GgaINT1024547 @ galGal4
Intron Retention
Gene
ENSGALG00000006112 | SCN5A
Description
sodium channel, voltage gated, type V alpha subunit [Source:HGNC Symbol;Acc:HGNC:10593]
Coordinates
chr2:5450441-5455660:+
Coord C1 exon
chr2:5450441-5450561
Coord A exon
chr2:5450562-5455572
Coord C2 exon
chr2:5455573-5455660
Length
5011 bp
Sequences
Splice sites
5' ss Seq
CATATCCTT
5' ss Score
-20.06
3' ss Seq
CTTAATTCACCTATTTACATTGT
3' ss Score
-3.35
Exon sequences
Seq C1 exon
ACATTTGTAGTACTGAACAAAGGGAAGACAATATTTCGATTTAGTGCCACTCCTGCCTTGTATATACTTAGTCCTTTCCATCCAGTCAGAAGAGCAGCAATTAAAATTTTGGTACATTCAT
Seq A exon
ATCCTTTCTGTTGATGTCCCTCCTAGTGTATTTTATACTATTATTTTTTAAACACAGAAAGTGAGAAAGCAGTTAATTTAATGAAGTTGTGTTAGACCTTTCTGATGCATTTGTTTATATACACAGAAAAACTTTATTTTTTTTTCCCCCTTTTATATTGTAATTTGAGCTACGACAATGATTATATTATGGTACTGAAAGATGATGTGAGCCTCTCTTGAGAGTTTGATGAGATTTAGTTTTAAAAGGCGTGAAGTGGCTGACCATGGCTGGGAAGGAGTCAGAAGATGGAAGGAAAGGTCCTTTTCCTGAGACAGGAAAGGAATTGTGAGGCTGGAGCATGTCCAGGGAGATGCGAGCTATGGGAGAGCTTCGCTACTGAGGGCTTAAGCAGTGTCTCCCATGAGACTCTGTGACCATATGCAGACAAAATTTAATTTTGAGTTGCCTCAGAATAATTTTTCTTCCTGAAAGAACATATTTTAAAGCTTGTTTTGTTGTTTTGTTTTTTTGTTTGTTTGTTTGTTTGTTTTGTTCAACTTGCTGCCCAGCTAGGAATGAGTGGTGTGCACGAGGGACTCAATAGTGATAATTCAAAGACTGTACATGGTGATGTGATGACTGTGTGGCATTTCAGTGGTGGAAATCCCTCAGCTGCAATGCCTGTGTCCATCAGAGAGAACTAACACTAAGCAAGTATCCTCTTAGAATCACTTGCTTATTATCAAATGTTGTGGAAAAAATAGGGGAAGAAACCAGATTGCAGTGATACATGCAGTGGAGAAAATATAAGAAGTGGGAATATAGGTGTTCTAGCAAGGAGAGAAATAGGTAAAGCGATAAAATAGCAAAATGGCAACAATAATTATATGCAAAAAAAATGAGTATGGATATCATCTAATGTGTTTTTACAGTTATGAAGGAAAAACATAGCATTTTGCAGAGGTATTTGTTTCTGGGTCAGGTTACAACAGTGAAGCAGACACTGCTGCATACCCAGAGCCCAGCAGTGTTTACGAGGTACGGTTACACCAGCACAGCTTTGCTGAAGTTCTTGATTTCCACAGCTGCAGCTAAGAGAAGAATATGAAAACGGAGATTCTTAGAAAAGGTATGTGTAAATATTGGCTCCAGGTCTGGATGTCTGTTCCGTCTTCTCCCTTTCTTGCACACAGGCCATGAAGCCACGAGGTCACAGGTGTGTGTAATACACAGAAACGACATGCCCTTGGTAGCAGTCAGCCATAAGATAAGTGTGCAAGAAATCCTTATCACGTTTCTTCCTAGGATAAAGGGCACAAAGGAGTGAATTTCAAAGACCTATCAGGAGCAGAAATATGGGAGATAAGAAGTGTAACGTTTCGGGAGTGGAAGGCTGCAATCCTAACAGCATTTTAGTTCCGGAAAGAGCCAAGTTATCACCTTGTGTTGATAACGTCAGACAATCCAACGGCTCAGCCCTCAGCCAACATGGGCAGGAGGCAGCAGCTTCAGTCTCAGCCACTTAGTGGTGAGGTTCCTGCATTAGGCACTGTGTTGTTTTCTGTCAATAAAGGGCTTTTGAACCATCCTGAAGCACAAAGGGCAAATGGCTGAGCAGGAAGTCAATATCCCAGGCAGAAAGGAGCCTGAATCGGCAAGTACTCAAGCGGATAATATCACAGACATGAATCTGGGAACCAGATCTGTTGCCTTGCGTGAGTGTAATCAAGCAGTCTTTATTTCCCCTGGAGCAAGGCCAAAAAAGAGCATTAACAAATGGTACTCTGTCACGTAAGTGTCTGAAGCAACATCTTTAGTAGAGGCCATATTTCCTTTGCTTGTCGCTGAATGTACCTCGAAGGCCAACAGTAGAACAGAAGAGAGAGGACAGAATAAGATCGTCCTCTATAGAAGCTGTGGGGGTCACATTTCTTGGTTAAGTGGCTTTCTATGGAGTTCTTCCACTGAGACTTCAGGCAGGATAGATCCTGTGTGCTGACTGCTCATCCATCCAAGCATGGTTACTCTTGTCATTCAGAAGCACACCCTTCCATGGGAAAGCATCCACAGGATAACAGCCTCCAGTAATGTGAATCGCTTCAATTAACAGCATGGCCCTGAACCTCTTCCAGGTATTTCCCCTCTTCTTCAGACTATGAGGTGCAGACAGATGCCCCAACAAGGCTCTGGCCCATTTCTGTCATAGAGGACATGGGTGGTGAAGGTCTGCATCCCTTTGGTCTGTAGCAAATGCAAAATAGAAGTAGTGGTTGAAAACTTTTTACCTTCTATTGGCTATTAGCATCTTTATTTACTAAGATTAAGTCGCTGCTAGCACTTCACTTATGCCTTATGCTTAAAAGGCTCCTCTTAGTTACTCTTGCCTGCAAGCCAAAGACAGCTCTGTGGTGTCCCTGGTTTCTCCAAGCAGTTTACTGTCCTGTATAAAAACATTGCAATTACTAGTTCCTGATTTTTCTAGGTATTATAGATAGTTGGTCTCAATTTATCACTGATTCAGAATAGGTTTTACGCCAAAATTACCTTCCTCGGTGTTAGAATTATGGATTCTGTCCCATCTAAAAAAAGTCTCCTTTTAGAATTTGTAATTTGTGTTCACATTTTGTGATTGCAGCCTTTCTTCTATCTGATTTTATACATTTTCCTTGGTAATAGAAAATGAGACCTTGTGAAGCACCAATTATGTGTACTATTGATTGGGACTAACCTTTGGTTGCCCATATTATATGTAATTTGGCAATGATTACTTAAAGAGCCACCAATGTTCAGTCTGCTAATTAGCTATTATCCATCATAATGAAGTCTAGAATAGAAGTATGCGGTGTTTTACTCAGTATCTTTGTGCTGGAAGATAAAATTTATAACTTTCAGGAATTCTTCATGAAGTCTGCATAAGATGTCATTCTGTAACTTCAGATTGGAAATAAATGTCAGGTTCAATTTATTGCAGAAAGGATCCTAATGTGTAGCTTACTATATTGGATTTGTGGTCCATAACAGAGTGTGCAACCCATGCACCCTTTTGGAGTGTGTTAGCTATGTGCATGATTCATGTCAGCTCATGGATCAGTGGGCTTTCAAATACTGGAAGTAATAGCAGCTGTAAGATAGGTAACAGACAGTAGTGATAACACAGGTTGCATCAATTTCATCCCCTTCACTTGGTCTTTTCTGAGTAGTTAATGATCAACAACTTCGATGTGAACAATTGCATTAGATTTCAGATAGCAATGCTAATTTTCCTTGTTTAGGAATTTCTGTTTTCACTTTCTAGCACAAACCTCTGACTTCAGTGCCTAAGTAGCTAGAGTGATTATTTCTTTTAAATTATTTGTAGTTTTGAGGTTGGTCGTGAAACTCAGTTAGAGTTAGTTGATAGATCGTTTGATGTCCCAAAGCTGACCCCTTGCATTTTCAAACTGTATCCTCATGTATATTCTCTTCGGTGTTCAAACAAGAAGGTGATGTCACCTTGGGAAAGCTCACTTTTAGATTCAGCTTACACCACAAGGAAATAGGGATGTATAAATCAGACTAGTGAGCCTAAATTGAGTGGTTATAGAGAAATTTCTTTGCTTGGAATTGAAGGATAGTTCTTGTTTGGCATGGCCTGAAGATACCATTCTGCCATATTATTATTGTTTTCATTGCTTTTCACTGGAGGTGAAAAGTAACGTAGCTCATTCTAGGCCAGCTGCAGTTTACCACCTCATTGTGTTAACCAGGTAGATGACTCTGAGAGATGTATCTCAAGCTGACTTTGGTCTGGATATCATCCATCTTCCCAGTCCTTCAGCAGAACGTGTCAGCCCCGTAAGTGGAAAATGTTTGTGAGACGAGCAGTCCCTCTGGGTTCAATTACTGCTCTCTGAATGGCATGGGGGAACATGCAGATTGGTTACTACCAATTTAATGTCACAGTGCCTTATGGGGCCCTGTGGAAAACATTCCACTCTGTACTCAGCAGAGATTTTGGGTCTGCAATAGAACAGCTCTACTATTCTCAGAAAACTACCACCGATGGGATTGGTAAATGGATAAAACAAGGAGACAAGTAAACTTTTCTTCTGAAGAAGTCAAAAGAAGTTTACATTTGGATAGTGCTTTCCTTCTCTGAGAAGGATCCCAGGCTGTTGACTGGATTGTAGGATGTTTAACTTCTGTCCACTTAAACTCATTCCTTAAACTTTCTTTCCAGGAGCGTGGGATGCCCTATTTATGCAGGACAACTCCATCGTAGTTAAAAAGAGTAGCACGTGCTTTTAGCAGAGCAGTTCAGTGAACTATGTTTTGAATTTCAGGAATTTGATTTAGGGTGCTCTTCTTTGTATTTATGGCCTCAGCTTAGCAGTTAAGTGTACAGACTATACACAAGGGAGGTTCATCCTAGCCTCCAGATAGGGAAGCTGGTTCCTCAGCTGAAACAGCTTTGCAGATCAACACTGCACATTTGCCAGTGAGCTTTGCTGACCAAGCCTTGAAATTAATGCTGAAAACTCATATTAGCTTTTGGTGAAACGTATACTGATCGTGAGACCTCAAGTCTGTTAGACAGATTAGAGTTTGGATTTATAGCTTTGCCTGCTGCCTGAGAAAAGTTTCAGGATGCAAAATAAGATCAGAATTTGCAGACACGGGTTTTTCTGTATATACTTGCATGAGTCTAATCCTGCTTTTCATGCAAAGTTGTGTACCTATGCATTTTGTCATCTGACGAGCACAGCTGTAAGTTTGAAGTATTGTGTTTTCAGAACACTGCCGAGGCAGTGTGTTTCCTGCATAAAGTGTGCATAAAAGATGTATGCAATGGAAAAAACAGACAGGAGTCACTCGGTTTTTCTGTGTTTCTGTAATTACTTTTTTCCTTATGCAATAGAAAACAAATGTCTGCAGTGATTTTTTAAAATGCTGGAAATCATGAGTGATTTGTTGCGTCTCGTATGAAATGATAAAAATGTATGTAGTCTCATAACAAATGCATTGTTTTCCTTAATTCACCTATTTACAT
Seq C2 exon
TGTTCAGTATGTTTATTATGTGCACTATTTTAACTAATTGTGTGTTCATGGCACAATCAGAGACTCCATCATGGAATAAATATGTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006112:ENSGALT00000031281:3
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(0.8=6.7)
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:
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]