HsaINT0158311 @ hg38
Intron Retention
Gene
ENSG00000163554 | SPTA1
Description
spectrin alpha, erythrocytic 1 [Source:HGNC Symbol;Acc:HGNC:11272]
Coordinates
chr1:158669709-158671453:-
Coord C1 exon
chr1:158671343-158671453
Coord A exon
chr1:158669787-158671342
Coord C2 exon
chr1:158669709-158669786
Length
1556 bp
Sequences
Splice sites
5' ss Seq
ATAGTAAGA
5' ss Score
4.74
3' ss Seq
TTTTATTTTTATTTTTTCAGACT
3' ss Score
9.69
Exon sequences
Seq C1 exon
GCCTTCCTGGAAAACGAGGATCTGGGAAACTCACTGGGCAGTGCAGAAGCCCTTCTTCAGAAGCATGAAGACTTTGAGGAAGCCTTTACTGCCCAGGAAGAGAAGATCATA
Seq A exon
GTAAGAAATTGGCCCTAGTTTGGGCATTGGCTCCCTCTCTGTATACATAATTTTACACAATACCTGTCCCCAGACAGCATTGCTCCTGTAACTACCAGACATAGCCTGAGGATTATCCCTAATCAAGTTGCATCTCTTCTTTCGTTGTTGGTGTGTTTATTTGTGTGTTTTTCAAACTCTTTAATTTTATAAACATAAAATGTTTATATAGTGAGAAAGCCAAAACTTAATACTAATCTTTAGAAAAAAAGTGAAAATAGCCAGAAAAATACTCATACCAATTTTTATCACACCATTCTTGTTCTACAAAGCATATCTGGAAAGTTTTTCTAGATGGTAGCCATGTTTTTTTTTTCTGATGAAGTGTATGGTTTTGTTTTATATTTTCTTCAGTGTAAATAGAAATTATTGAATTCTTATTCAGTATAGAATCATTACTTAGAAATTTTATTTTTTTTCATTTCTTCCTCTCTAGCAATATCTTAATATAATTTTCTCTTCCTTGGTAACATCTAGATATCTAAGTACTGTCTACTCTTTTCCTTTACAGCATATTTTTCCTTTATAGTATATCTTTATCTCTGTTTTTCATCATATATGACTACAGAGTTTTCCTGTGAGCCTTAAGTTACAATGTCCCAGAAAGCTGGTGAATGTGAAGGCAGGACTCAGAGAAGTGAAAGGAAGACTTCATGGGTCCAATACATTGTATGTCTCTGGCTGTTCCTAGGATGATGCTGACTTTAACACCACCCTTGCCACATGCACATACATACCACTACCTCCACCACCAGCAGCAGCAACAACAAAAATAACAGGCAAATTCCTAGTCTTCTCTGTTAATCTTAAATCAATATGGTGAAGAGGTGGAAGTCCAATTAATATCAAGTCCCTCATTAATTGATATGTGTGTCCTTTCTGTTGATTCTCATTGGTCAAAGCTAACAGTGTAAAATAATTTATTGTTTATAAAGTGTTATCATTTATTTTAGATCATTTTCTTATTCCAATCAATTAATTCTGAGCTCTAGCAATTTGGGGGATTTCTGGTTAAACAAGGGTGAAAACTTACCTCTATAATTTCTGACTCTTCTCCTATGTAACTGGAGATAGAGATAGAGATATAGCTAGAGCTAGAGATAGAAGGAGATAGAGATAGAGGTAGAGATGAGATAGAGATAGAGATATATTTGAGAGATGAATACACGGATAGATAGATGGATGGACAGACTGGCCATGGACATGGCTATATCATTGGTAGTGCTTCCCCTTGAAGACAAGAATAAATCAATCATCTCATAGCAACATCTGCATTCATTTACTGTAACCTGTATTTAAAAAATATTGTGGTACAGAGAATGTAATTGACATGCCCTGAGGTATATATTTTGAAATACAATTTATAACAGAAACCTGAATAAGGACTTACATCTGCTGGCCTTCAAACTTCTCCTCCCACATTGCTGTTCTTCATCTTTAAACAGCTACCCAAACTATGGCCACTTACTCAGTGGTCACTGAAGGAAAAGCATTCATTTTTATTTTTATTTTTTCAG
Seq C2 exon
ACTGTAGACAAGACTGCAACCAAATTGATTGGTGATGACCATTATGATTCAGAGAACATCAAGGCTATCCGTGACGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163554:ENST00000368147:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.027 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(34.3=100)
A:
NA
C2:
PF0043516=Spectrin=FE(23.8=100)
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:
CCTGGAAAACGAGGATCTGGG
R:
CGTCACGGATAGCCTTGATGT
Band lengths:
182-1738
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