HsaINT0145868 @ hg19
Intron Retention
Gene
ENSG00000007314 | SCN4A
Description
sodium channel, voltage-gated, type IV, alpha subunit [Source:HGNC Symbol;Acc:10591]
Coordinates
chr17:62026753-62029260:-
Coord C1 exon
chr17:62028784-62029260
Coord A exon
chr17:62026889-62028783
Coord C2 exon
chr17:62026753-62026888
Length
1895 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TGACCCTGTGGCCTCCGCAGAAG
3' ss Score
8.68
Exon sequences
Seq C1 exon
GTCCTGAACCTGTTCCTGGCTCTGCTGCTGAGCTCCTTCAGCGCCGACAGTCTGGCAGCCTCGGATGAGGATGGCGAGATGAACAACCTGCAGATTGCCATCGGGCGCATCAAGTTGGGCATCGGCTTTGCCAAGGCCTTCCTCCTGGGGCTGCTGCATGGCAAGATCCTGAGCCCCAAGGACATCATGCTCAGCCTCGGGGAGGCTGACGGGGCCGGGGAGGCTGGAGAGGCGGGGGAGACTGCCCCCGAGGATGAGAAGAAGGAGCCGCCCGAGGAGGACCTGAAGAAGGACAATCACATCCTGAACCACATGGGCCTGGCTGACGGCCCCCCATCCAGCCTCGAGCTGGACCACCTTAACTTCATCAACAACCCCTACCTGACCATACAGGTGCCCATCGCCTCCGAGGAGTCCGACCTGGAGATGCCCACCGAGGAGGAAACCGACACTTTCTCAGAGCCTGAGGATAGCAAG
Seq A exon
GTGAGCCGGGGCTGGGGCTCAGACAGACCCGGCTTCAAATTCTCCTGTGACCTGGAGCAAGCCCTAAGTCCTCTCTGAGCCTCAGTTTCTCCAGCTGTAAAATGGGGGTGGTGCCCTATGGCATTGTTGCAAGCATTATGTGAGACGCTGTATGTAAAGCATGCAGTCCGCGCCCTGTGAGTGGTGGCAGTCACTATCGTTATTGATGTGGTTATTATGATCAACCCTGTCTGTCCAGAAACCCTGATTCCCTCGGACCAGAACACCTGGGCCCCTCTCACCAGCAGGTGGTGCCCTTGGACATGCTGCTTTTACCTGGGCACCGCAGCTCCAGGACCAGGACCTGAGAGGCCTCTCTTACATATTCTCCTCTGGGTTTGAGGCCCCTTGCCCAGTCCTCACACTTATCCTCTATCTCTGTTTAGACCCCACCTGGGTCTGCTCCCAACCTCCCAGTGTGGGCCAAAGTGCCAGATCCAGGCAGGGGATTCAGGAGAGGAGCTAGGGGCCAACGGGAGTTGAGGACAAGGAGGACAGAAGCCTCAGGCAGGAGCCCTGACCCCTCAGCCATGCAGGGGGTGTGCTGCTGGGCTCAGATGCCCCTCCCCACCCCTCCACTGCGAGGTCGAGGAAGGGACAGGAACGCAGCGGTGGTAACCCCCAGCAGCTGAGGCTGAGGCTGAGGCTGACCCTGCCTGGGTCTTGAGCCCCCTTCCCCACTGTCCAGCTCTGGCAGGGAAAGGACTCATACAGGAGCTAGGACGAGGGCCCCTGCCCACCCCTGCACCATCAGCCTGAGCCTAATGAACTTTGCCCTGAAAGCTTTTGACTCCTTATTCCCCCCAAATATGCTGGCTTACCAGGAAGCGAGTGCCTGTGAGCTATAAATACCCAGGCAACTGTGGCACAGACCTCGGTATGAGGCACTCAGGTGGCGGGGGAGCTGGAGAGCACCAAAGTCCCAGGCTCCCCGGGGCCGGGGCCGGGGCCTGGGGACTTGTTCAAGGAGGGCGAGCACAACTCCAAGGGAGATTTAGGGAGTTGAGTGCACAATCGGGGCAAGCAACTCAGTGGATGCCCTGGCTGACCTAACACTCTGTGCCTCAGTTTCCCTTTTAGTCTAATGAAAACAAGGACCCCCACCCCGGCCATGGTGGTTTTCTGGTCACCACTCTGGATACAGAGCTGCCCCCCAAGTTGCCCTCTTCTTCCTTCTCTTCAGAGGCCTCACCCTCAGCCTTGAAGGGGTCCCCTGCCGGGTGGAGTCTGGGGCCGGGAAGCTGGCCTGGCCCAGCAGGAGGAGGTGGGAGGAAGCCTGGCCCGGCTGGAGCACCCGCCTCCCCCACTCCCGCTCCCAACACTGATCAGGTTCCCTTGGCACTGGATGGAGGCTTTGGCTGGGGAACATTTTCCACCCTTTCTGGATTCCTCAGCCAAACAGACCCTGCGGGTGGGAAGGCTCAGACGCTAGGGGCACCACACGCCCATGTTCTGAGGGCTGTGATAGCCTGGCTCCATCCTGACCCCTTTTCATACCCCTGCCCCCTCAGAGCTACCTTCAGGCCCCCCATGCCTCCCAGACCCCCCACTCGGGCCGGGGTCCCCGCCTCCTCCCTTATCTGAGGCCTTCGCATGTGTCCTCATGCCCTTACCGTCCCTTCCCAGGCATCAGCCCCGCCCCACTCCTTATATAAGTGTCATGCGGGCATGACCAGGGCCACCTACGTCCCCGTGGTTCCTCGACCATCCAGGGCTGGATGAATGAATGAATGGATGAGTTTGCTCCTCCCTCTCTTCTTCCCTTCCCTTCTGGTCTCCCATCCTGCCCCATCTGGTAGGAGGATGAGGGGGTCTCTCAGGGACCCAGATGTCATGTGACCCTGTGGCCTCCGCAG
Seq C2 exon
AAGCCGCCGCAGCCTCTCTATGATGGGAACTCGTCCGTCTGCAGCACAGCTGACTACAAGCCCCCCGAGGAGGACCCTGAGGAGCAGGCAGAGGAGAACCCCGAGGGGGAGCAGCCTGAGGAGTGCTTCACTGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000007314-SCN4A:NM_000334:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.484 A=NA C2=0.870
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.0),PF065128=Na_trans_assoc=PU(59.7=84.9)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(19.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCAAGGACATCATGCTCAG
R:
AGACGGACGAGTTCCCATCAT
Band lengths:
344-2239
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)