DreINT0132859 @ danRer10
Intron Retention
Gene
ENSDARG00000002748 | sema6d
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:ZFIN;Acc:ZDB-GENE-040426-1933]
Coordinates
chr19:414488-414748:+
Coord C1 exon
chr19:414488-414565
Coord A exon
chr19:414566-414689
Coord C2 exon
chr19:414690-414748
Length
124 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
GCGCATGTGCGTGTGTGCAGGGC
3' ss Score
6.5
Exon sequences
Seq C1 exon
ACGCTGCCTCTACACACATGACCCATACTGCATCTGGCTGCGGACGGGACGCTGTGCTGACATGGCCCCGGGGTTCAA
Seq A exon
GTAAGAGTGACATCACTTCCTGCTGCACCAATAAACCTGATCAGTTATTGAACAAATCAAATTTGATGCAACTGATCTGCCTGTCTCTCTTTCTGTGTGTGTGTGCGCATGTGCGTGTGTGCAG
Seq C2 exon
GGCGGGATTTGAACAGGACATTGATGGTGAACAAACTCATTTATTTGACACATGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002748:ENSDART00000136361:15
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:
PF0143720=PSI=FE(47.3=100)
A:
NA
C2:
PF0143720=PSI=PD(34.5=90.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGCCTCTACACACATGACC
R:
CAGTGCATGTGTCAAATAAATGAGT
Band lengths:
135-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]