HsaALTA0005741-1/3 @ hg19
Alternative 3'ss
Gene
ENSG00000183072 | NKX2-5
Description
NK2 homeobox 5 [Source:HGNC Symbol;Acc:2488]
Coordinates
chr5:172660112-172662360:-
Coord C1 exon
chr5:172661753-172662360
Coord A exon
NA
Coord C2 exon
chr5:172660112-172660212
Length
0 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
GCCTCTCTGTTCCCCCTCAGAGC
3' ss Score
11.07
Exon sequences
Seq C1 exon
GCCTCTCCTGCCCCTTGTGCTCAGCGCTACCTGCTGCCCGGACACATCCAGAGCTGGCCGACGGGTGCGCGGGCGGGCGGCGGCACCATGCAGGGAAGCTGCCAGGGGCCGTGGGCAGCGCCGCTTTCTGCCGCCCACCTGGCGCTGTGAGACTGGCGCTGCCACCATGTTCCCCAGCCCTGCTCTCACGCCCACGCCCTTCTCAGTCAAAGACATCCTAAACCTGGAACAGCAGCAGCGCAGCCTGGCTGCCGCCGGAGAGCTCTCTGCCCGCCTGGAGGCGACCCTGGCGCCCTCCTCCTGCATGCTGGCCGCCTTCAAGCCAGAGGCCTACGCTGGGCCCGAGGCGGCTGCGCCGGGCCTCCCAGAGCTGCGCGCAGAGCTGGGCCGCGCGCCTTCACCGGCCAAGTGTGCGTCTGCCTTTCCCGCCGCCCCCGCCTTCTATCCACGTGCCTACAGCGACCCCGACCCAGCCAAGGACCCTAGAGCCGAAAAGAAAG
Seq A exon
NA
Seq C2 exon
AGCTGTGCGCGCTGCAGAAGGCGGTGGAGCTGGAGAAGACAGAGGCGGACAACGCGGAGCGGCCCCGGGCGCGACGGCGGAGGAAGCCGCGCGTGCTCTTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000183072-0-3,0-2,0-1-1/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.368 A=NA C2=0.209
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=26.6)


Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGGAGAGCTCTCTGCCC
R:
GTTGTCCGCCTCTGTCTTCTC
Band lengths:
299-554
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
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)