SMED30019379

Overview
NameSMED30019379
Smed IDSMED30019379
Length (bp)766
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 SMED30019379 (SMED30019379) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30019379 (SMED30019379) 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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Homology
BLAST of SMED30019379 vs. TrEMBL
Match: A0A5J4NT45 (FAS-associated factor 1 (Fragment) OS=Paragonimus westermani OX=34504 GN=DEA37_0009957 PE=4 SV=1)

HSP 1 Score: 57.3806 bits (137), Expect = 9.333e-6
Identity = 30/109 (27.52%), Postives = 54/109 (49.54%), Query Frame = 2
Query:   83 DMMTPSFLKCGFNEAVMSTV-ANRPATSKPFIVYMHDSKDDMHRLFFKENICNEIVCEYLIKEDWPIWPIDISNQNEKQQFFNLMSNRLDAKEIFAYPL-----PMLMM 391
            + M P F     + A+ STV A   A  KP  +Y+H+ +     +F ++ +C+  VC++  + D+ +WP D++    K++ F  + N+L        PL     P+L M
Sbjct:   68 EAMAPPFTTGSLDTALNSTVGATTVAERKPLFIYLHNDESVACHVFCQKILCSTSVCQFFGENDFSLWPWDVTRSRAKERLFGWLENKLPNLASVVIPLSVDNYPVLAM 176          
BLAST of SMED30019379 vs. Planmine SMEST
Match: SMESG000077914.1 (SMESG000077914.1)

HSP 1 Score: 414.075 bits (1063), Expect = 4.765e-147
Identity = 244/251 (97.21%), Postives = 248/251 (98.80%), Query Frame = 2
Query:   14 MTSEHFVDCNLRFFEYLENSIGKDMMTPSFLKCGFNEAVMSTVANRPATSKPFIVYMHDSKDDMHRLFFKENICNEIVCEYLIKEDWPIWPIDISNQNEKQQFFNLMSNRLDAKEIFAYPLPMLMMCIREGLSTVIREYMWSPDPTMNVRKLFDCGVTFQTDKEXXXXXXXXXXXXXXXXXXXXXAXXXXXXXXXXXXXXXXXXXXXXXDKENLQTVEEFNRSNAIEFAKSQLVDFSPSPSNFTFRIRLPN 766
            MT+E+FVDCNLRFFEYLENSIGKDMMTPSFLKCGFNEAVMSTVANRPATSKPFIVYMHDSKDDMHRLFFKENICNEIVCEYLIKEDWPIWPIDISNQNEKQQFFNLMSNRLDAKEIFAYPLPMLMMCIREGLSTVIREYMWSPDPTMNVRKLFDCGVTFQT+KE+KMNMINSSSKK SISRKIKNAEIEKDLKDLELKKKALLEQLERLDKENLQTVEE NRSNAIEFAKSQLVD SPSPSNFTFRIRLPN
Sbjct:    1 MTNENFVDCNLRFFEYLENSIGKDMMTPSFLKCGFNEAVMSTVANRPATSKPFIVYMHDSKDDMHRLFFKENICNEIVCEYLIKEDWPIWPIDISNQNEKQQFFNLMSNRLDAKEIFAYPLPMLMMCIREGLSTVIREYMWSPDPTMNVRKLFDCGVTFQTNKELKMNMINSSSKKSSISRKIKNAEIEKDLKDLELKKKALLEQLERLDKENLQTVEESNRSNAIEFAKSQLVDVSPSPSNFTFRIRLPN 251          
BLAST of SMED30019379 vs. Planmine SMEST
Match: SMESG000077910.1 (SMESG000077910.1)

