Mmp1 protein

Overview
NameMmp1 protein
Smed IDSMED30023225
Length (bp)395
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 Mmp1 protein (SMED30023225) t-SNE clustered cells

Violin plots show distribution of expression levels for Mmp1 protein (SMED30023225) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

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



SMED30023225

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30023225h1SMcG0011380 SmedASXL_019211SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30023225h1SMcG0011380 SmedASXL_019211SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
prepharyngeal regionSMED30023225h1SMcG0011380 SmedASXL_019185SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30023225h1SMcG0011380 SmedASXL_019185SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30023225h1SMcG0011380 Contig36896newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023225h1SMcG0011380 Contig36896uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023225h1SMcG0011379 Contig36896newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023225h1SMcG0011379 Contig36896uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of Mmp1 protein vs. TrEMBL
Match: K0JBS3 (Mmp1 protein OS=Schmidtea mediterranea OX=79327 GN=mmp1 PE=2 SV=1)

HSP 1 Score: 230.72 bits (587), Expect = 2.596e-71
Identity = 106/129 (82.17%), Postives = 118/129 (91.47%), Query Frame = 2 
Query:    2 LKVEEMKIGGHGTYLGKSSAAFAREISTDESMQYFWLIQNNEVISGEILNHKIMFSRRVRPLSEVILMENGVKFPPSIDAALLSGEKDNLKLYLFVGNSYYIGKPNGRKKLKYHISADYPKSYKQLLKC 388
            LKVEEMKIGGHG YLGKSSAAFAR++S +E MQYFWLIQ+NEVISGE+L +KI+FSRR RPLSEVI M NG KFPPSIDAALLSGEKDNL+LYLFVGNSYY+GKP GRK+ +Y ISADYPKSYKQ+LKC
Sbjct:  367 LKVEEMKIGGHGAYLGKSSAAFARQVSAEEGMQYFWLIQDNEVISGEVLKNKIVFSRRTRPLSEVITMSNGAKFPPSIDAALLSGEKDNLQLYLFVGNSYYVGKPTGRKQFQYSISADYPKSYKQVLKC 495
[Close]
BLAST of Mmp1 protein vs. TrEMBL
Match: K0JBI8 (Mmp2 protein OS=Schmidtea mediterranea OX=79327 GN=mmp2 PE=2 SV=1)

HSP 1 Score: 121.324 bits (303), Expect = 1.332e-29
Identity = 55/129 (42.64%), Postives = 84/129 (65.12%), Query Frame = 2 
Query:    2 LKVEEMKIGGHGTYLGKSSAAFAREISTDESMQYFWLIQNNEVISGEILNHKIMFSRRVRPLSEVILMENGVKFPPSIDAALLSGEKDNLKLYLFVGNSYYIGKPNGRKKLKYHISADYPKSYKQLLKC 388
            + + E+ I   G + G+ +AAF R+ +   +   FW +Q+ E+I+G +  +++ FSRR   LSE++ M  G K   +ID A + G+KDN +L LFVGNS Y+G PNGRK +KY I A YPK++KQ++ C
Sbjct:  374 MALSELNITRFGAFQGRVNAAFVRDKAGKSNTLKFWALQDGELIAGRVKGNQVKFSRRTTKLSEILKMPTGTKTLSNIDGAFVLGKKDNKRLILFVGNSVYVGNPNGRKLVKYSIPAQYPKTFKQIIHC 502
[Close]
BLAST of Mmp1 protein vs. Planmine SMEST
Match: SMESG000040786.1 (SMESG000040786.1)

