BtaINT0129342 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017174 | SCN11A
Description
sodium channel, voltage gated, type XI alpha subunit [Source:HGNC Symbol;Acc:HGNC:10583]
Coordinates
chr22:12275353-12283141:-
Coord C1 exon
chr22:12282871-12283141
Coord A exon
chr22:12276384-12282870
Coord C2 exon
chr22:12275353-12276383
Length
6487 bp
Sequences
Splice sites
5' ss Seq
TTAGTAAGT
5' ss Score
7.79
3' ss Seq
ACCCTCCTCCTTGTCTTCAGGTT
3' ss Score
11.27
Exon sequences
Seq C1 exon
AACAAATGCCAAGGCTTTGTGTTTGACCTCGTCACACACCAGGTCTTTGACATCATTATCATCATCCTCATTCTCCTCAACATGCTTAGCATGATGGCTGAAACACATAAGCAGTCGGAGACCATGAAACATTTACTTGAGAGTCTCAACATGGCCTTTGTGGTCATCTTTGCAATTGAGTGTTTCATCAAAATCTTTGCTTTGAGGCAATACTACTTCGCCAATGGCTGGAATTTATTTGATTGTGTGATCGTGCTCCTTTCTATTGTTA
Seq A exon
GTAAGTAAAACTGGCAACCAGAGGGGCTTTAGTCTGAGAGCAAGAAGTAAACTTGTAAGTCTTATCATTTGGAATTTTCTCCAGAGTAGCCACAGAGCATAAAATTAAATTTAATGTGGTTTTTGAAAAAAAAAAAAAAAATAGATGAATAAATGCCATTCTCTTTGGGGAGTTGCTAGAAAATACAGAGTATTTCCACTCCCTTGATTATCTACACAATTGAAACAGAGTTAAGTAATTATGTGGATCATTTATTCAATGGGGATAGATGAAATTAAGATGACTTAGAAGTTTTTGTGGGGCTACCTGCTTTATCCAGGGAATTGAGTCAAAGTTCCATTTTCTTCTACAACTATAAGGCCTAAAGAGCATTTCTTGTTTTAAGGATTTGGCATTTAGTTTCCATGTTTTTCCCTAGTTCAAAATCCTTCTGGATGTCAGATCACAATTACTAGGCCCCAGTGACATTGCTGGGCCTTCCTGTACCTCCTCCTTATAGTGGGCCTCCGTGGCTCAACCTGGATGGGGCTTGCAAGAGTGTGTCATAAGGACAAACAGTGCTTTTCTTCTTTCTGTATCTCATGTTAACTTAAATTATAGTGGAAACGACATAGTGTGTCAACTGCTTGGGTTTCACTCACCAACTAGCTTCACTCTATAATTGCTATATTTTTCTTAACTGTGCACAGAAATTAACCTTAAGGTTTATAGAAGAAGACTAGGGAGAAAAAGAGGGTTATTGCCATACACCTTTTCATGAAACATGTACACACACATGCACATACATTAACTTCGAAGGTAAATTCTTCATGACTAAGCTATGAGATTTTACTCTGGGTTTTTGAAGTCTGCTTTAATTAAACTGATAATTTAACTATAATTGCGTAAAACTGCCTATGGGTTTTTCTCATCGTTCAAAGAGCATGAAGGCAGTGAAAACGGATTTCACAAGTGGAAGCTTCTGTTTTATCTCAGAAAGGATGCAATAAACAGATATGCTGGATCAAAATATTTTGGTTCTTAACATGATAGCAGCAATCCAGATGTTTCAGGGACCAAGAAAATGGTACAGTTCATAGTCTGTTCTACTTTTTAGCCATGGAAACTTATGTAGATAAAGTTCAGTAATAAATCTTTCAACATGCTTATGGTTAGTTCAGTTCAGTTCAGTAGCTCAGTTGTGTCCAACTCTTTGCAACCCCATGAACTGCAGCACACCAGGCCTCCCTGTCCATCACCAACTTCCGGAGTTCACTCAAACTCACATCCATCGAGTTGGTGATGCCATCCAGCCATCTCATCCTCTGTCATCCCCTTTTCCTCCTGCCCCCAATCTCTCTCAGCATCAGAGTCTTTTCCAATGAGTCAACTCTTCGCATGAGGTGGTCAAAGTACTAGAGTTTCAGCTTCAGCATCATTCTTCCAAAGAACACCCAGGGCTGATCTCCTTTAGAATGGACTGGTTGGATCTCCTTGCAGTCCAAGGGACTCTCAAGAGTCTTCTCCAACACCACAGTTCAAAAACATCAATTCTTCAGCGCTCAGTTTTCTTCACAGTCCAACTCTCACATCCATACATGACTACTGGAAAAACCATAGCCTTGACTAGACAGACCTTTGTTGGCAAAGTAATGTCTCTGCTTTATAATATGCTATCTAGGTTGGTCATAGCTTTCCTTCCAAGGTTAAGTAGACTGTTAATCTTTATTAGTCAGTTTCAAGCACAAGTCCTGGTGAAATTGACAGCAGCAATAAAGTTAGAAAATGAGTCTGGGGCAACCATCTGAGCACTTAAAGAGCTCTTCCTCCAACATTCAGAGAGCAGCTCCTTCATTCCACTATTTGCTGAACTTTTTCCAGGCAGTGCCAGGCATCGTAGAGCTCACAGTAACTGAAGGAGGTCGCCATTACCCCTACCATACAGCCTATAGCCTACCATGGAGACTGAAGACTCTAGGACAGGGCTGCCTCAGGTCAAACTACAGGCACAGCCCCTCCCATCAGCAGAAAATTGGATTAAAGATTAACTGAGCAAGGTACAGCCCTCCCAAGCAAGGCCCAGTTTTCCCTGAAGCCAGTCCCTCCTATCAGGAAGCTTGCACAAACTCTTACCCTCATCCCTCAGAGGGCAGACAGAATGAAAACCACAATCACAGAAAACTAACCAAAATGATCACATGGATCACAGCCTTGTATAACTCAATGAAACTATGAGCCATGCTGTGTAGGGCCACCCAAGACGAATGAGTCATGGTGAGTTCTAACAAAACGTGGTCCACTGGAGAAGGGAATGGCAAATCACTTCAGCATTCTTGCCTTGAGAACCCCACGAACGGTATGAAAAGGCAGAAAGATATGACACTGAAAGATTAAACACTCACCCCACCCCTAGGTGTCCAATATGCTACTGGAGAGGAGTGGAGAAATAGCTCCAGAAGGAATGAAGAGGCTTAGCCAGAGCGGAAATGATGCCCAGTTGTGGTTGTGTCTGGTGGTGAAAGTAAAGTCTGGTGCTGTAAAGACCAATGTTGCATAGGAACCTGGAACATTAGGTCCATGAATCAAGGTAAATCGGAAGTGGTCAAACAGGAGATGGCAAGAGTCAACATTGACATTTTAGGAATCAATGAACTAAAATGGACCAGAGTGGGCAAATTTAATTCAGATGACCATTATATCTGCAACTGTGGGCAAGAATCCCTTAGACAAAATGGGGTAGCCCTCAAAGTCAACAGAAGTGTCTGAAATGCACTACTTGGGTGCATTCTCAAAAATGACAGAATAATCTCTGTTCGTTTCCAAGGCAAACTGTTCAACATGACAGTAATCCAAGTCTGTGCCCTAACCATTATGCTGAAGAGTATAAAGTTGAATGTTTCTATGAAGACCTACAAGACCTTCTAGAACTAACATCAAAAAAGATGTCCTTTTCATCACAGGGGACTGGAATGCAAAAGTAGGAAGTCAAGAGATACCTGGAGTGACAGGTAAGTTTGACCTCAGAGTAGAAAATGAAGCAGGGAAAAGACTAACAGAGTTTTTCCAAGAGAATGCTCTGGTGATAGCAAACACCCTTTTCCAACAACACAAGAGACGACTGTACACATGGACATCACCAGATGGTCAATACTGAAATTAGGTTGATTATATTCTTTGTAAGCTGAAGATGGAGAAGCTCTATATCATCAGCAAAAACAAGACTGGGAGCTAACTGTGGCTCAGATCATAAGCTCCTTATTGTAAAATTCAGACTTAAATTGAAGTAAGTAGGGAAAACTACTAGACCATTCAGGTATGACCTAAATCAAATCCCTTATGATTAAACAGTGAAAGTGACAAATAGATTCAAGGGATTAGATCTGACAGACGGAGTGCCTGAAGAACTATGGACAGAGATTTGTAATGTTGTACAGGAGGCAGTGATCAAAACCATCCCCAAGAAAAAGAAATACAACAAGGCAAAATGGTTGTCTGAGGAAGCCTTACAAATAGTTGAGAAGAGAAGCGAAAGACAAAGGAGAAATGGAAAGGTATATCCATCTGAATTCAGAGTTCCAAAGAATAGCAATGAGAGATAAGACAGCCTTCCTAAGTGATCAATGCAAAAAAATAGAGGAAAACAACAGAATGGGAAAGACTAGAGATCTCTTTAAGAAAATTAGAGATACCAAGGGAACATTTCATGCAAAGATGGGCACAATAAAGGAAAGAAATGGTATGGACCTAACAGAAGCAGAAGAGATTAAGAAGAGGTGGCAAGAATACACAGAAGAACTATACAAAAAAGAGCTTCGTGGCACAGATAGCCATGATGGTGTGATCATCATCTAGCGCCAGACATCCTGGAGTCCGAAGTCAAATAGGCCTTAGGAAGCATTACTACAAACAGGAGATGGCAAGTTTGATTACTACAAACAAAGCTAATGGGGGTGATGGAATTCTGTCTGAGCTATTTCAAATCCTAAAAGATGATGCTATGAAAGTGCTGTACTCAATGTGTCAGCAAATTTGGAAAACTCAACTGTGGCCCCAGGACTGGAAAAGGTCAGTTTTCATTCCAATCCCAAAGAAGGGCAATGTCAAAGAACATTCAAACTACCATACAATTACACTCATTTTACATGTTAGCAAGGTTATACTTAAAATCCTTCAAGCTAGGCTCCAGCAGTACATGAACTGAGAACTTCTAGGTGTAAAACTGGGTTTAGAAGTCAGAGGAATCAGAGATCAAATTGCCAACATCTGTTGAATCATAGAAAAAGCAGGTGAATTCTGGAAAAATATCTACTTCTGCTTCACTAACTACGCTAAAACCTTTGACTCTGAGGATCATAACAAATTGTAGATAACTCTACAAGAGATAGGAGTACCAGACCACCTCACCTGCCTCCTGGGAAACCTGTATGCAGGTCAAGAAGCAACAGTTAGAACCGGACATGGACTGCTTCAAAAGGAATACGTCAAGGCTGTACATTGTCACCCTGTTTATTTAACTTATATGCAGAGTACACCATGTGAAATGCTGGGCTGTGAAGCACAGCTGGAATCAAAATTGCCTTGAGAAATATCTGTAACTTCAGATATGCAAATGATACCACCTTAATGGCAGAAAGTGAACAGAAACTAAAGAGCCTCTTGAAGGTGAGAGAAGAGAGAGAAAAAGTTGACTTAAGAATTCAACATTCAGAAAATGAAGATCATGGCATCTAGTCCCATAACTTCATGCCAAATAGATGGGGGGAAAATGAAGACAACGACAGACTTTATTTTCTTGGGCTCACAAATCACTGCAGATAGTGACTGCTACCATGAAATTAAAAGATGCTTCCTCCTTGGAAGAAAAGCTATGACAAAACTACACAGCGTATTAAAAAGCAGAGACATCACTTTGCTGACAAAGGTCCTTATAGTCAAAACTATGGTTTTTCCAGTAGTCATGTATGCATTTGAGGGTTGGACCATAAAGAGGGCCGAGTGCTGAAGAATTGATGCTTTTGAACTATGGTGCTGGAGAAGACTCTAGAGAGTCTCTTGGACAGCCAGGAGATCAAACCAGTCAATTCTAAATGAAATCAACCCTGAACTTTCATTGGAAGGACTGATGCTGAAGCTGAAGCTCCAGTACTTTGGCCACCTGATTCAAATAGCTGACTCATTGGAAAAGACCCTAATGCTGGGAAAGATTGAAGGCAGGAGGAGAAGCGGGTGACATAGGATGAGATGGTTGGATGACATCACCAACTTAATGGACATGAGTTTGAGCAAACTCTGGGAGATAGTGAAGGACAGGCATGCTGCAGGAGTCACAAAGTATTGGACACAACTGAGTGACTGAACAACAACAAAATTAAGACCTACCGCATTAAGGAATCAGAAAAAGAGAAATTAATTGAACCCCAAATCACTTGCTACATGAAAGAACTGAGCTCACAGGAAAGACAAATTACTGTGAGCTTGATTACTCAAAGAAATATGCACAGAGGAAGTGGACCTTAAAGGAGGGACTTCCTCCAGTTGTTGCTGAAATGGTAAAAATTCCACATCTCAAAAAAAGTGGCTGTCCACATCTCTAATGACCTTAGAGGATCCTCAGAGGAAGAACAAGGCCCTGTGTATATGAGGCAAGCATGTTCAAGCCATTCTGTAATATCTGGATCAAAATGTGTGTTGTTTTAAATTCTTATATCACTTGCTTGCAGAGCAAGCAATGAGAAAACAGGATGTTTTAGGCCAAATATTCAGCAGACTGCAGAAACTTCTGCTTGAGATGCCACTTCTGGGATATTTACAATAACAGAGAAACTGTCTCTGATTTATTCCCATAGCTTTTTGAGTTTGGACTTCCAGAAGTCCTTGGAATGAGTGTATTGACAAGCATCACAACACTACCTTCTTTCTCTAGCTCTGTCCTTGCCTATAGCAGGCTGTGTTCAAATTCCTCTAAAGTAAGAACCTGTTTGTTTAAGAAACCTTGGGGTTAGGGGTGTACAACTTCCACTGATAGCTCACACTCAAGCCAGCCTTCAGTAGAAGAAATTTCTCTTCGCATTCTAATCTAAATGACTCCTTCAATAGTTTATATGTTTTCCATTCTATGTATATAATAAATATGGAAAACTGTTATATTTGCTACCCCATGCGTGATTTTAAATGCCCAACATAGATGATAATGTATTTCAAGTCCATTAGGTAACTTACAAAATAGTAATAAACTACATTTTATTTATTTTCTTTGAAGGGTCTTCTTAGATGTCCTGTCCCATCTAAATTCCTATCTAAATTGTATGAACCTTGAAAATTGCTCTCCAGTTTAAGGCACATATATATTTTTTCCCTGATGTGGGTAAAAAAAATTCTTAATTTTGTACATAAGCTGAAAAGTAATGGTAAAAAGTTGGTCTCACTCAGATTGAAAGCAGGAGAGACAGGCTATGTCTAAAATCAATCTGTCTGCTGGAAATTCATTGACCCTCCTCCTTGTCTTCAG
Seq C2 exon
GTTCCGTGGTTTCTGCCTTGAAAACCCAGGCCCAGATTCCTTTCCCTCCAACACTGTTCAGAATGGTTCGCTTGGTTCGGATTGGCCGAATCCTGAGACTTGTTCGAGCAGCACGAAGAATCAGAACTCTGCTTTTTGCTCTGATGATGTCCCTGCCCTCTCTATTTAATATTGGTCTTCTCCTCTTTCTGGTTATGTTTATTTATGCCATTTTTGGTATGAACTCTTTTCGAAAAGTGAAGGAAGAGTCTGGAATCGATGACATCTTCAACTTCCAAACTTTTACAAGCAGCATGCTCTGCCTCTTCCAGATAACCACGACAGCAGGCTGGGATGCCCTCCTCAGCCCCATGTTGAAATCAAACAAGTCCTGTGACCCCAAGACAGAGAGCTGCCACCTCTCTACCATAGCCATAATCTACTTCGTCACTTATATCATCATCTCCTCTCTCATTGTGGTCAACATGTATATTGCTGTGATTTTAGAAAACTTCAATGTAGCCACTGAAGAAAGTGAGGACCCTTTGGGTGAAGATGACTTTGAAATGTTCTACGAAGTCTGGGAAAAGTTTGACCCAGAAGCAACACAATTTATCAAATATTCTGCCCTTTCTGACTTTGCTGATGCCCTTCCTGAGCCTCTGCGTGTGGCAAAGCCAAATAAATACCAATTTTTAGTCATGGACTTGCCAATGGTGAGTGGAGAGCGTCTCCATTGCTTGGATATTCTCTTCGCTTTCACCACGAGGGTACTTGGTGAGTCCAGTGGCCTGGATAGCATGAAAGCAGCAATAGAAGAGAAGTTCATGGAGGCCAACCCTTTCAAGAAGTTATATGAACCCATAGTCACCACCACCAAAAGGAATGAAGAGGAAAGATGTGCTGCTGCTGTTATTCAAAAGGCCTTTCGAAAGTACATGCTGAAGACCAGGTGTACCTTGAAAGACAGGCCTCATTCAACCCTCCAGACACTCTCCAATGGAGACTTACCCAGCTCTGGGGTGGCCGAGGGCAAGGTCCATTATGACTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017174:ENSBTAT00000022822:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.023
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(21.1=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(78.4=46.5)
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]