DreINT0018787 @ 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
chr21:2761089-2762557:-
Coord C1 exon
chr21:2762401-2762557
Coord A exon
chr21:2761312-2762400
Coord C2 exon
chr21:2761089-2761311
Length
1089 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGT
5' ss Score
10.49
3' ss Seq
TTCATTTCTTTGTGTTTCAGTGC
3' ss Score
10.23
Exon sequences
Seq C1 exon
GGGGAATGTAGGTCTGTCGGCGGTCTGTGCGTATAACATGAGCTCAGTGCATGAGGTTTTCTCCAGAGGAAAGTACATGCAGAAGGTCACGGTTGAACAGTCCCACACAAAGTGGGTCCGCTTTAATGGAGCGCCGCCCAGTCCCAGACCTGGAGCG
Seq A exon
GTGAGTGTTTCTCCAAAACATGGCTTTGTGGTGTGTTTAGGTGTCAAGATTAGATTAGAGGAGGAGAGAAGGATTAGTCATGTAAATAAAAAGTTGAAAATATTTAAATAATTATATAGTAGATAAATGGAGGGGGGGGGGGGTCACCATATATCAAATTGAGTTACTATATATTAAGAAATGTAAATATTTCATTGAAATCAATTACAGTTTAAAATTAATAATAACATTTGTTGAAATTATTAGATGTGAAAACAATAATTTAATTAGTATTATATTTAATAAAATAACTTTTATAGAAAAAAAAGTACAAATTTTGTTTATTAAATGTATATATAAAAACATAAAATACAACTAAATAAACTAAATTATATTATAATAATTATAATGCATATATATGAGTTTGGTCTGATAGTTTTGAACGGATAGATAGTCAGATGGATGGACAGACAGATGGATAGAAGGATAGATAGACGGACAGATAGACGGACAGCCGGATAGAAGTATAGATGGAGTCAGAGTAAGTATAGACCGATAGACAGACGGACGGACGGACGGACGGACAGACAGACAGACAGACAGACAGATAGATAGATAGATATACAGATGGATAGAAGATAAGATAGATGGACATGGGTAGATAGACGGATATATAGAAGGATAGAAAGACAGACAGATGGACGGATAGATATATAGACGGATGAACGAATAGATAAAGGATAGACAGATGGAGATATAGAAAGATAAATAGACAGATGGATAGAAGGATAGACAGATGGACAGATAGATAGACAGACAGACGGATAGAAAGACGGATGCATAGATGGAAAGAGACAGATGGAAAGACAGACAGACAGGCAGACAGGTAGATAGTATACATAGACACAAGGACAGATAGAAGGATAGACAGATGGACAGAGGGATAGATTGATAGATAGATGGAAAGAAAGATGGATGGACGGACAGACAGACAGACAGATGGATGGATAGAAGGATAGATAGACGTAAAGACAGACAGATTGATTCATTCATATTCCTTAATCAGCCAGGCAGTCAGCTTTCTGAATCATTCATTTCTTTGTGTTTCAG
Seq C2 exon
TGCATCAATAACATGAACCGTCAGCAGAACATGAGCTCGTCTCTTCATCTGCCTGATAAGACGCTTCAGTTTGTGAGGGATCATCCGCTGCTGGAGGACCCGGTGCTGCCCATAGGAAACGGCCCTCGCCTCATCACTAAAGATGTGAACTACACACAGATCGCCGTGCAGAGGGTGCAAGCGCTCGACAACAGCATACACCACGTCATTTTCACAGCCACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000067801:ENSDART00000097664:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.113 A=NA C2=0.093
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(12.0=100)
A:
NA
C2:
PF0140314=Sema=FE(17.1=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:
GGCGGTCTGTGCGTATAACAT
R:
TGGTGTATGCTGTTGTCGAGC
Band lengths:
342-1431
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]