DreINT0132857 @ 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
chr19:412802-413194:+
Coord C1 exon
chr19:412802-412975
Coord A exon
chr19:412976-413065
Coord C2 exon
chr19:413066-413194
Length
90 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGT
5' ss Score
11.81
3' ss Seq
GCGCGTGTGTGTTTGCTCAGGTG
3' ss Score
6.9
Exon sequences
Seq C1 exon
TTATAAGCTGACTCAGATTGTGGTGGACACTGCTGCTGGGCCTCATAAGAACCGCACCGTAGTGTTTCTGGGCTCTGAAGACGGACGCGTGCTGAAGATCCTGACCAACACACACACCAACAGCTCACACACATCCCAGCTGCTGGAGGACATCGACGTGTTTAATCCTACACG
Seq A exon
GTAAGTGTTTTTAACCAACACACACCTTTAGCTCGTGTGTGTTTTTCTCAGTGCACTGATGTGTGTGTGTGCGCGTGTGTGTTTGCTCAG
Seq C2 exon
GTGTGTTGGTGAGCGTGCAGTGTTGGGTCTGGAGCTGGATAAGGAGCATCACGCTCTGTTTGTGGCCTTCTCCAGCTGTGTGATCAGAGTTCCTCTCAGCCGCTGCGCTCAGCACGCCACCTGCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002748:ENSDART00000136361:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.068 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(13.6=100)
A:
NA
C2:
PF0140314=Sema=PD(1.9=18.2),PF0143720=PSI=PU(16.4=20.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACCGCACCGTAGTGTTTCT
R:
CCTTATCCAGCTCCAGACCCA
Band lengths:
170-260
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]