SMED30010141

Overview
NameSMED30010141
Smed IDSMED30010141
Length (bp)579
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 SMED30010141 (SMED30010141) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30010141 (SMED30010141) 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



SMED30010141

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
reproductive organSMED30010141SMESG000053924.1 SMESG000053923.1 Contig18481newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30010141SMESG000053924.1 SMESG000053923.1 Contig18481uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30010141 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004240:10024..10649 -2870
Homology
[Close]
BLAST of SMED30010141 vs. TrEMBL
Match: A0A401NZ49 (Uncharacterized protein OS=Scyliorhinus torazame OX=75743 GN=scyTo_0011960 PE=4 SV=1)

HSP 1 Score: 67.3958 bits (163), Expect = 6.809e-11
Identity = 46/118 (38.98%), Postives = 63/118 (53.39%), Query Frame = 3 
Query:   57 YAEQINKEKDAVNNFEQRWGFVKGKLTDILTKEEICKLIDPCRPPIVIPDHLKLPECSEKVPKGVVAKPSPKPFPQTTAAEIGWRAQDRELLLELTSPPSR--MTFLRSMNWPMEAVD 404
            +   I  E DA   +  RWGF+  +   I+ ++E  KL + CR  +  PDHLK+   S  + K +   PSP P PQTT   IGWR+   EL LE  + PSR   +FL  M WP + +D
Sbjct:   20 WTNAILLEADAARKWVNRWGFLVTERDQIVAEQE--KLRNKCR--LHTPDHLKVRPASP-ISKYIKVGPSP-PLPQTTQGLIGWRSAVPELKLEKYAGPSRGKWSFLSQMKWPEDCID 131
[Close]
BLAST of SMED30010141 vs. TrEMBL
Match: A0A5K4F780 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 PE=4 SV=1)

HSP 1 Score: 67.3958 bits (163), Expect = 7.907e-11
Identity = 46/126 (36.51%), Postives = 67/126 (53.17%), Query Frame = 3 
Query:   36 YQLSPDAYAEQINKEKDAVNNFEQRWGFVKGKLTDILTKEEICKLIDPCRPPIVIPDHLKLPECSEKVPKGVVAK--PSPKPFPQTTAAEIGWRAQDRELLLELTSPPSR--MTFLRSMNWPMEAV 401
            Y  S   + +   KE  A   + + W F+     ++L K+E+ +LIDP R PI IP +LK+   +E VP     K  PSPKP PQTT+  IGWR+   +  L+      R   + L+  NWP+EA+
Sbjct:   17 YVASDKIWRDNCIKEASAAKAWSKNWSFLTLTPRELL-KDELHELIDPNRKPIEIPQYLKV---AEAVPISAYIKVEPSPKPIPQTTSRMIGWRSGLPQYKLDKYEVAKRPQGSLLKRFNWPIEAL 138
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BLAST of SMED30010141 vs. TrEMBL
Match: A0A4Z2D7W7 (Uncharacterized protein OS=Schistosoma japonicum OX=6182 GN=EWB00_003587 PE=4 SV=1)

HSP 1 Score: 67.0106 bits (162), Expect = 9.026e-11
Identity = 41/111 (36.94%), Postives = 64/111 (57.66%), Query Frame = 3 
Query:   75 KEKDAVNNFEQRWGFVKGKLTDILTKEEICKLIDPCRPPIVIPDHLKLPECSEKVPKGVVAKPSPKPFPQTTAAEIGWRAQDRELLLE--LTSPPSRMTFLRSMNWPMEAV 401
            KE  A   + + W F+     ++L K+E+ +LID  R PI +P HLK+ E    +   +  +PSPKP PQTT+  IGWR+   +  L+  + S P + + L+  NWP+EA+
Sbjct:   28 KEASASRTWSKNWNFLTLTPEELL-KDEMNQLIDTQRKPIEVPQHLKVTEAIP-ISDYIKVEPSPKPIPQTTSKMIGWRSGLSQYKLDKYIVSKP-QGSLLKRFNWPIEAL 135
[Close]
BLAST of SMED30010141 vs. TrEMBL
Match: C1L3T8 (Uncharacterized protein OS=Schistosoma japonicum OX=6182 PE=2 SV=1)

