SMED30001000

Overview
NameSMED30001000
Smed IDSMED30001000
Length (bp)458
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 SMED30001000 (SMED30001000) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30001000 (SMED30001000) 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



SMED30001000

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 organSMED30001000SMESG000001671.1 SMESG000001665.1 SMESG000001654.1 SMESG000001642.1 Contig46811newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30001000SMESG000001671.1 SMESG000001665.1 SMESG000001654.1 SMESG000001642.1 Contig46811uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30001000 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007422:1519..2823 +2272
v31.006552:11048..12310 -2157
v31.002073:43205..44507 +2130
v31.017738:5256..6552 +2112
Homology
[Close]
BLAST of SMED30001000 vs. Ensembl Zebrafish
Match: CR762475.1 (pep chromosome:GRCz11:4:55494751:55498830:1 gene:ENSDARG00000098243.2 transcript:ENSDART00000172605.2 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:CR762475.1)

HSP 1 Score: 40.817 bits (94), Expect = 7.732e-7
Identity = 17/36 (47.22%), Postives = 24/36 (66.67%), Query Frame = 2 
Query:    8 LLQYLRKIGLDLNN*RGMGFDGDSNMSGQYNAVQQK 115
            ++  L+  GLDL N RG G+DG +NMSG Y  +Q +
Sbjct:  455 VISLLQDNGLDLKNIRGQGYDGAANMSGMYKGLQSR 490

HSP 2 Score: 29.6462 bits (65), Expect = 7.732e-7
Identity = 11/24 (45.83%), Postives = 14/24 (58.33%), Query Frame = 1 
Query:  109 AKIRKILPNVIYVHCANHCLNLAF 180
            ++IR      +YVHC  HCLNL  
Sbjct:  489 SRIRAHNEKALYVHCQAHCLNLVL 512
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BLAST of SMED30001000 vs. TrEMBL
Match: A0A0J7NMX6 (Zinc finger mym-type protein 1-like protein OS=Lasius niger OX=67767 GN=RF55_5998 PE=4 SV=1)

HSP 1 Score: 45.4394 bits (106), Expect = 1.858e-9
Identity = 19/31 (61.29%), Postives = 23/31 (74.19%), Query Frame = 1 
Query:  106 AAKIRKILPNVIYVHCANHCLNLAFSRACTV 198
            AAKI +   N +YVHCANH LNLA S +C+V
Sbjct:  363 AAKINEQYTNALYVHCANHSLNLALSHSCSV 393

HSP 2 Score: 44.2838 bits (103), Expect = 1.858e-9
Identity = 21/41 (51.22%), Postives = 26/41 (63.41%), Query Frame = 2 
Query:    8 LLQYLRKIGLDLNN*RGMGFDGDSNMSGQYNAVQQK*EKYY 130
            LLQ L  +GLDL   RG+GFDG +NMSG +N    K  + Y
Sbjct:  330 LLQSLNDVGLDLKKMRGLGFDGAANMSGAFNGCAAKINEQY 370
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BLAST of SMED30001000 vs. TrEMBL
Match: A0A3S2KX46 (TTF-type domain-containing protein OS=Chilo suppressalis OX=168631 GN=evm_014807 PE=4 SV=1)

HSP 1 Score: 44.669 bits (104), Expect = 6.514e-7
Identity = 17/36 (47.22%), Postives = 27/36 (75.00%), Query Frame = 2 
Query:    8 LLQYLRKIGLDLNN*RGMGFDGDSNMSGQYNAVQQK 115
            ++Q L ++GL + N RG G+DG +NMSG+Y+ VQ +
Sbjct:  365 IIQELNQVGLQIENLRGQGYDGGANMSGKYSGVQSQ 400

HSP 2 Score: 36.5798 bits (83), Expect = 6.514e-7
Identity = 14/32 (43.75%), Postives = 23/32 (71.88%), Query Frame = 1 
Query:  109 AKIRKILPNVIYVHCANHCLNLAFSRACTVLS 204
            ++I+++ P   Y+HCA H LNLA  +AC++ S
Sbjct:  399 SQIKQLQPLATYMHCAAHKLNLAIVKACSLPS 430
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BLAST of SMED30001000 vs. TrEMBL
Match: J9LNR5 (DUF4371 domain-containing protein OS=Acyrthosiphon pisum OX=7029 PE=4 SV=1)

