SMED30020164

Overview
NameSMED30020164
Smed IDSMED30020164
Length (bp)828
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 SMED30020164 (SMED30020164) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020164 (SMED30020164) in cells (dots) of each of the 12 neoblast clusters.

 

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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




SMED30020164

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
posterior region of the whole animalSMED30020164SMESG000061910.1 dd_Smed_v4_14161_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
headSMED30020164SMESG000061910.1 SmedASXL_014738SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
medial muscle cellSMED30020164SMESG000061910.1 dd_Smed_v4_14161_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
headSMED30020164SMESG000061910.1 dd_Smed_v6_14161_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
enteric muscle cellSMED30020164SMESG000061910.1 dd_Smed_v4_14161_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30020164 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000666:13826..22296 +3800
Homology
BLAST of SMED30020164 vs. TrEMBL
Match: A0A068YG28 (Uncharacterized protein OS=Echinococcus multilocularis OX=6211 GN=EmuJ_000880700 PE=4 SV=1)

HSP 1 Score: 129.798 bits (325), Expect = 3.662e-30
Identity = 82/269 (30.48%), Postives = 129/269 (47.96%), Query Frame = 3
Query:   12 IWIPDLTKYSKR-KWTPCLLNGGFQIKHMINRQYLDAKEK-CTLSIYVNLECDCLIGEGCEWNFNEATCNPFEKKIKSRFQCYSNWYSGGHNYTILVKKQLDDNHIVITMKYKD--IRYPYFKTKYEKFQSMTIFSGLQIDQANRHFGGSTMRYSYNVFDSKKFWGFVVMNKS-----HVRG--------------GCKADSRNQFFCHRTCPTNGEICDFTNHDSCTFKTRYIGEWDLISRSYSGS------------IKITNHSITF 713
            +WIP+L+KY  R + + C + GGFQ K  I    +++K + CT S+Y  ++ +C+ GEG E +FNE  CNPFE  + +RF C+  W   G+  TIL K++    +IV +M Y++   +      +Y  F  + I  G+    A     G+ + Y   ++D + F      + +      +RG              GC AD+RN+ FC R+CP+    C  T+ DSC     Y G W LI    S              I I++ ++TF
Sbjct:   82 LWIPNLSKYVSRYRRSRCPIVGGFQAKSFIK---MNSKSQICTSSVYATVDSECIRGEGIEMHFNEPGCNPFESTLVTRFMCFVQWVEMGNVNTILFKEKSPTEYIVASMFYQEAPTQVDTVNNEYSSFAKVYIGLGIFRPTAQSTKDGANVAYPAYLYDLEPFGMTAKTSPAAFYEVQMRGAFGVCDDELEQCERGCNADARNRLFCRRSCPSAQRECSMTHSDSCEISASYRGFWLLIDPLPSAPGQGEPRPHLRKLIGISDRTVTF 347          
BLAST of SMED30020164 vs. TrEMBL
Match: W6UUK3 (Uncharacterized protein OS=Echinococcus granulosus OX=6210 GN=EGR_08078 PE=4 SV=1)

HSP 1 Score: 127.872 bits (320), Expect = 1.825e-29
Identity = 81/269 (30.11%), Postives = 129/269 (47.96%), Query Frame = 3
Query:   12 IWIPDLTKYSKR-KWTPCLLNGGFQIKHMINRQYLDAKEK-CTLSIYVNLECDCLIGEGCEWNFNEATCNPFEKKIKSRFQCYSNWYSGGHNYTILVKKQLDDNHIVITMKYKD--IRYPYFKTKYEKFQSMTIFSGLQIDQANRHFGGSTMRYSYNVFDSKKF-----WGFVVMNKSHVRG--------------GCKADSRNQFFCHRTCPTNGEICDFTNHDSCTFKTRYIGEWDLISRSYSGS------------IKITNHSITF 713
            +WIP+L+KY  R + + C + GGFQ K+ I    +++K + CT S+Y  ++ +C+ GEG E +FNE  CNPFE  + ++F C+  W   G+  TIL K++    +IV +M Y++   +      +Y  F  + I  G+    A     G+ + Y   ++D + F            +  +RG              GC AD+RN+ FC R+CP+    C  T+ DSC     Y G W LI    S              I I++ ++TF
Sbjct:  253 LWIPNLSKYVSRYRRSRCPIVGGFQAKNFIK---MNSKSQICTSSVYATVDSECIRGEGIEMHFNEPGCNPFESTLVTKFMCFVQWVEMGNVNTILFKEKSPTEYIVASMFYQEAPTQVDTVNNEYGSFAKVYIGLGIFRPTAQSTKDGANVAYPAYLYDLEPFDMTAKTSPAAFYEVQMRGAFGVCDDELEQCERGCNADARNRLFCRRSCPSAQRECSMTHSDSCEINASYRGFWLLIDPLPSAPGQSEPRPHLRKLIDISDRTVTF 518          
BLAST of SMED30020164 vs. TrEMBL
Match: A0A183QCT6 (Uncharacterized protein OS=Schistosoma rodhaini OX=6188 PE=4 SV=1)

