HsaINT0158329 @ hg19
Intron Retention
Gene
ENSG00000163554 | SPTA1
Description
spectrin, alpha, erythrocytic 1 (elliptocytosis 2) [Source:HGNC Symbol;Acc:11272]
Coordinates
chr1:158614043-158615175:-
Coord C1 exon
chr1:158614978-158615175
Coord A exon
chr1:158614187-158614977
Coord C2 exon
chr1:158614043-158614186
Length
791 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
TCTCATTTGATTCCTCATAGATG
3' ss Score
8.29
Exon sequences
Seq C1 exon
GAGCACCGTGCTGACATGGAGGCAGAGGCTCCCACCTTCCAGGCCTTAGAGGACTTCAGTGCAGAACTTATCGACAGTGGGCACCATGCTAGCCCTGAAATTGAAAAAAAGCTTCAAGCTGTCAAGCTAGAGAGAGATGATTTGGAGAAGGCTTGGGAAAAACGCAAGAAGATCCTAGACCAGTGCCTGGAGTTGCAG
Seq A exon
GTACAGCAAATTTCCCAATTGTTAAGCAGGTTCAGTAGTCTGTTTCTCCTATGCAATTTCATATGGTCATTACAGGCTCCGTTCACTAGACTTTCCACGTTATAAACACAAAGGGAGCTCATCTCTTAATTACCTAGCATTGTACTATGCTTTCTATACCGATCATTGTCATATTCTCTGCTCTTTCTTGTTAGAAGAGCCAAACAAGATGGTGATCAGTCCTGAGCATGAGGTGGGTTGACTATCATTTGTTGATTGACTGAGGAATTGATTGGCTGATTTTTGTTGAGACTCTACTCTGTGGAGGCTCGGAGTGCCACAAAGATTAGTAAGATAGTTTCCCATTTCTTAAATAGTGAAATTAGACATATAGATAAATTTTACTAGTACAGTGAGATGATTATTAATAAACCAAAATGTACGAGTGCTTTGAGGCTAAAAAACAAGAAGTGATTAAAGCTTTTGGGGGAAGTAAGTGGTTGTGTCACAGGCTACCCTGAAGGATAACGTTTCACAAAGTCTTAAGGAAATGACCAGCCAGTATTAACAAGGTTTAAGAAATAGGAAATAGCACCCCAGGAATTGGAGGTAGCATATACAGAAACATAAAGTGTATGTTTGGAAAAGAGGAAAAGTTCCAGTACAGCTAAGATTTGTCACATGAGTGTTTCTTGGAAGATGGTAAGTACTCCTTGCAAAACCCTTTGTGTCATGATCCTGAAAGAGGTGTAACATCATTTCCTCCACACCACATGGACTATACCATACCCCTCTCATTTGATTCCTCATAG
Seq C2 exon
ATGTTCCAGGGGAACTGTGATCAAGTTGAGAGCTGGATGGTGGCACGTGAGAATTCCCTGAGGTCAGATGACAAAAGTTCCTTAGACAGTCTGGAGGCTTTGATGAAGAAACGGGACGATTTGGACAAAGCAATCACTGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163554-SPTA1:NM_003126:29
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.258 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(57.1=90.9),PF0043516=Spectrin=PU(2.9=4.5)
A:
NA
C2:
PF0043516=Spectrin=FE(45.2=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:
TGACATGGAGGCAGAGGCT
R:
CAGTGATTGCTTTGTCCAAATCGT
Band lengths:
326-1117
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)