HSP 1 Score: 265.003 bits (676), Expect = 3.430e-88
Identity = 127/129 (98.45%), Postives = 129/129 (100.00%), Query Frame = 2 
Query:    2 LKVEEMKIGGHGTYLGKSSAAFAREISTDESMQYFWLIQNNEVISGEILNHKIMFSRRVRPLSEVILMENGVKFPPSIDAALLSGEKDNLKLYLFVGNSYYIGKPNGRKKLKYHISADYPKSYKQLLKC 388
            LKVEEMKIGGHGTYLGKSSAAFAREISTDESMQYFWLIQNNEVISGEILNHKIMFSRRVRPLSEVILMENGVKFPPSIDAALLSGEKDNL+LYLFVGNSYYIGKPNGRK+LKYHISADYPKSYKQLLKC
Sbjct:  367 LKVEEMKIGGHGTYLGKSSAAFAREISTDESMQYFWLIQNNEVISGEILNHKIMFSRRVRPLSEVILMENGVKFPPSIDAALLSGEKDNLQLYLFVGNSYYIGKPNGRKQLKYHISADYPKSYKQLLKC 495
[Close]
BLAST of Mmp1 protein vs. Planmine SMEST
Match: SMESG000040772.1 (SMESG000040772.1)

HSP 1 Score: 230.335 bits (586), Expect = 1.236e-74
Identity = 106/129 (82.17%), Postives = 118/129 (91.47%), Query Frame = 2 
Query:    2 LKVEEMKIGGHGTYLGKSSAAFAREISTDESMQYFWLIQNNEVISGEILNHKIMFSRRVRPLSEVILMENGVKFPPSIDAALLSGEKDNLKLYLFVGNSYYIGKPNGRKKLKYHISADYPKSYKQLLKC 388
            LKVEEMKIGGHG YLGKSSAAFAR++S +E MQYFWLIQ+NEVISGE+L +KI+FSRR RPLSEVI M NG KFPPSIDAALLSGEKDNL+LYLFVGNSYY+GKP GRK+ +Y ISADYPKSYKQ+LKC
Sbjct:  367 LKVEEMKIGGHGAYLGKSSAAFARQVSAEEGMQYFWLIQDNEVISGELLKNKIVFSRRARPLSEVITMSNGAKFPPSIDAALLSGEKDNLQLYLFVGNSYYVGKPTGRKQFQYSISADYPKSYKQVLKC 495
[Close]
BLAST of Mmp1 protein vs. Planmine SMEST
Match: SMESG000040780.1 (SMESG000040780.1)

HSP 1 Score: 230.335 bits (586), Expect = 1.309e-74
Identity = 106/129 (82.17%), Postives = 118/129 (91.47%), Query Frame = 2 
Query:    2 LKVEEMKIGGHGTYLGKSSAAFAREISTDESMQYFWLIQNNEVISGEILNHKIMFSRRVRPLSEVILMENGVKFPPSIDAALLSGEKDNLKLYLFVGNSYYIGKPNGRKKLKYHISADYPKSYKQLLKC 388
            LKVEEMKIGGHG YLGKSSAAFAR++S +E MQYFWLIQ+NEVISGE+L +KI+FSRR RPLSEVI M NG KFPPSIDAALLSGEKDNL+LYLFVGNSYY+GKP GRK+ +Y ISADYPKSYKQ+LKC
Sbjct:  382 LKVEEMKIGGHGAYLGKSSAAFARQVSAEEGMQYFWLIQDNEVISGELLKNKIVFSRRARPLSEVITMSNGAKFPPSIDAALLSGEKDNLQLYLFVGNSYYVGKPTGRKQFQYSISADYPKSYKQVLKC 510
[Close]
BLAST of Mmp1 protein vs. Planmine SMEST
Match: SMESG000040780.1 (SMESG000040780.1)

HSP 1 Score: 230.335 bits (586), Expect = 1.584e-74
Identity = 106/129 (82.17%), Postives = 118/129 (91.47%), Query Frame = 2 
Query:    2 LKVEEMKIGGHGTYLGKSSAAFAREISTDESMQYFWLIQNNEVISGEILNHKIMFSRRVRPLSEVILMENGVKFPPSIDAALLSGEKDNLKLYLFVGNSYYIGKPNGRKKLKYHISADYPKSYKQLLKC 388
            LKVEEMKIGGHG YLGKSSAAFAR++S +E MQYFWLIQ+NEVISGE+L +KI+FSRR RPLSEVI M NG KFPPSIDAALLSGEKDNL+LYLFVGNSYY+GKP GRK+ +Y ISADYPKSYKQ+LKC
Sbjct:  386 LKVEEMKIGGHGAYLGKSSAAFARQVSAEEGMQYFWLIQDNEVISGELLKNKIVFSRRARPLSEVITMSNGAKFPPSIDAALLSGEKDNLQLYLFVGNSYYVGKPTGRKQFQYSISADYPKSYKQVLKC 514
[Close]
BLAST of Mmp1 protein vs. Planmine SMEST
Match: SMESG000014326.1 (SMESG000014326.1)

