HsaINT0145815 @ hg19
Intron Retention
Gene
ENSG00000136531 | SCN2A
Description
sodium channel, voltage-gated, type II, alpha subunit [Source:HGNC Symbol;Acc:10588]
Coordinates
chr2:166243256-166248820:+
Coord C1 exon
chr2:166243256-166243526
Coord A exon
chr2:166243527-166245138
Coord C2 exon
chr2:166245139-166248820
Length
1612 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGA
5' ss Score
9.14
3' ss Seq
TATTTGTTGATTTTCTACAGGAA
3' ss Score
8.79
Exon sequences
Seq C1 exon
AACAAATTCCAAGGAATGGTCTTTGATTTTGTAACCAAACAAGTCTTTGATATCAGCATCATGATCCTCATCTGCCTTAACATGGTCACCATGATGGTGGAAACCGATGACCAGAGTCAAGAAATGACAAACATTCTGTACTGGATTAATCTGGTGTTTATTGTTCTGTTCACTGGAGAATGTGTGCTGAAACTGATCTCTCTTCGTTACTACTATTTCACTATTGGATGGAATATTTTTGATTTTGTGGTGGTCATTCTCTCCATTGTAG
Seq A exon
GTAAGAAGAGGTGCTTTTATTCAGTTAAGGAATATAGTGGTAAAAATATGTGTTTTAAAACTTTAGAGGTGTTTTTCACTAATCTTTCTCATTCATCCCAAACTCCCAAATAAAAATCTAATAGTCCATTGTTTTAGTTTTAGTTTGCCATTTCTCTAATTGCATGCTGTGCTTGAAATGATGAGTGGAATACAAGGAATTTATATTTTCAGCTTTCATTTATTCTCATTTAATATTTTCATCTGTTCTCATCTCAGAAGACAATAACTGCAACTTTGGTAGAATAGTCTTGTACCTGGTCATACTCCTGTGGTATTGACAGTTACTGCTTTGAATAAACAATCAATCCACACACATATATACATAAATCATTTGAAGTAGTCACATAATTCATAAATATGACCTCTTAAATAATTGGAATAGTGTATATGTGCAGTTATATATATAATAACACATATATAAGTTTCATGTTATCTTTGGGTGCAGACAGTTTTCTGTGGTTTGCAATATCTCTTTTTGGAAGCAGATAGTTTGTTTGAAAATCCAAAACAGATTTGTTATCATCAATGATACATTAATGTTAGGATACATACATACATTAAGTCCTAGGAATGCAAAAGATTTATTGGAAAAAATATATATATACAGTGTTTATGTATAAGATATTAAATGAGGTACTGGAAGTAAATATAAGAAGATTTAAGAGAAGGTTCTACCTATTTGGGGAAACAGAACATTCACATGGAGGGGAAAATTATATAGCACTCTTTAAACTACTTTCTTTAGTCGAATAGAACATTGTAACAATGTTCCACTGCATTTGATTCTCACATAAGTGCTATGAGGTAGCATTAAGAGGTAAGATTTGAGATCTGACCTGGAGCTTCCCTATTTACACTACTTACCTTCTCAGTGACCTAAGAGAAGTTACCTCAGCTCTCCAATCTCTGGTTTTGCAAGGAATTTTTCTGTAAAATGTTATTGTGAGGATTAAATCAGATTATGTATATATATGCACTTAGCACTGTGCCTAGCATGAAGAAAAGACTTAGTAAATGTTCAGTTTGACCACAAGAAAAAGTTGATATTATCACCATTTACTCATGCATAAAAGCAAGTGCCAGGATTCAGTCCCAAGTACATCTGTCTCCAAAGCCTATGTTTTCTTCTGTACATCACGCTGCCTACTCCCAAATAACATAGAATCTCAGAAAGTAAAGAACTCTCATATTCCTGACCCAAAATCATACACCTTTAGTTCTTATGCAAATACTAGAACTAGTATTTTGGACATATAAATTAATTTCTGTACTTGGCCACTGTATGCTTCATGATGTCTTTGGACCTTCCAGGGTTGAGTCATTTTTTTGATAGATGCTTTCCTTGAACTAGGAAAAATGGCCCTTATTATCTTCATTTAATATAAAGATGTAAATGTTATAACACCAAACATACCAGTTTCATTTTGCTCAACAAACATTGCAGATTATTTGCATATATACATGTACCTAACTGTCCTGTTCACATTTTGTAAAACTAATGTACTTATGTAAACTTTCATTTGCTACTATTAAGTATAACAATATTTTTGTTATTTGTTGATTTTCTACAG
