HsaINT0158345 @ hg19
Intron Retention
Gene
ENSG00000163554 | SPTA1
Description
spectrin, alpha, erythrocytic 1 (elliptocytosis 2) [Source:HGNC Symbol;Acc:11272]
Coordinates
chr1:158589960-158592982:-
Coord C1 exon
chr1:158592773-158592982
Coord A exon
chr1:158590257-158592772
Coord C2 exon
chr1:158589960-158590256
Length
2516 bp
Sequences
Splice sites
5' ss Seq
AAGGTTTAA
5' ss Score
1.88
3' ss Seq
TCTTTTTTTTCTCTCTGCAGGCT
3' ss Score
12.9
Exon sequences
Seq C1 exon
GACACTCTGGATGCCAGTCTGCAGAGTTTCCAGCAAGAGAGACTTCCCGAGATCACTGACCTGAAGGACAAACTGATTTCTGCTCAACACAACCAGTCTAAAGCCATTGAAGAGCGTTATGCCGCTCTGCTGAAGCGCTGGGAACAGTTGCTGGAAGCCTCGGCAGTCCACAGACAGAAATTGCTGGAGAAACAGCTGCCTCTACAGAAG
Seq A exon
GTTTAAAAAAATTATGAGGCATGATCAGTTCTCTGTTACCTGTATATTAGCCATGAAATTCGGAAACAGATATTGGAAACTCAGTTTGGATAATACAAAAACCTTTTATTGCATTGAAAGATGTTGGGAAGACATTCTTACTGAGCAAAAAGTAGATTGAAAAGAAGCTTTAAAAATTTTTTTTAGATTGATTGATTAGTTGCATAACTAACTTGAGATGGAAGCCAGGCAAACAGTGGAAGAGGTGGATGGAACAAGAGGATGGGAGGTCTTTGTGTATGATAGAATTAAAACTGTCAGGCAAAAGTCAAGGTTGTCCCTGTACTTTTCCTAACCCAAATAAAAGGAGCACTGGACAAGTTGTCATAAAACATGTTCTCACCTTATATCAAGCTTTCCTAGGTTGAAGACCTTGTAAAAGTCATTTAATATCTCTAAACCTTGATATCCCCATTTAGAAAATTGAGTAGCATCACCATTCTATTCTGCCTTTCTGTTATCACTATTAAAAAAGATAATGAATCTAAAAGTGTAATAATTCCATATTATTACATTATTACATTCATATAAATATGTATGGTTGTAATATGTGTGTATTAATAATACATAATTATATGTACATTATATGTACCTAAATATATGTACATTAATAATACATAATAAATATGTATGATTAATATGGATTAATATAATAATGTAACATTATTACATTACTACATCCATATAAAATTCCATATAAATATGTAATCAAAATATTCCTTCAAATGTTGGCTGCTAAGGCATTGGATGTTGATCATAAAAATATCAATAATGGAAGGAGGCCAGGTGCAGTGGCTCACGCCTATAATCCCAGCACTTTGGTAGGGCAAGGCAGGTGGATCACTAGATCAGAAGATCAAGATCATCCTGGCTAACACGGTGAAACACCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGCGGGCACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAACGGCGTGATCCCGGGAGATGGAGCTTGCAGTGAGCCCAGATCGCGGCCACTGTACTCCAGCCTGAGCGACAGAGCAAGACTCCATCTCAAAAAATAAATAAAAGGAAATCAGAATGGTCAGTGGAATTACTGAGCACTCCTAGACCCTAAGAATCATTGTACTTGGTAACAAATTAAGTCAAGGAGTTAGGGAATTTAGGAAATAACACATGAGTAAAAGTCAAATCAGAGTCTTAGTTAATTTCCACACTTTTGAAAAACATAGGGCCTACATCAAATAAATCTTAGGTGAAAAATTAAATCAATTAAGTGGGCAACTTTACACATATATGTGCATTCTATATAGGAAGCTCCTTCATATTTTTAATCTTCTTTTTAAAATAATTTCAAACTACAATGAGTTTTGTTTATTTTCTGATTACAAGATATTTATAAAATATTCACTCAATCTATAACATTATGAAAAAGATATTAAATACTTTATAGGTTTCTGTGTCCTTTCTGTGTAGAGGTCATGTTAATTTTCTCTGTATTGATCTATTTTGGCATATAGATTGCTGAAATGAGTACAGGGTCAGATGTAACGGTTTAATACCTTTGAAATCCTCCCTCCATTTGGGCCAGTTTTCTTCTTTTTAATTCTTGTATTTGGGAATGAAAAATTCATTTTTATGTTTGCTCAAGACAAACCTCTTTAGAAGTACTATCTGCTGACCCAAAATCTGTAATGTATTTTAAGTATAAAAGTATATTTGATCACTTGCTGTTTGAAAAAATTCATGCTTTTTCTGTCATTCAGTAATACAGAAAATTCAGAGCTATTCAGAGCACTTGGATAATGCCAGACAGTAATACAATGATACATATATTTGTGCTAAGGATACAGGTTAGAGGGTAGAAGATAAGTTTAAGCAGTGGTTTGAAAAGCTTCAGGCATAAAATGAGGCCTGAACAAGGTTTAAAAGGAAGGTAGGAAAATGACATAGCCTTGTCAAAGAGAAGTCAGCTGGGTGTGGTCTACAGAAGCTTGTAGGATAATAAGATAAAGGAGATAACAGATTTTCTTGGTTTGTTTATTCAATCATTATTTCATCCATTCATTCAATGCTTTTTTTTTTTTTTTTTTTTTCATGTTTACTACTTGCCGGGTAGAACTGGAGGATAGACTTTAGAACAAGAAATCATATAATTGAAAACTACCTTTGCTACTTTTGGAATTTTAAAACTGAAATAATTTTAGAAATAATTCGACCTCCCTCATTTGTAAATGATGAAAGACTTAAACAATTTCACACAATGAGAAAATGCCAGAACCAGGGCTCGTACCGCTAACTCACATGTTCAACCATCAAAGTACACAGTCCCTATTGGTTTTAGTTCTGCCCTTTTAGATTGGTGGCCCTGCAGATATTTAAAGACAGGCATTATTTTTATCCTCAATCTTCTCTTCTGCTGAGAGGCTTTATCAGGAAAGATGGTAGTGTCTTTTTTTTCTCTCTGCAG
Seq C2 exon
GCTGAGGACCTGTTCGTGGAATTTGCACATAAGGCTTCAGCTTTGAACAACTGGTGTGAAAAGATGGAAGAAAACTTGTCAGAGCCTGTGCACTGTGTCTCCCTGAATGAAATTCGGCAGCTGCAGAAAGACCATGAGGACTTCTTGGCCTCCCTGGCTAGGGCTCAAGCAGACTTTAAATGTTTGCTGGAGCTAGACCAGCAGATTAAGGCCTTAGGTGTGCCTTCCAGCCCTTATACCTGGTTAACAGTGGAGGTGCTGGAAAGGACCTGGAAGCACCTATCTGACATCATTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163554-SPTA1:NM_003126:43
Average complexity
IR-S
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(58.5=88.6)
A:
NA
C2:
PF0043516=Spectrin=PU(91.4=97.0)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)