HsaINT0026556 @ hg19
Intron Retention
Gene
ENSG00000165995 | CACNB2
Description
calcium channel, voltage-dependent, beta 2 subunit [Source:HGNC Symbol;Acc:1402]
Coordinates
chr10:18823005-18825125:+
Coord C1 exon
chr10:18823005-18823156
Coord A exon
chr10:18823157-18825029
Coord C2 exon
chr10:18825030-18825125
Length
1873 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
AAACTCATTATCTTTTACAGGTT
3' ss Score
8.08
Exon sequences
Seq C1 exon
CGGAAGTTCAGAGTGAAATCGAAAGGATTTTTGAACTTGCAAGAACATTGCAGTTGGTGGTCCTTGACGCGGATACAATTAATCATCCAGCTCAACTCAGTAAAACCTCCTTGGCCCCTATTATAGTATATGTAAAGATTTCTTCTCCTAAG
Seq A exon
GTAAGTAGGACTGCTACTGTTTGCTCTATAATCAAACTTTCCTAAAATGTATTTTATGTTCTGCTTTCTATAATTAGGCTATTGTAATAGCCTTTATGATGTATAGAGAATTTGAGGAGACATGATAGTCAAGAATTTTTAAATTGATATAGTTTCATGGCTTAGAACAGCTGTTCTCAAAGTGTGGTCCATGGATCCCTGGAGAGTGTTGAGACACTTTTAGAGGGTCCATTTAGTCAAAACTACTTCCATGATAATACTAAGACATTATTTGCCATTTTCACTGTTTTGATATTTGCATGGCTGATGCAAAAGCAATGGTGGGTAAAACTGCTGGCGTCTAAACATAAATCAAGACTGTGGTATCAAAGTACCAGCAGTTACTGTATTCACCGCCACCATGCTTTCGCAGTTTGAGGGGAAAAAAAGCCAATTTCACTTAATGTCCTTATAAAGTAGTAAAGTTTATTACTTTTATTAAATCTTGACTTTTAATATTCAGTGTACTAAAACAAAGTACACACAAAGCTCCTGCTGTATACCAAAAAGTAAGGACAAGCACTGGTTTGATTGAGTTGTGAACTAAACTAGCCATGTTTTTCATAGAATACCATTTTTATCTCAAACAACAACTGACAGGCTATGCTTATTCCGACTTGGTGTAGCAGATATTTTCTTGGACAAAATAAGCCTGTCACTTAAAGGAGAACAGCATGTGTTGCCAATGATAAAACTCAAGCTTTCAGACAACAATCAGAATTTTAGAAAACTTGTATGCATCTCTGAGAACTTGCAAGCTTCCCAATAAAGTTTTCTCTGAGATCAATGGTAATATTAATGAATATGATGTTTTAATAATGTATAATGAAATATGTCAACATTTGGAAGATCTGAAGTCAGTGAACCATTATTGTTTGTATGATCAATGAATAACATTAATTTTCAAGACAGACCAATGGAATGTCATGGAGTAAGAAAATTGCACTGCAGGTTCAGATTCCACATAACAAATAGTCTTTAAGGAACCACCATTTGTTGAGTTTTAGTGTAGTATCAAAGAAGACTATACTAAATTGTTTCTCCTTTTCTCAATTACAAATCTGTAGGAGGTTGGATTTTCTTCACGTATTTCAACCAAAACATGACATTGCAGCAGGTTGACTGTAGAAGCAAACAGGAGACTGCAATTGTCTTCTATGAAGCCAGCCAGCCAGCCATTAGAGAGATGTGTAAAAATGTAGCTATTTTTATTAAAAAAAATTCGGCCGGGCGCAGTGGCTCATACCTGTAATCCCAGCACTCTACTAGGCTGAGGTGGGAGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACACAGTGAAACCCCGTCTCTACTAAAAATACAAAAAAATTAGCCGGGCGTGGTGGCGGGTGCCTGTAGTCCTAGCTACTTGGGAGGCTGAGGCAGGAGAATGGTGTGAACCTGGGAGGTGGAGCTTGCAGTGAGCCGAGATCGCACCACTGCACTCCAGCCTGGGCAACAGAGCGAGACTACATCTCAAAAATATATATATATATATTTTAACATGTATCAGATTTATTGTGAATTTTTAAATAAATGTTTTAATAGTTTTCCATTTTAGCTTCTTTAAAGAGGTTGTGAGATAAAATGTTTGAGAGCTGCTAGCATAGAAAAAATGTGAGTGCTTAAAGCTTGCAACTGTGATTTATGTTAACATGTTAATTTTGCAGATAATCTTATAGCTCCATCTATTATAAGCCCCTTGTGCTGTATATAAAAAGGCCCCAGAGAAAGGAGTCAATAATGTACCTTGTACTTTACCTGGATGTAGTTATTACTCTGTTAAAAACTCATTATCTTTTACAG
Seq C2 exon
GTTTTACAAAGGTTAATAAAATCTCGAGGGAAATCTCAAGCTAAACACCTCAACGTCCAGATGGTAGCAGCTGATAAACTGGCTCAGTGTCCTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165995-CACNB2:NM_000724:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.037
Domain overlap (PFAM):
C1:
PF0062516=Guanylate_kin=FE(27.6=100)
A:
NA
C2:
PF0062516=Guanylate_kin=FE(17.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGAAGTTCAGAGTGAAATCGA
R:
TGGAGGACACTGAGCCAGTTT
Band lengths:
248-2121
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)