BtaINT0129391 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038180 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr2:31066082-31067407:-
Coord C1 exon
chr2:31067090-31067407
Coord A exon
chr2:31066201-31067089
Coord C2 exon
chr2:31066082-31066200
Length
889 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
GTGTTTGTTTTCTTTTTCAGACA
3' ss Score
12.31
Exon sequences
Seq C1 exon
CACTTTCTTATGCAAGGAGCTAAACAGTGATTAAAGAAGCAGGATGAAAAGATGGCACAGTCAGTGCTGGTACCGCCAGGACCTGACAGCTTCCGCTTCTTTACCAGGGAATCCCTTGCTGCTATTGAACAACGCATTGCAGAAGAGAAAGCTAAGAGACCCAAACAAGAGCGCAAGGATGAGGATGATGAAAGTGGCCCAAAGCCAAATAGTGACTTGGAAGCAGGAAAATCCCTTCCATTTATTTATGGAGACATTCCTCCAGAGATGGTGTCAGAGCCGCTGGAGGATCTGGATCCCTATTATATCAATAAGAAA
Seq A exon
GTGAGTTCTTAGTCAAGTTGCCTTTATTTCCTCTACTTCCTAATTGCTTCTGGGCTAGTGCGAGGCATGTTAGGTGAAGAATGTTGTGCCACCTCCCCTCTGTCTGAAGTATCACTATGGTAGTAATGGGCTTGACCATGCCATGGCCCCGTTGTCCTAGAGTCTTTGGGAAGCACTTATTTGAACCCACGACCAGGACAGGCAGAGAGCTGAAAGAGCATCTTGCAGTGGGGGAAATGAGGAAGGGCAAAAGTCTGCTGACCTTACAGTGTGGTGAAGCAGAAAGTAAAGACAAGGAGTTTATTTTTTATGCATTAAAAACAATATTTCCAGGAGTCGTATACAAAGTTCTCTTTATAATATCTAGCTCTACAAAAGGTACTTTGATTTTCAGCACATTTATTCCCTCACATATAAATTTGGCCCATTCCATGGTTCCCTCAAGAAGAAATAAAAGCAGGTGACTTCCAAGTGCCCCCTAAAAGCATTTGATCAACTACCACCTCCAGAAAACACTGAAGTTCCTGTGAGAAGGCTTTTATCAAATTGAAAAAGTAGTCAAAGCCTCATTCTTGAACTCTTTGTGAATTATAAATACAGTTTGAAAATACTGATATTAAAACTTGATGGTGATGCTAAGTATTCCTATGGTAATGACTATATATTTTCTTTATGTTCCTTAAATCCTCATATCCCTCGCCAAATTAGGGGAGTTTATAGCATTCAGAAAGAGAAAATACGTAGCATCATGTCATATGTTAGTAGTTAGTATATTATTATTTTATAAAATCATATTTCTAAAAAAATTTTATCACTTTTTTCTCAAATTGTTCTTAGTTTTAATATTGCATTTCTAACTTCTGTTTTATGTGTTTGTTTTCTTTTTCAG
Seq C2 exon
ACATTTATAGTATTGAATAAAGGGAAAGCAATCTCTCGATTCAGTGCCACCCCTGCCCTGTACATTTTAACTCCCTTCAACCCTATTAGAAAATTAGCTATTAAGATTTTGGTACATTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038180:ENSBTAT00000061380:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.360 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
AGCAGGATGAAAAGATGGCAC
R:
AAAATGTACAGGGCAGGGGTG
Band lengths:
349-1238
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]