DreINT0132720 @ danRer10
Intron Retention
Gene
ENSDARG00000079611 | sema4c
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C [Source:ZFIN;Acc:ZDB-GENE-080303-16]
Coordinates
chr5:14060761-14061059:-
Coord C1 exon
chr5:14060997-14061059
Coord A exon
chr5:14060860-14060996
Coord C2 exon
chr5:14060761-14060859
Length
137 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCG
5' ss Score
10.05
3' ss Seq
TGTCGTCGACGTCTTTGCAGACT
3' ss Score
7.82
Exon sequences
Seq C1 exon
ATTGAGTGGTCTGCTCCTGCAGAAAAGAAAAAAGAGTGTGCAGCGAAGGGGAAGAATAACCAG
Seq A exon
GTACCGGCTGATGTTGCATCCTTTATGTTTTAACAGCTTTATTTTGTCTGCCTTCACCGAAATGCATTTACTCTCCCTCCATCTCACCTATTTTCTCTTTGTGTGTCTCTCTCTCTCTGTCGTCGACGTCTTTGCAG
Seq C2 exon
ACTGAGTGCTTCAACTACATTCGCTTCCTGCAGAGCTACAATCACACGCACCTGTATACATGCGGGACGTACGCCTTCCAGCCCAAATGCACCTACATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079611:ENSDART00000160511:2
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(4.7=100)
A:
NA
C2:
PF0140314=Sema=FE(7.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTGAGTGGTCTGCTCCTGC
R:
AATGTAGGTGCATTTGGGCTGG
Band lengths:
162-299
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]