HsaINT0113817 @ hg19
Intron Retention
Gene
ENSG00000119919 | NKX2-3
Description
NK2 homeobox 3 [Source:HGNC Symbol;Acc:7836]
Coordinates
chr10:101292690-101296280:+
Coord C1 exon
chr10:101292690-101293246
Coord A exon
chr10:101293247-101294741
Coord C2 exon
chr10:101294742-101296280
Length
1495 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
GTTGTTTGCTTCTTCCGCAGAAA
3' ss Score
9.22
Exon sequences
Seq C1 exon
AGTCCCTGCAGTGGCTGTAACAAAACCCAGACCCCCAGGTCCCGGCCAATGGAGGCGATTTAGACTGGAGTGGGACCGCGTCTGTCAAAAGCCCGACTCGGCAGCAGCGGCGGAGTCCAGGAGGAGAGCTGGAGCCGCCGCGCTGCCTCCCCGCCCCCGCCGGGATTTATTATTTGGACTGGACAATTAAGTGGCCCTGATGATGTTACCAAGCCCGGTCACCTCCACCCCTTTCTCAGTCAAAGACATTTTGAATCTGGAGCAGCAGCACCAGCACTTCCATGGTGCGCACTTGCAGGCGGACTTGGAGCACCACTTCCACTCTGCGCCCTGCATGCTGGCCGCCGCTGAGGGGACGCAATTTTCTGACGGAGGGGAGGAGGACGAGGAAGACGAGGGCGAGAAATTGTCCTATTTGAACTCACTAGCCGCAGCAGACGGCCACGGGGATTCAGGGCTGTGTCCCCAGGGCTATGTCCACACGGTCCTGCGAGACTCGTGCAGCGAGCCCAAGGAACATGAAGAGGAGCCCGAGGTCGTGAGGGACCGGAGCCAAA
Seq A exon
GTGAGTAGAGGGGGAAAGAAAACGCACCCGCACACCTGGAGCAATGGCAGAGCGCACACAAACAGCCCACAGACCTTGCCAGCGCAGCTGCCCATCCCTTTACCCTTTGGCTGGGGCCATGCCTCCGCCCTGGTCACCGACAGCTCCACAAAGCGCAGGTACCTGCAAGGGAGCCGGGGTGGAGAGACAAGGACGAGGTGACCCTGACAACTACTCCCCCCAAAAGGGGGAAATGAGGGAAGGGAAGGTGGTTACTGCTGCCCTGATGCTGAGAGGCGACGTGGGCTCAGCGCCTGGGTCCTCATAACTGGCAGTATTTTTGCTCTTCCCCCCGCCCCAAAAGGCTCTTCCCCCAAAAAGGGCAGGAGCCTGGACCTTTTTCGTTTTCCCTCTAGGGTGAGATGAGTTCTCTTAGCCCAGGGCAGCCACCCCTTCTTCTCCGAAAAGACAGCCCAAGCAGCCTGTGTCTCTCGCACCCGCAGGGGCAGGAACTTTGGTGGAGGCCAGCTGGGCGGTTTCCTCCCTTCTCTGCTTGGAGCTCAGCGTCCTTGAACCCGTGGCACTCGGTAGAGAGAGAGGAGATGATCGGAAAGTGCGTGGGAACAATGTCTATTCCGCGCGACCATAGCTCTCACATCCCTAAGGCGCCAGCCTTTTTTGAAAATCCGTAACGTTTTGCTTTGTGTCCCAGGCTGCGGGCCTAATAGAAAACGCGCCGAACTTGAGTCCGAGATCTTGGCTGCTCACATCGGATGGGAAGTGAATTGATAGGGAGATGGGATAATCAAATAAAGTCCCCAAGGAAGTGTATTTAAGAGGACAGAATCACAGTCTTTCCCCAAGAGGCGGTTTGATGTGGCAGAGGCCAAGGCCTATGCTCTCATAGTTCCCAGAGCCGAAAATCGGCATGAAACTGTCTATAACTAGTCAATCAAACTTCATTTTCAAAGTGCACACAGATGTCGTCATAACATTCGCTTGTAGTCTTTTATAAGCCACACACACACACAAGTCCCTGAGCCATGCACAAGCGTTACACTCAGAACAGATTTTCGCGCAACCCATGCCCACCGGCCCACTCATACCAACACGCCTCACACCTTCAGTTATCCTTGGTGGAGTAGAATGCAAACGAGTTTGCAAATACTGTAGTTATTATGTAGTTGCAAGCCTTCATCCTGAAAATAGTCATTAGCACGTCGAGCCGCATATTTAATACAGAGTAATCTCTTCTCTCGCAGATGCTCAAGATCCAAATAAACACGCACTAACTACCCCTCTCCACGAAACGCGCCTCCGCCTGCTAAGGGCGTTCTTTGGGTACTGGGGCTGTCTCAGGGTCCCACAGCGCCAGGAGCCACAAACGTTCCCAAAAGTCCAGCCATTTACTACCGCACGCTCTGCGCAGCCACCAAAAAGGGTCACGGTGCTCCAGGACAGGAGCCGCGGTGCGGCCGGGAACAGCTAAGGACGCTGTTGTTTGCTTCTTCCGCAG
