GgaINT0047351 @ galGal4
Intron Retention
Gene
ENSGALG00000011040 | SCN3A
Description
sodium channel, voltage gated, type III alpha subunit [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr7:19463966-19468431:+
Coord C1 exon
chr7:19463966-19464236
Coord A exon
chr7:19464237-19465187
Coord C2 exon
chr7:19465188-19468431
Length
951 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGA
5' ss Score
9.14
3' ss Seq
CTCTTTTTTTCCTTCTCTAGGTA
3' ss Score
13.29
Exon sequences
Seq C1 exon
AACAAATTCCAAGGCATGGTCTTTGATTTTGTCACCAAACAAGTATTTGACATCAGCATCATGATACTTATCTGCCTTAATATGGTCACAATGATGGTAGAAACAGATGACCAGAGTAAGGAAATGGAAACAATTTTATCCCGGATTAACCTTGTGTTCATTATCCTTTTCACTGGAGAATTTGTCCTCAAACTGATTTCTCTTCGCCATTACTACTTCACTATAGGCTGGAATATTTTTGATTTCGTGGTTGTGATTCTCTCCATAGTAG
Seq A exon
GTAAGAGCAATTCCCTTTCAAGAAAGAACTAGTGGACAGAAAAGACAGCAGCTGTTTCAAGAATATGAATTTTTCTGTGTTCTATACAATTTGGTTGATCTTTATACTTTTTAGCATAAAATATGTTAAATGTTGCATATGAGATTTTTATTACTCTTATTAGGATCAGTTACCATCTTTAACATAAAGGACATGAAAGATCTATTTGGCACGTTAAATTAGTACATACACATTTGTAAGTGTTTATTGGTATACGCTAACCACAGATTTGCTTTCATTAGTAGAACTGAAGAGTCTATGAAGGCGGAGGGATTTTTAATTGCTTTTTCTAACTAAGGTCTTGGTGAATATTTAGATTTTGCCAGCTAGAAGTTGCTGACTCTCCAATGTGTAGATTAGTCATATGAAAAAATAGTCTCAAAGACTTTCCGATAAACCTAAGAGAAGCTTTGCTGAATATAGTGCAGATCCTCAGGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAACATTAATTCGCATAAATTAAGCCAATATATTCTTTCCTAAATGAAGGCAGTAGGCTCATCATCAAGAACTAATGATATCTAAGAGAAACTTCTCTTTCTGGCCTTTTTAGAACAAACGAGAACTCTGATAGACACTAAACTACCTTGTCATAAAACGACTTCTTTCTTTTACTTCTTTCCTTTCTTAGATATCATATCAGTATAAGGAAAACACAGTACTATTATAATTCTTTTAAATAAAAAGTAAGAACTTGTATGATGTTCTGCAATAACTAACTTTTCTAGGAATTCTGACATCACCTTTCATTTCTGAAAATAAAAAAGCAGAGACTTCCTATACTGATTGTTTTCAAGACAGCAAGAAATAAATATTTCCATAATTAATAAATAAATTAAAATGTTATTTTATGCACTCTTTTTTTCCTTCTCTAG
Seq C2 exon
GTATGTTCTTAGCTGAGATGATTGAGAAATATTTTGTGTCCCCTACTTTGTTCCGAGTCATCCGACTTGCCAGAATAGGCCGCATTCTGCGCCTCATTAAAGGCGCAAAGGGAATCCGCACTCTGCTTTTCGCTCTGATGATGTCTCTTCCTGCTTTGTTCAACATTGGCCTGCTGCTCTTCTTGGTCATGTTTATCTATGCGATATTTGGCATGTCCAACTTTGCCTACGTTAAGAGGGAAGTTGGGATTGATGACATGTTCAACTTTGAAACATTTGGCAACAGCATGATCTGCCTATTTCAAATTACCACATCTGCTGGCTGGGATGGCTTGTTAGCCCCAATTCTTAACAGTGGGGAGCCGGACTGTGACCCTCATAAAGATCATCCAGGGAGCTCTGTTAAAGGCGACTGTGGCAACCCTTCGGTTGGGATTTTCTTCTTTGTCAGCTACATCATCATATCCTTTTTGGTGGTGGTGAACATGTACATTGCTGTCATTCTGGAGAACTTCAGTGTTGCAACTGAAGAAAGTGCTGAGCCCTTGAGCGAGGATGACTTTGAGATGTTCTATGAGGTCTGGGAGAAGTTTGATCCAGATGCAACACAATTCATAGAATACAGTAAACTATCAGATTTTGCAGCTTCGTTAGATCCTCCTCTTCTCATAGCAAAACCAAACAAGGTCCAGCTGATTGCAATGGATCTGCCCATGGTAAGCGGTGACAGAATTCACTGCCTTGACATCTTGTTTGCTTTCACAAAGCGTGTGTTAGGGGAAAGTGGGGAGATGGATGCCCTCAGAATACAGATGGAAGATCGTTTTATGGCAGCCAATCCTTCCAAAGTCTCCTATGAACCAATCACAACCACATTAAAACGGAAACAGGAGGAGGTATCTGCTCTCATTATTCAGCGTGCTTACAGGTGTTACCTTTTAAAGCAAAAGGTTAAAAAAGTATCTAGTATATATAACAAAAATAAAAACAACGAAGGAGATGGACAAGTTATAAAAGAGACAATTATTGATAAACTAAATGGGAACTCCACTCCAGAGAAAACAGATGAGAGCTCCTCTACAACTTCCCCACCATCCTATGACAGTGTAACAAAGCCGGATAAAGAAAAATATGAGAAAGACAAAGCAGAAAAGAACTACAAAGGTAAAGATGTCAGGGAAAATAAAAAGTAAAAATGTAAGAATTCTGCTTGTGGGACAGCTTGTTTACAGTCTTTGAGAATGAAGCATCACCTGGACTCCTGCAGGAGGTTTATGCCAAACTGACAGTTTTTACATATATGTGTGTGTGTGTGCGCGCGTGTGTGCATATATATACATTATATATATACACTTAAGGTCAGTGCCTATAACAGAACAGTAAACCTTCATCATCAAACTGTGACTGTGAACCAGAGTAACAAACCTGACAACAGGTTTCTGTTTTCACTACAGCAGACACTGCTAAGAATGAGGGATAAAGCGGCTCCACAGAGAACAGGGAGCTTGAAATACGTGCAAAGCTATAGTTTGTTGTGTTTCACATACTGCAAAACATGTAGAACAGTACTTCTATTCACTGTTTGTAATTCAATGGCTACATCTGTCATATTTTTACAAAACTGGTATTAGTGTATCATTTTTTTAATTCACAGGTTGTTTACTATTATATGTGACTATTTTTGTAAATGGGTTTTATGTTGGGGAAAGAGGTATAAGGACCAAGTGTTCTACTCTCAGATTCACTATAACATACAGACGCAAGTGATTTGCATAGGCATGTTACACTTATCAGTCATGCCCAAATAAAAATATGACATTGCACAAAGCTAAAGACTTTAAGAACTTCCACGTTTTAGAGTGGGTTTTTAATTTGAGGCATCCTGACCACATGTATGGATGCATCTAGATTACGTACATCCAGATTAATGTGCCTGGAAAGTCTCCTCTAATTTCGAGGAATTTGCAATGACTTATTTTTATGCAAATCATTAAGCATGAACAAGTTCTTGTGTGAAAATAATCACAGCTAAAAAAAATATTGTACGGTTTCTACACTAGAAAAAAACAGCTTCACCAAAATACACCTGGGAGGTTTTTTTTTCTTTTTCAAACAGTTTAAGCTTTTTTCCTGGATTATTTAGTTATTGTGTTCTCTCATTAAGGCCAACATCCAATAAATATCTTTTGCTATGTAAATACTAACGGCATACTGCCGTGCACATTTGAGCATAGAACTAAATGGCTTTGCCACATTGAATTGCATCAGATATGTACCACAGTGTGGGTAATTTGCAAAAGCTCAACAGAACACTTTGTATTCTGTGTCATTATAGATAGTTTGGAGAGCATCACTGATGCATGTCAATGCTTTTGCTGCTGTATCTTGCTCCTTCCACTGTCTCCAATGTAGGAAGCCATATGTCAGTGGTGAGTTGAATAAAGTTGTCCAACCAGACCTCATTCTTTCAAATCATTAAGCAATAGTTTGCAGCTATTGATGAGCTTCTTTAGTTTTGCATTTTAAATTTGAAGTGGCTACTATATTGTGTAGAATCAGACTGTACAGGACATATTTCAAACTGTTTAACCTGTTGAAAATGTGGTTAGCATATATAAATACTGTAAAGAAATACCATTTGGCAACAGTTTTGTATATAAGAAGAGTGTCTTCAAGTTTAGGTCACTGTTTCTTATATTTCTTTCCTCATTCACTCAGTTTACTTTCTAACCACAGTAATTTCAAACTGAAATCATACCATAAGAAAAAAGTATTTGTAGACTATCATGTTTTAATATTATATTTGCATATATTTCAATGTGAAGTAAATTGTGTAAATCTGGAACCCAGCTTATTGTTTCCAAATAGGTATATCTGGTAACTGGACATAGCAAGGAAATACTAGGGAAATGTGTGAATTACCAGTGCTGATCACATCAGAAGTTCCAAGATAGTCTCATTGTTCATGAAATCCTTGCTATTTCACAGTATCTGTTTACATAGACTATTATTCTTTTTGAATCACACTGCACTAGACCTCTACAAATAGAACCCACAATATTTCTCAAGAATAAAGATGGCACATTTGTATAATCAAGGACAGCAGGACACTTTGCGTTTCATACACAAGCAAACATTAAATGTATGATATTTCTTTTACTAATGCTTTTGACTTGTAATGTGTTGGTGAAATGCATGCAGGAAATTGTTATCATAAACAACAAAAATATAACAAATGAGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011040:ENSGALT00000017981:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.212
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=42.0),PF0061222=IQ=WD(100=5.3)
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:
TCGTGGTTGTGATTCTCTCCA
R:
CCAGCCAGCAGATGTGGTAAT
Band lengths:
353-1304
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]