SMED30011688

Overview
NameSMED30011688
Smed IDSMED30011688
Length (bp)4059
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 SMED30011688 (SMED30011688) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30011688 (SMED30011688) 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.
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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



SMED30011688

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
epidermisSMED30011688SMESG000010591.1 dd_Smed_v4_10661_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30011688SMESG000038869.1 OX_Smed_1.0.03638ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Category 4 cellSMED30011688SMESG000010591.1 dd_Smed_v4_10661_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30011688 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001170:25328..29387 +19932
Homology
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BLAST of SMED30011688 vs. Planmine SMEST
Match: SMESG000020037.1 (SMESG000020037.1)

HSP 1 Score: 89.3521 bits (220), Expect = 1.969e-20
Identity = 45/84 (53.57%), Postives = 58/84 (69.05%), Query Frame = 1 
Query: 2878 Q*QAKWFKPTKVK*IYQ*LTAKREGLKEERQQFQMRKVKIKALETALSSSQNGNAVTYPLVFVPDQLAYKERAVTSSTYQNPTP 3129
            Q +A W +P KVK +YQ +TA + G  EE+Q  Q +KV+I++LE ALS+ Q GNAVTYPLVF P QLAY+E   T+     PTP
Sbjct:   34 QIKATWVEPGKVKSLYQKMTAAQRGWAEEKQLHQTQKVQIRSLEVALSACQEGNAVTYPLVFAPAQLAYREATETTKPATKPTP 117
[Close]
BLAST of SMED30011688 vs. Planmine SMEST
Match: SMESG000054288.1 (SMESG000054288.1)

HSP 1 Score: 85.8853 bits (211), Expect = 2.876e-19
Identity = 43/82 (52.44%), Postives = 56/82 (68.29%), Query Frame = 1 
Query: 2878 Q*QAKWFKPTKVK*IYQ*LTAKREGLKEERQQFQMRKVKIKALETALSSSQNGNAVTYPLVFVPDQLAYKERAVTSSTYQNP 3123
            Q +A W  P K+K +YQ LTA ++G  EE+Q  Q  + +I+ LE ALS+SQ G AVTYPLVF P QLAY+E A  S++  NP
Sbjct:   34 QIRATWIDPAKIKPLYQRLTAAQKGWAEEKQINQSLRTQIRGLEVALSASQEGAAVTYPLVFAPAQLAYRESAAASTSVPNP 115
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BLAST of SMED30011688 vs. Planmine SMEST
Match: SMESG000003397.1 (SMESG000003397.1)

HSP 1 Score: 86.2705 bits (212), Expect = 3.806e-19
Identity = 43/82 (52.44%), Postives = 56/82 (68.29%), Query Frame = 1 
Query: 2878 Q*QAKWFKPTKVK*IYQ*LTAKREGLKEERQQFQMRKVKIKALETALSSSQNGNAVTYPLVFVPDQLAYKERAVTSSTYQNP 3123
            Q +A W  P K+K +YQ LTA ++G  EE+Q  Q  + +I+ LE ALS+SQ G AVTYPLVF P QLAY+E A  S++  NP
Sbjct:   47 QIRATWIDPAKIKPLYQRLTAAQKGWAEEKQINQSLRTQIRGLEVALSASQEGAAVTYPLVFAPAQLAYRESAAASTSVPNP 128
[Close]
BLAST of SMED30011688 vs. Planmine SMEST
Match: SMESG000011429.1 (SMESG000011429.1)

HSP 1 Score: 83.5741 bits (205), Expect = 1.130e-18
Identity = 42/81 (51.85%), Postives = 55/81 (67.90%), Query Frame = 1 
Query: 2878 Q*QAKWFKPTKVK*IYQ*LTAKREGLKEERQQFQMRKVKIKALETALSSSQNGNAVTYPLVFVPDQLAYKERAVTSSTYQN 3120
            Q +A W  P K+K +YQ LTA ++G  EE+Q  Q  + +I+ LE ALS+SQ G AVTYPLVF P QLAY+E A  S++  N
Sbjct:   27 QIRATWVDPAKIKPLYQRLTAAQKGWAEEKQINQSLRTQIRGLEVALSASQEGAAVTYPLVFAPAQLAYRESAAASTSVSN 107
[Close]
BLAST of SMED30011688 vs. Planmine SMEST
Match: SMESG000029996.1 (SMESG000029996.1)