Seq C2 exon
AAAGCTGCCAGCTGAAGAAGTCTCTAGAGACGGCCGGAGACTGCAAGGCGGCGGAGGAGAGCGAGAGGCCGAAGCCACGCAGCCGCCGGAAGCCCCGGGTCCTCTTCTCGCAAGCCCAGGTCTTCGAGCTGGAACGCAGGTTCAAGCAGCAGCGGTACCTGTCGGCACCCGAGCGCGAGCACCTCGCCAGCAGCCTGAAGCTCACATCCACTCAGGTGAAAATCTGGTTCCAGAATCGCAGGTACAAGTGCAAGAGACAGCGGCAGGACAAGTCTCTGGAGCTTGGCGCACACGCGCCCCCGCCGCCGCCGCGCCGCGTGGCTGTCCCGGTGCTGGTGCGGGACGGCAAGCCGTGCGTCACGCCCAGCGCGCAGGCCTACGGCGCGCCCTACAGCGTGGGCGCCAGCGCCTACTCCTACAACAGCTTCCCCGCCTACGGCTATGGGAACTCGGCCGCGGCCGCCGCCGCCGCCGCCGCCGCCGCCGCAGCAGCGGCGGCCTACAGCAGCAGCTATGGCTGTGCGTACCCGGCGGGCGGCGGCGGCGGCGGCGGCGGGACCTCCGCGGCGACCACTGCCATGCAGCCCGCCTGCAGCGCGGCCGGAGGCGGCCCCTTTGTGAACGTGAGCAACCTAGGAGGCTTCGGCAGCGGCGGCAGCGCACAGCCGTTGCACCAGGGTACTGCAGCCGGGGCCGCGTGCGCTCAGGGCACCTTGCAGGGCATCCGGGCCTGGTAGGGACGGGGCGGGTCACGCGGCGGGCACCCCAGCGCAGCCTGGCGCCGCGGGACTGAAGCTCGAGAAGGGCCTGACCTAAAGGTCAGGTCCCCTCGTTAAAAAAATATGTACGTCTAGCTCCTCAGGGCTTCGGATCGCAGCTCACTCGAGGCCTGGGGAAGGGGACTCAGGGGCGAGGAGGATGACTGGGTCCGGTCGCCAGGACTGTCTCTGAGGCAGAAACGCCGGCTGGGCGCCGGGGAGGACGATGGCCCCGACCCTGGCAGCGAGAGGAGACCAGGAGGCTAGGACCCTGGCCGCGCTTGGTTCTTCCAAAGCGAGAAGGGCTTCTCTCCCTCTGCCTTTCCGCGGCCTCCGCGAAGCGTTGGCGGGGAGCCCAAGGACATAACAAATTAAAAGCATGAAGGAGAGAAAAATGGGGGTCGTGGCTTGAGAAATTCCAGGCCCTACCGATCCTCTGCCCCCTTTGCGGGCCTGGAGCGCCATAGCACAGTCGATTTCGTTTCGCAGCTGTCTCCCCTCCGCAGCAGATACCTCGGTCCAGATCTCCGGATTGTCGGGGGACGCAGGACTCTTCGAGGAAAACCAGCCGAATGAGATCAAAAGTTGGGGGTGGGGGGAGGCTGAACAAACTCAGGACCTGGTGGCCCACCGGAGGTGTTACCGGGTTTCCTTTCTGTTTCGTATTCTGTATTCAGCACATGTTATCTATCTATCTATCTATATAACTATAACCACACGCCGTGTAGACACCCGCTGCCACACACTACAGGAGTCAATAAACAAGGTGCAATATTTTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000119919-NKX2-3:NM_145285:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.700 A=NA C2=0.216
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=23.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTGAACTCACTAGCCGCAGC
R:
GAGTGGATGTGAGCTTCAGGC
Band lengths:
356-1851
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)