Basic Information

Symbol
HOPX
RNA class
mRNA
Alias
HOP Homeobox NECC1 LAGY HOP OB1 SMAP31 Lung Cancer-Associated Y Protein Homeodomain-Only Protein Odd Homeobox Protein 1 HOD Not Expressed In Choriocarcinoma Protein 1 Not Expressed In Choriocarcinoma Clone 1 Homeobox Only Domain CAMEO TOTO
Location (GRCh38)
4:56647989-56681877
UCSC Genome Browser Search in Marker Scope
Forensic tag(s)
Postmortem interval inference
External database
HGNC NCBI Ensembl OMIM UniProt GTEx

MANE select

Transcript ID
NM_032495.6
Sequence length
1123.0 nt
GC content
0.4417

Secondary Structure

Generated by RNAfold
Minimum free energy (MFE) structure:
Secondary structure that contributes a minimum of free energy.
Ensemble properties:
Thermodynamic properties of the Boltzmann ensemble.
Minimum free energy
-329.60 kcal/mol
Thermodynamic ensemble
Free energy: -353.02 kcal/mol
Frequency: 0.0000
Diversity: 301.03
MFE Structure Visualization
Structure Prediction
MFE Structure Prediction
.........(((((((((((.((((..((..(((.((((((......................)).)))))))..))..)))).)))))).....)))))(((((....((((((((((((((....(((((....(((.((((((..(((.......)))((.(((.((((((.(.....((..((((...))))..))((.((......)).)).(((((((.(((((((((...))))))....((((.....).))).)))))))))).).))))))))).)))))))).)))(((((((((((((((((((((..((((.(((((......((((((.(.((...)).)))))))......((((((((((..(((...............)))...)))..)))))))........(((((.....)))))))))).))))....))))))))((((....))))(((((........)))))((((((.((((((((((.((((((((...(((((((((.((((((((((((.((((((((((((..........))))))))))))))))))..((((.((.....)).)))))))))).)))))))))...(((((......))))).)))))))).(((((((((.((((.(..((((((((((......)))))))..)))..)...))))))....(((((...((((...)))).((((((((..(((((((...........)))))))..)))..))))))))))))))))).......(((((((.(((((......)))))(((((.((((((((((......)))).)))).))..)))))......)))))))((((((((((.........))))...))))))....)))))))).)).))))))..))))))))..))))).)))))..)))))).............((((((((.((.....................(((((.((..((((((.......))))))..)).)))))..(((((((((((.....)))))))))))))))))))))((......)).................)))))))))))))..
Thermodynamic Ensemble Prediction
.........(((((((((((.(((({{((..((({((((((.......,..,{,,{{.....{||{|,,},||{{||{{|,||.,,,))}.,,.})))))|..,.,}}||{{{|{||||||{{....(((({....,.|}}}}..,..,||..,.,}.}))}})|)}.|||||{|(.{,..{{,.((((...)))),,}}||{||,...{,||.,|,((((({(((((((((((...))))))....((({.....}.))).)))))))))).}.}))}})))).,},,||||,|||(((({((((((((((((((((..((((.(((((....,.((((((.{.(,...}},))))))|{.,...((((((({((.,{{(,,......,}}.,..})}...)))..))))))).,},....(((((.....)))))))))).))))....))))))))((((....))))(((((........)))))((((((.((((((((({.((((((((,.{({(((((((.((((((((((((.((((((((((((.{......,.)))))))))))))))))),,{(({.{{.....)}.})},)))))).))))))))),..(((((......})))).))))))))...{,,,,,..((((...})))(((((((......)))))))..,{{{{{{{.,({{{{{{{..,,.({{.,((...{||({.,,,,,,,,..,,,||||}.....}}..})),}}},..|||.,||||||||(((((((({....,)))))))|{.{((((......)))))||,,|}||||||||||,.....,,,,..))))))}})))))},....,,}}|||((((((((({.........}}},..,))))),.,,,))))))))},).))))))..))))))))..)))))})}))}}.}}}},},{,,...,.....|{{{{,,,{||,,,,.................(((((.((..((((((.......))))))..)).)))))..(((((((((((.....)))))))))))))))))))))........}}..,,,,..........,||||,}}}})))),.

Transcripts

ID Sequence Length GC content
NM_001145459.2 NCBI
AGAAGGCCGCCUACCGGGGAGGCCGGAGGCCGGCUAGUCGCGGACUCGG… 1174 nt 0.4668
NM_001145460.2 NCBI
GCUUCCAAACCCAGGGCUUGCGCUUGCCUUUGCCUCUUCCACACUAAUG… 1253 nt 0.4477
NM_032495.6 NCBI
GCUUCCAAACCCAGGGCUUGCGCUUGCCUUUGCCUCUUCCACACUAAUG… 1123 nt 0.4417
NM_139211.5 NCBI
AGAAGGCCGCCUACCGGGGAGGCCGGAGGCCGGCUAGUCGCGGACUCGG… 1130 nt 0.4584
NM_139212.4 NCBI
GCUUCCAAACCCAGGGCUUGCGCUUGCCUUUGCCUCUUCCACCGCGCAG… 998 nt 0.4349
Summary

The protein encoded by this gene is a homeodomain protein that lacks certain conserved residues required for DNA binding. It was reported that choriocarcinoma cell lines and tissues failed to express this gene, which suggested the possible involvement of this gene in malignant conversion of placental trophoblasts. Studies in mice suggest that this protein may interact with serum response factor (SRF) and modulate SRF-dependent cardiac-specific gene expression and cardiac development. Multiple alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Feb 2009]

Forensic Context

A study in Sprague Dawley rats demonstrated that the HOPX transcript in brain tissue is a potential marker for early postmortem interval estimation, showing a high coefficient of determination (>80%) and low error (<3 h) in verification experiments where its expression remained nearly unchanged at low temperatures but was strongly correlated with PMI at higher temperatures [Wang et al. DOI:10.1016/j.legalmed.2019.04.008].