HSP 1 Score: 84.7297 bits (208), Expect = 1.272e-18
Identity = 42/82 (51.22%), Postives = 55/82 (67.07%), Query Frame = 1 
Query: 2878 Q*QAKWFKPTKVK*IYQ*LTAKREGLKEERQQFQMRKVKIKALETALSSSQNGNAVTYPLVFVPDQLAYKERAVTSSTYQNP 3123
            Q +A W  P K+K +YQ LTA ++G  EE+Q  Q  + +I+ LE ALS+SQ G AVTYPLVF P QLAY+E    S++  NP
Sbjct:   45 QIRATWIDPVKIKPLYQRLTAAQKGWAEEKQINQSLRTQIRGLEVALSASQEGAAVTYPLVFAPAQLAYRESVAASTSVPNP 126
The following BLAST results are available for this feature:
BLAST of SMED30011688 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 SMED30011688 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 SMED30011688 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 SMED30011688 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 SMED30011688 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 SMED30011688 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 SMED30011688 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 SMED30011688 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 SMED30011688 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 SMED30011688 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 SMED30011688 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 SMED30011688 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 SMED30011688 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 SMED30011688 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000020037.11.969e-2053.57SMESG000020037.1[more]
SMESG000054288.12.876e-1952.44SMESG000054288.1[more]
SMESG000003397.13.806e-1952.44SMESG000003397.1[more]
SMESG000011429.11.130e-1851.85SMESG000011429.1[more]
SMESG000029996.11.272e-1851.22SMESG000029996.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011688 ID=SMED30011688|Name=SMED30011688|organism=Schmidtea mediterranea sexual|type=transcript|length=4059bp
GTGATTTTGAATAATTAATTCATAAATTATTCGTTGATTTAAATATTTAA
TTTAGGTTATTTATTTTAGAATAGGAAGTGTCTGCTGGATGTGGTAAACA
ACAAAATTGCGTGAAATGTGTGTAATTATTGCCTCACCTGGAGAATGTAT
GCATTATTTCATAATGAATCTGTTTTCTGAATAAATGTTTCATTTATTCG
CTGCAATCGAATATGGAATGATTCATTCGCATCCGATGATTTGCTCAAAT
TTTGTGATTTTAAAACTCAAAATATTTATATAAATTTATGAGGTTTTGAT
TGGTTTGTAATCAATATTCAGCTGTGCTGAACAAGAACAATCGAGTGCAA
TTCAGACATTAAATGCATCTTTTGTAAATCTGTTGTTTATAAAGTTTGGT
