HsaINT0077278 @ hg19
Intron Retention
Gene
ENSG00000105996 | HOXA2
Description
homeobox A2 [Source:HGNC Symbol;Acc:5103]
Coordinates
chr7:27139973-27142394:-
Coord C1 exon
chr7:27141729-27142394
Coord A exon
chr7:27141085-27141728
Coord C2 exon
chr7:27139973-27141084
Length
644 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
GTTGGTTTCCCTTTCCGCAGAAT
3' ss Score
9.3
Exon sequences
Seq C1 exon
TCTTTTGATTAAAGCCCAAATTGTCATTGGGCAGAAGCAATCATGTGACAGCCAATTCGGTCCAATTTCAACCTTGTCTCCATGAATTCAATAGTTTAATAGTAGCGCGGTCCCCATACGGCTGTAATCAGTGAATTAGAAAAAAAACACCCTAGCAGCGATATTCTATGATAGATTTTTTTTCCTCTGCGCTCGCCTTTTTCCTAGGCCTTGCCCCCCCAAAGCCCCTCCAAAAGAGGGAACTTTTTCTCTGAGGGGGCTCCAAGGAGAAGGCCATGAATTACGAATTTGAGCGAGAGATTGGTTTTATCAATAGCCAGCCGTCGCTCGCTGAGTGCCTGACATCTTTTCCCCCTGTCGCTGATACATTTCAAAGTTCATCAATCAAGACCTCGACGCTTTCACACTCGACACTGATTCCTCCTCCTTTTGAGCAGACCATTCCCAGCCTGAACCCCGGCAGTCACCCTCGCCACGGCGCTGGCGGCCGCCCCAAGCCGAGCCCCGCGGGCAGCCGCGGCAGCCCGGTGCCCGCCGGCGCCCTGCAGCCGCCCGAGTACCCCTGGATGAAGGAGAAGAAGGCGGCCAAGAAAACCGCACTTCTGCCGGCCGCCGCCGCCGCCGCCACCGCCGCAGCCACCGGCCCTGCTTGCCTCAGCCACAAAG
Seq A exon
GTCAGTCCAAAGACTTGGCCCCAGGTCTCTGGGACCCTCTTCCTTCTCCGGGCTGCCCCGAGAGTGGCTGTGGGGGGAGGGGAGAGTGGGCTGGGAGAGAAGGAGGAGAGGGAGAGATGCTTGGTTGCCTTGTCCCTGCCCCTGTGGGTTCAGGAGTGGGTTTGATGGAGAGGAAAGGGGATCCTGCGCTCTACAATGAGACATATATATTTTTAGGAAGTGGGGGGAAACTTTCCCGAACTTGTGTAATGTGGGATGATTTATTTGAGTTGGAACTGACCTCCTCCTGTCTAGTTGTCCTAGAGTTTGGCTTTTTGACAGTAATGAAGAGTGATAGATCGCTCTTGCTCAGCTAAGCAGCTGACGCATTAATTATAAATTGTGTTGTGGCTAATATAAAGTTTGCTCCCGGATGAAGAGGTTGGGGGGAGCCACAGGCATGAATTCGATAGAGATGGAGGGGACGGGGTCTGCCCAGGCTGGGCTCCCAGGAAAGGCAGCACAATAGCTCTACTGCATCCAGGGGCGGCCATTTTGTTGCAGTTGATCTTTTCTGCTATATTTATTCTCCAGTGGAATAACCCCGCTCGGACCCCTCCACCTCCAACTGTGCGTGTGTCTCTTGTTGGTTTCCCTTTCCGCAG
Seq C2 exon
AATCCCTGGAAATCGCCGATGGCAGCGGCGGGGGATCGCGGCGCCTGAGAACTGCTTACACCAACACACAGCTTCTAGAGCTGGAAAAAGAATTTCATTTCAACAAGTACCTTTGCAGACCCCGAAGGGTGGAGATTGCAGCGCTGCTGGATTTGACTGAGAGACAAGTGAAAGTGTGGTTTCAGAACCGGAGGATGAAGCACAAGAGGCAGACCCAGTGCAAGGAAAACCAAAACAGCGAAGGGAAATGTAAAAGCCTTGAGGACTCCGAGAAAGTAGAGGAGGACGAGGAAGAGAAGACGCTCTTTGAGCAAGCCCTTAGCGTCTCTGGGGCCCTTCTGGAGAGGGAAGGCTACACTTTTCAGCAAAATGCCCTCTCTCAGCAGCAGGCTCCCAATGGACACAATGGCGACTCCCAAAGTTTCCCAGTCTCGCCTTTAACCAGCAATGAGAAAAATCTGAAACATTTTCAGCACCAGTCACCCACTGTTCCCAACTGCTTGTCAACAATGGGCCAGAACTGTGGAGCTGGCCTAAACAATGACAGTCCTGAGGCCCTTGAGGTCCCCTCTTTGCAGGACTTTAGCGTTTTCTCCACAGATTCCTGCCTGCAGCTTTCAGATGCAGTTTCACCCAGTTTGCCAGGTTCCCTCGACAGTCCCGTAGATATTTCAGCTGACAGCTTAGACTTTTTTACAGACACACTCACCACAATCGACTTGCAGCATCTGAATTACTAAAAACATTAAAGCAAAACAAAGCATCACCAAACAAAAACTCCTTTGACCAGGTGGTTTTGCCTTCTTTTATTTGGGAGTTTATTTTTTATTTTCTTCTTGACCTACCCCTTCCCTCCTTTAAGTGTTGAGGATTTTCTGTTTAGTGATTCCCTGACCCAGTTTCAAACAGAGCCATCTTTTACAGATTATTTTGGAGTTTTAGTTGTTTTAAACCTAACTCAACAACCCTTTATGTGATTCCTGAGAGCAGTATGAGGCCTGCAAGAAAGTGATCATATAATTGTATCTTCACTTTCTTTTTATTTTTGTATTACATTGGGATGCATTGTCATGCATATTTTTTGTAGAATAAATTCTCCTTTGCTATAAGTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000105996-HOXA2:NM_006735:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.603 A=NA C2=0.516
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=23.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTGACATCTTTTCCCCCTG
R:
CATCGGCGATTTCCAGGGATT
Band lengths:
351-995
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)