thbs1b thrombospondin 1b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: thbs1bprovided by ZNC
Official Full Name: thrombospondin 1bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-020708-1
See related: Ensembl:ENSDARG00000010785 AllianceGenome:ZFIN:ZDB-GENE-020708-1
Gene type: protein coding
RefSeq status: MODEL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: Tsp-1; thbs1; wu:fc48c03; si:dkey-11e23.1
Summary: Predicted to enable calcium ion binding activity and heparin binding activity. Predicted to be involved in negative regulation of angiogenesis. Predicted to act upstream of or within cell adhesion. Predicted to be located in extracellular region. Predicted to be active in collagen-containing extracellular matrix. Is expressed in several structures, including axial vasculature; head mesenchyme; nervous system; pectoral fin; and somite. Human ortholog(s) of this gene implicated in cholangiocarcinoma; pancreatic cancer; pancreatic ductal carcinoma; and primary open angle glaucoma. Orthologous to human THBS1 (thrombospondin 1). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 20

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	20	NC_007131.7 (29038562..29051694, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	20	NC_007131.6 (29134741..29148827, complement)

Chromosome 20 - NC_007131.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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?

ELL (Eleven-Nineteen Lysine-rich Leukemia) acts as a transcription factor for direct thrombospondin-1 regulation
Title: Elongation factor ELL (Eleven-Nineteen Lysine-rich Leukemia) acts as a transcription factor for direct thrombospondin-1 regulation.

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General gene information

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Markers

fc48c03 (e-PCR), detects polymorphism
- UniSTS:189227

fk36g02.y1 (e-PCR)
- UniSTS:200914

Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables heparin binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of angiogenesis	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: thrombospondin-1

Names: thrombospondin 1

NCBI Reference Sequences (RefSeq)

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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_007131.7 Reference GRCz11 Primary Assembly

Range

29038562..29051694 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_685303.10 → XP_690395.4 thrombospondin-1 isoform X2

UniProtKB/TrEMBL

A0A8N7TB12, F1QEE7

Related

ENSDARP00000012255.8, ENSDART00000017090.10

Conserved Domains (9) summary

smart00209
Location:495 → 547

TSP1; Thrombospondin type 1 repeats

sd00001
Location:763 → 785

TSP3; TSP3 repeat_short [structural motif]

sd00002
Location:787 → 821

TSP3; TSP3 repeat_long [structural motif]

sd00003
Location:691 → 726

TSP3_1C; TSP3 repeat_1C [structural motif]

pfam00093
Location:317 → 371

VWC; von Willebrand factor type C domain

pfam02412
Location:846 → 882

TSP_3; Thrombospondin type 3 repeat

pfam05735
Location:972 → 1169

TSP_C; Thrombospondin C-terminal region

pfam12947
Location:650 → 689

EGF_3; EGF domain

cl22861
Location:25 → 220

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
XM_005160762.5 → XP_005160819.1 thrombospondin-1 isoform X1

UniProtKB/TrEMBL

A0A8M2B7Q1, F1QL35

Related

ENSDARP00000120705.2, ENSDART00000140350.3

Conserved Domains (9) summary

smart00209
Location:496 → 548

TSP1; Thrombospondin type 1 repeats

sd00001
Location:764 → 786

TSP3; TSP3 repeat_short [structural motif]

sd00002
Location:788 → 822

TSP3; TSP3 repeat_long [structural motif]

sd00003
Location:692 → 727

TSP3_1C; TSP3 repeat_1C [structural motif]

pfam00093
Location:318 → 372

VWC; von Willebrand factor type C domain

pfam02412
Location:847 → 883

TSP_3; Thrombospondin type 3 repeat

pfam05735
Location:973 → 1170

TSP_C; Thrombospondin C-terminal region

pfam12947
Location:651 → 690

EGF_3; EGF domain

cl22861
Location:25 → 220

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...