robo3 roundabout, axon guidance receptor, homolog 3 (Drosophila) [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: robo3provided by ZNC
Official Full Name: roundabout, axon guidance receptor, homolog 3 (Drosophila)provided by ZNC
Primary source: ZFIN:ZDB-GENE-000209-4
See related: Ensembl:ENSDARG00000005645 AllianceGenome:ZFIN:ZDB-GENE-000209-4
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: cb503
Summary: Predicted to enable cell-cell adhesion mediator activity. Acts upstream of or within axonogenesis and determination of ventral identity. Located in plasma membrane. Is expressed in several structures, including EVL; digestive system; fin; nervous system; and neural tube. Orthologous to human ROBO3 (roundabout guidance receptor 3). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 10

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	10	NC_007121.7 (31300589..31563079, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	10	NC_007121.6 (31414249..31619883, complement)

Chromosome 10 - NC_007121.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

In the absence of Sim1a and Arnt2, expression of robo3 splice isoform robo3a.1 is increased in the hypothalamus, indicating negative control of robo3a.1 transcription by these factors.
Title: Sim1a and Arnt2 contribute to hypothalamo-spinal axon guidance by regulating Robo2 activity via a Robo3-dependent mechanism.
Slit-Robo signaling downregulates N-cadherin activity to allow apical retraction in newly generated retinal ganglion cells.
Title: Slit1b-Robo3 signaling and N-cadherin regulate apical process retraction in developing retinal ganglion cells.
The Mauthner neurons are essential for the startle response, and in twitch twice/robo3 mutants misguidance of the Mauthner axons results in a unidirectional startle response.
Title: Unidirectional startle responses and disrupted left-right co-ordination of motor behaviors in robo3 mutant zebrafish.
These results demonstrate a key role for Robo-Slit signaling in vertebrate longitudinal axon guidance; Robo1 and Robo3 restricted the extent of defasciculation of the tract of the postoptic commissure.
Title: Robo-Slit interactions regulate longitudinal axon pathfinding in the embryonic vertebrate brain.

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General gene information

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Markers

AI558309 (e-PCR)
- UniSTS:206262

fb78e10.x1 (e-PCR)
- UniSTS:191432

fb78e10.x1 (e-PCR)
- UniSTS:191433

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables axon guidance receptor activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within Roundabout signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within axon extension	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within axon guidance	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within axon guidance	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within axon midline choice point recognition	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within axon midline choice point recognition	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within commissural neuron axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within determination of ventral identity	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: roundabout homolog 3

Names: roundabout (axon guidance receptor, Drosophila) homolog 3; twi; twitch twice

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001328416.1 → NP_001315345.1 roundabout homolog 3 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1). The encoded isoform (1) lacks a predicted signal peptide compared to isoform 2.

Source sequence(s)

AL845320, BX571852

UniProtKB/TrEMBL

A0A8M1P948, F1QFK4

Related

ENSDARP00000027377.8, ENSDART00000023575.9

Conserved Domains (7) summary

cd05725
Location:274 → 342

Ig3_Robo; Third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors

cd07693
Location:62 → 161

Ig1_Robo; First immunoglobulin (Ig)-like domain in Robo (roundabout) receptors and similar proteins

smart00408
Location:463 → 524

IGc2; Immunoglobulin C-2 Type

smart00410
Location:456 → 537

IG_like; Immunoglobulin like

cd00063
Location:555 → 649

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam07679
Location:257 → 342

I-set; Immunoglobulin I-set domain

cl11960
Location:360 → 449

Ig; Immunoglobulin domain
NM_131482.3 → NP_571557.2 roundabout homolog 3 isoform 2 precursor

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, uses an alternate translation start site, and uses an alternate splice site in the 3' coding region compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus compared to isoform 1.

Source sequence(s)

AL845320

UniProtKB/TrEMBL

A8DZ85, B3DK49

Related

ENSDARP00000003540.7, ENSDART00000024778.9

Conserved Domains (7) summary

cd05725
Location:243 → 311

Ig3_Robo; Third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors

cd07693
Location:31 → 130

Ig1_Robo; First immunoglobulin (Ig)-like domain in Robo (roundabout) receptors and similar proteins

smart00408
Location:432 → 493

IGc2; Immunoglobulin C-2 Type

smart00410
Location:425 → 506

IG_like; Immunoglobulin like

cd00063
Location:524 → 618

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam07679
Location:226 → 311

I-set; Immunoglobulin I-set domain

cl11960
Location:329 → 418

Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

NC_007121.7 Reference GRCz11 Primary Assembly

Range

31300589..31563079 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005172638.5 → XP_005172695.1 roundabout homolog 3 isoform X3

UniProtKB/TrEMBL

A0A2R8QRK0, A0A8M2BJW1

Related

ENSDARP00000157596.1, ENSDART00000186456.1

Conserved Domains (7) summary

cd05725
Location:274 → 342

Ig3_Robo; Third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors

cd07693
Location:62 → 161

Ig1_Robo; First immunoglobulin (Ig)-like domain in Robo (roundabout) receptors and similar proteins

smart00408
Location:463 → 524

IGc2; Immunoglobulin C-2 Type

smart00410
Location:456 → 537

IG_like; Immunoglobulin like

cd00063
Location:555 → 649

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam07679
Location:257 → 342

I-set; Immunoglobulin I-set domain

cl11960
Location:360 → 449

Ig; Immunoglobulin domain
XM_005172637.5 → XP_005172694.1 roundabout homolog 3 isoform X2

UniProtKB/TrEMBL

A0A8M2BKE7

Conserved Domains (7) summary

cd05725
Location:274 → 342

Ig3_Robo; Third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors

cd07693
Location:62 → 161

Ig1_Robo; First immunoglobulin (Ig)-like domain in Robo (roundabout) receptors and similar proteins

smart00408
Location:467 → 528

IGc2; Immunoglobulin C-2 Type

smart00410
Location:460 → 541

IG_like; Immunoglobulin like

cd00063
Location:559 → 653

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam07679
Location:257 → 342

I-set; Immunoglobulin I-set domain

cl11960
Location:364 → 453

Ig; Immunoglobulin domain
XM_005172636.5 → XP_005172693.1 roundabout homolog 3 isoform X1

UniProtKB/TrEMBL

A0A8M2BJU1

Conserved Domains (7) summary

cd05725
Location:274 → 342

Ig3_Robo; Third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors

cd07693
Location:62 → 161

Ig1_Robo; First immunoglobulin (Ig)-like domain in Robo (roundabout) receptors and similar proteins

smart00408
Location:467 → 528

IGc2; Immunoglobulin C-2 Type

smart00410
Location:460 → 541

IG_like; Immunoglobulin like

cd00063
Location:559 → 653

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam07679
Location:257 → 342

I-set; Immunoglobulin I-set domain

cl11960
Location:364 → 453

Ig; Immunoglobulin domain
XM_017357931.3 → XP_017213420.1 roundabout homolog 3 isoform X4

UniProtKB/TrEMBL

A0A8M6Z192