HSP 1 Score: 127.872 bits (320), Expect = 1.900e-29
Identity = 78/244 (31.97%), Postives = 120/244 (49.18%), Query Frame = 3
Query:    6 SMIWIPDLTKYSKRKWTPCLLNGGFQIKHMINRQYLDAKEKCTLSIYVNLECDCLIGEGCEWNFNEATCNPFEKKIKSRFQCYSNWYSGGHNYTILVKKQLDDNHIVITMKYKDIRYPYFKTKYEKFQS--MTIFSGLQ----------IDQANRHFGGSTMRYSYN---VFDS-------KKFWGFVVMNKSHVRGGCKADSRNQFFCHRTCPTNGEICDFTNHDSCTFKTRYIGEWDLISRS 671
            S++WIP L+K     + PC   GGFQI  +   +    K  C    +  LE DC+I EG EW F++  CN FE    S   CY++W   G  YT+L + + DD + + TM + DI  P   + Y   QS  + I+SGL           +D  + H   +T+  ++N    ++S       ++ +G      +    GC  D RN+ FC+++CP + + C  +  DSCTFK  Y G W+LI  +
Sbjct:  247 SILWIPSLSKKLNDLFIPCPFVGGFQITSL--SRVTSEKPICQYQTFATLESDCVINEGIEWTFDDPKCNIFEVNSISHHNCYASWKKDGLTYTLLHQDRKDDGYSIFTMVFSDIPEPLNPSDYTYGQSKPLWIYSGLSSKHYQYSTLLLDSHSSHID-TTITKNWNDQRTYESPAYRLQIRRAFGICDDEPTSCTKGCDHDIRNRLFCYKSCPVDDKKCKSSQWDSCTFKQNYQGHWNLIEST 487          
BLAST of SMED30020164 vs. TrEMBL
Match: A0A068WFF3 (Uncharacterized protein OS=Echinococcus granulosus OX=6210 GN=EgrG_000880700 PE=4 SV=1)

HSP 1 Score: 127.487 bits (319), Expect = 2.259e-29
Identity = 81/269 (30.11%), Postives = 129/269 (47.96%), Query Frame = 3
Query:   12 IWIPDLTKYSKR-KWTPCLLNGGFQIKHMINRQYLDAKEK-CTLSIYVNLECDCLIGEGCEWNFNEATCNPFEKKIKSRFQCYSNWYSGGHNYTILVKKQLDDNHIVITMKYKD--IRYPYFKTKYEKFQSMTIFSGLQIDQANRHFGGSTMRYSYNVFDSKKF-----WGFVVMNKSHVRG--------------GCKADSRNQFFCHRTCPTNGEICDFTNHDSCTFKTRYIGEWDLISRSYSGS------------IKITNHSITF 713
            +WIP+L+KY  R + + C + GGFQ K+ I    +++K + CT S+Y  ++ +C+ GEG E +FNE  CNPFE  + ++F C+  W   G+  TIL K++    +IV +M Y++   +      +Y  F  + I  G+    A     G+ + Y   ++D + F            +  +RG              GC AD+RN+ FC R+CP+    C  T+ DSC     Y G W LI    S              I I++ ++TF
Sbjct:   82 LWIPNLSKYVSRYRRSRCPIVGGFQAKNFIK---MNSKSQICTSSVYATVDSECIRGEGIEMHFNEPGCNPFESTLVTKFMCFVQWVEMGNVNTILFKEKSPTEYIVASMFYQEAPTQVDTVNNEYGSFAKVYIGLGIFRPTAQSTKDGANVAYPAYLYDLEPFDMTAKTSPAAFYEVQMRGAFGVCDDELEQCERGCNADARNRLFCRRSCPSAQRECSMTHSDSCEINASYRGFWLLIDPLPSAPGQSEPRPHLRKLIDISDRTVTF 347          
BLAST of SMED30020164 vs. TrEMBL
Match: G4VIZ4 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 GN=Smp_150880 PE=4 SV=1)

HSP 1 Score: 127.487 bits (319), Expect = 2.723e-29
Identity = 76/244 (31.15%), Postives = 119/244 (48.77%), Query Frame = 3
Query:    6 SMIWIPDLTKYSKRKWTPCLLNGGFQIKHMINRQYLDAKEKCTLSIYVNLECDCLIGEGCEWNFNEATCNPFEKKIKSRFQCYSNWYSGGHNYTILVKKQLDDNHIVITMKYKDIRYPYFKTKYEKFQSMTI------------FSGLQIDQANRHFGGSTMRYSYN---VFDS-------KKFWGFVVMNKSHVRGGCKADSRNQFFCHRTCPTNGEICDFTNHDSCTFKTRYIGEWDLISRS 671
            S++WIP L+K     + PC   GGFQI  +   +    K  C    +  LE DC+I EG EW F++  CN FE    S   CY++W   G  YT+L + + DD + + TM + DI  P   + Y   +S  +            +S L +D  + HF  +T+  ++N    ++S       ++ +G      +    GC  D RN+ FC+++CP + + C  +  DSCTFK  Y G W+LI  +
Sbjct:  258 SILWIPSLSKKLNDLFIPCPFVGGFQITSLT--RVSSEKPICEYQTFATLESDCVINEGIEWTFDDPKCNIFEVNSISHHNCYASWKKDGLTYTLLHQDRKDDGYSIFTMVFSDIPEPLNPSDYTYGRSKPLWIYPGLSSKHYQYSTLLLDSHSSHF-DTTITKNWNDQRTYESPAYRLQIRRAFGICDDEPTSCTKGCDHDIRNRLFCYKSCPVDDKKCKSSQWDSCTFKQNYQGHWNLIEST 498          
BLAST of SMED30020164 vs. Planmine SMEST
Match: SMESG000061910.1 (SMESG000061910.1)

HSP 1 Score: 459.529 bits (1181), Expect = 9.659e-159
Identity = 220/237 (92.83%), Postives = 222/237 (93.67%), Query Frame = 3
Query:    3 SSMIWIPDLTKYSKRKWTPCLLNGGFQIKHMINRQYLDAKEKCTLSIYVNLECDCLIGEGCEWNFNEATCNPFEKKIKSRFQCYSNWYSGGHNYTILVKKQLDDNHIVITMKYKDIRYPYFKTKYEKFQSMTIFSGLQIDQANRHFGGSTMRYSYNVFDSKKFWGFVVMNKSHVRGGCKADSRNQFFCHRTCPTNGEICDFTNHDSCTFKTRYIGEWDLISRSYSGSIKITNHSITF 713
            SSMIWIPDLTKYSKRKWTPCLLNGGFQIKHMINRQYLDAKEKCTLSIYVNLECDCLIGEGCEWNFNEATCNPFEKKIKSRFQCYSNWYSGGHNYTILVKKQLDDNHIVITMKYKDIRYPYFKTKYEKFQSMTIFSGLQIDQANRHFGGSTMRYSYNV   + F G     +     GCKADSRNQFFCHRTCPTNGEICDFTNHDSCTFKTRYIGEWDLISRSYSGSIKITNHSITF
Sbjct:  176 SSMIWIPDLTKYSKRKWTPCLLNGGFQIKHMINRQYLDAKEKCTLSIYVNLECDCLIGEGCEWNFNEATCNPFEKKIKSRFQCYSNWYSGGHNYTILVKKQLDDNHIVITMKYKDIRYPYFKTKYEKFQSMTIFSGLQIDQANRHFGGSTMRYSYNVLIRRSF-GICDDEQESCERGCKADSRNQFFCHRTCPTNGEICDFTNHDSCTFKTRYIGEWDLISRSYSGSIKITNHSITF 411          

