Details for: RORB

Gene ID: 6096

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: RORB

Ensembl ID: ENSG00000198963

Description: RAR related orphan receptor B

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • retina horizontal cell CL0000745
    CSI 45.48
    rCSI 69.32%
    PRS 90.13
  • L4 intratelencephalic projecting glutamatergic neuron CL4030063
    CSI 27.01
    rCSI 64.6%
    PRS 84.42
  • Mueller cell CL0000636
    CSI 21.92
    rCSI 50.02%
    PRS 87.5
  • ON-bipolar cell CL0000749
    CSI 21.81
    rCSI 32.42%
    PRS 91.64
  • retinal bipolar neuron CL0000748
    CSI 20.82
    rCSI 38.99%
    PRS 86.01
  • L2/3-6 intratelencephalic projecting glutamatergic neuron CL4023040
    CSI 20.66
    rCSI 50.21%
    PRS 80.25
  • astrocyte of the cerebral cortex CL0002605
    CSI 20.45
    rCSI 45.85%
    PRS 82.61
  • amacrine cell CL0000561
    CSI 20.35
    rCSI 58.98%
    PRS 85.88
  • glycinergic amacrine cell CL4030028
    CSI 19.06
    rCSI 49.64%
    PRS 87.95
  • H1 horizontal cell CL0004217
    CSI 17.86
    rCSI 70.73%
    PRS 87.84
  • neuroblast (sensu Vertebrata) CL0000031
    CSI 16.22
    rCSI 20.82%
    PRS 89.76
  • retinal ganglion cell CL0000740
    CSI 15.75
    rCSI 34.79%
    PRS 84.23
  • GABAergic amacrine cell CL4030027
    CSI 15.49
    rCSI 53.07%
    PRS 82.04
  • neuroblast (sensu Nematoda and Protostomia) CL0000338
    CSI 14.76
    rCSI 17.05%
    PRS 86.33
  • L2/3 intratelencephalic projecting glutamatergic neuron CL4030059
    CSI 14.69
    rCSI 31.87%
    PRS 83.45
  • H2 horizontal cell CL0004218
    CSI 14.05
    rCSI 69.83%
    PRS 88.38
  • retinal pigment epithelial cell CL0002586
    CSI 13.86
    rCSI 27.51%
    PRS 90.08
  • diffuse bipolar 6 cell CL4033032
    CSI 11.13
    rCSI 58.52%
    PRS 84.24
  • rod bipolar cell CL0000751
    CSI 10.84
    rCSI 19.48%
    PRS 88.81
  • adipocyte CL0000136
    CSI 10.81
    rCSI 13.87%
    PRS 86.06
  • glutamatergic neuron CL0000679
    CSI 10.78
    rCSI 22.16%
    PRS 82.88
  • retinal rod cell CL0000604
    CSI 10.66
    rCSI 18.79%
    PRS 89.51
  • neural cell CL0002319
    CSI 10.26
    rCSI 38.7%
    PRS 80.67
  • glioblast CL0000030
    CSI 9.36
    rCSI 14.93%
    PRS 86.56
  • retinal cone cell CL0000573
    CSI 9.25
    rCSI 14.89%
    PRS 86.2
  • Bergmann glial cell CL0000644
    CSI 9.1
    rCSI 12.45%
    PRS 86.76
  • invaginating midget bipolar cell CL4033034
    CSI 8.47
    rCSI 50.04%
    PRS 85.46
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 8.19
    rCSI 14.46%
    PRS 81.71
  • cerebral cortex neuron CL0010012
    CSI 8.15
    rCSI 33.23%
    PRS 86.88
  • diffuse bipolar 1 cell CL4033027
    CSI 7.76
    rCSI 58.36%
    PRS 83.5
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 7.72
    rCSI 9.61%
    PRS 80.23
  • neural crest cell CL0011012
    CSI 7.54
    rCSI 5.96%
    PRS 87.29
  • OFF-bipolar cell CL0000750
    CSI 7.08
    rCSI 9.67%
    PRS 91.04
  • regular ventricular cardiac myocyte CL0002131
    CSI 6.55
    rCSI 40.9%
    PRS 87.52
  • pancreatic D cell CL0000173
    CSI 6.5
    rCSI 6.39%
    PRS 94.1
  • vascular leptomeningeal cell CL4023051
    CSI 6.33
    rCSI 11.1%
    PRS 90.33
  • mature astrocyte CL0002627
