DreINT0018777 @ 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
chr21:2757103-2758394:-
Coord C1 exon
chr21:2758279-2758394
Coord A exon
chr21:2757273-2758278
Coord C2 exon
chr21:2757103-2757272
Length
1006 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAA
5' ss Score
7.09
3' ss Seq
TGAGTCTCTCTGTCTCTCAGGCT
3' ss Score
8.79
Exon sequences
Seq C1 exon
ATAAAGGTTTCCTGCATAAGTCAGTGGTGTTGGAGAATGAGGTTCACACGGTGGAGGAGGTTCAGCTGCTGAAGAACTCAGAGCCCATCAAAACACTCCTGCTCTCCACAGACCAG
Seq A exon
GTACAAAACCCAGAAACACTTCATCTTCTCTTCTAGCAGAGCGTCTGAACACTGCTGAATCATGGGAAATCAGATCCAGAGGAACCAGCTTTATTCACTGTGATTTCACAGCAGGAGGGAAGTTTCCATTTGATGGTGACACACAGTCTGACAGAGTCTGCTCCAGTTTCTTCTTTCTCACACATCAAGGCACACACACACACACACACACACACACGCACAGATACACACATATATTACAGACACACATGGATTGTTCTGAACTGTTTGATTCACTCTTTCAGACTCAGGATTGTTCTGAACTGTTTGATTCATTCATTGAGACTCAGGATTTTTATGAACTGTTTGATTCACTCATTCAGACTCAGGATTGTTCTGAACTGTTTGATTCACTCATTCAGACTCAGGATTGTTCTGAACTGTTTGATTCTCTTATTCAGACTTAGGATTGTTCTGAACTGTTTGATTCACTTATTCAGACTCAATATTGTTCTGAACTGTTTGATTCACTCATTCAGACTCATGATTGTTCTAAACTGTTTGATTCACTCATTCAGACTTAGGATTGCTCTGAACTGTTTGATCCACTTATTCAGACTGAGAATTGTTCTGAGCTGTTTGATTCACTCATTCAGACTAAATATTGTTCCGAACTGTTTGATTCACTTATTCAGACTTAGCATTGTTTTGAACTGTGTGATTGACTTATTTAGACTCAGGATTGTTCTGAACTGTTTGATTCACTCTTTAAGATTCATTGTTGTTCTGAACTGTTTGATTCATTCTTTCATATTTAGGATCATTTGAATCATTTGAACTGTTTGATTCTCTCTTTCATGGTCAGGATTGTTCTGAACGGTTTGATTCACTCTTTAAGACTCATTGTTGTTCTGAACTGTTTGATTCATTCTTTAAGATTTAGGATCATTTGAATCATTTCAACTATTTGATTCTCTCTTTCACGGTCAGAATTGTTCTGAACGGTTTGAGTCTCTCTGTCTCTCAG
Seq C2 exon
GCTCAGTTTCTGTATGCGGGTTCAGACTCAGGAGTGGTTCAGTCACCCACAGCGTTCTGTCAGAAATACGGCTCCTGTGTGGACTGTGTTCTGGCCCGGGACCCATACTGCGCCTGGGACACTCAATCCAAAGCCTGTGTGAACATCTTCCAGAGCAAAGCTGATCCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000067801:ENSDART00000097664:11
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(8.8=100)
A:
NA
C2:
PF0143720=PSI=PU(71.7=66.7)
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:
ATAAAGGTTTCCTGCATAAGTCAGTG
R:
CGTGGATCAGCTTTGCTCTGG
Band lengths:
286-1292
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]