HSP 2 Score: 48.521 bits (114), Expect = 3.023e-6
Identity = 29/54 (53.70%), Postives = 35/54 (64.81%), Query Frame = 1
Query:  658 SYPGHIRVPSRSQTILSPSNNTLSKDQEVTLTCN*KKNNEYIQDLVYVSNAISK 819
            SY G I++ + S T     NNTLSKDQEVTLTC  K+NNEYIQD   ++    K
Sbjct:  397 SYSGSIKITNHSITF----NNTLSKDQEVTLTCI-KENNEYIQDWFMLAMPFQK 445          
The following BLAST results are available for this feature:
BLAST of SMED30020164 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 SMED30020164 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 SMED30020164 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 SMED30020164 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 SMED30020164 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 SMED30020164 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 SMED30020164 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 SMED30020164 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A068YG283.662e-3030.48Uncharacterized protein OS=Echinococcus multilocul... [more]
W6UUK31.825e-2930.11Uncharacterized protein OS=Echinococcus granulosus... [more]
A0A183QCT61.900e-2931.97Uncharacterized protein OS=Schistosoma rodhaini OX... [more]
A0A068WFF32.259e-2930.11Uncharacterized protein OS=Echinococcus granulosus... [more]
G4VIZ42.723e-2931.15Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
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BLAST of SMED30020164 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 SMED30020164 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 SMED30020164 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 SMED30020164 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 SMED30020164 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 SMED30020164 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000061910.19.659e-15992.83SMESG000061910.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020164 ID=SMED30020164|Name=SMED30020164|organism=Schmidtea mediterranea sexual|type=transcript|length=828bp
AATCTTCAATGATTTGGATACCTGATTTAACAAAATACAGTAAAAGAAAA
TGGACTCCATGTCTACTGAACGGTGGGTTTCAAATTAAACATATGATAAA
TCGCCAATATTTAGATGCCAAAGAAAAATGCACGTTGTCGATCTACGTCA
ATTTAGAGTGTGACTGTTTGATTGGAGAAGGCTGCGAATGGAACTTTAAT
GAAGCAACTTGTAATCCATTTGAGAAGAAAATAAAATCGAGATTCCAATG
CTATTCAAATTGGTATTCTGGAGGGCACAACTATACAATTTTGGTGAAAA
AACAACTCGATGACAACCATATAGTTATTACAATGAAATACAAAGATATT
AGATATCCTTATTTTAAAACGAAATACGAAAAATTTCAATCTATGACCAT
CTTTTCCGGATTGCAAATTGATCAAGCGAATCGTCACTTTGGGGGATCCA
CTATGAGATATTCGTACAATGTTTTTGATTCGAAGAAGTTTTGGGGATTT
GTGGTGATGAACAAGAGTCATGTGAGAGGGGGTTGCAAGGCTGATTCAAG
AAATCAGTTTTTTTGCCATAGAACCTGTCCAACGAATGGGGAAATTTGTG
ATTTTACCAACCACGACAGCTGCACATTCAAAACCAGATATATTGGAGAA
TGGGATCTCATATCCCGGTCATATTCGGGTTCCATCAAGATCACAAACCA
TTCTATCACCTTCAAATAACACTTTATCCAAAGATCAAGAAGTCACTCTG
ACCTGTAATTAAAAGAAAAATAATGAATATATTCAGGATTTGGTTTATGT
TAGCAATGCCATTTCAAAAGAATGGATG
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protein sequence of SMED30020164-orf-1

>SMED30020164-orf-1 ID=SMED30020164-orf-1|Name=SMED30020164-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=239bp
SSMIWIPDLTKYSKRKWTPCLLNGGFQIKHMINRQYLDAKEKCTLSIYVN
LECDCLIGEGCEWNFNEATCNPFEKKIKSRFQCYSNWYSGGHNYTILVKK
QLDDNHIVITMKYKDIRYPYFKTKYEKFQSMTIFSGLQIDQANRHFGGST
MRYSYNVFDSKKFWGFVVMNKSHVRGGCKADSRNQFFCHRTCPTNGEICD
FTNHDSCTFKTRYIGEWDLISRSYSGSIKITNHSITFK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000142posterior region of the whole animal
PLANA:0000418head
PLANA:0002056medial muscle cell
PLANA:0003104enteric muscle cell