HsaINT0145842 @ hg38
Intron Retention
Gene
ENSG00000153253 | SCN3A
Description
sodium voltage-gated channel alpha subunit 3 [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr2:165112885-165113970:-
Coord C1 exon
chr2:165113816-165113970
Coord A exon
chr2:165113059-165113815
Coord C2 exon
chr2:165112885-165113058
Length
757 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
AAAATATTTTTGATTCATAGGCC
3' ss Score
6.95
Exon sequences
Seq C1 exon
GATGTATTAAAAAGTTTCCATTCTGTCAAGTAAGTACAGAAGAAGGCAAAGGGAAGATCTGGTGGAATCTTCGAAAAACCTGCTACAGTATTGTTGAGCACAACTGGTTTGAGACTTTCATTGTGTTCATGATCCTTCTCAGTAGTGGTGCATTG
Seq A exon
GTAAGTGAAATGCATATTGGCAAGAATCAGATTCTGGTGAAATAGTTTATTCTCCAAAATTACCAGATGCAAACACTGAGCTTCAGAATCAAAAGAAAAGGCATATCTGTGTCTTGCAGAGCTTGGCACCCAAGGTTTAACGATGCAAAATTCAGTTCTGAACAAATCAGCACCATGAAACAGCCAGATGGAATTTCTCATCTGGTGTTTATCTAACAGATGTTTTCCTCACTGAGACAACCATTTGCAGAGACATTCTGTAACCACGTTACTTTCCCTGTCAAATACTATCCAGTTCTCCCTAATAATTGTATTAACATTTATGGACTAAAAGTGTATTTTAGGTTTTTTTTTCATGTATAATCAACTTATTCTCTCAAAATAAGCCAGATCATTCAGGAAATTGTAGAAAGTAATGTTTGAATAGGCCAATTCTGTCCCTCATTAACAGAACTTCTAGTTATTTCTGAGTTCATATTACTTCATTAAAAGCATGTCTTTGTAACAGTAATTGAGATAGAGACTTAGGGGTGAGAAGTAGGAAAGAAAGCACATTCTAAATCACTAAAGGCATGACGTTTCCCTGCCAGCATTTTCACACTTAGTTTAGTCTTTAGATTTTGTCTGATGTTCAATGTTTATGTAAAATATCAATAATCAAATTATTGTTTTGTACTCACTATTATACTAAGCAATTTTTTCAAATATTTAGAAGAAGCAAGCCATTTAAGTAAAATAAAATATTTTTGATTCATAG
Seq C2 exon
GCCTTTGAAGATATATACATTGAACAGCGAAAGACTATCAAAACCATGCTAGAATATGCTGACAAAGTCTTTACCTATATATTCATTCTGGAAATGCTTCTCAAATGGGTTGCTTATGGATTTCAAACATATTTCACTAATGCCTGGTGCTGGCTAGATTTCTTGATCGTTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000153253:ENST00000283254:20
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(20.1=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.3=67.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAAGTTTCCATTCTGTCAAGTAAGT
R:
CAACGATCAAGAAATCTAGCCAGC
Band lengths:
318-1075
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development