HsaINT0158350 @ hg19
Intron Retention
Gene
ENSG00000163554 | SPTA1
Description
spectrin, alpha, erythrocytic 1 (elliptocytosis 2) [Source:HGNC Symbol;Acc:11272]
Coordinates
chr1:158584043-158585193:-
Coord C1 exon
chr1:158585006-158585193
Coord A exon
chr1:158584097-158585005
Coord C2 exon
chr1:158584043-158584096
Length
909 bp
Sequences
Splice sites
5' ss Seq
CAAGTATTG
5' ss Score
-0.57
3' ss Seq
GTTTTTTTTTTTTCTTTCAGGGA
3' ss Score
12.46
Exon sequences
Seq C1 exon
AGAAAACAGAAGGAGATCCAGGCGATGAAGCGTCAACTAACCAAGATTGTGGACCTGGGGGACAACTTGGAAGACGCTCTGATCCTTGATATCAAATACAGCACCATTGGATTGGCTCAGCAGTGGGACCAGCTCTACCAGCTTGGGTTGCGGATGCAACACAACCTGGAGCAACAGATCCAGGCCAA
Seq A exon
GTATTGAGGGCGTGTGGCCAGAGCAGGGAGGGATGCAGGTGGTGTTAGGTGTTAGGACCTTAACTAAGGGCGAGAGTTTGGTGCACCAGATAAAAGAGTTGCTTCAGAGAACCAATATTCTGGGTCTTTACTGCCCCACGGAATGACTATTTCTCTTTATACTGAAATCCATCATGAAATAAAAGACAGTGCTCTCCATCCACCTGAGCCTACTCATCACCCACTTGGACAACAACTGACTTTTATACCCAATTTCTCAGAGTTCTTTCACCATCTTATGTGATCTCTTAGGAAACCATTCCCTTTCATAGAATTTTATCTAAAATGTAATGTCTAGATTAAAAGAAACATTTAAAGTGTGGCCAAATAGAGCAGAAGGGCAGAAACTCATTTTCTAGATAAATTCACTATATCAAAGCAGCTCTAGGTCTCAATAGCATTTTGGCAACATTTTTATCTAGATTAGGATTGGCAAACTTTTTCTGTAAATGGTCTGATAATAAATAATTTAACTTTGTAAGGCACATATATTTTCTGCTGTAACTCCTTGATTCTGCTGTTGTAGTGAAAAAAGCAGCTATGATAAGTGAATGACCGTGGCCATGTTCCAATAAAGCTTTATATATGGACATTGAAATTTAAATTTTATGTAATTTTCATGTTTCAAAAAATTTTCTTTTGATTGTCTTCAACCATATGAAAATGTAAAATCTACTCTTGGCTCATGGACTGTACAAAAGCAGGTGGCAGCCTAGATTTGGCCCATGGACTATAGTTTGCCAACTCTTGAACTAGATGACTCAAATAGCAAATTGTCCATTAAAATTCCTCTCTCTTCCATGTGGCTTGTGTTCTGCTAACCTGTGTTTCATATACAGGGAAAATTCATGTTTTTTTTTTTTCTTTCAG
Seq C2 exon
GGACATCAAAGGTGTGAGTGAAGAGACTCTAAAGGAATTTAGCACAATCTATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000163554-SPTA1:NM_003126:48
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(55.9=90.5)
A:
NA
C2:
PF134991=EF-hand_7=PU(14.9=57.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAAAACAGAAGGAGATCCAGGC
R:
AGATTGTGCTAAATTCCTTTAGAGTC
Band lengths:
238-1147
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)