HsaINT0158320 @ hg38
Intron Retention
Gene
ENSG00000163554 | SPTA1
Description
spectrin alpha, erythrocytic 1 [Source:HGNC Symbol;Acc:HGNC:11272]
Coordinates
chr1:158654611-158656656:-
Coord C1 exon
chr1:158656564-158656656
Coord A exon
chr1:158654749-158656563
Coord C2 exon
chr1:158654611-158654748
Length
1815 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TGCTTCCTGTTTTTATTCAGCAA
3' ss Score
7.55
Exon sequences
Seq C1 exon
GCTCTTCTAAAGAAGCATGAGGCCTTTCTATTAGATCTCAATTCATTTGGAGACAGTATGAAAGCTCTGCGGAATCAGGCAAACGCCTGCCAG
Seq A exon
GTAAGACTAACTTAGCGATGACAGGATTCACACTTCCCACCACAAAGAAAAAGAAATTGTCTTTATTGCTGATTTTTTACTTTCTACAACCCCAAAAACAATGGCAAAGAAAACACTAAGTTCTATGACCCTTGTATGCAGGAACTGTAGCATCCACAATTTAGTCCAAAGGAGACTTTGTCCAAAAGAGGTTTTTGATAAATGGTATCATGTCTTCATTGATGTATTTTTGGCTTTCCTCTTTCCTTCCTTTTATATTTCTACCCTTCTTTCTTTCTTACTTTTCTTCATTTATGTCTCTCCTTCTTATCTTTCTTCTTTACTCCCTTCTTTTGTTTCTTAATTTTTAATGCCAAAACTTATTAAATGTCTACTATATGTAAGTATGAATAAAAAATCCTGATTTGCAGGAAAATTACAGTCTATTAGGAGGCCAGATGTTTAACAGTAAGTGCATATAATAGATGTATGAACAGGACAAAGAGTCTCAAAGAAAGGCCTCTTGTGTTCTCTTGAAATAACAGTACTGGAAAACAGGAAAATTTTTGTAAGCTAAGGGAAACCGCCTGATCTGAATTATTAAGGAAAGACAGATGGGTAGTTTACTGTGCAGAGAAAGAGGATAAGCGTTTTTCTAGTCAATAAACCATGAGAGCAAATGCACTGAGGCACAAAACAATCAAGTTTTGTGGAAAATGCAATTGGTTAAGAATGTGAGAATGGAAGATGCAATTGGTTGAGAATATGAGAATGGCTCAGGTACAGGGCAAAACTGGGTGTCATGAAGATTAATTGAACTGGAATCAAATAAATGTTATAACAATGTCTACTATATGTAGTGGTAGAAAAAAAGAGACACACTTCTTACCTTCAAGGAATTCTTTCTAATGAGAGGTTGTTAATCCACACATTCAGAGTAAACAAAAGACGTAGACTCAGTCTGTCAAATCAGTGTATATTTACAGACCTCCTATACTGTGCCTTCACCAGGCTCTGCACAGTGGGTGCCTAAACAAGAACAGAAGGATTTATATATTGTGTGGTATGAGGAAACATGTTACCTAAAGGAGATGAAATTAGAGGGCTCTGTCGGTGGAGGTGCATATTCAACTCCAACCTGAGGAAGGGGTGGGTCATTCCTTAGGAAGAGGGGTTATGTTTTGCTTGATTTCTCAGAGACATGAAATTGGCAGAAAGTAAAAATCAGAGAAAATTCTACCTTAGAATGCAGGCTGCTTACTAAACTGAGACACAAGATACTTTTAATGATCTCAGTTAATGTTCTCAGTTTTTAAAATTCTGTGGCCTTTCCTGTGCTATTGATCACTCATATCTCAAATAGAAGGTCCGGAGCTCCTGACATAGTAACTTAAAGGCCAGAAGGAGTGGGAAGAATTATCACTGGAGGTACAGGGAAAGGTGACGACAGAGAGTGGGTCTTTTCACTTTCTCAAACAATTTTTTGAAATGTTGATGTGTATAATCCTGTTGGACCTTCTTAAGGGAGTACACTTCTTAAAATGTACTCCTCCCATTTTAAGAACTGATGGCTTAGAGCATTTAATACGTTTCTGACAAATTATGTATTTCCTTCCTTGCTTTGGGTTTATAGTTCCCAACCTGCCTGTCCCCGATAAGTGTCAGAATGGAGCAGTCTCTCTGAAGACCACATACTTTAATCTCTGCAGCCACGTAAGAGGTTCCAGCCAGAGGCTCTTTTCTCCTGGGAAGCCTAAAGGACTACTCACCCCTGGTAAGCTGTACAGGGAGATATTTCCAGTGCGTGACTGACACCTGCTTCCTGTTTTTATTCAG
Seq C2 exon
CAACAACAGGCTGCACCAGTGGAGGGAGTTGCTGGAGAACAAAGGGTCATGGCTTTATATGACTTCCAGGCCCGCAGCCCCCGAGAAGTCACCATGAAGAAAGGTGATGTCTTAACGCTGCTCAGTTCCATCAATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163554:ENST00000368147:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.151 A=NA C2=0.174
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(36.6=100)
A:
NA
C2:
PF0043516=Spectrin=PD(15.9=28.3),PF0001823=SH3_1=PU(63.0=63.0)
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:
CTTCTAAAGAAGCATGAGGCCT
R:
TTGATGGAACTGAGCAGCGTT
Band lengths:
224-2039
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