HsaINT0145934 @ hg19
Intron Retention
Gene
ENSG00000136546 | SCN7A
Description
sodium channel, voltage-gated, type VII, alpha subunit [Source:HGNC Symbol;Acc:10594]
Coordinates
chr2:167261539-167266445:-
Coord C1 exon
chr2:167266175-167266445
Coord A exon
chr2:167263157-167266174
Coord C2 exon
chr2:167261539-167263156
Length
3018 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TTTATCTTTCCCACCCCCAGGAC
3' ss Score
11.62
Exon sequences
Seq C1 exon
AACAAGCTCCAAGGATTCATCTTTGATGTGGTAACAAGCCAAGCTTTTAATGTCATTGTTATGGTTCTTATATGTTTCCAAGCAATAGCCATGATGATAGACACTGATGTTCAGAGTCTACAAATGTCCATTGCTCTCTACTGGATTAACTCAATTTTTGTTATGCTATATACTATGGAATGTATACTGAAGCTCATCGCTTTCCGTTGTTTTTATTTCACCATTGCGTGGAACATTTTTGATTTTATGGTGGTTATTTTCTCCATCACAG
Seq A exon
GTAAGATTTTGTTTAGTCAAATTTTTACTGATAATAATATTAATTCAAGTAAGCTCTTACAGTAAATATGAAATATAGTCTCCTACATTTCAAAATCATGAAATATAGTCTCCTAATAAGCAAAACAGGTAGAGATCTTTTTTTATTTTCAACAGGAATGCTTCACATTTGTATTCATATGTGTACCACCCATGCCTAATAGAGATAAGATGTTCAAAAATATTTCTAATAACATAGACTTTGCATACAAGCCACCAGGTGAATGTTTAGTCAACCCTTCATTCTATAATATACACTAATTTTCTAGATGACACTAGAAAGACGTTTATGTCTTAGAATGATGTAATCTTTCAGGTTCACTATTATTTCCTTCCCTCTAATCTCTAAAACTATTTACAACTTATACAACATTAGAGTTTCAGGCTTTAACAAATTTGTTGCTTGTTTTCTCTTACTTTGGAGATCTCTCTCTTATTTAATAAATACACTTGATAATTCTCTTTGAGAATAAAGACTGTTATATGCAAAAAATTCAGTAGTAAACAAGACAAGTATAATTTCTGTGTACACATAGCTTAGAGTCTATTAAAGGATATAGATAATTAAACAGTACATTTTAATGTGTGCTATTAAGGTTATGGTAGGGAAGTCACAGGGTGCTGCAGCAACACAGCAGAAGGAGGTCACCTAATCAGTAAGTAGAGGTCAGAGAAAACTTTATGGAAGACGTGAAATCTAATTAGAGACTTTTCAGATAAGGAGATAGCCAAGCAAAGAATTTAGTGTCAAAGAGTTTCAGGCAGAGAGAAGTTTGTCTGTTTCCACATAACACACATATTAGGGTGTAAGTTCCATGAGAGTAGGAACAATATTTAAGTTTACTGCATCAAGCACTATTCTATGCATTGAGTAGTAGAAAATATAGATAAACTGTTTGCCCAGATCTGCTTCCAAATATTCACTCATTCAGTTGATAGTGGAAACAATGCAACTAACTACTGAAAAAAACCGTAAGAAGCTTCAGAAAAGAAGAAGCTATCAGAAAAACTGATAGAAAAGTACATGAAGACAAGAGGGAGCTGATAGGAAGAAGGCAGAGAAATGATGGAATTAGGGTCCTATGAGACTGAAGGGGACTTCATCAGAGAACTGGAAGGAAAAGCAATTGCAGTCAGAGAGAAAGCAGTTTGAATTTGCAGTTTCAGAAGGCAAGGTATCTTGGGTCCAGAATGTGATTATAAATGTAGATTTGTAAAATGATGGAAGAGAGTGTAATAACTTGAGAAGACCAAAGACAGAAACCGGCTTTTAAATGGATTGTTGATGGTAGGTGCTAAGGTGAAATGAGAGACAGTGAGTCAATTATTGAAGTCTTCAATGAATGTGAATGAAGAATGAGTAGGCTATAGAGCCAAGGAATGGTAGGAAATGATATAGCTGAATGGCATGATCCACAAAGTGTCAAAAATCTCTTTTATTTTTTCTTTATAAAAATAATAGGAAGGAAAAGTGACCAGAAATCACATTGGAAAGAAAGAAAGATACCTATTTTTTCTTTCTAACCTGAGGAAAGTGGAGTGGGGAAGAATGAGCTCCCTGTATTTGAGAGGGTTGCAAGGGAAATAGAGTCTTCAAGATAGAGCCAGATTTAGCCATCATCCTCTGAAAACTGAAACAGGAACAGAAATCCAAACACCACATATTCTCACTTATAAGTGGGAGTTGAACAATGAGAACACATGGACACAGAAAGGGGAACAACACACACCAGGGCTTGTTGGAGGGTGGGGCGTGAGGGGAAGGAACTTAGAGGACAGGTCGATAGGTGCAGCAAACCACCATGGCACATGTATACCTGTGTAACAAACCTGCATGTTCTGCACATGTATCCTGGTGGGTTTTTTTTAGAAGAAATAAAAACAAAGATTAAAAAAAGAACTTCCCCCCAAAAAAGAGACTGGGTTAAAAAAAAATTAGTGATGAGAATGTAGAGGAATTTATTCACAATTTAGTGATACTTCCTGCATAATGAAAAAGTTTGGAAGGTTGAAGGGAAATGAGAATTTGGGTCAGAGTAGAAGATTCACTAAAGCACTATAGAGATAGGGTATTGATAGGATAGAACATCAGAGAGAAATATCATCTTAGGCAGAGACCAAGTTTAACAAAAATGTGAGACATGATTCCTCCAGATTCAACAAACCTACCATATCACTTAGAAGCCTCGTGGGATTCCTTCTTCCACTACCTTCTCAACTCAAAATAAACTACATTCTCTCTAATACTTCCAGAGAACATCTCTTATACCTTTAATGAATTATAATTCTACCTTGTTTTATAGTTCTTGTGTTAATCACTGCCATACTTCCCTCATCTAACTACCACAGCTACAAAAAAGTTCTAAACAAAGACTTATTTATTCAATTCACATTTAAAGTTCCTGGAGCCCCAGTACTATTTATGAAATAAGGAAATTAAATTACAATCTATGAATCACTGAATGCCAGACATTTCTGTAATTATATTTATCAATTTCTGTCTTATAATTATTTTAAATGTCTGTCACTATTTTCTAAATTATAAGGTTCCTGAAGACAGAAATCATGTCATTCATCTTTGTATATTGGTGTGATATATTTATTGGGCATTCAATAAAGATTGCATGGAACTAAGTTTCTTAATCCAATAGCAATAAAAAATTATGACTATTGTCCTACATTATAGAATCAGGTCATCTGTAATTCCAGAACTACTTGATCTGTAATACTCTTAGATGATGTTACAGAAAAATAATCTTCCAAATTTAGCTAGATACCCTGAGCATTGATACAATAGGTGTTTGGCTGACCCAAACTTTCAACATGCTAACTGTTAAATGAGAATGATTAGTAAAATGGAAGGGATCAATAAAGGATTAATAAAACAGGGAAAAACAATTAAGTGTAAAATAATTTATAGTCCTCAAAATACTATTGTGTTTGAATAATGTATAGCCTGCTTTATCTTTCCCACCCCCAG
Seq C2 exon
GACTATGTCTGCCTATGACAGTAGGATCCTACCTTGTGCCTCCTTCACTTGTGCAACTGATACTTCTCTCACGGATCATTCACATGCTGCGTCTTGGAAAAGGACCAAAGGTGTTTCATAATCTGATGCTTCCTTTGATGCTGTCCCTCCCAGCATTATTGAACATCATTCTTCTCATCTTCCTGGTCATGTTCATCTATGCCGTATTTGGAATGTATAATTTTGCCTATGTTAAAAAAGAAGCTGGAATTAATGATGTGTCTAATTTTGAAACCTTTGGCAACAGTATGCTCTGTCTTTTTCAAGTTGCAATATTTGCTGGTTGGGATGGGATGCTTGATGCAATTTTCAACAGTAAATGGTCTGACTGTGATCCTGATAAAATTAACCCTGGGACTCAAGTTAGAGGAGATTGTGGGAACCCCTCTGTTGGGATTTTTTATTTTGTCAGTTATATCCTCATATCATGGCTGATCATTGTAAATATGTACATTGTTGTTGTCATGGAGTTTTTAAATATTGCTTCTAAGAAGAAAAACAAGACCTTGAGTGAAGATGATTTTAGGAAATTCTTTCAGGTATGGAAAAGGTTTGATCCTGATAGGACCCAGTACATAGACTCTAGCAAGCTTTCAGATTTTGCAGCTGCTCTTGATCCTCCTCTTTTCATGGCAAAACCAAACAAGGGCCAGCTCATTGCTTTGGACCTCCCCATGGCTGTTGGGGACAGAATTCATTGCCTCGATATCTTACTTGCTTTTACAAAGAGAGTTATGGGTCAAGATGTGAGGATGGAGAAAGTTGTTTCAGAAATAGAATCAGGGTTTTTGTTAGCCAACCCTTTTAAGATCACATGTGAGCCAATTACGACTACTTTGAAACGAAAACAAGAGGCAGTTTCAGCAACCATCATTCAACGTGCTTATAAAAATTACCGCTTGAGGCGAAATGACAAAAATACATCAGATATTCATATGATAGATGGTGACAGAGATGTTCATGCTACTAAAGAAGGTGCCTATTTTGACAAAGCTAAGGAAAAGTCACCTATTCAAAGCCAGATCTAATACCACTTACCACCTCTTTTCATATTTCTTCACATATCTGAAAAATGTTGAAAGCCTAAGCCAGGAATAAAAGAAAAGTAGAGATAATAATCAGTTCTTTACAACCGATGGTAATTAAGCTTGTATTCACAAGACTTCATGCCAAATTCACTTTTTAGCATTATATCTAACAAATCAAGAGAATCCTTAATATTGCTGCAGTGAGTTTAAAGTGGGTTAAAGTGGCCATTTGACAATCTCATATTTGTTTTCTCTACATGGCTTATATGATGTGTGCCTTCTAGGGAATGAAGGGAAGTGGTGATAGAGATCAGCAGCAGCAGGGGCTTTCTTTTATATTTTATGTATAATTTAATGGGCTTTAAGTCACCACTATTAAGACTTACAAATAAGCAAATACTTTCCTGATGTGGGATGGTGAAATGCTAATGGCCATTAAATCATAAACTTGCCTAGACAAAAGCCAATTGGAAGAAGGGAGAGAGCAGTTCTTTAGAAAGTGCCTTTGAGATCAACCTCAGAGATTCTTGGGCTGATTAAAACTGCATTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136546-SCN7A:NM_002976:24
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=0.045
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=46.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
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
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)