GgaINT0099744 @ galGal4
Intron Retention
Gene
ENSGALG00000006072 | SCN10A
Description
sodium channel, voltage gated, type X alpha subunit [Source:HGNC Symbol;Acc:HGNC:10582]
Coordinates
chr2:5362095-5364221:+
Coord C1 exon
chr2:5362095-5362215
Coord A exon
chr2:5362216-5364127
Coord C2 exon
chr2:5364128-5364221
Length
1912 bp
Sequences
Splice sites
5' ss Seq
CATATCCTT
5' ss Score
-20.06
3' ss Seq
TTCACTCCCATGTCTTACATTAT
3' ss Score
-0.64
Exon sequences
Seq C1 exon
ATCTTCATAGTGTTAAACAAACAGAAAACAATCTTCCGGTTCACAGCTACGCGTGCCTTATGGATCCTCAGTCCTTTCCATCCAATCCGAAGAGCAGCAATTAAAATTTCAATACATTCAT
Seq A exon
ATCCTTTTTTTTTTTTTTTTTGCTTCATTCACTCTCTTTTGTTACGAAGATGTGTGCTATCCTTTCCTGTTATGTTTTAGAGCATTGAATAAATCTAGGTTTTCCTCTTTCCACACAACTTCTAATTACGGTTTACATTAGATATTACCATTTTCTTGTTCTATTTAGTAATAAATACTTTTATGAGTACTAAGGGTTGTGAAGCCTGACTTTCTACTTTATTTTGTATTATAAGCATGATCTCTGATGTTGATTACCTGATGTCTCATAAACAAGCATCTCATGCTGAGGCCCTTCTCAGTGAGAAAACTAATAAGGTCTCTAATCTTTATCTCATGTTCTGTTTACCCAAGCTATAAGAATTAAATTCAACTCCCGTGCTGAAGCAGATTGCTGACTTATTTTAAGAATAAAACACAGAGGTAGGCACACATATGAAAACACATAGAGCAATTATGCATACTATATTTCTTCTGGAAATCAGATTACAATATATGCCTTTAATATATGAAAGTAAAAATTATCAGGGATACTATTGTAGGGAAAGGATGCCTTTGGAATAAAAAAGTAATACACATCCCAAATCACACACTTAGAAAATGGGACTTATTAGTATATTTTTCAAATTTGGCACTTGAAAACGACACCAGGGCAAAAATGCTGTCACTCAGGAATGACTCAGGGCAACTGCAGTCTGTGGTGTTACTGCACTGAGGTTAGGTTTTCAGCCATCTCCCCTCCACGTAACATTGAAACAGATCCAAAGCTGTGGTCATAGCAGGGTACCGGCATCCCTGGAGGAGTGATGCCTCTCATCTGAGAGCTTTTTTGGGTAACAAGTTGGCTGTTATTGGCATTTCAGCACTTGTGGTCCATCTCCTGAGTTTGTGGCAATATTTGGCTGTGCCTACAGTTAAATCCAAGACATTTTTTGGGAGGATTGAAAGAACTGTTGATCGGAAGTGTAGATGTCTTTCCCATGCTCATCTACATCCTAGGTTGCCAAAGGTGTGGTATGACACTAAGCATGAGGTTCAACTCCAGAGACAGGCACTTCATCTTAAGTATCAACTTGAGCTAGATGCCTGTGTTCTACTTCTGAACTTACAGTCAGTAGTTCCTAGGGAATAGCTGGGCAACACCAAGAGCTGGCATCTAATATCCTTTGAGCCATCCACAAGTATCATGGCAGACTTTGCCCTGCCTGTACATAGGAATAGAGGTCTCACAGTTTAGAGATGAGTGACTCTGGATGTTCAACTTCTATGAACTATTCATTTCACTTAAAAATAAATATCCTTCCACTGGAGTTCCATGAGAACTGCTTTATTACCATCACTGCTTACACTGCAATGGTAATCAGGAACTTCAGTTTGTTACCTGCAAACCTTTGCTCTCAGAACTGTCAAGCTCCCATTTTTTTTAAAGATAAAATTCCATAAATTACGTAAGTTGTGAAAAAGGAAAGAAAAGGGAGAAGAGAACAGCAAAATATGTTTTATTCACACGACCTTCCTTGTGCAAGGAAAACTGAAATTATGTGATACCAAATGGGTTCAGTTCTCAGTTGTATCCTGCTGAGACCTTGGGCGAGTCAGACAGTCTCTATTTAACAATTTTTTTTGCTGTAAAATTAAATTAAAAAGGCATCCTTCCTCTTGCTCTGTCTCAGTGGTTAGGGATCATTTTACTATGTCTGCAATGCGTAGTACCTCCACAGCAATTAAGACAACATAAATAATGATGTCAGTGTGTTGTCATCTAATGTGACTCAGAATCAGTAAATGCGTGCGCTTGTAGTCCTTACATGTGCTTTAGAAAGTATTGAAAATATTAATTTCATAGACATCAGGATATGTAACTGTTTCTTATTTGATGCCGTATTCTTTGCCTTCACTCCCATGTCTTACAT
Seq C2 exon
TATTCACCTGGTTTATAATATGCACAATTATAACTAATTGTGTGTTCATGGCTCAGAATGAGTCCTCCAGGAGTTCATCTCCATCGTGGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006072:ENSGALT00000038879:2
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=6.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTAAACAAACAGAAAACAATCTTCCG
R:
GAGATGAACTCCTGGAGGACTCA
Band lengths:
190-2102
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]