HsaINT0158312 @ hg38
Intron Retention
Gene
ENSG00000163554 | SPTA1
Description
spectrin alpha, erythrocytic 1 [Source:HGNC Symbol;Acc:HGNC:11272]
Coordinates
chr1:158669408-158669786:-
Coord C1 exon
chr1:158669709-158669786
Coord A exon
chr1:158669564-158669708
Coord C2 exon
chr1:158669408-158669563
Length
145 bp
Sequences
Splice sites
5' ss Seq
GGGGTATGT
5' ss Score
7.48
3' ss Seq
TTTACTCATGGTTTTTGCAGCTG
3' ss Score
8.48
Exon sequences
Seq C1 exon
ACTGTAGACAAGACTGCAACCAAATTGATTGGTGATGACCATTATGATTCAGAGAACATCAAGGCTATCCGTGACGGG
Seq A exon
GTATGTCCAAGGGCCTAGAGCTTCTGTGTGCCTACACACTAGAATCAAGAAGAGTTTTGGTGGGCATGGTGACCAGGGTGGTCAGCGAATCTCACATGTCCATATTTGGTTGTGCTGACAGTAAGTTTACTCATGGTTTTTGCAG
Seq C2 exon
CTGTTAGCCCGGCGGGATGCCCTACGTGAAAAGGCTGCCACTAGACGTAGATTGCTGAAGGAGTCATTGCTTCTGCAAAAACTGTATGAGGACTCAGATGACCTAAAGAACTGGATCAACAAGAAGAAAAAGTTGGCAGATGATGAAGATTACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163554:ENST00000368147:13
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=0.019
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(23.8=100)
A:
NA
C2:
PF0043516=Spectrin=PD(19.0=38.5),PF0043516=Spectrin=PU(27.9=55.8)
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:
ACTGTAGACAAGACTGCAACCA
R:
CTTGTAATCTTCATCATCTGCCAACT
Band lengths:
234-379
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains