HsaINT0077286 @ hg38
Intron Retention
Gene
ENSG00000122592 | HOXA7
Description
homeobox A7 [Source:HGNC Symbol;Acc:HGNC:5108]
Coordinates
chr7:27153716-27156677:-
Coord C1 exon
chr7:27156167-27156677
Coord A exon
chr7:27155223-27156166
Coord C2 exon
chr7:27153716-27155222
Length
944 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGC
5' ss Score
9.88
3' ss Seq
GTCTGCATGTCTGTTCTCAGGAC
3' ss Score
9.45
Exon sequences
Seq C1 exon
GTGCTGCGGCGAGCTCCGTCCAAAAGAAAATGGGGTTTGGTGTAAATCTGGGGGTGTAATGTTATCATATATCACTCTACCTCGTAAAACCGACACTGAAAGCTGCCGGACAACAAATCACAGGTCAAAATTATGAGTTCTTCGTATTATGTGAACGCGCTTTTTAGCAAATATACGGCGGGGGCTTCTCTGTTCCAAAATGCCGAGCCGACTTCTTGCTCCTTTGCTCCCAACTCACAGAGAAGCGGCTACGGGGCGGGCGCCGGCGCCTTCGCCTCGACCGTTCCGGGCTTATACAATGTCAACAGCCCCCTTTATCAGAGCCCCTTTGCGTCCGGCTACGGCCTGGGCGCCGACGCCTACGGCAACCTGCCCTGCGCCTCCTACGACCAAAACATCCCCGGGCTCTGCAGTGACCTCGCCAAAGGCGCCTGCGACAAGACGGACGAGGGCGCGCTGCATGGCGCGGCTGAGGCCAATTTCCGCATCTACCCCTGGATGCGGTCTTCAG
Seq A exon
GTAGGCGCAGTCGCTAGGCGGGCCAGGCTGGCGGAGCGGGACCGGGAGCGGGGAGCGCAGCGCTGGGGAGCGCGGAGCGCGGGGCGCGGGGCCGGAAGAGCGGAGCCAGGCTGTTGCGAGCCGGTAGCCCCGTGACTCCCGGCGCAGCCTTTCTGGTTTTAATTGGAGCGGAGGCGCCATTGCGTGGAGCCCATAGCATTGTATGTAAATGAGGCTCATAAAACTTTTTATGGCCCAATTAATGGGTTCGATCCTCGTAAATTTATTTAACTCCATTTGTCTTGGAATTTTAACATTAAGTTTGTTCGCTATTCTGTCTCTCTTTCTCCCTCCTCTGTCACCCTCCCTCCCTTTCTTCTTCTCTCTCTCCTCATTTTCCTTGCTGCCTGACATTTCTTTCTCAAAAGCTAGGAGAGCCAAGCCCTCCAGGGCCTCTCACCCGACCCTGTGCCAGGGTCCATTTCAAGATGGGGGCGAGGGAATGAGGACAGAGGGTCGGGGTGCCCTAGGAAGGTCCTGGGGATGAGGGCTCAGGCTGCTGGGAAGAGTCGCCCACTTGCCTAGCAAGGCAGGGGAATGGCCGGGCTCATCTTTGAATGGCAAAAGTGCAGCGTTTCCCACTTGCTCACACTCTATATTTACAGTTTTCCTTTGTCAGAGGAAGCAGGACATTGTGGAAGCTTAGCCGGCTGGAAAGGTCGGTTGTAAAGTTGAGATTCTGTGCCTTTGCTCATTACAGAGCTGCCTGCGCGTCTGGCACTGCAGTTGGGGTCTTTCCCTAACACTCCCCCTCCTCCCCTAGCTCAGTTCGGGGCCTGGGGCAGAGGGGGATGCTCGCTGGGGACTAGGCCAGGAGGAAGGTGCGGGCTCTGGGACAGCAGCCTAACGAGTGCCCTGTCTACTTGTCTGTCCTTGTGTTCATGTGTCTGCATGTCTGTTCTCAG
Seq C2 exon
GACCTGACAGGAAGCGGGGCCGCCAGACCTACACGCGCTACCAGACGCTGGAGCTGGAGAAGGAGTTCCACTTCAACCGCTACCTGACGCGGCGCCGCCGCATTGAAATCGCCCACGCGCTCTGCCTCACCGAGCGCCAGATTAAGATCTGGTTCCAGAACCGCCGCATGAAGTGGAAGAAAGAGCATAAGGACGAAGGTCCGACTGCCGCCGCAGCTCCCGAGGGCGCCGTGCCCTCTGCCGCCGCCACTGCTGCCGCGGACAAGGCCGACGAGGAGGACGATGATGAAGAAGAGGAAGACGAGGAGGAATGAGGGGCCGATCCGGGGCCCTCTCTGCACCGGACAGTCGGAAAAGCGTCTTTAAGAGACTCACTGGTTTTACTTACAAAAATGGGAAAAATAAAAGAAAATGTAAAAAACAAAAACAAAAACAAAAAAGCAACCCAGTCCCCAACCTGCACTCTACCCACCCCCATCACCTACTCCAGCTCCCAACTTTTGTGGACTGAGCGGCCGCAGAGACTGGGTCGCCTTGGATTCCCTCTGCCTCCGAGGACCCCAAAAGACACCCCCAACCCCAGGCCAGCCGGCCCTGCTCTGGCGCGTCCAAAATACTACCTAGCACAGGCCTCTGCTCGAGGCACCCCCAAACTACCTATGTATCCAGCCCCAGAGGGCCTCCATTCCCAGGAAGTCCCTATGTATCCCAACACTGGCAGACACCCAGCACCACCCTCCCAGACCCGCAAGAAAGTGAATCTCACTACTACCTACTCCCCTAAAACTACCTATTTTGTGCTGGCTGGCTTGCCTGCTACCTAGTGCCGACTGCTCCCAGGCAAGTCCCCTGCTGCTTACAGCCCGCAGCTTTTGGGGTCCCTGAGGCTGCCCTGAGAATGTGCTGAGGTCCAGGATCAGGGTATTGGCATCTATTTAAATCGAAAAATAATATATTTATTCCAAAAAGCATCCTAAGTGCTTGCACCCTAGAATCAATCCCTCCTTCTCTGGCTTGGCACCCACAGCTCAGGCCCATCAACCCCCACTTCTGGAGGGGAATGTTCCTGAGCTGGCTGCAGATCTGTGGGTTAGCTTCTGCTTAGCAGGACTGTGGAGATGCTTCCAGCTTCGCTGTCCTTTCCTCTGGCTCCTGTATCTTACTGTTCAGCTGTGTTAAATATGTACGCCCTGATGTTTCCTATAATAGCAGATACTGTATATTTGAACAAGATTTTTTTTTATCATTTCTATAGTCTTGGAGTTCATTTGTAAGGCAGTGTCTTGACTTGGAAAGGATGTGTTAATGGGGTGACTTTGTAGCATGGTATGTTGTCTTGAGTTAACTGTAGTGGGTGGGGAGGTCCAATGCCCTCCGCAATGCCCTTCATCTCCTGTGTTGTCCTGTACCCTGCTCAGCTCCATCCTGGGGTTCAGGGAAGGCACACTTCCCAGCCCAGCTGTGTTTTATGTAACCGAAAATAAAGATGCGTGGTGACAAAGAAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000122592:ENST00000242159:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.500
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=54.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTCCGCATCTACCCCTGGAT
R:
CCCCTCATTCCTCCTCGTCTT
Band lengths:
350-1294
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