RnoINT0131626 @ rn6
Intron Retention
Gene
ENSRNOG00000012134 | Scn4a
Description
sodium voltage-gated channel alpha subunit 4 [Source:RGD Symbol;Acc:3636]
Coordinates
chr10:94505026-94508783:-
Coord C1 exon
chr10:94508513-94508783
Coord A exon
chr10:94507269-94508512
Coord C2 exon
chr10:94505026-94507268
Length
1244 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGC
5' ss Score
7.23
3' ss Seq
GAGCCTGTTTCTCTCTGCAGGCC
3' ss Score
10.53
Exon sequences
Seq C1 exon
AACAAGATCCAGGGCATGGTGTACGACTTCGTGACGAAGCAGGTGTTTGACATCTCCATCATGATCCTCATCTGCCTCAACATGGTTACTATGATGGTGGAGACAGATGACCAGAGCCAGCTCAAGGTGGACATCCTGTACAACATCAACATGGTCTTCATTATCATCTTCACAGGGGAGTGTGTGCTGAAGATGTTTGCCCTACGCCATTACTACTTCACCATTGGCTGGAACATCTTTGACTTTGTGGTTGTCATCTTGTCCATCGTGG
Seq A exon
GTGAGCTGGCAGGGCTGCACTAAGATGAGCTATTCAAGGAAACCCTTCCTCCTGCATGCAGACCTGCTATGGCCCCGAAAAACCCACACGCCTTATACAAACACACCTTTAATGCACAAAGACACTGCTCACAGGCCTCTGATCACCCCAAGAAACACTGGCCGGATCAGCACATGTGTACTTGGGTGGCCGCACGCTGAATCAAAAGCACAAGATGGGGCTGGAGTGGTAGCTCAGTGGGTAACGCGCTTGCGGCAGAGGCATGAGGGTCTGAGTACATGGTAGCACATGCTTGTTGGGACCCTGGGTGTGTGTGTGTGGGGGGGGTGTGGTCACTGACCAGACAGCCTAGCCTAATCATTGGACCCCAGGGCCAGTAAGAGACCCTGTTTCAAAAATCAAGGTGGATGGCATTGAGAAATGACACATTAGGTTTTCCTCTGGCCTATGTTCACACACACATGCACACACACACACAATGTATTATGTATTATATACATAATAATGTGTATAAGAATGTACATGCGGGGTTGGGGATTTAGCTCAGTGGTAGAGCGCTTGCCTAGGAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCCAGCTCCAAAAAAAAGAACCAAAAAAAAAAAAAAAAGAATGTACATGCATGCATGTACACATGTATGAACACATATGTACAGATAAGTATATAATACATGAAAAAACACACTAATGTGTACAAGTAAGAATGTGCATACAAGCATGGACACACACATGAACACATATGTACAGATAAGTATATAATACACGTAAACACACGCACACGCACACGCGCTCGCATGCACACACACACACACACACACACAAATGAGAAAAGGGATCCAGAATCTTTATACACCGAGAGGAGAACAGATCTGTCTACAACCATGGCAGTAAGTAGCTACTGCCCATTGAGTGTTTACTGTAGGCCAGGCATTTGCTATGTACTTAACAGGCTCAGCTCTGTTCTTTCACAGAGGGGCCATCTCAGTCCCATCTTTCAGATGAGAACAAGTCACACAGCTACCCTCTCTTCCCTTGTCTCTCACCTGTGGTATCTAAAAGCAGATTTCAGGATGAACCCTCGTCAGTTTTAGTATATCCCACCTCCAACCATCAGGGCACAGTAATCCCCTGCATCCCCAAGAGCTCTAGGGACCATGCTCAGGGGACCCCAGTCCTCCCTGCTCCCAGTTCCCTGACGGAGCCTGTTTCTCTCTGCAG
Seq C2 exon
