SMED30022237

Overview
NameSMED30022237
Smed IDSMED30022237
Length (bp)2280
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 SMED30022237 (SMED30022237) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30022237 (SMED30022237) 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 SMED30022237 (SMED30022237) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30022237 (SMED30022237) 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




SMED30022237

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
head regionSMED30022237 SmedASXL_071740SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30022237 dd_Smed_v4_15266_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30022237 dd_Smed_v4_15266_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30022237 dd_Smed_v4_15266_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022237 Contig55517uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022237 Contig55517newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30022237 dd_Smed_v6_15266_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30022237 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000968:82498..84771 -10858
Homology
BLAST of SMED30022237 vs. Planmine SMEST
Match: SMESG000047293.1 (SMESG000047293.1)

HSP 1 Score: 95.9005 bits (237), Expect = 7.181e-28
Identity = 81/225 (36.00%), Postives = 110/225 (48.89%), Query Frame = -1
Query:  535 FDRKGVARRLLVREMAYRIDIIPAHHLPGSIINLSTNPVAQSTPSVTTTTGIPQKTP*STRHKPHKNRSRREKQ*SANALLQATLGAVKTPILNMSAIQK*IPLPAFSFPRHMDPSLDVVYALPM-------CQPVQHEQRSLNLNAWLPTNLQLAIKFVATTRTLIDFSTSSAGSTPLIISDPITSRNDSFTNLVPGRTSRENLHRFQRKPRHRYFPVYIDADD 1188
            F  K +  RL  R +A +IDIIPAHHL GS    S+  +  +    T     PQ +  + +HKP+KNR RREK+ + NALLQA L   +    N +     IP       R  D  LD +YA  M        +P+       NL   LP+NLQL +    +       + +S GSTP I S     + +++ NL+ GR SR +L R  R+P  RY PV ID  D
Sbjct:   84 FAEKELQARLPSRSIAQKIDIIPAHHLLGS----SSGRIGHNDIKATAIGEAPQTSKPTIKHKPNKNRRRREKRRAENALLQANLNTTRNETSNETTKISKIPAALDLILRTSDSDLDAIYAPRMINFFTQNSEPMHINVSKENLMVSLPSNLQLVVTAEPSNIRDERSTVTSGGSTPQITSMSEAPQTNTYVNLITGRASRRDLDRIPRRPGKRYCPVDIDVKD 304          

HSP 2 Score: 48.1358 bits (113), Expect = 7.181e-28
Identity = 27/56 (48.21%), Postives = 34/56 (60.71%), Query Frame = -2
Query: 1164 KGTWSSPKKTQELYKKISQISRAHNDLIIENRSQLILIVGQSAELQQILTEKELQG 1331
            KGTW SP+ T+      S   ++   LIIENR+Q + I  QSA L+QI  EKELQ 
Sbjct:   42 KGTWCSPEATK------SSTRKSLEGLIIENRAQRLTIAEQSATLRQIFAEKELQA 91          
BLAST of SMED30022237 vs. Planmine SMEST
Match: SMESG000023296.1 (SMESG000023296.1)

HSP 1 Score: 100.138 bits (248), Expect = 5.930e-24
Identity = 59/133 (44.36%), Postives = 77/133 (57.89%), Query Frame = -1
Query:  505 FSFPRHMDPSLDVVYALPMCQPVQHEQRSL-------NLNAWLPTNLQLAIKFVATTRTLIDFSTSSAGSTPLIISDPITSRNDSFTNLVPGRTSRENLHRFQRKPRHRYF----PVYIDADDK*AIMYFLCY 870
            F+FP  ++ S +VVY LP CQPVQ E RS+       NLN  LP N+ L+I+  A T T +D +TSSA STP  ISDP+T R++SFTNL+ GR SR N+      PR R           A+     + FLC+
Sbjct:   53 FTFPPPLETSQEVVYGLPTCQPVQPESRSVQMQVSIGNLNVKLPKNMHLSIESGAVTHTAVDLTTSSAESTPQRISDPVTPRDNSFTNLITGRASRGNM------PRDRSMLSSTRTLTKANSGSTYIKFLCF 179          
BLAST of SMED30022237 vs. Planmine SMEST
Match: SMESG000032225.1 (SMESG000032225.1)

