HsaINT0077320 @ hg38
Intron Retention
Gene
ENSG00000128709 | HOXD9
Description
homeobox D9 [Source:HGNC Symbol;Acc:HGNC:5140]
Coordinates
chr2:176122720-176124937:+
Coord C1 exon
chr2:176122720-176123585
Coord A exon
chr2:176123586-176123933
Coord C2 exon
chr2:176123934-176124937
Length
348 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
CCAAACCTCCCTCTTTGTAGACA
3' ss Score
7.04
Exon sequences
Seq C1 exon
GTCGGTGGCTCGGGCGCCGGCGGGGAGCTGCTCGGCGGCGGACAGTGTAATGTTGGGTGGGAGTGCGGGACGCCTCAAAATGTCTTCCAGTGGCACCCTCAGCAACTACTACGTGGACTCGCTTATAGGCCATGAGGGCGACGAGGTGTTCGCGGCGCGCTTCGGGCCGCCGGGGCCAGGCGCGCAGGGCCGGCCTGCAGGTGTGGCTGATGGCCCGGCCGCCACCGCCGCCGAGTTCGCCTCGTGTAGTTTTGCCCCCAGATCGGCCGTGTTCTCTGCCTCGTGGTCCGCGGTGCCCTCCCAGCCCCCGGCAGCGGCGGCGATGAGCGGCCTCTACCACCCGTACGTTCCCCCGCCGCCCCTGGCCGCCTCTGCCTCCGAGCCCGGCCGCTACGTGCGCTCCTGGATGGAGCCGCTGCCCGGCTTCCCGGGCGGTGCGGGCGGTGGCGGTGGTGGTGGAGGCGGCGGTCCGGGCCGCGGTCCCAGCCCTGGCCCCAGCGGCCCAGCCAACGGGCGCCACTACGGGATTAAGCCTGAAACCCGAGCGGCCCCGGCCCCCGCCACGGCCGCCTCCACCACCTCCTCCTCCTCCACTTCCTTATCCTCCTCCTCCAAACGGACTGAGTGCTCCGTGGCCCGGGAGTCCCAGGGGAGCAGCGGCCCCGAGTTCTCGTGCAACTCGTTCCTGCAGGAGAAGGCGGCAGCGGCGACGGGGGGAACCGGGCCTGGGGCAGGGATCGGGGCCGCGACTGGGACGGGCGGCTCGTCGGAGCCCTCAGCTTGCAGCGACCACCCGATCCCAGGCTGTTCGCTGAAGGAGGAGGAGAAGCAGCATTCGCAGCCGCAGCAGCAGCAACTTGACCCAA
Seq A exon
GTAAGTGCAAAAGAAATTGCCCCCTGATTTATTGCTGAAACCTGTAAGGCTCGAATGTGCAAAACTGATAGTTTTACTAACCTATAAAAACGTCTAGACGCCTACCCAAGCCTAGGCGAACAACATGCATCCATAAAAAGAGCTTCCCATAACCACCTACCCTGGGCGCTCAGTTAGTACGGTAAACAGAGCGCGAGCATTAAGGCTTTTTATGATAATTCCCCACAAGTTGTGAAAAGCGACCATCCTTGGTGAAATTAATTTAACGACCTCTCTTCCCCACCCTGTGGTCTCTCCCTGCCTCCCCTCCTCTCCTCTCTCCCCGTCTCCAAACCTCCCTCTTTGTAG
Seq C2 exon
ACAACCCCGCCGCGAACTGGATCCACGCTCGCTCCACCCGGAAAAAGCGCTGTCCCTACACCAAATACCAGACGCTTGAGCTGGAGAAAGAATTCCTCTTCAACATGTACCTCACCCGGGACCGGCGCTACGAGGTGGCCAGGATTCTCAACCTAACAGAGAGACAGGTCAAAATCTGGTTTCAGAACCGTAGGATGAAAATGAAAAAGATGAGCAAGGAGAAATGCCCCAAAGGAGACTGACCCGGCGCGGTGCTGGCGGGAGCGCTCAAGGGCAGCGGATTTGTTGTTGTTGCTGTTTTCCTTTGTGGGTGTTTGGTGCTTGATTTCCAGAAACTCTCCAGCGACTTGGACTTCTTCTTCTTTTTTTTTTTCTTTTTAGATAGAAGTGACTGTGTGGTTGGTCTCTGAGGTATTTGGGGGACTCTGTATTTGCTCGTTTACGTGTTGGAAAAACCAAGTGGCTTTGGGGTTTCGCCCTATCCCACTCCCTCTCTTTCCTGCTCCATTGGTTCCTTAAGAAATGCTATATTTTGTGAGTGCAAGCTGGCTTGGGGAGCCCTCTCTTGTGTAAATGTCCCCCATGTTTCTGAAAAGTGCTGTAGTTTAGTCCCCTCACCCCCAGCACTGCCCAAACAGGGGCCAAGTGCGCCCCAATTCCAAGAATGAAGGCAGAGCGACAACAGTGCGGACACCCCGGCTGCTAGCCCACGGTGAAGCCCGGCGGGGTTGCCCACCAGTTGCGAAAGCCCCCTTTCCTCAGGGAGCACGCGGGACCTCGGTGGAGATCTCCAGTGAGGCTTAGAGGAGCCCAGGGCCTCGGGCGGGTTGGGGTTTGTCCTCAGTGCATTGGACGCGCTGCTCTCTCCCCTGAAGGCTGGGCTCGCGTGGGCGGCCGCGGGTGGTGGCCCTCCCGGTTCCTGCCCGAGGACCAGTTGTAAATGTTACTGCTTCCTACTAATAAATGCTGACCTGATCAAATGGAGCCCAGACGCTGGCCCTAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000128709:ENST00000249499:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.747 A=NA C2=0.312
Domain overlap (PFAM):
C1:
PF046178=Hox9_act=WD(100=45.4)
A:
NA
C2:
PF0004624=Homeobox=WD(100=70.4)
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:
CACCTCCTCCTCCTCCACTTC
R:
TGTAGGGACAGCGCTTTTTCC
Band lengths:
350-698
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