Special

DreINT0018781 @ danRer10

Intron Retention

Gene
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D [Source:HGNC Symbol;Acc:HGNC:10732]
Coordinates
chr21:2781698-2781964:-
Coord C1 exon
chr21:2781902-2781964
Coord A exon
chr21:2781797-2781901
Coord C2 exon
chr21:2781698-2781796
Length
105 bp
Sequences
Splice sites
5' ss Seq
GAGGTAATG
5' ss Score
8.73
3' ss Seq
TTTCTGTTTTTGTGGAACAGACG
3' ss Score
6.67
Exon sequences
Seq C1 exon
CTCCTGTGGAAAGTTCCAGACATTGACATGTCCATGTGTATTTTAAAGGGGAAATCTAAAGAG
Seq A exon
GTAATGTGGAAAAATACACTCAAAATGCCCTTACTCTGAGTATTCAGTCACTGATGCTGGAATCTTTGTAAATGTTTGTGGTTTATTTCTGTTTTTGTGGAACAG
Seq C2 exon
ACGGACTGTCGAAACTACATTCGAGTTTTGCAAGTGCTGGATGAAGAACATCTGTATGTTTGCGGGACTCACGCGTTTCAGCCTCTCTGTGATTATCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000067801:ENSDART00000097664:3
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(4.6=100)
A:
NA
C2:
PF0140314=Sema=FE(7.4=100)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Associated events
Primers PCR
Suggestions for RT-PCR validation
F:
TGTCCATGTGTATTTTAAAGGGGA
R:
GAGAGGCTGAAACGCGTGAG
Band lengths:
122-227
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]