HsaINT0147330 @ hg19
Intron Retention
Gene
ENSG00000196189 | SEMA4A
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A [Source:HGNC Symbol;Acc:10729]
Coordinates
chr1:156128510-156130350:+
Coord C1 exon
chr1:156128510-156128615
Coord A exon
chr1:156128616-156130233
Coord C2 exon
chr1:156130234-156130350
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-SEMA4A:NM_022367:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.102 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
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)