HSP 1 Score: 77.7962 bits (190), Expect = 6.478e-24
Identity = 35/56 (62.50%), Postives = 45/56 (80.36%), Query Frame = -2
Query: 1164 KGTWSSPKKTQELYKKISQISRAHNDLIIENRSQLILIVGQSAELQQILTEKELQG 1331
            KGTW SP+ T+ELYK I++ISRA +DLI+ENR+Q I IV +S  L+Q+ TEKELQ 
Sbjct:   34 KGTWCSPEATKELYKNITRISRARDDLIVENRTQRITIVDKSPALRQLFTEKELQA 89          

HSP 2 Score: 53.1434 bits (126), Expect = 6.478e-24
Identity = 44/123 (35.77%), Postives = 64/123 (52.03%), Query Frame = -1
Query:  823 FDRKGVARRLLVREMAYRIDIIPAHHLPGSIINLSTNPVAQS-TPSVTTTTGIPQKTP*STRHKPHKNRSRREKQ*SANALLQATLGAVKTPILNMSAIQK*IPLPAFSFPRHMDPSLDVVYA 1188
            F  K +  RL  R  A +++II  HHLP      S+N + +  T +V T   +P     + +HKP+KN+ RREK+ + NALLQA L A++  I     I +  P    S P   D  L ++YA
Sbjct:   82 FTEKELQARLPGRSTAQQLNIISVHHLPV----YSSNRIERDVTNAVMTRPVLPIC---NRKHKPNKNQRRREKRRTENALLQANLNAIENVI--SIGISETTPYEPISMP--ADSDLAIIYA 193          
BLAST of SMED30022237 vs. Planmine SMEST
Match: SMESG000033974.1 (SMESG000033974.1)

HSP 1 Score: 78.1814 bits (191), Expect = 9.447e-22
Identity = 35/56 (62.50%), Postives = 45/56 (80.36%), Query Frame = -2
Query: 1164 KGTWSSPKKTQELYKKISQISRAHNDLIIENRSQLILIVGQSAELQQILTEKELQG 1331
            KGTW SP+ T++LYKKI+++SRA +DLI++NRSQ I I  Q A L+QI TEKELQ 
Sbjct:    2 KGTWCSPEATKKLYKKITRVSRARDDLIVKNRSQRITIADQCATLRQIFTEKELQA 57          

HSP 2 Score: 45.4394 bits (106), Expect = 9.447e-22
Identity = 69/212 (32.55%), Postives = 100/212 (47.17%), Query Frame = -1
Query:  580 FDRKGVARRLLVREMAYRIDIIPAHHLPGSIINLSTNPVAQSTPSVTTTTGIPQKTP*STRHKPHKNRSRREKQ*SANALLQATLGAVKTPILNMSAIQK*IPLPAFSFPRHMDPS-------LDVVYALPMCQPVQHEQRSLNLNAWLPTNLQLAIKFVATTRTLIDFSTSSAGSTPLIIS--DPITSRNDSFTNLVPGRTSRENLHRFQR 1188
            F  K +  RL  R +  ++++IP  HLP   +NLS N V     +V T   +P   P + +HKP+KNR R+EK+ + NALLQ  L  ++ P  N+  I +     +   P + D         +D   + P+  P Q      NL+    TN Q+ I   ++        TSS  STP IIS  +P   RN    N   G TSR+N  +F R
Sbjct:   50 FTEKELQARLPDRSITQQLNMIPVQHLP---VNLS-NCVEWDATNVFTLAPVP-SIP-NRKHKPNKNRRRKEKRRTENALLQVNLITIENP--NVIKIPEVTSYESNEMPANSDLEIISPPRLMDFPQSAPI--PFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNS--INSTAGDTSRQNQTQFHR 249          
BLAST of SMED30022237 vs. Planmine SMEST
Match: SMESG000047586.1 (SMESG000047586.1)

