RnoINT0131680 @ rn6
Intron Retention
Gene
ENSRNOG00000029342 | Scn7a
Description
sodium voltage-gated channel alpha subunit 7 [Source:RGD Symbol;Acc:61922]
Coordinates
chr3:52777214-52781749:-
Coord C1 exon
chr3:52781479-52781749
Coord A exon
chr3:52778284-52781478
Coord C2 exon
chr3:52777214-52778283
Length
3195 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TCCTTGTATCTTTTTCTCACACC
3' ss Score
1.01
Exon sequences
Seq C1 exon
AACAAGTTCCAAGGCTTCATTTGTGACGTAGTAACACATCGTGTCTTTAATGTCATCATCATACTTCTTATCTGTTTCCAAGCAACAACCATTATGATACAAAATGATGAGCAGAGTCCACAAATTGAAACCGCTGTCTTCTGGATGAACTCCCTTTTTACCATGCTGTTCACTCTGGAATGCATACTGAAGCTCACCGCCTTCCGCTGCCACTATTTCACCAGCGCATGGAATGTTCATGACTTTATGGTGGTCGTTTTCTCCATTACAG
Seq A exon
GTAAGGTTGGCTGCTGTCAAATTTTCCTTTATATTTTAATTTAGTCTATCACTGTATGTATCAAGATAATGACTTTGAAGAAGCAAAATCATAAGACCATTTTCATCCCCAAAAGAATGAATCATTATTTGCAATTGTGTGTGTGTGTGTGTGTGTGTACTATCACTATTTTTAGATGAAAACATTTTATCTGTTTAGAAACTTAAGCATGTGTCACAAACACAGGATATGTACTTGGTTATCTGTAACATTCTAAGCTGCCATGAGAAGAGCTCTGTGTATTGAAATGACATGGTTTTCAAAGCTCACTAAAAGTCCTTACTTTTAATTTTTTTAAATGTTCCCCACCATCCCATCATTACAATTTTAGTATTTAAATGACTTTGTTCCTAGTCTCATAGTTCTGGGGTTTAATGAATTTGTCTCTAGTTTCTCTTACCTGAGTAATTTTATATTGGTTGACAAACACATTTTGTTATGTTGTTAAATAAGTAGAACTGTGTATAGTAAGGTTAGGGACACTTTCTCTACACATATCGTTTAAGGACTATCAGGGAGTAAGTACATTTGCAGAGCAGAACATTCTCTTATGGGCTGAATCACAGAGTTCTATTACACAGGGTAAAAGAAAGAGCACCTTATCAGTAACTGGTGGTCAGAGAAAATGCCATTTAAGAAGGAAATTTAAACAGAGACCTACTGGGTAAGGGCTATCAGGCAAAATTATACCAGGAATAAAGAAGTTTCTTTAGTGTTTGCTTCTGCATAACCAGGATATGGTCTCCATGAGAGTAGGGGATAACATTTAAAATGTAAATTAAAAATATCCAATAAAAAAACAATCAATGATGTCAATGCTGCACTTAAGGCTCGGGGATCATCGGAGAAAAGGGGTAGGTAGGATGGATGCAGGAACCAAAGAACCAAGGAGTTTGCTGTGAGAATCTATCTCCTAAGAATATCAGAAACTATGCCCATGAAGTCTCACCAATGTGTCTGTATAAACATTGGATGAGTAAGGATGAAGATATGCTACAAGGGAGAGCCCAGGATATCTCTACTAGACACAAAGAACTAGAAGAAACAAGGAATATTGTGAGTAGAAGGACTACTCCTTCCAGGGAAGCGCACACCAATTGGTTATCCTATGCCAAATGGTCAATCCTGAAAGTAACATTACAGAGAATGGGCAGGTTGTATTTACATATTAAGAAACAAATATGTATGCATGTGTTTATGTATATATACATTGTTTTATATATACATACATAGACATATATAAGTATATATGTGGAACAGTAGTAAATGTAAAAACAGGCCATAAATTGAAAAGAGAGAAAGGAAGGATATATAGAAAGGTTTAGATGAAGGGAAGGAAAGGAAATCTAGTGGGATTATATTGTAATCTTAGAAAGTAAAAAAAAATTAAAAGGTTAGTGATATCAACCAGAACTTTCGTAAAAGAAAACATAAACTACCTGCCTAATATGAGTTCAGAAATTTCACTCTTTCAGTAGAACAGTGAATTCATGTCACTGACTACTGAAAGAAAAGTATAAGCTGGAGAGAAAAGTGTATGGAGATTGGAGGGGCAACAGGAAAGAAACAAGGGAAGTATAAGCTACAGTGTCTGAAGTAGGAGTTACAGAGTGTACAGGAAGAGAAAAGCAGCCATAGTGAAAGCCATTCAACTTGAATTTCCAGTCTCCTGAGGCAATCATCTGGCCAAGGCACTGATGTTGCCAACTTAACTAAAATAATGAGTATTGTTAAATTGAGATGGTTAAAGGCTGAGGTGAGTCCTTGGATTGTTCATTAAGGGAGACGCTGTAAACAGGGAGACCATGAGCCACTTATTAAGTCTCCAGCTGTGTGTAAGTGATGAGAACTGTGTGAATCATAGAGCAAGGGAATGATAAAAAATTGAGTTGGACAGCATAATCCACAGAGGGCAGGAAATGTATCATAATTTTTAATAAAACTTATTGGACAAAATGTGCCTAGAAATGTAATTGGAAAGTGACAAGGTACTTATGCTGCTGTTTTGCCTTAGAAATGTAGAGAAGAAGAGAGTATGCATTCTTCATTTTAAAGTGTTACGTGGAAAATAATGTCATCAGCAGAGTAAGAGTTTAGATAAGGGGTTTAATTTCCTGGTAGGGAGCAGGAGTATATGCACAGGAAGTGAGGATGCCTCTTTATTAATGGAAGAGCTTGAAAGATTGGGGAGAGATGGGAATTTGTCTAGTGTAAAAGAGTCACTGATATACTTTAGAGGGGGTGTAGGCATGACAGAATATAGAATATAAAATAGACATGACCCACCAAAAAGTTCATCTTAGAGAGTGCACATGTTAACAAAAGTATTAGGCCTGATACTTCCTCTCAGCAAATACACAAAAGCCTCATGACACTGTCCTCCATGACCTTTGCAACAAAAACTAAAACGAAGTTATAAGGAGATGTTCACATGTTATACTCATATTTAAAGTTCTTTAGACTCAAATACTACTTATAAAAGAAATAAATTACAATCTATGAACCCCTAAATTATATACATATATAGAGAGATAGTCTTGGTTATCAATAATGGAGCAATATCTCAGGAGTTAAGAGCACTGTCTGCCCTTCCAGAGGTCCTGAGTTCAATTCCCAGCAACCACATAGTGACTCACATGGGACTTTATGCCCTCTTCTAGTGTGTCCGAAGACAGCTGCAGTGCACGCACATACATTAAATAAATAAATCTCTAAAAAAATAATGTCTCCCTGCTTTACATTCTCTTCATCTTTAAGAACTCTCATAAGTTAATGCATTAAAAAATCTTTGAGGGAAATTATATTCTATATTTACATGATGCATTAGTGAGATTGGTCAAATTCCTTAATCCAACAATCTTAAGAAAAGTGTGGACTATTGAACTACAGTATGGATCTGGTCACCTGTGATTTCAAAACTATCTTAAAATAGTAGCACAGAAGAATTCTATTTTAAACTTTGGCACAGAGCCTGATCATTGATAAAAATAATATTTAATTAACCTAATGTTCAATATGCTGTTCTATGAGATAGGTTAAGTGATGGAGTAATAGTAGATTCATGAACCATACAAAACTAGAGCAGTTGGGAAATTATCTTTTCTATATACAATTGCATTTGGATAATTTTGTTTCTTCCTTGTATCTTTTTCTCAC
Seq C2 exon
ACCAAGGACTGCTGCTGCCTTTGTCAATAGGACAATACTTTGTGCCTCCTTCACTGGTGCAGCTGCTTCTTCTCTCTCGCATCATCCATGTCCTGCGTCCTGGGAAAGGACCAAAGGTGTTCCATGATCTGATGCTTCCCTTGATGCTGTCACTCCCAGCACTGCTCAACATTGCTCTTCTCATCTTCCTGGTCATGTTCATCTACGCCATCTTTGGAATGTACAACTTCGCCTACGTAAAGAAAGAAGCCGGAATTAATGATGTGTCCAACTTTGAGACCTTTGGAAGCAGTATGCTTTGTCTCTTTCAAGTTACAACATTTTCTGGTTGGGACGGGATGCTGGATGCAATTTTCAACAGTCAGTGGTCTGACTGCGATCCTGATAAAATTAACCCAGGGACTCAGGTCAGGGGAGACTGTGGGAGCCCTTCTGTTGGGATTTTTTATTTTGTCAGTTACATCCTCATATCATGGTTGATCATTGTTAATATGTACGTTGTTTTGATCATGGAGTTCTTAAGTATTCCTTCTAAGAGAAAAAACAGGACCTTGAGCGAAGATGACTTTAGGAGATTCTTCAAGGTATGGAACAGGTTTGACCCTGACAGGACCCAGTACATAGACTCTACTAAGCTTTCTGATTTTGCAGCTGCTCTCGATCCTCCTCTTTTCATGGCAAAACCAAACAAGGGCCAGCTTGTAGCCATGGATCTCCCCATGGCTGCAGGAGACAGAATCCATTGCCTTGATATTTTGCTTGCCTTTACGAAAAGAGTGATGGGAAAGGATGAGCGGGTGGAGAAGATCCTTTCAGAGATAGAATCTGGGTTTATGTTAGCGAACCCTTTCAAAATTACGTATGAGCCGATTACAACGACTTTGAAACGCAAACAAGAGGCAGTCTCAGCCACTATCATCCAGCGGGCATACAAAAGTTACCGCTTAAGGCAAAGTGACAAAAAGATACAAGATATCCCGGAAATAGATGATGGCAGGGAGGATCCTAACTCTAAAGGTGTCCACTCTGGTCAAATCGAGGAAAAGGCATCTATTCAGACCCAGATCTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000029342:ENSRNOT00000041096:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.079
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.2=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.3=47.3)
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
Chicken
(galGal3)
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]