HsaINT0147330 @ hg38
Intron Retention
Gene
ENSG00000196189 | SEMA4A
Description
semaphorin 4A [Source:HGNC Symbol;Acc:HGNC:10729]
Coordinates
chr1:156158719-156160559:+
Coord C1 exon
chr1:156158719-156158824
Coord A exon
chr1:156158825-156160442
Coord C2 exon
chr1:156160443-156160559
Length
1618 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TCTCCTCTCCTCCACCCTAGATG
3' ss Score
11.09
Exon sequences
Seq C1 exon
GAACTTCAAGATTCCTACCTGTTGCCCATCTCGGAGGACAAGGTCATGGAGGGAAAAGGCCAAAGCCCCTTTGACCCCGCTCACAAGCATACGGCTGTCTTGGTGG
Seq A exon
GTGAGTATCAGGTTTCCCACTTCATCCCAACATCTACTTTCTCCAGTCACGCTGTGAAATATGGAATATTACAGAGTTTTCCAAAAGGCAGGGGAAACTGGGTGTGGTGATGCGTGCATATGGTCCCAGTTATTTGGAAGCTGAAGTTGAAGGATGCTTGAGTTTAGGGGTTTGAGTCTAGCCTGGGCAACACAGCGAGATCGTCTCAAAAAAAAAAAAAAAAAGCCTCAGTGCCTCATGCCTGTAATCCTAGCAGTCTAGCAGTTTGGGAGGCTGAGGTGGGTGGATCATGTGACCCCAGGAGTCTGAGACCAGCCTGGTAAACATGGTGAAACCCCATCTCTACTAAAAATACAAAAATTATCCAGGCGTGGTAGGGCGCACCTATGGTCCCAGCTACTCGGGAGGCTGAGTCACAAGAATTGCTTGAACCCAGGAGGTGGAGGTTGCAGTGAGCCAAGATCGCGCCACTGCACTCCAGCCTGCGCAACAAAGCAAGACTCTGTCTCAAAACAAAACAAAACAGAAAATGCAGAGGACAGAGAGAGAGAGGGAAGCCAGAAGCCTCAGAACACAAGATCAGAGGGAGAATTAAGCACCCCAACCACCAGCTCCTGCTGAAATTGCCACAAAAAGTGGTGGAGAAAGATGCATGTGGAGAGACAGAGGCACGAGGGCCCGGGAAGGGTATTGGGTAGAGAAGAGGCCTGAGACTGAGCCACTGTTCAACAATTGTGTGAACACTTCCTCTGGTGTACTGGGCACTGTGCTGGGTAGTATAGGAGTTATAAACAAGAAATCAGGCTGGGTGCAGTGGCTCACACCTGAAATCTCAGCACTTTAGGAGGCTGAGGCGGGTGGATCACTTGAGCCCAGGAGTTTGAGACCAGCTTGGGCAATAGTATAGTGAGACCTCGTCTCTACTAAAAACAAAACAAAACAAAAACAACAACAACAAAATTAGCCGGACAAGCGCCTGTGATCCCAGCTACTTGGGAGGCTGAGGTGGGAGGATCGCTTGAGATGGTCAAGGCTACGGTGAGTTGTGATGGCACCACTGCACTCCAGCCTGGATGTGAGCAAGACCCTGTCTTGAAAAAAAAAAAAAAAAAAAGGGAGAGAGAAACCATGTATCAATGCACTACTGGACACCAACCATTACAGACTTCCCACCTGCCTTCCTGGAGGAGATGGCCTTCGGCTTTTCAGCAGGACCTTGAAAAGATAGGTAGACAGATGGCAGGGAAGGTGTTCCAGGGAGAGAAGGGTAGGACCCAAGGTGTGGAAGTGGAAAACACAGTCACCTTCCAGGATCAGTAAGTGATTCTACTTGGCAAGTGGTTCAGCTAGGTATGTGACGAAGTAGCCACAGAAAGGCTGGAAAAGTGCCCAAACACGGAGGGCCACACAGGATGGCCATTTCCTGTGGAGAGAGGAAGCTAAGAGGGGTGCTTAGTGAGGAGGGGGAGCTGGCCTTTGAGGCTCCCCAGGAAGGTGCAGAACTGATGCAGGGCCCCCGAGACTGATATGGATGCCAGCCCCAGTCAGAGGCAGGTCTGTGGAGGGCAGAGGAACCCTCCACCCCATCAGTTCTCTCTTCTCCTCTCCTCCACCCTAG
Seq C2 exon
ATGGGATGCTCTATTCTGGTACTATGAACAACTTCCTGGGCAGTGAGCCCATCCTGATGCGCACACTGGGATCCCAGCCTGTCCTCAAGACCGACAACTTCCTCCGCTGGCTGCATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196189:ENST00000368285:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.096 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=PD(10.6=19.4),PF0140314=Sema=FE(30.2=100)
A:
NA
C2:
PF0140314=Sema=FE(11.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAAGATTCCTACCTGTTGCCC
R:
CAGCCAGCGGAGGAAGTTG
Band lengths:
214-1832
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