SMED30029305

Overview
NameSMED30029305
Smed IDSMED30029305
Length (bp)897
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell 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 SMED30029305 (SMED30029305) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30029305 (SMED30029305) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30029305 (SMED30029305) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30029305 (SMED30029305) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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




SMED30029305

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
intestinal phagocyteSMED30029305SMESG000061791.1 Contig2041GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30029305SMESG000016407.1 Contig2041GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
gutSMED30029305SMESG000016407.1 dd_Smed_v4_2791_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
SMED30029305 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.008934:8588..9485 +4419
v31.009249:15530..16427 -4410
Homology
BLAST of SMED30029305 vs. TrEMBL
Match: A0A194ALC9 (Uncharacterized protein OS=Pinctada fucata OX=50426 PE=4 SV=1)

HSP 1 Score: 73.9442 bits (180), Expect = 3.076e-12
Identity = 49/130 (37.69%), Postives = 68/130 (52.31%), Query Frame = 2
Query:  185 WCLDKKIQTPLILPRIGKYSESCPH-VWSWNVLFHSWLYYNSTYLELIGNKSGGFVRISTSAPYAANRCKTFFTQLHSE-SNVSLECLRNCANQYLGYYGKYNYIFNNCHDFVNRLSKILCQGKPCPKWC 568
            WC+ K         + GK S    H +WS   L HS++YY+  Y E    K+   V  + +    +NRCK+   +  +  S +S+ECL+ C   Y G YGKY  + +NCH F NR+S ILC  K CP WC
Sbjct:   51 WCMMK-------YGKKGKRSAPKRHNLWS---LSHSFIYYDGWYFEFGVGKTHKAVYNTRAVK--SNRCKSRRDKKPAGYSTLSVECLKKCTKNYKGKYGKYRLLTHNCHHFANRISNILCNWKSCPSWC 168          
BLAST of SMED30029305 vs. TrEMBL
Match: A0A210QSH2 (Uncharacterized protein OS=Mizuhopecten yessoensis OX=6573 GN=KP79_PYT11711 PE=4 SV=1)

HSP 1 Score: 73.9442 bits (180), Expect = 4.872e-12
Identity = 37/101 (36.63%), Postives = 55/101 (54.46%), Query Frame = 2
Query:  281 FHSWLYYNSTYLE--LIGNKSGGF-VRISTSAPYAANRCKTFFTQL-HSESNVSLECLRNCANQYLGYYGKYNYIFNNCHDFVNRLSKILCQGKPCPKWCI 571
             HSW+ Y+  Y+E  +  N S  +   +S   P   ++C     Q     S++ ++C++ CA  Y+  YGKY    NNCH F+NR+SKILC    CP WC+
Sbjct:   81 IHSWIQYDGHYVEFGIYHNYSKPYNYSVSIERPAVGDKCNYRLQQTPKGYSSLGIDCIKGCARNYMRKYGKYRLFLNNCHVFINRISKILCHSTSCPSWCL 181          
BLAST of SMED30029305 vs. TrEMBL
Match: K1RU64 (Uncharacterized protein OS=Crassostrea gigas OX=29159 GN=CGI_10020876 PE=4 SV=1)

HSP 1 Score: 72.0182 bits (175), Expect = 3.884e-11
Identity = 43/139 (30.94%), Postives = 71/139 (51.08%), Query Frame = 2
Query:  221 LPRIGKYSESCPHVWSWNVLFHSWLYYNSTYLELIGNKSG-GFVRISTSAPYAANRCKTFFTQLHSE-SNVSLECLRNCANQYLGYYGKYNYIFNNCHDFVNRLSKILCQGKPCPKWCIS*PWPTG--DTHNYFYLTIA 625
            + R+ ++  + P  +++    H W++    YLE  GN+ G     + T+ P   N C     +  +  + +S  C+R+C   Y+  +G Y++  NNCH FVN++S +LC GK CPKWC   P   G  D  N   + +A
Sbjct:   64 IRRLNRHRRTPPSRFTFK-FSHRWIWTAGMYLEF-GNRIGRDAALVKTTYPNLGNVCTMTKEKTPAGYTRLSPGCIRSCIENYVDKFGNYSFYTNNCHHFVNKISILLCMGKKCPKWCKYTPEDDGEFDQENEHQMDLA 200          
BLAST of SMED30029305 vs. TrEMBL
Match: K1RAD8 (Uncharacterized protein OS=Crassostrea gigas OX=29159 GN=CGI_10020875 PE=4 SV=1)

