matrix metalloproteinase

Overview
Namematrix metalloproteinase (CCM73860.1)
Smed IDSMED30026322
Length (bp)916
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 



 

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




 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of matrix metalloproteinase (SMED30026322) t-SNE clustered cells

Violin plots show distribution of expression levels for matrix metalloproteinase (SMED30026322) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of matrix metalloproteinase (SMED30026322) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for matrix metalloproteinase (SMED30026322) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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

 

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Anatomical Expression

PAGE et. al., 2020




SMED30026322

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
cephalic gangliaSMED30026322SMESG000049445.1 dd_Smed_v4_2972_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30026322SMESG000049445.1 dd_Smed_v4_2972_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
anterior sideSMED30026322SMESG000049445.1 dd_Smed_v4_2972_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026322SMESG000049445.1 Contig48552uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026322SMESG000049445.1 Contig48552newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026322SMESG000049445.1 Contig6240uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026322SMESG000049445.1 Contig6240newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
muscle cellSMED30026322SMESG000049445.1 dd_Smed_v4_2972_0_1dd_Smed_v4PMID:30962434
Cote et al., 2019
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30026322SMESG000049445.1 HE998773.1smed_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 matrix metalloproteinase vs. TrEMBL
Match: A0A090C5X6 (Matrix metalloproteinase OS=Schmidtea mediterranea OX=79327 GN=mmpb PE=2 SV=1)

HSP 1 Score: 340.117 bits (871), Expect = 1.965e-109
Identity = 193/201 (96.02%), Postives = 195/201 (97.01%), Query Frame = 2
Query:  143 TNNLMFQSTGKDGDFYLVIKNEHSQWVYRNSNSSSLIKKDWPYKFDLFFKRLEMKTTPNIDAILYSTLVRKFLIFSGTKLFSFDEFGYFIRQDETGKDVSYAFNSEKSPIVVTKDNSAWQFDPRTNEFKSSQPISSIFPGXXXXXXXXXXXXPWPQEIEYIYFFKGREXXXXXXXXXXXXXTGNFGDSFFGCRQYPVPKFK 745
            +  L+    GKDGDFYLVIKNEHSQWVYRNSNSSSLIKKDWPYKFDLFFKRLEMKTTPNIDAILYSTLVRKFLIFSGTKLFSFDEFGYFIRQDETGKDVSYAFNSEKSPIVVTKDNSAWQFDPRTNEFKSSQPISSIFPGIASDIDAAAEDDPWPQEIEYIYFFKGREYYKYQVKKKQIVKTGNFGDSFFGCRQYPVPKFK
Sbjct:  428 STKLLSAFMGKDGDFYLVIKNEHSQWVYRNSNSSSLIKKDWPYKFDLFFKRLEMKTTPNIDAILYSTLVRKFLIFSGTKLFSFDEFGYFIRQDETGKDVSYAFNSEKSPIVVTKDNSAWQFDPRTNEFKSSQPISSIFPGIASDIDAAAEDDPWPQEIEYIYFFKGREYYKYQVKKKQIVKTGNFGDSFFGCRQYPVPKFK 628          
BLAST of matrix metalloproteinase vs. Planmine SMEST
Match: SMESG000049445.1 (SMESG000049445.1)

HSP 1 Score: 340.117 bits (871), Expect = 1.645e-113
Identity = 193/201 (96.02%), Postives = 195/201 (97.01%), Query Frame = 2
Query:  143 TNNLMFQSTGKDGDFYLVIKNEHSQWVYRNSNSSSLIKKDWPYKFDLFFKRLEMKTTPNIDAILYSTLVRKFLIFSGTKLFSFDEFGYFIRQDETGKDVSYAFNSEKSPIVVTKDNSAWQFDPRTNEFKSSQPISSIFPGXXXXXXXXXXXXPWPQEIEYIYFFKGREXXXXXXXXXXXXXTGNFGDSFFGCRQYPVPKFK 745
            +  L+    GKDGDFYLVIKNEHSQWVYRNSNSSSLIKKDWPYKFDLFFKRLEMKTTPNIDAILYSTLVRKFLIFSGTKLFSFDEFGYFIRQDETGKDVSYAFNSEKSPIVVTKDNSAWQFDPRTNEFKSSQPISSIFPGIASDIDAAAEDDPWPQEIEYIYFFKGREYYKYQVKKKQIVKTGNFGDSFFGCRQYPVPKFK
Sbjct:  379 STKLLSAFMGKDGDFYLVIKNEHSQWVYRNSNSSSLIKKDWPYKFDLFFKRLEMKTTPNIDAILYSTLVRKFLIFSGTKLFSFDEFGYFIRQDETGKDVSYAFNSEKSPIVVTKDNSAWQFDPRTNEFKSSQPISSIFPGIASDIDAAAEDDPWPQEIEYIYFFKGREYYKYQVKKKQIVKTGNFGDSFFGCRQYPVPKFK 579          
BLAST of matrix metalloproteinase vs. Planmine SMEST
Match: SMESG000049445.1 (SMESG000049445.1)

HSP 1 Score: 340.117 bits (871), Expect = 5.087e-113
Identity = 193/201 (96.02%), Postives = 195/201 (97.01%), Query Frame = 2
Query:  143 TNNLMFQSTGKDGDFYLVIKNEHSQWVYRNSNSSSLIKKDWPYKFDLFFKRLEMKTTPNIDAILYSTLVRKFLIFSGTKLFSFDEFGYFIRQDETGKDVSYAFNSEKSPIVVTKDNSAWQFDPRTNEFKSSQPISSIFPGXXXXXXXXXXXXPWPQEIEYIYFFKGREXXXXXXXXXXXXXTGNFGDSFFGCRQYPVPKFK 745
            +  L+    GKDGDFYLVIKNEHSQWVYRNSNSSSLIKKDWPYKFDLFFKRLEMKTTPNIDAILYSTLVRKFLIFSGTKLFSFDEFGYFIRQDETGKDVSYAFNSEKSPIVVTKDNSAWQFDPRTNEFKSSQPISSIFPGIASDIDAAAEDDPWPQEIEYIYFFKGREYYKYQVKKKQIVKTGNFGDSFFGCRQYPVPKFK
Sbjct:  417 STKLLSAFMGKDGDFYLVIKNEHSQWVYRNSNSSSLIKKDWPYKFDLFFKRLEMKTTPNIDAILYSTLVRKFLIFSGTKLFSFDEFGYFIRQDETGKDVSYAFNSEKSPIVVTKDNSAWQFDPRTNEFKSSQPISSIFPGIASDIDAAAEDDPWPQEIEYIYFFKGREYYKYQVKKKQIVKTGNFGDSFFGCRQYPVPKFK 617          
The following BLAST results are available for this feature:
BLAST of matrix metalloproteinase vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of matrix metalloproteinase vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of matrix metalloproteinase vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of matrix metalloproteinase vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of matrix metalloproteinase vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of matrix metalloproteinase vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of matrix metalloproteinase vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of matrix metalloproteinase vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A090C5X61.965e-10996.02Matrix metalloproteinase OS=Schmidtea mediterranea... [more]
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BLAST of matrix metalloproteinase vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of matrix metalloproteinase vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of matrix metalloproteinase vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of matrix metalloproteinase vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of matrix metalloproteinase vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of matrix metalloproteinase vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000049445.11.645e-11396.02SMESG000049445.1[more]
SMESG000049445.15.087e-11396.02SMESG000049445.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30026322
GenBankCCM73860.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026322 ID=SMED30026322|Name=matrix metalloproteinase|organism=Schmidtea mediterranea sexual|type=transcript|length=916bp
AAACTTTTGAGTGCTTTCATGGGTAAATAATGCTTTTCACCCCGATTACA
TGAAAATTTATTTATAAAAATATTATTATTTATTCGGTCATCACTTTTTT
GTGAGTTGCCGTATTTGATGAATTGAAATGAAAATACAAAAAACCAATAA
CCTTATGTTCCAATCAACAGGAAAGGATGGGGATTTTTATCTGGTCATAA
AGAACGAACATTCACAGTGGGTCTATCGCAATTCGAATTCTTCATCCTTG
ATAAAAAAGGACTGGCCATATAAATTTGATTTATTTTTCAAGAGATTGGA
AATGAAGACGACGCCAAACATCGACGCTATTCTCTACAGTACCTTAGTAA
GGAAATTTTTAATATTTTCTGGAACGAAACTGTTTTCCTTTGACGAATTT
GGTTATTTTATTCGCCAAGACGAAACAGGAAAAGATGTCAGCTACGCCTT
CAATTCAGAGAAGTCACCTATTGTTGTTACAAAGGATAATTCTGCTTGGC
AATTCGATCCGCGCACAAATGAATTTAAATCATCCCAACCAATCAGCAGC
ATCTTTCCCGGAATCGCGTCAGACATCGACGCAGCTGCTGAAGATGACCC
ATGGCCCCAAGAAATAGAATACATTTATTTTTTTAAAGGCAGAGAATACT
ATAAATATCAAGTAAAGAAAAAACAAATAGTTAAAACCGGAAATTTTGGA
GATTCGTTTTTCGGATGTCGACAATATCCGGTTCCAAAATTTAAATAATT
TACGAATGATCATTAAATATCAATATTTGTATCTTGGCATTGAAACATAG
CTTTGAATCATGGCTTTGGTTCCTTTGCACAAATTTATTGAATATTATGC
ATTTTTCATTTATCATTTTCTTTTGCTTTTCTTTGGTCTTGGGTTGAATA
AATTAAAAAAATTGCA
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protein sequence of SMED30026322-orf-1

