RnoINT0131561 @ rn6
Intron Retention
Gene
ENSRNOG00000005018 | Scn2a
Description
sodium voltage-gated channel alpha subunit 2 [Source:RGD Symbol;Acc:3632]
Coordinates
chr3:51800888-51802782:+
Coord C1 exon
chr3:51800888-51801042
Coord A exon
chr3:51801043-51802608
Coord C2 exon
chr3:51802609-51802782
Length
1566 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGT
5' ss Score
8.37
3' ss Seq
TACCATGCTTCCATTCCTAGGCC
3' ss Score
9.56
Exon sequences
Seq C1 exon
ACTGTGTGAGAAAGTTCAAGTGTTGTCAGATAAGCATAGAAGAGGGCAAAGGCAAGCTCTGGTGGAACTTGAGGAAAACGTGCTACAAGATAGTAGAGCATAACTGGTTTGAAACCTTCATCGTCTTTATGATTCTGCTCAGCAGTGGTGCTCTG
Seq A exon
GTAGGTGGTGCGGGGCCTGCCCCCTCAGCGTTTCCCCTTCCTGTCCATTGAACGTCACTTCACCCATTCATAAAATACAACGTTGGGGAAATATGTGTGCGGAAGGGCTGGCAAGAGTGGCTTATACTGCTCTATCTGGAGGAGCCAGACAGGATCACTCTGAGACAGTGTGTGTTCACATGATATTTCAAAAGGAATCTCTCTGATTTGCGCCAATGGCAGTTGTTTATTTTTGTGTCATCTTTATTCTTTTGTTTTCCGGGCCATTGTTATACTTTCCAGCATCTACTGAATTTCATCCATACAATACAGTACAAATGCAACTATGTTCCTATTTAAGAAATAGATTTTAGGGTCTGCAATACATCCTCGGGCCCTGAGATAGATTAGAACCACTTCTTCAGAAGGGCCAAGCGGTTAAGATGTGGGGTTGCCCACTGAAGTGGGGATCTGCTTAATAGAAGTCCCTTCCTGAGAGAAGTCACCTGACTCAGTCATACCGATCAGGTGCCAGCCACCTGGACTGGTAACTAGTTGGCTACCTTAATCTCTAAAAGCAACACGAGCCTACTTTGCATCTGACTTCATTTAATGGAATGAGTAATTTAGTCAAATTCTCGTTGATATGACAGAAATAAAGTCACCCATTTCCCCACATTGTGGTGTGAAGGGAGATGCAGTCCCTTTGCTTTGAATTTGCTGACCCTGTCTGTGAGTACATTTCATTGTGAGGATGAGTGCACTACTTCAGGAGGCCTTTTAGGGCCGCCCCTGAATTGACCGAGTCCTGTATCCTGCCCTACAGGGTGTGACCTTGCTGTAATAGCTCTTGGCTCCCTGGTACATTCAGTCACAGGTCTTCGAAGCACAAGCGCATGCTCACACTGGAGCTGGCTTCTGGGGGCTTTCTGCTTCAGGGACAAGCTAAGCTCGGTAGCTCTCGGTAGCACTTGTGCTGGGCCCTGTCACAAACCTGGATCCCTCGTTCTCTAAAAACAAAACCTTCTTAGTTCTTTGATGCAGGACACTATGCACTCTGTGTTAATGTTTCCTGTCAAAAGAACTTGTGTAAAATGGTCTTTTCATTCCAGGCCAGGGGCTGCTGGAAAATGACCACGCCCTTTTTGTTCCTAAGTGTTACAGAATGACAGTAGCTTCCAGACACCCCCACTGGAGAAAGCGAGATAATCTTTTCCCCCTTTCCTGGGTCAGGAAACTCCTTGTCACATATTTACACATTCCTCGGAGAGGGATGCCAGTGACTCTAGATTTTGAGCGACTTGACACTTCACCTCTTGCTTAAGAGAACATTTGGCCTTCTCTTGAAAATCTTATGCTTTTTGGTATATGCTCTCAACATTCAGACTTGAAAACTACATGAGTCTCCCCCGTAGACTGCAAAGCCCAGGTATTCTTCACACACCCAGATAACTGTGAGATCAGGACAGTGTAATGACCCTTCTCCTGCCCCTGACCAAAGACGCCTTGCATCATCCCCCGCTCCCCAATATATGAAGCAGGAACTGCTCAGGACAGTGAAATGCAATACCATGCTTCCATTCCTAG
Seq C2 exon
GCCTTTGAAGACATTTATATTGAGCAGCGAAAGACCATCAAGACCATGCTGGAGTATGCTGACAAGGTTTTCACTTATATCTTCATCCTGGAGATGCTTCTAAAGTGGGTGGCCTATGGTTTCCAAATGTATTTCACCAATGCCTGGTGCTGGCTGGACTTCCTGATCGTTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005018:ENSRNOT00000007069:18
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:
PF065128=Na_trans_assoc=PD(19.8=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.0=67.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTGTGTGAGAAAGTTCAAGTGT
R:
CAACGATCAGGAAGTCCAGCC
Band lengths:
327-1893
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]