BtaINT0129352 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018520 | SCN1A
Description
sodium channel, voltage gated, type I alpha subunit [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr2:30359922-30361685:+
Coord C1 exon
chr2:30359922-30360269
Coord A exon
chr2:30360270-30361552
Coord C2 exon
chr2:30361553-30361685
Length
1283 bp
Sequences
Splice sites
5' ss Seq
GAGGTGATA
5' ss Score
3.13
3' ss Seq
CATTAACATTTTTTTTACAGGGA
3' ss Score
8.07
Exon sequences
Seq C1 exon
TCTTTGTTGAGCATCCGTGGCTCCTTATTTTCTCCAAGGCGAAATAGCAGAACAAGCCTTTTCAGCTTCAGAGGGCGAGCAAAGGATGTGGGATCAGAGAACGACTTTGCTGATGATGAGCACAGCACCTTCGAGGATAACGAGAGCCGCAGAGACTCCTTATTTGTGCCCCGACGGCATGGAGAGCGACGCAACAGTAACTTAAGTCAGACCAGTAGGTCGTCCCGAATGCTGGCCGTGTTTCCAGCCAATGGGAAGATGCACAGCACTGTGGATTGCAATGGTGTGGTTTCCTTGGTTGGTGGACCTTCGGTTCCTACATCGCCTGTTGGACAGCTTCTGCCAGAG
Seq A exon
GTGATAATAGATAAGCCAGCTACTGATGACAATGTAAGGAAGTTTTAAATAGTTCAGGCATGGAAGGCCCATGATTGCTGTACCAGCCAGTGTTTCTACAGAATGGAACCCCTTGAGAATGATTCCTGGTTGGTCAAGCTGTGAATGCACCTGCATCTTGTAATACCTTTAAAAGACTAACCAACTAAAACTTAAGGCCTCAACACTCTCTTGCATAACACCTGAATGCATTTATTTATTAAATGTGCTAAGGATAAATTATACACAGTAATAAATGACTGCCTCCAGTTGGAGGATTTGCTATATACCCATGCTGAACTACCTTTAGATAGCAGGCCATCCACTAAAGACCTGGTATAAGAATAAATGAACGATTCCTATATTTAAGTGTAAAGGGTGTATAATAAATCTTTCCAACAGATTCTTCGATATACCTTGCTTTAGTGTAGAAGATTTCAAGAACACTGTGCCTAAATAGATAGCTTTATTATTATCTTCAAATTTCTAGTACTCATACTTGTCTTACTAAAAAACAATGCTGATATAGGTCTTCTCAAAACTAATCTAAATGAAGAGACACACAAAATTATTAATACAGACAGTTAAAAGAATTCTCTGTGTACAAAGGTATGTGTTTGTGAATATATACCCGGATAAGGAATTTCTAAACACGTGCTGCCTCTTATTAGACCTGGATATATATCAGCATGAATGAGGCATGATCAAGTCAGAACTAGATGACTTATTGCTTTGGTACCCTGGATGAAACTGTTGTCCATGCAGCATGTATTGTTGTTTTTTTTAATATACAGCTTGTGTTGTCGATGACCATCTATGTCTTGTGTCCAGAAAATGAGATGGCAGCTACGTGTGTTCTAATTATTTGTATTCCTTTAAAAATAAAGGGCTACCTTCTCAAAATAAAATGCTGTGATCATTTAGGTGACTTTTCAAGTTATTGCTTTCTGCTGTTAGTTCTGACATAAGCAAATTGTTAAATATGTCACTCACAGGGTTTATCAAGGATATCAAAATTACATTGTCACCTAAAACTATAAAATCAGAGGGTAAAAAGAAAACCCTTAGTTCTGGTGTATGAATAAATGGCTAACAGTTTGGACAGTCCAGGTTAATGCTACAATAAGTCAGCAATATCTGCCATCACTAATTAAATATGAATGTGCATGATGCATGTATTTCATGAATTTCACTGTGTCACAATGGTTGTTTGCTTATCATATTGCCCACGTTAAGCATTGAATACATTAACATTTTTTTTACAG
Seq C2 exon
GGAACAACCACTGAAACTGAAATGAGAAAGAGAAGGTCAAGTTCTTTTCATGTTTCCATGGACTTTCTAGAAGATCCATCTCAAAGGCAAAGAGCAATGAGCATAGCCAGCATTTTAACAAATACAGTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018520:ENSBTAT00000021951:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.655 A=NA C2=0.244
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=PD(16.8=27.6),PF119333=DUF3451=FE(51.1=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.4=82.2)
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:
ATGATGAGCACAGCACCTTCG
R:
TGCTGGCTATGCTCATTGCTC
Band lengths:
348-1631
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]