GgaINT0029095 @ galGal3
Intron Retention
Gene
ENSGALG00000004844 | SEMA6D
Description
NA
Coordinates
chr10:11369109-11370160:+
Coord C1 exon
chr10:11369109-11369197
Coord A exon
chr10:11369198-11369942
Coord C2 exon
chr10:11369943-11370160
Length
745 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
CTTTTTTCCACCCTTCACAGGCT
3' ss Score
9.78
Exon sequences
Seq C1 exon
AGCCACACTTTCTCCATGCCATAGAATATGGGAACTACGTGTATTTCTTCTTTCGAGAAATTGCTGTAGAGCACAATAATTTAGGCAAG
Seq A exon
GTGGGTATCCTTCCAGCAAGCTCTCATTAGCCATGAGCCTTGGCAGAATTAGATCATCCGAAAAGTAGCAGTAACAAGTACAGCTTACAGTGTGAAATAAGGCTGTAGTACCAAATTTATGCAATTATTCCAAAATTATAGTTTACAGGCAGAGAAAAAAAACACAACGGTGCATTCTTCTACCAAAAAGTTATTGATATTCCACATGCCCTGCAATTAGGAGAGCTCTATGCAGGTATCTTTTGGTGTAGCTGTTCCCTTAACACTTGTGACAGTTAATGGAATATCTGAGGGTTTTTTTTTCATGCTTATAAGAGAAACAAAAGAACACAAAAGAAGAGTTTCAAAGAAGTTTCTCTTATGTCCGTAGATATTGAATAATTCAGTCATACCACTGCAGAGTATAATGCTAATGCCTCACCATGGAAGGATATTCTGTAATAAATTATTAATGTCTTTACACGTGGTTAATTAAAGTCTTTAAATCTCACTAACAATATGATTTTGAATGGAAAAAAAAAGGGTGGGGACAAGCTGGCAGAGTTGCATTTGCCTGGCGATGCTTTAAGATGCCTATGTACTGGCAGCTAAACATTGCTTGCTCTCTTTCTTTCTGCACAGATAAATGGCAACTGTCTTCCTGTTAAAATTATCTGCAGTGTTTTACTAACAGCTCAGAAACGAGCACTTTTGCCCTTGAATCTCTCAAGCCTTTCTTCCTTTTCCTTTTTTCCACCCTTCACAG
Seq C2 exon
GCTGTGTATTCCCGTGTGGCACGCATATGCAAAAATGACATGGGGGGTTCCCAGAGAGTACTGGAAAAACATTGGACATCCTTTCTGAAAGCTCGGCTCAACTGCTCCGTTCCTGGGGATTCGTTCTTCTACTTTGATGTTCTACAGTCTATCACGGACATAATAGAAATCAATGGAATCCCCACGGTTGTCGGTGTATTCACTACACAGCTTAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004844:ENSGALT00000007734:8
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(6.8=100)
A:
NA
C2:
PF0140314=Sema=FE(16.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCACACTTTCTCCATGCCAT
R:
GTAGTGAATACACCGACAACCGT
Band lengths:
294-1039
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]