HsaINT0145784 @ hg19
Intron Retention
Gene
ENSG00000144285 | SCN1A
Description
sodium channel, voltage-gated, type I, alpha subunit [Source:HGNC Symbol;Acc:10585]
Coordinates
chr2:166852523-166854685:-
Coord C1 exon
chr2:166854548-166854685
Coord A exon
chr2:166852628-166854547
Coord C2 exon
chr2:166852523-166852627
Length
1920 bp
Sequences
Splice sites
5' ss Seq
AAGATAAGT
5' ss Score
2.82
3' ss Seq
TTGATTTTTCTTTTCTATACTTT
3' ss Score
0.52
Exon sequences
Seq C1 exon
GTGGAACTCCAGCCTAAGTATGAAGAAAGTCTGTACATGTATCTTTACTTTGTTATTTTCATCATCTTTGGGTCCTTCTTCACCTTGAACCTGTTTATTGGTGTCATCATAGATAATTTCAACCAGCAGAAAAAGAAG
Seq A exon
ATAAGTATTTCTAATATTTTCTCTCCCACTGAGATAGAAAATTATTCCTTGGAGTGTTTTCTCTGCCAAATGAGTACTTGAATTTAGAAACAAAATGGGAGTATATATTATAACTGATTTTTCCTTCCTCTTCCTCTGTCATTCACTATCCATATATTTCCGGCTATAGAAAGCTAAGAATAACTGTGTTCCACACTCTTGTTCATAGGTTCATAAAGTTTTTCCTCCTCTTATTCATTATCAAGAAACATTTTCTATCTTTTAAAAAATAATAATTAGAATAAAACTAGAAAGCAACCGAATATGCCTCTTTCCCAAAAGCAATTTGTTACTTTATCCCTACAACTACCCACTCCCCCTTGAAAATATATTTTCCAACTAATTCTTTGCAATAAATTAGGCACTGGATGTAAGCTTCTTCTAGTGTTTATTTTTACGCTTTTTTCTGTCATTGATTTCTTTTATATATTCCCATTTCTTTCTCCAAGATATTTAAATACAAGCTATCCGTTTCAGTCTTGAATTGTATGACTATTATTTATCATTTATAAGGCTCATTTGATTGTCCCAATTACCTATGTACATTATAGAACATATGGAAAGTAAATAAATATCATCACTTGGAAGTAACTGCTGCCATTCACATTTTGTTTTCTGTTCAGAGTATTTCTGCACATACTCTTATTGTTGTACTTTTTATCTATAATTATAAATTCCACTTTAGACTTAACATAAGTATTTTCTCATTTTGTTAAGTCTTCATATATGCATTATCATAATTTACTTATTCATTCCCCAGTAGGTTGATAATTTAGATTGTTTTTAATCTTTAATGATTTAAATAGTACCTTGTTGAAAGTTTTGTACAAAAAAAAAGAGAGAGGGACAGAAAATAAGGCTTTAATTATTTCCTGAGAATAAATTCCCACAATGAAGTATTTTACTCCCCTAGAGTAATATAACTACTCAAACTCCCAATATCAGTGTATGAACACCCATGCCACCGTTCCCTCACTGTCACCAAACATTCTGTTTTTGAATATTTGATATTTAATAGGTGAAAACTGTATTTAATTTTAATTTTTATGACTTTTATAACCTTAATTGTTATGACTTTTATGTATTTTATTACATTTGAACATGTTCTTAAATGCTCATTGGCCATTTGTATTTCTTCCTTTATGTACTGTTGCTTCATCTCACTTGTTCAGTAGGTTTGCTTTTTGTATAATGAATGAGTGCTTTCTTAGACTACAGAACATTCTCCCCTCAATTCCCTTTTCTTATTACCAGTAGTATTCTTAAGTCAATATCAGGCTACTCTATTTCACTTACTTGCCAGTGTTCCAATCTTCTATCCCTACTGGTCTGTCCCATACTTACTATGCTATGAGCTCTGATTTATCCCCTAAATCTCTCACTAACTCATCCAGTTTTCTTTTTATCCCTTTCCTCCAATTCTTGACAGAGTTAGAGTGACTTTTTTAATGAGTAACTCCAAACTGTCTTGCAGTATACATCCTCTAACTCTTTGCTACATTTAAATAAGAAAATTATTGCCTTTAACATCATAAAGGTAGTATGTATAGTATAAGGTACCAAGTATTTATTATCTCAGTGAACCAAATTTCGCCACTCACTAAGCATAAGGTCTTGGGTAAAATACTTAACCTTTTTGAGATTTGGGGGTGTTTGTCTTCATAAGATAATAATAATAAAGTCAATTTTGAATTATTTAGGGAATTAAATATTATCATACCTAAAGAGTACAATTTTTTTTACATTTTAAATCCCAGATATAATTATACTAATCAGTTGAATTTTGTATTTCTTTTTTTAGCCATCCATTTTCTATTTTAACATTGAAAAAAATGTACAAAAGGACACAGTTTTAACCAGTTTGATTTTTCTTTTCTATAC
Seq C2 exon
TTTGGAGGTCAAGACATCTTTATGACAGAAGAACAGAAGAAATACTATAATGCAATGAAAAAATTAGGATCGAAAAAACCGCAAAAGCCTATACCTCGACCAGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144285-SCN1A:NM_001165963:23
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(15.3=76.1)
A:
NA
C2:
NO
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:
TGGAACTCCAGCCTAAGTATGA
R:
TCCTGGTCGAGGTATAGGCTT
Band lengths:
242-2162
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)