HsaINT0145813 @ hg19
Intron Retention
Gene
ENSG00000136531 | SCN2A
Description
sodium channel, voltage-gated, type II, alpha subunit [Source:HGNC Symbol;Acc:10588]
Coordinates
chr2:166237102-166237707:+
Coord C1 exon
chr2:166237102-166237239
Coord A exon
chr2:166237240-166237602
Coord C2 exon
chr2:166237603-166237707
Length
363 bp
Sequences
Splice sites
5' ss Seq
AAGATAAGT
5' ss Score
2.82
3' ss Seq
TGTTGCTTTCATTTCTTTACTTT
3' ss Score
0.77
Exon sequences
Seq C1 exon
GTAGAATTACAACCCAAGTATGAAGACAACCTGTACATGTATCTTTATTTTGTCATCTTTATTATTTTTGGTTCATTCTTTACCTTGAATCTTTTCATTGGTGTCATCATAGATAACTTCAACCAACAGAAAAAGAAG
Seq A exon
ATAAGTATATTAAAACTTCATCCTTGCTCTGAAATATGAACTAAATATTTCATACTCTTTCCTTTAGCCTCCAAAATGCAATCACCAAAAAAAGAATATAAAATTCAGAAATTATTTTGAGACATTTGATAATCGATAAGCTTTTAAGCAATTAATAATTCAGATAGCATGTTTTTGATATTTTTAGTCTAGAAATATGACTAATATGGCATAATTTATATATTGAATAAAGGCATCTCTATAAATACAGATATTAGTAACAATAGAATGAAATGTGGGAGCCAATTTTCACATGATTACTAAGGTGGATTTTATAGCCAGCAAAGAACACAATTTTAACAAGTGTTGCTTTCATTTCTTTAC
Seq C2 exon
TTTGGAGGTCAAGACATTTTTATGACAGAAGAACAGAAGAAATACTACAATGCAATGAAAAAACTGGGTTCAAAGAAACCACAAAAACCCATACCTCGACCTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136531-SCN2A:NM_001040142:24
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=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(15.3=76.1)
A:
NA
C2:
NO
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:
ATTACAACCCAAGTATGAAGACAACC
R:
AGCAGGTCGAGGTATGGGTTT
Band lengths:
238-601
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)