HSP 1 Score: 66.6254 bits (161), Expect = 1.303e-10
Identity = 41/111 (36.94%), Postives = 64/111 (57.66%), Query Frame = 3 
Query:   75 KEKDAVNNFEQRWGFVKGKLTDILTKEEICKLIDPCRPPIVIPDHLKLPECSEKVPKGVVAKPSPKPFPQTTAAEIGWRAQDRELLLE--LTSPPSRMTFLRSMNWPMEAV 401
            KE  A   + + W F+     ++L K+E+ +LID  R PI +P HLK+ E    +   +  +PSPKP PQTT+  IGWR+   +  L+  + S P + + L+  NWP+EA+
Sbjct:   28 KEASASRTWSKNWNFLTLTPEELL-KDEMNELIDTQRKPIEVPQHLKVTEAIP-ISDYIKVEPSPKPIPQTTSKMIGWRSGLSQYKLDKYIVSKP-QGSLLKRFNWPIEAL 135
[Close]
BLAST of SMED30010141 vs. TrEMBL
Match: A0A183NYV9 (Uncharacterized protein OS=Schistosoma mattheei OX=31246 GN=SMTD_LOCUS7295 PE=4 SV=1)

HSP 1 Score: 66.2402 bits (160), Expect = 1.648e-10
Identity = 45/126 (35.71%), Postives = 67/126 (53.17%), Query Frame = 3 
Query:   36 YQLSPDAYAEQINKEKDAVNNFEQRWGFVKGKLTDILTKEEICKLIDPCRPPIVIPDHLKLPECSEKVPKGVVAK--PSPKPFPQTTAAEIGWRAQDRELLLELTSPPSR--MTFLRSMNWPMEAV 401
            Y  S   + +   KE  A   + + W F+     ++L K+EI +LIDP R P+ IP +L++   +E VP     K  PSPKP PQTT+  IGWR+   +  L+      R   + L+  NWP+EA+
Sbjct:   17 YVASDKIWRDNCVKEASASKAWSKNWSFLTLTPRELL-KDEIHELIDPNRKPVEIPQYLRV---AEAVPISAYIKVEPSPKPIPQTTSRMIGWRSGLPQYKLDKYEVARRPQGSLLKRFNWPIEAL 138
[Close]
BLAST of SMED30010141 vs. Ensembl Nematostella
Match: EDO34523 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SP27])

HSP 1 Score: 51.9878 bits (123), Expect = 5.638e-9
Identity = 31/117 (26.50%), Postives = 54/117 (46.15%), Query Frame = 3 
Query:   57 YAEQINKEKDAVNNFEQRWGFVKGKLTDILTKEEICKLIDPCRPPIVIPDHLKLPECSEKVPKGVVAKPSPKPFPQTTAAEIGWRAQDRELLLELTSPPSRM--TFLRSMNWPMEAV 401
            + + I  E  A  ++ + WGF+  +   +  ++   +  +         ++LKLP     V   +    S   +P TTA+EIGWR+  R+  LE     ++   +FL  M WP EA+
Sbjct:   19 WKDHIGHEHGAAKHWPENWGFLIEQYKQLANEDNNIENGEAAVRVKQRRENLKLPPIDSSVASQLSVGRSKARYPSTTASEIGWRSSQRQCNLERYGRYTKQKSSFLGQMKWPPEAI 135
[Close]
BLAST of SMED30010141 vs. Planmine SMEST
Match: SMESG000053923.1 (SMESG000053923.1)

HSP 1 Score: 262.307 bits (669), Expect = 4.763e-91
Identity = 127/127 (100.00%), Postives = 127/127 (100.00%), Query Frame = 3 
Query:   24 MSKLYQLSPDAYAEQINKEKDAVNNFEQRWGFVKGKLTDILTKEEICKLIDPCRPPIVIPDHLKLPECSEKVPKGVVAKPSPKPFPQTTAAEIGWRAQDRELLLELTSPPSRMTFLRSMNWPMEAVD 404
            MSKLYQLSPDAYAEQINKEKDAVNNFEQRWGFVKGKLTDILTKEEICKLIDPCRPPIVIPDHLKLPECSEKVPKGVVAKPSPKPFPQTTAAEIGWRAQDRELLLELTSPPSRMTFLRSMNWPMEAVD
Sbjct:    1 MSKLYQLSPDAYAEQINKEKDAVNNFEQRWGFVKGKLTDILTKEEICKLIDPCRPPIVIPDHLKLPECSEKVPKGVVAKPSPKPFPQTTAAEIGWRAQDRELLLELTSPPSRMTFLRSMNWPMEAVD 127
[Close]
BLAST of SMED30010141 vs. Planmine SMEST
Match: SMESG000060159.1 (SMESG000060159.1)

