SMED30016108

Overview
NameSMED30016108
Smed IDSMED30016108
Length (bp)1124
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.
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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



SMED30016108

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30016108 dd_Smed_v4_59338_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30016108 dd_Smed_v4_59338_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30016108 dd_Smed_v4_59338_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30016108 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.010170:21777..22895 +5118
v31.003491:41748..42866 +5112
v31.007245:26706..27822 +4427
v31.012191:2697..3841 +4162
v31.009755:7235..8379 +4161
v31.002917:15966..17021 -3895
Homology
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BLAST of SMED30016108 vs. Planmine SMEST
Match: SMESG000020037.1 (SMESG000020037.1)

HSP 1 Score: 157.918 bits (398), Expect = 2.755e-47
Identity = 89/136 (65.44%), Postives = 101/136 (74.26%), Query Frame = 1 
Query:  688 MNTCQTLQRKLNKARTVNKGLQQQLRQLNKEIQQVKATWIEPGKAKMVYQEMTAVQRG*AEEKQLT*SQKIQIPGLEVALLACHEGNAVTYPLVFAPDQLAYRDXXXXXXXXXXXXXHRPVKSERAKRRAAQMKDC 1095
            M   +   R+L K+R  N  L QQL Q+ KEI Q+KATW+EPGK K +YQ+MTA QRG AEEKQL  +QK+QI  LEVAL AC EGNAVTYPLVFAP QLAYR+A   TKPATK    RP K+ERAKRRAAQ KDC
Sbjct:    1 MGPYKISSRELEKSRRENAELHQQLIQMTKEIHQIKATWVEPGKVKSLYQKMTAAQRGWAEEKQLHQTQKVQIRSLEVALSACQEGNAVTYPLVFAPAQLAYREATETTKPATKPTPRRPGKAERAKRRAAQAKDC 136
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BLAST of SMED30016108 vs. Planmine SMEST
Match: SMESG000071419.1 (SMESG000071419.1)

HSP 1 Score: 159.844 bits (403), Expect = 7.352e-46
Identity = 88/134 (65.67%), Postives = 107/134 (79.85%), Query Frame = 1 
Query:  685 DMNTCQTLQRKLNKARTVNKGLQQQLRQLNKEIQQVKATWIEPGKAKMVYQEMTAVQRG*AEEKQLT*SQKIQIPGLEVALLACHEGNAVTYPLVFAPDQLAYRDXXXXXXXXXXXXXHRPVKSERAKRRAAQM 1086
            +M+    L+ KL+KA   N+ L +QL Q+N EIQ++KATWIEPGKAK++YQ+M A QRG AEEKQLT SQK+QI GLEVAL AC EG AVTYPLVFAP QLAYR++  ATK ATK  +HRP +S+RAKRRAAQ+
Sbjct:  183 NMHPPLGLRDKLDKAHVKNRELHRQLTQVNSEIQRIKATWIEPGKAKLIYQKMMAAQRGWAEEKQLTQSQKVQIRGLEVALSACQEGKAVTYPLVFAPAQLAYRESTTATKIATKPPRHRPGRSQRAKRRAAQL 316

HSP 2 Score: 66.6254 bits (161), Expect = 9.001e-19
Identity = 54/152 (35.53%), Postives = 73/152 (48.03%), Query Frame = 1 
Query:   76 DVGFLISPVRELRSGNRGDPEEVELPFIAIKREPG-------PGNPSFC*LASTNTREKPTAKWRKTSST*FK*TQISRRAKYPVRMGTLP-----PDRKL--QEWI-AAMNVVIPLKILPREIRNEERYTENRRDHPFARERSSQRYNQIR 486
            D GF ISPVRE R GNR + ++V+LPF+ IKREPG        G   +  LA     ++ T   R+         +I+R     +  G +P     P R      W+ +AMNVV+P + L R      +      DHP ARER S+R N  R
Sbjct:   33 DAGFSISPVRESRIGNRSNTDDVDLPFVTIKREPGRNLAREIRGLAEYL-LARLEEHQRQTD--RQVDKARRHLEEINR----DIAAGLIPSLTGMPGRTTLRSTWMTSAMNVVVPREALIRGWGEANKPANEHHDHPHARERPSRRDNSKR 177

