HsaINT0147308 @ hg19
Intron Retention
Gene
ENSG00000010319 | SEMA3G
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G [Source:HGNC Symbol;Acc:30400]
Coordinates
chr3:52467268-52471682:-
Coord C1 exon
chr3:52471543-52471682
Coord A exon
chr3:52470090-52471542
Coord C2 exon
chr3:52467268-52470089
Length
1453 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CCCTCCCGCCCGCATGGCAGGTG
3' ss Score
8.87
Exon sequences
Seq C1 exon
AAGAGGCAGTGGGACTTGTGGCAGCCACCATGGTCTACGGCACGGAGCACAATAGCACCTTCCTGGAGTGCCTGCCCAAGTCTCCCCAGGCTGCTGTGCGCTGGCTCTTGCAGAGGCCAGGGGATGAGGGGCCTGACCAG
Seq A exon
GTGAGTGAGGAGACCCCTGCCTCTAGCCTCTGTGTGTCCTGAGGTCACCTCCCATCCTGAACCCCAAGACCTGAGCCCCAGAAAGGGGTTCTGGGGGGAATCTGCCAAGATTAACCTAAAAAAAGTTTGTATTAGGCTCCTGGGGTGCCTAGAAGGAGGTGCCCTATTTTTGCCTTTTGGGAATGCCCAGGCCAGATGTGGCTGGAACTCCCCCAGTCTGAGGGGTGGGTGATGGAAGAGAGAGAAGAGGGTCTGGGCAGGCCAGTAAGTCTCCCATGTTTACACACATGGCTCATCTTTGAAGGATTCTCTTCTCCAGGGGTTCTTGGTTCTCTTCTGCCCCAGGCAGGGGAGGGGGCTGTGCCCTGGGCCCAGGACTAGGCTTCAGAACCTCCCTATGCTACACACACACAACAGAAGAGAACCTTCTGGGTCCCTAACCACTGGTCCTTGCCCTCCACCCTCAAAGCCTGGCCCCACACTTCCTCCCTGGAGTCCAGCTGTCTGCTCAGGGCCTCTCCTCCCCCATCCGGAAAGGTCTATCAACCCCAGGGATGGTTTAAGTCTGGGGCCTGAGGATGGGCATTGGCCGGGGCAGGGAAGGGGAGGGGCAGGAGTGGATTGATTACAGGAGGGGCTCTCCCTCCAGCCTGGGAACTGGGGGAGGCCAGCCTTGGGCCAGCTGTTGGGCTGGGCACTGAGAAGATTCCCCAGGGGAGGAGGGGAGCAACAAGATGGTGTTTCACAACACTAGCTAATGGCTCAAGCAATCCACCCCCAACACACAGATGTGCAGACTAAAACCCACACAGGGTCCAGGCCAGAGGCGGGCTGGGATCAGGGCGGCACTCCCACTTCCCACGCTGTGATGGGCGATCAGCCCACCCTGGGCTGGGGCTGTCAGCTCGCACCGTTGGGGGAATGAACGGTTCAGACCAGGATGGGAAGGCCCTGTGTGTGTCTCTGTGTGTGTGTGCGTGCACGTGCATGTGTGCGTGGGCACACGCACATTGTATGTGTGTAGCATAGGGAGTTTCTGAAGCCCAGTTCTGGGCCAGGGGGCACAGCCCCTCCCTTGAGAAAAGCCTGTAGATGGGATGGTACCTCCAGAAGGGCTAAGGGGATAACATCTTAGCCCCTATGTTCCTTGGGAATGTGTGCCAGGGCCCTCTGAGGCCAAGATTGGAGTCCTCTGACTAAGGGAGAAACCAGCCAGTCAAATCCTTGAGAAGGCCCCTTCCTGGGCTATGGGAAGGTGAGGCCCCACCTGAATTAGCTGGTGGTCTAGAGGAGGCCCAGACTGCCACGCTGCTGGTCCCCTCCTGGGAAGGGGAGAATAGGGCAAGAAGTGCCCAGGCACTGGGCCCCAAGGATGGCAGAAAAGCTGGGGCAGAGAAGCCGATGGTAAACTCCCACCTTGCACCCTACTCACGCCCTCCCGCCCGCATGGCAG
Seq C2 exon
GTGAAGACGGACGAGCGAGTCTTGCACACGGAGCGGGGGCTGCTGTTCCGCAGGCTTAGCCGTTTCGATGCGGGCACCTACACCTGCACCACTCTGGAGCATGGCTTCTCCCAGACTGTGGTCCGCCTGGCTCTGGTGGTGATTGTGGCCTCACAGCTGGACAACCTGTTCCCTCCGGAGCCAAAGCCAGAGGAGCCCCCAGCCCGGGGAGGCCTGGCTTCCACCCCACCCAAGGCCTGGTACAAGGACATCCTGCAGCTCATTGGCTTCGCCAACCTGCCCCGGGTGGATGAGTACTGTGAGCGCGTGTGGTGCAGGGGCACCACGGAATGCTCAGGCTGCTTCCGGAGCCGGAGCCGGGGCAAGCAGGCCAGGGGCAAGAGCTGGGCAGGGCTGGAGCTAGGCAAGAAGATGAAGAGCCGGGTGCATGCCGAGCACAATCGGACGCCCCGGGAGGTGGAGGCCACGTAGAAGGGGGCAGAGGAGGGGTGGTCAGGATGGGCTGGGGGGCCCACTAGCAGCCCCCAGCATCTCCCACCCACCCAGCTAGGGCAGAGGGGTCAGGATGTCTGTTTGCCTCTTAGAGACAGGTGTCTCTGCCCCCACACCGCTACTGGGGTCTAATGGAGGGGCTGGGTTCTTGAAGCCTGTTCCCTGCCCTTCTCTGTGCTCTTAGACCCAGCTGGAGCCAGCACCCTCTGGCTGCTGGCAGCCCCAAGGGATCTGCCATTTGTTCTCAGAGATGGCCTGGCTTCCGCAACACATTTCCGGGTGTGCCCAGAGGCAAGAGGGTTGGGTGGTTCTTTCCCAGCCTACAGAACAATGGCCATTCTGAGTGACCCTCAGAGTGGGTGTGTGGGTGCGTCTAGGGGGTATCCCGGTAGGGGGCCTGCAGGGAGCCAGAGGGTGGAAATGGCCTCTAAGCTAGCACCCCGTAAGAAGAGCCTACCTGACCGACTTGGGGAGGGAACACAGAGGTGTTGGGAAGGTGGAGCAACAATGCACCTCCCCTCCTGTCGCGCCGTGATATCTTGGTGGCTCCCTGCCACTGCCCACCGCCTCTTCTCCATCTGAGAATCACGGAGAGGTGTAGATAATCTAGAGGCATAGACTGCTAGAGCCCCCAGGGATCTGGGGTGGTCAGGGCTCAGGCTTCACTTTGTAAACCAGGTGGGGGCATCTCACAGCCTGACTTCCCTTCCCCAGGCCAGGGTTGCTGGGATGCCTGCCCCTCCTGAGAGGACCCCCTCCCCATTGTCAGGCTCTCCATGTCCACGAGCGGGGAGGGGTGGGTTCTGGGGCATTGTTGTCCCTTGTGTCTGTGGACTAGAGATAGGGTGGGGGAGCTGGGGAAGGGTGCAGGCGGGAAGAGTGGGCTGTCTTTCCCAGGGTGATGCAAGCATGCCGCAGCCCTGGAGGCTGGGAATGTGGAGGCTCTGTGAGCCCTGCAGCCCTCAGAATCAGGGCCAGGGATGCAGAAGATTGAGAGGATATGGAGATGGATAGAGGGCAGGAGACCCTTAGGATAGATTGTGGGACCCAGGCAGGAACAGGTGTCCACAAGAACTCAGGATGGCATCAGTTAGCTCAGAAGCCACCTGGAAGACCCAGTGTTTCCATCTCTGGAATCTCTGTTTTATGCTAAATGGATTTAGGAAGACTGTTTTTCTTTTAAGGGGGAAACAAGGTAGAGAAAAGGACGAAGAAGTGTAAGTCCCGCTGATTCTCGGGGGTAAGGCTCGGATGGCAAGGACGCGTTCTGCCTGGGCATGTAGGGGAGGTGTTTTTGCCATCACCAGTTTCTCAGGCTGGGGAGCACAGAGGGGAGGAGGAGGACTAAATGAAAAGTTGTTCCCAGCCTGCACATGAACACATTCATGACACACAAAACTGGCTGGAAGGAGATAAGAGCACTGGGTTTGAGATTCCCTCCATTAAAACAACCAAGACAAAGAAAGGAGGGGAAAAAAAGATAAAAAGCAAGCCAGGGTTCCCTGCCCTATTGAAACTCAAACCCAGACTGCCTTGGGTTTTATCTTTCCCTTACCCCTGGCACCTCCAGAGAACTGGGACCTGAAATAGTCCCTCCGTTCTCCCCTTTGACCATGTAATAAATGAACCAGAAGCACTGAGATTAACCTATCAACGCCCTGAGAAGCCTTCCAGCCTGCGGTGCTGTCTGCTGGGAGGTCAGCTGGTCAAGGCAGAGGAGGAGAGGAGGAAAGGATGGGGGCTGAAGAGCAGAAGGGAGGGGAGACAGAGGGGATTAAAGAGGGGAGGAGAGAGTGCAGAGCTCCAGGAAAGGGTATCAGAGCTGCAGCCAGCTCTGCCCTCTACCCTAGGGAGGCCAGAAAGACACAAACAGCCCTCCGGGCCTTTACGCTGGACTCTGGCTTGGCAGGCTCCAGGCAGGGTCCTCTGGGAAGTTACTCTAGAAAACGAAGGGAGGAGGAGCACAAGATCCTCAGCAACGAACACCTGCACTTAGAAAAAGTGGACAGCTTCTGCCAACCACACCCTACCCATGGTACTGTATGCTATTAACTCCTGGAAACGCCCCGTAAATGCGAGTTGTTTTTGTATTTGTGTGTTGAGATGGGCCTTGTGGTTTCTCTGTACTCAGAGCACATTTCTTGTAATTACTATTGTTATTTTTATTGTCATGACTGCCCCTGAGCTCTGGTGAGAAAAGCTGAATTTACAAGGAAAGGGATGAAGTTAATATTTGCATCACATAATTATATCATTACTGTGTATCTGTGTATTGTACTAAATGGACTGATGCTGCGCACATGAGCTGAAAATGAAGAGCCCTCCCATCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000010319-SEMA3G:NM_020163:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.191 A=NA C2=0.269
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(1.6=2.1),PF0004720=ig=PU(48.4=63.8)
A:
NA
C2:
PF0004720=ig=PD(48.4=19.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGGAGCACAATAGCACCTTC
R:
GCTGCAGGATGTCCTTGTACC
Band lengths:
358-1811
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)