HsaINT0158355 @ hg38
Intron Retention
Gene
ENSG00000163554 | SPTA1
Description
spectrin alpha, erythrocytic 1 [Source:HGNC Symbol;Acc:HGNC:11272]
Coordinates
chr1:158677690-158678534:-
Coord C1 exon
chr1:158678401-158678534
Coord A exon
chr1:158677835-158678400
Coord C2 exon
chr1:158677690-158677834
Length
566 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
GCTCTTGTTAATGACTGCAGGGA
3' ss Score
4
Exon sequences
Seq C1 exon
GAAAACCATCCTGACCTACCCTTAATTCAGTCTAAGCAAAATGAGGTGAATGCTGCCTGGGAGCGCCTTCGTGGTTTGGCTCTCCAGAGACAGAAAGCTCTGTCCAATGCTGCAAACTTACAACGATTCAAAAG
Seq A exon
GTATGGATCTGGCCACTGCTTTATAGAAAACTTTGAAGTGCTTTATAAAAACCGTGTCTTTGTATTAGGCTCTTTCTACTTCTGTTAGCAATTAATGGTCAACACTTCAAACAAAAGTGGATCATGTACTTGCCTTTGGGACAGCAAAGGAGAAGGTAAAGAAATCTGTGACCTACTCTATGGCCAAGGATGTAGAGATTGGAGATCAAAATAACTAAAAAAGTAGCATTGGTAATTTAGGAATGGAAGCGCTGCAGACGGAAGGGAAGCAGGTTAATAATTAAATGGAAGGTGGAGTTAGGAAGAAGAAAAGCATTCGTAAGGAGCTGACCCAGATATGGAACATATCTCTAGAGGCTCAGCTGTCAAGAAGCCCAGGACCTTAACATCTCAATAGAAATAACCATTAAGTAAGAACATTTTATATTACTTTTTGCTAGTATGTAGGAAGAAAGGATAATTGCTCCTGGGTCAACTAGGATGGTCCTTGCTGTGAGTTCTGTTGGACCGTTTGCCCTGTAATGCTTGCTATCTTCTTTGGTTGGAGCTCTTGTTAATGACTGCAG
Seq C2 exon
GGATGTGACTGAAGCCATCCAGTGGATCAAGGAGAAGGAACCTGTACTCACCTCTGAGGACTATGGCAAAGACCTTGTTGCCTCTGAAGGACTGTTTCACAGTCACAAGGGACTTGAGAGAAATCTTGCTGTCATGAGTGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163554:ENST00000368147:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.128 A=NA C2=0.002
Domain overlap (PFAM):
C1:
PF081246=Lyase_8_N=FE(40.4=100),PF0043516=Spectrin=PD(47.9=77.8),PF0043516=Spectrin=PU(16.3=15.6)
A:
NA
C2:
PF0043516=Spectrin=FE(45.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAAACCATCCTGACCTACCCT
R:
ACTCATGACAGCAAGATTTCTCTCA
Band lengths:
273-839
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains