HsaINT0147322 @ hg38
Intron Retention
Gene
ENSG00000196189 | SEMA4A
Description
semaphorin 4A [Source:HGNC Symbol;Acc:HGNC:10729]
Coordinates
chr1:156172826-156174940:+
Coord C1 exon
chr1:156172826-156173006
Coord A exon
chr1:156173007-156174821
Coord C2 exon
chr1:156174822-156174940
Length
1815 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
CTCTCTCTGTCTCCCCATAGCCA
3' ss Score
12.08
Exon sequences
Seq C1 exon
TGCTCAGTGGGCCCCTCCTCTGATAAGGCCCTGACCTTCATGAAGGACCATTTCCTGATGGATGAGCAAGTGGTGGGGACGCCCCTGCTGGTGAAATCTGGCGTGGAGTATACACGGCTTGCAGTGGAGACAGCCCAGGGCCTTGATGGGCACAGCCATCTTGTCATGTACCTGGGAACCA
Seq A exon
GTGAGTAAAGAGTTCCGGGACATCCCCCAGAGGACTAGAGCAGAGGATGCCCCCAGGTTGAGGAGGGAAACCCTTGAGTTCATTCACTTATTCATTCAACAACTGTTTACTGAGCACCTGCTATGTGCCTGGCATTCTGCTAGGTTCTGGAAATACAGCAGAGGAGCAAAACAGTCCACTCCCTACCCTTTCTGAGCTTCCTATGGTGGGGGAGGCAGACAGGGAGGTCTTTGGTGGCTTTATCAAGAGCTGTGTGTCTTATGAGGGAAGCTATGTTAGAGGAATGAAAGGTGAGTGGGTGGAGGGGAGCTGGAAACCGCACATGTAGAGATCACTCCTTCAGGAAGCTCGTCTGTGAAGGGAGAGAGGAAGGAGGTGGTGGCTGGAGCACGGAGTGGGGCGCAGCTGGGGTTCTTGGTTTTGTTTTTTCCCCCTCCTTGCCCCCAGGGTTCTTGTTTTGTAGACAGGAAGGACTAAGCATCTAGTAGACAGGGGGATGGCAAAGAGATGGGTAGAAGAAGGGATAAGTGGCAGGTAAAGTTGTGGCGGGAGCAGGCGGCCAGAGTCCAGGACACATGTCGAGCTGGGCAGCTGTGGGTGGCGGGGGGGACAGCACCTGAGCTGGGCTGGGAGTGAAGCTGTAGCAGCGGGGTGTGACTTGGTGGGTGTGCAGGCTCAGGGTAGGAAGCCAAGGGAGCTCTTATTTGAAGGCTTTTGTGTTCTCTATGTAGGTGGAGGACACAAGGTCATGAGCTGGGAGTGAGGGGGCAGGAAAGGTGGGAGGTTTGAGGAGAGAGAGGTAGATTCAAATAGCCATTGTGGGCTGGGCACAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGTGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATTGTGAAACCCGTTTCTACTAAAAATACAAACAAATTAGCAGTGTGTAGTGGCACGCACCTGTAATCCCAGCTACTCGGGAGGCTGAGTCAGGAGAATCACTTGAACCTGGGAGGCAGAGGTTGCAATGAGCCAAAATTGTGCCACTGCCCTCCAGCCTGGGTGACAAGAGTGAAAATCCGTCTCAAAAAAAAAAATAGCCATTGTGGAAAGAGGGAGACGGAGTCAGCAGAGAATGCAGCAAGACTGCCCAGGCAGACTGCTCAGGCAGGATAACCTTGAGGGTCAGTGGAAGAAATTTGTCAAGTTCATTCATTCCTTCAGGACAGATTACTAGGCACTGTATCAGCTGTGCATGTATTGGGTATACAGCAGAGAACAAAACAGTCAAAAATCTCAGTCTTTGTGGAGTGGATGGAGACAGACAATAGCATCCTGAATAAGTAAATTACATGGCACATCATGAGATTTGAGTCACGTAGAGGTGTGTGCGGGGGAATCAGGAATGCCAGGTAAGGAGGTTGCACCTGTTAAAAGGGTGGCCAGGTAGACCTCACTGAGGTGCTTGATGGATGTGAGGGAGGCAGGTGATGTGATTTTCTACAGAAGCACCCAGCCGCCCACTGTTTCATGCCTATGGAGAAATAGCTGGGTTTCTCCAGGGACAAAGTTTTGTCAGGGAGTTGCAAAGGAAGGACAGGGGTCCAAGGGATTTTAGTCATTTACAAGAGACTGCCATCTCCATGGCACAGAGGAAGGTGAATGATCTGGCTGACCCGCGCCCAGTACATATCACCCTCAGAAGGAGCTTTCTTACAGCTGGGGAGGCCCCCGGAAGTTGGGAAGGGATCTGTGGATGAGATGAGATGACTTCCACTCTCTCTGTCTCCCCATAG
Seq C2 exon
CCACAGGGTCGCTCCACAAGGCTGTGGTAAGTGGGGACAGCAGTGCTCATCTGGTGGAAGAGATTCAGCTGTTCCCTGACCCTGAACCTGTTCGCAACCTGCAGCTGGCCCCCACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196189:ENST00000368285:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.049 A=NA C2=0.050
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(14.5=100)
A:
NA
C2:
PF0140314=Sema=FE(11.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGGGCCCCTCCTCTGATAA
R:
GCAGGTTGCGAACAGGTTCAG
Band lengths:
278-2093
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