HsaINT0077317 @ hg19
Intron Retention
Gene
ENSG00000128652 | HOXD3
Description
homeobox D3 [Source:HGNC Symbol;Acc:5137]
Coordinates
chr2:177033759-177037826:+
Coord C1 exon
chr2:177033759-177034383
Coord A exon
chr2:177034384-177036244
Coord C2 exon
chr2:177036245-177037826
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
GAGAGAGCTGCGAGGACAAGAGCCCGCCAGGCCCAGCATCCAAGCGGGTACGCACGGCATACACGAGCGCGCAGCTGGTGGAATTGGAAAAGGAATTCCACTTCAACCGCTACTTGTGCCGGCCGCGCCGCGTGGAGATGGCCAACCTGCTGAATCTCACGGAACGCCAGATCAAGATCTGGTTCCAGAACCGGCGCATGAAGTACAAGAAGGACCAGAAGGCCAAGGGCATCCTGCACTCGCCGGCTAGCCAGTCCCCTGAGCGCAGCCCACCGCTCGGCGGCGCCGCTGGCCACGTGGCCTACTCCGGCCAGCTGCCGCCAGTGCCCGGCCTGGCCTACGACGCGCCCTCGCCGCCTGCTTTCGCCAAATCACAGCCCAATATGTACGGCCTGGCCGCCTACACGGCGCCACTCAGCAGCTGCCTGCCACAACAGAAGCGCTACGCAGCGCCGGAGTTCGAGCCCCATCCCATGGCGAGCAACGGCGGCGGCTTCGCCAGCGCCAACTTGCAGGGCAGCCCGGTGTACGTGGGCGGCAACTTCGTCGAGTCCATGGCGCCCGCGTCCGGGCCTGTCTTCAACCTGGGCCACCTCTCGCACCCGTCGTCGGCCAGCGTGGACTACAGTTGCGCCGCGCAGATTCCAGGCAACCACCACCATGGACCTTGCGACCCTCATCCCACCTACACAGATCTCTCGGCCCACCACTCGTCTCAGGGACGACTGCCGGAGGCTCCCAAACTGACGCATCTGTAGCGGCCGCCGCCAGCCCGAACTCGCGGCAAAATTACCTCTCTTGCTGTAGTGGTGGGGTAGAGGGTGGGGCCCGCGGGGCAGTTCGGGAACCCCCTTCCCCGCTCTTGCCCTGCCGCCGCCTCCCGGGTCTCAGGCCTCCAGCGGCGGAGGCGCAGGCGACCGGGCCTCCCCTCCATGGGCGTCCTTTGGGTGACTCGCCATAAATCAGCCGCAAGGATCCTTCCCTGTAAATTTGACAGTGCCACATACTGCGGACCAAGGGACTCCAATCTGGTAATGGTGTCCCAAAGGTAAGTCTGAGACCCATCAGCGGCGCGCCCTGCAGAGGGACCAGAGCTTGGAGAGTCTTGGGCCTGGCCCGCGTCTAGCTTAGTTTCAGAGACCTTAATTTATATTCTCCTTCCTGTGCCGTAAGGATTGCATCGGACTAAACTATCTGTATTTATTATTTGAAGCGAGTCATTTCGTTCCCTGATTATTTATCCTTGTCTGAATGTATTTATGTGTATATTTGTAGATTTATCCAGCCGAGCTTAGGAATTCGCTTCCAGGCCGTGGGGGCCACATTTCACCTCCTTAGTCCCCCTGGTCTGAACTAGTTGAGAGAGTAGTTTTGAACAGTCGTAACCGTGGCTGGTGTTTGTAGTTGACATAAAGGATTAAGACCGCAAATTGTCCTTCATGGGTAGAGTCAGGAAGCCCGGTGGCGTGGCACAACACACTTTGGTCATTTCTCAAAAACCACAGTCCTCACCACAGTTTATTGATTTCAAATTGTCTGGTACTATTGGAACAAATATTTAGAATAAAAAAATTTCCCAGTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000128652-HOXD3:NM_006898:2
Average complexity
IR-S
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
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)