HsaINT0077273 @ hg19
Intron Retention
Gene
ENSG00000253293 | HOXA10
Description
homeobox A10 [Source:HGNC Symbol;Acc:5100]
Coordinates
chr7:27210210-27213955:-
Coord C1 exon
chr7:27212968-27213955
Coord A exon
chr7:27211793-27212967
Coord C2 exon
chr7:27210210-27211792
Length
1175 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGC
5' ss Score
8.84
3' ss Seq
TTTATTCTCTTACATGCCAGGCA
3' ss Score
6.46
Exon sequences
Seq C1 exon
TAATCGTATTCAGCATGTTTTGCACAAGAAATGTCAGCCAGAAAGGGCTATCTGCTCCCTTCGCCAAATTATCCCACAACAATGTCATGCTCGGAGAGCCCCGCCGCGAACTCTTTTTTGGTCGACTCGCTCATCAGCTCGGGCAGAGGCGAGGCAGGCGGCGGTGGTGGTGGCGCGGGGGGCGGCGGCGGTGGCGGTTACTACGCCCACGGCGGGGTCTACCTGCCGCCCGCCGCCGACCTGCCCTACGGGCTGCAGAGCTGCGGGCTCTTCCCCACGCTGGGCGGCAAGCGCAATGAGGCAGCGTCGCCGGGCAGCGGTGGCGGTGGCGGGGGTCTAGGTCCCGGGGCGCACGGCTACGGGCCCTCGCCCATAGACCTGTGGCTAGACGCGCCCCGGTCTTGCCGGATGGAGCCGCCTGACGGGCCGCCGCCGCCGCCCCAGCAGCAGCCGCCGCCCCCGCCGCAACCACCCCAGCCAGCGCCGCAGGCCACCTCGTGCTCTTTCGCGCAGAACATCAAAGAAGAGAGCTCCTACTGCCTCTACGACTCGGCGGACAAATGCCCCAAAGTCTCGGCCACCGCCGCCGAACTGGCTCCCTTCCCGCGGGGCCCGCCGCCCGACGGCTGCGCCCTGGGCACCTCCAGCGGGGTGCCAGTGCCTGGCTACTTCCGCCTTTCTCAGGCCTACGGCACCGCCAAGGGCTATGGCAGCGGCGGCGGCGGCGCGCAGCAACTCGGGGCTGGCCCGTTCCCCGCGCAGCCCCCGGGGCGCGGTTTCGATCTCCCGCCCGCGCTAGCCTCCGGCTCGGCCGATGCGGCCCGGAAGGAGCGAGCCCTCGATTCGCCGCCGCCCCCCACGCTGGCTTGCGGCAGCGGCGGGGGCTCGCAGGGCGACGAGGAGGCGCACGCGTCGTCCTCGGCCGCGGAGGAGCTCTCCCCGGCCCCTTCCGAGAGCAGCAAAGCCTCGCCGGAGAAGGATTCCCTGG
Seq A exon
GTAAGCAGGGCTGCAGAGGGCTGCAGTCAGGCGGGCAGACAGGCAGACACAAGGAGGAGAAGGATCAGAAAACTAGGAGCCCGCGCAGCAGCCGGCCGGCCTTGGCCCAAGCTGCAGGCAGGCTGACCTTGTGAACTTGCTTTTTAATATTTGGGCGTGGGGACGCAGTAAAATTCATGTCCGGCTTAGCGCCCCACAGCAAGACGTCCTCGGCGCTGGCCTCAGCTCCCCCTGACTAGGGACGAGGACACCAGCGAGCAGGCCCCCTCCTGTGCGCTCTTTCCTGTGGCCGGGAGGACCCAGAGCCCTGGTCCCTGCCCAGCCTGCGCGGCGCGGCCCACGCGGGGGGAGGGGGAGGGAGGGAAAGTAGCTCGCCCGCAGATAGCGCGGATGTTTGTAAGGCATCCAAAATAAGCAGCCGCCAGCGCCAATAAATAAGCCCATTAACCGGCGAAGTTCGAGTTTACGATCCCCCATGCTTTTTTCAAAGTTGCTGAGGGGCGGGAATCTTCGTTGCGGGAAGAAGAAAAGGCAAATCCGGCCTGGAAGCGGGGGGCCCTGAGCTGAGAGCCAGAGAAGGGCCATTTCCCTTCCCCTGGACCTCGGAATCGCCCAGCTATCTATCCCTGGCTCCTGGAGAAACTTGAGGGAGGGCCCTTGACCCCCGAATCGGTTTTTCCTGCCTTCCCCATTGGACCAATGATGCCCTTCTTTCTCCCCTTATCGAGTCTTGGGCAATCAGGGCCCTGGGGTGAGACAGCCAAGCTGCCTGGCCCATCTTCCAAGTAAGCACCCCGCGCTCCTAGCCTGGGGGCTACAGGAAATGCTTGTCTGCCATATGGCAAGAGGCAAAGAAAAGCGTTAAGTTCAAGATGTACAGCCTGCCCTCCCAGGCCTTTCCTTCTGCAAGCATCTACGGCTTAGCGCTAAAACAGGTGTTTGGAAAAGTGGGGGAAATGTAAATTGGAAGGGTCATGTAGATTGAAGGCCCACTCAATTTTTGTCATGACTTTTGGAGGAACTGCTTGCTCTCAGCAAGCCAAAAACGGGGGCACGACTCTCTTCTCTGTGACTTGGGACATCTCTCTTATGGGAGAAACGGAGGCAATTCACCCCCGCGGGCAGCCCGTGTGGCCTCGACTTAATCATCCCCTCTTTATTCTCTTACATGCCAG
