HsaINT0145878 @ hg19
Intron Retention
Gene
ENSG00000007314 | SCN4A
Description
sodium channel, voltage-gated, type IV, alpha subunit [Source:HGNC Symbol;Acc:10591]
Coordinates
chr17:62015914-62020456:-
Coord C1 exon
chr17:62020186-62020456
Coord A exon
chr17:62019354-62020185
Coord C2 exon
chr17:62015914-62019353
Length
832 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGC
5' ss Score
7.23
3' ss Seq
TCACTAGCTTCTCCCCGCAGGCC
3' ss Score
10.45
Exon sequences
Seq C1 exon
AACAAGATCCAGGGCATGGTGTATGACCTCGTGACGAAGCAGGCCTTCGACATCACCATCATGATCCTCATCTGCCTCAACATGGTCACCATGATGGTGGAGACAGACAACCAGAGCCAGCTCAAGGTGGACATCCTGTACAACATCAACATGATCTTCATCATCATCTTCACAGGGGAGTGCGTGCTCAAGATGCTCGCCCTGCGCCAGTACTACTTCACCGTTGGCTGGAACATCTTTGACTTCGTGGTCGTCATCCTGTCCATTGTGG
Seq A exon
GTGAGCGGGGCGGGCTGGACCGGCAGGGCAGCACTGAGCTGAGGCACTCGGGAAGACCCATCCTCACACGGACACACCTGCCCCTGCACCCTCACACGCTCACCCAGACACATGCCTGTGCGTGCCTGCCATTCACTCTCAATGCACAAAGGCACATGGTGTGCACACAGGCAGATCGTCACCCGCGCACACATGGATGCACCTCAGGACACACAACTGACCAGAAGACGTGCACTCAGGTGCCCACATACTGAGCGAAAAGTGTAAAAGATGGTTCCATGTCTGTGTGCACTGAGAAGTGCACAGTCATGCGTGTGCTTATGATAGAAAGTAGCTGCCATTTATTATCAACTGTGCTGTGCGCTTGACAGGTGTTATCTCACCTGTTGTTCATAACAATGTCATGATCAGGAACTGTTGTTCCCATTTTACAGGTAAGGAAATTGAGGCACAAACAAGTGAAGTGGAGACCCAGAGTCACGCAGCTGTTCTGTCTCCCTCTCTCTCTGTCTCTCTCTCTCTGTCTCTTTCACACACACACACACACACACACACACACACACACACCAGTGGCATTTGCAAACAGCCTTGGGAATGGGCCTTACACTCCCCCACTTCAGGGTATCCCACCTCCAGTTCCATCAAGACAAAGCTGCAGCCCCTGGCCCCAAGACCCGTGGGAGAGCCCAGCCTCACCTGTCAGTCATCTGGGCTGTGCTCTGAGACTTGAGCAGAGCACACCAGGCCGGGCCCCCTGAGCCCCGCATGCTCCCCACACCCTGTGCCGGCCCCCCTCCCCAGTGGCAGCGTCCTCACTAGCTTCTCCCCGCAG
Seq C2 exon
GCCTTGCCCTCTCTGACCTGATCCAGAAGTACTTCGTGTCACCCACGCTGTTCCGTGTGATCCGCCTGGCGCGGATTGGGCGTGTCCTGCGGCTGATCCGCGGGGCCAAGGGCATCCGGACGCTGCTGTTCGCCCTCATGATGTCGCTGCCTGCCCTCTTCAACATCGGCCTCCTCCTCTTCCTGGTCATGTTCATCTACTCCATCTTCGGCATGTCCAACTTTGCCTACGTCAAGAAGGAGTCGGGCATCGATGATATGTTCAACTTCGAGACCTTCGGCAACAGCATCATCTGCCTGTTCGAGATCACCACGTCGGCCGGCTGGGACGGGCTCCTCAACCCCATCCTCAACAGCGGGCCCCCAGACTGTGACCCCAACCTGGAGAACCCGGGCACCAGTGTCAAGGGTGACTGCGGCAACCCCTCCATCGGCATCTGCTTCTTCTGCAGCTATATCATCATCTCCTTCCTCATCGTGGTCAACATGTACATCGCCATCATCCTGGAGAACTTCAATGTGGCCACAGAGGAGAGCAGCGAGCCCCTTGGTGAAGATGACTTTGAGATGTTCTACGAGACATGGGAGAAGTTCGACCCCGACGCCACCCAGTTCATCGCCTACAGCCGCCTCTCAGACTTCGTGGACACCCTGCAGGAACCGCTGAGGATTGCCAAGCCCAACAAGATCAAGCTCATCACACTGGACTTGCCCATGGTGCCAGGGGACAAGATCCACTGCCTGGACATCCTCTTTGCCCTGACCAAAGAGGTCCTGGGTGACTCTGGGGAAATGGACGCCCTCAAGCAGACCATGGAGGAGAAGTTCATGGCAGCCAACCCCTCCAAGGTGTCCTACGAGCCCATCACCACCACCCTCAAGAGGAAGCACGAGGAGGTGTGCGCCATCAAGATCCAGAGGGCCTACCGCCGGCACCTGCTACAGCGCTCCATGAAGCAGGCATCCTACATGTACCGCCACAGCCACGACGGCAGCGGGGATGACGCCCCTGAGAAGGAGGGGCTGCTTGCCAACACCATGAGCAAGATGTATGGCCACGAGAATGGGAACAGCAGCTCGCCAAGCCCGGAGGAGAAGGGCGAGGCAGGGGACGCCGGACCCACTATGGGGCTGATGCCCATCAGCCCCTCAGACACTGCCTGGCCTCCCGCCCCTCCCCCAGGGCAGACTGTGCGCCCAGGTGTCAAGGAGTCTCTTGTCTAGCAGGCAGCATCGGGGTGGCCCACTGAGTCTCGGCATAGTCCCCAGAGCTCCCCCGTGGTGCCTGCACACAGAGTGAGGGAGGAGGGCTTTGAATCTGGGACTGTGCCTGGCTCCCTGATGGGGGACAGGATTTGGCCACACTGGGGCTGACACCCAGGCCCGAGCGCCTGCGTTCCCAGACCATGGGAAATGGGAATTGCGCTCAGGGGCTCCATGCTGGGTCTGAGGCCCCTGCCTCCAAGATTTAACCTGCAAGTTGCTCTGACCTCCTCTGGGCCCTGTCGCCCCTCCTTTTGGCCTGGGGGAGGTCAGAACATTCGAATCTCTGCCCCTCACTTGAGGAGGAGCTGGCCTGCGGTGGAGGGATCAGTTGCCCCCCATCACCAGAGTCTTAAGGGTCACTGGCCTCTCCCCAGGAAGTGGCTCAGACCCCTCAGCCCCAGCCCAGACAAAGATGTCTTAACCTCAGGGAGTGCAGACACCTAACCCCAGGGCACTGCCAGCCCACCCCCTTTGACTCTGGGGTGCAGCTTCACCCACCAGGCCAGCTCAGGAATTCCCTGGAAAAGGGAAATGTGACTGGTTCAGAAATAGCTCCTCAAAGCCTCAAAACCTGATTGGCCACTGGATCCTGCTGCTTTGGGCTGGGATGGTGACTCCTGAAACCTCTTCCTAGGCCACGTCCAGGTCCGTAGCTCCCCTGGCTGGCTCCTAGGGGAAGAGCAGAAGGAAGGATGCCACTTGGGAATGAATTGTCCTTTTCTAGGAAGCACGGGGGAGTGAGACAGGCTGGGTCCTGCCAGCTGGATCGCTGCACATGGCCTGAGCATCCAGACCTGAGCGGGAGTCAGGGACCTGCTGCTCAGTAAGAAGATTCTCGCCCCTTCCCTCTCTCCCTGCCTCACTCCTCCGTGAGCACCACCAGGGCTCCAGGAGCCTCATCCAGCCTCAGAGATCTCCCTTCTCATCTCCCCACGCCCGTCTCTTTCTCACCTTTCCCACCTCTCTCCCCAAAGTGATCCTAAGAATGTACAGTTGAGCTCAGGTTAGATATTTCGACCCTGGGGCGTGCAGCAGGGAAGGCCCAACTGGTTCAGGCTCAACCTTCCAACTTCCTGTGGCCTGAAGAAGCACTTCTGCTGCATCGCTGTTCTGGGCATGGCAGGGCCAGGCCTCTGCTGGCTCAGGAGGAGGGGTGAGAGACCTGCTCAGGCGTCGCTGGATTTATTCACTTGTGTGTGTACCTGTGGCTGTGTGTCTGCTTGTATGCTTTTATAGGCCTGTGTGTATAGCTGTGTGTGTGTTCAAGTGCGTGACTGTATGTGTGTGTGTGAACCACTGTGTACTGGAGCCTGCATTATGCACGTGTCTGGGTATCTTTGTATATATGTGTATATATGTGTGCCCTGGACTGTTTCAAGGTCCATGGAGTACGGCTGGTGTGTCATACTGTGCAGGCCTGTCCCTGGGAGTGTTCCCGTGCCTGGGAGAGTGGACCTGTGCTGTGAGTGTGTGGATGCGTGTGAACGCATGTGGTAAGGTGTGTACTCAGGGCATTCTGTTGGCCTAAGTGCCTCTTCTTTTTCTTCTTGTTTCTCATGAAAAGTTTGATTAAAATTCAGGAAGCAGCAAAACCTTCAAAACAAGACATGTATGTGTGCTTGAGTGTGTGAACACGTGTGTGTGTGTGCACATCTACATGCCATGCCTATGGGCCAGAGTTGTCTTTATTGTCCACCATGCTCTCTCACCTGCTCCCAGTCCTGCCTGAACAGCCCTCTCTCTCACTCCCCTCTCCTCCCCTTCCTGTTTCTCGTTGTCACACCCATGGCCTCAGCCCTGCTCCCTGCCTCCTGCCTATGTCTCCTCTATGGAAGGAGGCCTCCACTCCTTCCATCTCTTCCTTCAGAAGTTTCGTCTAATGGGGGCAGTCTCCCCTTCCTGGCACATTGCCCCTCTGCCTTGCCCTCCTGGGCCCTGGGCTGGCACAGCCCCTGGAGCCTCAGAAATCTGTTTGATTGGATATTCTCCTCGGACTGTGTGCAGGTTGCAGAGGAAGAGTAGATGAGCCGGGTCCGGCCTCTCCCTGCCTGTGGCCCCTCCCCTGCAGACGGATGCCCATTCCTGCCTGGTCCAGTGGGGAACAGGTCCCACGCCAGGCCAGCAGGCGGGCTCCTTTGTACAGTTCTTACAATAAACCCTCCTTGGTGCCTCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000007314-SCN4A:NM_000334:23
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=0.260
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=40.9),PF0061222=IQ=WD(100=5.1)
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:
TGACTTCGTGGTCGTCATCCT
R:
GTGGTGATCTCGAACAGGCAG
Band lengths:
345-1177
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)