HSP 1 Score: 75.485 bits (184), Expect = 1.553e-17
Identity = 42/124 (33.87%), Postives = 67/124 (54.03%), Query Frame = 3 
Query:   36 YQLSPDAYAEQINKEKDAVNNFEQRWGFVKGKLTDILTKEEICKLIDPCRPPIVIPDHLKLPECSEKVPKGVVAKPSPKPFPQTTAAEIGWRAQDRELLLELT--SPPSRMTFLRSMNWPMEAV 401
            Y      + +   +E      +E  W F+K    DI+ K+++ +L+D  RP   +P H+ +   + K  K V  KPS  PFP+TT+ E+GWR+  R+L LE    S  ++ + L+ +NWP EAV
Sbjct:   15 YTAQDQIWRDHCTQEMKKAGIWEHNWSFLKQSYRDII-KDDMDRLVDKDRPKAELPLHMHVQPATPK-SKYVSVKPSITPFPKTTSGEVGWRSAHRDLQLETIGKSKYAKGSILKQLNWPAEAV 136
The following BLAST results are available for this feature:
BLAST of SMED30010141 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 SMED30010141 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 SMED30010141 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 SMED30010141 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 SMED30010141 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 SMED30010141 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 SMED30010141 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 SMED30010141 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A401NZ496.809e-1138.98Uncharacterized protein OS=Scyliorhinus torazame O... [more]
A0A5K4F7807.907e-1136.51Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
A0A4Z2D7W79.026e-1136.94Uncharacterized protein OS=Schistosoma japonicum O... [more]
C1L3T81.303e-1036.94Uncharacterized protein OS=Schistosoma japonicum O... [more]
A0A183NYV91.648e-1035.71Uncharacterized protein OS=Schistosoma mattheei OX... [more]
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BLAST of SMED30010141 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 SMED30010141 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 SMED30010141 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 SMED30010141 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO345235.638e-926.50Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30010141 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 SMED30010141 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000053923.14.763e-91100.00SMESG000053923.1[more]
SMESG000060159.11.553e-1733.87SMESG000060159.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010141 ID=SMED30010141|Name=SMED30010141|organism=Schmidtea mediterranea sexual|type=transcript|length=579bp
TTATTGACGAAAAGCAGTAAATTATGTCAAAATTATATCAGTTATCCCCT
GATGCTTATGCAGAGCAAATTAATAAAGAAAAAGATGCTGTTAATAATTT
TGAACAGAGATGGGGATTTGTTAAAGGAAAACTGACAGATATCTTAACGA
AAGAAGAAATATGCAAATTAATAGATCCATGCCGACCACCAATAGTAATA
CCAGACCATTTGAAACTTCCAGAATGCAGTGAAAAAGTACCAAAAGGTGT
TGTTGCAAAACCTTCACCGAAACCTTTTCCACAAACTACGGCTGCCGAAA
TCGGTTGGAGAGCCCAAGACAGAGAGTTGTTACTGGAACTTACTTCACCT
CCATCTCGAATGACTTTCCTTAGATCTATGAATTGGCCAATGGAAGCTGT
AGACTAACATTGAGAAAATGCAGCGTCAATTTTACAAGCTTTAATTTGCA
AATATAATAGTTTTTAATTATTGTAAGTTCATTAATACAGTACCAAAATT
TGGTAAAAAATAGATGAGGATTATTTTCGTTTGCAATATGTGTTTGTCTA
ACCGCTTTCTTTGAATTTTTAGTCAAAAA
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protein sequence of SMED30010141-orf-1

>SMED30010141-orf-1 ID=SMED30010141-orf-1|Name=SMED30010141-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=128bp
MSKLYQLSPDAYAEQINKEKDAVNNFEQRWGFVKGKLTDILTKEEICKLI
DPCRPPIVIPDHLKLPECSEKVPKGVVAKPSPKPFPQTTAAEIGWRAQDR
ELLLELTSPPSRMTFLRSMNWPMEAVD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR020339Uncharacterised_C20orf85
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR020339Uncharacterised protein family C20orf85PFAMPF14945LLC1coord: 12..125
e-value: 1.3E-16
score: 61.3
NoneNo IPR availablePANTHERPTHR31909:SF3CHROMOSOME 20 OPEN READING FRAME 85coord: 14..127
NoneNo IPR availablePANTHERPTHR31909FAMILY NOT NAMEDcoord: 14..127
NoneNo IPR availablePRODOMPD297655coord: 10..126
e-value: 5.0E-5
score: 105.0