GgaINT0029099 @ galGal4
Intron Retention
Gene
ENSGALG00000004844 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr10:9409256-9410149:+
Coord C1 exon
chr10:9409256-9409438
Coord A exon
chr10:9409439-9410008
Coord C2 exon
chr10:9410009-9410149
Length
570 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGT
5' ss Score
9.82
3' ss Seq
CCATTATTTTTGCTGACCAGGTG
3' ss Score
7.77
Exon sequences
Seq C1 exon
CCTTGACAGATACAGATTGACAGCAATTGCTGTAGATCACGCTGCTGGACCACACCAGAACTACACAGTCATATTTGTTGGCTCCGAAGCAGGAGTAGTACTTAAAATCTTGGCAAAGACCAGACCTTTCTCTTTGAATGACAGTGTATTACTGGAAGAGATTGAAGCATATAATCATGCGAA
Seq A exon
GTAAGTGTTATGAGAACACCTGAAATATGTAGCTTTTTATCTAGTTTGGTACCAAGCTAAACAAAAATGATAGTGAACCAAAACTAATTCATTAATGCCAACTTCATTGCTTGTTTGTCATTTCACAGTGTCTCTCATGTTGACTAACCTGAAAATATTTGGTTATTTGCCATTTTGCTTGGGTTGAGTGAACATCGTAATTCCACTGTAGTGACGTCAGTGATACAGTCTTAATTCTTCCACAAATACACTTCTTCCTGAATATCAAACATCAGAACAATCTGCAGTTGTTAAAAAGAAATGATGAGAGCTTATCTTGAGTGTTTCTCAACAGTAACCAATAATATATAAACTATATCTAATCATTGTAAACTTGTTTATTCTGGAGTGAAGAATTTGGGAGTGGAAGCATTCCAATTTGACTGGCACCCAGTGAGAACTCTTGTTCTGCTCTGTTGAGATATTTATGCCAACTCTGAGAACAAAAAAAAAAAAGAAGTTTTCAATGTAAACTCTGACCAAAGGACTACAGTTGTAAAACAATGGCTTCCCATTATTTTTGCTGACCAG
Seq C2 exon
GTGTAATGCTGAGAGCGAGGAAGACAGAAGAGTCATTTCCCTTCAGCTGGATAGAGACCACCATGCTCTGTTTGTGGCGTTCTCCAGCTGTGTCGTTAGAATTCCTCTGAGCCGGTGTGAGCGTCACGGGTCATGTAAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004844:ENSGALT00000007734:12
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(14.3=100)
A:
NA
C2:
PF0140314=Sema=PD(1.2=10.4),PF0143720=PSI=PU(15.0=18.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTTGACAGATACAGATTGACAGCA
R:
TTTACATGACCCGTGACGCTC
Band lengths:
322-892
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]