HsaINT0145786 @ hg19
Intron Retention
Gene
ENSG00000144285 | SCN1A
Description
sodium channel, voltage-gated, type I, alpha subunit [Source:HGNC Symbol;Acc:10585]
Coordinates
chr2:166845670-166850926:-
Coord C1 exon
chr2:166850656-166850926
Coord A exon
chr2:166848933-166850655
Coord C2 exon
chr2:166845670-166848932
Length
1723 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGA
5' ss Score
9.14
3' ss Seq
TTCTCATTGTTTATTCATAGGTA
3' ss Score
8.89
Exon sequences
Seq C1 exon
AACAAATTTCAAGGAATGGTCTTTGACTTCGTAACCAGACAAGTTTTTGACATAAGCATCATGATTCTCATCTGTCTTAACATGGTCACAATGATGGTGGAAACAGATGACCAGAGTGAATATGTGACTACCATTTTGTCACGCATCAATCTGGTGTTCATTGTGCTATTTACTGGAGAGTGTGTACTGAAACTCATCTCTCTACGCCATTATTATTTTACCATTGGATGGAATATTTTTGATTTTGTGGTTGTCATTCTCTCCATTGTAG
Seq A exon
GTAAGAAATATTTAAAGTTCTTAAATTCAGTTAAATAAAAGTGAAAGCTGAAACAATCAAGATTAGATTCAAGATCATCCCAGCAATCAGAGATAATCACTGTAAATATTTTGATACATTTTATCCAAGTGTGTTTGTTTTTTTAACAAAATGTCTCCTACTATATGTCAGTATTGTTTCTTATTCTATCCATTTAGAACAATATACTTAGTGTAAATGTAGTAAAACCTCATTCATTTGAACTAGAACTGTGCTATTAACTAAAATAAAAATGTTTTTGACATGTTGAGATTGAAGAACCAATATAGTATCTAGATGGTTCTGTTAACAAGACTAGAAATGTAGTCTGGTACTCACGAAAATTGCTTTAGAGAATAGACATGGAGTCACCAGCATATAGATATTAGTGGAAAGTGGTTTCAAGATAAGGAAAAGTATTGCATAAAAAGAGAATAAAGACAAGGACTAAACATTAGCAAATGCATATAGTAGGTTCTCTGCAAGTGTCATGTAGAGATTTTCTAGACTACCTTAAAAATGGGTTTATCATAATGATGCACAAGGGAAATAAGGTGGCATGGGACATCATCAGTACTATACTTCAAAGCCTGGAACACATAACTAGCCTCATGAGCAATAGCTCATTTCATTAGACAAAACTAAAGCTCTAGTAAAGTAAAAAGCATCTGTCTGTGGGCCTATTCATTCTTCCCTAAACAGGATGATATGATTGGGTCAATATTTTACTATCCAAAACGAGGCACCTGTGTTGGACAGATTTTCATGCCACTCCCCTCTCTGAAGAAACTGGCCTTATATCCAGCTCATTGTATATAGCCTTTGATTCCCACTAATTATAATCCTTGGTTATAACTAGTGTGGCTAAGGTATAAAAGTTGTATTCTCACACGTCTCCTTCTCTCTCTCTCTCTCTCACACACACACACACACACACACACACACACTCTTACACTTCGTCTTTTCAGAATGAGGCATTTAAACTTGAAGGCATTTAGTTTCTTGAGCTCTTCTTTTTAACTTTACAAGTATTGTTTTTATCTAAAAAGCAAATGGAGAGAGAAGCTGAAAATAAGAAGACTGAGATTACAGTGTTAGGTACAGGAGACCAAAAAGAATTGAAATACAACATTAAGTACAGGATACTAAAAAGAGCATCAACCTGGGATCCTTTCAGAAATGCACCAGAACATACATAAATGAGTATATAAAAATATTAGAGTGGAATTTAAGTAAGTACCAAGATCATGGGGAGATGAAAGTAGCATCAAAAGCTACCAATACTTTCAGATGGAAAAGGAGTAAATAGAGAATTTAGAATATGGCAATTTCAGAAAAAGTCACTGTATACATATAAACTTGTACCTATACTGTTGGGCTGCTACTGTTCGGCCAAATGTGCATTTTTAACTTATTTTCTTTTTAAATTCTGACTTGGGACTTTACATAAACTAAAAGTAGTTTATAAACATCTCTTAAAGATAAAAAAAAGTACTATAATCCTTATAATTGAAATTATTGCTGAATTTCAAAATTAAGATTTATAATATATTATGTACAATTATATATATATTATATATAGTTGTCATATTTAATATAACTGGGTTCAGGACTCTGAACCTTACCTTGGAGCTTTAGAAGAAACATATGTTTATTTTAACGCATGATTTCTTCACTGGTTGGTATTCTCATTGTTTATTCATAG
Seq C2 exon
GTATGTTTCTTGCCGAGCTGATAGAAAAGTATTTCGTGTCCCCTACCCTGTTCCGAGTGATCCGTCTTGCTAGGATTGGCCGAATCCTACGTCTGATCAAAGGAGCAAAGGGGATCCGCACGCTGCTCTTTGCTTTGATGATGTCCCTTCCTGCGTTGTTTAACATCGGCCTCCTACTCTTCCTAGTCATGTTCATCTACGCCATCTTTGGGATGTCCAACTTTGCCTATGTTAAGAGGGAAGTTGGGATCGATGACATGTTCAACTTTGAGACCTTTGGCAACAGCATGATCTGCCTATTCCAAATTACAACCTCTGCTGGCTGGGATGGATTGCTAGCACCCATTCTCAACAGTAAGCCACCCGACTGTGACCCTAATAAAGTTAACCCTGGAAGCTCAGTTAAGGGAGACTGTGGGAACCCATCTGTTGGAATTTTCTTTTTTGTCAGTTACATCATCATATCCTTCCTGGTTGTGGTGAACATGTACATCGCGGTCATCCTGGAGAACTTCAGTGTTGCTACTGAAGAAAGTGCAGAGCCTCTGAGTGAGGATGACTTTGAGATGTTCTATGAGGTTTGGGAGAAGTTTGATCCCGATGCAACTCAGTTCATGGAATTTGAAAAATTATCTCAGTTTGCAGCTGCGCTTGAACCGCCTCTCAATCTGCCACAACCAAACAAACTCCAGCTCATTGCCATGGATTTGCCCATGGTGAGTGGTGACCGGATCCACTGTCTTGATATCTTATTTGCTTTTACAAAGCGGGTTCTAGGAGAGAGTGGAGAGATGGATGCTCTACGAATACAGATGGAAGAGCGATTCATGGCTTCCAATCCTTCCAAGGTCTCCTATCAGCCAATCACTACTACTTTAAAACGAAAACAAGAGGAAGTATCTGCTGTCATTATTCAGCGTGCTTACAGACGCCACCTTTTAAAGCGAACTGTAAAACAAGCTTCCTTTACGTACAATAAAAACAAAATCAAAGGTGGGGCTAATCTTCTTATAAAAGAAGACATGATAATTGACAGAATAAATGAAAACTCTATTACAGAAAAAACTGATCTGACCATGTCCACTGCAGCTTGTCCACCTTCCTATGACCGGGTGACAAAGCCAATTGTGGAAAAACATGAGCAAGAAGGCAAAGATGAAAAAGCCAAAGGGAAATAAATGAAAATAAATAAAAATAATTGGGTGACAAATTGTTTACAGCCTGTGAAGGTGATGTATTTTTATCAACAGGACTCCTTTAGGAGGTCAATGCCAAACTGACTGTTTTTACACAAATCTCCTTAAGGTCAGTGCCTACAATAAGACAGTGACCCCTTGTCAGCAAACTGTGACTCTGTGTAAAGGGGAGATGACCTTGACAGGAGGTTACTGTTCTCACTACCAGCTGACACTGCTGAAGATAAGATGCACAATGGCTAGTCAGACTGTAGGGACCAGTTTCAAGGGGTGCAAACCTGTGATTTTGGGGTTGTTTAACATGAAACACTTTAGTGTAGTAATTGTATCCACTGTTTGCATTTCAACTGCCACATTTGTCACATTTTTATGGAATCTGTTAGTGGATTCATCTTTTTGTTAATCCATGTGTTTATTATATGTGACTATTTTTGTAAACGAAGTTTCTGTTGAGAAATAGGCTAAGGACCTCTATAACAGGTATGCCACCTGGGGGGTATGGCAACCACATGGCCCTCCCAGCTACACAAAGTCGTGGTTTGCATGAGGGCATGCTGCACTTAGAGATCATGCATGAGAAAAAGTCACAAGAAAAACAAATTCTTAAATTTCACCATATTTCTGGGAGGGGTAATTGGGTGATAAGTGGAGGTGCTTTGTTGATCTTGTTTTGCGAAATCCAGCCCCTAGACCAAGTAGATTATTTGTGGGTAGGCCAGTAAATCTTAGCAGGTGCAAACTTCATTCAAATGTTTGGAGTCATAAATGTTATGTTTCTTTTTGTTGTATTAAAAAAAAAACCTGAATAGTGAATATTGCCCCTCACCCTCCACCGCCAGAAGACTGAATTGACCAAAATTACTCTTTATAAATTTCTGCTTTTTCCTGCACTTTGTTTAGCCATCTTCGGCTCTCAGCAAGGTTGACACTGTATATGTTAATGAAATGCTATTTATTATGTAAATAGTCATTTTACCCTGTGGTGCACGTTTGAGCAAACAAATAATGACCTAAGCACAGTATTTATTGCATCAAATATGTACCACAAGAAATGTAGAGTGCAAGCTTTACACAGGTAATAAAATGTATTCTGTACCATTTATAGATAGTTTGGATGCTATCAATGCATGTTTATATTACCATGCTGCTGTATCTGGTTTCTCTCACTGCTCAGAATCTCATTTATGAGAAACCATATGTCAGTGGTAAAGTCAAGGAAATTGTTCAACAGATCTCATTTATTTAAGTCATTAAGCAATAGTTTGCAGCACTTTAACAGCTTTTTGGTTATTTTTACATTTTAAGTGGATAACATATGGTATATAGCCAGACTGTACAGACATGTTTAAAAAAACACACTGCTTAACCTATTAAATATGTGTTTAGAATTTTATAAGCAAATATAAATACTGTAAAAAGTCACTTTATTTTATTTTTCAGCATTATGTACATAAATATGAAGAGGAAATTATCTTCAGGTTGATATCACAATCACTTTTCTTACTTTCTGTCCATAGTACTTTTTCATGAAAGAAATTTGCTAAATAAGACATGAAAACAAGACTGGGTAGTTGTAGATTTCTGCTTTTTAAATTACATTTGCTAATTTTAGATTATTTCACAATTTTAAGGAGCAAAATAGGTTCACGATTCATATCCAAATTATGCTTTGCAATTGGAAAAGGGTTTAAAATTTTATTTATATTTCTGGTAGTACCTGCACTAACTGAATTGAAGGTAGTGCTTATGTTATTTTTGTTCTTTTTTTCTGACTTCGGTTTATGTTTTCATTTCTTTGGAGTAATGCTGCTCTAGATTGTTCTAAATAGAATGTGGGCTTCATAATTTTTTTTTCCACAAAAACAGAGTAGTCAACTTATATAGTCAATTACATCAGGACATTTTGTGTTTCTTACAGAAGCAAACCATAGGCTCCTCTTTTCCTTAAAACTACTTAGATAAACTGTATTCGTGAACTGCATGCTGGAAAATGCTACTATTATGCTAAATAATGCTAACCAACATTTAAAATGTGCAAAACTAATAAAGATTACATTTTTTATTTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144285-SCN1A:NM_001165963:25
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=0.120
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=42.5),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:
ACATGGTCACAATGATGGTGGA
R:
AACAACGCAGGAAGGGACATC
Band lengths:
352-2075
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)