>SMED30026322-orf-1 ID=SMED30026322-orf-1|Name=SMED30026322-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=207bp
MKIQKTNNLMFQSTGKDGDFYLVIKNEHSQWVYRNSNSSSLIKKDWPYKF
DLFFKRLEMKTTPNIDAILYSTLVRKFLIFSGTKLFSFDEFGYFIRQDET
GKDVSYAFNSEKSPIVVTKDNSAWQFDPRTNEFKSSQPISSIFPGIASDI
DAAAEDDPWPQEIEYIYFFKGREYYKYQVKKKQIVKTGNFGDSFFGCRQY
PVPKFK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0000140anterior region of the whole animal
PLANA:0002142parenchyma
Vocabulary: INTERPRO
TermDefinition
IPR036375Hemopexin-like_dom_sf
IPR018487Hemopexin-like_repeat
IPR000585Hemopexin-like_dom
Vocabulary: molecular function
TermDefinition
GO:0004222metalloendopeptidase activity
GO:0005509calcium ion binding
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
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR018487Hemopexin-like repeatsSMARTSM00120HX_rpt_3coord: 65..112
e-value: 6.8
score: 9.2
coord: 150..197
e-value: 0.002
score: 27.4
IPR018487Hemopexin-like repeatsPFAMPF00045Hemopexincoord: 150..180
e-value: 2.1E-6
score: 27.6
IPR018487Hemopexin-like repeatsPROSITEPS51642HEMOPEXIN_2coord: 147..197
score: 10.806
IPR018487Hemopexin-like repeatsPROSITEPS51642HEMOPEXIN_2coord: 62..104
score: 7.182
IPR036375Hemopexin-like domain superfamilyGENE3DG3DSA:2.110.10.10coord: 8..197
e-value: 3.2E-15
score: 58.5
IPR036375Hemopexin-like domain superfamilySUPERFAMILYSSF50923Hemopexin-like domaincoord: 30..197