HSP 3 Score: 45.8246 bits (107), Expect = 9.001e-19
Identity = 19/28 (67.86%), Postives = 21/28 (75.00%), Query Frame = 2 
Query:    2 DNLWIDASRIIARFPAHSVA*CRQATWD 85
            +N WIDASR+  RFPAHS   CRQA WD
Sbjct:    6 ENSWIDASRVTLRFPAHSAVRCRQAMWD 33

HSP 4 Score: 60.077 bits (144), Expect = 5.957e-10
Identity = 29/53 (54.72%), Postives = 41/53 (77.36%), Query Frame = 3 
Query:  183 GKSEFLLARLNEHQRETNRQVEKDKQYLIQVNADIAAGKIPSTDGYTPSRSEI 341
            G +E+LLARL EHQR+T+RQV+K +++L ++N DIAAG IPS  G  P R+ +
Sbjct:   76 GLAEYLLARLEEHQRQTDRQVDKARRHLEEINRDIAAGLIPSLTGM-PGRTTL 127
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BLAST of SMED30016108 vs. Planmine SMEST
Match: SMESG000033890.1 (SMESG000033890.1)

HSP 1 Score: 150.599 bits (379), Expect = 2.767e-44
Identity = 84/138 (60.87%), Postives = 102/138 (73.91%), Query Frame = 1 
Query:  679 IVDMNTCQTLQRKLNKARTVNKGLQQQLRQLNKEIQQVKATWIEPGKAKMVYQEMTAVQRG*AEEKQLT*SQKIQIPGLEVALLACHEGNAVTYPLVFAPDQLAYRDXXXXXXXXXXXXXHRPVKSERAKRRAAQMKD 1092
            I+DMN   TL ++L K+R  N+ L  QL QLNKEIQQ++A+WIEP + K +YQ +TA QRG  +EKQL  SQKIQI  LEVAL AC EGNA+TY LVFAP QLAY +   ATKPA K  + RP K+ERAKRRA Q+K+
Sbjct:    5 ILDMNRIGTLTKELTKSRQQNEKLHSQLLQLNKEIQQIRASWIEPARPKRIYQRLTAAQRGWEDEKQLGQSQKIQILSLEVALSACQEGNAITYQLVFAPAQLAYMETTEATKPAKKPAERRPGKAERAKRRAFQIKE 142
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BLAST of SMED30016108 vs. Planmine SMEST
Match: SMESG000043722.1 (SMESG000043722.1)

HSP 1 Score: 143.28 bits (360), Expect = 4.963e-41
Identity = 79/141 (56.03%), Postives = 105/141 (74.47%), Query Frame = 1 
Query:  673 FIIVDMNTCQTLQRKLNKARTVNKGLQQQLRQLNKEIQQVKATWIEPGKAKMVYQEMTAVQRG*AEEKQLT*SQKIQIPGLEVALLACHEGNAVTYPLVFAPDQLAYRDXXXXXXXXXXXXXHRPVKSERAKRRAAQMKDC 1095
            + +  +++ Q LQ++L +AR +N  L QQ+ QL KE+Q +K+T +E  K K +YQ++TA Q+G AEEKQL  SQK+Q+ GLEVAL AC EG AVTYPLVFAP QL YR+A + +KPAT+  KHRP ++ERAKRR AQ KD 
Sbjct:   43 YYLAMLDSHQFLQQELTQARKINADLHQQILQLTKEMQTIKSTLVELSKVKRLYQKLTAAQKGWAEEKQLNQSQKMQLIGLEVALSACQEGAAVTYPLVFAPAQLTYREAMSNSKPATRPFKHRPGRNERAKRRVAQTKDA 183
[Close]
BLAST of SMED30016108 vs. Planmine SMEST
Match: SMESG000059789.1 (SMESG000059789.1)

