DreINT0018783 @ danRer10
Intron Retention
Gene
ENSDARG00000067801 | SEMA4D
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D [Source:HGNC Symbol;Acc:HGNC:10732]
Coordinates
chr21:2779091-2779711:-
Coord C1 exon
chr21:2779618-2779711
Coord A exon
chr21:2779208-2779617
Coord C2 exon
chr21:2779091-2779207
Length
410 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
TATCTGTGTTTGTTGTTCAGATG
3' ss Score
8.74
Exon sequences
Seq C1 exon
TCTCTGCAAGATTTCCGGCTGCTCGAGAAAGCAGAGGACGGAAGAGGGAAATGTTCCTATGATCCGTCTCAAAGCTTCACCACTGTGATGGTTG
Seq A exon
GTAAGTTAACCGTCCTGACCTTTTGTCTAAACCACATTTCTACATGTTTTGTTAGACCTCATATACAGTAGAAGTCAAAGTTATTTGCCCTCCTGTGAATTTTATTTATTTTCTTTTCACAGAAAAGTCAATATTATTAGCTCTCTAAACCAATATTTTTCTCAGATTGTCTACAGTACAAACCACTGTTATACAATGACTTGCCTAATTACCTTTAAATGTCACTTTAAGCTGAATACTAGTCCTGAAAAAGAACTAGTCAAATATTATCCACTGTTATGATGTTTAAACTAAATTTAGTTATTAAATCAGTTAAAACTTCACTTTGTTAAACAACACTTAGAAATATATATTTTAAAAGTATTAAAATTCCCTAGAAACTAATGTTTTTATCTGTGTTTGTTGTTCAG
Seq C2 exon
ATGGCGAGTTGTACTCAGGAACTGCTTATAACTTTCTGGGCAGTGAACCGATCATCTCCAGATCGTCTCCGTCTCAGAGTTTACTGAGAACTGAGTACTCAACATCCTGGCTCAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000067801:ENSDART00000097664:5
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(7.1=100)
A:
NA
C2:
PF0140314=Sema=FE(9.0=100)
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:
TCTCTGCAAGATTTCCGGCTG
R:
TGAGCCAGGATGTTGAGTACTCA
Band lengths:
208-618
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]