HsaINT0026589 @ hg19
Intron Retention
Gene
ENSG00000182389 | CACNB4
Description
calcium channel, voltage-dependent, beta 4 subunit [Source:HGNC Symbol;Acc:1404]
Coordinates
chr2:152709962-152711889:-
Coord C1 exon
chr2:152711738-152711889
Coord A exon
chr2:152710058-152711737
Coord C2 exon
chr2:152709962-152710057
Length
1680 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATT
5' ss Score
8.83
3' ss Seq
TTCATGTCTTCTTCTATCAGGTT
3' ss Score
10.04
Exon sequences
Seq C1 exon
CGGAAGTACAAAGTGAAATTGAAAGAATCTTTGAGTTGGCAAGATCTTTGCAACTGGTTGTTCTTGATGCAGACACCATCAATCACCCAGCACAACTTATAAAGACTTCCTTAGCACCAATTATTGTTCATGTAAAAGTCTCATCTCCAAAG
Seq A exon
GTAATTAGCTCCTTTCTGCCTTAAGGTTTAGAAGTGCATCTTTTAAAAATGTGTTTTGCTCTGTGGTTTTTTGTTAGTGGACAAAGGAGAACGTCTTGCTGATTATTAATAAGCACATTTAAAATCTTTCCACAGTGTACAGATTCTATGAATTTTCAGATAGTGAAGAATATAATAGTTCATTTCTTCTAAAAGCTACTATTGTAGATCCCAAACAAGACAGTTATGCAAGTGTATAATAGAAACAAAACATTAAGACAGATGTGGAAAAGTAGACTCTGGCTTATCATAGACTATGAATTCTATATTGGTAAATTTCTTGGATCCTGTTGATTCCTGTGTCATCCATACTCTGTACCTAGTTGAGAGAGTACATCTATATTGATCAAAAAAGGCATCTATGTTGATCATATATAAAATAGAATATCACTGTTTAAACATCTCCTATGGAAGCATTATAGACCCTGACATTTGTGCTTAGGTTGAGTTCTTGAAAGAATGTGGTTATTCCACGATAAGCACAATGGGAAATTTGCTTTGTATCTTTATGCCATTGTGGGAGGTAAAAATAAAAGTGAAATAGCCCCAAATTGGTTTCTTTTGATTTGGGTGTTCTTTCATTTTTAAAAAAGGATGTTGTTCTTAAAAAGTTAACGTGAAATGGTTACCCTTGGGAAGTACTATCTTAATAATCAGTTTCTTCTCTGTGCCTCCTAGTGTATTTTGGTGCCTAAATACAAATTCAACTGCCAACCAGCATGGCAGTCTTCTCTCATGGGTGGAGAATGTCTAAAGAAGCTGTACTCTCCTCCAGATGTTCTGAGATCCTAGCCTTCCATCTATCTCTGCAGACACTGCTTTGGTGCAGTGGACTTGGGAATCCTGAACAAACTAGGGCCTTTTGAGAATCAGTAGAATGGATTGAAAGAGCTGCTGGGGGTTCAAGCACTTCACTGCAGTGCAGGAGAGTTCAGCCCTTCCCACTGCCCATGACACTGTGGTGTCCTTAAGTGCAAGAACAGGAGTTCCCAGACACCTATGTCCTGGGGTATTATAGAGCTCATAGATTAGCATTGTTTGCAGGGGAAGGGCCACGGGACATGGCAGTATATGACCAAATGCAGTTACAGCAGTGGCCAAAAGACATAGATATATCACTGGTTTACATGTAGCAATATACTAATACAAATGTTTTGCCTGGGTCTCCAATCACAGAATAGTCTGATTAATTTAAAATTAAACTGAAATGTCCCATTAATAATCGGTGACAAAAATAACCAGAAAATGACTCTGACATTTATCTGACATGGAGATAGTGAGCTAAAACATTATTCAGGTGAATAATATTAAAGTATTACTTAACATAAATGACCTGGTACAGTCCACTCCCTCCATTTTTACAGGTCTCTCTTTGAAATCTCTGGGAAAAATCTAGGATGGGAACTCAGGCTCCTCCTGAGACTTCACACAGAGTTAGAATAGGATGAACATATCAAATCCATGGAACTGAGAGCCAATGTAAGCAGATGACATCATTACAGGTTTAAATATATGATTTCTCACACTGCATTTCCTCTCTGATAATACTCAGGGCCAAGCAGACCATTAAAAAGATCCTGGCTTATTTGATTTTCTTTCAACTCATCTACAATACCTCAGGTTCATGTCTTCTTCTATCAG
Seq C2 exon
GTTTTACAGCGGTTGATTAAATCTAGAGGAAAGTCACAAAGTAAACACTTGAATGTTCAACTGGTGGCAGCTGATAAACTTGCACAATGCCCCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000182389-CACNB4:NM_000726:11
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=0.094
Domain overlap (PFAM):
C1:
PF0062516=Guanylate_kin=FE(24.6=100)
A:
NA
C2:
PF0062516=Guanylate_kin=FE(15.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGAAGTACAAAGTGAAATTGAAAGA
R:
TGTGCAAGTTTATCAGCTGCCA
Band lengths:
238-1918
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)