HsaINT0145786 @ hg38
Intron Retention
Gene
ENSG00000144285 | SCN1A
Description
sodium voltage-gated channel alpha subunit 1 [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr2:165989160-165994416:-
Coord C1 exon
chr2:165994146-165994416
Coord A exon
chr2:165992423-165994145
Coord C2 exon
chr2:165989160-165992422
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:ENST00000303395:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.118
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=42.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
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