HSP 1 Score: 373.244 bits (957), Expect = 6.539e-131
Identity = 204/251 (81.27%), Postives = 227/251 (90.44%), Query Frame = 2
Query:   14 MTSEHFVDCNLRFFEYLENSIGKDMMTPSFLKCGFNEAVMSTVANRPATSKPFIVYMHDSKDDMHRLFFKENICNEIVCEYLIKEDWPIWPIDISNQNEKQQFFNLMSNRLDAKEIFAYPLPMLMMCIREGLSTVIREYMWSPDPTMNVRKLFDCGVTFQTDKEXXXXXXXXXXXXXXXXXXXXXAXXXXXXXXXXXXXXXXXXXXXXXDKENLQTVEEFNRSNAIEFAKSQLVDFSPSPSNFTFRIRLPN 766
            M +E+FVDCNLRFFEYLENSIGK+MMTPSFLKCGFNEAVMSTVANRPATSKPFIVYMHDSKDDMHRLFFKEN+CN+IVCEYLIKEDWPIWPIDISNQNEKQQFFNLMSNRLDAKEIFA+PLPMLMMCIREGLST I E+M S DP MNV KLFDCG  FQTDKE+KMN+INS  +K  I++K K +E+E+  +  EL++KA+LE+ ER+ KENL+ V+E NRSNAIEFAKSQLVD SPSPSNFTFRIRLPN
Sbjct:    1 MANENFVDCNLRFFEYLENSIGKNMMTPSFLKCGFNEAVMSTVANRPATSKPFIVYMHDSKDDMHRLFFKENVCNDIVCEYLIKEDWPIWPIDISNQNEKQQFFNLMSNRLDAKEIFAHPLPMLMMCIREGLSTFITEFMCSTDPMMNVGKLFDCGGAFQTDKELKMNIINSVREKSLIAKKKKESELEEKRQKQELERKAILEEQERISKENLRLVKESNRSNAIEFAKSQLVDVSPSPSNFTFRIRLPN 251          
BLAST of SMED30019379 vs. Planmine SMEST
Match: SMESG000039424.1 (SMESG000039424.1)

HSP 1 Score: 324.709 bits (831), Expect = 4.411e-111
Identity = 175/237 (73.84%), Postives = 193/237 (81.43%), Query Frame = 2
Query:   56 EYLENSIGKDMMTPSFLKCGFNEAVMSTVANRPATSKPFIVYMHDSKDDMHRLFFKENICNEIVCEYLIKEDWPIWPIDISNQNEKQQFFNLMSNRLDAKEIFAYPLPMLMMCIREGLSTVIREYMWSPDPTMNVRKLFDCGVTFQTDKEXXXXXXXXXXXXXXXXXXXXXAXXXXXXXXXXXXXXXXXXXXXXXDKENLQTVEEFNRSNAIEFAKSQLVDFSPSPSNFTFRIRLPN 766
            E   NSIGKDMMTPSFLKC F+EA+MSTVANRPATSKPFIVYMHDS DDMH LFF EN+CNEIVCEYLIKEDWPIWPID+SNQNEKQQFFNLMSNRL+AKEIFAYPLPMLMMCIREGLST I EYM SPDP MNV KLFDCG  FQTDKE+K+NM                   ++  +  EL++KA+LE+ ER++KENL+ VEE NR+NAIEFAK QLVD SPS SNF FRIRLPN
Sbjct:   78 EECTNSIGKDMMTPSFLKCDFDEALMSTVANRPATSKPFIVYMHDSNDDMHSLFFMENVCNEIVCEYLIKEDWPIWPIDLSNQNEKQQFFNLMSNRLEAKEIFAYPLPMLMMCIREGLSTFITEYMCSPDPMMNVGKLFDCGGAFQTDKELKINM-----------------INKEKRQKEELERKAILEEQERIEKENLRLVEESNRNNAIEFAKGQLVDASPSHSNFIFRIRLPN 297          
BLAST of SMED30019379 vs. Planmine SMEST
Match: SMESG000055685.1 (SMESG000055685.1)

HSP 1 Score: 200.29 bits (508), Expect = 2.332e-64
Identity = 96/120 (80.00%), Postives = 107/120 (89.17%), Query Frame = 2
Query:    8 LIMTSEHFVDCNLRFFEYLENSIGKDMMTPSFLKCGFNEAVMSTVANRPATSKPFIVYMHDSKDDMHRLFFKENICNEIVCEYLIKEDWPIWPIDISNQNEKQQFF---NLMSNRLDAKE 358
            LI+T+E+FVDCNLRFFEYLENSIGKDMMTPSFLKCGF+EA+MSTVANRPATSKPFIVYMHDS DDMH LFF EN+CNEIVCEYLIKE WPI PID+SNQNEKQQ F   N+  N +D ++
Sbjct:    9 LIVTNENFVDCNLRFFEYLENSIGKDMMTPSFLKCGFDEALMSTVANRPATSKPFIVYMHDSNDDMHSLFFMENVCNEIVCEYLIKEYWPIRPIDLSNQNEKQQLFSIKNMYRNLIDNQQ 128          
BLAST of SMED30019379 vs. Planmine SMEST
Match: SMESG000055685.1 (SMESG000055685.1)

