HsaINT0145823 @ hg19
Intron Retention
Gene
ENSG00000136531 | SCN2A
Description
sodium channel, voltage-gated, type II, alpha subunit [Source:HGNC Symbol;Acc:10588]
Coordinates
chr2:166165176-166165766:+
Coord C1 exon
chr2:166165176-166165304
Coord A exon
chr2:166165305-166165674
Coord C2 exon
chr2:166165675-166165766
Length
370 bp
Sequences
Splice sites
5' ss Seq
TGCGTAAGT
5' ss Score
9.73
3' ss Seq
ACTCTGATTTAATTCTACAGGTA
3' ss Score
9.49
Exon sequences
Seq C1 exon
GTATACCTTTACAGGAATTTATACTTTTGAATCACTTATTAAAATACTTGCAAGGGGCTTTTGTTTAGAAGATTTCACATTTTTACGGGATCCATGGAATTGGTTGGATTTCACAGTCATTACTTTTGC
Seq A exon
GTAAGTATCTTAATACATTTTCTATCCTGGAAGAGTAAATCACTGGTGGGAGCCTATACTATATTTTCCTTGGTGGCTTGCCTTGACAGACCAAGCATTTTTCTTAGTAATCATAGTTTTCTTCCAATCAAATTATCCAGTTTGGAGAAATTAGGAACTATCATAGTAAATTACATGGCTTTGGTTTCAATTAGCACTGTAAAGTAATAAAGTTTCCCAAATAACAGAGATTATGATTGATGACAATGCCATTTTCCTCTTAATTGGGAAAGCTGATGGCGACACTCATGAAATTAAAAAGGTCTTGATGAAAGACCAAGGAAGACGTAGATTTCCCTAAATTCTGAATAACTCTGATTTAATTCTACAG
Seq C2 exon
GTATGTAACAGAATTTGTAAACCTAGGCAATGTTTCAGCTCTTCGAACTTTCAGAGTCTTGAGAGCTTTGAAAACTATTTCTGTAATTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136531-SCN2A:NM_001040143:4
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=FE(16.0=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(11.6=100)
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:
CACTTATTAAAATACTTGCAAGGGGC
R:
TACAGAAATAGTTTTCAAAGCTCTCA
Band lengths:
182-552
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)