HsaINT0145856 @ hg38
Intron Retention
Gene
ENSG00000153253 | SCN3A
Description
sodium voltage-gated channel alpha subunit 3 [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr2:165155762-165162371:-
Coord C1 exon
chr2:165162308-165162371
Coord A exon
chr2:165155904-165162307
Coord C2 exon
chr2:165155762-165155903
Length
6404 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGA
5' ss Score
9.21
3' ss Seq
TCCATTTCTCTCTCTTATAGCCA
3' ss Score
10.75
Exon sequences
Seq C1 exon
GTCACTTTTATGTTTTGGATGGGCAAAAAGACCCTTTACTCTGTGGAAATGGCTCAGATGCAGG
Seq A exon
GTAAGAAACATAATATATTTTTTAAGATATAGAACTCTTTGCGAAAAAAAAAAGTAGGTAGGAAAACAACTACATGGTTATATGTGTAGCCTTACCATGTATGCAATAAAGAGCAGTGCTGCTCCCCTAGGAAGTGCCTTGTCTGCCTTACCGGATTGCCACTGGTCCTAAACTCACAGCAATTAAAAATTATCCCTTTGTGAAGACCTTTCCCCAAAATTTCACAGTTAAGATGTTCTTAAATTGATGCTCCAATGTGTGAAGGCCCAGAGTCTGTCTTTGCTGTACATCTATCAGAGCTGTTAGGAAACACAGGAACACAAGATGGGCCCCTTTTTATTGGTGTACATATGTATCAATGGGATGAGTTTTGTCGTGACTGGAAAAGACCCAGACTATAATGTGGTCTTCAGGGTGGAAGCACACTTGGGGAAGTGCTTTGAAATATTTAAGTATTCTTGAAGGAGCATGTATTTCTGTATACAAAGAAGCCAAGGGTGCATGTGTGCCAAAGGCATGTCCAAGTATCAGTTGACATAATGAATAGTTCTTTTAGGCCACACGTTACAACAAAAGATGCCATAATATCTTAGTCATGCTGTTATTCTCTAACCCTTAAATATTTTCCTAAGAGTATTGTAAGTTAATTTTAAATCAAAATAGGGAATTTTTTAAGAGCTGAGAGATAGCAATAGTAAGTGACTCTTAGGACACGGAACTTAAATATATTTTGAGTCATCCTTTAAAAAGGGAAACTGGTGTAGCCATAAAAATCTAAGAGAGTTAATGAAAATGTATACTAGTCATATAAATAGAGCTTTGGGGAATTTTTTTTCCTGACAGTTTTCCTAGCCTTATTATGAATGTAGGGGGTAAGAGCATAGGTTGTAGAGTTCATGTATACCAGGGTTCAAATCCTAACTTCACCACTTGTAAGCTCTTTGACCTTGGAAAAGTGTCCTAAGCTCTCTGTACCTTAGTTTACTCATCGTTAAAATGGAGAGAGTAATATTCTGTCCCTTTAATAGTTGTGATGATTAATGATTTAATACACATAAAGTATTTGAACTATCACATGGACAATTGTAAGAATTTATTGTATGTACCAGCCTAAGCAACAAAGCAAGACCCTACCTCTACAAAACAAAAAAAAAAAAAAAAAAAAAAAAAGAAAGAAAGAAAAAAAAGAAAAGAAAAGAAGAAGAAAAAAAGAAAAACTTAGCCAGGCATTGTGATGCACACGTGTAGTCCTAACTTCTCAGGGGGCTAAAGTAGAAGGATTGCTTGAGCCTAGGAATTCCAAGCCACAGTGAGCTATGATCATGCCACTGCACTCCAGCCTAGGTGATAGGCTGTCTCTGAAAAATGGCTGGGAGCGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAAGCAGAGGCAGGGGGATTACTTGAGGCCAGGAGATCTAGACCAGCCTGGCCAACATGGCGAAACCTTGTCTCTACTACAAAATGCAAAAATTAGCTGGGTGTGGTGGGGCACACCTGTATCTCAGCTACTCTGGAGGCTGAGGCACAATAATCTCTTAAACGTGAAAGATGGAGGTAGCAGTGAGCTGAGATGGCACCACTACACTCCAGCCTGGATGACAAAGCGAGACCCTGTCCCCCCAAAAAATTTTTTTAATAAATTTAAAAAAAAAGCACACTCTAAAAAAAGAAAAGAATTTATTGCCTATTAACTATTATTTATTATGATGATGATTAACATAAAAGCCCAGATAAAATTTTGGATAAATTTGGTTAATACATACTTTATTCCTATTAAACCATAATAATCTATTCCCCTTAATGAATTCCTATTATGGCTTAAGTAATTTACATCAACAGTCCCCAGCCTTTTTGGCACCAGGGACTGTTTTGTGGAAGACAATTTTTCCACCGACCAAGGGTGGTGGTGGGAAATGATTTCAGGATGATTCAAGCACGTTACATTTATTGTGTACATTATTTATATTATTAGCATACTGTAATATATAATGAAATAATTGTACAAGTCACCATAATGTAGAATCAGTGGGAGCCTGATCTCAAATGATTCACCTGCCTCGGCCTCCCAAAGTGCTGGGGATTACAGGCATGAGCCACTGCGCCTGGCCATTGGTGATGAGATTTTTGTTTTTGTTTTTGTTTTTTTTTGAGACGGAGTTTAGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGTTCCGCCTCCCGGGTTCAAGCTATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACCACAGGCGCCCGCCACCACGCCCGGCTAATTTTGTATTCTTAATAGATACCAGGTTTCACCATGTTAGCCAGGATGGTCTCAATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGAGTGAGCCAGGTGATGAGTTTTAAATACAAAACCATTTTGTATTTAAGCGGCACATTCCATTAAAGAAATAAATGATTTGTATTTTATTAAAATTAAAAGCTGCTGTTTTACAAAGATATTCTTAAGAGAATGAAAAGACAAACCAGCAACTGGAAGACAATATTTGCAAAGCACATATCTGATTTAAAAAAAAAAAAAAAAAGACTGGGGCTAGGTGAAGTAGCTCATTCCTGTAATCCAGCACTTTGGGAAGCTGAGAGGGGAAGATCATTTGAGCCCAAGAGTTTGAGACTGGCCTGGGCAGCATAGGGAGACACTGTTTCTCCAAAAAATAAAAATAAAAAAATTAGCCAGGCATGGTGTAGTGTATCTGTGGTACCAGCTACTCAGGAGGCTGAGGCAGAAGGATTACTTGAGCCTGGGAGGTCGAGGCTGCAGTGAGCCATGATCAGACCACTGCACTATAGCCTGGGCAACAGAATTATACCCTGTCTCAAAAGAAAACAAAACAAAACAAAACAACAAACCAGTGTCCAGAATATCTAAAGAACTCTTAAAACTCAACAATAAGAAAACAAATGACCCAATTTAAAACTGGCAAAAGATCTGAACAGATACCCCACACGAGTATATAGTACAGGTGGTTATTAAGGAGGTAAAAAGGCACTCGACATCATTTGTCATTAGGGAATTGCAAACTAAAACAACAAGGAGTTACCACTGCACATCTGTTAGAATGACTGAAAAATGTATCTGGCAATACCAACTTCTGATGAGGATGCAGAATAACAGGAACTCTTGCTTATTGCTGGTGGGAATGCAAAACTAGACAACCGCCTTGGAAGACAGTTTGGCGGTTTCTTACAAAATAAACATAGTCTTACCATATGATCCAACAACTGCACTTCTAGGTATTTAGCTGATCAATTTGAAAACTTATGTCTTCACAAAAAACCTGCATGTGAATATTTATAGCAGCTGTATTCATAATGACCCCAAACTGGAAGTAACCAAGATGCCCTTCAATGACCCCAAACTGGAAGCAACCAAGATGTCCTTCAATAGTTGTATAGATAAATAAATTGTTATGCCCATACAATAAAATATTACTGAGTGATTAAAAAGAAATGAGCTATCAAGATACAAACAAATATTAATGAATATTAAATGCACATTTCTAAGTGAGAAAAAGCCAACCTCAAAAAGCTACATACTGTATGATTTCAATTACCTGACATTCTAGAAAACACAAAGCAACAGAGATGATAAGAAAATAGTGTTTTCCAGGGGTTCATGGTGAGGGATTATCTAGGTAAAGCAAAGGGGATTTTTTTTTAGGGTGAGAACCTGTTCTCTAAGATTCTATAATGGTGAATATGAAACTTAATGCATTTGTTAAAACTCATAGACCTTTATAACACAAAGAGTGAATCTTAATATATACAAATTAAAAAAAAAATCTTTTGTGAGGTTTGGGGATCCCAGGAAGAAATGGAATATGTGACAAAAATATATACATGTATTGCAAAATATGAAATGACCTCACTGTAGGTGGTGGGGTAATAACATGCTAACCTAAGTAACTTTGGAAATGAGTGGAGTCTGTAAGACTAAAGGTAAAAGGAACAATACCCTAGTTGATAAAGTTGTTTCCAATGGTAGTATAGATTAACAATCCTGAAACCACTGTGCATGTGTACCAGTACTGAGCAATTACAAACATGTGTATCTCCTTGTTCTGTCAGCTGAGAGGGCCTAGAAGCAATGACACCCCAGTAGCAACAAACACAGCTAGCACTCAGATCTTGGTTTCTAATACCATTTTCCAATAAAAAGAACTAGGGCTCCTTGGAGAAATGGTTGATTCTAGGACTGCGGCAGAAATTATAAAAGATGAGCCTGGAGCATCTGATAGTACCTAAAACTAAGAAAGTGTTAAAAAACAAAAAAAAATGCAACCCACAACCATGGTGTATGTCAAACTGTTACAGGTGTCAACTGAAAGAGCTTCCAGTGGCCAAAGATGAAGCCATTTGAACAAATAAATGAAATATCATTGAATTGTAATCCAAAATATAAAATGACTATCCATGACTACATGTTAATTGAAATGATTGAATAATTAAATAAAATATGAATGGACAAATATCCTATGCAGAATAATTTCAAATAATTTTGGTATATACTTAAGATCATAACTGCGGGTTCCTTAAATGTGGTCTGTACACAGTGACTTTATTTCAAAGAGCACATATGGAAAAGGAAGAAAAGGGAGTAAATTTACAGTAGAGAAACCTAACACTACCTCAAGACAGGTGGTGAAAGTTAACATCAAGAGTGATAAGTCATAGTGAGTGATAAGTATGTACCCTTGGCATGATGTGATGTGATGACAGTGACATTTTACCTCTGTAGTCTTCCACCCAAAAATCCATAACCTAAATATAATCATGAGACAAACATTAGACAAATCCCAATTGAAGGGTATTCTATAAAATATCTGACCAGTAATCCTCAAAACTGTTGTGGTCATCAAAAACAAGGGAAGTCTGAGAGATTGTCACAGCCAAGAGGAGCCTAAAAAGACATAACTACTAAATGCGATGTGTATCCTGAATGGGATCCTGGAACAAAAAAAGGACATTAAGAAAAAAACTGAGGGCTGGGCACGGTGGCTCTCGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCGGATCACGAGGTCAGGAGATGGAGACCATCCTGGCTAACACTGTGAAACCCTGTCTCCACTAAAAATACAAAAAATTAGCTGGGCGTGATGGCAGGCACCTGTAGTCCCAGCTATTTGGGAGGCTGAGGCAGGAGAATGGTGTGAACCTGGGAGGCGGAGCTTGCATTGAGCCGAGATTGCACCACTGCACTCCAGCTTGGGCGACAGAACGAGACTACATCTCAAAACAAAACAAAAAAAAAGAAAAAAACTGATGAAATCTGAATAAAATAGTAACTTTAGGTAATAATAATGTATTAAGGCTGGGTGCGGTGGCTCGCACCTGTAATCCCAGTACTTCAGGAGGCCAAGGCAGGAGATTGCTTGAGCCCAGAAGTTTCAGACCAGCCTGGGCAGCGTAGCAAGATCCCATCTCAATTAAATAATAACAATATATCAATATTGAAAATGGCATGGAATGTATGAAGCCTGTACTATCCTCATACTTTTTCTGTAAATAAAAAATTGTTATAAATATTAACTTTATTTTAGAAAATTCTACAAAACCAGCTAATGAAATGGTTGATTCCCCACTCTTTGTCTGTTTTCTGGCTTTTAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGTCAGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAATGGCACAATATCGGCTCACTGCAAGCTCCACCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCACCCACCACAACGCCCAGCTAATTGTTTTTTTTTTGTATTTTTAGTAGAGATGGAGTTTCACTGTGTTAGCCAGGATAGTCTCGATCTCCTGACCTTATGATCCGCCCGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCACCCGGCCTTAATTTTTAACTATTGATTCTTGCCACTTTGTAAAGAGTAGAAATATGGTAATGTCAGAGCCAAAAGTGTGTGGTTGCTAGCTTTCTGCCATTCTAAATGTCCGTAAATATTTATTTGCATCTAAATTTTCTATCGGTCTTCCTAGTGAATTTCATCTGATAAGTTTCACGGTGGGCAATCACCTAAAGTGTTCTGGAAATTAAAGCAAGATAATTCGTCACAGATAGCAGCTTTGGGTTTTGAAAATTCCTATAAGTCAAATAAATTGAAATTGCTGTAATTTCTAAACTGACCCTACCTCCATTTCTCTCTCTTATAG
Seq C2 exon
CCAGTGTCCAGAAGGATACATCTGTGTGAAGGCTGGTCGAAACCCCAACTATGGCTACACAAGCTTTGACACCTTTAGCTGGGCTTTCCTGTCTCTATTTCGACTCATGACTCAAGACTACTGGGAAAATCTTTACCAGTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000153253:ENST00000283254:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(7.8=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(17.5=100)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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