GgaINT0048560 @ galGal4
Intron Retention
Gene
ENSGALG00000011040 | SCN3A
Description
sodium channel, voltage gated, type III alpha subunit [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr7:19433846-19436971:+
Coord C1 exon
chr7:19433846-19434202
Coord A exon
chr7:19434203-19436485
Coord C2 exon
chr7:19436486-19436971
Length
2283 bp
Sequences
Splice sites
5' ss Seq
GTGGTATGT
5' ss Score
7.64
3' ss Seq
TGTATTCTCTCATCTTTTAGGTT
3' ss Score
12.52
Exon sequences
Seq C1 exon
CTTCGAGTTTTTAAGCTGGCAAAATCTTGGCCAACTCTAAATATGCTGATTAAGATTATTGGCAACTCAGTGGGGGCTTTGGGTAATTTGACCCTGGTGCTGGCCATCATTGTGTTCATTTTTGCTGTGGTTGGGATGCAGCTGTTTGGAAAAAGCTACAAGGAATGTGTCTGCAAGATCTCCAGTGACTGTGTGCTTCCACGCTGGCACATGCATGACTTTTTCCACTCTTTCTTGATTGTATTCCGAGTTCTGTGTGGAGAATGGATAGAAACAATGTGGGACTGCATGGAGGTTGCAGGCCAAACCATGTGCCTTATTGTTTTCATGCTGGTCATGGTGATTGGAAACCTAGTG
Seq A exon
GTATGTGATGAACACTTTTAAATTGTGATACAAAAATATATATTATGTACAGCTAGACAATAAGAATGTTATGCTTCTATTTGGAAGAAAGAGATAACTGCTTGAGCTAGATTTTGGGTAAAAAAAAAATCATTCTCTTTGCTTTTTCACTTTTATTTCCATTCAGTGAACTGCTGTTACTAGGGCTGTAGGAATGTATGAATGCACCAAAATGACTCACTGTGCACCCTACCATGGGAGTGATGGAACTAATTCACAGATGTTATTTAAATCCAGATGTTATCAGAACTCATCTTGAAATAATAAAGATTATGCTGCACCAGCTCATGGGCAGCATCTTGTTTGGAGATTTAAAAATAAAAAAGGACTTTCTTGCACTCATTGCAGATAATTCTGACACTAATACTTCTGACTTAATTAAAACAAAGTATGATATAGTTGTTATAGTAGCATATATTGAATTTAAGTACTCAACTTTTTGCCCTGCTTAGGTGTAGAAAGAAACCCCTAATATTTTCAGAGCGATTGGTCTTCCCTACAAAAAATGTGCTTCAAAAAATGAAAGTTTCTAATGCAAAATCACAGAATATTTTTTTATAGAAAAATTTTAATTCATGCTGACAATTAATGATGAAAGGTTCACATATATCATTGTGAAAACTTCTTAGAAATCAGGATTACAATTGGAATGCACAATTCATGTTTACACTTTAAGATTTCTTTTAATGTTCACAGTTAATTCTGAAATGCCTGGAATTTATATTTCATTGTATGTCAAAATTCTCTTCCTTTTGTGATTGACTTTAGTGATTTATTTTTATGATGAATTCACAATGTTTGTGTCCTAGTTGTTCAGACAACTTTGCAATCTTAACATTAGATTTGCAGAAATGTGAAAGCCTGAGAAAATTATTTATGATCAGTAATGCACTCCTTATTTTTTCAGCATTAACTTCTGGATATAAATACTGTTTCAGATTCATATTGCTTCATCTTTCTTTCAAATATTTACTTATTCAGATCTGTTGTTGTTGTTGTTTTTCCTGGAATTGTGAAGGTCTGAAGAATTACATGTTGAATAGAGTTAAAATGAGAGGTCTAACACATTTAAATAAGGGGAAATTTATTTCAGATAGGACTTGAGGTTTTTTTGGTAGCTTAGAGGGTGTTTTTGTTTGTTTGTTTGTTTGTTTGTTTTGTATCTTGAAATTATATAAATATGATAGAGAACAAAGCATTTTTTCTCAAATTCAGTAGAAGGAAGTTGATGTAGGCTGTCATTTTGCAGTGTCATGACAGCTTTTGATGCCTTGTGGCCTCCACTTAATCCAAATATAGGAAAGACCATGTTGAAGTCTTTTCAGCCATTTACCAATCCATTCCTTTAATAATGTGATTTTATACAAAGTTGTCATATATAAAACTGAAGGTATGAAATGATTTGTTGCTTGTAGGCTTTAGGGAAATAACTGTAGTTTATTGGAGGTGACATTAAAACAACAATAACGATGTTTGAATTTTGAAGTAACAAGCCACAGTTAGGACTGGTATCTGCTGATGAGGAAAGTCTGTTTTACTTTGAATTCCTATGTAAGATCAAATAAATTTTTCTTCTTTGCCAAGAGAAAAAGGAAAAAATCCAATTATAAATAATGTAATTATTAGTAACTGAGATTAAAGTAAAAATTTCATTTTGAAATATTCTTTCTATTCTTTTTACAACAAGCTTTATAGGACTTAAGAGAAAAGCTCAGAATTAACAGAATATCACAGTTTTATGATATAATCCTTCAAACACTATGTAGAAAATATAAGTAGGTTATTATAGCATTAACTGATGTAAGTTTCTAAAATAAATGCACCATAGAAATCTATCTAATTTTATAGGATGATACTTTTAAATTCTACTTAACTTCCAGGTGATTCCACTAAGAGATTTAGAAAGAAGCATTTCAGACCTCTGATGGATGTGTATAGCTACAGTTTTGTAATTTTTTAAATTTTATCTTACACTTCAAACAACCATGCTATATCAATAAAATAAAATAAAATAAAATCAGGAAAGAAAAAATGTTTAGATGTTAGCTTGTCCGTTTCCATCTTCTTAATATTGACCAGACCAGTAAGGAGAGGTTTTGTAATGGGAAGTACTAATTGGTTGTCTAAAATTAGCAAGTGTGAATGTTCTTCAAAACAAGCTGTGCTTTTTTTACACTATCCTATAAAAATATTAACTTCTTTACGCATGTATTTATTATACAGTTGTATTCTCTCATCTTTTAG
Seq C2 exon
GTTCTGAACCTGTTTCTGGCCTTGCTGCTGAGCTCGTTTAGCTCAGACAACCTTGCTGCTACAGATGATGATAATGAAATGAACAATCTCCAGATTGCTGTGGCAAGAATTCAGAAGGGAATAGATTATATTAAAAAAAAGATACAGGAATTCATACAAAAAGCCTTCGTTAGAAAACAGAAGGCTTTAGAAGAAATCAAAGCACTTGAAGAGATAAACAACAAGAAAGACAGCTGCATTTCCAATCATACTGCTGTTGAAATAAGCAAAGATATGAATTATCTTAAAGATGGGAATGGAACTACCAGTGGTGTAGGCACAGGCAGCAGTGTGGAAAAATATGTTGTTGATGAAAGTGATTACATGTCCTTCATAAACAACCCAGGCCTCACCGTGACAGTGCCAATTGCTGTTGGAGAATCTGACTTTGAAAATTTAAATACAGAAGAATTTAGCAGTGAATCTGATATGGAAGAAAGCAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011040:ENSGALT00000017981:15
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=0.160
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(62.1=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(4.2=4.9),PF065128=Na_trans_assoc=PU(61.6=85.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
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]