HSP 1 Score: 61.6178 bits (148), Expect = 4.008e-20
Identity = 29/50 (58.00%), Postives = 37/50 (74.00%), Query Frame = -2
Query: 1164 PKKTQELYKKISQISRAHNDLIIENRSQLILIVGQSAELQQILTEKELQG 1313
            P+ ++E YKKI+++SRA +D  IEN SQ I I  QSA L+QI TEKELQ 
Sbjct:    4 PRSSREFYKKITRLSRARDDFNIENWSQRITISDQSAALRQIFTEKELQS 53          

HSP 2 Score: 56.6102 bits (135), Expect = 4.008e-20
Identity = 42/120 (35.00%), Postives = 60/120 (50.00%), Query Frame = -1
Query:  829 FDRKGVARRLLVREMAYRIDIIPAHHLPGSIINLSTNPVAQSTPSVTTTTGIPQKTP*STRHKPHKNRSRREKQ*SANALLQATLGAVKTPILNMSAIQK*IPLPAFSFPRHMDPSLDVV 1188
            F  K +   L  R M  R+DII  HHL  +  NL+ N  A +       T +P  +  S RHKP+KN  RR+K+ + N   QA LG ++ P  N S   +  PL   S   H D +L+++
Sbjct:   46 FTEKELQSWLPRRNMVQRLDIISTHHLLINSSNLTNNDDANAA------TAMPAPSTSSRRHKPNKNWRRRQKRRAENGSQQANLGVIENP--NPSRTAEIFPLEPTSM--HNDKNLNII 155          
The following BLAST results are available for this feature:
BLAST of SMED30022237 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 SMED30022237 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 SMED30022237 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 SMED30022237 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 SMED30022237 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 SMED30022237 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 SMED30022237 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 SMED30022237 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30022237 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 SMED30022237 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 SMED30022237 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 SMED30022237 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 SMED30022237 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 SMED30022237 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000047293.17.181e-2836.00SMESG000047293.1[more]
SMESG000023296.15.930e-2444.36SMESG000023296.1[more]
SMESG000032225.16.478e-2462.50SMESG000032225.1[more]
SMESG000033974.19.447e-2262.50SMESG000033974.1[more]
SMESG000047586.14.008e-2058.00SMESG000047586.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022237 ID=SMED30022237|Name=SMED30022237|organism=Schmidtea mediterranea sexual|type=transcript|length=2280bp
CTCAAAATCAGTTTGAAAATAAAAATAACGAATTTCAAATTTAATCTTTT
TAATTAACAAAATCCAAATTATAATCTTTTGACAATTTCTTCAAAAATAA
AAACAACTTTATTTCGGATAAACAAACATACAAACTAAATGTAAATTTTT
ACATAAAAAATAAAAAAAGAACTTTTATTTCAAGATTCAACAGTGAACAA