    CSI 6.25
    rCSI 26.54%
    PRS 87.2
  • VIP GABAergic cortical interneuron CL4023016
    CSI 6.15
    rCSI 7.34%
    PRS 82.43
  • glial cell CL0000125
    CSI 6.03
    rCSI 22.96%
    PRS 87.49
  • forebrain radial glial cell CL0013000
    CSI 5.84
    rCSI 18.74%
    PRS 92.64
  • myofibroblast cell CL0000186
    CSI 5.39
    rCSI 7.46%
    PRS 90.23
  • midbrain dopaminergic neuron CL2000097
    CSI 4.84
    rCSI 31.03%
    PRS 87.47
  • dopaminergic neuron CL0000700
    CSI 4.62
    rCSI 26.13%
    PRS 83.93
  • cardiac muscle cell CL0000746
    CSI 4.62
    rCSI 6.63%
    PRS 85.98
  • sncg GABAergic cortical interneuron CL4023015
    CSI 4.54
    rCSI 7.3%
    PRS 83.37
  • eye photoreceptor cell CL0000287
    CSI 4.51
    rCSI 50.79%
    PRS 94.19
  • diffuse bipolar 4 cell CL4033031
    CSI 4.39
    rCSI 50.23%
    PRS 82.24
  • GABAergic neuron CL0000617
    CSI 4.27
    rCSI 14.32%
    PRS 81.57
  • enteroglial cell CL4040002
    CSI 4.17
    rCSI 21.92%
    PRS 93.13
  • sst GABAergic cortical interneuron CL4023017
    CSI 4.16
    rCSI 5.36%
    PRS 83.41
  • serotonergic neuron CL0000850
    CSI 4.11
    rCSI 18.38%
    PRS 80.4
  • macroglial cell CL0000126
    CSI 4
    rCSI 10.3%
    PRS 89.67
  • cerebral cortex pyramidal neuron CL4023111
    CSI 3.83
    rCSI 23.6%
    PRS 93.12
  • lamp5 GABAergic cortical interneuron CL4023011
    CSI 3.79
    rCSI 6.37%
    PRS 82.41
  • keratocyte CL0002363
    CSI 3.71
    rCSI 8.91%
    PRS 93.54
  • OFFx cell CL4033036
    CSI 2.7
    rCSI 12.69%
    PRS 84.46
  • OFF midget ganglion cell CL4033047
    CSI 2.6
    rCSI 53.01%
    PRS 86.35
  • regular atrial cardiac myocyte CL0002129
    CSI 2.51
    rCSI 8.08%
    PRS 89.81
  • ON midget ganglion cell CL4033046
    CSI 2.49
    rCSI 50.73%
    PRS 85.69
  • stromal cell CL0000499
    CSI 2.41
    rCSI 6.78%
    PRS 89.65
  • L5/6 near-projecting glutamatergic neuron CL4030067
    CSI 2.32
    rCSI 7.63%
    PRS 83.25
  • cone retinal bipolar cell CL0000752
    CSI 2.24
    rCSI 29.19%
    PRS 89.26
  • starburst amacrine cell CL0004232
    CSI 2.13
    rCSI 17.96%
    PRS 81.18
  • ON parasol ganglion cell CL4033052
    CSI 1.56
    rCSI 22.16%
    PRS 86.57
  • flat midget bipolar cell CL4033033
    CSI 1.37
    rCSI 9.76%
    PRS 84.82
  • S cone cell CL0003050
    CSI 1.36
    rCSI 5.95%
    PRS 89.73
  • L5 extratelencephalic projecting glutamatergic cortical neuron CL4023041
    CSI 1
    rCSI 3.59%
    PRS 80.52
  • diffuse bipolar 2 cell CL4033028
    CSI 0.77
    rCSI 5.99%
    PRS 86.44
  • diffuse bipolar 3a cell CL4033029
    CSI 0.68
    rCSI 4.6%
    PRS 85.89
  • diffuse bipolar 3b cell CL4033030
    CSI 0.64
    rCSI 4.26%
    PRS 87.88
  • GABAergic interneuron CL0011005
    CSI 0.56
    rCSI 8.88%
    PRS 93.36

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
Network Configuration

Explore relationships of the current gene. Select an Interaction Source: 'ONTOLOGY' for shared pathways (GO/Reactome) or 'STRING' for protein-protein interactions. Further refine by selecting context genes and comparing Cell Significance Index (CSI) scores between baseline and target cell types and their specific contexts.