HSP 1 Score: 70.0922 bits (170), Expect = 1.634e-10
Identity = 35/99 (35.35%), Postives = 53/99 (53.54%), Query Frame = 2
Query:  284 HSWLYYNSTYLELIGNKSG-GFVRISTSAPYAANRCK-TFFTQLHSESNVSLECLRNCANQYLGYYGKYNYIFNNCHDFVNRLSKILCQGKPCPKWCIS 574
            H W+YY   +LE  GN+ G     ++   P+  + C      +    S +S EC++ C   Y   YG Y+   NNCH FVN++SKI+C+   CP+WC+ 
Sbjct:   95 HRWIYYADMFLEF-GNRIGKDAALVNYYVPHLGDVCPLDLEPEPAGFSRLSPECVKGCVENYTDKYGNYHVYTNNCHHFVNKISKIMCESVICPEWCLP 192          
BLAST of SMED30029305 vs. TrEMBL
Match: A0A3L5TRF4 (Uncharacterized protein (Fragment) OS=Mytilus galloprovincialis OX=29158 GN=AM593_01840 PE=4 SV=1)

HSP 1 Score: 67.0106 bits (162), Expect = 1.191e-9
Identity = 38/102 (37.25%), Postives = 55/102 (53.92%), Query Frame = 2
Query:  275 VLFHSWLYYNSTYLELIGNKSGGFVRISTSAPYAANRCKTFFTQLHSE----SNVSLECLRNCANQYLGYYGKYNYIFNNCHDFVNRLSKILCQGKPCPKWC 568
            VL H W+ Y   Y E I   SG      +S    +++C T   Q  S+    S++S++C++ C N+Y   YG Y +  NNCH + NR+S+ILC    CP WC
Sbjct:   91 VLSHRWIQYKGYYFERIN--SGDIYTYGSSTE--SDKCST---QRESKPAGYSSLSVDCIKRCTNKYQRKYGSYGWWGNNCHHYANRISEILCTKTTCPSWC 185          
BLAST of SMED30029305 vs. Planmine SMEST
Match: SMESG000016407.1 (SMESG000016407.1)