TGATTTATTGATTGATATAATTATTATTTGCACTAATAAGAAATCAATTA
TGCAATAAAAGAGCTGAAAGCAAGAAAATGGATTAATAGAAATACAGGAA
AGAATGACCAGATAGAATCACGTCAAAGTTGAACCAAAGTAATGCAAAAG
CAGTAATTTTTAATTAATCTGATTAATTATCAAAGTCAATTTCAGATTTT
TGTACTTTCACAATTTGCATCATTGATAATGCGCTGATATGATGCAACGT
ATTCTAAATCGCCCTTTATTCAAATACTGAAGTATGTGTTTATATAAATG
AACAAGTCCATATATTTGCAGATATTGGAACTGTATTGTCATTGGTGAAT
TTTCTAGTTCAAAAAGTTGCGCCAGATTTATGCAGCAATACTAACTCGAT
ACAAACACATGAAGCAAAGTAAATCAGCCGAGTATTCTAAATATTTATTT
AGTATTCGCAAACTCCTTTACATGAGGCAATTGCGAGTGGATTGGGTGGT
AATTGCGGATATTTAATTGGTCGACCAATTGATATTGACCAGCCTGGATT
TGTGAGTTTTGATTTATTGATTGAATAATTATGTGAGATATAAATGGTAT
TGACTATTCCGTAATGTGCTGTGATTTGAAGAATGATAAATGTTTGTGCA
AAGCTGATGAACTGAGGTGATAATTATGTGAAATCTATTGAGGTGAACAA
TTTTCAAAATTTCTGTCACTTATAAATTATTTAACCTATCGATTCAAATA
CAAATATTTATATTATTTGCAGGTTATTAATCGATATTCCAGAAATGAAA
ATGTTTAATTATTTATTTGGTCGTGATTGTTGAATTTTTTGTTTTAATTC
AAATAAAAGTGCAAACCTATATTATTGGACCTGGATTATACGGATAGAAC
AAAAAAAATTATTCGCAAAAATACAGAATTTGTTATATAGCACGCGCACA
TCAATGATTGCAACAAATTTGCACAGGTCCATGGTAGAATAAACTACAAG
TACTTCCGTAAAGTTGTGGCTGCCTTCTGGTCTACAATTTCTTATGACCG
AATCAGTAATCTTATTTTGATTCTGTAAAGAGATTCTTCGAAATGAAGGC
GTGGACTATCAGTAAAAATAAGTTGAATATTATCAATGACAAATAAGCGT
TTCTGGAAGTTTTTGATTAATAAATTTGGACTGGGAATCCCTCAACAATG
TCGGATATAAACAAACAAATATTATACCGTTTACTAATAGTCTAATGGCT
GAGATTGCTGCTCAGAGCATAAAGTCATGAAAAAATTACGAATTGAAGAA
AATGAAGAGAGTATTTTCATGTGATTCATTTGAAAGAGGTAATCTGGACA
GCTGATTTCTAGACTATTATTACAAAAAAGAACGAAATAAAAATAGATCC
AAACTTTAAAGAACAACATGGTATTAGGGAACTACAAATCCATTGGGTAA
GAGCTTACTTTGGAAATATATTTAGCTAAAATGAATAGAGTCGAGTTAAA
TGTGTTTGTGGAAGAAGAATAATACGCGAAAGGTTTATTTATAATGCTGG
TGAGACAGGTTTAAATTGGGAAAGTTTTCCCATCAAATCTTTAGTGTCGA
AATTACTATTACGCCGAGAGATCTCACAAAAATAGTACAAAACCATCAGA
TAAAGAAAATAAACCTTATAAAAGATCGATAAAATAATTTTATGAGTTTG
TATTGATTTATTGCAATTTAGATGTGCAACATATGCCAGGATTATCAGGT
GAATATTGTATTCCAAGTGGCCATTTGACATGCTATGCTTGTTTCTATCA
GTTATTCTTTTGTCCCTTCTGTAACACTGACATTTTGAGGTGGACATAAT
TATTCAGATATTTTCATCAATTTTCAACTGATATTTTCATTGATGTTTAC
GATTGATTAAAATTTATTGCTAATTGGTGCAGGTCAAATTATCGATTAAA
TTATTTGTTTATTTCCTTGTGTAATTTTATCATTTTACTAGCTTTCTCAC
CTTGCCATGCTCATATAGATTCGAATTCATTATAATTGATTTTAATAATT
TTTTATTACAAATATATGTCAATACTTGGCTATGTACAACCTTCCATAAA
CTTTTGTTGATGAACAATGTTGAAAGATCCTTTGACATCTCTACATACAG
CTGTCAATGCAAGACGTACTTGTCTATTATCTTCAATTTATTTTCAATTC
