DreINT0132856 @ 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
chr19:412428-412975:+
Coord C1 exon
chr19:412428-412583
Coord A exon
chr19:412584-412801
Coord C2 exon
chr19:412802-412975
Length
218 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGC
5' ss Score
6.46
3' ss Seq
TGTGTGTGTGTGTTGTGCAGTTA
3' ss Score
8.19
Exon sequences
Seq C1 exon
TCCAGGTTCGTGTGCAGGTGAGGGTTCTGCCTCCTCCTATTCCTCTTCTGTTCAGTTTCCAGACTCTGTGCTGTCGTTCATCAAAACACACCCGCTGATGGAGGAGAGCGTGCCGTCAGTCAACAGCCAACCGCTGATCACCAACACCGCCAGCAG
Seq A exon
GTGTGCAGACATGAGCGCACACATGCACACACAGCCAACTGGTGACCAACACCACCAGCAGGAACACACACACAAAAACTCGCTTACACACACACATCAGAAGCATCCCATGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTGCGTGTGTGTGTGTGTGTGTGTGTGTATATGTGTGTGTGTGTGTGTGTGTGTTGTGCAG
Seq C2 exon
TTATAAGCTGACTCAGATTGTGGTGGACACTGCTGCTGGGCCTCATAAGAACCGCACCGTAGTGTTTCTGGGCTCTGAAGACGGACGCGTGCTGAAGATCCTGACCAACACACACACCAACAGCTCACACACATCCCAGCTGCTGGAGGACATCGACGTGTTTAATCCTACACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002748:ENSDART00000136361:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.238 A=NA C2=0.068
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(12.2=100)
A:
NA
C2:
PF0140314=Sema=FE(13.6=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:
GAGGGTTCTGCCTCCTCCTAT
R:
AAACACGTCGATGTCCTCCAG
Band lengths:
300-518
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]