SMED30009927

Overview
NameSMED30009927
Smed IDSMED30009927
Length (bp)818
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ 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




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 SMED30009927 (SMED30009927) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30009927 (SMED30009927) 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.
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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




SMED30009927

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30009927SMESG000032093.1 dd_Smed_v6_60023_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30009927 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007062:13126..23145 +4030
v31.009054:3379..13206 +4012
Homology
BLAST of SMED30009927 vs. TrEMBL
Match: A0A2G8LFR2 (G_PROTEIN_RECEP_F2_4 domain-containing protein OS=Stichopus japonicus OX=307972 GN=BSL78_04029 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 9.180e-6
Identity = 63/232 (27.16%), Postives = 109/232 (46.98%), Query Frame = 1
Query:   46 TYCGFLAIAFSANYAIDCNWIVMITHFALLSCLCWMMLIAADAAMTFSRLKAVTNTKGKLKKKFIIALIEVHLIV---LIFW-SPGVINYACG-YQCLGLLS--VTYGRIPTCWLSGSLS--ILYGVTSPATLTLLISMISLASSVFGIIRSIRKTSKVIQSKXXXXXXXXXXXXXXXXXXXTGVTIGMMQLSILFEWKSVNL-VFSAINSSLGVAIMVLFTCNNRVLNLYR 711
            T+   L +  S    + C  I +  HF  LS   W  +IA +   TF          G      I A +  HLI+   +I W SP +    C  +Q   +L     YG+  TCWL+  L+  +L+G+  PA L L  ++I   ++V GI R  ++TS V      +      ++  +K+ +L G++     L   F   +V L + + +N S+GV + +++ CN RV+++++
Sbjct:  637 TFLAQLLLLVSPANEVMCTLIAIFGHFIWLSTFIWTTVIAYNVTQTF----------GGTSSLLIDASVTSHLILRNTVIGWISPAMFVGICFVFQRSTILEERFDYGKGETCWLTPPLANFLLFGI--PAILCLTCNIIFYVTTVRGI-RDTKRTSLVATQTDESTLVKEEIVLFLKISVLMGLSWIWAILYGCFPQVTVLLYIHTFLNPSIGVFVFLIYVCNRRVISMWK 855          
BLAST of SMED30009927 vs. Ensembl Nematostella
Match: EDO31226 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SYI9])

HSP 1 Score: 46.2098 bits (108), Expect = 3.379e-6
Identity = 32/116 (27.59%), Postives = 53/116 (45.69%), Query Frame = 1
Query:   97 CNWIVMITHFALLSCLCWMMLIAADA--AMTFSRLKAVTNTKGKLK----KKFIIALIEVHLIVLIFWSPGVINYACGYQCLGLLSVTYGRIPTCWLSGSLSILYGVTSPATLTLL 426
            C +I ++ HFA L+   WM +IA D   A +FS   A+ + K K +    K+  I  + V ++V+I                G  ++ YG    CW++   + LY    P +L L+
Sbjct:   28 CVFIAIVLHFAFLASFSWMSIIAFDTWRAFSFSGQSAMRSDKAKQRQRIMKRLAIGYLSVFVLVIIL---------TALDQSGAFAIRYGGSKGCWINNGDANLYIFVIPVSLALV 134          
BLAST of SMED30009927 vs. Ensembl Nematostella
Match: EDO34420 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SPE2])

HSP 1 Score: 46.9802 bits (110), Expect = 4.440e-6
Identity = 52/202 (25.74%), Postives = 89/202 (44.06%), Query Frame = 1
Query:  121 HFALLSCLCWMMLIAADAAMTFSRL-KAVTNTKGKLKKKFIIALIEVHLIVLIFWSPGVINYACGYQCLGLLSVTYGRIPTCWLSGSLSILYGVTSPATLTLLISMISLASSVFGIIRSIRKTSKVIQSKXXXXXXXXXXXXXXXXXXXTGVTIGMMQLSILFEWKSVNLVFSAINSSLGVAIMVLFTCNNRVLNLYRKLLK 723
            HFALLS  CWM ++A D   TF++  +  T ++G     + I       I L      ++  +      G   + YGR   C++    ++LY    P  + LL + I+L  +++ I    +KTSK    +R      +    +  +GI   +       +  F W      F  +NS  G  I++ +  N RVL++YR+ L+
Sbjct:  481 HFALLSAFCWMNVLAFDVHHTFTKPGQRRTASRGHCPGTYAIYAAYSWGIPL-----AIVTISFSVDLSGSWRIGYGRGEYCFIENPSAMLYLFLLPVAIILLYNFIALFHTMWHIRAVRKKTSKASNQQRKPNLPIICFKMTSAMGITWVLAYFASTQATSFLW----YAFVILNSLQGFLILLSYVLNRRVLSMYRETLQ 673          
BLAST of SMED30009927 vs. Planmine SMEST
Match: SMESG000032093.1 (SMESG000032093.1)