Seq C2 exon
GCAATTCCAAAGGTGAAAACGCAGCCAACTGGCTCACGGCAAAGAGTGGTCGGAAGAAGCGCTGCCCCTACACGAAGCACCAGACACTGGAGCTGGAGAAGGAGTTTCTGTTCAATATGTACCTTACTCGAGAGCGGCGCCTAGAGATTAGCCGCAGCGTCCACCTCACGGACAGACAAGTGAAAATCTGGTTTCAGAACCGCAGGATGAAACTGAAGAAAATGAATCGAGAAAACCGGATCCGGGAGCTCACAGCCAACTTTAATTTTTCCTGATGAATCTCCAGGCGACGCGGTTTTTTCACTTCCCGAGCGCTGGTCCCCTCCCTCTGTCTTCAGGCTCTGCCCAGGAACTCGCACCTGTGCTGGAGCCCTGTTCCTCCCTCCCACACTCGCCATCTCCTGGGCCGTTACATCTGTGCAGGGCTGGTTTGTTCTGACTTTTTGTTTCTTTGTGTTTGCTTGGTGCTGGTTTATTTGTTGTTTTCTGGGGGAAAAAGCCATATCATGCTAAAATTCTATAGAGATAGATATTGTCCTAAGTGTCAAGTCCTGACTGGGCTGGGTTTGCTGTCTTGGGGTCCCACTGCTCGAAATGGCCCCTGTCTTCGGCCGAGCTGGTTTCCTGCCCAGCCTGGGGCAAACCTAGCCGGAAGGCCGAGGTCCCATTGTTGGCGCTGAGGTGTCTGGCCTGAGGTCAATGGTGCAAAGGAGCCGCCACCGGGCATGTCTGCCTGGAGTGCTGTGCTGTGTTTAATCAGGGGATACAGGCCCCTGGGTTTCTTTTTTCTTTCTTCCTTTCTTCCTTGGCCAAGAGAAGGGCTTACAGGCATGGACATGCAGGTTGGCAAACGGGCTTGACTTTGGCTGATTTAAAAAGTGAGAAAGAAAGTAAAAAAGGTTAATTTTTCCTTCCTCTGTAAGATATCCCAGCTTTAAAAAGAAAAAAAAAGAATTACCAAGAGAAGGGGACTTCTCTTCCAGTTTCTGTAAGGTCTTACATTGCCTGACTAAAATGTTTCATTTACCTCTAAATTTCCATATCCTTCTGGCTGTAGATAAATAATGTAGTTTTGTTTATGCATTTGGAATTAGTGGATTTTTTTGTCATTAAAATTGTTACCACTGGTAACATGTGACAAGCACACCACAATTCTCCCTATCTTGTGAAGTTGTTTTTTTAAATCGCCTTGAACAAAAAGTTTTTTTTTTGTTTGTTTTTGCTTTCTGAAATTCACAGAAGCCTAGGAGGACTGGGGTAAGCGGAATAAACTAGAGAAGGGAGACATTGTTTGGATTTCCTTTATACTGTGAAGTTACATGCATAAAAGGGTCAAACCTGTAGATGCAGAAAAAGAAAAAAACTATAAATACAAATCTGTATAAATGTCTATTATTATGAAGAATTGCCAATCTTGTTTTAAGCAAATGCATTCTATCGTTATTATAAATGTTAGTTCTAGCTCTATTTACTTCTAATCTTAAATCAGAATAAATTAATATTGTATTGCTGCTGTGCGTGGAAAAAGACGATGTTTATGTTCTTATAGAATAAAAGCTGTGGAATGAAGCTTTTTAATTTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000253293-HOXA10:NM_018951:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.757 A=NA C2=0.332
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=62.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTACTTCCGCCTTTCTCAG
R:
AGTTGGCTGCGTTTTCACCTT
Band lengths:
355-1530
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)