Comma-separated if multiple.
Comma-separated if multiple.
Legend:
  • Query Gene
  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
    • Low
    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

Loading network (please wait)...

Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [RORB](/details-gene/6096) (RAR related orphan receptor B) is a protein-coding gene located on chromosome 9q21.13 that encodes a nuclear receptor transcription factor. This protein plays a crucial role in neurodevelopment, particularly in the retina and cerebral cortex. Functional annotations indicate its involvement in processes such as retinal cell differentiation, regulation of circadian rhythm, and both positive and negative control of DNA-templated transcription. Expression data reveals that [RORB](/details-gene/6096) is a highly specific marker for several neuronal subtypes, most notably [retina horizontal cells](/details-cell/CL0000745) and layer 4 glutamatergic neurons of the neocortex, underscoring its importance in the development and function of the visual and somatosensory systems. A clinical association for this gene is noted in OMIM ([601972](https://omim.org/entry/601972)). ## Cellular Roles and Expression Landscape **Overall**, the expression profile of [RORB](/details-gene/6096) demonstrates a highly specialized role within the central nervous system, with a striking concentration in specific cell types of the retina and cerebral cortex. The gene exhibits its highest significance in the retina, where it is the top marker for [retina horizontal cells](/details-cell/CL0000745) (CSI: 45.48). It also shows prominent expression in other retinal interneurons and glia, including [Mueller cells](/details-cell/CL0000636), [ON-bipolar cells](/details-cell/CL0000749), [retinal bipolar neurons](/details-cell/CL0000748), and various types of [amacrine cells](/details-cell/CL0000561). This pattern strongly suggests a fundamental role for [RORB](/details-gene/6096) in the development, lamination, and signal processing functions of the inner nuclear and plexiform layers of the retina. In the cerebral cortex, [RORB](/details-gene/6096) is a key identifier for specific excitatory neuron populations. It shows very high significance in [L4 intratelencephalic projecting glutamatergic neurons](/details-cell/CL4030063) (CSI: 27.01) and is also significantly expressed in [L2/3-6](/details-cell/CL4023040) and [L2/3 intratelencephalic projecting glutamatergic neurons](/details-cell/CL4030059). This specific expression in layer 4, the primary recipient layer for thalamocortical sensory inputs, positions [RORB](/details-gene/6096) as a critical factor in establishing the architecture and function of sensory processing circuits in the cortex. ## Pathways and Molecular Function Functionally, [RORB](/details-gene/6096) is a nuclear transcription factor, consistent with its localization to the [nucleus](/details-cell/GO:0005634) and its annotated molecular functions, which include [DNA-binding transcription factor activity](/details-cell/GO:0003700) and [nuclear receptor activity](/details-cell/GO:0004879). The Reactome database places it within the [Nuclear receptor transcription pathway](/details-cell/R-HSA-383280) and more broadly in [Gene expression (transcription)](/details-cell/R-HSA-74160). Its biological roles are tightly aligned with its cellular expression pattern. Gene Ontology annotations highlight its critical involvement in retinal development, including [eye photoreceptor cell development](/details-cell/GO:0042462), [retinal cone cell development](/details-cell/GO:0046549), [retinal rod cell development](/details-cell/GO:0046548), and [amacrine cell differentiation](/details-cell/GO:0035881). Furthermore, its role in the [regulation of circadian rhythm](/details-cell/GO:0042752) is particularly relevant given its high expression in the retina, an organ that provides primary light input to the central circadian clock. As a transcription factor, it can exert both [positive](/details-cell/GO:0045893) and [negative regulation of DNA-templated transcription](/details-cell/GO:0045892), suggesting it can act as a molecular switch to fine-tune gene expression programs during neuronal differentiation and function. ## Research Directions The highly specific expression pattern of [RORB](/details-gene/6096) in distinct neuronal subtypes, coupled with its function as a transcription factor, presents several avenues for future investigation. **Testable Hypotheses:** 1. Given its high and specific expression in [L4 intratelencephalic projecting glutamatergic neurons](/details-cell/CL4030063), [RORB](/details-gene/6096) is likely a master regulator required for the specification and functional maturation of these neurons. Its loss would be hypothesized to disrupt the formation of layer 4 and impair the processing of thalamocortical sensory information. 2. The dual role of [RORB](/details-gene/6096) in retinal development and circadian rhythm regulation ([GO:0042752](https://www.ebi.ac.uk/QuickGO/term/GO:0042752)) suggests it may integrate light-dependent signals with the intrinsic molecular clock within retinal cells. It could be hypothesized that [RORB](/details-gene/6096) transcriptionally regulates key clock components or output genes in retinal neurons, thereby tuning their daily physiological rhythms. **Proposed Experimental Approach:** To test the first hypothesis regarding the role of [RORB](/details-gene/6096) in layer 4 cortical neuron identity, a conditional knockout mouse model could be employed. Using a Cre-Lox system with a Cre driver specific to layer 4 progenitors or early postmitotic neurons, *Rorb* could be selectively deleted. The resulting phenotype could be assessed using a combination of techniques: immunohistochemistry to analyze cortical lamination and cell-type marker expression, single-cell RNA sequencing to define transcriptomic changes and cell fate specification errors, and in vivo electrophysiology or calcium imaging to measure functional deficits in sensory-evoked responses within the primary somatosensory or visual cortex. **Therapeutic Potential:** As a nuclear transcription factor, [RORB](/details-gene/6096) is a challenging therapeutic target for traditional small molecule inhibitors. However, its high cell-type specificity presents an opportunity for targeted therapies for neurodevelopmental disorders or retinal diseases linked to its dysregulation. Therapeutic strategies would likely focus on modulating its expression levels rather than inhibiting its function directly. For instance, antisense oligonucleotides or gene therapy approaches could be explored to correct either loss-of-function or gain-of-function mutations associated with a specific pathology. Such interventions would require careful consideration due to the gene's critical role in the development of the central nervous system.

