BtaINT0129344 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017174 | SCN11A
Description
sodium channel, voltage gated, type XI alpha subunit [Source:HGNC Symbol;Acc:HGNC:10583]
Coordinates
chr22:12347474-12349278:-
Coord C1 exon
chr22:12349150-12349278
Coord A exon
chr22:12347578-12349149
Coord C2 exon
chr22:12347474-12347577
Length
1572 bp
Sequences
Splice sites
5' ss Seq
AGCGTAAGA
5' ss Score
6.21
3' ss Seq
CCTTGTGCTTTGTCTTATAGATT
3' ss Score
10.61
Exon sequences
Seq C1 exon
GTATGTCTTCCTTGGGATTTATTTATTTGAAGCATTAGTTAAAATATTGGCAAGAGGTTTTATTCTGGATGAGTTTTCTTTCCTGCGAGATCCGTGGAACTGGCTGGACTCCATTGTCATTGCAACAGC
Seq A exon
GTAAGAATGTTAAGATTTTTGCTGGTGGGAAAGAAGCCCTTTGGCTTCCATCTGGGTTCTTTGTGGATCCACATGAGTGGCTGAGTACAGCCAAGTAGTTGGTTGGCACTGAACTGCACCATGTAGCCAACTGGCCAGAGGACTTCACACACACAAATCCACTTCATCCTTTCTATCTGTTCCCCCCCAACCCCCCAACCAGGGACTGAATCTGGGCCATGGCAGTGAGAGTGCTGAGTCGTAACCACTGGACTGCCAGGGAATCCCCCACAAATCCATTTCTGGTCAAATACTCATGGTCTTACTTTTTCAGCCATTTACTCACCAAACACTGACCTGTTATGGGGCCAGGCTCTGTGGACCCAGGGTTGTGATAATGAGAAAACCATCATTCATGATTCTCACTCTGTTCGCAGTTCAGAGGGGATGTGAAACATTTGTGTGTGTGCTTAGTCGCTCAGTCGTGTCCGACTCTTTGAGACCCCATGGACTGTAGCCCTCTAGGCTCCTCTGTCCATGGGATTCTCCAGGCAAGAATACTGGAGTGGGTAGCCTTTCCCTTCTTTGGGTGATCTTCCTGACTCAGGGATCAAACCCAGGTCTCCTGCCTTGCAGGCGGATTCTTTATCATCTGAGCCACTAGGGAAGCCCAATGAAGCATGACCATTAAAACCGGCTACAGTTAGTGCTAGCATGGGATGCTGTGCATCGTTCTGGCTGTCAGAAGATGGAGCGGGAACAAAGGGTCTAGAACATCTTTGTCTACTGAAAGCTCAAGGAGTTTCTGTCATGTTTCCTTCTAGAAGTGTTATTATTTTGGCTCTTGTGTTTATGTTTATGGTCCATTTTGAGTTAGTTGTTGTATATAGCAAGAGTGAGAGTTGAAGTTCTTTTTGAAGGAGAGGACATCAATCTGGCATCTGAATGATGAGCAAAATAAAAAGCAAGAGAAACAATGGCCCATTGCCAGCACAGTAATAATAAACCCAACCTTATTTAATTAGTACCAGCCATTGTCTTAAGCACTTTGCGTATATTTTTGTTTAATATTCACAAAAGCCCTTTGAGGTAAGTACTAGTAATTTCAGAGTTTTACATTTCAAGGTCAATAGTCAGATGTTATTGAGAGGTGGTATAGTACAATGCCGAAGAATACGGGCTCTGAAGCCAGGCTGCCTAGGCTCCTTCTGGACTTGACCGCATGGTTGAGAGACCTTAGGGACGTGTACTGGGGCCTGGAACTTGGTAGCAAGTCAATAAATGTTTAAGTTGATTTCTGTTATCCATGAATGTAGCTACAGCTGCCATGACTATTTCAAGGAATCCCCAACTATGTCCAAATATAAAGATCAGCTGAGAAGAGTCTCCTGTGCAATCTATGGTCCCTGGGTCCACAGCAATAGAGAGTGACATTGCCAGGTCTTGAGATGATGGTGGGGCTGGAAGGGGAGGCTGCAGATTTCATGCTGGTGGACAGAACCCAGGCTGTAATTACTTGGGACTTTTGTGGAGATGTGTAGGACAGATACATGACTGAGCAAGCCTGGACTTTCCTTGTGCTTTGTCTTATAG
Seq C2 exon
ATTTGTATCATATTCTCCATATATCAATGACAGCAGCTTCAGTCTGTCATCCCTGCGTACCTTCCGAGTATTCAGAGCTTTGAAAGCAATTTCAGTAATTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017174:ENSBTAT00000022822:4
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(17.8=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(14.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCTTGGGATTTATTTATTTGAAGCA
R:
TTTCAAAGCTCTGAATACTCGGA
Band lengths:
206-1778
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]