HsaINT0175320 @ hg19
Intron Retention
Gene
ENSG00000188229 | TUBB2C
Description
tubulin, beta 4B class IVb [Source:HGNC Symbol;Acc:20771]
Coordinates
chr9:140136173-140136473:+
Coord C1 exon
chr9:140136173-140136281
Coord A exon
chr9:140136282-140136362
Coord C2 exon
chr9:140136363-140136473
Length
81 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGG
5' ss Score
9.35
3' ss Seq
ACGCCCTCCCGTCCCCGCAGGCG
3' ss Score
12.15
Exon sequences
Seq C1 exon
TTTTGGGAGGTGATCAGCGATGAGCACGGCATCGACCCCACGGGCACCTACCACGGGGACAGCGACCTGCAGCTGGAACGCATCAACGTGTACTACAATGAGGCCACCG
Seq A exon
GTGAGGCCCCGGCCCCTTCCCCGACCGCCCTCCGGGGACCCCGCGGCCCCTGCCTTGGCTGACGCCCTCCCGTCCCCGCAG
Seq C2 exon
GCGGCAAGTACGTGCCCCGCGCCGTGCTCGTGGATCTGGAGCCCGGCACCATGGACTCCGTGCGCTCGGGGCCCTTCGGGCAGATCTTCCGGCCGGACAACTTCGTTTTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000188229-TUBB2C:NM_006088:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.135 A=NA C2=0.026
Domain overlap (PFAM):
C1:
PF0009120=Tubulin=FE(16.2=100)
A:
NA
C2:
PF0009120=Tubulin=FE(16.7=100)
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:
TTGGGAGGTGATCAGCGATGA
R:
GAGCGCACGGAGTCCATG
Band lengths:
174-255
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
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)