HsaINT0145878 @ hg38
Intron Retention
Gene
ENSG00000007314 | SCN4A
Description
sodium voltage-gated channel alpha subunit 4 [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr17:63938554-63943096:-
Coord C1 exon
chr17:63942826-63943096
Coord A exon
chr17:63941994-63942825
Coord C2 exon
chr17:63938554-63941993
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:ENST00000435607:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.260
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=40.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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