HsaINT0145834 @ hg19
Intron Retention
Gene
ENSG00000153253 | SCN3A
Description
sodium channel, voltage-gated, type III, alpha subunit [Source:HGNC Symbol;Acc:10590]
Coordinates
chr2:165995986-165997508:-
Coord C1 exon
chr2:165997161-165997508
Coord A exon
chr2:165996119-165997160
Coord C2 exon
chr2:165995986-165996118
Length
1042 bp
Sequences
Splice sites
5' ss Seq
GAGGTGATA
5' ss Score
3.13
3' ss Seq
CATCAGTATTTGGTTTGCAGGGC
3' ss Score
5.44
Exon sequences
Seq C1 exon
TCTCTCTTGAGTATCCGTGGCTCCCTGTTTTCCCCAAGACGCAATAGCAAAACAAGCATTTTCAGTTTCAGAGGTCGGGCAAAGGATGTTGGATCTGAAAATGACTTTGCTGATGATGAACACAGCACATTTGAAGACAGCGAAAGCAGGAGAGACTCACTGTTTGTGCCGCACAGACATGGAGAGCGACGCAACAGTAACGTTAGTCAGGCCAGTATGTCATCCAGGATGGTGCCAGGGCTTCCAGCAAATGGGAAGATGCACAGCACTGTGGATTGCAATGGTGTGGTTTCCTTGGTGGGTGGACCTTCAGCTCTAACGTCACCTACTGGACAACTTCCCCCAGAG
Seq A exon
GTGATAATAGATGACCTAGCTGCTACTGACATTATTCACCAATTTGAAATAATCAAAGCCTGGACAGTTTAGGCTGTCATACCGTCCTGCTTCCTCAAAATGAAAGTTGGTAAAAATAATACATGATTAATCAAAGGGAAAACAATAGAATATTGAGAATCAATTGAATTGTATGGGACCATTAGCTTTTGTTGTATGGGAATTACTTGTAAGGGACCATGGCTTTAGGTTAAAAGGGCCCCGTTTTTAGAGTCTGCTATGAAATACATATCTGCAAATTTGGTAGACCTACCGAGACAAATAATGGACATTTTCACCATCAAATCTATAAGATGTATATTCACCAAGAATTGTATAATTATCTATTCATATTCTGGAAAATTCATATTCTTAAAATTAAATATTATAACCAATTTGTTGATAATGGGCAATTTCATACAACTGTCAATATTTACAGTGCTATTTTAAAATGACTCTAAAATGTGTTGTTTTTTAATAGGATAAGATATAGAAATAATTAAAGAAATTTCAGGAAAGCACACACATTTCATCGTACATCTGTGTTTGTGCATGGAAAAAATTGGCCCACATATGTCAATATTGTCAATATAGCCTCAAAGAAAATAATTCAGCCTTGAGACTATATAATCATAATATTTATTGGGGGGAGATTGATCTGATTATTAATCATTGATAGAAGATAAAAATAATTTTCACCTGAATGAAATAAAATAATAAATGACTTTAGCATGTTTACAACAAATTTCCTTGAAAATTGTGACAGGTTAATTAAAATAGTTCTGTAATATAATTGTGTTATAAAACTGCATCCCACTGGTGAATTCCTCTTAAAGAGTACTACCTGTGATAACTTTTTTTTAAAAAAAAAACTGTTTATAACTTAGCAATAATTCAATATTTTATTCCTTGAAAATTCTTACCTGGAAAAATTGCATGTAGCATGATTTGCCAAAGAAATGCTATGTGGTGTTGTATTACTTATTGGGAAGAGTGGTTTGAGCCATCAGTATTTGGTTTGCAG
Seq C2 exon
GGCACCACCACAGAAACGGAAGTCAGAAAGAGAAGGTTAAGCTCTTACCAGATTTCAATGGAGATGCTGGAGGATTCCTCTGGAAGGCAAAGAGCCGTGAGCATAGCCAGCATTCTGACCAACACAATGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000153253-SCN3A:NM_006922:13
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.634 A=NA C2=0.189
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(50.9=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.4=82.2)
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:
CTCCCTGTTTTCCCCAAGACG
R:
ACTTCCGTTTCTGTGGTGGTG
Band lengths:
351-1393
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)