HsaINT0077316 @ hg19
Intron Retention
Gene
ENSG00000128652 | HOXD3
Description
homeobox D3 [Source:HGNC Symbol;Acc:5137]
Coordinates
chr2:177028805-177034383:+
Coord C1 exon
chr2:177028805-177028896
Coord A exon
chr2:177028897-177033758
Coord C2 exon
chr2:177033759-177034383
Length
4862 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TCTTGCTTTTCTTCTGACAGGTC
3' ss Score
11.91
Exon sequences
Seq C1 exon
GCCTCCACAGATATCAAAAGAAACCTGAAGAGCCTACAAAAAAAAAAGAGATAAAGACAAAATTCAAGAAAACACACACATACATAATTGTG
Seq A exon
GTGAGTGGGCATCATTTAAATAATAATTTCCAGTACATTTCCCTCTGCAACTCAAGGTGGCCATCTCAAAATTCATACATCAAGACATAGAACAAAGGGCAGCTTTGAAGTGGGTCACTTCAGTATGAAGTACCACCCGTTACATGAAAACCGATCATTGGCCTTCAAATTTATGGCGCTTTAATGGGGCAAGCCCAGTGCCTTAAATACAGGGTGCATTACAGTATTGAGTTATCTGGGCTAAATAAGAGTGATTTAGAAGGCGCGTCCAGGTCTTCTTATAGAGCAAAAGAGGCTCAAGCTTAGAGATCGGGAGAACTTGGGCGGAACGTAAAGAAGTCTCCTTTCGAGCAAACCCAAAAACCAGTGGTTTCGAATCCCGAAGTAGCAAAGCCAACAGGAAAGGGAGAATCGTTGCTCGGTTCCAGTGAATTCGTGGGGATGCTCAGCAAAAGTCTTGGCCGCCAGAAAGAGATCCGTGGGCTTCTGACCCTGGTTTAGGCAAAACAGGGGGAGGCGCCGAGACCAGCTCGAGCACTAGCGGATTTTGAGAGAAACTGACCGCAACCTCCATCGCCTTCCCCCTCTCTTTCAACTTGGATGGGCTGACTCTACCCGTCGGTGATTTACGACGATTGCAGCGCTAGTCACAGCCTGGCGCCTGGTGTCCCCTCCCTTCCCAAGCCCCCTCAGCTTTTCCACTGCCACCGGCGTACAAGCAAGTGCCGAGCCGGCCTCCGCAAGTCGGACTAGCCTCCCGGCGTCCGAGGCCACCACGGGCAGCAGATTTTTGGTCCCCAGCGAGGCTGCGCGCGTTCGTCCCGCCTCCGACCGCCGAGCAGAGCTGCTAGCAGAAGCAGGCGCCGGTCACTTTATATAATCCTGCTGCTCGCAGGGTGCAAGAGCGGGAAAAGTGCGGAGTAGGGAATTCTTTTGCTGCGCTGCCTCCTACGCGGAGCCTGCTTTCCACTGCTGAAAAGTGCCGGGCCTTGGGAAGTGTTTTTCTTTTCATTCCTTACCGAAGCGTTTACTGCCGCCGTGGTCGCAGTCATAAATTTTGCTACAAACCACAATGACAGGTGCATTGATATGCACCGTGAGAGCTCCAGCTGCTTAATAACCCCGTCCCCTGGTCGCTGTGAGCGCCTTTTATTTATTTGGTATCATATTAGGTATTGATCTCTAGTAGCATTAAGTGCGGTGAGCAAGTATCAGGGTTCGGCTGCTTTGGAGGCGCAGCGGTTGCGGCGGGCCGGCGGGCCCGGGGAAGCGGGCGGTGGCCGCTCAGAGAATACCTTCCTTCCGGCAGGAGACCGTTTGGCCCTGTATTCCGGGCCTGCGGTTGGGCCTCCAAGCTGAGTTGGGCAACTTCCCAGCACCGCAAGAAAGGGCGAGCCAGACCTATTTGGCACCCCTTTCCCAGGAGGAGCAGGGGATGGCGCCGGCGGAGTTTGGGGAGGCTGCCCTGGCCAGTTCCCCGGGCTAGAGGGTGGAGGAGAGGAGGAGGGAGAGGAAAGGGCAGCTGAGGACTTGGAAGAAATGAGAAGCCGTGCTCGACCACCCCTCCCCCAACACTGGCTCATCTTCACCCCAAGACATTTGGGTCTTGGAGCCCAAATGAGCAAAGGTACCAAAGGGCGAGAAAAGAAAGGCTTTAAAAAAAGGGTGAGGGGGTGATCGAAAAGATGAGCCACTGAACAGTTGACCATTGTCCAAGTGATTTATGACCCGTTCCTGCTTTTTAGGTTCAAGCAGAGTTCACAAGGAGTAGGGATTTCTGAAAAGAAATAAGCCTTTTTACCAGTTTTGTAACTATATTCTCAGGTTTTGTTTTAAGAGGGATCACTTTTGGGAAACTGCATTTTTGGGGGACTGCAAAGCCATTTCCAGTAAGGACAGCACCATCACTGGCTCTTGCTTTTGGGGAAATGGACATTAAGGTAGTGGATTGTCATTGAGTGGGAAATTTCTTGAGACAATGTAAACAGTTAGGAAAACAGACTCTGGTTTTTCAGGAAGATGCCCAATGTTTGTACTTTTGAGGTCTGTACACAGAACTTTTTCTAGGAATATGCCATAGAAGCAAATATATATATAAAGCCATCTGTCCCAGAAGAACTGGTCAGTTCCTAAGTAAGCTATTTTAACGTGACTGGTTCACCTATCTAGATCAACTTTGTCAACTTGGGAGGCAGGAGGGTGAATGTTTTGCTTCCACAGTTGTAAATGGAATGACAGAGCAGCAGCAAGTTCTGGTAGTCTGAGTGTCCGATGTGACCATTAGGCCTCCAGAGGGTTAAGACTGAAAGCAGGATACCAGAAAAGCCTGAAACATAACCAAATCCAGAGTGCCTCTTTCTTCAGCAGGGGGCAAACATATGTAAGTATTAGTCACAGAATGAAGACTTAGCTGTCCATTTGATATCCAGTAACTTTTAACAGAGAATGATATATAAAATTAATCAAAAGAAAAATTAAGTCCAGCTTTGTTAAGTAGATATCCTACCTACATACATTTAAGAACAATAATGGAAACAATTTCTACAACATAGTATCTTGGTATTAAGGGCCTGTTCCTCATCAAGACAAATGGCATACTCACTTATATTCTAAAACAAGACAAAACAAAAAGGGCAACAACACTACCTACCAAAGACTAATTAGAAGAATTTTAAAATTTGGGTTAGGCTGTTTGGTGCAGGTGGAGGGAAAACTAGTGAATCATTCTGGTACCTGTGGTCAAATCCATTAGGCCACATAAGCTGTCTAGATGATGTGGTACATCATGATGACCAGGATGGAAGCCAGGGAGAGTTTCTAGGAAGGAAAGTTGCCTGAAAGACAGATCAAGAATTGAGACCAGGGAGCTGACCTATGAGTTTTCTTTATCAAACAGACAAAGTGATTGAATGGTATTAGTTATACTTTAACTCTTTAGGAGCCTTTCAGAAGAAGTAGGGAGGCAGGGAGAGAAGGGAAACCCCCATAAAGAAGGGAATACAAAAGGGGTAGGATTTTTCTTAGCTTTTTTTTCTTCTTCTAATTCTGGGTCCATTCATCATGTCATGAAAGGTTCTCTCATTGGTTGTGGTTTGGGTGGGAGGTAGGGTAGAATAGATTATCCAGAGCAGATGTCAATAATATCTATTTATACAATAGATCCAAGGCAAAAATAATAAAGTTATAAAGCATTCTCCACTCACCCATGTTCCATGCATTTCAAATTCTAGATCTCTTTGCCCATTTCCAGTGGTATCTGTTTAAAAGTAGGGGAGGTCAAAAGTAAAAGGTCTAGAAAAATGTAAATGAAAGAGAAGAAACATTTTCTAGCCTCAAAATGAGTCTGGAAGTCTGCAAGTCCTCCTGTTGGTGTTTATCCCCTAGTTTTCTACATTGTAGATTTTACACTGCTGATTCATAGAGCTTACTCAGCTGATTTTCACCCTGTCATCGTTAAGTGGACTATCTGGACTTTCATGCAAGATGCTGTGATTTTGAAACCAGGTGGGGGGAGACCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAGTTCTGGCTGTTCTGAGCATGTTATAGGACTTTCATTTCCCATCAAAACCTTGTGCTGACCCAATGATTGACTGATTGATCCACTTATTAATTCACCTATTCAACAAGCATTTATTGCACTAACTACATGCAGGGCACTGTGCTGGATGTTAGGAACAGTAGACAAATGACACAGCCCCTGCCTGCAAGGAGCTTACAGTTTAGTGGGCGAATCAGCCAACAAAATGTCTGAGGCTATAAGTACTTTTCCACACAGAAGAAAGGCTAAATGGACAATCTTGAAGAAAGTAAATTGTATCTGGAGGTAGAGGGAAGCCCTTTCCCTCAGCTACAGTTGAGCTAAAAAGAAGGAAACTCTTCTTACATTTAGGAAAAATTCCTTCTGATACTTCCAGAGGTTCAAATAAGTTGAACTTCATAAAATCTGCCAGGCGCAGTGGCTCATGCCTGTAATTCCAGCACTTTGGGAGGCCAAGACGGGAGGATCACAAGAGCCCAGGAACTCAAGACCAGCCTGGGCAACATTGTAAGACCCTGTCTCTACAAAAAAAAAAAAAAAAAAACTAAGAGCTGGCGCAGTGGCTCACACCTGTAATCCCAGCACTTAGGGAGGCCCAGGCGGGTTGATCACCTGAGGTCAGGAGTTCAAGACCAACCTGACCAACATGGTGAAACCCTGTCTCTACTAAAAATATAAAAAATTAGCCAGGTGTGGTGGCAGGTGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCCAGAGGCGTAGGTTGCAGTAAGCTGAGATCATGACACTGCACTCCAGCCTTGGCAACAGGAGCAAAATTCCATCTAAAACAAAACAAAACAAAACACTAAGACATGTAGCCAGGCATGGTGGGCACCTGTAGCTACTGCAGAGTAGCTGGGACTCTGAAATACTCTGAAATAGCTATTAATACTGCAGAATAGCTGGGACTTTGAAATACTCTGAAATAGCTATTAATACTGCAGAATAGCTGGGACTTTGAAATACTCTGAAATAGCTATTAATACCAGGCTAAAGTGGGAGGATCGCTTGAGCCCAGTAAATTGAGGCTGCAGTGAGCCATGTTCATGCCACTGCACTCCAGCCTGGGCAACAAGCAAGACACTGTATTAATAAATAAATAGATAAGTAAATAAACTCAGATCCAGCACCTTGCCCATCTCCCCGCCGTGAAGTGGGTAGGAAGCAGAGAGCATGGGCTAGTCCTTCTATATTGACTGGTCTTGCCAATGACACTCCCTCTGGGGCCTCTTGCTTTTCTTCTGACAG
Seq C2 exon
GTCACCTGGAGCCTGGGGGCCGGCCCAGCTCTCTCAGGATTCAGCAGACATTGGAGGTGGCAGTGAAGGATACAGTGGTAGTCAATGTTATTTGAGCAGGGTCAGCAGGCCCTGGAGCTTCCTGAGTGCACAATGCAGAAGGCTGCTTACTATGAAAACCCAGGACTGTTTGGAGGCTATGGCTACAGCAAAACTACGGACACTTACGGCTACAGCACCCCCCACCAGCCCTACCCACCCCCTGCTGCTGCCAGCTCCCTGGACACTGACTATCCAGGTTCTGCCTGCTCCATCCAGAGCTCTGCCCCTCTGAGAGCCCCAGCCCACAAAGGAGCTGAACTCAATGGCAGCTGCATGCGGCCGGGCACTGGGAACAGCCAGGGTGGGGGTGGTGGCAGCCAGCCTCCTGGTCTGAACTCAGAGCAGCAGCCACCACAACCCCCTCCTCCACCACCGACCCTGCCCCCATCTTCACCCACCAATCCTGGAGGTGGAGTGCCTGCCAAGAAGCCCAAAGGTGGGCCCAATGCTTCTAGCTCCTCAGCCACCATCAGCAAGCAGATCTTCCCCTGGATGAAAGAGTCTCGACAGAACTCCAAGCAGAAGAACAGCTGTGCCACTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000128652-HOXD3:NM_006898:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.862
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)