HSP 1 Score: 140.584 bits (353), Expect = 1.138e-40
Identity = 80/120 (66.67%), Postives = 98/120 (81.67%), Query Frame = 1 
Query:  688 MNTCQTLQRKLNKARTVNKGLQQQLRQLNKEIQQVKATWIEPGKAKMVYQEMTAVQRG*AEEKQLT*SQKIQIPGLEVALLACHEGNAVTYPLVFAPDQLAYRDXXXXXXXXXXXXXHRP 1047
            M++ + LQ++L+KA T N+ L+QQ+ QL++EIQQ KA WIEP KAK +YQ+MTA Q+G AEEKQLT SQKIQI GLEVAL AC EGNAVTYPLVFA  QLAYR+A +AT  ATK+ K+RP
Sbjct:    1 MSSTRWLQQELHKAHTANQNLRQQITQLSQEIQQTKAAWIEPRKAKKIYQKMTAAQQGWAEEKQLTQSQKIQIRGLEVALSACQEGNAVTYPLVFARAQLAYREATSATTTATKVSKNRP 120
The following BLAST results are available for this feature:
BLAST of SMED30016108 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 SMED30016108 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 SMED30016108 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 SMED30016108 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 SMED30016108 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 SMED30016108 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 SMED30016108 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 SMED30016108 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 SMED30016108 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 SMED30016108 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 SMED30016108 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 SMED30016108 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 SMED30016108 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 SMED30016108 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000020037.12.755e-4765.44SMESG000020037.1[more]
SMESG000071419.17.352e-4665.67SMESG000071419.1[more]
SMESG000033890.12.767e-4460.87SMESG000033890.1[more]
SMESG000043722.14.963e-4156.03SMESG000043722.1[more]
SMESG000059789.11.138e-4066.67SMESG000059789.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016108 ID=SMED30016108|Name=SMED30016108|organism=Schmidtea mediterranea sexual|type=transcript|length=1124bp
AGATAACTTGTGGATCGACGCGTCCAGAATCATCGCACGATTCCCCGCAC
ACTCGGTCGCCTGATGCAGGCAGGCGACGTGGGATTTTTGATATCCCCGG
TACGAGAACTCAGATCAGGCAATCGAGGAGACCCAGAGGAGGTCGAACTT
CCCTTTATAGCGATAAAGCGGGAACCCGGCCCGGGAAATCCGAGTTTCTG
TTAGCTCGCCTCAACGAACACCAGAGAGAAACCAACCGCCAAGTGGAGAA
AGACAAGCAGTACCTGATTCAAGTAAACGCAGATATCGCGGCGGGCAAAA
TACCCAGTACGGATGGGTACACTCCCTCCCGATCGGAAATTACAGGAATG
GATCGCAGCTATGAACGTGGTGATACCGCTAAAGATTCTTCCCCGAGAAA
TACGGAATGAAGAGAGATACACTGAGAACCGTCGCGACCACCCATTTGCT
CGCGAGCGCTCGAGCCAGAGATATAATCAAATTCGTTCCAAATTTAGGCG
TCGATGAATGTAATAGAATAAATATTTAGGAAAAAGTTTTTGCTTTTTTA
TTTTTGATAACCCTTAAGGAAATAAATAAGAGGACGATGCACTGGCCGAT
GGTAAACCTTGATATAAACCTATAAGCAATAAATTGACGAAACCTGTTAA
AAGAACTTAAACTTAATGAGTATTTATCATTGTAGACATGAATACATGCC
AAACCTTGCAACGGAAGCTCAACAAGGCCCGTACAGTCAATAAAGGACTA
CAACAACAGCTCAGACAGTTAAATAAAGAAATACAGCAGGTCAAAGCGAC
CTGGATCGAGCCGGGGAAGGCAAAAATGGTTTATCAGGAAATGACCGCGG
TACAACGAGGGTGAGCTGAGGAGAAGCAGCTCACCTAGTCGCAAAAAATT
CAGATACCTGGTCTGGAGGTAGCGTTATTGGCGTGCCATGAAGGCAACGC
GGTAACCTACCCTCTGGTATTTGCGCCAGACCAACTGGCCTACAGAGATG
CAGCGGCCGCCACGAAGCCAGCAACCAAGATAATTAAACATCGGCCGGTA
AAATCCGAGCGTGCTAAACGTCGGGCCGCTCAAATGAAAGACTGTTGGGC
TAGAACACAAACGGCCTTGTAAAT
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protein sequence of SMED30016108-orf-1

>SMED30016108-orf-1 ID=SMED30016108-orf-1|Name=SMED30016108-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=136bp
ITCGSTRPESSHDSPHTRSPDAGRRRGIFDIPGTRTQIRQSRRPRGGRTS
LYSDKAGTRPGKSEFLLARLNEHQRETNRQVEKDKQYLIQVNADIAAGKI
PSTDGYTPSRSEITGMDRSYERGDTAKDSSPRNTE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron