DreINT0132761 @ danRer10
Intron Retention
Gene
ENSDARG00000088143 | sema4gb
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Gb [Source:ZFIN;Acc:ZDB-GENE-111117-1]
Coordinates
chr12:33754794-33755079:-
Coord C1 exon
chr12:33754989-33755079
Coord A exon
chr12:33754908-33754988
Coord C2 exon
chr12:33754794-33754907
Length
81 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAAT
5' ss Score
6.8
3' ss Seq
ACAGTTTTGCTGTTTTACAGATG
3' ss Score
9.69
Exon sequences
Seq C1 exon
GATGTGGCACGTTTTACCTTTGTGCGTTTTGAGGAGGGAAAAGAGAAATGCCCTTATGATCCCACTAAGGGGTACACTGGATTTATTATCG
Seq A exon
GTAAATCACTCGGATTCATATTGATTTTGTATTTTTTTGTGGTTGGTGCTTGTTTTTGAGCACAGTTTTGCTGTTTTACAG
Seq C2 exon
ATGGCGAGATGTACTCTGCCTCCCAGTATGAATTTCGTAACATCGCTGATATAAGGCGAAACTTTCCCTTCCCCAATTTGAGAATAGATGATTCCCCAACAAGATGGCTTTTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000088143:ENSDART00000131181:3
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(7.7=100)
A:
NA
C2:
PF0140314=Sema=PU(11.5=97.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGCGTTTTGAGGAGGGAAA
R:
AGCCATCTTGTTGGGGAATCA
Band lengths:
180-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]