RnoINT0131482 @ rn6
Intron Retention
Gene
ENSRNOG00000032473 | Scn10a
Description
sodium voltage-gated channel alpha subunit 10 [Source:RGD Symbol;Acc:3629]
Coordinates
chr8:128387744-128391077:-
Coord C1 exon
chr8:128390776-128391077
Coord A exon
chr8:128387863-128390775
Coord C2 exon
chr8:128387744-128387862
Length
2913 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGA
5' ss Score
9.84
3' ss Seq
CGCGCTTTGCTTTCTTCTAGACA
3' ss Score
9.77
Exon sequences
Seq C1 exon
AGTGTAAATTCTTCCCCAAGAAGAATGAGAAGATGGAGCTCCCCTTTGCGTCCGTGGGAACTACCAATTTCAGACGGTTCACTCCAGAGTCACTGGCAGAGATCGAGAAGCAGATTGCTGCTCACCGCGCAGCCAAGAAGGCCAGAACCAAGCACAGAGGACAGGAGGACAAGGGCGAGAAGCCCAGGCCTCAGCTGGACTTGAAAGCCTGTAACCAGCTGCCCAAGTTCTATGGTGAGCTCCCAGCAGAACTGGTCGGGGAGCCCCTGGAGGACCTAGACCCTTTCTACAGCACACACCGG
Seq A exon
GTAAGAGCTGCCACCGGGAGCATCTGCACTGAGCTCTCGGGAGTGAGCCTCAGTCCCACCCAGCCCAGGAAGTCCTCACCCTCCCTCATCCTGTGAAGTAGCTGTTAATGAATGAATAGGCTGGTGTGAAGCAAGGTGAACACACCTCCCTCTCTGAATCTTTAGGAACTCTGCGATGGGGCAAACTAAGCCAAACCCCCCAAATCCCCAAAGCAGACTGCTGCTGCAGAACTTACTTGGAAAGCTGTTTTTTTCCCCATGGGTGAGACCCAGCTTGGAGCCTCTGGAGATGTTCTTTCTCTTTGCAGATCAAGAGCATGGATTTTTGAAGTTGAGAGGGATGCTTTAAGCCAGGGTTCTCTAACATATAGTCTCAGAGCCTCTGGAGTTTTCCAAGCTCTCTCATGGGTTACAGAAGTCAAAACTGTCTTGAAATAATAGTTTACTGTCACCTGTCTCTTACTTAGATCATCTCGTAAGCATGTAGCAGTACCCAAGGGAGCAGCACCATTCACAGCAGCTACTGGAAGATGTATCTATGTGCTCCTGGGTTTTAAAGTTTTACACACACACACACACACACACACACACACACACACACACACACACCATTTCTAATATAGTATGTGCCCCACTTTCCTTCCAGGTTGCTGTGATAACATACCTGGGCATAAGCAACTTAAGGGAGAAAGGATTTATTAGTTCATAGTTCCAAGCTACACGCTATCGAGGTAGCAAAGTCATGGGAAGGGAAGCATGAGGGAGCAGAATACATCACGCCTGGAGTCTGAAGACGATGAATGTAGCATACGTGTGCTCAATTTTCTTTCTCTCCTCTTATGTGGATGGCATCTTCTGCTCTGGGATAGAGGCATGCACAGTGATTGGGTCTTCCCACCTTAATTTCCACTGTCAAGATAATTCCCCCATCTTAATTAGGGTTCCATTGTTGTGAAGAGACACCATGACCAGGGCAACTCAAAGGCAAACATTCAGAGGTTCAATCCACTATCATCATGGTGGGAGCACAGCAATGGGCAGGCAGTACGCAAGCATACATGGGACTGGAGGAGCTGAGAGGTATAGAAGGCAGCCAGGAGGAGACTGAAATTCTACACTGGGTGAAGCATAAGTTTAGGAGACCTCACCCCCTCCCCAGTGACACATTTCCTCCAACACAGCCACACCTGCTCCAGCAAGGTCTCCTAATAGTGCCAATCCCTATGGCCAAGCATTCAAACACATGAATCTATAGGGGCCAAGTCTATTCAAACCCCTACACTCCCACAGACATGCCACCAGGACAACTCAGTCTAGACAATCACTTATGGAGGGTCTCTTCCTGGGTTATTCTAGATTGTGTCAAGCTGACGACACTGGCCATCAAGGATGTATACACATATACAAACATGATATGTGTACATAGACATTGTGTGTGTGTTGGTGTGGGTGTGTTCCTTTGTTATAACAAAATATCACAGAAAATAAATTTGAAGGAGGAAAGGGTCATTTCATGCATAGTTTTAGAGGGCTCTGCTCGTCCATGCTCTCTTGGCCTTGGCACTTTGGGTGAAACAGTTCATCAGGTAGCACGTACACACTGAGGAAAAGTGCTCACCTCACAGTGGCCTGGAAGCCAACAGAGAAAGAGGAAGAGCCTGGGGCCCCGGTTTACCCTCAATGGAATACCTCTCGTGATCTAACACTCTCTCCCTTGACCACAACTTTTAGGCTTTGATCGCCTTACAGTAGTGCTATAGTGCAGTGGGCTGACAAATAAGCCTCCAGTACCTGAGCTTTGAAGCCATCTTAGATCATAGATCTAAGGTAGGTAGATGATAGATAGATAGGCAGATAATGATAGATAGATGATAAATAGATGAGTTGCATAGATATACAAACTTCTATCATATATATATATATACATACATACAAATACACATGAACAAAGCGAGAAAGTTTTAAACATCATAAACTAGAGTATTCAATGATTTTTTGATCAGAAGAGTGAGACCTGATAGTCTAATGAGGCTACCATGACAGTTTCCTCTCCCGTACTGCACCTTGGATGTTTATCGCAGCCCAAATATGGTAAGTACACGTTCGGAAATGACAAAGAACTGGGACAAGCAAATAGAGTTGTAGAAGAGATAAGACACAGAGGGTGTCCTTTTCCCGCCTCTCTCTTTCCAAGAACGCATCCCTCCTAAATACACAGAGGAGGGGACTGAGATGGTTTAGAGCCGAGACTCAGGTAGTAGAAAACAGGAACATCACAGGACCAGTGTCCTCTTGTCAGAGGGGAATTAAATTCTGGAGCTGGGGAGCTGGCTCAGTCAGTACAGAACTTTGCTGAGTTTAATCTCTAGAAAACAGGTAGGGAAAAAAGTGGAACACACTTGTAATGTCGCTCCTGAGGTGGAAGAGGAGGGAGAGGGAGGAGAGGGAGGGGGAGCAGAAGCAGGAAGTGGGGAACAGGGGAAGGAGGAGGCAGAGGCAGGTGGGCCCTTGGGGATCACTGTCTGGCCAGCCTAGCCTTCTCAGTGAGCTCCAGGCCAGTGAGAGTTTGGGGGAGGCTCCTGAGGAATGACGATAGAATTTCTTCATCAACGTACTCACACACATACACACACACACACACACACACACACACACACACACACACACGTTGGATTAAATGCAACTGTGCTCAACCATCTGTAGTCAGAATCCTGCCCTGGGTGTACTGTATATATCCAGCCCTTGAGGTAGCAGCCTGTCCATGAAGCACTCTCAGCGGGCTTGCCTTGGTTCACAGTCAACCACGGAGTCCAGGGATGGTCAGTGGCCATGGTTCTTCAAACAGATCCTACGAGGAGGCCACTCCGGATTCTTGTTTCTCACGGAACCCACTCGCGCTTTGCTTTCTTCTAG
Seq C2 exon
ACATTCATGGTGTTGAATAAAAGCAGGACCATTTCCAGATTCAGTGCCACTTGGGCCCTGTGGCTCTTCAGTCCCTTCAACCTGATCAGAAGAACAGCCATCAAAGTGTCTGTCCATTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000032473:ENSRNOT00000046864:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.256 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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]