HsaINT0077317 @ hg38
Intron Retention
Gene
ENSG00000128652 | HOXD3
Description
homeobox D3 [Source:HGNC Symbol;Acc:HGNC:5137]
Coordinates
chr2:176169031-176173102:+
Coord C1 exon
chr2:176169031-176169655
Coord A exon
chr2:176169656-176171516
Coord C2 exon
chr2:176171517-176173102
Length
1861 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGCT
5' ss Score
6.52
3' ss Seq
CTCTCTCCCTCCCTGCCCAGGAG
3' ss Score
10.59
Exon sequences
Seq C1 exon
GTCACCTGGAGCCTGGGGGCCGGCCCAGCTCTCTCAGGATTCAGCAGACATTGGAGGTGGCAGTGAAGGATACAGTGGTAGTCAATGTTATTTGAGCAGGGTCAGCAGGCCCTGGAGCTTCCTGAGTGCACAATGCAGAAGGCTGCTTACTATGAAAACCCAGGACTGTTTGGAGGCTATGGCTACAGCAAAACTACGGACACTTACGGCTACAGCACCCCCCACCAGCCCTACCCACCCCCTGCTGCTGCCAGCTCCCTGGACACTGACTATCCAGGTTCTGCCTGCTCCATCCAGAGCTCTGCCCCTCTGAGAGCCCCAGCCCACAAAGGAGCTGAACTCAATGGCAGCTGCATGCGGCCGGGCACTGGGAACAGCCAGGGTGGGGGTGGTGGCAGCCAGCCTCCTGGTCTGAACTCAGAGCAGCAGCCACCACAACCCCCTCCTCCACCACCGACCCTGCCCCCATCTTCACCCACCAATCCTGGAGGTGGAGTGCCTGCCAAGAAGCCCAAAGGTGGGCCCAATGCTTCTAGCTCCTCAGCCACCATCAGCAAGCAGATCTTCCCCTGGATGAAAGAGTCTCGACAGAACTCCAAGCAGAAGAACAGCTGTGCCACTGCAG
Seq A exon
GTAGCTCCCTGAGGTGGCCTACTGCCAGACCAAGCCCCCTCCAGATTGACCCAAGGAAGCCTAGTCAGGGCTGGAAATGCAACCTTGGAGGTCATATGTCTAAACTCCTACTCACGTCAAAATGTTCTTTTTTTTAGTGTTCCTGATTGGGGTCATGACCTTGCAGTGACAGGGTGCTCCCTTCCATTCCAGGCTGCTGGTGCTGTTGCTGGACAGGTCTTATAGCTATTAATAGAGAGTGCTTCCTTATATGGGCATATCTGTTTTCCTGGGCTGCTAATTATAACTCCATTCCCTCTTCCACCCAACAGCTCTTCAAGATTTGAAGATAGGTATTACAATCCCCAAGCCTAGGTGATTATATAGCCCATATCACACGAATCTCATTCCCTTAAACTCATAAAAACTAAAGTCTTAGAAAGTACCATACTAAGTACTTTCTAAGCATTATCTAATTTAATTTTTCAAAGAACCTTTTGAGGTAGGTATATGATAACATCCCCATTTTACAGATAAGAAAACTGTTAGAGAGGATAGGCAACTTGCCCAAGATTCTGAAACTGCAAAGTGGTGGATTTGAATCCAGTCAGTCTGGCTTTAGGGGCTGCTAAGCATAACCATGAGTCTCTATTTGGCCCACCTCAGCCCAATTCTCCCACTCCAGCAAATCCATAATGGGGAGGTGCCTGTCCTAGTAGGAGAGGATATTCTGGGAGACAGTAACAGCCTTGGATTTCTCTAACTGGAAGGGGAGCCCCTCCAGTTGGGGCCTTCTCTAGGTCCACCCAGGGCATGTAGAAGATAGGCATGGCCAGGAACTCTGAGGGCTGTTCCTTCTCTCTGCTTAGACTGCTTGGTTCCTGAAATTTTCTGACCTTGTGGTATCTGATGTGGTTTATCTTCAGGTAGATGAACTTGCTTCCAGGTCCAGGGCAAGTTTGGGGCCTGGGGTGTGGCTTGCTATCAGGGATCTGGTTTGCCTGATGTTTTCTGGGGCTGCTGCTCCTAGGGAGAGGGTATTATCCTGCCTGCAACCTCCTTTTCCTGCCCCTCCTTCCTCAGCTGCAGGCTCAGGCCCTCCCTCCCAGGAGAAATCCATTTGTCTTCCCTGGGAGGGAGTGGACAAGCAGCTGAGAGGTGGCAGGGTAGTAAAAGCCAGTGTTGAGGCTGCTGCTCCTAGCACTGTGAATACTCAAAATGCTTCCAGCCTGGCCTTGGACTCCCTAAAATACCCAGGCAGTGTTTTTTTTTGTTTGTTTGTTTGGTTGGTTTTTTTTTATTTTTTATTTTTTGGTTTGTCACCTCCCTGGCTTTGAGTGCAGTTGGGCTGCAGTGGGGCGCCAAGATCTCCATCCCCATACTTTGCTGGGGGTTGGTGGGGGGCTTTGCCCAGAGGCCAGCTCCTAAGCAAGGCAGGCTGGAGCTATTTCCTCTTCCTTTCCTTCTCCATACCCCACCCCTGGCAGCAGAGGCTGGGAGGAGTGTTCAAAGGAGTCTGGCCCTTCTTTGACAGAGGGAGGCCTTACCAGCTGCTCCTGGTCTCTCATTAAACTCTTTCATGGCCTTTGGGTGGGTATGGGATGATGGACTAGGCTGCAGGGGAGAGGGTGGGCAGAGTGAACTGGATCTCAGAAGGCTGATGGAGGTTTCAGGTGCGACTGATAGGTAGGCCTAGTAGGGGGTTGGTAGGTAGGTGAATTCCCCCTTGGAATCATACCTCTCAAACGGCCCTTCCCCTCCCCAGCCAGGATTGGAGGTGGGGGGAGGGAGGAGGAAAAGAGAACCAGGGAAGCACCCCTCTCCAGTCCTGAGGGTCCCCACCCACTCGCTCAGCGCCCTCCCTCTCTCCCTCCCTGCCCAG
Seq C2 exon
GAGAGAGCTGCGAGGACAAGAGCCCGCCAGGCCCAGCATCCAAGCGGGTACGCACGGCATACACGAGCGCGCAGCTGGTGGAATTGGAAAAGGAATTCCACTTCAACCGCTACTTGTGCCGGCCGCGCCGCGTGGAGATGGCCAACCTGCTGAATCTCACGGAACGCCAGATCAAGATCTGGTTCCAGAACCGGCGCATGAAGTACAAGAAGGACCAGAAGGCCAAGGGCATCCTGCACTCGCCGGCTAGCCAGTCCCCTGAGCGCAGCCCACCGCTCGGCGGCGCCGCTGGCCACGTGGCCTACTCCGGCCAGCTGCCGCCAGTGCCCGGCCTGGCCTACGACGCGCCCTCGCCGCCTGCTTTCGCCAAATCACAGCCCAATATGTACGGCCTGGCCGCCTACACGGCGCCACTCAGCAGCTGCCTGCCACAACAGAAGCGCTACGCAGCGCCGGAGTTCGAGCCCCATCCCATGGCGAGCAACGGCGGCGGCTTCGCCAGCGCCAACTTGCAGGGCAGCCCGGTGTACGTGGGCGGCAACTTCGTCGAGTCCATGGCGCCCGCGTCCGGGCCTGTCTTCAACCTGGGCCACCTCTCGCACCCGTCGTCGGCCAGCGTGGACTACAGTTGCGCCGCGCAGATTCCAGGCAACCACCACCATGGACCTTGCGACCCTCATCCCACCTACACAGATCTCTCGGCCCACCACTCGTCTCAGGGACGACTGCCGGAGGCTCCCAAACTGACGCATCTGTAGCGGCCGCCGCCAGCCCGAACTCGCGGCAAAATTACCTCTCTTGCTGTAGTGGTGGGGTAGAGGGTGGGGCCCGCGGGGCAGTTCGGGAACCCCCTTCCCCGCTCTTGCCCTGCCGCCGCCTCCCGGGTCTCAGGCCTCCAGCGGCGGAGGCGCAGGCGACCGGGCCTCCCCTCCATGGGCGTCCTTTGGGTGACTCGCCATAAATCAGCCGCAAGGATCCTTCCCTGTAAATTTGACAGTGCCACATACTGCGGACCAAGGGACTCCAATCTGGTAATGGTGTCCCAAAGGTAAGTCTGAGACCCATCAGCGGCGCGCCCTGCAGAGGGACCAGAGCTTGGAGAGTCTTGGGCCTGGCCCGCGTCTAGCTTAGTTTCAGAGACCTTAATTTATATTCTCCTTCCTGTGCCGTAAGGATTGCATCGGACTAAACTATCTGTATTTATTATTTGAAGCGAGTCATTTCGTTCCCTGATTATTTATCCTTGTCTGAATGTATTTATGTGTATATTTGTAGATTTATCCAGCCGAGCTTAGGAATTCGCTTCCAGGCCGTGGGGGCCACATTTCACCTCCTTAGTCCCCCTGGTCTGAACTAGTTGAGAGAGTAGTTTTGAACAGTCGTAACCGTGGCTGGTGTTTGTAGTTGACATAAAGGATTAAGACCGCAAATTGTCCTTCATGGGTAGAGTCAGGAAGCCCGGTGGCGTGGCACAACACACTTTGGTCATTTCTCAAAAACCACAGTCCTCACCACAGTTTATTGATTTCAAATTGTCTGGTACTATTGGAACAAATATTTAGAATAAAAAAATTTCCCAGTCGGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000128652:ENST00000249440:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.862 A=NA C2=0.484
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=22.5),PF132931=DUF4074=WD(100=24.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCCTCCTGGTCTGAACTCAG
R:
GGCACAAGTAGCGGTTGAAGT
Band lengths:
345-2206
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