HsaINT0158337 @ hg38
Intron Retention
Gene
ENSG00000163554 | SPTA1
Description
spectrin alpha, erythrocytic 1 [Source:HGNC Symbol;Acc:HGNC:11272]
Coordinates
chr1:158636641-158638241:-
Coord C1 exon
chr1:158638033-158638241
Coord A exon
chr1:158636762-158638032
Coord C2 exon
chr1:158636641-158636761
Length
1271 bp
Sequences
Splice sites
5' ss Seq
AGAGTATGT
5' ss Score
5.66
3' ss Seq
GTTTTCTTCCTTGATTTTAGGGA
3' ss Score
10.09
Exon sequences
Seq C1 exon
GATGCACTCAAGGACCTGAATACATTGGCTGAAGATTTGCTCTCCAGCGGGACTTTCAACGTTGATCAGATTGTGAAGAAAAAAGATAATGTCAACAAGCGTTTCCTGAATGTCCAAGAATTGGCAGCTGCACACCACGAAAAATTGAAAGAGGCCTATGCCTTGTTCCAGTTCTTCCAGGATCTAGATGATGAGGAATCCTGGATAGA
Seq A exon
GTATGTGCCACCAGCTCAAAAATGTGTGGATAATACAAGCGAGTAGATAATCCACCAAACTTGTTCCAATTTATGCTGAAATGAAATTTGTACTTGTTTCTTGAAGATAGCACTACTTCATGTTTGCCTCAGCTTAAGGTTAACATTGGTTTTATTTTTCCCAAATTCCCTTACTGGATGCAAGCCAGAGAAAGACAGGTGTGGAGGAAGTGAAGAGCAGTTAACATACATGACAGGAACAAAACTAAGAAGCCATCTGCATTTGCTCTGTAGTTCATTGAATAATATGCAATACTCACAGAGACACCTGGACATTTACACAGCTGATCAGAACCTTGTCATTCTATATCCAGTATATCTTATATGACACTGAATTGGACACTCAATAGAGAATATTACAAAGTATCTACCAAGGTTTCATTACTCATTCCATTTTTGGTTACACAGCTGGTCAGAACCTTGTCATTCTATATCCAGTATATCTTATATGACACTGAATTGGACACTCAATAGAGAATATTACAAAGTATCTACCAAGGTTTCATTACTCATTCCATTTTTGTTGTAAAATATGATTTGGAAAATCTTAGCACATTACACTATTTTGCCTACTTCCCATTTAACCTGCCTCATCACGCTTCTCTTCTACAAAGCTGCTTGATTATTATGAGTAATCAATAAATTAGAGGGAAGCACCATGCACAGGGCAACAAATAACATGTTTTAAAAACCTTTTTGGATAAGACCATAAGATAGAATAATCTTGTCCATGTAGTCTTCGACTGTACTTCGTGGTGATGCTCAAACCTTTTGCACTTGGAAGCATCCCAACTGCCATGACTCCTATGAAATCAGCTCTTTATACCCATTCTAGCTGAATTTATTATTGACATTAATAAATGAAAATAACAAAACCTGTGGAGGTCATATATAATTTTCACATTTTTTTGAAATAGGAAACATTAGTGTGTATTCTTGAGCAAAAAAGAGAAGATATACAAGTGGAGAAGCAAAGGGACTAATGGAAAGGCTGTTACAGTTGTGACTATGGTGGAGATCAGTATGTTACTTTAATTTGTATTGGCTCAGTCAGAAGTTTTGCTGCAAGCCTCTTCCACTAATTATATTTTTGGTCATTGGCACCAGGGTATTACAGAATTTACAACCACCTCCCTCACCACCAGCCACACACATAGTCATAGAAAGCTATTGCTGTAGGATGACATTAGATGTCTAGACTCCAAACTTTCTGTTTTCTTCCTTGATTTTAG
Seq C2 exon
GGAGAAGTTGATACGAGTGAGCTCCCAGGACTATGGGAGAGATCTTCAGGGGGTTCAGAACTTGCTGAAGAAGCACAAACGCCTAGAGGGGGAGCTGGTGGCCCATGAGCCTGCCATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163554:ENST00000368147:36
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=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(47.6=71.4),PF0043516=Spectrin=PU(16.2=24.3)
A:
NA
C2:
PF0043516=Spectrin=FE(38.1=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:
TGCACTCAAGGACCTGAATACA
R:
CTGGATGGCAGGCTCATGG
Band lengths:
328-1599
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