BtaINT0129508 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019137 | SCN7A
Description
sodium channel, voltage gated, type VII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10594]
Coordinates
chr2:29987937-29990022:+
Coord C1 exon
chr2:29987937-29988074
Coord A exon
chr2:29988075-29989917
Coord C2 exon
chr2:29989918-29990022
Length
1843 bp
Sequences
Splice sites
5' ss Seq
AAGATAAGT
5' ss Score
2.82
3' ss Seq
TTTTTCTTTCATTGCTTTACCAG
3' ss Score
-0.24
Exon sequences
Seq C1 exon
GTAGATATGCAACCTAATTTTGAAAACAACATCTATATGTATTGTTACTTTATTGACTTTATTATCATTGGATTATTTCTTCCTCTGAGTATGTTGATTGGTGCTATTGTTGCCAATTTCCACAAGCATAAAATAAAG
Seq A exon
ATAAGTATAAATATTCTTTCTCAATCAGTGCCCATGGGGGGAAAATGTCCTGCTTCAAATAATTGGTTTTAGATTCAGCTTAATAGCATTTTTGTCTGGTACTTATCTTTAAAAATTATTTATGTTCCTGCAGATTGAATATTGCTAAAATGTTTATCTTTACATTATTTTCTATATTCAAATAAGCACAGACAAGTTTAAACATTAAACATTACAACTGTTTCCGTGTATGTGTTTGTAAATCATGACATGCTGAAAAATAGCATTCTTTTGTATCTGCACAAATATGTGAAGATGTTCAAGAAAAATAAACCACACTTTTTTATTCTTTGATGTACTCAAAGTGGTTCAAAATTGTACCCAGCAGAGACATCTTTGTCAGTTGAAATGGCTTTTTCTGCTAGAAGTAGAGGGTCATAAATCCTAATTAGGTGACCTAAATAGGAGTTCCTTGAAACAAATAAGAAAATTCAGAGGCAGAATTCAAAAACCCATATTCAGTGTCATCTCCACATGAAGACTCCCTTCAGGGCTTCTGTTAATACAAATGCCTCAAATGTCATATAAATCCACTTATTTTAACCTCAGGGATCTACTTTCTATTAAGTGTAGAAATGCCTTCTAGTGAATCAAAGAAAAGAATAGTTTAATCTTGAAATTTTGTATTTAGCAAAGTCATCAATCTGGTGTAGAATCTGGTGAACAAACCATTCTGAGTCTGCACTAATTAGATGGGGTTAGAGTACTTAGATGGGCTTAGAGGGACTGAAGCTAGTTAGCATGCATGCATGCAGAAGGATCAGTGGTCATTGGACTGTATACTTCAGCTTCTTAAGGATTTCAGCCCAATGGAATAATATCCTAGGATTTGCCCAGGGGCTTCAAATTGGTGAACCGCGTCAACTTAAGTGACCCAGGCCTGACATCGGGGAAGGCAATGGCAACCCGCTCCAGTACTCTTGCCTGGCAAATCCCATGGACGGAGGGGCCTGGTGGGCTGCAGTCCATGGGGTCGCTAGGAGTTGGACATGATTGACCGACCTCACTTTCACTTTTCACTTTAATGCATTGGAGAAGGAAATGGCAACCCACTCCAGTGTTCTTGCCTGGAGAATCCCAGGGACAGGGGAGCCTGGAGGGCTGCCATCTATGGGGTCGTGCAGAGTCGGACACGACTGAAGCAACTTAGCAGCAGCAGCAGTCCTGACATGGACAGTAACAATTCCTAACTCCTAGATTAACTCATTAAATGTTCACCTCTTATTCACTTTGCTTTTTCTATATAAGATACTGAAATTAACACTAGAAACACAAAATGAATAATTCCTAGAAGGTATTATGAAGGGTTGTAAGTACTAGGTGCTTTTGGAATAATAATGAAAAGATATCTTCTGATAGTATTTTGAAAATTAAGTAACCTATGAACATATAAAAACAAGTATATGACCAGTTCTATTTTTTCTTGATTACTGAAAGGTACAAATCAAGTTCAGCTTTTGAGGTTAACTATTCTTAGTAACCTTTCCAGATATCCTCTGCTGTTTCTCTTTTGTCTCTAACAAGAGGTAGGTCCCAGTAACTAAAAAGTTAAAATAGGGTTGACTACCACAGAAAAATGCATCAAAATATAATTGAATATCAATCTTTTCCAGTGTATACTCTGTATTTTGAATGGATTTTTGTGCAGAAAGTCAGACATGTTTAAACATTATATAGTTCATTGCAGTTAAGCATTCTTTAGAGGATTAAATCAATAATTGCCAAGCTTTAGAAAATGCATATTAATATAAGGTGAAGTGTGGATTAAATATGATTTTAGTATCTTTTTCTTTCATTGCTTTAC
Seq C2 exon
CAGGGAGGCTCAAATATCTTTATAACAGTGAAACAGAAGAAACAGTATCGTGCACTGAAGAAGCTGATGTATGAAGACTCTCAACAACCAGTACCTCTCCCAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019137:ENSBTAT00000038441:25
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=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(15.7=76.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TATGCAACCTAATTTTGAAAACAACA
R:
TTCTGGGAGAGGTACTGGTTGT
Band lengths:
238-2081
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]