BtaINT0129500 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019137 | SCN7A
Description
sodium channel, voltage gated, type VII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10594]
Coordinates
chr2:29972266-29975833:+
Coord C1 exon
chr2:29972266-29972706
Coord A exon
chr2:29972707-29975730
Coord C2 exon
chr2:29975731-29975833
Length
3024 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
TGGTGGGACTTACTTTTCAGAAA
3' ss Score
6.07
Exon sequences
Seq C1 exon
ATACTTTACCTGTTTCTGGCGTTGATCATCTCATTTAGTTCATACAAGCCTGCAACAACTGAAGAATTCTCTGAAGAAGCAAAAAATCTCCAGCGTGCAATGGCAAGAATTAAAAAAGGAATAAATTATCTGCTTTCTAAAATAGTATGCAAAAAACAAAATGTTCTAGAGGAAACAATGGACAATATAAGTGACGTCTATGTTAAAGAGAATATTTCTGACCATACTCTCTCTGAATTGAGCAACACCCAAGATTTCCTCAAGGATAAGGAAAAAAGCAGCGGCACAGAGAAAAACACAATGACCGAAAATGAGAGTCAGTCACTAATCCCCAGTCCCAGTGTCTCAGAAACTGTACCCATTGCTTCAGAAGAATCTGATATAGAAAATCCAGACAATAAGGAGATTCAGAGCAAGTCAGGTGATGGAAGCAGCAAAGAG
Seq A exon
GTAAGTTGTTTTAACATTATGGTTTCGTACTGTTGATTGATGGCACTATTGACAAGGAAGTGAAGCAATGCTGAAGTTCCAAAGTTAGGTTATTATCCATTCAGTCCTAGCTGTAGCACTTCTTCTCCTGATCCAGTTTCTTAAACTTCCTAAGTTTCTTCATCTGTGAATGAGGATAAAATTGTATCTATTTCTCAGAAGAGATAGAAGGATTAAGAAAAATAGTTCAATAGTGCATAGAATAATGTCTAAAATATGGAAGCACTTAGCAAACACTAGATAACATAATTGTAATATCTTCAGTTAATGGGGTGATAAAAAGCATATTGAAGAAACCTAGATTTTTATAATTAATGCATACTACTGGAGAAGTCACTAAACTGTCCTAGGCTTTATCATCTTTAAAATATAAGATGGGACTAGAAGAGTGCTAAGATACAGATATTTTCCTACTTGCTAATATTTTAAGATTCTTGTCAGTTTATTTCTGCAACATACATTATAACATGGGAGAAGGCAATAGCACCCCACTCCAGTACTCTTGCCTGGAAAATCCCATGGATGGAGGAGCCTGGTGGGCTGCAGTCCATGGGGTCGCTAAGAGTCGGACACGACTGAGTGACTTCACTTTCACTTTTCACTTTCATGCATTGGAGAAGGAATGGCAACCCACTCCAGTGTTCTTGCCTGGAGAATCCCAGGGACACGGCAGCTTGGTGGGCTTCCGTCTATGGGGTCGCATAGAGTCGGACACAACTGAAGTGACTTAGCAGCAGCAGCAGTTGAGTTGGACTTAAAGACCAAAGGGTAAAAGAAACATCAGTTGTAAATGTAAACAATTTGTTGTTGTTGTTTAGACACTAAGTCGTGTCAAACTCCTTTGTGGCCTCATGGATTGTAACACACCAGTCTCCTCTGTCTGTGGGATTTTCCAGGCAAGAATCCTGGAGTGGGTTGCCATTTCCTTCTCCAGGGGATCTTCCTGACTCAGGGACTGAACCCACATCTTCTGCATTGTAGGCAGATTCTTTACTGCCTACAATGAGCCACCAGGAAACCCAAAGGAAAAAAAAAAAGGATCACCTTTAAAGAAGGGCAGATACTGCCTTTCACTTAGCTTTAAAAATGTATACCTTAGTGAATCCAGTCTTACTGTCTTCATTTGCAAGTAGCACAGTGTCTTAGTAGGAGGTGCCATTTAATCTACAGGGATCACGTGCAGTGTAAGCCACTTCCATTGAACTTCACTAAAGAATTGTTTTATTTCATTCACTGGCATGGGGCAGGGAAGATAATGTCTTTTTCCAGATCCTCAAAGTCTCTGGCACCATCTTATCTCCCAGACCTCTTCCACCTTATCAGCTGCTCTCTGTAATAGCTTATCAAATTGCCCTTCTAACAGGAATTAAGTTTCAATTATCTAGAGCCCTTCTAGTTTCTGGTAAAGGCATCTTTGTTTCAGAGAAACATTTTCACTCCTTATCATACCTAATCTTGTCAGGTCCATTTTCCTTCAATTAATAGCATTATTAGGAAATGAAAAACATTCTTCTTTTGCACACTGATTTTATTTAAACTATAACAACATTATAAGGCATGTGCTACCATACATTTCTGGGTAAAATTGCTATTTATCGCAACACATTATATGTTGCGATAAACTTCTTGTCAATCTGAAAAACTTCTTGTCAGTCTCATTAGAAAGTCTGAGATATGAAATATATAGGAAAGATGGAACTTAATATAACTGTAAATGTTGAAGTTTTAGAAGTTATTACTTAAGATGCATAATTATTTGGTTCTTTTGATTGATTAAGTACTCAAAGAAGATTTTATCATTTATATATTTCATTATATATTTAATTAATCACTTTCCAGATTATGTAGCCCAAGAGTATTTAGGATGTTGATCTAAAAAAGCAAAGAATAAAATATAAAAATTACAAGTGGTATGATCATTCAGAGATTCATGTTCTTGTTTCTTTGGTATTTGAACTTTTATCTTTTAGTACAAATATATAATTATATAAATTTCATAAAAATAACATCAAACTTAAATCAGATTTTGAAACACTTTTTTTCATAATGTAGCCATATATATTGGTCACTAAGTAATCTTTTACTAAAATGGTTTATAATTTTGAATTTTGATTTATTTATAAATTTAAAATAATAAATACAGGATTTTGAGAAAATCATATCAAATAATTTATGTGTGAGGGTTTTAAATACTCTAATGAATCATTTAAATATATAGTGTATGATTTTCAATTATTGTATGCTTGAATATTACATAATATTAATTTATTATCTACTCCCAAATCAATGCATTGCTATACCTTATTTTATCAATAATAAAGAGAATACAAAGGGAAATCAAATAACCTTTTAAAAGGTTTGTTTGTTTAAAAGTAATATCCTGCTGACTATTTTATGTTTTTAATAGAGAAGTATAATGTCTTAAAATTGACAATATATGGCTTAAAGCAAACAAAACTTGCTAATTTTATTTCTTTGACATTTATTGTGCAAAAGACAGAGGTAGAACAAAATATTTGTAGTTTTTTATATATTCTAGCTAGATTTTTCAGAAATTTGGGATAGCCTATACATCTTTTAGAACAGTGTTATTCACTATATATTCATTTTAATGTGAAAATTATTTTATCTTAAATTAATTTTTAAAATATCTTTAAACATTTCAACTCCCAGAGATATGTATACATTTAAAATTTATTTTTAATTTCGTTTTTACTTTTTGTCCATGCCACATGGCACGTGAGATCTTAATTCCCTGACCAGGGATCGAACCCCTGCACCCTGCCTTGAAGCTCAGAGTCTTAACCACCAGGGAAGTCTCTGTATGCATTTTAATATCAATCATGAAATTGGCATAAAGTCTTTTACTTTGACAGTAGTTTTTCTGTACATAATTTTTCTTTTTCCTGAAAATGACATAAACTTTAGCTATAGTGAGTAAATGAAACTTTAATGGCAACTTTCTTGGTGGGACTTACTTTTCAG
Seq C2 exon
AAAGTAAAGCAGTCGAGCTCATCTGAATGTAGTACAGTTGATATTGTTCTCTCTGAAGAAGAAATGGTCTACGAATGTGAAAAGCCAAAGCATCTTAGAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019137:ENSBTAT00000038441:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.429 A=NA C2=0.114
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.4),PF065128=Na_trans_assoc=PU(60.6=83.7)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(16.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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]