HsaINT0113819 @ hg19
Intron Retention
Gene
ENSG00000183072 | NKX2-5
Description
NK2 homeobox 5 [Source:HGNC Symbol;Acc:2488]
Coordinates
chr5:172659107-172662315:-
Coord C1 exon
chr5:172661753-172662315
Coord A exon
chr5:172660505-172661752
Coord C2 exon
chr5:172659107-172660504
Length
1248 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
GCTCCTGTCATCGAGGCCCCTGGCCCAATGGCAGGCTGAGTCCCCCTCCTCTGGCCTGGTCCCGCCTCTCCTGCCCCTTGTGCTCAGCGCTACCTGCTGCCCGGACACATCCAGAGCTGGCCGACGGGTGCGCGGGCGGGCGGCGGCACCATGCAGGGAAGCTGCCAGGGGCCGTGGGCAGCGCCGCTTTCTGCCGCCCACCTGGCGCTGTGAGACTGGCGCTGCCACCATGTTCCCCAGCCCTGCTCTCACGCCCACGCCCTTCTCAGTCAAAGACATCCTAAACCTGGAACAGCAGCAGCGCAGCCTGGCTGCCGCCGGAGAGCTCTCTGCCCGCCTGGAGGCGACCCTGGCGCCCTCCTCCTGCATGCTGGCCGCCTTCAAGCCAGAGGCCTACGCTGGGCCCGAGGCGGCTGCGCCGGGCCTCCCAGAGCTGCGCGCAGAGCTGGGCCGCGCGCCTTCACCGGCCAAGTGTGCGTCTGCCTTTCCCGCCGCCCCCGCCTTCTATCCACGTGCCTACAGCGACCCCGACCCAGCCAAGGACCCTAGAGCCGAAAAGAAAG
Seq A exon
GTGAGGAGGAAACACAGGCCCCCTTCTCCCCTCCTGGGTCGCTTTCGTCCCCAAGAAACTCAGGGCCAGGAGGAGGAGACACGCGCCCTTGGGCCGAGGGCTGGGCTGCGGCGGGGGGTTCAGAATGTAAGATGCCTGGTGTTGTCGCCAGGCTCCCGCGCCCCGCGTCCAATCGGAGGTTCAGAGGAAATGCCGGATTGAAAGGATCAGAAGCAAGAGACCAAAAAACGTTTCCCCCCGGCCTAACAAAGCCCCGGGCGGCTTCGGCTCTGCTCCTGGGTCTGGTAGGAAGTTGAGAAATCGGTTTATGGTAGACAGAACAGAGAGACAAGCAGATAATCTCTGTTTTTAAATCTCCTTTGGATTTACGAATCTTTTTAAAGATCTGATGAGAACCGCTAAACAGAAATTGAAATGTTGCTCACCAGACAGCTTTTGCGTACAATCGGAGGAGGGTCCTGGACCTTCTTTCTGCAGCCCACCCACGACCCGGGTTTCTGGTGCCTTTCTTTCTTTGCGCCAGGAAAGTGGAGTCTGGGATCGAGGGCCTTGATTTTAAAATGGGATACTGCGGACCCTCAGGAATCTGACTTCACTTTATTTTTTCAGCACAACTTGCCGGCGCGGCCAGGGCGGAGAGGTTCCCTCGTGGAAAAGTTAGGAAATGCTGCGCTACCGCGGGCACAAGGGAGTGGACGAGATGAGTGCGGGATCATCCCGCAGGCCATCCCAGGATCGGGGAGGGAGGCCGGCCCCGCTGCAGAAAGGGGCCTTCTGGGAGACCCCCCAGCCCAAGGCAGGAGCCCGGGCGATTCCCGGGAGGCCGCAGGCGCTGGGCGAAGCGCTGGGCGAAGGGCCGCTGCCAGCCGGGAGAGAATTCATAGGTTTGTTGAGGAGCAGAGGCCTGGGAACAAATTCGGGCGGGCACGGCGGCTAGAACTGATCGCTACCAATTCGAGGAAGCCAGCAAGGCAGGTTCCGAGGCCGCCTGCCCACCCGCAGCTTCTTGGACACTGCGCAAACCCTGCTGCGGCCAGGCTGGAGCCTCCGATCACCAAACCAACACTCCCTGGCCTTCTGTTTCTTGATTCCTTAATTTTGAGATAAGACCGTCCCTAGCAGTGAGGCCTCGGCCTCTGTTCATTTAACTTCTCAAACCAAACTAGCCCTAATTCAGTTCACCCCAGAGCATCACCTGGTTTTATTTTTATTTTTTTATTTTTTTATTTATTTTTTTTTTTTTTGCAG
