HsaINT0077278 @ hg38
Intron Retention
Gene
ENSG00000105996 | HOXA2
Description
homeobox A2 [Source:HGNC Symbol;Acc:HGNC:5103]
Coordinates
chr7:27100354-27102811:-
Coord C1 exon
chr7:27102110-27102811
Coord A exon
chr7:27101466-27102109
Coord C2 exon
chr7:27100354-27101465
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
CCCGACTTTTTTGGATCAATCAAACAGACAGTGGCTTCTTTTGATTAAAGCCCAAATTGTCATTGGGCAGAAGCAATCATGTGACAGCCAATTCGGTCCAATTTCAACCTTGTCTCCATGAATTCAATAGTTTAATAGTAGCGCGGTCCCCATACGGCTGTAATCAGTGAATTAGAAAAAAAACACCCTAGCAGCGATATTCTATGATAGATTTTTTTTCCTCTGCGCTCGCCTTTTTCCTAGGCCTTGCCCCCCCAAAGCCCCTCCAAAAGAGGGAACTTTTTCTCTGAGGGGGCTCCAAGGAGAAGGCCATGAATTACGAATTTGAGCGAGAGATTGGTTTTATCAATAGCCAGCCGTCGCTCGCTGAGTGCCTGACATCTTTTCCCCCTGTCGCTGATACATTTCAAAGTTCATCAATCAAGACCTCGACGCTTTCACACTCGACACTGATTCCTCCTCCTTTTGAGCAGACCATTCCCAGCCTGAACCCCGGCAGTCACCCTCGCCACGGCGCTGGCGGCCGCCCCAAGCCGAGCCCCGCGGGCAGCCGCGGCAGCCCGGTGCCCGCCGGCGCCCTGCAGCCGCCCGAGTACCCCTGGATGAAGGAGAAGAAGGCGGCCAAGAAAACCGCACTTCTGCCGGCCGCCGCCGCCGCCGCCACCGCCGCAGCCACCGGCCCTGCTTGCCTCAGCCACAAAG
Seq A exon
GTCAGTCCAAAGACTTGGCCCCAGGTCTCTGGGACCCTCTTCCTTCTCCGGGCTGCCCCGAGAGTGGCTGTGGGGGGAGGGGAGAGTGGGCTGGGAGAGAAGGAGGAGAGGGAGAGATGCTTGGTTGCCTTGTCCCTGCCCCTGTGGGTTCAGGAGTGGGTTTGATGGAGAGGAAAGGGGATCCTGCGCTCTACAATGAGACATATATATTTTTAGGAAGTGGGGGGAAACTTTCCCGAACTTGTGTAATGTGGGATGATTTATTTGAGTTGGAACTGACCTCCTCCTGTCTAGTTGTCCTAGAGTTTGGCTTTTTGACAGTAATGAAGAGTGATAGATCGCTCTTGCTCAGCTAAGCAGCTGACGCATTAATTATAAATTGTGTTGTGGCTAATATAAAGTTTGCTCCCGGATGAAGAGGTTGGGGGGAGCCACAGGCATGAATTCGATAGAGATGGAGGAGACGGGGTCTGCCCAGGCTGGGCTCCCAGGAAAGGCAGCACAATAGCTCTACTGCATCCAGGGGCGGCCATTTTGTTGCAGTTGATCTTTTCTGCTATATTTATTCTCCAGTGGAATAACCCCGCTCGGACCCCTCCACCTCCAACTGTGCGTGTGTCTCTTGTTGGTTTCCCTTTCCGCAG
Seq C2 exon
AATCCCTGGAAATCGCCGATGGCAGCGGCGGGGGATCGCGGCGCCTGAGAACTGCTTACACCAACACACAGCTTCTAGAGCTGGAAAAAGAATTTCATTTCAACAAGTACCTTTGCAGACCCCGAAGGGTGGAGATTGCAGCGCTGCTGGATTTGACTGAGAGACAAGTGAAAGTGTGGTTTCAGAACCGGAGGATGAAGCACAAGAGGCAGACCCAGTGCAAGGAAAACCAAAACAGCGAAGGGAAATGTAAAAGCCTTGAGGACTCCGAGAAAGTAGAGGAGGACGAGGAAGAGAAGACGCTCTTTGAGCAAGCCCTTAGCGTCTCTGGGGCCCTTCTGGAGAGGGAAGGCTACACTTTTCAGCAAAATGCCCTCTCTCAGCAGCAGGCTCCCAATGGACACAATGGCGACTCCCAAAGTTTCCCAGTCTCGCCTTTAACCAGCAATGAGAAAAATCTGAAACATTTTCAGCACCAGTCACCCACTGTTCCCAACTGCTTGTCAACAATGGGCCAGAACTGTGGAGCTGGCCTAAACAATGACAGTCCTGAGGCCCTTGAGGTCCCCTCTTTGCAGGACTTTAGCGTTTTCTCCACAGATTCCTGCCTGCAGCTTTCAGATGCAGTTTCACCCAGTTTGCCAGGTTCCCTCGACAGTCCCGTAGATATTTCAGCTGACAGCTTAGACTTTTTTACAGACACACTCACCACAATCGACTTGCAGCATCTGAATTACTAAAAACATTAAAGCAAAACAAAGCATCACCAAACAAAAACTCCTTTGACCAGGTGGTTTTGCCTTCTTTTATTTGGGAGTTTATTTTTTATTTTCTTCTTGACCTACCCCTTCCCTCCTTTAAGTGTTGAGGATTTTCTGTTTAGTGATTCCCTGACCCAGTTTCAAACAGAGCCATCTTTTACAGATTATTTTGGAGTTTTAGTTGTTTTAAACCTAACTCAACAACCCTTTATGTGATTCCTGAGAGCAGTATGAGGCCTGCAAGAAAGTGATCATATAATTGTATCTTCACTTTCTTTTTATTTTTGTATTACATTGGGATGCATTGTCATGCATATTTTTTGTAGAATAAATTCTCCTTTGCTATAAGTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000105996:ENST00000222718:1
Average complexity
IR
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