BtaINT0129404 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038180 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr2:31044782-31046508:-
Coord C1 exon
chr2:31046445-31046508
Coord A exon
chr2:31044924-31046444
Coord C2 exon
chr2:31044782-31044923
Length
1521 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
TTCTTTTCACCTAATCACAGCCA
3' ss Score
5.24
Exon sequences
Seq C1 exon
GTCACTTTTATTTTTTGGAAGGGCAAAATGATGCTCTGCTTTGTGGCAACAGCTCTGATGCAGG
Seq A exon
GTAAGTGCTGTTTTGTGTCGAGCCTCAGTCTACACTGCTCCATAGGCCTTAACCTGCCACTTCCCGCCCACCCTGCCCCCACCTGCTCCTCATTCAAAGCCCTCCATAAATTCCACTTCACGCTGACTCAAAATAGCTGGGATAAGTGTGGATTCTCACCTCCTTCACACACTCAGGCAGCAATTATTTCTCCATACTAGGTCACAGCTAATCTTCCAAATTAGTTCAATGGAAAATAGAAAGAAAAACAATACATATACATAAAAAGCTCAAATTAATAGAATTCATAACCATGTTCTTTTGTAAGTGTGATATTCTATATATACTAATGTGGTCTCCATGGCATAAAATATATCTGAGGATAATGTCAGTATCTGATCTGTGGTGAGTACGCGTTTAGCATATTTTAGCAAAATGGTTAAGAGCATAGACCGGAGAGTTTACACAAATTCAAACCCGAACTTCACCATATAATGTCACCTTTCCTTGCCCTGATTTCCCCATGGGATAAGTGGGAATAAATTATAAGGTGGCTGTGAGAATTAAATGGATTAATGAATGTATAGCTATTACAGCATTCTCTAAGTACTTTTAATTATCATAACTCGCATTATGTGAATGCTTGTTTTTAAGAAGCATTTTCCCTGGAGCTAAAGCTAGGAGGAAAATTCAGAGAAATAGTTCTTTTTGTATTTACAAGATTTTAGAATCATAAATGGAAGGCTGATGTTCTTTCTGAGGAAGGTGCTATTGTGGACATTAGTAACTAGTACCTGTAGCAGAATCCCCAACTGTAACAAGCTTTGCATTTGGCTCATATGATGTTGTGCTGCGTTTATCTCCAGATCTTAATGATAAGTAACACAGACTGATTTTAACTCTTCTCTGTACTGTACTGAGTGTTTTACATACGATGCCTTATTCAGTGATTGTAAGTTTGGAGGCAGGTTGTGTTATTAGCCTTTTCTTACATACAAGGTGTCCCAAACCAGCAACTTGCCCAAGATCACACAGCCCAGAGTGTCAAGCACAATGTTGAGTCCAGGTCAGCTCAATCATTAAGGTCATGCTGTGAGATGTTCACTCTGCAGACTCATTCACTCTTCTTGGTATGTACCCCCCCGATCTTTTTCTTACCCCGCTTTCCTACCTCCACACTCAACACACTTCTGCCTTTAGGTATCTTCAGTGAAAATCAAATTTTTCCCTGCAGACTTATTTTTCTGTTCATCTTCACAAATATCAGAAGATAGTAATCATAATATGATTGCTCTTATAGGGAGACATGATAAATATAATAATGGCAATCATAAATCACAGAGAAATCCACAAATAGACTTAGCAGATCCTGTTGTTATGTAAATCAGTCCCCTTAGTCCTGGACTCAGCACTGAGTAAAGTGAGAACACTCTGCTTTTTCTTGTGTTGCATAAAATAGACATCAGGATCTATAAAAACAGGAAAGCCAGCCATCCAACTTTCAGTGACTGATGTCCCCTCTTTCTTTTCACCTAATCACAG
Seq C2 exon
CCAGTGTCCAGAAGGATACATCTGTGTGAAGGCTGGTCGAAACCCCAACTATGGCTACACAAGCTTTGACACCTTTAGCTGGGCTTTCCTGTCCTTATTTCGTCTCATGACTCAAGACTTCTGGGAAAACCTTTATCAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038180:ENSBTAT00000061380:8
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=FE(7.8=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(17.5=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:
TTGGAAGGGCAAAATGATGCT
R:
CAGCTGATAAAGGTTTTCCCAGA
Band lengths:
192-1713
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]