HsaINT0026534 @ hg19
Intron Retention
Gene
ENSG00000151062 | CACNA2D4
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4 [Source:HGNC Symbol;Acc:20202]
Coordinates
chr12:1901123-1904545:-
Coord C1 exon
chr12:1904465-1904545
Coord A exon
chr12:1902926-1904464
Coord C2 exon
chr12:1901123-1902925
Length
1539 bp
Sequences
Splice sites
5' ss Seq
GAGGTGCGG
5' ss Score
6.79
3' ss Seq
CCTCTGCTCTGCGTTCGCAGGAG
3' ss Score
9.92
Exon sequences
Seq C1 exon
AATGCCTCTGTCAAATGTGACCGGATGCGCTCCCAGAAGCTCCGCCGGCGACCAGACTCCTGCCACGCCTTCCATCCAGAG
Seq A exon
GTGCGGGTTGAGGCGGATCGAGGGTGGGCTGGATTTTCATCCCCAAACCCTCTGTGCCTGGGTCTGTGCCCCTGCAGACAGGAGCATATAGGGATGCCAATGAACACACCTGTGCCTGTGCTTCTCGGGGGAAACATTCGCGTTTATGCCCTGTGACACTGTGATATAATAAGAAACAGATCTTTATTTAGTCTTTGTCCTGATTCCTGGCAAGCTCCTAAAACGCTTGTTATTTCCTGATTAGGGTGATAGGTGCATCTTTTGTTATAGTGTTTGGTCTTAGTCCCTGGTTCCTTCACAGGTGCCTCTAAGACCCTTGGAATGATAGAGGTATCTTTGTATGCTAATTAGATGACTGGTGGCTGGGGGCCCTAGACAGGATGAGAGCTGGCCACAGGAAACACCAAGTTAGGATTAGAGGGTTGGGACTTTTGGCTCCAAGCCCCTGGCTTCTGGGAAAGGAAGGGGGCTGGAGACTGAGTTGATCACCAGTGGCCAAAGATTTAATCAATGATCATAATGAGGCCTCCATAAAATCCCCGAGCCACTGTGTTTGGAGAGTGTCCGAATTGGTGAAAGGGTGTGGGAGCTCTGCGTACCCCGTGCCTTGGCCTACGTGTCTCTTCCACTCAGCCGCCTGACCTGCGTCCTTTATAATAAACGGGTCATGGTGAGGGAAGCACCTTCCTGAGTTGAGTGAGCCACGCTAACAACTCACGGAGCCTGAGACAGGCTCATGGGAACCCTAGATTTACAGCCAGTCTGTCAGAAGGACAGGAGACCTGGGGCTTGCGATTGGCATCTGAAGTGACGGCCACCTTGTGGGACCGAGCCCTGTAACTTGCGAGCTCTAATGCTAACTCTCAATAGTGTCAGACTTGAATTGAGTTTCAGGACAGACACCCAGTTGGTGTCCAGAGAGTGGGGTGGGAAAAACCCTTCACATTTGTTGAAGTGCTGGTGTGAAAGCACAGCAGAGCCCCTGTGTCATTAAAATACGAAGTCAACCAGGATCCCAAGGTGCTTTAACGAAGAGCCACGCTTCCTAGGGCTTGGGCCCTAGGTGAATTAGAATGCAGTTTTCCCATCTTGTCCTCATTCCCGCTACACTTAGTTCCGAATGATCGAGCAATGTGAGGGGGCCGTCACGTGGATAATAGTCATAGTGGCTGGTACGGATCCAGAACCCAGACCCAGGTGTCAGGCCCTGAGCCGGGTGCTTCATACAGTCTGGTCTGCTGGGACCAGAAACCCCCATCAGAGATGCTCCCAGAGTTGAGGACATTCTGAGAGGATGACCTCGCAGCCACTCCAAGCCTGAGGGCAAGCAGAGAAGGCCGGTGCCCCCCTCCCAGGCTGAGGGGCCAGCCTTTGCTTTTCCCCCAAAAGGTAGGGGCCTAAGAGAGGTAGCAGTGCTTCCCCGGCTTTCCAAAACTCCCCTTTCCCCAGGATTTTGGCCCAAATTAGTGGTGGAAGCCCCTCCCTTTTTGAGGGTCCTCCTCTGAGCGCCGCGCTGTCACCTCTGCTCTGCGTTCGCAG
Seq C2 exon