HSP 1 Score: 121.324 bits (303), Expect = 3.653e-33
Identity = 55/129 (42.64%), Postives = 84/129 (65.12%), Query Frame = 2 
Query:    2 LKVEEMKIGGHGTYLGKSSAAFAREISTDESMQYFWLIQNNEVISGEILNHKIMFSRRVRPLSEVILMENGVKFPPSIDAALLSGEKDNLKLYLFVGNSYYIGKPNGRKKLKYHISADYPKSYKQLLKC 388
            + + E+ I   G + G+ +AAF R+ +   +   FW +Q+ E+I+G +  +++ FSRR   LSE++ M  G K   +ID A + G+KDN +L LFVGNS Y+G PNGRK +KY I A YPK++KQ++ C
Sbjct:  376 MALSELNITRFGAFQGRVNAAFVRDKAGKSNTLKFWALQDGELIAGRVKGNQVKFSRRTTKLSEILKMPTGTKTLSNIDGAFVLGKKDNKRLILFVGNSVYVGNPNGRKLVKYSIPAQYPKTFKQIIHC 504
The following BLAST results are available for this feature:
BLAST of Mmp1 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 Mmp1 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 Mmp1 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 Mmp1 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 Mmp1 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 Mmp1 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 Mmp1 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 Mmp1 protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
K0JBS32.596e-7182.17Mmp1 protein OS=Schmidtea mediterranea OX=79327 GN... [more]
K0JBI81.332e-2942.64Mmp2 protein OS=Schmidtea mediterranea OX=79327 GN... [more]
back to top
BLAST of Mmp1 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 Mmp1 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 Mmp1 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 Mmp1 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 Mmp1 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 Mmp1 protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000040786.13.430e-8898.45SMESG000040786.1[more]
SMESG000040772.11.236e-7482.17SMESG000040772.1[more]
SMESG000040780.11.309e-7482.17SMESG000040780.1[more]
SMESG000040780.11.584e-7482.17SMESG000040780.1[more]
SMESG000014326.13.653e-3342.64SMESG000014326.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023225 ID=SMED30023225|Name=Mmp1 protein|organism=Schmidtea mediterranea sexual|type=transcript|length=395bp
TCTAAAAGTAGAAGAAATGAAAATTGGAGGTCATGGAACCTATCTAGGAA
AAAGTTCTGCAGCCTTTGCAAGAGAAATTTCTACTGATGAAAGCATGCAA
TATTTTTGGCTTATTCAAAATAACGAAGTTATCTCTGGTGAAATTTTGAA
CCACAAAATTATGTTTTCAAGACGGGTTCGTCCTCTGTCGGAAGTTATTT
TAATGGAAAACGGAGTTAAATTTCCCCCTAGCATCGATGCGGCTCTTTTG
AGTGGTGAAAAAGATAATTTAAAATTATATTTATTTGTAGGAAATAGTTA
TTACATCGGTAAACCGAATGGAAGAAAAAAATTAAAATATCACATTTCAG
CCGATTATCCCAAATCTTACAAACAACTTCTGAAATGTTAAAAAC
back to top

protein sequence of SMED30023225-orf-1

>SMED30023225-orf-1 ID=SMED30023225-orf-1|Name=SMED30023225-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=130bp
LKVEEMKIGGHGTYLGKSSAAFAREISTDESMQYFWLIQNNEVISGEILN
HKIMFSRRVRPLSEVILMENGVKFPPSIDAALLSGEKDNLKLYLFVGNSY
YIGKPNGRKKLKYHISADYPKSYKQLLKC*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR000585Hemopexin-like_dom
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