Seq C2 exon
CCTGAAATTTTAAGTCACCGTCTGTCTCCCTCACCAGGGTGTGAACTGCCCCGAGGGCAGAGACCTCCCGTTTTGTTCTCCAGCGCCTTGAGCCAGCCTGACTTTCTACAAATGCTGAGTGAGACGTGTCGGTGGCTCCCAGTGCACTTGGCAGAGTGAGCCGCAGCCAGCTGGGCGCTCCAGGCAGGACACAGTGGCCTCCACGAGGATCCCTTACCATTACTGTGCGGCCGCGCTCCGTAGGTCAAGCCGCTCTTACCAAGCGTCTCTCTGCCTCTCTGTTCCCCCTCAGAGCTGTGCGCGCTGCAGAAGGCGGTGGAGCTGGAGAAGACAGAGGCGGACAACGCGGAGCGGCCCCGGGCGCGACGGCGGAGGAAGCCGCGCGTGCTCTTCTCGCAGGCGCAGGTCTATGAGCTGGAGCGGCGCTTCAAGCAGCAGCGGTACCTGTCGGCCCCCGAACGCGACCAGCTGGCCAGCGTGCTGAAACTCACGTCCACGCAGGTCAAGATCTGGTTCCAGAACCGGCGCTACAAGTGCAAGCGGCAGCGGCAGGACCAGACTCTGGAGCTGGTGGGGCTGCCCCCGCCGCCGCCGCCGCCTGCCCGCAGGATCGCGGTGCCAGTGCTGGTGCGCGATGGCAAGCCATGCCTAGGGGACTCGGCGCCCTACGCGCCTGCCTACGGCGTGGGCCTCAATCCCTACGGTTATAACGCCTACCCCGCCTATCCGGGTTACGGCGGCGCGGCCTGCAGCCCTGGCTACAGCTGCACTGCCGCTTACCCCGCCGGGCCTTCCCCAGCGCAGCCGGCCACTGCCGCCGCCAACAACAACTTCGTGAACTTCGGCGTCGGGGACTTGAATGCGGTTCAGAGCCCCGGGATTCCGCAGAGCAACTCGGGAGTGTCCACGCTGCATGGTATCCGAGCCTGGTAGGGAAGGGACCCGCGTGGCGCGACCCTGACCGATCCCACCTCAACAGCTCCCTGACTCTCGGGGGGAGAAGGGGCTCCCAACATGACCCTGAGTCCCCTGGATTTTGCATTCACTCCTGCGGAGACCTAGGAACTTTTTCTGTCCCACGCGCGTTTGTTCTTGCGCACGGGAGAGTTTGTGGCGGCGATTATGCAGCGTGCAATGAGTGATCCTGCAGCCTGGTGTCTTAGCTGTCCCCCCAGGAGTGCCCTCCGAGAGTCCATGGGCACCCCCGGTTGGAACTGGGACTGAGCTCGGGCACGCAGGGCCTGAGATCTGGCCGCCCATTCCGCGAGCCAGGGCCGGGCGCCCGGGCCTTTGCTATCTCGCCGTCGCCCGCCCACGCACCCACCCGTATTTATGTTTTTACCTATTGCTGTAAGAAATGACGATCCCCTTCCCATTAAAGAGAGTGCGTTGACCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000183072-NKX2-5:NM_001166175:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.368 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GCCTTCTATCCACGTGCCTAC
R:
GGGAACAGAGAGGCAGAGAGA
Band lengths:
350-1598
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)