BtaINT0129325 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017174 | SCN11A
Description
sodium channel, voltage gated, type XI alpha subunit [Source:HGNC Symbol;Acc:HGNC:10583]
Coordinates
chr22:12353016-12356183:-
Coord C1 exon
chr22:12355917-12356183
Coord A exon
chr22:12353135-12355916
Coord C2 exon
chr22:12353016-12353134
Length
2782 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCT
5' ss Score
8.49
3' ss Seq
CCTTTTTTTTTTTTTGGCAGACA
3' ss Score
9.31
Exon sequences
Seq C1 exon
ATGGATGACAGGTGCTACCCAGTGATCTTTCCAGATGGGAGGAATTTCCGCCCCTTCACTCCTGACTCTTTGGCTGCAATCAAGAAGCGGATCGCCATCCAAAAGGAGAAAAATAAGTCCAAAGATCGGAAAGCAGCAGAATGCGAGCCTCGACCTCAACTTGACCTAAAGGTCTCCAGAAAGTTGCCCAAGCTTTATGGTGACATTCCCCGTGACCTGATAGCAAAGCCCCTAGAAGACCTGGACCCATTCTACCACAATCATAAG
Seq A exon
GTACCTCTGTGAGGAGACGGGAGTGTTGTAACCACAAAGTACAACTGGCACTGCAAGGATCTCCTTGGGCTATAAAGAGGCCAGACCCCACTTCTCCTTTGCTGTCACCCTGTCTTTGATTTCCAATCCTAAGAATGGCTTTCAGTACTAATTTATCTCTATAATAATGCATATCTTGGAGAAGATAAGGACTAGGAGCAGTAGAAGGGTAAAACGGTGTCAGGAAAGAACTGGACCAGCAGTCAGAAAGGTTGAATACAGACCATTTCAAGTGCTTGAATTTATAAGTTTGGGTAAATAATTTCACTAATTGTCACTTTTATAATCAGTAAAATGAGAACAACGCCTGCTTTCCCTTCATTACAGCATAGACATGCGATGGAGGCACTTTATAAACTGTAAAACATGATGCTGATATGAAGGATTAATACCACTGTCCATGAATGTCTGTTTCAGCAACTAAAGTTTACCTTGAGAAACTCTTAACCAGTAGGCTTGTTAGGTTATTAATATGAAGGTCAAAGCCCCAAACCAACACTTGACACAAAAGAGGATCTCAATAAATAAAGTTTAAGAATATTGTAATCAAGTGGGCACATGCAGATTCTATGTAAACTCCATACGTGATAGTCTTGCTGTTTTATCTACCTAGATGTAGGGAAATTCTAATAAAAGTTTCTCAAAGAGGTTCCTGAATGAGGAAGTATGAGCTCAAGCTCTTCTGATGGCTGGTCAAAAACCCAGGGCAGTGAGGAAAGTCCTCTATAACCCATGAGAAACTGACTTCTCCAAAGGAAGATTGCCTGGTTTGTACGTCCTTGAACTGAACAGACTTGGGATTACCAGGCCAAATGAGGACTGTGTAATGGAGGAAAGTGTGGTATGAGTGGGAAGAACAAGAAAGGAGAAAGGAGATGAAAGAACAAAAACACTTCATTATCTCTCCCTCTCCTAATGCTCCAGGATTCCAGGGGCTTCTTAGAGGCAGAGTCATTGGAAATAAGTTAACTCCAGGAGACCTCCTTCTGCCTCAGGTCTGGGTAGGGAACCCAGGAGGTAGGCAGCAGCTTGGTGTGTTATGGAGAATCCTGGGAGGACAGACTCTGTTCCAGCTGGGGTGGGTGTTCTAGGACCATCTCTTCTAAATCTGGGTCCTCCCTTTAAATCAGGAGACATGATACTTGTTCGGAGCTCTTACACCCACAGCCTCACATGCCAGTGCTCTCAGCACTCCTGTGAACCATGGGTGGTGTCATTAGCACTTCACCTTACAGATGGGGAAACAAAGCTTTGATGGGGAAGTGGCTTACACCAGGTCAAGCAGCCCGTTAGTGGTGGAGCTGGGACTCAAACCCAAGGGTTCTTTCTGTAGTCACAGGTCACTTCTTATCTTTCAAAGCTTCCATTTTTGAAAGAGAAAAGAGTGGAGATGTGTCAGCAAGCAGACAGGAAATACCTATATTTTAAATCATTAAAACCTTGGGAAGTGTAGTTAAATACACCATTAGTTGAAATATTTAAAGCAGTCAGAGGAGGCATTAATAAAATATCTAGGTCAAAGGGCACAGAAATAGAGCCATAGCATGCCACATATTAATCTGGGTGACCCACCTCAGGAGAGGTTTACTCTCTGCCCTAAAATCATCTTTCTGTCCAGAGGAAGTACACGGAATCCCTAAAATGAGTCTTAGACTCCTGGGCTCATAGCTTTCAAGGAATCCTGTAGCCCATTTCATTTTGTTATGGAGTAAAAAGAAAGCATCCTAGTCCACATTCTCCCTGCTGCCAGATAGCCAGCAGACAAGTTCCACAACTCGGTGAAGGAAGCTGATGCTTGGCAGTGGCTGAAGTTCTGGTCCCTCAACCAAGGTGGCAGCTAACCTGCTGTTTCTGTGCCTGGATGACAAGACCTGTTTTCCCTGTCTGAGAACATGCTGAATTACATGTCAAGGAGTACTTTCTGCAAGTCTGAAAAAAGCAGTGACATGGAAGACAGGAATGACCCTAGTTCTATGAAGGCTTTTATAACTAACAGCCTTGGGAACCGATAAGGGGACAGCAGATGACTGTTATATGGAAAGGGGATGGTTTGAAGGTTATGTTAGAAGCCTGTGAGTCATTGGTTTTGTCCAGAGGCAGCTTCATGCCCAGAGCCCAGGAAGAGATGCAAGGAGGAAGCAGGCGTTTTTCAGCAGGGCCCAATTGGACACTTTGGGTGAGAAGTGCACCAAATCTTTCCTGGATTTGGCATCCCTGGTTATACCCATGACAAGGCAGCAGAGACTCCAGTGAATGTTCAGTTCTACTTCTGTCTCTTCAAGTTCTCTTCTAATTCTCATCTCCATAAATAGTACAATACAAAGGGTTTTATTTGACCCAGTTATTACTCTTTATCTCTTTTTTGTTTGTTTGCAGGGCCCATGCACTTCATTTCTGTGGCCTCCAGAATATGTCACTGGGTGAAAAGTCCATAGCTCAACAGTTATTTTAGGCGTGAGGACTGACTTTCAACAGATCAGAGTCTTGGAGCCCTGAGAGAGACCTAAGCCACATGGGTGGGGGGGATCTACTGGCTTCCAAAGTGAAGTGTAAGCTGCTCAGAAAGTACCTCTGGCTTCAGAAGGTAACTCTCTAGTCAGAAGCTGCTGTCATAATATGACAAGCCATACCTCAACCTATGGTTCCACTAGATTTTCTCTAAGATGAACTCATGATAAATATTGTTTTGTCACTGCATATAATTCCTGTTGTGTGGTTTTTTGCCTTTTTTTTTTTTTGGCAG
Seq C2 exon
ACATTTATGGTGTTGAACAAAAAGAGAACAATCTACCGCTTCAGCGCCAAACGTGCCTTGTTCATTTTGGGGCCTTTCAATTCAATCAGAAGTTTGGCCATTAGAATCTCAGTCCATTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017174:ENSBTAT00000022822:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.090 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
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]