HsaINT0158354 @ hg19
Intron Retention
Gene
ENSG00000163554 | SPTA1
Description
spectrin, alpha, erythrocytic 1 (elliptocytosis 2) [Source:HGNC Symbol;Acc:11272]
Coordinates
chr1:158580496-158582751:-
Coord C1 exon
chr1:158582607-158582751
Coord A exon
chr1:158581180-158582606
Coord C2 exon
chr1:158580496-158581179
Length
1427 bp
Sequences
Splice sites
5' ss Seq
CAGGTCCGA
5' ss Score
4.4
3' ss Seq
TCTCTTTTTATACTTTTCAGGCC
3' ss Score
9.81
Exon sequences
Seq C1 exon
GAAGGGCTATGTCTCACTGGAGGACTATACTGCTTTCCTGATTGACAAGGAGTCAGAAAACATCAAGTCCAGTGATGAAATAGAGAATGCCTTCCAAGCCCTGGCAGAGGGCAAGTCATATATTACCAAAGAAGACATGAAGCAG
Seq A exon
GTCCGATTCTGGTTGCTTCCCCTACTACACTGTCATCCTAATTTGAATTCTGGTCATCTCAGGCCCGGTGGCCTACTTTGAAAAAACCCACCCACTTGTTTTTTTTTTTCAGACCTCCCCTTTCACAAGATGTCATTTGCTTTGGTAACCACTTCATTTTGTCTTGACCCAACTCAAAAACGTACTGTGGTACTCTATTGAATGTGAGAGTCAATTCAAAATCTGCAACTCAGTTTTTAAGGCTATTTCTTTTTTTTTTCCTCATTAATTCAAAGAGCATTTATTGAATGCTTACTATGTTCCAGGCATGAGGAGTGCAAACTTTAGTAAGACACAGTCCCTAAATTCAGGTGTAGTGGGGAAGACAGAACTTTACAAGTTAAAAACACTGTAACAGAAGCAAACACATCTGTCATGGGAACAAAGATGTGGGGAATTTTATTACAACCAGAAGTAATCTCTCTTCTCTCTGATTCCAAGAGCTTTCTTCATTCCTCTCCTTAAAATACTTGCATCAGGGAAAGTATCATCTATGATTAACACAGGGTGAGTGTTGAAGGACGTGCAGGAACTCATCAAGTCATCAAAGGAAAGCCTAAGTGTTTCAGGCAAAGGCAAGTGTGTGTGCAAAGGAACTTGAGAAAACAGATTTTCCTAATACCTAAAGCATAAGGTAAGAAGATAGTAACAGAAAGTGAAAGGGAAAACAATTAAGCAGAAACCAGATTACAAAGGGTCACATACATGATGGTATCGTTTTGCACAAACTCATCCAATTGTCTAAACTCATCAAACTGTACACATTAAAGGTGCAATTCTTTATCAATCATACCTCGACAAAGCTGTTACAAAAAGAAAATGATGTGGTCTTCCAGACACTATCTGGAGCCACCCACCCACACGCTAACTTATTGGAGTCTTTAGGGATCCACTTGGTAATCAAACAGCACAGTGAATAGAGGAACTCTTTGGCATAAGAGGATCATAGGTTCAAGTCCCAGCTCTACCACTTTCTGGCAGTGTAACCACTGGTGAGTTATTCTACCTTCTTGAGTATTTTACCTTACTCATAAAACATGCTAGTCCCCACATCTCAAAGCAGCCAGGAAGATGAAATAGATCAAGTGGTCAACAAATGTTGTTAGGCATATAATTCCTTCTATTTAATAAAACAACTTTAGGGAATGAGATTTACAGAATAATCAAAGTGAGTAAGCTCTCTTTTTCAAGAAAGGGCTGAGATTAAAAGTTAAGTTACTCATTAGAAATTATAAATTTATGAGATAAAAATTGTGTGTAATAGAAATAGGGCTTGCGTCTTCCAGAGACTCTCCATCTCCTGCATTTATGGCGTAATATGGGAAGCCCCAAGGAACCAGCTATTTTGAATCCCTATAACTGTATTTTTCTCTTTTTATACTTTTCAG
Seq C2 exon
GCCCTTACCCCAGAGCAAGTGTCATTCTGTGCCACACATATGCAGCAATATATGGACCCACGGGGTCGAAGCCATCTCTCTGGCTATGACTACGTTGGCTTCACCAATTCCTACTTTGGCAACTAATAAGCAGCTCCTCGTGGATCGTAGAAAATCTTAGTGTCGTGGGAAATTTACTGGGGGGCAAAGAGTACAGGCAAATGTGGAAGATAAAGATGGCCTCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCTTGTGTTTGTGTGCATATTACATTTATTGTAGGATCTTAAAAAATCTCAAGGGTGGGAGATAGAAAGGTTAATAGAGTTGGAGGAGTGGAAGCTATTTTGTATGCAACTAGTCACTGCTGAGGGGTGTCAAAGTTTCTATTTTTATTTGTTCTGTTTTGCACGTCTTTATCATTTTGCTTTATTCCGATTATAGAATAAAGTAATTCTTTTTAAAAATATTTTTTGGGGCAAAGTTAAGTAAAATGTTGAGCTTCTATATTTCTGGGAACTGTACTCATATAAGAGTGGGCAGCTAATTTTACTGTAAAGAAGGGCCATGGTATAGTAGATAAATAAAATCCAAGGCAATTTTCAAACAATTTTTTTAAACTTTGGAATGTGTTTAAATTTAAATTTGAAAATAAAGATATTTGATTTTCTGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163554-SPTA1:NM_003126:51
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF134991=EF-hand_7=PD(17.6=26.5),PF087265=EFhand_Ca_insen=PU(40.6=57.1)
A:
NA
C2:
PF087265=EFhand_Ca_insen=PD(56.5=92.9)
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:
AGGGCTATGTCTCACTGGAGG
R:
TTTGCCTGTACTCTTTGCCCC
Band lengths:
344-1771
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)