BtaINT0129510 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019137 | SCN7A
Description
sodium channel, voltage gated, type VII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10594]
Coordinates
chr2:29990336-29994583:+
Coord C1 exon
chr2:29990336-29990606
Coord A exon
chr2:29990607-29993510
Coord C2 exon
chr2:29993511-29994583
Length
2904 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CCTGCTTTATTTTTTCCTACACC
3' ss Score
1.03
Exon sequences
Seq C1 exon
AACAAGTTCCAACGATTCATCTTTGACTTGGTAACAAGTCGAGTTTTTAATATCATCATTATGACTCTTATATGTTTCCAAGCAATAACCATTATGATACAAAGTGATGAACAGAGCCCAAAAATCAACACTGCTCTGTTTTGGATTAACTCAGTTTATGTTATGCTATATATTGGAGAATGTGTACTAAAGCTCATCGTTTTCCATTGTAACTATTTCACCAGTGGATGGAACATTTTTGACTTCATGGTGGTTGTTTTCTCTATTACAG
Seq A exon
GTAAGATTTTGTTTACTCAGATTTTCACTTGTAATAATATTAATTCAGTCAACCTCTTATAGTAATCATCTTCTGAGGTATAGTCTCTTAATAAACACAGGAGGTGGAGGACTCTTTATTTCCAGCAGGAATGCCTTGAAAAAAGTGAAAGTGTTAGTCCATCTGGGACACCAGGAGAGCCCCAACTTCCCCCAAGGAATACTGGAGTGGGTAGCCGTTCCTTTCTCCAAGGAATCTTCCTGACCCAGGGATCAAACTCAGGTCTCCCACATTGCGGACAGATTCTTTACCGTCTAAGTCACCGGGGAACACCTTACATTTTTACATTTACATATGTACACATGCCTGAAAGATATATAACATACTGAAAAATACTTTCTGAGTTAATATATAGACTTTATTACACAGACCACCCGATAAATGCTTAATTATCCCTTCAGTATATCACATACATTATTTAAGATGACACCAGCAGGACCTTTATGTTTTAGTGTGATAGAACCTTTCGAACTCATTGTTTTCTTTCCTCTAATCTCTAAAATCATTTACTACTTTCACAACACTAGAGTTTTAGGCTTTTATGAAATGGTCACAAGTTTTCTCTTACTCTGGAGATCTCAGTCCTTTATTTAACAGATATATTTGATTATCCTCTTTGTGAATAGGTATTATGCTATATGCAAAGAATTCAGTAGCAAATGAGGTAGGCATAATTCCTGTATATACATAGTTTATAATCTATCAAAGGATACAGATAATTAAATAGGACATTTTAATGTGCTATTAAGGTATTGGTAAGGGAAGAAGCACAGGGTGCCACGGCAGCACAATAAAGTGAGATGCACATAATCAGTAAGTAGAGGTCAGAGAAAGCTTCACAGAAGAGGCAGAAAACTAATGGAGACCCACTGGTTAAGGAGGTAGCCAAGAATCTAGGATAAAAGTGTTCTAGGCAGAAAAGGCTTACTGTCTGCCTCCCATAAACACATACTAGAATGTTATCTCCATAAGAGTATGGACAATACCTCAGTGTTACTGTCAAGTACTATTCTGTGCAGTCAGTAGTGAAAATGTGGATAAACTTTCTGCGCAGTTGTACCTCCAGAAAATTAACTCGTTCAGCAGGTAATAGAGGCAGTGCAGGCAACACTGATAGACAGTAGCAAGAAGCTTCCTAGAAAAGTACATGAAGTCAGGAGAGAGCTGAAAGGAGGAAAACGGAGGAAAATGAAAGTAAGGAGCCATGTGGTTTGAAATGAGAGTGAGTAATTGAATCAGACATATAGAAGGAGAGGAAATTGCAGTCTGAGACAAAATGTTTAAATTTGAGATCTCAGAAGGTCAGCTATCCTGGGTTCAGAACATACTGATAGATAGGTATAACTAAAGTAAAATGATGGAGAGTCTTAAAGTTAACAAAGCCAAAGACTGAAAGATGGGTGCTGGTGGAATGGACAACACTGAGCCGTGTACTAAAGTCTGTAATGAATATGAATGAGGGGGAATGAACAGATCATAGAGCTAAGGAATGGTAGGAGATGGTATAGTTGAATGGCATGATCCACAAACTGTCAAAATTTTTTTCTTTATAAAATTAATGTGAAAGAGAAGTATCTGGAAATCACACTGGAAAGAAGGAAAGATGCTTGCTCGTTCCATCTTTCTACACTGAGAAATGTTGAGTGGGAAAGAATGAGCTGTCTGTGCTTGAGGGGAAGTAGTGTCCTCAAGATAGACAATTTTCTTCACTTCCTTTCTTATCTAAAATCTTAGTGAACAAGGAGTAAAGATGTGTTTACAATTAAAGAGGGAAACCTCCTGCATAATGTAAGAGTTTGGAAGATTGAAGAGAAATGAACATTTGAGTCAGAGTAGAAGGTTCACTCGGAGAAGTCAATGGCAACCCACTCCAGTATTCTTGCCTGGAGAATCCCAGGGACAGAGGAGCCTGTTCGGCTGCCGTCTATGGGGTAGCACAGAGTTGGACACAACTGACGCGACTTAGCAGCAGCAGCAGCAGAAGGTTCACTAAAGCACAATGGAGAGGGGGATACATGTAAGATATAACCATATCAACAGAAATGTGAGACACAATCCTTCCAGATTCAGCAAATATACCATCTCATTTAGAAGCTCCATAGGATTTTCCCCTTCTCCATCTTTTCAACTCAAAATGAACCACACTGTTTCCGTACTTCCAAAGAACTTTCCTTATATATTTTTTATGGTAATTATAATTTCACCTTGTTTTATAGTTATATGTCTCACTCTCATAGTTCTCTTTTCACCACAGCAGGAAAGAAAAATTCTAGACCGAAACTTGTTTATTCACATTTAAAGTTCCTAAGGGTCCATATGGTATTTATCAAGTTAATAAACCAAATTATAATCTATGAATCTGAATGCAAAGTATTTTTTCAATTATATTTATCAACTTGGTCTTTCTGCTTTGCATAATAATTAGTTTAAATGTCTACCTCTACTGTGTATATCATATGGTCTTTGAGGATAGAAGTCATGTCATTTATCTTTGCATATTTTCATGGTACCTTTATTAGGTATCCAGTAAAAGTTGATTTGAACTAAATTGCTGGGTCTAACTGCAATCAGAAAAAAAAAATATGACTACTGTCCTACATTATGGATATATGCCATCTGTGACTCCAGAAGTGTCTGATCCCTAATACCCTGGAAATTATGGTAGAAATAATTCTCATCCAAATCCTCATCCAAATTTGTTAGATGCTGAATATTGCCACTATTAGTATTTGGCTTAGCCAAACTTTCAATGTGTGCCAAATGTTATAGGGGAAGGATTAATTATCTGAACATGTAGAAAAAAACAAATGTAAAATAATTTATATTCCTCTAAATAATTGTATTGCCTGCTTTATTTTTTCCTAC
Seq C2 exon
ACCAAGGACTATTTCTGCCTCTGATGGTAGGATATTACCTTGTATCTCCTTCCCTTGTGCAACTGATACTTCTCTCACGGATCATCCACATTCTGCATCCTGAGAAAGGACTAAAGTTGTTCCATAATCTGCTGCTTCCTTTGATGCTGTCCCTCCCCGCCTTGTTGAACATCAGTCTTCTCATCTTCCTGATTATGTTTATCTACGCCATCTTCGGAATGTACAATTTTGCCTATGTTAAAAAGGAAGCTGGAATTGACGATATGTCCAACTTTGAAACCTTTAGCAGCAGTATGCTCTGTCTTTTCCGAGTTACAATATTTGCTGGTTGGGATGGGATGCTCAATGCAGTTTTCAATAGTAAATGGTCTGACTGTGATCCTAATAAAATTAACCCTGGGACTCAGGTTAGAGGAGATTGTGGCAATCCCTTTCTTGGGATTATTTATTTTGTCAGTTACATCCTCTTAACTAGGCTGATCATTGTAAACATGTACATTGTTGTTGTCATGGAGTTTTTAAATATTGCTTCTAAAAAAAAAGCCAAGACATTGAGTGAGGAAGATTTTAGGAAATTCTTTCAGGTATGGAAGAGGTTCGATCCTGAGAGAACCCAGTACATAGACTCTAGCAAGCTTTCAGACTTTGCAGCTGCTCTTGATCCTCCTCTTTTCATGGCAAAACCCAACAAGGGCCAGCTTGTTGCCATGGATCTTCCCATGGCTGTTGGAGACAGAATTCATTGCCTTGACGTCTTACTTGCTTTAACAAAGAGAGTTTTGGGTAAAGATCTGAGCATGGAGAAAGTTCTTTCAGAGATGGAATCAGGATTGACATTAGCTAACACTTTTAAGATCACATATGAGCCAATTACAACTACTCTGAAACGAAAACAAGAGGTAGTCTCAGCAACCATCATTCAGCGTGCTTACAAAAGCTACCGTTTGAGGCAGAATGACAAAAATACTTCAGATACTCATATGATAGATGGTGACAGGGAAGTTCAAGCTATCAAAGAAGATTCCTATATTGATAAAGCTGAGGGAGTGTCAATACTTCAAAGCCAGATATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019137:ENSBTAT00000038441:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.036
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.2=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.3=47.2)
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]