HsaINT0158311 @ hg19
Intron Retention
Gene
ENSG00000163554 | SPTA1
Description
spectrin, alpha, erythrocytic 1 (elliptocytosis 2) [Source:HGNC Symbol;Acc:11272]
Coordinates
chr1:158639499-158641243:-
Coord C1 exon
chr1:158641133-158641243
Coord A exon
chr1:158639577-158641132
Coord C2 exon
chr1:158639499-158639576
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-SPTA1:NM_003126:12
Average complexity
IR-S
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
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
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)