GAGAATGCCCAGGACTGCGGCGGCGCCTCGGACACCTCAGCCTCGCCGCCCCTACTCCTGCTGCCTGTGTGTGCCTGGGGGCTACTGCCCCAACTCCTGCGGTGACACCACCCAGCCTGACCTGTGTTTTGGCAAGGTGATCCTTCCAGAGCCATCCCAAAAAGTCAGCACTGACATGGGATGCAGCTAACTGCAGTTGGGTCGCCCCCAGGCCAACGCTCCTCTCAATCCTGGGCTGGTGGCCCCTGGCTCCGGAGAATGCTGGATGGAACAGGAAACCAATCACCTGGCACCACTTTCAAGATGCTTCATGGTGCCCGGTACCATCTGCCCTAGGTCTCAACATGAGCATACTTCTGACCTAACCTTCCTGTCTCCTCTTCGGGAAGCCAGCGTGAGCTCAGCTTGGACCAAGACAAAATAATTTAGTTCTTCCTGTACTCCAGAGTCCAGACCCAGCCAAGAAAGGGTCAGTTGTTTCTGACCCTTTCTGTCGGAGTGGTCTCTGGTAGAACCCAAGGACTTCTGGGTACTGAGAAGCAGCAGCAGAATGAGGCCAAATGCAGAGATGAGGCTAAGGCAAGAATATGCCCCAACTAAAGCATAGATTCCCCAAAGTGAGGCTCATGGTGGGAGGCCACTCACCTTCCTAGCTGCTGCTCGAAAAGGTTTTGACTGTGTTGGGGTGGGGGTTGGGTAAGGGAATGGTCAAGACTGAGAAAGGAATGAAATCCATTCAGGAAATATCGACAGGGCTACACGTGATGTCCCCAAACTGCTGCTATTGAAGAACTTCCCAAAACTTCTTTACAAAGCCCTAAAGGAAAGTTTGCATCTATGAAAAGCCAATAGGCTGAGACATCCAATTGCTGCATGGAAATTGATGTACATTCAGGGGACGGCAAAAATAGCTGTAAAATAGTGAAAAAGAGCAGTGGTTGTGCTCTTTTCTGGCCAATGATTTACAAAAGAATCTACTTGACTCTGTCCCTGGAGTGAAATCCTTAGGGTTGGAACTTGTGGGAACATTCCAACTTGCTAAGCAGGGTCCACTGGGAGGGAAGCTCTATCTGGGAACTCACCCCCAGCGCACACACATCTCCCCCAGGGTCCCAAGGCCCCGCAGCTTCCTCCCCCGACCAAACCCCAAGACCTGGATCCCAGGAGACAACAGTCTCCACAGTGAGAGCAACATTAAGGGCAAAGCCATGGAGAAATGTGGGAGAGGCCGGCCTCAAATCTTTCCATTTAACAAACCCCAGTGATGGGTATGGACAGCATGCAGGGCTTTTGGGGCGCTTCCCCCCGCTCCTCCATCACCCTCAGCCTCCACACTTCAAAGTTCAAGTTCAAAGCTGTTCAAGTTTCCTACCAGCAAATAGCCCTAACTTGCCTCTAGAGTAGGCCAAATGCCAACTCTGTAAAACACACTTACATTATCGGTTACAGAATGTCACTCTTACCGTCATGTCTTGCAACAACCCTGTGAGGGCAGTATTAATGCCCCCTTACAGCAGAAGACACTGCAGCTCGAAGACAGCTTAAGTGGCAGAATAATGCTAGAACAGCTAAGGTTTACATGTACCAAATAACATGTTTCAGCTCATTCCATCCTCACAACAGCCCCCTGAAAGTGGGTACTATCATTAGTCCCATGTTATAGAAACTGCAGCAGAGTTGAAAATTGCCTCCAAATTACCGGAAGAGTGTATGAAGATTGAATGTGATGTATTCACGTAACATGCTTGAAACTGCCTGGCATATACTAAACGCTAAATAAATACATGCTAACTGCGATCATTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000151062-CACNA2D4:NM_172364:37
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.111 A=NA C2=0.118
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAATGTGACCGGATGCGCTC
R:
GTTCCATCCAGCATTCTCCGG
Band lengths:
342-1881
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
- 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)