HsaINT0158343 @ hg19
Intron Retention
Gene
ENSG00000163554 | SPTA1
Description
spectrin, alpha, erythrocytic 1 (elliptocytosis 2) [Source:HGNC Symbol;Acc:11272]
Coordinates
chr1:158595936-158596797:-
Coord C1 exon
chr1:158596629-158596797
Coord A exon
chr1:158596013-158596628
Coord C2 exon
chr1:158595936-158596012
Length
616 bp
Sequences
Splice sites
5' ss Seq
TAGGTATGA
5' ss Score
6.99
3' ss Seq
TAATTGTTTTTGCCTTTTAGCTG
3' ss Score
8.18
Exon sequences
Seq C1 exon
GTGTTGCAGGAGGAAAGTCAGAACAAAGAGATTTCTTCCAAGATAGAGGCTCTGAATGAAAAGACCCCTTCTCTGGCTAAGGCAATAGCTGCTTGGAAGTTGCAATTGGAAGACGATTATGCCTTTCAGGAATTCAACTGGAAGGCTGATGTGGTAGAGGCTTGGATAG
Seq A exon
GTATGATGTGTCAGGTTCAGGGTCCCTTGGGTTTGAGAAACCCTAATAAATCCCATCCATGTGTAGAATGGTCTCTGGGACTTTTACTGTATGAAAGGAGGTGTTTCCATCACTACCCATTCCTATCCTTTCTGGACAGAATTACACTCACATTTGCACACACATACACACACACATAAACACACACACACAAAGTGAGAAAGAGATAGAAATGATGATGCAGTAATTATGTACCGTAACTCCAGAGAACACATTTTTGGAGAATTGGAGATTTTGTGTGTGACATTGAGAAAGGGAAAGCCATAGCAAAATGTTCTAAGAAACAATCTAAAATGTTTGTTAGATTTACTTACAATTCATATCTAATCTACAATTTCTCTTTTTTTTTCTATGAAGTACTCAAAAGCTCTCAAGACCCTAGCTCTGTTTCGTTAAGTTTTATCCTGCCTAGGTAGAAAAACGATCCATTGGTCCCACTGCTCACATATTCCAATTAATCATCAACTTTGAGAGTCAAGAAGCTTTCTTGTTGTGTGTTGTAAATATTCCTTTTCTGCTTCCCAGGACTCAAACAAGACCAAATGTCTTTCTCTTCTTAATTGTTTTTGCCTTTTAG
Seq C2 exon
CTGATAAGGAAACAAGCCTAAAGACCAATGGCAATGGTGCAGACCTTGGTGACTTCCTCACTCTTCTGGCAAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163554-SPTA1:NM_003126:41
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(34.3=64.9),PF0043516=Spectrin=PU(16.0=29.8)
A:
NA
C2:
PF0043516=Spectrin=FE(23.6=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:
GTGTTGCAGGAGGAAAGTCAGA
R:
CTGTTTTGCCAGAAGAGTGAGGA
Band lengths:
246-862
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)