GTATAAAAGAAAACGAAAGCTCAATTAAGGTTGACTTTCGATGAATACCT
AACTTCCTGGTTCCTCCAACACTCGTATTATTCTATATTTATAGATATGA
TGAGATTTAGATTTCAGATGCTAAACTTGTTTTGCAATAAATCGAAAAAT
ACAAATACATTTCCAGTTGGATCGCAATTCATAGGATTTCCACACATTCT
GAATTTTCAGTCACTACTCTCAAATGATTTTCAAATATCAATTCACTCAA
AAAAGAGAAGGACAAATATTAACTACAACGTTTATTTCTTATTACATTTT
ACTTATAACACAGAAAATACATTATTGCTCATTTATCGTCGGCGTCGATG
TAAACGGGGAAATAACGGTGTCTCGGTTTTCGCTGGAATCGATGGAGGTT
TTCTCGAGATGTCCTTCCAGGGACCAGGTTGGTAAATGAATCATTTCTAG
AAGTTATAGGATCCGATATAATTAGAGGCGTTGATCCTGCGCTGGAGGTT
GAGAAATCGATGAGCGTGCGAGTGGTCGCTACAAATTTGATGGCTAACTG
TAGATTAGTGGGTAGCCATGCATTCAGATTTAAGGACCTCTGTTCATGTT
GAACTGGTTGGCACATAGGTAGTGCATACACTACGTCTAGACTGGGATCC
ATGTGTCTGGGAAATGAGAAAGCTGGCAATGGGATTTATTTTTGAATAGC
CGACATATTCAAGATTGGAGTTTTCACAGCTCCGAGAGTCGCCTGAAGTA
AGGCGTTCGCTGATCATTGCTTTTCTCGCCGACTTCTATTTTTGTGTGGC
TTGTGCCTCGTTGATTAGGGAGTCTTTTGAGGTATCCCAGTGGTAGTAGT
CACACTCGGTGTTGACTGTGCAACTGGGTTCGTAGAGAGATTGATTATCG
ATCCCGGCAGATGATGGGCCGGTATAATATCAATGCGATAGGCCATTTCG
CGGACCAGTAGACGCCTTGCAACTCCTTTTCTGTCAAAATCTGCTGGAGT
TCAGCGCTTTGACCCACTATGAGAATCAGCTGAGAACGGTTCTCGATGAT
AAGATCGTTATGAGCTCGGGAAATTTGAGAGATTTTCTTATAAAGTTCTT
GAGTCTTCTTGGGAGAAGACCACGTACCTTTTCAATTTCTTTTACTTTTG
GACTAGCTCATTATACTTGACTTCTAAGTGCGAGATGGAGGTTGGAGCTG
GATAAATTTTCGGTATCTTGGGAAGTTTCTATATCATTGCTACTAAATAC
TAAATTTTCTATAACAAAAGAAATTAAGGAAAATGAATATGATAACAAAA
AAAGATAATATTTACGTAAATAATTAATAAATGATTAATATATTCAAATT
TTTGAGGCAATCAGAGTTGAACAATTTTATACAACTTATTTTCCTTTATT
TGGTTCAAGCAAACCACAATCATACAAAAAGGGTAATCGTATATCCATAA
TCTAATTATATGCATACTTTACTAGTCCCTGCTGTGCAGATTTATATTAA
TTAGGAAGTGCTATCCAAGCCGAACTCTGGGTTGATGAAAATTTTGTGAA
GTATATTATCGAAAAAGGTTTTGATTATATCTACATGATTGTCGATGTTG
CGGTGTAATTACTGTTCAATCTAAAGGATAATATATAGCTTTAACTCGTG
TAATCATGATTGAATTTACTTATGAAATTTTGTATAAATATTTTCGACAT
TGTTGAATTTATTTCATGTCAGTTTTCTTAAGAACAGTAAATATGATGTC
GTTTGATTTGACTATTAATTCCATAATGTAACAACATCGTAACTCAAAAA
TCATTTAAAGTATTTGATTTAATAATCTAAATTAATCTCTTTTTAATATA
TTAAAATTAAAACTTAATTTAGATCAAATTATAACCACTTATTTTAAAAG
ATAGAATATAAATTATCAATAATTACAATACAATTAAAGATAACTAAATT
TCATTAATAATTAAAAATAAGAAAACTAAAATGAATAATAAAAACCAAAC
AATGTTTTATAACTGAAATTTAAAAAACTGAAAATTAAAATCCCCCTGAT
TTCATTGTACTTGTAAGCTAAAAAATTGTG
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protein sequence of SMED30022237-orf-1

>SMED30022237-orf-1 ID=SMED30022237-orf-1|Name=SMED30022237-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=113bp
MMRFRFQMLNLFCNKSKNTNTFPVGSQFIGFPHILNFQSLLSNDFQISIH
SKKRRTNINYNVYFLLHFTYNTENTLLLIYRRRRCKRGNNGVSVFAGIDG
GFLEMSFQGPGW*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000099neuron
PLANA:0000418head