Seq C2 exon
GAATGTTTCTGGCTGAACTGATAGAAAAGTATTTTGTGTCCCCTACCCTGTTCCGAGTGATCCGTCTTGCCAGGATTGGCCGAATCCTACGTCTGATCAAAGGAGCAAAGGGGATCCGCACGCTGCTCTTTGCTTTGATGATGTCCCTTCCTGCGTTGTTTAACATCGGCCTCCTTCTTTTCCTGGTCATGTTCATCTACGCCATCTTTGGGATGTCCAATTTTGCCTATGTTAAGAGGGAAGTTGGGATCGATGACATGTTCAACTTTGAGACCTTTGGCAACAGCATGATCTGCCTGTTCCAAATTACAACCTCTGCTGGCTGGGATGGATTGCTAGCACCTATTCTTAATAGTGGACCTCCAGACTGTGACCCTGACAAAGATCACCCTGGAAGCTCAGTTAAAGGAGACTGTGGGAACCCATCTGTTGGGATTTTCTTTTTTGTCAGTTACATCATCATATCCTTCCTGGTTGTGGTGAACATGTACATCGCGGTCATCCTGGAGAACTTCAGTGTTGCTACTGAAGAAAGTGCAGAGCCTCTGAGTGAGGATGACTTTGAGATGTTCTATGAGGTTTGGGAGAAGTTTGATCCCGATGCGACCCAGTTTATAGAGTTTGCCAAACTTTCTGATTTTGCAGATGCCCTGGATCCTCCTCTTCTCATAGCAAAACCCAACAAAGTCCAGCTCATTGCCATGGATCTGCCCATGGTGAGTGGTGACCGGATCCACTGTCTTGACATCTTATTTGCTTTTACAAAGCGTGTTTTGGGTGAGAGTGGAGAGATGGATGCCCTTCGAATACAGATGGAAGAGCGATTCATGGCATCAAACCCCTCCAAAGTCTCTTATGAGCCCATTACGACCACGTTGAAACGCAAACAAGAGGAGGTGTCTGCTATTATTATCCAGAGGGCTTACAGACGCTACCTCTTGAAGCAAAAAGTTAAAAAGGTATCAAGTATATACAAGAAAGACAAAGGCAAAGAATGTGATGGAACACCCATCAAAGAAGATACTCTCATTGATAAACTGAATGAGAATTCAACTCCAGAGAAAACCGATATGACGCCTTCCACCACGTCTCCACCCTCGTATGATAGTGTGACCAAACCAGAAAAAGAAAAATTTGAAAAAGACAAATCAGAAAAGGAAGACAAAGGGAAAGATATCAGGGAAAGTAAAAAGTAAAAAGAAACCAAGAATTTTCCATTTTGTGATCAATTGTTTACAGCCCGTGATGGTGATGTGTTTGTGTCAACAGGACTCCCACAGGAGGTCTATGCCAAACTGACTGTTTTTACAAATGTATACTTAAGGTCAGTGCCTATAACAAGACAGAGACCTCTGGTCAGCAAACTGGAACTCAGTAAACTGGAGAAATAGTATCGATGGGAGGTTTCTATTTTCACAACCAGCTGACACTGCTGAAGAGCAGAGGCGTAATGGCTACTCAGACGATAGGAACCAATTTAAAGGGGGGAGGGAAGTTAAATTTTTATGTAAATTCAACATGTGACACTTGATAATAGTAATTGTCACCAGTGTTTATGTTTTAACTGCCACACCTGCCATATTTTTACAAAACGTGTGCTGTGAATTTATCACTTTTCTTTTTAATTCACAGGTTGTTTACTATTATATGTGACTATTTTTGTAAATGGGTTTGTGTTTGGGGAGAGGGATTAAAGGGAGGGAATTCTACATTTCTCTATTGTATTGTATAACTGGATATATTTTAAATGGAGGCATGCTGCAATTCTCATTCACACATAAAAAAATCACATCACAAAAGGGAAGAGTTTACTTCTTGTTTCAGGATGTTTTTAGATTTTTGAGGTGCTTAAATAGCTATTCGTATTTTTAAGGTGTCTCATCCAGAAAAAATTTAATGTGCCTGTAAATGTTCCATAGAATCACAAGCATTAAAGAGTTGTTTTATTTTTACATAACCCATTAAATGTACATGTATATATGTATATATGTATATGTGCGTGTATATACATATATATGTATACACACATGCACACACAGAGATATACACATACCATTACATTGTCATTCACAGTCCCAGCAGCATGACTATCACATTTTTGATAAGTGTCCTTTGGCATAAAATAAAAATATCCTATCAGTCCTTTCTAAGAAGCCTGAATTGACCAAAAAACATCCCCACCACCACTTTATAAAGTTGATTCTGCTTTATCCTGCAGTATTGTTTAGCCATCTTCTGCTCTTGGTAAGGTTGACATAGTATATGTCAATTTAAAAAATAAAAGTCTGCTTTGTAAATAGTAATTTTACCCAGTGGTGCATGTTTGAGCAAACAAAAATGATGATTTAAGCACACTACTTATTGCATCAAATATGTACCACAGTAAGTATAGTTTGCAAGCTTTCAACAGGTAATATGATGTAATTGGTTCCATTATAGTTTGAAGCTGTCACTGCTGCATGTTTATCTTGCCTATGCTGCTGTATCTTATTCCTTCCACTGTTCAGAAGTCTAATATGGGAAGCCATATATCAGTGGTAAAGTGAAGCAAATTGTTCTACCAAGACCTCATTCTTCATGTCATTAAGCAATAGGTTGCAGCAAACAAGGAAGAGCTTCTTGCTTTTTATTCTTCCAACCTTAATTGAACACTCAATGATGAAAAGCCCGACTGTACAAACATGTTGCAAGCTGCTTAAATCTGTTTAAAATATATGGTTAGAGTTTTCTAAGAAAATATAAATACTGTAAAAAGTTCATTTTATTTTATTTTTCAGCCTTTTGTACGTAAAATGAGAAATTAAAAGTATCTTCAGGTGGATGTCACAGTCACTATTGTTAGTTTCTGTTCCTAGCACTTTTAAATTGAAGCACTTCACAAAATAAGAAGCAAGGACTAGGATGCAGTGTAGGTTTCTGCTTTTTTATTAGTACTGTAAACTTGCACACATTTCAATGTGAAACAAATCTCAAACTGAGTTCAATGTTTATTTGCTTTCAATAGTAATGCCTTATCATTGAAAGAGGCTTAAAGAAAAAAAAAATCAGCTGATACTCTTGGCATTGCTTGAATCCAATGTTTCCACCTAGTCTTTTTATTCAGTAATCATCAGTCTTTTCCAATGTTTGTTTACACAGATAGATCTTATTGACCCATATGGCACTAGAACTGTATCAGATATAATATGGGATCCCAGCTTTTTTTCCTCTCCCACAAAACCAGGTAGTGAAGTTATATTACCAGTTACAGCAAAATACTTTGTGTTTCACAAGCAACAATAAATGTAGATTCTTTATACTGAAGCTATTGACTTGTAGTGTGTTGGTGAAATGCATGCAGGAAAATGCTGTTACCATAAAGAACGGTAAACCACATTACAATCAAGCCAAAAGAATAAAGGTTTCGCTTTTGTTTTTGTATTTAATTGTTGTCTTTGTTTCTATCTTTGAAATGCCATTTAAAGGTAGATTTCTATCATGTAAAAATAATCTATCTGAAAAACAAATGTAAAGAACACACATTAATTACTATAATTCATCTTTCAATTTTTTCATGGAATGGAAGTTAATTAAGAAGAGTGTATTGGATAACTACTTTAATATTGGCCAAAAAGCTAGATATGGCATCAGGTAGACTAGTGGAAAGTTACAAAAATTAATAAAAAATTGACTAACATTTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136531-SCN2A:NM_001040142:26
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.204
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=41.9),PF0061222=IQ=WD(100=5.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGGAAACCGATGACCAGAG
R:
AGGCCGATGTTAAACAACGCA
Band lengths:
348-1960
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)