BtaINT0129364 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018520 | SCN1A
Description
sodium channel, voltage gated, type I alpha subunit [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr2:30406249-30408428:+
Coord C1 exon
chr2:30406249-30406302
Coord A exon
chr2:30406303-30408290
Coord C2 exon
chr2:30408291-30408428
Length
1988 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGT
5' ss Score
8.62
3' ss Seq
AAAGTATTCTCCTTTGGTAGGTG
3' ss Score
5.53
Exon sequences
Seq C1 exon
GCCACATTTAAGGGATGGATGGATATAATGTATGCAGCAGTTGATTCCAGAAAT
Seq A exon
GTAAGTATTCTTTACATTCTAAGTCTTTTCACAATTTTGATTAGACATTAAAAATAATTTAACAGAGCATAGCAGCTAAATGGAATGATTTTACAATGATTTTTTAAAAAGAAAAAGTATGATTCAAGACTCAAGTATAGCAGTAGTATGCACGCATATAGCAGTATTTATCAGAAATCTTACTAAGATATATCAAAACAGAAGTGCAACGAAAGTAACACAGTCATATATTTAACAACTAACAAATATCCTTCTATTGACTATTTTTCTATTTTGTTTCCTTTCAATCTATCAATTACATACTCATTAATAATTTTGGCATGATAAAACAAATGTGAAGAAATATATGATTGCTATCCATAGTTTACCCTCCATATTGGACAAGTAAAGGATGTTGTCTAGGCAGTGTAAGATTTCTGTAACAGTCACTTTAAAATCCATTCCTTTATGTGATGATACACTGTGCTCAGTCACTTCAGTCGTGTCTGACTCTTTGTGACCCTATGGACTGTAGCCCACCAGGCTCCTCTGTCCATGGGATTCTCCAGGCAAGAATATTGGAGTGGTTGCCCTTCTCTTCTCCAGGGGATCTTCCTGACCCAGGAAATGAATCTGTGTCTCCTGTGTTGTAGGCAGATTCTTTACCACTGAGCCATCTGGGAAGCGCCCTTTATATGATCCATAAATTTACTGGAGCCTTTACAGACTGTTATCATTTCTATGATCAACAGTTTCCTTTAAGTTTCTATCACCTAAGACCTACTTTTTTGATTTTTCCTACTACAGCCTTTTTTAGACTTCAAGAAGAATTAAAATCCATGCTCATTCCAAATCTGCTCTTCAAATTTTGTACAATTTAGTATTTTCTCTTTATCTTTCCATTCTTAGGTCCCATCTGTTTAGCCTATAAACATGATGGATGACCTTTGCCCCCATAATCTTTAAACTGACCTAAGAAGCTCCCTTTTATCTTTCCTGATATACATTTTCCATAAATGATTCTAGTTTTGTGTTGAGTACCTTCCTGATATCCTCCAGAGTTATTTTACTTTGTTATTTTGTTTTGTGTGTTTGGTTGGTTTTTAACTCTAATATCTTTAGGAGGACATGAATATATTAGGGCATTGTCTTATAGTGACTCATTTATGTCTTTGTTACATGCTAAGTAAAAGCTCAAATGCTTATTTCTCATGAGTACACTCTAGAGATTAAATTACTGGTTGAGGATTTAGCAGATGGCATGTCCAGTTGGATGCTAAGTCCCCTTCAGTTGGATCTGACTCTTCGCAATCCTATGGACTGTAGCCCACCAGTCTCCTCTGTCCATGGGATTTTCCAGGCAAGAATACTGGAGTGGGTTGCCATGCCCTTCTCCAGGGGATATTCCCAACCCAGGGATAGAACCCAAGTCTTTAATGTCTCCAGCATTGGCAGGCAGGTTCCTTACCACTAGTGCCAGTTAATGTCTACTTAATCTGAAAAATTCAGTGACTGTTACACTGTTATAGGCAGTGTCAAACTGCCTATTTATTTAGATGTCAAACATCTAAATAAATAAATAACTAAATTGTTTGCTAAATAAATTCACACATCAGGAATGATTATTTCTAAACATAATCTATACATATTTACTGATGTAAAATGTTTTCACTAGTAATTTTTAAATTATAAAAATGTAGTATGTTAAAAATTGCCAAATTTAGTATACTACTGTTCAAATGGCAACATATTGGTTGTATTTGTAGTTAGAAAAAAAATAATTTCTAAATCATTTTATGGTATTTTTTTACATAACACCTCCTTTTTTACTTAAAAAATTATCCTAAAGGCTAATTTCAGAGATTATTTTTAGAAGTAGCTGATTTATAAGAAATAAAAGTACTGCTTAAGTATTACTAAAAATTTTATTATCTATTCTCATGAAAAAGCAACAATTACTTCCAGCATCAAATGTATTATAATGTCTAAAAAGTATTCTCCTTTGGTAG
Seq C2 exon
GTGGAACTCCAGCCTAAGTATGAGGAAAGTCTATACATGTATCTTTACTTTGTTATTTTCATCATCTTTGGGTCCTTCTTCACCTTGAACCTGTTTATTGGTGTCATCATAGATAATTTCAACCAGCAAAAAAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018520:ENSBTAT00000021951:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(7.4=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(15.3=76.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCACATTTAAGGGATGGATGGA
R:
TGCTGGTTGAAATTATCTATGATGAC
Band lengths:
182-2170
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]