HsaINT0147362 @ hg38
Intron Retention
Gene
ENSG00000187764 | SEMA4D
Description
semaphorin 4D [Source:HGNC Symbol;Acc:HGNC:10732]
Coordinates
chr9:89391264-89392536:-
Coord C1 exon
chr9:89392423-89392536
Coord A exon
chr9:89391416-89392422
Coord C2 exon
chr9:89391264-89391415
Length
1007 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGG
5' ss Score
10.38
3' ss Seq
TCACTGTCCTCTCTCTGCAGAGC
3' ss Score
12.82
Exon sequences
Seq C1 exon
ATGGAGAACTTTATTCGGGGACGTCGTATAATTTTTTGGGAAGTGAACCCATCATCTCCCGAAATTCTTCCCACAGTCCTCTGAGGACAGAATATGCAATCCCTTGGCTGAACG
Seq A exon
GTAAGGAAGAGCAGTGCACCTTAGTGGGAGGTGCGTGTCTCCTCATGAGTGCACACCTGTTGATCTCTCCTTTTCTGTCTCTGAGCCCTGGGGGCCCCCGAGCTTGTGTTAGCCCCTGTTTGTGGGGGATACTTCCCAAACTGTCCAGCAATGGCCAGAGTCCCAGGGCACCTTGTTGGGTGTTTTCACTGGTAACAGAGTACTGTTTTAAGACAGCTCCCCACTAACCCCCCAAAAATGGATTTGGGAGACTCTCATAAAATTGAGAATCTGATAGTAGATGGTAAACTAAGACTAATCAGATGGGGACATGGTATAATTTCCAGAATGATATTAAAGTGTGGCACCAACACTGGTGTGGGACCTGCCTCCGGGCCCAGCCTCTAGTGCCCGGTCAGATGGGCTCTGGGTGCCTTGTTGCTGCCAGCAGCACATGTCCGATGTCCGTCTTCAATGTGCAGGAAGAAGCTGGTGGCTGTTCATGGGGGCTTTTCTTGTGGGTGCCAGCCAGTAGAGCCTTGGGTTTTGAACCTCTTGACCTTAGGGCAGATCCCAAGACCCCAGATTCAGGGACAGTCGGCCATTCCTCAGGGTGGGGCAGGATCTGGTGGTTAGAGTTTGTTTATGTGAAGCATGTGTTGTTTAAACCAGCAAATGCATGCCTTACGTAGGTCTCTGATGCTGGTACCATCTGGCTCCCTGCCTTCCAGTCAGGAGGCCCAGCCTCAGTTCTTGGGGTGAACCTGGGTGGGATGCACTGCAGAACCACTGTCGGGGGCACCTCTCTGAGGCCGAGGAGGTGGGGGTAGGGCACCATCTGGGCTCAGGGCTGTCATCATCCTCAGATCCTGGAGTTTCTGTTTGGATTGTGGCATGTGCACACTCCAGACATCCTTGCAGGGAAGCCCTCAGGCCCCCAAGGTAGTGTTGGCCGGCCTCGTGACCTCATGGGTGCAGGCAGTCCCCCAGCTCTGTGTTCTGGGATAATCACTGTCCTCTCTCTGCAG
Seq C2 exon
AGCCTAGTTTCGTGTTTGCTGACGTGATCCGAAAAAGCCCAGACAGCCCCGACGGCGAGGATGACAGGGTCTACTTCTTCTTCACGGAGGTGTCTGTGGAGTATGAGTTTGTGTTCAGGGTGCTGATCCCACGGATAGCAAGAGTGTGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000187764:ENST00000455551:9
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(8.8=100)
A:
NA
C2:
PF0140314=Sema=FE(11.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAGAACTTTATTCGGGGAC
R:
TGCACACTCTTGCTATCCGTG
Band lengths:
263-1270
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development