HSP 1 Score: 153.295 bits (386), Expect = 1.825e-46
Identity = 73/94 (77.66%), Postives = 81/94 (86.17%), Query Frame = 2
Query:   86 MMTPSFLKCGFNEAVMSTVANRPATSKPFIVYMHDSKDDMHRLFFKENICNEIVCEYLIKEDWPIWPIDISNQNEKQQFF---NLMSNRLDAKE 358
            MMTPSFLKCGF+EA+MSTVANRPATSKPFIVYMHDS DDMH LFF EN+CNEIVCEYLIKE WPI PID+SNQNEKQQ F   N+  N +D ++
Sbjct:    1 MMTPSFLKCGFDEALMSTVANRPATSKPFIVYMHDSNDDMHSLFFMENVCNEIVCEYLIKEYWPIRPIDLSNQNEKQQLFSIKNMYRNLIDNQQ 94          
The following BLAST results are available for this feature:
BLAST of SMED30019379 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 SMED30019379 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 SMED30019379 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 SMED30019379 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 SMED30019379 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 SMED30019379 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 SMED30019379 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 SMED30019379 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A5J4NT459.333e-627.52FAS-associated factor 1 (Fragment) OS=Paragonimus ... [more]
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BLAST of SMED30019379 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 SMED30019379 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 SMED30019379 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 SMED30019379 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 SMED30019379 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 SMED30019379 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000077914.14.765e-14797.21SMESG000077914.1[more]
SMESG000077910.16.539e-13181.27SMESG000077910.1[more]
SMESG000039424.14.411e-11173.84SMESG000039424.1[more]
SMESG000055685.12.332e-6480.00SMESG000055685.1[more]
SMESG000055685.11.825e-4677.66SMESG000055685.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30019379 ID=SMED30019379|Name=SMED30019379|organism=Schmidtea mediterranea sexual|type=transcript|length=766bp
AACATACTTAATAATGACTAGTGAACATTTCGTTGATTGTAACCTAAGGT
TCTTCGAATATTTAGAAAACTCAATTGGAAAAGATATGATGACACCTTCA
TTCTTGAAATGTGGTTTTAATGAAGCAGTTATGTCTACGGTTGCCAATAG
ACCTGCAACATCAAAGCCATTCATCGTTTATATGCATGATTCCAAAGATG
ATATGCATAGATTATTTTTCAAGGAAAATATTTGCAATGAGATCGTTTGT
GAATATCTTATCAAAGAAGATTGGCCAATTTGGCCGATAGATATCTCCAA
TCAAAATGAAAAACAACAATTTTTCAATTTGATGAGCAATCGTCTCGACG
CCAAGGAAATATTTGCGTATCCCTTACCAATGTTGATGATGTGTATAAGA
GAAGGATTGAGTACTGTCATTAGAGAATATATGTGGAGCCCTGATCCAAC
GATGAATGTTAGAAAATTATTCGACTGTGGCGTTACATTTCAGACAGATA
AAGAAATAAAAATGAATATGATTAATAGTAGTAGCAAAAAATTGTCTATT
TCGAGAAAGATTAAAAACGCTGAAATTGAAAAAGATCTAAAAGATTTAGA
ACTAAAGAAAAAAGCCTTATTGGAACAGCTAGAAAGGTTAGATAAAGAAA
ACCTTCAAACGGTTGAAGAATTCAATCGCAGTAATGCCATTGAATTCGCA
AAGAGTCAACTTGTTGATTTTTCTCCATCTCCTTCAAATTTTACATTTAG
AATACGTCTACCTAAC
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protein sequence of SMED30019379-orf-1

>SMED30019379-orf-1 ID=SMED30019379-orf-1|Name=SMED30019379-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=255bp
TYLIMTSEHFVDCNLRFFEYLENSIGKDMMTPSFLKCGFNEAVMSTVANR
PATSKPFIVYMHDSKDDMHRLFFKENICNEIVCEYLIKEDWPIWPIDISN
QNEKQQFFNLMSNRLDAKEIFAYPLPMLMMCIREGLSTVIREYMWSPDPT
MNVRKLFDCGVTFQTDKEIKMNMINSSSKKLSISRKIKNAEIEKDLKDLE
LKKKALLEQLERLDKENLQTVEEFNRSNAIEFAKSQLVDFSPSPSNFTFR
IRLPN
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
Vocabulary: INTERPRO
TermDefinition
IPR036249Thioredoxin-like_sf
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 189..223
IPR036249Thioredoxin-like superfamilyGENE3DG3DSA:3.40.30.10coord: 6..191
e-value: 4.7E-14
score: 54.3