BtaINT0129340 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017174 | SCN11A
Description
sodium channel, voltage gated, type XI alpha subunit [Source:HGNC Symbol;Acc:HGNC:10583]
Coordinates
chr22:12290113-12296404:-
Coord C1 exon
chr22:12296263-12296404
Coord A exon
chr22:12290214-12296262
Coord C2 exon
chr22:12290113-12290213
Length
6049 bp
Sequences
Splice sites
5' ss Seq
TAAGTATGG
5' ss Score
1.55
3' ss Seq
CATCTTCTCCACATACTTAGGTG
3' ss Score
6.73
Exon sequences
Seq C1 exon
GAAGGACAACAGCCACAGTTTGAGGCACGTTCTTCCATGTACCTTTACTTCGTAGTTTTTATCATCTTTGGCTCATTCTTCACTCTGAATCTCTTTACTGGTGTTATTATTGACAACTTCAACCAACAGCAGAAAAAGATAA
Seq A exon
GTATGGGGATTGTCCTGATTTGGTATTTTTACCTCCTCATTTCTCCAAAGAGCTTGGATGGAGCATAAATCAGTTCTAGATTGTTGTGCAAAGTAGCCTTTATCATCTGCATAAGAATGAAGAGGGAGCCTCTTAAGGAAAGAGTCTTGAGGATATGGCTGAAAAGGGACTGCATTAGCTGGGTTTTATTAATCATTGTTTTTATTCTTCACTCTACCCTCTTAAACAAAGGCCATTGTTGAACTCTAATAGAAAAACAAATATCAGGATTAGTATTTATGTCAAATTGTAGTAACCTTGCAAGTGTATCTTGTTATTCAGGATAAAAAGAGTACAATCCCTGACTTAGGATAGTTCAATTTACATGATTTTTCAACTTTTACAATGAGGCAGAAATGATACGCATTGAGTAGAAACTTTACTACAGGTTTTGAACTGTGATCTTTTCCTTGGCTAGAGATATATAGTACAATACTTTCCTGTGACACTGAGTGGCAGCAGCCACAGCTCCCAATCATCCGTGGCTCACTGAGGATAAACAGTAGGTATATATTTACAACATTCTGTATCCATACAACCATTCTGTTTTTCACTTTCAGTACAGTATTTGATAAACTAAATGAGATATTCAACGTTTATTTTCAAATAGGGTTTGTGTTACATGATTTTGCCCATCTGTAATCTAATTTCTGGGCTTCCCTGATAGCTTGCAATGCAGGAGACTCCAATTCGATTCCTGGGTTGGAATCGAATAAGATCTCCTGGAGAAGGGATAGGCTACCCCCTCCAGTATTCTTGGGCTTCCCTTGTGGCTCAGCTGGTAAAGAATCCACCTGCAATGTGGGAGATCTGGGTTCAATCCCTGGATTGGGAAGATCCCCTGGAGAAGGAAAAGGCTACCCACCTCAGTATTCTGGCCTGGAGAATTCCAAGGACTGTATAGTCCATGGGGTCACAAAGAGTCAGACATGACTGAGTGACTTTCACACACATGTGAAAGCTAATTTCTAAGTGTTCTGAGCATGTTTAAGGTAGGCAAGGCTAAGCTGTGATGTTCAGCAAGTTAAGTGTATTAAATGCATTTCAAGTTACATACAATATTTTCAACTTAACATGGGTTTATCAGGATGTATAATCATTGTAAGTGCAGGAAAAATCTATAAACTCTCCTCTTTCCGTAAACTTGCATCCTGCCTCTCAATACCCAAGTCTCAGCAGATTTATTGAACTTACTTGGAAAGAAGATGGTAGGGAAGAGACAGGTTTTTTCCCCCATGTGTTGTGACAAACACATATTTATTTTTCTGATTCAATAATATATAGGGGCATTGTAGTAAATGTGGAAAAAAGATGAAGAGAAAAAGAAAATTTAAATCATCCATAAGGTGACCACCAAATGATAACTATTTTAGATTAAGCCTCATCATTTTGGTACCATCTTTTCCAGTTACTACTAAATAATACTAAATGTTTCTTTTACACTGTTGAGATTATATAATATTTTTAACTGTCTTCTCCATTAGTTATGAGTTCATATCATGAGATCATCTTTATTATAAGAATTTTCATGGATGAATTACATCCCATATTATGGATAGACCATAATTTATTCCAACTATTCCCCCCACTCTCCCTTTTAAGGACATTTAGGTCATTTCCAAATTTCTTGCTCTTCTAAAATAATCATGAACATTCTTGAAAGTCTCTCTGTATATCTCTGATTATTTCCTCAGGATAAGTTCCTAGAATTTAAGGCATTAAAGATAGATTGTCAAATTACCTTTCAGAAATTCTATTCTGGGTACCCTCCTTTTGTAAGACATGAAGTGCCTGTTTATTCTGTTCTCATCGTTCTGACTTTTGTAATTTTAAATTATTTTTTCTAGCTTGATGGGTAAAAGTGTTACCTCACAGTTTTACATTCATTCATTTGACCATTTCTGAAGTTAAACACTTTTTCACAGGTTGATGGCCATAACTATTTATTTCTTCCTTGAGTTTTCTGTTTTTAAACAGAAAACTCTTCTTAAAATTTAAAAATAAAATAAAATTAGAAAAAAAAATTTATATTATCATTTTTTCTTATGGTTTTATATAGTATGTTCAATTTGACTTACCTCTTACATTTTTGTAATGACATTTTAAATTTATAGACATTTAGCAGATGTATGAAGTCAAGCTTTCAATCTTGTCCTTTTGCCCTCTTTTCTTGAATTTATATACTGAAGGCATTTCTCAATCCTAAAATCAGGTGGCTAAATATTCACCTTTGGTTTTTCCCTTGTTGTTTTGTGACCTTCTTTATTTTTATGTTGAACTTTTTTTAATCCATCTAAAATGTGTCCTGATACTGCTGAGCTTTCTTAGTGTCTGCTGGGAGAGTCATTCACAGTCCCAGGCAACTATATGGCTGCTGTTACTCAACAGTGTGCTATATGGAGTCACCTCTGTAATATGCAGCTTGTATTGCATATTGCAGGTATTGCAACCAATACCTACAATCTGAATGTCAGGCCTTGTGATTTTAGATTTAAACTTGCATTTGAAATCACTGTTTTGATCAGTCCATAGCATTTTTGTTCCATTTTGTTTTACTTTTATTATAGAAAATCTCAAACACTCACAAGAATATAGTAAAATGAATCTAAAATACCCAGCACCCAGCATATTTACTGATTTAAGAACATCCTTATACCTTCAGTGTCTTTCCCCACTGGATCCTTCCACTGGATTTTTTTATAGAGCATCACATACATCGTATTATTTCATCCACCAATTTTTCAGAACATATCTCTTTTTAAACATAACTACAATTCCATGATCATATCTAAAAAGTTTAATATGAGTTCTTTAAATTAATCAAAAATCCAGTCAATGTTCAAATTTCCTCCAGTCTCTTATATTCTCAAAATATTTATTCATTCTTTAACTGATTAGTTGATTGATTGTATTAAAGTTTGCTTCTTTTCAAATTAGGATTCAAATCAGGTCCTTGCACTGGATGACTTCCTTGCTCTCTGGATTGACAGTATGTTCTAGGCATTGTTTGTACACTTTTTGCTCCAGATCTGGAATCAGCCATTTCTCTAGGGCGTTCTCAGAGGTGGTGTTCTAATACCGCAATCTAGAATGCTCATTGTGATTATTTTGAGACTTTTTCAGTGGACAGAGCTACTTCAAATTTAGGACTACAAAGTTTTCATTTAACTAGTACATCTGTATCTCCTCTTTTTCACACTGAGAAAGCTGGTTCTTGTGGGTACAGAAGATGATAGCCTTTAAAATTTCCATAGCTGTTCATTTTATTTATCTCACCACACACAAAGGGCAGTCTCATAATAATAGTATTAATACTATCATGATGCATATGATTACTGAAGATAGTTAATATCTGCCAGGCATCATGAAAAAAACCTGGTTAACTTCTAGGGCTGGGTTATTTATTTATTTATTTATTTATTTTTACTGTGGCAAAATGGTCATAACATCAGATTTATCATCTTATCCATTTTTAATGTACAGCTCAGTGATGTTAAATACATTCATAATGTTGGGCAACCATCATCATCATCCATCTGTATAACTCTTCATCTTATAGACTGAAACTCTACACCCATTAAGCAATAACTCCCCGTACTTCCCACCAGCCCCTGGCAGCTCCCATTCCACTTTCTGTCTTCATGATTTTGATTATTCTACGTATCTCGTGTAAGTGGAATCATGCAGTGCTTGTCTTTCTGTGAGTAGCTTACTTCATTTAGCATAATGTCCTTAAGGTTCATGGATGTTGTTGCGTATTTCAGGATTTCCTTCTTGTTTAAGGCTATGTATACATCATGTTCTGCTCTTTCATCCATGTATTGATGGACAGTTGGGTTTCTTCCATGTTTTACTTATTGTGAATAAAGGTCCTATGAATATGGGTGTGCAAACATCTCTTTGAGACCCTGCTTCAATTCTTTTAGGTCTATATAGAAGTGGCATTGCTGTATCATGTGGTGATATGTACAGTATACAAAGTTTCTAATTTCTCTACATCCTCACGGACACTTGTTTGCTGTGTTATTGATAGTAGCCATTCTAATGGATGTGAGGTGGTATCTCATTTTGATTTTGATTTGCATTTCCCTAATGATTAGTGACACTGAACATTTTCTCATGTGCTTATTGGCCATTCATATATCTTCTTTAGAGAAATATCTATTCAAACCTTTTGCTCTTTTAAAAATCAGGTTGTTTGTCTTTTTGTTTTTATATTTTCAGAGTCCTCTATATAATATTAATCTCTTGTCAGATATATGATTTTCAAATATTTCCCCACTCTGTGTGTTGCCTTTACTTCATTGAGAGTGTCTCTGATGCTCCAAAATTTAAAGTTATGAAGTCCAATTGATCTGTTTTTTCTTTTGCCTTTTGTGTCGTATCCAAGAAATTATTACCAAATCTAATGCTTTGAAGCTTCTGTTCTGTGTTTTATTCTGAGAGTTTTATTGTTCTAGATATTACATTTATGTCTTTGATCCATTTTGAGTTAATTTTTGTATATGGTGTTAGGTAATGATTCAGCTTCATTCTTTTGTATGTTGATGTCCAGTGGCACCCCACTCCAGTACTCTTGCCTGGAAAATCCCATGGACGGAAGACCCTGGAAGGCTGCAGTCCATGAGGTCGCTAAGAGTCAGACACAACTGGGCGACTTCGCTTTGACTTTTCACTTTCATGCATTGGAGAAGGAAATGGCAACCCACTCCAGTATTCTTGCATGGAGAATCCCAGGGACGAGGGAGCCTGGTGGGCTGCCATCTATGGGGTCACACCGAGTCAGACACGACTGAAGTGACTTAGCAGCAGCAGTGTTGACTTTTCACTTTCATGCATTGGAGAAGGAAATGGCAACCCACTCCAGTATTCTTGCCTGGAGAATCCCAGGAACGGGGGAGCCTGGTGGGCTGCTGTCTATGGGGTCGCACAGAGTCGGACACGACTGAAGTGACTTAGCAGTAGCAGCAGTATCCAGTTTTCCTGGTGCCATTTGTTGGAAAGACTGTTCTAGGACTGTATTTTTTGGTCCATACTGTAGTGTAAATTTAAACCCCACACCCTCATCAAGGCAGGCTTGGATTCACAAATTACCAGTGAAGAGTATAGACTAAGACAATGTCCTGGTTGTCTTCTCTCCCCAACAGATACGTTTGGTTTTCTTCTTCACTCTTTAATGGCAGCACTTGGAGAATTCCATTACCAACACACAGCGTTCTTGGACTAACCACACTGTCTTTTCCCCATGACCCCCTTGTAGTTATTAAATCCTAAGATTCTCATTTTTGCAGAAATTAGCAAATGCCCTTAGGCCAGCCATGACTTCAGGACTAATTTACTTCTCTTTTTTCTCTCTCTTGATTTTCAGATGATGGAAATTTTCCTTACTTTTTGGGCAAGTTCAGCTATGTCTTTTAAAAGTAATTCTGTTCTATTTTATCCAGCATTTCTAGATGTTTTACCACTTCTCCCACCAAATTTCATGAAAATCCTTCTTCATTTTTCTGTTCTTTATTACTCAGTGGTGAAGACACTCAAAGCTCTCTTTTTTTTTTTTTGTAAGAATGGCTCTAGACAGATGTTTTTGGAAATTTTATTAGTGATATATGCATTCATATATTTAGGAGAATTTTAATTGTCACTTTTTAGGACTTTTCATTTAGATTTTTATTACTAATTTCTATGTTTGTTTCACTGTAGTTTGATTTACACAACTTGAAGTATGTTCAGTTTTTGTAAAGCTTCTGTGGATGTTTGCAAAGAATTTGTAGTCTTATTTATATTATAAAAAGAGACATATAACTGATAAAAGTAACATTTCTCCCTTAATCCTTAATTTAAACCCTGTTTCCTTTAGGCCCTTCCTTATAGTCTCATTCTGCTTCAAACTGGAATTTTAGGAATTGTTGATAGAAATGCAATATAACTTTAAAACTATTTCTGAAAATTCAGAATTCATTTCCAAAAATCTGTTAATGATAATTAGCTCTCATCTTCTCCACATACTTAG
Seq C2 exon
GTGGCCAAGATGTCTTTCTGACAGAAGAACAGAAGAAATACTATAATGCAATGAAAAAATTAGGATCCAAAAAACCTCAAAGGCCCATTCCAAGGCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017174:ENSBTAT00000022822:23
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=0.059
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(16.1=72.9)
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]