HsaINT0145840 @ hg19
Intron Retention
Gene
ENSG00000153253 | SCN3A
Description
sodium channel, voltage-gated, type III, alpha subunit [Source:HGNC Symbol;Acc:10590]
Coordinates
chr2:165970326-165972085:-
Coord C1 exon
chr2:165971965-165972085
Coord A exon
chr2:165970481-165971964
Coord C2 exon
chr2:165970326-165970480
Length
1484 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAC
5' ss Score
8.14
3' ss Seq
TAACTATATTTGATTTTTAGGAT
3' ss Score
8.93
Exon sequences
Seq C1 exon
AAATTAAATGCAACCAGCTCATCTGAAGGAAGCACAGTTGATGTTGTTCTACCCCGAGAAGGTGAACAAGCTGAAACTGAACCCGAAGAAGACCTTAAACCGGAAGCTTGTTTTACTGAAG
Seq A exon
GTAAACAAGCTCTGATGTGATTAAATACAATCTCCCCTTGTTCTTTACGGAGACTGAATATGCCTCATTTAAAAAAAAAAATTTATGAAACGAGGTGTGGTGGCTTATGCCTGTAACCCCAAAATTTTGGGAGGCTACGGTAGGAGGATTGCTTGACCCCAGGAGTTTGAGACCACCCTGGGAAATGTAGTAAGGCTTTGCCTCTACAAAAAAAAAAATAAAGAAAGAAAAAATAAATTAGCTCAACATGGTGGTACATGCCTGTAGTCGCTGCTACCTCAGCCACAGCTGTATCTTAGAGCTTTTGCAGGGAGTCGAGGCTACAGTGAGCCATGATTATGCCACTGCACTTCAGCCTGGGCAATAGAGCAAGACCCTGTCTCAAAATAAATACATAAATTAAATTAAATAAGAAAAATATTTAAAATAAATAGTGAAGGCATGTTTATCTTTATTTTCCTTTTTTGTCTTTTAAAAAGTTAATCTCTCTAGATTTCTGGATTATACTTATGGCAGTGACTATTCCTGGACAGTTAAAATGATCTGATAGGTCTTTTTGTTTTCTCATTCTCCATAATGTGAGGAAGCTGACCCTATGAGATAAATGGCATTCTAGAATGTCATGTCATTGATATTGTAATCCCTTCAGAACTCCTTGGCAATGGTGTGATTTGATTTATAGATGCTACAGTAATTACATTCCCTCCCTTACAGTTCCAATGTGGTTAATGTGCTTTGGCTAGAGCTGTTTTGAGATGTAACTGTATTGTGAAGCTTTGGCAGGGAAAGCAATAGCTGTTCTCACAGAAAGCAGCACAATGTCTTGAACACAAATCAATGAATATCTATTATTCAATGTGACTGGACTTAATCAGATGAGTAGTAGCTCAGAGACTTACAGCAGAAGAGTGGATGGGAGTTAGAAATAATGCGAAAGCTAGGAGGGGGAGGACAAAGGGAAAGAGATACTGACTGACGAGCTGAGTCATAGGTGTGACTAAGAGAAGCACTGAGGCTGAAAAATAAATTAGCTTCGGAAAATTGACAGTGGCTGATGCCTGGGAAGACAGCGAGATTTTCTGTGCATGTGTGCATGAAAAGAATTAAAAACCCAGGATCACATCAAAATATGAATAAACAAATCGAACATGTAGTTTTTGCCTCAAACCTGAGAGATGCACCTGGACTATTTTCATCAATGGCCTTGAGGCAAAATAATCCTGACTGGTGGTGAAGAATGAAACCATTGTTACTTAAGCAAATCTAGATAAAATATTTCCTTGAATTCTAAGTAGCTGGCTGAGTATATAAGTCTGAGAATAATTCATTATACAGGAGGGATGCTGACGATAACTAGGAAATGAAGGAGATGGTTACCCTATGAAATGATTACCTGGAAGTGGAGTGGGGAAGGGGCAAGAAAGTTTATTTTTTCCTATTTAAGATTAAAATATATTTTTTAATTAACTATATTTGATTTTTAG
Seq C2 exon
GATGTATTAAAAAGTTTCCATTCTGTCAAGTAAGTACAGAAGAAGGCAAAGGGAAGATCTGGTGGAATCTTCGAAAAACCTGCTACAGTATTGTTGAGCACAACTGGTTTGAGACTTTCATTGTGTTCATGATCCTTCTCAGTAGTGGTGCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000153253-SCN3A:NM_006922:19
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.659 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(18.3=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(20.1=84.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATGCAACCAGCTCATCTGAAGG
R:
CAATGCACCACTACTGAGAAGGA
Band lengths:
270-1754
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)