BtaINT0129417 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019385 | SCN3A
Description
sodium channel, voltage gated, type III alpha subunit [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr2:31257975-31259379:+
Coord C1 exon
chr2:31257975-31258095
Coord A exon
chr2:31258096-31259224
Coord C2 exon
chr2:31259225-31259379
Length
1129 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAC
5' ss Score
8.14
3' ss Seq
CAATGTATGCTATCTTTTAGGAT
3' ss Score
8.38
Exon sequences
Seq C1 exon
AAATTAAATGCAACCAGCTCATCTGAAGGAAGTACAGTTGATGTTGCTCCACCTCGAGAAGGTGAACAAGCTGAAATTGAACCTGAGGAGGACCTTAAACCAGAAGCTTGTTTTACTGAAG
Seq A exon
GTAAACTAGCTCTAAAATGGTTAAATCCAATCTCCCCCTCTTTCCTTACAGACTAAATATACCTCACTTGAACAAAATATTTCAAAGAAACAGTGAAGGCATATTTATCTTTGTTTTGCTCTTTTCTTCCAAAAAGTTCATTTATCTGTATTTCCTGATTATACTATAGTAGTTACTGTGCCTGGACAATAAGATAATTTGACATGTCCTTTTTTTCATCCCAGAATGTGGAGAAGTGAACCCTAGGAGATAAATGGTATTCTGGAACATCTTCTCATTATTGACAAAGCAATCCCTTCAGACTTCACTGGCAATGTTGTGATTTGATTTATAGATGCCGCAATAACTATACCCCATCTCTTACAGCTTCAAATGTGGTTAATTTGTGCTGTGACCAGAGGTGTTGGGGGATATAGATGCATTGCAGAGCCTTGGCAGGGAGACCAAGTTATTTTCACAGCCACCAGTACAGTGTCCAGCACACAAATCAATAAAGATTTGCTGATTCCATGTGATTGGACTGAATCCCATAAGTAGTAACTCAGACAGTTAGAGCCCAAGAGTGGATGGAAGTTAGAAATAATATGAAAGCGAAGAGGGGGAGGACAAAGGAAGAGAGATACTGACTGACAAGATGAGTCATAGGTGTGACTAAGAAAAGCTCTGAGGTTGAAAATAAATAGCTTGGGAAAACTGACAGAGGATGAGACCCAGGAAGACAGAGGGATTTTCCATGTGAAAAGAAGTGAGTAAAAATCTAGGATCACACAAAAAATGAATAAACAATTTGAACATGTAGTTTTTCCCCAAACCTCAGAGATGTCCTTATCTATGATTGGCCTTGAGGCAAAGAGAGATCCTATGCAGTGTTCAAGAATGGAACTGTTTGTACTCAGGTAACTCTCGGTAAAGTAATTCCTTGATTTCTAGGTAGCTGGCTCATATGTAAGTCTGAGAATAATTCCCTATACAGGAGGGAAGCTGAAAATAACTACGAAATGAAGTAGCCAGTTACTATATAAAATGATGATTTGAGACTAGGATGGGGAGGGAGCAGCAAAGTTAATTTCTTCCTACAGAAGATGGAAATATATTTTTCTAATGTATTACAATGTATGCTATCTTTTAG
Seq C2 exon
GATGTATTAAAAAGTTTCCATTCTGCCAAGTAAGTATAGAAGAAGGCAAAGGAAAAATCTGGTGGAATCTTCGGAAAACCTGCTACAGCATTGTTGAACACAACTGGTTTGAGACTTTCATTGTCTTCATGATTCTTCTCAGTAGTGGTGCTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019385:ENSBTAT00000025829:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.756 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(18.3=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(20.1=84.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATGCAACCAGCTCATCTGAAGG
R:
CAAAGCACCACTACTGAGAAGA
Band lengths:
270-1399
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]