Genular Protein ID: 142935994

Symbol: Q58EY0_HUMAN

Name: N/A

UniProtKB Accession Codes:

Q58EY0

Database IDs:

ARBA 10 AlphaFoldDB 1 Antibodypedia 1 BindingDB 1 BioGRID-ORCS 1 CDD 2 CTD 1 ChiTaRS 1 DNASU 1 DisGeNET 1 EMBL 13 ExpressionAtlas 1 GO 9 Gene3D 2 HOGENOM 1 IntAct 1 InterPro 7 NCBI Taxonomy 1 OrthoDB 1 PANTHER 2 PRINTS 3 PROSITE 5 Pfam 2 PharmGKB 1 RefSeq 1 RuleBase 1 SAM 1 SMART 2 SMR 1 SUPFAM 2 VEuPathDB 1

Citations:

PubMed ID: 11181995

Title: The sequence of the human genome.

PubMed ID: 11181995

DOI: 10.1126/science.1058040

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

Sequence Information:

  • Length: 459
  • Mass: 52073
  • Checksum: E15FD91422CCD67C
  • Sequence:
    • MRAQIEVIPC KICGDKSSGI HYGVITCEGC KGFFRRSQQN NASYSCPRQR NCLIDRTNRN 
RCQHCRLQKC LALGMSRDAV KFGRMSKKQR DSLYAEVQKH QQRLQEQRQQ QSGEAEALAR 
VYSSSISNGL SNLNNETSGT YANGHVIDLP KSEGYYNVDS GQPSPDQSGL DMTGIKQIKQ 
EPIYDLTSVP NLFTYSSFNN GQLAPGITMT EIDRIAQNII KSHLETCQYT MEELHQLAWQ 
THTYEEIKAY QSKSREALWQ QCAIQITHAI QYVVEFAKRI TGFMELCQND QILLLKSGCL 
EVVLVRMCRA FNPLNNTVLF EGKYGGMQMF KALGSDDLVN EAFDFAKNLC SLQLTEEEIA 
LFSSAVLISP DRAWLIEPRK VQKLQEKIYF ALQHVIQKNH LDDETLAKLI AKIPTITAVC 
NLHGEKLQVF KQSHPEIVNT LFPPLYKELF NPDCATGCK