HSP 1 Score: 43.5134 bits (101), Expect = 7.848e-7
Identity = 18/30 (60.00%), Postives = 24/30 (80.00%), Query Frame = 1 
Query:  109 AKIRKILPNVIYVHCANHCLNLAFSRACTV 198
            A I++I PN IYVHC+ H LNLA S++C+V
Sbjct:  320 AHIQEIYPNAIYVHCSAHSLNLAVSKSCSV 349

HSP 2 Score: 37.3502 bits (85), Expect = 7.848e-7
Identity = 17/42 (40.48%), Postives = 27/42 (64.29%), Query Frame = 2 
Query:    8 LLQYLRKIGLDLNN*RGMGFDGDSNMSGQYNAVQQK*EKYYQ 133
            +L+ L++ G+D    RG G+DG + MSG+YN VQ   ++ Y 
Sbjct:  286 ILESLKQFGVDTKYLRGQGYDGAAAMSGKYNGVQAHIQEIYP 327
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BLAST of SMED30001000 vs. TrEMBL
Match: J9LUK6 (TTF-type domain-containing protein OS=Acyrthosiphon pisum OX=7029 PE=4 SV=2)

HSP 1 Score: 41.5874 bits (96), Expect = 2.852e-6
Identity = 20/45 (44.44%), Postives = 27/45 (60.00%), Query Frame = 2 
Query:    2 QTLLQYLRKIGLDLNN*RGMGFDGDSNMSGQYNAVQQK*EKYYQM 136
            + L+  L+ IGLDLN  RG G+DG S M G +N VQ    + Y +
Sbjct:  375 EVLIDSLKNIGLDLNFLRGQGYDGASAMRGHFNGVQAVVRRSYPL 419

HSP 2 Score: 37.3502 bits (85), Expect = 2.852e-6
Identity = 15/32 (46.88%), Postives = 21/32 (65.62%), Query Frame = 1 
Query:  109 AKIRKILPNVIYVHCANHCLNLAFSRACTVLS 204
            A +R+  P  +Y HC++H LNLA S AC + S
Sbjct:  411 AVVRRSYPLALYSHCSSHSLNLAISDACNIKS 442
[Close]
BLAST of SMED30001000 vs. TrEMBL
Match: J9M5M7 (Uncharacterized protein OS=Acyrthosiphon pisum OX=7029 PE=4 SV=2)

HSP 1 Score: 44.669 bits (104), Expect = 3.311e-6
Identity = 22/44 (50.00%), Postives = 27/44 (61.36%), Query Frame = 2 
Query:    5 TLLQYLRKIGLDLNN*RGMGFDGDSNMSGQYNAVQQK*EKYYQM 136
            TLL  L K+G+DL   RG GFDG + MSG +N VQ    K Y +
Sbjct:  298 TLLNTLDKLGIDLKYLRGKGFDGAATMSGCFNGVQSHVTKKYSL 341

HSP 2 Score: 33.8834 bits (76), Expect = 3.311e-6
Identity = 12/21 (57.14%), Postives = 15/21 (71.43%), Query Frame = 1 
Query:  142 YVHCANHCLNLAFSRACTVLS 204
            Y+HC +HCLNLA S  C + S
Sbjct:  344 YIHCTSHCLNLAISDTCNIQS 364
[Close]
BLAST of SMED30001000 vs. Ensembl Cavefish
Match: ENSAMXT00000035789.1 (pep primary_assembly:Astyanax_mexicanus-2.0:APWO02000101.1:2843018:2852765:1 gene:ENSAMXG00000037827.1 transcript:ENSAMXT00000035789.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 35.8094 bits (81), Expect = 1.091e-6
Identity = 13/21 (61.90%), Postives = 15/21 (71.43%), Query Frame = 1 
Query:  130 PNVIYVHCANHCLNLAFSRAC 192
            PN +YVHCA H LNL  + AC
Sbjct:  224 PNAVYVHCAAHNLNLVLNDAC 244

HSP 2 Score: 33.8834 bits (76), Expect = 1.091e-6
Identity = 15/36 (41.67%), Postives = 24/36 (66.67%), Query Frame = 2 
Query:    8 LLQYLRKIGLDLNN*RGMGFDGDSNMSGQYNAVQQK 115
            + + ++  GL L+  RG G+DG S MSG Y+ VQ++
Sbjct:  183 ITELIQSKGLPLHKCRGQGYDGASTMSGIYSGVQKR 218
[Close]
BLAST of SMED30001000 vs. Ensembl Cavefish
Match: ENSAMXT00000042930.1 (pep primary_assembly:Astyanax_mexicanus-2.0:12:25471427:25473738:-1 gene:ENSAMXG00000037442.1 transcript:ENSAMXT00000042930.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 35.8094 bits (81), Expect = 1.458e-6
Identity = 13/21 (61.90%), Postives = 15/21 (71.43%), Query Frame = 1 
Query:  130 PNVIYVHCANHCLNLAFSRAC 192
            PN +YVHCA H LNL  + AC
Sbjct:  266 PNAVYVHCAAHNLNLVLNDAC 286

