Mmp2 protein

Overview
NameMmp2 protein
Smed IDSMED30003191
Length (bp)540
Neoblast Clusters

Zeng et. al., 2018




 



 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)




Explore this single cell expression dataset with our NB Cluster Shiny App




Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

back to top
Anatomical Expression

PAGE et. al., 2020




SMED30003191

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymaSMED30003191SMESG000014326.1 dd_Smed_v4_321_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30003191SMESG000014326.1 dd_Smed_v6_321_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30003191SMESG000014326.1 OX_Smed_1.0.22204ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
dorsal region of the whole animalSMED30003191SMESG000014326.1 HE577119.1smed_ncbi_20200123PMID:23405188
Isolani et al., 2013
whole organism asexual adult colorimetric in situ hybridization evidence
ventral region of the whole animalSMED30003191SMESG000014326.1 HE577119.1smed_ncbi_20200123PMID:23405188
Isolani et al., 2013
whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30003191SMESG000014326.1 HE577119.1smed_ncbi_20200123PMID:23405188
Isolani et al., 2013
whole organism asexual adult colorimetric in situ hybridization evidence
basophilic gland cellSMED30003191SMESG000014326.1 HE577119.1smed_ncbi_20200123PMID:23405188
Isolani et al., 2013
whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Mmp2 protein vs. TrEMBL
Match: K0JBI8 (Mmp2 protein OS=Schmidtea mediterranea OX=79327 GN=mmp2 PE=2 SV=1)

HSP 1 Score: 98.5969 bits (244), Expect = 1.234e-20
Identity = 46/46 (100.00%), Postives = 46/46 (100.00%), Query Frame = 1
Query:    1 STAADIYFGKVSSKQGSMFSLSFADAEHKMYDVHNNFAESRDPYPL 138
            STAADIYFGKVSSKQGSMFSLSFADAEHKMYDVHNNFAESRDPYPL
Sbjct:  130 STAADIYFGKVSSKQGSMFSLSFADAEHKMYDVHNNFAESRDPYPL 175          
BLAST of Mmp2 protein vs. Planmine SMEST
Match: SMESG000014326.1 (SMESG000014326.1)

HSP 1 Score: 98.5969 bits (244), Expect = 3.631e-24
Identity = 46/46 (100.00%), Postives = 46/46 (100.00%), Query Frame = 1
Query:    1 STAADIYFGKVSSKQGSMFSLSFADAEHKMYDVHNNFAESRDPYPL 138
            STAADIYFGKVSSKQGSMFSLSFADAEHKMYDVHNNFAESRDPYPL
Sbjct:  132 STAADIYFGKVSSKQGSMFSLSFADAEHKMYDVHNNFAESRDPYPL 177          
BLAST of Mmp2 protein vs. Planmine SMEST
Match: SMESG000014326.1 (SMESG000014326.1)

HSP 1 Score: 98.2117 bits (243), Expect = 3.703e-24
Identity = 46/46 (100.00%), Postives = 46/46 (100.00%), Query Frame = 1
Query:    1 STAADIYFGKVSSKQGSMFSLSFADAEHKMYDVHNNFAESRDPYPL 138
            STAADIYFGKVSSKQGSMFSLSFADAEHKMYDVHNNFAESRDPYPL
Sbjct:  132 STAADIYFGKVSSKQGSMFSLSFADAEHKMYDVHNNFAESRDPYPL 177          
BLAST of Mmp2 protein vs. Planmine SMEST
Match: SMESG000040772.1 (SMESG000040772.1)

HSP 1 Score: 45.8246 bits (107), Expect = 5.456e-6
Identity = 20/44 (45.45%), Postives = 28/44 (63.64%), Query Frame = 1
Query:    7 AADIYFGKVSSKQGSMFSLSFADAEHKMYDVHNNFAESRDPYPL 138
             +++ F     K G MFS+SF+  +H  YDV+ NF  S+DPYPL
Sbjct:  133 VSNLGFAASRDKAGCMFSVSFSGRDHLQYDVNKNFQPSKDPYPL 176          
The following BLAST results are available for this feature:
BLAST of Mmp2 protein vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Mmp2 protein vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Mmp2 protein vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Mmp2 protein vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Mmp2 protein vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Mmp2 protein vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Mmp2 protein vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Mmp2 protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
K0JBI81.234e-20100.00Mmp2 protein OS=Schmidtea mediterranea OX=79327 GN... [more]
back to top
BLAST of Mmp2 protein vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Mmp2 protein vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Mmp2 protein vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Mmp2 protein vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Mmp2 protein vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of Mmp2 protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000014326.13.631e-24100.00SMESG000014326.1[more]
SMESG000014326.13.703e-24100.00SMESG000014326.1[more]
SMESG000040772.15.456e-645.45SMESG000040772.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003191 ID=SMED30003191|Name=Mmp2 protein|organism=Schmidtea mediterranea sexual|type=transcript|length=540bp
TCAACAGCAGCAGATATATACTTCGGAAAAGTTAGCAGTAAACAAGGATC
TATGTTTTCTTTGAGTTTTGCTGATGCTGAACATAAAATGTACGATGTCC
ACAACAATTTTGCAGAGTCTAGAGATCCATATCCATTGGGATAATGTACC
TGGGAAAATGGTTTNGGCACACGCCTTTTTTTNCCCAAAAAGTGGGAAAT
TTACATTTCCGATTTCAGCTGAAGAAATGGGACTGAAGGGTAAAGAATTG
ATNGGAATTAAATCTTTCGGTGGTAGTTNGCTGGCCCATGAAAATGGGGG
ACACCGCCTAATTNGGGCTTTGGTATTCATAAGTAAATNGATCCCNAAAA
GCCTTAAATGGGCTNCCANNGGNTAATTGGGNGGACTTATNNTTCCTTGA
AAAGTGGATTTTCCGGCCTTTCCCGNACNGACNNATTTCNCNANGGAGGC
AATTTTCTCCTTTATGGGAAAATNNCGAAAAAAATGGGAAAAACGGAATT
CCGTTCCGNAAGTGNANNGANCCAAAACCGANGAACCNNT
back to top

protein sequence of SMED30003191-orf-1

>SMED30003191-orf-1 ID=SMED30003191-orf-1|Name=SMED30003191-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=101bp
MLNIKCTMSTTILQSLEIHIHWDNVPGKMVXAHAFFXPKSGKFTFPISAE
EMGLKGKELXGIKSFGGSXLAHENGGHRLIXALVFISKXIXKSLKWAXXX
*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000141dorsal region of the whole animal
PLANA:0000143ventral region of the whole animal
PLANA:0000418head
PLANA:0000420parapharyngeal region
PLANA:0000488basophilic gland cell
Vocabulary: molecular function
TermDefinition
GO:0004222metalloendopeptidase activity
GO:0008233peptidase activity
GO:0008237metallopeptidase activity
GO:0008270zinc ion binding
GO:0016787hydrolase activity
GO:0046872metal ion binding
Vocabulary: biological process
TermDefinition
GO:0006508proteolysis
Vocabulary: cellular component
TermDefinition
GO:0031012extracellular matrix