HsaINT0147333 @ hg38
Intron Retention
Gene
ENSG00000196189 | SEMA4A
Description
semaphorin 4A [Source:HGNC Symbol;Acc:HGNC:10729]
Coordinates
chr1:156161346-156163094:+
Coord C1 exon
chr1:156161346-156161518
Coord A exon
chr1:156161519-156162943
Coord C2 exon
chr1:156162944-156163094
Length
1425 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGC
5' ss Score
6.64
3' ss Seq
TTCCCTCTGGCTGTCTCCAGGCA
3' ss Score
10.26
Exon sequences
Seq C1 exon
AATGACGTGGGCGGCGAAAAGCTGCTGCAGAAGAAGTGGACCACCTTCCTGAAGGCCCAGCTGCTCTGCACCCAGCCGGGGCAGCTGCCCTTCAACGTCATCCGCCACGCGGTCCTGCTCCCCGCCGATTCTCCCACAGCTCCCCACATCTACGCAGTCTTCACCTCCCAGTG
Seq A exon
GTGAGCAGCAGGGCTGGACCATGGGGGCTGGACACGGGACTTGACGCCAGTGAGGCCCCAGCTCGTGAGCGGAGGCAGGAATTGACATGAGCCAGCACCTACTCAGCACTTTCACATAGGAAGGCATTAAATCGTCACCACCTCTCAGGAATTTGACTCATGCCCTTTTTGTAAATGGGAAAAATAAGACGCAGAGAGGTTCTAACTAGTTTATATTCTGCCTAGTTCCAAAAGGGATAGGAAGCATTTTACAAAAGGCAAATATTAAAATCGATAAAATAGATACAGAAATGGGAATAAAAGGAGAATATGAGAAGCCAAGGGTAAGGCCAACACACTACAAATGCTTGTCATAAGATGTAGGATAGTCCCTGGATGCCAGCCACAAATTTAGCTCTGCATTTCCTAATGGCCAGGGCAAACAGGGAAACGCTATCCGTATCAGAAGATAAAAATAAAGTCGGCCGGGTGCGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCAGATCACGAGGTCAGGAGATCAAGACCATCCTGGCCAATATGGTGAAACCCCGTCTCTACTAAAAACACAAAAATTAGCTAGGTGTGGTGGCGCATGCCTGTAGTCCCAGCTACTCGTGAGCCTGGGGCAGGAGGATCCCATGAACCCGGGAGGCGGAGGTTGCAGTGAGCCAAGATCGCACCACTGCACGCCAGCCTGGCAACACAGTGAGACTCCGTCTCAAAAAAAATAAATAAAAATAAAGTCATTGCTTGAAGGTTGAGAAAGGTTAACCAATTTGTCCAAGGTCCCCGAGTCATGGTCTGGCCCCACAGTGTTTAGGTACCTGCTGACAATGTGTCAGGTACCAAAGGTATTTGGGGTAAGTGGGATCTGGTATCCACAGGATCCAGAATTGAGAGCCTGGTGTATACAGTAGTCAGCTTCAAGAGAGCAGAGAAACAGACCTCCTGTCTCCACAGACCAGGGTTGAGGAATAATAACAGTCTGGTAGTCAGGCACTGGTCGGTTCTCTGAGGACCAGGGATCCAAGAGACTCAAAGGAAGAGGGGTTTGTGTGGAGCCAGGCTAGAGCTGGTTACACTGTCCCTCCAATGGGTGCAGCCCAGTGTAGGCAGGACAGGCAGGGGCCACCCCAGGGCCTGAGCCCCAATTAATTCTCATTAAGGATAATCAGACTTCAGATCCCAAGATGGGCCTAGAGCCAGGCCCTGGGCCAGAGTCAGGGAATTCCATGGGGCTCCCTTGGCCCTTATCAACACAGTGAGGGGAAGGAGTGGTAGCTGGAGGCTGGCCCAGCTCTCCACACTCTTGCCTCCTGGGTTTTCTCACTGAGGGCCAGCGCTGGAGAGAGAGCTGCTGGTGTGGCAGAGACCACAGACAATGTTCCCTCTGGCTGTCTCCAG
Seq C2 exon
GCAGGTTGGCGGGACCAGGAGCTCTGCGGTTTGTGCCTTCTCTCTCTTGGACATTGAACGTGTCTTTAAGGGGAAATACAAAGAGTTGAACAAAGAAACTTCACGCTGGACTACTTATAGGGGCCCTGAGACCAACCCCCGGCCAGGCAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196189:ENST00000368285:9
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=0.333
Domain overlap (PFAM):
C1:
PF0140314=Sema=PD(21.5=94.0)
A:
NA
C2:
PF0140314=Sema=FE(12.0=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:
GACGTGGGCGGCGAAAAG
R:
CGGGGGTTGGTCTCAGGG
Band lengths:
311-1736
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