HsaEX0013870 @ hg19
Exon Skipping
Gene
ENSG00000117335 | CD46
Description
CD46 molecule, complement regulatory protein [Source:HGNC Symbol;Acc:6953]
Coordinates
chr1:207958964-207968858:+
Coord C1 exon
chr1:207958964-207959027
Coord A exon
chr1:207963598-207963690
Coord C2 exon
chr1:207966864-207968858
Length
93 bp
Sequences
Splice sites
3' ss Seq
TTTTCTCTTCCTCTGTTCAGCAC
3' ss Score
9.4
5' ss Seq
AAGGTATCT
5' ss Score
7.56
Exon sequences
Seq C1 exon
TTGTTGGAGTTGCAGTAATTTGTGTTGTCCCGTACAGATATCTTCAAAGGAGGAAGAAGAAAGG
Seq A exon
CACATACCTAACTGATGAGACCCACAGAGAAGTAAAATTTACTTCTCTCTGAGAAGGAGAGATGAGAGAAAGGTTTGCTTTTATCATTAAAAG
Seq C2 exon
GAAAGCAGATGGTGGAGCTGAATATGCCACTTACCAGACTAAATCAACCACTCCAGCAGAGCAGAGAGGCTGAATAGATTCCACAACCTGGTTTGCCAGTTCATCTTTTGACTCTATTAAAATCTTCAATAGTTGTTATTCTGTAGTTTCACTCTCATGAGTGCAACTGTGGCTTAGCTAATATTGCAATGTGGCTTGAATGTAGGTAGCATCCTTTGATGCTTCTTTGAAACTTGTATGAATTTGGGTATGAACAGATTGCCTGCTTTCCCTTAAATAACACTTAGATTTATTGGACCAGTCAGCACAGCATGCCTGGTTGTATTAAAGCAGGGATATGCTGTATTTTATAAAATTGGCAAAATTAGAGAAATATAGTTCACAATGAAATTATATTTTCTTTGTAAAGAAAGTGGCTTGAAATCTTTTTTGTTCAAAGATTAATGCCAACTCTTAAGATTATTCTTTCACCAACTATAGAATGTATTTTATATATCGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000117335-'18-25,'18-23,22-25
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (No Ref, Alt. Stop)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.036 C2=0.738
Domain overlap (PFAM):
C1:
PF0248011=Herpes_gE=FE(28.8=100),PF060117=TRP=FE(36.8=100),PF122163=m04gp34like=FE(36.2=100),PF128772=DUF3827=FE(32.8=100),PF054546=DAG1=FE(33.3=100),PF151761=LRR19-TM=FE(36.2=100),PF151021=TMEM154=FE(33.3=100),PF145751=EphA2_TM=FE(38.2=100),PF0200911=Rifin_STEVOR=FE(47.7=100),PF0265610=DUF202=PD(45.2=86.4),PF055686=ASFV_J13L=FE(36.8=100),PF126692=P12=FE(48.8=100)
A:
PF146101=DUF4448=PD(0.7=5.6)
C2:
PF0248011=Herpes_gE=PD(24.7=72.0),PF060117=TRP=PD(31.6=72.0),PF122163=m04gp34like=PD(6.9=16.0),PF128772=DUF3827=PD(29.7=76.0),PF054546=DAG1=PD(28.6=72.0),PF151761=LRR19-TM=PD(36.2=84.0),PF151021=TMEM154=PD(30.2=76.0),PF145751=EphA2_TM=PD(40.0=88.0),PF0200911=Rifin_STEVOR=PD(11.4=20.0),PF055686=ASFV_J13L=PD(31.6=72.0),PF126692=P12=PD(23.3=40.0)
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCAGTAATTTGTGTTGTCCCGT
R:
AGTCAAAAGATGAACTGGCAAACC
Band lengths:
167-260
Functional annotations
There are 1 annotated functions for this event
PMID: 33767911
This event
The skipping is unregulated in bladder cancer. In BCa cell lines, enforced expression of CD46-CYT2 (exon 13-skipping isoform) promoted, and CD46-CYT1 (exon 13-containing isoform) attenuated,cell growth, migration, and tumorigenicity in a xenograft model. Heterogeneous nuclear ribonucleoprotein (hnRNP)A1 is a novel CYT2 binding partner, and this interaction facilitates the interaction of hnRNPA1 with IRES RNA to promote IRES-dependent translation of HIF1a and c-Myc.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- 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)