TCTCCTGAACAGTCCAGCAGTCTGAAACAAAAATACTATCACTACGTTTA
ACTCCAGTGATATGAATATATCTTAGTGATTGATTATTGTTAGTTTGTCG
AGAGACATTATTTTCGTAATAAATCAAAATTACTTAAAACAGTTACCAAA
TAAATAAGATTAGTATTGGAAAGACACAAGTTTGAAGCTCACTCTTGCAG
TATAGGTAACTGATATGTAATTTACTTTCAATGCCCAGGCTCTTGGTTGA
GAGACTTACAAATTGAACTATCGCCTCCAATAACAGGCGAAATGGTTCAA
ACCAACTAAAGTGAAATAAATCTACCAGTAGTTGACAGCGAAACGAGAGG
GCCTCAAAGAGGAACGCCAACAGTTTCAAATGAGGAAAGTGAAGATTAAG
GCCCTCGAAACTGCCCTATCATCGAGTCAGAACGGAAACGCGGTGACCTA
TCCGCTGGTATTCGTTCCGGACCAACTAGCCTACAAAGAAAGAGCAGTTA
CAAGCTCCACTTACCAGAATCCAACCCCAGATAAATGGAAATGGTGAAAA
AAATAGATAATCAACCTTAATGGATTATTTTGTAATCAATTTCTGTCATT
AAAATTTAGAAAAGTTGTTTTGGATTTAATTTGTCATTAAAAGATCACGA
ATATAAGGAAAGAAGGGGTGAATCAGACCAAAAATGCATTGAAAGTCGAG
CAGATGCTTTCGACAGCTCGCTGAACCCAGAGTGTGTCTTATAGAAAGTA
GTCTTGGCGAAAATGCTGACCTTTGGCGGACCTACATCCACTCGTTACAT
TACCAAAGTTGCCTAGCAACGAGTAGCGAGTGGGCAAGGCAATCGCTTGT
ATGCATGGATTACTCAAGATCTGAAGTAGTAACCCACCAGTACGATATAT
TTTTAAAATATAAATTATTAATGAAGAAATAAGTTTGAAAAAAGAAATTT
AATTCTATTAAGTTTCAAGTTTGAATTTACATGACTATGACCATCAGTCT
ATCAAAATTAGGGTTTCCAAATATCCGGGTTTTCTGTAACCGAGGTTATT
GGATATTAATTTCAGAATTGTCCGCCGGATTCCAGATAACCGTATAAAAA
TAAACAAATAATATTGAACTTTAATTTTTTATAAATAAAATTTAAAATGC
ATACGTAATTATATTTTTTGAATTTTTTCATTTAAATAATAGTATTTCAG
GAAGGCTAATGCATTAAGTGGCGCACAAGAAAGACGAAATGTAATTTAGT
ATAGAAATTTCCAGAAACTGAAAAAATTCTCTCTGAATTTGTAGAAGTCG
GACTCGCTGTTTTTAGTGCTATATAGAGAAATTCAATATTTTGTGTTCTT
TTAATTGTTTTTTTGAAAATGCTAAATTCTTTCATAAGTACTATTAGTTA
TTGATATTCCTACTTGTTTATTGTTGGATTCATTTGAAATATATGAATTG
AGTGCTTCC
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protein sequence of SMED30011688-orf-1

>SMED30011688-orf-1 ID=SMED30011688-orf-1|Name=SMED30011688-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=103bp
MSTSKCQCYRRDKRITDRNKHSMSNGHLEYNIHLIILAYVAHLNCNKSIQ
THKIILSIFYKVYFLYLMVLYYFCEISRRNSNFDTKDLMGKLSQFKPVSP
AL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000418head
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR013083Znf_RING/FYVE/PHD
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR013083Zinc finger, RING/FYVE/PHD-typeGENE3DG3DSA:3.30.40.10coord: 6..38
e-value: 2.3E-5
score: 25.8
NoneNo IPR availableSUPERFAMILYSSF57850RING/U-boxcoord: 8..36
NoneNo IPR availableTMHMMTMhelixcoord: 10..32