BtaINT0129363 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018520 | SCN1A
Description
sodium channel, voltage gated, type I alpha subunit [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr2:30403688-30406302:+
Coord C1 exon
chr2:30403688-30403969
Coord A exon
chr2:30403970-30406248
Coord C2 exon
chr2:30406249-30406302
Length
2279 bp
Sequences
Splice sites
5' ss Seq
GTTGTAAGT
5' ss Score
8.3
3' ss Seq
ATGCATGTCCTTTTTAATAGGCC
3' ss Score
7.75
Exon sequences
Seq C1 exon
GTGGTTGTGAATGCCCTTTTAGGAGCAATTCCATCCATCATGAATGTACTTCTGGTTTGTCTTATATTCTGGCTAATTTTCAGCATCATGGGCGTAAATTTGTTTGCTGGCAAATTCTACCACTGTGTTAACACCACAACTGGTGACATGTTTGACATCAGCGAAGTGAATAATCATTCAGATTGCCTAATACTAATAGAAAGAAATGAGACTGCCCGATGGAAAAATGTGAAAGTAAACTTTGATAATGTAGGATTTGGGTATCTCTCTTTGCTTCAAGTT
Seq A exon
GTAAGTGAACACTCTTTTCTCTGAAATGTGTTTATTGTCTAGAATAATAACAAAGTGATGACATACAGCTGTTGTGTAGTACTAAGAAGAAAATTTATATATCCTTTTTTCTAATTTTGATTTATTAGTACGTTTATGAGCCCAGATGGGTGGAAGTGTCAGTATATTTAAACAGTGCAGACACAGTTTCTCATATGAACAAATTGATGACTAAATCAACAAATTTGCTAATATTTTTCCTATTGCAATTGGAAAGCTTGGTTCACTGATGGATCACCCCCTCCCCTCAAACACACACCCTAAACACACCTGACTGGATTGTAACAAATTGGTGAGAATTAATTGCTACTGAGTTATATCATTTGGATTGAAGATTGGGGAATGATATTTAGGCTTTAGGATTAGCTCCTCATAGTGAAATGGAATAATACCAGATAGCACTCAGAAACAGAAATGAAACACAAGCAGCTGTTATCCCATCGCAAATGGCCTTTAGTGCAATTATAGAAGTCTTTTTTTCCTCTAAATATTAATGTTTTCACTACTGGGTCTCTAAGACTGAAAAACCATTCACAATGTATAAAAATATAAAAGATGGTAGCCTCTTGAACATTTTCATTTGATGCAGCTTCTGACTGCAGCTGCATCACAAAGCAGTGGATAAAAAGAGTCCAGAGTATTTGAAAAACATTGTAAAAATACTGTTCTATTTTGGCCAGTGAAAACTCATATTTAAAAAAAAAAAAAACCTGCATAAATTTGTTCCTGTAGTTCTATAGTCCTTAGGGCAGAAATCTATTTTATTTCACCAGGGTTGTGTTTCCAACTGTTCAACCAGGAGATTAAGCAAGCAAACAAGCTTGTGCTGATCAAAATCCTCCTGCATCTCTTTCAGAGTACTATGGCTCTTTTGCAAGTTCTCTCTACCTTCTTGTTAGAAATTCTTACTTCTCTTGTAGATGTTTCTGATTTATTCTAAATGTTCATGGAATTAAAATAGAGATTTTTAATATTTGGACAAGTATGATTTCTTCGAATATTATAGTAGACACATGATGGTATTTCCTTGGGCACTTACCCTAACCCTTAACTGATAACCACACTTGTAAATATCACTAATATATATCACTTCCTCCATAAAATTGAGAAAGAAAAATTGAAAATTTCAAGCAATCCCTTAAAATGCTAGGGTAAAGATGCTGCACAAAGCCAGTAAATAAATTCTGCTACCAGAGTACTGATTTACACTTGGCTATATATACAGAATCATCTCTCTGTTGGTTAGCAATTCATTGAAATGGTTCCTTGAATCACCTTTTACTGCTTTTGTACCTAGTATATAATGAACTTGTTCTGTCATTGACCTCAGCCATTGACACATTCAAAATTTCCCTCTTTGATAGACAAATAAGTTCTATTTTCTAGCTAAGAGTCTTTACTTTTTCTTCATTGCCATCGCAAGCACCCATACTTGACTTTCTTCCCATGACATCTACCACTTCATAAGTGTTAGTGTTACAAAAACAAAGATGTGTTAAGATACAGATGCTAAAAGCTTTTTGGTAGACTTTCTGACTAAGGAATAATCCTCTCAGGTCCATAGTGTTCAAAACTCATATTCTAGAACAAGTATCAAGTTACTATAAATTATTACACTTGGAATACCAAGTGTCTACTGTACTATTTTCACTTTTCTTACCCAAATTAACTCACTCTCATCAAAAGTTGCAGAAAAGAAAGTGGAAGATAGGATTATTTCTGATGTTACGCTTCAAAATTCTTAAAATGTTAGCTGCAACTGACTTTTGGATACCTGTATGATCTTTAGAGTATTACAATCAAGAGAAATTGTAAGCTTTCAGTCACTTGGATCACCCTGTAGATAGGTGTTAGTGGATGATCATCAGGTCTAAGATGTAGTTGTTTTGCTGCTATGAACATTACTAAATGTGTTGGCATTTGTAAGACTTTCTAAAAGTATTCCACCAAATCTTGATAGCACTTTAAACTGCATGATTCCATTAACTAAAGAACTGAAAAGTATTTGTCAGTTGGTTGTCAAGCAGGAGGATATATCAAAGGACCATTCTATTCATTATATGGTGTAGAAATGAAGAGACTTACTGAGATATTGTTGGTCCAAAATCCATGTAAAATTTGTTTTGAGATATATTTTTAAAATGTTCCTTTTAAAGAAATGTATCAGTAAGGATATTTATTAAATATTGGATCTGAATTACTTTTACCCCAAAATAAAACATGCATGTCCTTTTTAATAG
Seq C2 exon
GCCACATTTAAGGGATGGATGGATATAATGTATGCAGCAGTTGATTCCAGAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018520:ENSBTAT00000021951:21
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(40.6=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.4=100)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]