Special

HsaALTA0005741-3/3 @ hg38

Alternative 3'ss

Gene
ENSG00000183072 | NKX2-5
Description
NK2 homeobox 5 [Source:HGNC Symbol;Acc:HGNC:2488]
Coordinates
chr5:173233109-173235357:-
Coord C1 exon
chr5:173234750-173235357
Coord A exon
chr5:173233210-173233501
Coord C2 exon
chr5:173233109-173233209
Length
292 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TATTTTTTTTTTTTTTGCAGCCT
3' ss Score
10
Exon sequences
Seq C1 exon
GCCTCTCCTGCCCCTTGTGCTCAGCGCTACCTGCTGCCCGGACACATCCAGAGCTGGCCGACGGGTGCGCGGGCGGGCGGCGGCACCATGCAGGGAAGCTGCCAGGGGCCGTGGGCAGCGCCGCTTTCTGCCGCCCACCTGGCGCTGTGAGACTGGCGCTGCCACCATGTTCCCCAGCCCTGCTCTCACGCCCACGCCCTTCTCAGTCAAAGACATCCTAAACCTGGAACAGCAGCAGCGCAGCCTGGCTGCCGCCGGAGAGCTCTCTGCCCGCCTGGAGGCGACCCTGGCGCCCTCCTCCTGCATGCTGGCCGCCTTCAAGCCAGAGGCCTACGCTGGGCCCGAGGCGGCTGCGCCGGGCCTCCCAGAGCTGCGCGCAGAGCTGGGCCGCGCGCCTTCACCGGCCAAGTGTGCGTCTGCCTTTCCCGCCGCCCCCGCCTTCTATCCACGTGCCTACAGCGACCCCGACCCAGCCAAGGACCCTAGAGCCGAAAAGAAAG
Seq A exon
CCTGAAATTTTAAGTCACCGTCTGTCTCCCTCACCAGGGTGTGAACTGCCCCGAGGGCAGAGACCTCCCGTTTTGTTCTCCAGCGCCTTGAGCCAGCCTGACTTTCTACAAATGCTGAGTGAGACGTGTCGGTGGCTCCCAGTGCACTTGGCAGAGTGAGCCGCAGCCAGCTGGGCGCTCCAGGCAGGACACAGTGGCCTCCACGAGGATCCCTTACCATTACTGTGCGGCCGCGCTCCGTAGGTCAAGCCGCTCTTACCAAGCGTCTCTCTGCCTCTCTGTTCCCCCTCAG
Seq C2 exon
AGCTGTGCGCGCTGCAGAAGGCGGTGGAGCTGGAGAAGACAGAGGCGGACAACGCGGAGCGGCCCCGGGCGCGACGGCGGAGGAAGCCGCGCGTGCTCTTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000183072-0-4,0-3,0-2-3/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact

Protein isoform when splice site is used (No Ref, Alt. Stop)

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)


Main Inclusion Isoform:


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
Chicken
(galGal3)
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:
299-591
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