BtaINT0129565 @ bosTau6
Intron Retention
Gene
ENSBTAG00000002425 | SCN9A
Description
sodium channel, voltage gated, type IX alpha subunit [Source:HGNC Symbol;Acc:HGNC:10597]
Coordinates
chr2:30110142-30111588:+
Coord C1 exon
chr2:30110142-30110205
Coord A exon
chr2:30110206-30111446
Coord C2 exon
chr2:30111447-30111588
Length
1241 bp
Sequences
Splice sites
5' ss Seq
AGGGTATGT
5' ss Score
8.34
3' ss Seq
ATATTCTTTCTCACATGTAGTCA
3' ss Score
6.78
Exon sequences
Seq C1 exon
AATATTTTTATTACTTGGAGGGATCCAAAGATGCTCTCCTTTGTGGTTTCAGCAGTGATTCAGG
Seq A exon
GTATGTAATATTTGTTTCAATTTTAGTCTAAAGACTGAAAAATAGAAAAAGCAAGTTCAATCAGTTTGCTAAGAAGGACCTTTGATTCTATGTTATTTTCTTATATTTCATGACATTACTTGACGCATTCTGTCCCACAGTGAGTCCAGACTTTAAAACGATCATGGTTAATGCGTACTTTTGAAAGCAAGACGTAGGTATGCTTGGATTAAAACAAGATACCAGTCATATATATCTTAAGGAAGTAGAAAGAAAGTGACTTCCAAAAAACCCAACCAAGAGTTGTTTGGATAGTTTCTAGCCTTTCTTGTTTCCAGAAAGAAGAGTGATAAAATCAGCTTTTCTTTCCATCCCTAAATTCTACTCATTCTCCCATCGAGTACAGTTCATGGGTGACAGAATGCAGTGACACTTTGGCCACTCTAAACAAAAGGGTCCCACGGACTTGGGTAAAGCTATTTTAAGATATCATATTTATGTAAGTACCTGCTGTTTCTCCCATACACAACTTTATTTCTGCTGTACGGCCTTTGTTCTTGTACTCTCCCTGCCCAGAGATCCCTTGACCAGACTCTGTGTACACAGGGAACATAAAAATAAACAAGATAAAGTTGCTGCTCCCAAAGACACATCAAAACACCTTTTATCTGTCATTGTGGATACCAATCTACCAACTTTAAAAAGACAAAAAGTCTAATTATAAATCTCCATGAACTTACACAATTGCTATCTGTTGACTGTTGTTGATTCTAGTTCACCTCAAGAATAATTTGAGGAAACAGTTTTATTAGAGACCTGTATATTAATATCAATCTTTGTGAATATAAGAATTTTTATATGATATCAAGTGAAAGTTTTCAAGTTTTGATGGTTGTTGATGATGATACTAATAGCAGCTACCATTTATCAAATGTTTTTATGTACAGGAAGTAGGTTAGGTAATTTGCATACATTATCTTTTTTAAACTTTAAAACAATCTTAACCTTTGGAAGTATGTATTATTATCTTGTCTCATGGAAAGAAGAAACTGGGCCTTGCAGAATTTAAGTAATTTGACAAAGTCAGCAACTAGTAAAAAGTAGGGATGGGGTTGAAACCCACTTCTTTCTGACTTCAAAAAGTGTGTTCTTAAAAATTATTCGATATTGTCCCCCTGAAAAGGAAATCTTGAGTTTTTGACTTCTCTGTAAGACTCTTCAGCTTGCATCCTCTGACTTGTGATATTCTTTCTCACATGTAG
Seq C2 exon
TCAGTGTCCAGAAGGGTACACCTGTAAGAAGATTGGCAGAAATCCTGACTATGGCTACACGAGCTTCGATACTTTCAGCTGGGCCTTCTTAGCCTTGTTTCGGCTAATGACCCAGGATTACTGGGAAAACCTTTACCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002425:ENSBTAT00000003146:8
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(8.5=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(19.0=100),PF0253517=Zip=PU(11.0=39.6)
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:
TGGAGGGATCCAAAGATGCTCT
R:
CTGTTGGTAAAGGTTTTCCCAGT
Band lengths:
191-1432
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]