DreINT0132868 @ 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
chr19:410103-410839:+
Coord C1 exon
chr19:410103-410228
Coord A exon
chr19:410229-410750
Coord C2 exon
chr19:410751-410839
Length
522 bp
Sequences
Splice sites
5' ss Seq
GAGGTGCAG
5' ss Score
2.03
3' ss Seq
GTGTTGTTTTGTTTCTGCAGAGC
3' ss Score
10.73
Exon sequences
Seq C1 exon
GTGGTCATTTCTATTCAGCCACAGTGACGGACTTCCAGGCGAGTGACGCTGTGATCTACAGGAGTTTAGGAGGAGAGGGTCGACCTGTTCTGCGCACTGTCAAATACGACTCCAAATGGCTCAGAG
Seq A exon
GTGCAGCTTTCCCTGATTTACCTTCATTATAATCACTAGATCTGTTTCTATCAGCCTAATTTTAAGCGCCTTTTGGATTATTGCATGAAAAAAATGCTTAACAGAATTGCCAAGATGTGCTTACATTTTAAATATGTGCATACAATAGTGTATGCATCTGTCTGCACTCCCAAAGAGTGTCTCACACCTCCAAAAGCCACCGCATTCATTGCATTTCATCTTCTGAGGCGCAACTCGTTTATTAGAGGAGAACAAACACCACAGTGGCAAATCCCAACAGTGCAGCAGACTCTGCTTCTCTCAGCAGGAGCTTCTCATTTTACTTCTCTTTTGTGTCTCACTGGAGGGAAACGCTGCTTCAGTCACTAATGCTTTATGTGCTGTTCCAGTTATTCCCTCTTTGCCTGGAAACACAGCTCGTGTCTGCTCAGATCATGTGTGCTTTTAGCAGAGAGACACACTGCTGTGAGAAATGCTCAACTGTTTATGTTGTTGGTGAATTGTGTTGTTTTGTTTCTGCAG
Seq C2 exon
AGCCTCATTTCCTGCACGCTGTCGAATACGGGAACTATGTGTATTTCTTCTTCAGTGAGATTGCTGTGGAGCACACTGCTGCTGGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002748:ENSDART00000136361:8
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(13.4=100)
A:
NA
C2:
PF0140314=Sema=FE(6.8=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:
TGGTCATTTCTATTCAGCCACAGT
R:
CTTCCCAGCAGCAGTGTGC
Band lengths:
214-736
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]