DreINT0132867 @ danRer10
Intron Retention
Gene
ENSDARG00000002748 | sema6d
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:ZFIN;Acc:ZDB-GENE-040426-1933]
Coordinates
chr19:409570-410228:+
Coord C1 exon
chr19:409570-409660
Coord A exon
chr19:409661-410102
Coord C2 exon
chr19:410103-410228
Length
442 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAA
5' ss Score
5.07
3' ss Seq
CCCTCTCCTCTATACTTCAGGTG
3' ss Score
10.13
Exon sequences
Seq C1 exon
TTGAGTTCACTGGAGCAGGTCGGACAGGAGCTCTTGGGTCAGGCAAGATGTCCATTTGAGTCTCGACAGTCCAATGTAGGAGTGTTTGCAG
Seq A exon
GTGAAACACACACAGAGACGGATGTGAAGATATATACACCTGCAAAATAAGACTAAATTTGTCTTCCAGGGGGATATTTTATTAACACTCTCACCAAATAACAATGTTAAAATAGATTTATTGCTTTGTTATTTTTGTTTTGAATTTAAATACAGAAAAACAACATGACTGCATTATTAAAAGTATATAATAAAGTATATTATTATTATTATTATCATTATTATTATTATTAAATAGTCATACTGAATAAGTTTCCTTTTTTGTTCTTATATGCCAGTAATTGATTGATTGATTGATTTGATTGATTGATTGATTGATTAATTATCTGATTGATTTGATTGATTGATTAATTGATAGATTATCTGATTGATTGGCAGGTAGACAGACAGTGAAGTGCTTCTTCATTTAAGTGTTTTACATTTCCCTCTCCTCTATACTTCAG
Seq C2 exon
GTGGTCATTTCTATTCAGCCACAGTGACGGACTTCCAGGCGAGTGACGCTGTGATCTACAGGAGTTTAGGAGGAGAGGGTCGACCTGTTCTGCGCACTGTCAAATACGACTCCAAATGGCTCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002748:ENSDART00000136361:7
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(7.0=100)
A:
NA
C2:
PF0140314=Sema=FE(13.4=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:
TGAGTTCACTGGAGCAGGTCG
R:
CTCTGAGCCATTTGGAGTCGT
Band lengths:
216-658
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]