HsaINT0026567 @ hg19
Intron Retention
Gene
ENSG00000165995 | CACNB2
Description
calcium channel, voltage-dependent, beta 2 subunit [Source:HGNC Symbol;Acc:1402]
Coordinates
chr10:18689513-18690972:+
Coord C1 exon
chr10:18689513-18690029
Coord A exon
chr10:18690030-18690852
Coord C2 exon
chr10:18690853-18690972
Length
823 bp
Sequences
Splice sites
5' ss Seq
TGTGTAAGC
5' ss Score
4.52
3' ss Seq
ATGTACATTTTCCTCTCCAGGGT
3' ss Score
10.24
Exon sequences
Seq C1 exon
AAAGATAAGGCTTGAACTTTGCACTTGCAAATGTCACTGCATACGTTTTTGCACTAGTTTTTTTTTTTTTTTTTCTGCGATTCTTTTACAACTAATTTCTTTTAACAATTTGAGCGCAGGGAAGAGAATGTTTAGGGTTATGAGATGCATTAAGTTTAGAACGAGTTGATGCTCGGCTTTTGAATGCACTTGTCTTCTTTATTTTTAAAGCAATATAAAGCACTCGAGTGTGTGTTTTCAGCCCCTCCTGGAATGGGAAAATAAGAATCTCCCTGGATGGGAGTCCTCTGGGGCAGGGAGTGAAAGCCCCGGAGGCAGAAAGGGACGGAGAACAGGGGCTTGCCCAGAGCATGGATAGGAAAGGAGCTGGGGTTCTCCGGGGCTCAGCGCGCACTGAGAACCTGTGCCCGGGGCTGCAGCTGCGGACGATAAAGGCGCTGTCTGGCTCATGAAGGCCACCTGGATCAGGCTTCTGAAAAGAGCCAAGGGAGGAAGGCTGAAGAATTCTGATATCTGT
Seq A exon
GTAAGCGCAAGGGCTTTCGTTTGTGGGGAGAGGTTATTTTGTCTCTGCTTTTCTGTTGTTGCAGTGAGTGCAGGTAGAGAGGGTGGTTTGATTTGGTTAATCGGATCATGATTGCAGGAGAGGGAAGCTAGGGAGATTCCTCTCATTTTTTGAGCTCCTTTTCCTAGGTTGTGATTAATTGCCAGATGAGCTATCCCAGGCAGGTGTTTTCTGTAGACGGCTTTTTATTAAATCTAGGTAAAGGTATTTTAAAATGTGTTGCTGGAAGATGGAGTGAAGTTAGCTGCTAGTGTCTTACAGTTTTATCAGAGAAAATAGCAGGTGTATAAAAAGGTAAACAAGGCTTTTTCAGATTAAAGTGGGAATCATGTCATGGTAGTGACATTTTGGAGAGTTCAAGTTTATAACTCAGACTTTCTTTCATGTTTTTGTTAAGCTTAATGTCCTCCTAGTTTCAAATACCTGCTTTAGCATGTAGATTGTTCTTGAAGCTATCCTTGAAACCCATCGTTGTCCTTCAGTTCTGCACTGCACCATCAAGCTGTTTAATTATAAAACCAACTTGTTCTGGCTTCCAGGAAGGATAGTTTTTTGGAATATAAAGCTTGGGAAGGAATGGCAACTCAGTAGACACAACTATTCTATTGAATGTCTGCAAACCAGAGCATGGTTTTCTAGATAGGTTGCTGCAAAATGAATTATTTTCTCCTCTTTTCAGGAAAGTATAGAACAATCCGGGAAGCTAACTGCTGTGTCGATGAGACTTTTCCAATGCAAACATCATAGACTGAATCTACTTTAAAATGTACATTTTCCTCTCCAG
Seq C2 exon
GGTTCGGCAGACTCCTACACTAGCCGTCCATCCGATTCCGATGTATCTCTGGAGGAGGACCGGGAGGCAGTGCGCAGAGAAGCGGAGCGGCAGGCCCAGGCACAGTTGGAAAAAGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000165995-CACNB2:NM_201570:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.868
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF120523=VGCC_beta4Aa_N=PU(92.9=97.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCGAGTGTGTGTTTTCAGCCC
R:
CCGGTCCTCCTCCAGAGATAC
Band lengths:
357-1180
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)