HsaINT0158355 @ hg19
Intron Retention
Gene
ENSG00000163554 | SPTA1
Description
spectrin, alpha, erythrocytic 1 (elliptocytosis 2) [Source:HGNC Symbol;Acc:11272]
Coordinates
chr1:158647480-158648324:-
Coord C1 exon
chr1:158648191-158648324
Coord A exon
chr1:158647625-158648190
Coord C2 exon
chr1:158647480-158647624
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-SPTA1:NM_003126:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.089 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(33.3=77.8),PF0043516=Spectrin=PU(6.7=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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)