HsaINT0158328 @ hg38
Intron Retention
Gene
ENSG00000163554 | SPTA1
Description
spectrin alpha, erythrocytic 1 [Source:HGNC Symbol;Acc:HGNC:11272]
Coordinates
chr1:158645188-158645594:-
Coord C1 exon
chr1:158645495-158645594
Coord A exon
chr1:158645386-158645494
Coord C2 exon
chr1:158645188-158645385
Length
109 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
CTTCCCCCTTTTTCCCACAGGAG
3' ss Score
13.07
Exon sequences
Seq C1 exon
GGATCTGCAGAACTGGATCAGTAGCATTGGTGGCATGGTATCATCACAGGAGCTGGCCGAAGACTTAACTGGCATAGAGATCTTGCTGGAGAGACATCAG
Seq A exon
GTAAAACTACAAAAGTCACAGCCACTGATCACTTGACCTGAAACCTCTACTAATTTTAAAATTTCCAATGGAGTTGGCCTCACTGATTTCTTCCCCCTTTTTCCCACAG
Seq C2 exon
GAGCACCGTGCTGACATGGAGGCAGAGGCTCCCACCTTCCAGGCCTTAGAGGACTTCAGTGCAGAACTTATCGACAGTGGGCACCATGCTAGCCCTGAAATTGAAAAAAAGCTTCAAGCTGTCAAGCTAGAGAGAGATGATTTGGAGAAGGCTTGGGAAAAACGCAAGAAGATCCTAGACCAGTGCCTGGAGTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163554:ENST00000368147:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.029 A=NA C2=0.258
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(31.4=100)
A:
NA
C2:
PF0043516=Spectrin=PD(57.1=90.9),PF0043516=Spectrin=PU(2.9=4.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGTAGCATTGGTGGCATGGT
R:
TGCGTTTTTCCCAAGCCTTCT
Band lengths:
248-357
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains