGCTGACAGTCCTCCTTCTCCTACAG
Seq C2 exon
AACCTGTATCGCCTCCAGAGACCCATATTGTGGGTGGGTAAAGGAAACTGGTTCCTGTGCCCATCTGTCACCCCTTAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004033:ENSRNOT00000005446:13
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=PD(3.4=31.2),PF0143720=PSI=PU(13.6=18.8)
A:
NA
C2:
PF0143720=PSI=FE(40.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATCATGGGTATGCAGCTCG
R:
ATGGGCACAGGAACCAGTTTC
Band lengths:
176-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]