GCCTTGCGCTCTCTGACTTGATACAGAAATACTTTGTGTCACCCACGCTGTTCCGTGTGATCCGCTTGGCTCGGATCGGGCGTGTCCTGCGTCTGATCCGCGGGGCCAAGGGCATCCGGACGCTGCTGTTCGCCCTGATGATGTCCCTGCCCGCCCTCTTCAACATCGGCCTCCTTCTCTTTCTGGTCATGTTCATCTACTCGATCTTCGGCATGTCTAACTTCGCCTACGTCAAGAAAGAGTCAGGCATCGACGACATGTTTAACTTTGAGACCTTTGGCAACAGTATCATCTGCCTCTTCGAGATCACCACGTCAGCCGGCTGGGACGGGCTTCTGAACCCCATCCTCAACAGTGGGCCCCCAGACTGTGACCCGACGTTGGAGAACCCGGGTACCAATGTCAGGGGGGACTGCGGCAACCCTTCCATCGGCATCTGTTTCTTCTGCAGCTACATCATCATCTCCTTCCTCATCGTGGTCAACATGTACATTGCTATCATCCTGGAGAATTTCAACGTGGCCACCGAAGAGAGCAGCGAGCCCCTCAGTGAGGATGACTTCGAGATGTTCTATGAGACCTGGGAGAAGTTCGACCCGGACGCCACTCAGTTCATCGACTACAGCCGCCTCTCGGACTTTGTGGACACCCTGCAGGAGCCGCTGAAAATCGCCAAACCCAATAAGATCAAGCTTATCACGTTAGACCTGCCCATGGTGCCCGGCGACAAGATCCACTGCTTGGACATCCTCTTTGCCCTGACCAAAGAGGTACTGGGTGACTCTGGGGAGATGGACGCCCTCAAGCAGACCATGGAGGAGAAGTTTATGGCAGCTAACCCTTCCAAGGTCTCCTATGAGCCCATCACCACCACCCTCAAGAGGAAGCAGGAGGAGGTGTGTGCTATCAAAATCCAGAGGGCCTACCGCCGCCACCTGCTGCAGCGCTCCGTGAAGCAGGCCTCTTACATGTACCGTCACAGCCAGGACGGCAATGGCGACGGGGCCCCCGAGAAGGAGGGATTGCTTGCCAACACCATGAACAAGATGTATGGCCATGAGAAAGAGGGTGATGGTGTGCAGAGCCAGGGGGAGGAAGAGAAGGCCTCTACAGAGGATGCTGGACCCACCGTGGAGCCCAAACCCACCAGCAGCTCAGATACTGCCCTGACTCCTTCTCCTCCACCACTACCCCCCTCATCATCACCGCCACAAGGGCAGACAGTTCGCCCAGGGGTCAAAGAGTCTCTTGTCTAGATGGCAGCGTCAAGGCTGCACGCAGAGTTGGAGGGGAAGGGCTTTGAGATGGGGGCTATACAGGACTTGACACCTGGGCTGAGGGGTATGGAAATTGTGCTCAGGGTTCAGGTGGGTCGGAAGCCCCTGCTGCCTGATTTCATCTTTACGATGCTCTGACATTCTGTTGGCCAGGGGAGGCCAGGACATCTGAATGCTGTTTCCTTCTTGGGGGAGAGCCAGCATACCTTGGAGGGGTTGGCCACCTTCCTGTCACTACTTTAAGGGCCCAGGACCCCAGCTCTAGCCAAGACAAAGACGAATCTTAACCCCCAAACCTACACCTGACCCCCAGAGCTTAGCTATCCCTCTCGCCCCCATAATTCTAGGGTGCAGCTTCCCCCTGACAGCTCAGGAATGCCCTGTAAAAGGGGAAATGGTTCTGGTACAGAACCAATTGGCCGCTGGATCCGGATGTATCAGGCTGGAAACATGACTTCTGAAACCTTTCACCCAGTCAGATCCAGGCCGGTGGGCAGCTCCCCTGGCTGGCCCCTGGGGGAAGAACTAAGGAAGGATTGCCCTGAGAAATTACCTTTCTCTAGATTGCGTGGATGGGTCAAACAGGCTGGGTCCTGCCAGCTGCATTCATGCCCTTGAGCCTGAGCGCCCACATCTGCCTGGGGTCAGGTTGGAAGCTCTCTATCAAGAATCTGCCCGTTCCCGCCTCCCTGCCTTCTTTCTTTGAATACCAGGGCTCCTGGGAGCCCCATCAAACACGAAAGACTGCCTTCCTCCTGTCTAATCTCTGCCCCCCCCCTTCCCTGCCCCTTCCCTGCTTCCTCAAGTGACTCTGAGAATGCTAGAACTCAGCACACGGGAGATGAGTTGATACTGGGGCATGCAGTGAGAAGGCTCACCAGGCTTGGCTTTGGTCTTCTCATTGCCTGAAAGCAAGTTTTCCCCTGAGACAGGGTTTCTTTTCTCCGTGTAGCCCTGGCTGCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012134:ENSRNOT00000016841:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.282
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=39.9),PF0061222=IQ=WD(100=5.0)
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:
GAAGATGTTTGCCCTACGCCA
R:
AACATGTCGTCGATGCCTGAC
Band lengths:
345-1589
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]