HsaINT0077312 @ hg19
Intron Retention
Gene
ENSG00000128710 | HOXD10
Description
homeobox D10 [Source:HGNC Symbol;Acc:5133]
Coordinates
chr2:176981492-176984670:+
Coord C1 exon
chr2:176981492-176982306
Coord A exon
chr2:176982307-176983681
Coord C2 exon
chr2:176983682-176984670
Length
1375 bp
Sequences
Splice sites
5' ss Seq
AAGGTCGGT
5' ss Score
7.13
3' ss Seq
TCTCCCTTTAATTTTGTTAGAGG
3' ss Score
4.45
Exon sequences
Seq C1 exon
CGGGGAATGTTTTCCTAGAGATGTCAGCCTACAAAGGACACAATCTCTCTTCTTCAAATTCTTCCCCAAAATGTCCTTTCCCAACAGCTCTCCTGCTGCTAATACTTTTTTAGTAGATTCCTTGATCAGTGCCTGCAGGAGTGACAGTTTTTATTCCAGCAGCGCCAGCATGTACATGCCACCACCTAGCGCAGACATGGGGACCTATGGAATGCAAACCTGTGGACTGCTCCCGTCTCTGGCCAAAAGAGAAGTGAACCACCAAAATATGGGTATGAATGTGCATCCTTATATACCTCAAGTAGACAGTTGGACAGATCCGAACAGATCTTGTCGAATAGAGCAACCTGTTACACAGCAAGTCCCCACTTGCTCCTTCACCACCAACATTAAGGAAGAATCCAATTGCTGCATGTATTCTGATAAGCGCAACAAACTCATTTCGGCCGAGGTCCCTTCGTACCAGAGGCTGGTCCCTGAGTCTTGTCCCGTTGAGAACCCTGAGGTTCCCGTCCCTGGATATTTTAGACTGAGTCAGACCTACGCCACCGGGAAAACCCAAGAGTACAATAATAGCCCCGAAGGCAGCTCCACTGTCATGCTCCAGCTCAACCCTCGTGGCGCGGCCAAGCCGCAGCTCTCCGCTGCCCAGCTGCAGATGGAAAAGAAGATGAACGAGCCCGTGAGCGGCCAGGAGCCCACCAAAGTCTCCCAGGTGGAGAGCCCCGAGGCCAAAGGCGGCCTTCCCGAAGAGAGGAGCTGCCTGGCTGAGGTCTCCGTGTCCAGTCCCGAAGTGCAGGAGAAGGAAAGCAAAG
Seq A exon
GTCGGTATGAGCAGAGTTGCCACCCCAGCGGGGCGCGCAGCCCGGGAACCCGGCAGAGAGGGAGTGCCGGGGTGCCCAGCGCCGAGCCGGAGCCCGACTTGGCAGGTGCTGCTCCGCCTGGTTTTAGAGGGGTGATCTCAGCCCTGAGATAGTCCCCGCTTCTCCCCTGCTGCCCTGGCCCTCTCCGCCAGTCCTGGCCCCACGCTGATGGCGCCCGGGCAGAGGAAAAGCTTGCCGGTTTTATTTTTCCTGAGCTAGACCTGAACACAACAAAAGAGCGCAAAGGAGACCTGCGGCTCATAAACACGACCACAGAGCCTCTTTTCTCCTGCTCAGATTTGCAGTTCCAGTTTTGCCTTGAGCCCAATGATCATGTTAAGGTGATCCAGGGCACCGTGTTCGTGTTCAAGTGTATGCACCCCGCATCCTGCGAGCTTGGGGGTGGTGAGGGGAAAGAGATGGCTGGGCTGGTTGGTGCTTGAGTTGGGAAACAGGGCTTACTGCCTTTGCTGGGCTAGGTAACCTTGGCTTTGTTTAGGAAAAGTGCTGCAGTCTTTGCAATCCGTCGGCAAAGAGGGCAAAGGCGGAGGGGGAGAGTGGAACCCGCATTGCCCTCCCTGCAAGGCCAGCCTTAGGGCTGGGCTAAGGCAAAGAGCCAGGGATCTGGCTTTTTGAGAAGGAACCCTCCTCCTCTCCCCCAGTGCTTAGAGGTGGGCCACAGTAGGGGGCTCCCTTTCTGGGGGAATGCTTTAGTGTGGGGGCAAGAAGACATGAAAATTAAGGAAATTCTGGGGAATGCAACAATACCCAGGCAAGGTGGGGGAAGGTGTCTCGCTTCCCCATTTATCTTTTGAAAGAGAATGGGCACCTATAAACCTGACTGTCAGGATTCCTGACTGCCTAGGAGAGGTGGGGAAGAAGTGGCAGATTTGGGGACCTGAGGCAGCAGTGGGGTTGGTAGGCTTGTCCAGGTCGTGGCGTATTCCCCTCCGTCCCTGTTAGGAGCTGAACCCTTAGAATGTTGCTGGGGAGATCTGGAAAGTTTACTATTCTACTAATGTTTTGTACAAGTGAGAAAGTTGAAAGAGAGAGCGAGAACCCAAATGCAGACTGTCCTGCCATCATGTCATTTAAGTAATGTGGCATCAATGTAAGATTCCCTTCCAAGGCCCACTTCATGTGAGTAATGTTTAATACTAGCATTTTCCAAAGCGGCCTGGCTGCCAGCAGGGTCACGGCCAAGGGTACATTTGAACAGTCTGAAGAAAAAAACAAAAACGAAAACCAAAACCAAAACCAAAACAAAAACAAAAACAAAAACAAACAAACAAAAAACCTCTTGATTTTTTTCTTCTTCTCCCTTTAATTTTGTTAG
Seq C2 exon
AGGAAATCAAGTCTGATACACCAACCAGCAATTGGCTCACTGCAAAGAGTGGCAGAAAGAAGAGGTGCCCTTACACTAAGCACCAAACGCTGGAATTAGAAAAAGAGTTCTTGTTCAATATGTACCTCACCCGCGAGCGCCGCCTAGAGATCAGTAAGAGCGTTAACCTCACCGACAGGCAGGTCAAGATTTGGTTTCAAAACCGCCGAATGAAACTCAAGAAGATGAGCCGAGAGAACCGGATCCGAGAACTGACCGCCAACCTCACGTTTTCTTAGGTCTGAGGCCGGTCTGAGGCCGGTCAGAGGCCAGGATTGGAGAGGGGGCACCGCGTTCCAGGGCCCAGTGCTGGAGGACTGGGAAAGCGGAAACAAAACCTTCACCGCTCTTTGTTTGTTGTTTTGTTGTATTTTGTTTTCCTGCTAGAATGTGACTTTGGGGTCATTATGTTCGTGCTGCAAGTGATCTGTAATCCCTATGAGTATATATATATATATATATATATATATATAAAAACTTAGCACGTGTAATTTATTATTTTTTCATCGTAATGCAGGGTAACTATTATTGCGCATTTTCATTTGGGTCTTAACTTATTGGAACTGTAGAGCATCCATCCATCCATCCATCCAGCAATGTGACTTTTTCATGTCTTTCCTAACACAAAAGGTCTATGTGTGTGGTTAGTCCATGAACTCATGGCATTTTGAATACATCCAGTACTTTAAAAATGACATATATATTTAAAAAAAAAAGATTAAGAAAACCCACAAGTTGGAGGGAGGGGGACTTAAAAAGCACATTACAATGTATCTTTTCACAAATGAATTTAGCAGTTGTCCTTGGTGAGATGGGATATTGGCGATTTATGCCTTGTAGCCTTTCCCTTGTGGTGCATCTGTGGTTTGGTAGAAGTACAACAGCAACCTGTCCTTTCTGTGCATGTTCTGGTCGCATGTATAATGCAATAAACTCTGGAAATGAGTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000128710-HOXD10:NM_002148:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.510 A=NA C2=0.293
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=61.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGACTGAGTCAGACCTACGCC
R:
GCACCTCTTCTTTCTGCCACT
Band lengths:
357-1732
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)