RnoINT0131705 @ rn6
Intron Retention
Gene
ENSRNOG00000005309 | Scn8a
Description
sodium voltage-gated channel alpha subunit 8 [Source:RGD Symbol;Acc:3638]
Coordinates
chr7:142678280-142683213:+
Coord C1 exon
chr7:142678280-142678550
Coord A exon
chr7:142678551-142682068
Coord C2 exon
chr7:142682069-142683213
Length
3518 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
ATCCTCTGTTCCTCCCTCAGGAA
3' ss Score
10.99
Exon sequences
Seq C1 exon
AACAAAATCCAAGGGATTGTCTTTGATTTCGTCACTCAACAAGCCTTTGACATTGTGATCATGATGCTCATCTGCCTTAACATGGTGACAATGATGGTGGAGACAGACACTCAGAGCAAGCAGATGGAGAACATTCTTTACTGGATTAATCTGGTCTTTGTCATCTTCTTCACCTGCGAGTGTGTGCTCAAAATGTTTGCCTTGAGACACTACTATTTCACCATTGGCTGGAACATCTTTGACTTTGTGGTGGTCATCCTCTCCATTGTGG
Seq A exon
GTGAGTAAGCGGGGCCACGGGAAGGACAAGGACCCCAGGTGTGAGGACCAGATTTCTGAGAGCAGTGACAAGCAGGGTGGGCTGGTGGTGGCTCTCATATCCCTGCTCTGTGTGCACCTCAGCCTCCCAGGAAGGTCGCATGGCTAGTGTGTTCCTCCTGGGAGCTCTCAGCACTCTTGGGTGCAAATGCTGCAGCTCAGAGGCAAGAGATAAAATCTGATTTGCCTGCAAGAGATTAAAAGTCTACCAGGAAAAGTAAAAGGAACTTGTTTTTTCCAGTGGCAATAGCCTGGGAGATGGCCCAGCTGGTAAAATGCTTGGCTGAGTGTCTTAGTCAGGGTTACTATTGCTGTGATGAAATACCATGACCAGAAGCAACTTGTGGAGGAAAGGGTGTTTTCATTCAGGGTTCATCGAAGGCAGTGAGGACAGGAACTTAAGCAGGGCAGGGACCTGGAGGCAGGAGCTGGTGCAGAGGCCATGGAGGGATGCTGCTTACTGGCTTGCTCATTATGGTTTGCTCAGCCTGCTTTCTTATAGAACCCAGCACCACCAGCCCTGGGATGGTCCCTCTCACAAAGGGTTGGGCCTGCCTCCATTCACTAATTAGGAAAATGCCCTCCAGGCTTGCCCACAGCCTGTTCCTATGGGGACGACATCTCAGTTGAGGCTCCCTTTTTTCCAGCTTGTGTCAGGTTGACATAAGCCAGCCAGTACACTGCACAAGCATGAGGGCCTGAGTTTGATTCCCAGCATCCATGTTCTGGGCGTGGTATACACACTTATAATCCCTTTACTCGGGAGGCAGACAGGGAAGAGCCCTGGGCTCACTGGCTAACCAATGTGGCCTAATTGATGGACTCCAGGCTAGTGAGAGACCCTGTCTCAAAAAACAAGATGGATAATACCTACAAAATGACACCCAAGGTTGACCTTGACGTGTAAGTACATACACACGTGCACGTGATGAGAAGAGTGGGCGGAGATTGCTAAGGGGACAGTAACTGCAGCAGTGATCACAGGTTCTGGCTACTGAGACAGCACTAACTGGAAAGTTCTCCCCACATTGTCTCACTGGGGCCTTACGATGTCACCAGAAAGGAGGTGTCTTATTATCTTCGCTGCATGGGTCATTTACCCAGGAGGTAAAAGAAACAGAACTCAGATTAGCCCCAGAGTTCCTGTTTTCTTCAACCTAAAAACACAGCAGGTTGGGGTTCTGGGGTGAAGAGAGAATGTGTGAGCCTGTTGACTCCTCAAAACATGCTGTCGCCTCCTGGAACAGCATCCCATGTGCTGTGTGCATGCCTTGGCTCCAGGCAGGCGTGACTGACTTCTAATACCACAAAACAGTGCTGAAAACAACAAAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGACAGTCAAGAGCACGGCTGGCTGCACCCTGGTCTGAGGTTGGTGACTGTGAACACAAGACAGGTGACCTCCCTTTACCTACATCACCCTGTAAGGACAAAGATGTCATGTGGGACACTGAGTCTTGGGGCATTTTCCCAAGAATCCCTAAGCTAGAGTATCTGAGGTGAGTCTGCACAAGGTCTTGGCTTTTGAGAGTCACTGCCTATACTCACCTTCTGAAGTACGCCTCACGTCTCTGGTTCCCATACCACCCCCTTCCTTTAGACTTATGTCAGGGCATGGTGCTACACACCCTTTAATCCCAGTACTCTGGAGACAGAAGCAGACAGATCTCTGTAAATTCAAGGCCAGTCTGGTCTACATAGCAAGTTCCAGAACAGCCAGGGCTACATAGTAAGACCCTGTCTCAAGCAAATAAAAAAGCTTATTTGTGTAACTGTTTTGCCTGCATATGGATATGCAAGGAGAGGACCTTTCCTGGGTTTTTATTAAGTGTGTTTGCCTGGAGATTTTTTATATATATATACATATATATATGTATATATATGTGTGTGTATATATATATATATATATATATATATATATATATAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATCCATACCCATGGAGGTCCAGAGAGTGCTGAATTCTCCAGAACTGGATATGCAGACATTTGTAAGATACCATGTGGTTGCTGGGAATTGAACCCAGGTTCTCTAGAAGAGCAGTCAGTGCTCTTAACCACTGAGCCATCTCTCTAACCCCAGTTTTTATTTTATTATATAGTGTGTGGGTGTTTGTGTGCATGTATAGCTGTGCACCATGTGCATGCAATGCCCTCGAGGCCAGAAGAAGTTGTCAGAGCCCCTGTGACTAGAGTTATGGGTGGCTGTACACTACCATGTGGATGCTGGGATTGGAGCCTGGGCCTTCTGCGTGGACAACAAGGGCTCTTAGCTGCTGTGCCCTTCTCCAGCCCTTCTCTTCTGGCTTGAAACCTTCAGAGGAGAGACTCTTGAGTTCTGAAGCTGGTCTCAATACTTGTGAATTCTTATGGCTAAGAGACCCTTCCCTAGTTAAAAGCTTCATTTGAGTGGGTGTTCATCTTGGCTCCTTGGCCTGTAGAAGGCAGAAAGTAAGGCTGATGTAGAGAGAACAACTCTAGCTCTCACTGATGGAAAGAGAACAGCTCTAACTCTCACCCCTGGCCTTTCCATCTCCTCTTTTATCCGTGGCCTTCCTTGGACCCCCCCCCATGCCACTCCAAGTCACTTCTTAGTTTTAAGACACGTGATCTGTGTAAGCTGGGTCACAGGGGGAAAGGGGAGGCAGTTGTCCACTTCTCCCCTGCTTTTGCTCCCTGCTTTGAAACTGCCCTCTGATTTACACCTTTCAGCTCAGAATCTTGGGGCACCAAGCAGAAGGCCCCCTGGGTGGGCCGCTTTAGTCTCCAAGGCGAGCTGTCTCGTGAAGATGGGGGTGAGAAGCGAAGAATAGGATGTTCTGAGAACGCAGAGCATCCGCAGAGGAATTAGACATGAAGTCAAAGGGTAGTGTGTCACGGGGAACATCTCGCTCCCTGTTTGCAGAGTAGAAATCTGGCGGTATTGTGGAGAACATTTGAAAGCTGTGTGTGCACACATGACACAGAGGGTCCTTGATAGGAGAACAGATTTTGCTCCAGCCACAGGAAGGGATAGTGTGAAGCCATTTCCATCTGAGGAGCCAGAGTTGCAGACAAAACCAGTGAACATCTTAATACAGAGCTACAGAGAGAGCCCTGTCCCAACTCCTAAACATAGAGGACACCTTGTTGTTAATGAATGCACACATAGTAAAACTATAAAAACACTAGAACCATTGTGGCCTGTGCATGCCTCCAGGGTTATGTGCTGGCCACGGTTAAGCCCTGAGCACACCGTCTCCACACTACTGCGTTCTCCACATTTCTGTCTTTGGAACGTGTCACTGTTCATCGTGACGCCCATTCTACACGCCCGTCCGTTGAACTCGTGCGCGTCACAGTGCCGGGTAAGAGGAGGGCAGGGGTCCCTGACCTCAGTACTCACATCCTCTGTTCCTCCCTCAG
Seq C2 exon
GAATGTTCCTGGCTGATATCATTGAGAAGTACTTCGTCTCCCCAACCCTATTCCGAGTTATCCGATTGGCCCGTATTGGGCGCATCTTGCGTCTGATCAAGGGCGCCAAAGGGATCCGCACCCTGCTCTTTGCCTTAATGATGTCGCTGCCCGCCCTGTTCAACATCGGCCTCCTGCTCTTCCTCGTCATGTTCATCTTCTCCATTTTTGGCATGTCCAACTTCGCATACGTGAAGCACGAGGCCGGCATTGACGACATGTTCAACTTCGAGACATTTGGCAACAGCATGATCTGTTTGTTCCAGATCACAACGTCTGCTGGCTGGGATGGCCTGCTGCTGCCAATCCTGAACCGCCCCCCTGACTGCAGCTTGGACAAAGAGCACCCAGGGAGTGGCTTCAAAGGGGACTGTGGGAACCCCTCGGTGGGCATCTTCTTCTTTGTGAGCTACATCATCATCTCCTTCCTGATTGTGGTGAACATGTACATCGCCATCATCCTGGAGAACTTCAGCGTGGCCACCGAGGAGAGCGCCGACCCTCTGAGTGAGGATGACTTCGAGACTTTCTATGAGATCTGGGAGAAGTTTGACCCAGACGCCACCCAGTTCATCGAGTACTGTAAGCTGGCAGACTTTGCCGACGCCCTGGAGCACCCGCTCCGAGTACCCAAGCCCAACACCATCGAGCTCATCGCCATGGACCTGCCCATGGTGAGCGGAGATCGCATCCACTGCTTGGACATCCTTTTCGCCTTCACCAAGCGAGTCCTGGGAGACAGTGGGGAGTTGGACATCCTGCGGCAGCAGATGGAGGAGCGGTTCGTGGCATCCAATCCTTCCAAAGTGTCTTACGAGCCTATCACAACCACTCTGCGGCGCAAGCAGGAGGAGGTGTCTGCAGTGGTCCTGCAGCGTGCCTACAGGGGACACTTGGCTAGGCGGGGCTTCATCTGCAGAAAGATGGCCTCCAACAAGCTGGAGAATGGAGGCACACACAGAGACAAGAAGGAGAGCACCCCGTCCACAGCCTCCCTCCCCTCTTACGACAGCGTCACAAAGCCAGACAAGGAGAAGCAGCAGCGTGCGGAGGAGGGCAGAAGGGAAAGAGCCAAGAGGCAAAAAGAGGTCAGGGAGTCCAAGTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005309:ENSRNOT00000008160:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.170
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.5=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.0=43.5),PF0061222=IQ=WD(100=5.5)
Main Inclusion Isoform:
NA
Other Inclusion 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]