HSP 2 Score: 33.113 bits (74), Expect = 1.458e-6
Identity = 15/36 (41.67%), Postives = 24/36 (66.67%), Query Frame = 2 
Query:    8 LLQYLRKIGLDLNN*RGMGFDGDSNMSGQYNAVQQK 115
            + + ++  GL L+  RG G+DG S MSG Y+ VQ++
Sbjct:  225 ITELIQSNGLLLHKCRGQGYDGASTMSGIYSGVQKR 260
[Close]
BLAST of SMED30001000 vs. Planmine SMEST
Match: SMESG000003943.1 (SMESG000003943.1)

HSP 1 Score: 42.3578 bits (98), Expect = 1.047e-10
Identity = 19/37 (51.35%), Postives = 28/37 (75.68%), Query Frame = 2 
Query:    5 TLLQYLRKIGLDLNN*RGMGFDGDSNMSGQYNAVQQK 115
            TL+Q+L  IGL+L+  +G G+DG + MSG++N VQ K
Sbjct: 1431 TLVQFLSSIGLNLSYLKGQGYDGAAAMSGRFNRVQAK 1467

HSP 2 Score: 40.4318 bits (93), Expect = 1.047e-10
Identity = 15/30 (50.00%), Postives = 21/30 (70.00%), Query Frame = 1 
Query:  109 AKIRKILPNVIYVHCANHCLNLAFSRACTV 198
            AKI  + P+ +YVHCA+H LNL+ S  C +
Sbjct: 1466 AKIMDLYPSTLYVHCASHSLNLSLSDVCQI 1495
The following BLAST results are available for this feature:
BLAST of SMED30001000 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 SMED30001000 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 SMED30001000 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 SMED30001000 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
CR762475.17.732e-747.22pep chromosome:GRCz11:4:55494751:55498830:1 gene:E... [more]
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BLAST of SMED30001000 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 SMED30001000 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 SMED30001000 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 SMED30001000 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A0J7NMX61.858e-961.29Zinc finger mym-type protein 1-like protein OS=Las... [more]
A0A3S2KX466.514e-747.22TTF-type domain-containing protein OS=Chilo suppre... [more]
J9LNR57.848e-760.00DUF4371 domain-containing protein OS=Acyrthosiphon... [more]
J9LUK62.852e-644.44TTF-type domain-containing protein OS=Acyrthosipho... [more]
J9M5M73.311e-650.00Uncharacterized protein OS=Acyrthosiphon pisum OX=... [more]
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BLAST of SMED30001000 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 2
Match NameE-valueIdentityDescription
ENSAMXT00000035789.11.091e-661.90pep primary_assembly:Astyanax_mexicanus-2.0:APWO02... [more]
ENSAMXT00000042930.11.458e-661.90pep primary_assembly:Astyanax_mexicanus-2.0:12:254... [more]
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BLAST of SMED30001000 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 SMED30001000 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 SMED30001000 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 SMED30001000 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 SMED30001000 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000003943.11.047e-1051.35SMESG000003943.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001000 ID=SMED30001000|Name=SMED30001000|organism=Schmidtea mediterranea sexual|type=transcript|length=458bp
TCAGACGCTACTTCAATATCTTAGAAAGATAGGCCTTGATCTTAATAATT
AGCGAGGTATGGGATTCGACGGGGATAGTAATATGAGTGGACAATATAAT
GCAGTGCAGCAAAAATAAGAAAAATATTACCAAATGTAATTTACGTACAT
TGTGCAAACCATTGTTTAAATCTAGCTTTTTCTCGCGCTTGCACTGTTCT
TTCTCATAGTTTCTAGGGCATTGATGAACTTTGCTAATATTGCATTTCCT
GCGACGTGCTTGCTGTCTTTCTAGCATTTTGAAAATCTTCATAATATTTA
CATCGCAATTTATTTACAGTTATTGGTTAGTAAATCAAGTTGTACAAACT
CCCTCGATTGTATCAATGTAAAAATATAACATTCAATTCACAAAAAAATA
ATTGCATTTATAAACTCACCCAAAATAAATAATAACTTTGTTGCTCTTTC
ATCGACTA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 52..74