HsaINT0147230 @ hg38
Intron Retention
Gene
ENSG00000012171 | SEMA3B
Description
semaphorin 3B [Source:HGNC Symbol;Acc:HGNC:10724]
Coordinates
chr3:50271361-50273443:+
Coord C1 exon
chr3:50271361-50271480
Coord A exon
chr3:50271481-50273297
Coord C2 exon
chr3:50273298-50273443
Length
1817 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGA
5' ss Score
7.23
3' ss Seq
ATGCCTCCTGCCGCGGTCAGAGC
3' ss Score
4.82
Exon sequences
Seq C1 exon
GGGAGGAGCTATACTCAGGGGTGGCAGCAGACCTCATGGGACGAGACTTTACCATCTTTCGCAGCCTAGGGCAACGTCCAAGTCTCCGAACAGAGCCACACGACTCCCGCTGGCTCAATG
Seq A exon
GTGAGAGGCTGGTGGGGTTGGTGGGTAGAGGTCGTCACCCTCCCACAGGGCAGGTGCCAAGCAAGGCCCATAAAGTAAGTGAGCAGTGGGTGTGGCCAGGTCTTACCAAATACCCTCCTTAATCAGGCACTGGCGTCACAGAGACAGACAAGACAGGTATGACCGTGACCTCTTTGAGTTCACAGATCACATACATGATAAGATCAAGTCCAATGGCCTTGAGGCCAGAGAGAGACAAGGGAGGAAGGGAAAAGGAGACTGGGTGGCTGGAGGGGGTTGGGTAAAGGAAGCCGCTGTGCTGAGGGGAGTATGAGCTAATTCCCAAGCACAAGACAGCTAGCCAGCAAAATTTAGGGATGAGCATTCCAGGCAGAGGGAGCATTCCAGGCAGAGGGAGCAACTAGTGCAAAGGCCTGGATGCAAGAACAAGCAAAGGAATAGACTTGCAGAGCTAGCAATGAAAAGGGGGCCTGGACTGTCAGGGGCCAGAGTCATTTATTCTAAGAGTCATGGGGGCTGGGCACAATGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCAGACAGATTGCTTGAAGACAGGAGTTTCATACCAGCCTGGGCTACAAAGCAAGACAAAAAATAAAATAAAATTAGCTGGGGGCAGTGGCATGCACACACCTGTAGTCCTGGCTAGTCAGGAGGCTGAGATGGAAGGATCACTTGAGCCCAGGAGTTGGAGGCTGCAGTGAGCCATGATGCTGCCACTGCAGGACAGAGCAGACCCTGTCTCTAAATCAAATAAAAATTAAATAAGGGCTATGGGCTGGTGGGCACAGTGGCTCACACCTGTAATCTCAGCACTTTGGGAGGCGGAGGCAGGCAAATCGCTTGAGGCCAGGAGTTTGAGACTAGCCTGGCCAACATGGTGAAACCCTGTCTCTACTAAAAAATACAAAAATTGGCCGGGTGCAGTGGTGTGCACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGGATCACCTGAGTTCAGGCATTTGAGACCAGCCTGGCCAACATGGTGTAACCCCGTCTCTACTAAATATACAAAAATTAGTCCGGCATGATGGTGTGCATCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTAGGAGGCGGAGGTTGCAGTGAATGGAGACTGTGCCACTGCATTCCAGCCTGGGCAATAGAGCGAGACTTCGTCTCAAAAAAAAAAAAAAAAGCCAGGTGTGGTGGTAGGCTCTGACTGTAATCTCAGCTACTTGGGAGGCTGAGGTTGCAGTGAGCCGAGATCGAGCACTCCAGCCTGGGCGACAGAGCGAGACTGTCTCAAAAAATAAATAAATAAACAAATAATAATAATAATAATAATAATAAAGAGCAATGGGACCCAGCAGAAGGATTTGAAGCAGGAGTGGGGAGCATCTGGTTATGCTAGAGAGGAAGATTCATGAGTGAAGGTGAAACCAGATTACCTCATCTCCCTCCTACCCCAGCCTAAGGTGCTGGGCGACGTGTGGGGCGAGATCGGAGGCTAGCCGGGCTTCACGCCTGCGCCCCCAGGTAGCCACGGTCTCTGCTGCCCCCTCGCGGCTGCTTCTTGCCTCGCAGGCCCTGATCCTTTGGATTCGGTCCGCGCAGAGCGCCAACTGGACATGGTGCTAGAGGTTGGGTGGTCAGACACTGTGATCCCGGGTGCTGTGCCCGCACTACGGGAAGGGGAAGCAGCGCGTGGGTCTCGCATCAGGAGGCAAGGCCAGGACCCGCTGACCCATGCCTCCTGCCGCGGTCAG
Seq C2 exon
AGCCCAAGTTTGTCAAGGTATTTTGGATCCCGGAGAGCGAGAACCCAGACGACGACAAAATCTACTTCTTCTTTCGTGAGACGGCGGTAGAGGCGGCGCCGGCACTGGGACGCCTGTCCGTGTCCCGCGTTGGCCAGATCTGCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000012171:ENST00000616701:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.100 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(20.0=100)
A:
NA
C2:
PF0140314=Sema=FE(10.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCTATACTCAGGGGTGGCA
R:
CAGATCTGGCCAACGCGG
Band lengths:
257-2074
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