HSP 1 Score: 314.694 bits (805), Expect = 2.020e-109
Identity = 149/151 (98.68%), Postives = 149/151 (98.68%), Query Frame = 2
Query:  122 TRKEQFRENDEAFVIGHTFPSWCLDKKIQTPLILPRIGKYSESCPHVWSWNVLFHSWLYYNSTYLELIGNKSGGFVRISTSAPYAANRCKTFFTQLHSESNVSLECLRNCANQYLGYYGKYNYIFNNCHDFVNRLSKILCQGKPCPKWCIS 574
            TRKEQFRENDEAFVIGHTFPSWCLDKKIQ PLILPRIGKYSESCPHVWSWNVLFHSWLYYNSTYLELIGNKSGGFVRISTSAPYAANRCKTFFTQLHSESNVSLECLRNC NQYLGYYGKYNYIFNNCHDFVNRLSKILCQGKPCPKWCIS
Sbjct:   17 TRKEQFRENDEAFVIGHTFPSWCLDKKIQNPLILPRIGKYSESCPHVWSWNVLFHSWLYYNSTYLELIGNKSGGFVRISTSAPYAANRCKTFFTQLHSESNVSLECLRNCTNQYLGYYGKYNYIFNNCHDFVNRLSKILCQGKPCPKWCIS 167          
The following BLAST results are available for this feature:
BLAST of SMED30029305 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 SMED30029305 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 SMED30029305 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 SMED30029305 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 SMED30029305 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 SMED30029305 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 SMED30029305 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 SMED30029305 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A194ALC93.076e-1237.69Uncharacterized protein OS=Pinctada fucata OX=5042... [more]
A0A210QSH24.872e-1236.63Uncharacterized protein OS=Mizuhopecten yessoensis... [more]
K1RU643.884e-1130.94Uncharacterized protein OS=Crassostrea gigas OX=29... [more]
K1RAD81.634e-1035.35Uncharacterized protein OS=Crassostrea gigas OX=29... [more]
A0A3L5TRF41.191e-937.25Uncharacterized protein (Fragment) OS=Mytilus gall... [more]
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BLAST of SMED30029305 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 SMED30029305 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 SMED30029305 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 SMED30029305 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 SMED30029305 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 SMED30029305 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000016407.12.020e-10998.68SMESG000016407.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029305 ID=SMED30029305|Name=SMED30029305|organism=Schmidtea mediterranea sexual|type=transcript|length=897bp
CGAATTCAAAATACATTTGGTAATTCAATAATTGACCTTTAACCGGAAAT
AAAAAATTTTATAGTCAAAAATTATGATAATAATATTATTTTTATTAACT
ATTATCAATATTTCATCGTCTACGAGAAAGGAACAGTTTCGAGAAAATGA
CGAAGCATTTGTAATTGGGCATACTTTTCCAAGTTGGTGTTTAGATAAGA
AAATCCAAACCCCTTTGATTTTACCAAGAATTGGAAAATATTCTGAATCT
TGTCCACATGTATGGAGTTGGAACGTCCTCTTTCATAGTTGGTTATATTA
TAATAGCACTTATCTGGAATTAATTGGGAACAAATCTGGTGGATTTGTCC
GAATTTCAACATCAGCACCTTACGCAGCGAATCGATGCAAAACGTTTTTC
ACCCAATTACACAGTGAAAGCAATGTGAGTCTGGAGTGCCTCCGTAACTG
CGCTAATCAATATCTTGGATACTATGGAAAATACAATTACATTTTTAATA
ATTGTCACGATTTTGTCAATCGCCTATCGAAAATCCTGTGCCAAGGAAAG
CCTTGTCCCAAATGGTGCATTTCTTAACCTTGGCCCACAGGAGATACGCA
CAACTATTTTTATCTGACCATTGCATGTTGAAATTTATTTTTAAATTTAT
TGTTTATTATTTTTATTTTGTCTCTGGGCCATCATTCCTTCAGTACATTA
GAAATCATGACTTTCTTGTTCAAAATAAACTTCCAATTAAACCTTTAAAT
TATGAAGGGTATGGTAATAAATGAATTTGCAAAATTCCAATAATTATATT
AAATATCTAAAATATTGCTTCTAAAATTGGATTATTATGAGTAGCAAGAA
ACAAGGATTCCAAAGCACGTTAACTTTACAATTTTTTTTAATTTATC
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protein sequence of SMED30029305-orf-1

>SMED30029305-orf-1 ID=SMED30029305-orf-1|Name=SMED30029305-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=168bp
MIIILFLLTIINISSSTRKEQFRENDEAFVIGHTFPSWCLDKKIQTPLIL
PRIGKYSESCPHVWSWNVLFHSWLYYNSTYLELIGNKSGGFVRISTSAPY
AANRCKTFFTQLHSESNVSLECLRNCANQYLGYYGKYNYIFNNCHDFVNR
LSKILCQGKPCPKWCIS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
Vocabulary: molecular function
TermDefinition
GO:0003677DNA binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..16
score: 0.766