HSP 1 Score: 447.588 bits (1150), Expect = 6.837e-153
Identity = 255/256 (99.61%), Postives = 256/256 (100.00%), Query Frame = 1
Query:    1 FPGXXXXXXXXXXXXTYCGFLAIAFSANYAIDCNWIVMITHFALLSCLCWMMLIAADAAMTFSRLKAVTNTKGKLKKKFIIALIEVHLIVLIFWSPGVINYACGYQCLGLLSVTYGRIPTCWLSGSLSILYGVTSPATLTLLISMISLASSVFGIIRSIRKTSKVIQSKXXXXXXXXXXXXXXXXXXXTGVTIGMMQLSILFEWKSVNLVFSAINSSLGVAIMVLFTCNNRVLNLYRKLLKFGCTPPPHGVPTSQS 768
            FPGLMVLSMSISLLITYCGFLAIAFSANYAIDCNWIVMITHFALLSCLCWMMLIAADAAMTFSRLKAVTNTKGKLKKKFII+LIEVHLIVLIFWSPGVINYACGYQCLGLLSVTYGRIPTCWLSGSLSILYGVTSPATLTLLISMISLASSVFGIIRSIRKTSKVIQSKRSNRNSNLLLLFSIKLGILTGVTIGMMQLSILFEWKSVNLVFSAINSSLGVAIMVLFTCNNRVLNLYRKLLKFGCTPPPHGVPTSQS
Sbjct:  580 FPGLMVLSMSISLLITYCGFLAIAFSANYAIDCNWIVMITHFALLSCLCWMMLIAADAAMTFSRLKAVTNTKGKLKKKFIISLIEVHLIVLIFWSPGVINYACGYQCLGLLSVTYGRIPTCWLSGSLSILYGVTSPATLTLLISMISLASSVFGIIRSIRKTSKVIQSKRSNRNSNLLLLFSIKLGILTGVTIGMMQLSILFEWKSVNLVFSAINSSLGVAIMVLFTCNNRVLNLYRKLLKFGCTPPPHGVPTSQS 835          
BLAST of SMED30009927 vs. Planmine SMEST
Match: SMESG000032103.1 (SMESG000032103.1)

HSP 1 Score: 231.876 bits (590), Expect = 1.249e-70
Identity = 140/238 (58.82%), Postives = 177/238 (74.37%), Query Frame = 1
Query:    1 FPGXXXXXXXXXXXXTYCGFLAIAFSANYAIDCNWIVMITHFALLSCLCWMMLIAADAAMTFSRLKAVTNTKGKLKKKFIIALIEVHLIVLIFWSPGVINYACGYQCLGLLSVTYGRIPTCWLSGSLSILYGVTSPATLTLLISMISLASSVFGIIRSIRKTSKVIQSKXXXXXXXXXXXXXXXXXXXTGVTIGMMQLSILFEWKSVNLVFSAINSSLGVAIMVLFTCNNRVLNLYRK 714
            FPGLM L+MS  LLITY GFL IAFS + A+DC+WIVMITHFALLSCLCWMMLIA D+AMTF+              KF I L+ V L V+IFW PGVIN+ACGY CL  L VTYGR+PTCWLSG++SIL+GVT PA  T  IS+IS   +++GI RSI+ T  +  +K  NRN+ L++LFSIKLG++TG+++G+MQ+SILF+WK +N + SA+NS LG+ I  +F CN R+  LY K
Sbjct:  517 FPGLMALAMSYCLLITYSGFLVIAFSGSLAMDCSWIVMITHFALLSCLCWMMLIAMDSAMTFAVRNMAHRRTTNSMNKFGIMLLFVLLTVMIFWIPGVINFACGYTCLYWLPVTYGRVPTCWLSGNISILFGVTGPAMATFGISLISFIVAIYGIYRSIQSTGSLTIAKSPNRNTKLIMLFSIKLGVITGMSLGIMQISILFDWKILNTISSAVNSCLGIFIGFVFNCNGRIWRLYFK 754          
BLAST of SMED30009927 vs. Planmine SMEST
Match: SMESG000032100.1 (SMESG000032100.1)

HSP 1 Score: 232.646 bits (592), Expect = 1.718e-70
Identity = 141/238 (59.24%), Postives = 178/238 (74.79%), Query Frame = 1
Query:    1 FPGXXXXXXXXXXXXTYCGFLAIAFSANYAIDCNWIVMITHFALLSCLCWMMLIAADAAMTFSRLKAVTNTKGKLKKKFIIALIEVHLIVLIFWSPGVINYACGYQCLGLLSVTYGRIPTCWLSGSLSILYGVTSPATLTLLISMISLASSVFGIIRSIRKTSKVIQSKXXXXXXXXXXXXXXXXXXXTGVTIGMMQLSILFEWKSVNLVFSAINSSLGVAIMVLFTCNNRVLNLYRK 714
            FPGLM L+MS  LLITY GFL IAFS + A+DC+WIVMITHFALLSCLCWMMLIA D+AMTF+              KF I L+ V L V+IFW PGVIN+ACGY CL  L VTYGR+PTCWLSG++SIL+GVT PA  T  IS+ISL  +++GI RSI+ T  +  +K  NRN+ L++LFSIKLG++TG+++G+MQ+SILF+WK +N + SA+NS LG+ I  +F CN R+  LY K
Sbjct:  597 FPGLMALAMSYCLLITYSGFLVIAFSGSLAMDCSWIVMITHFALLSCLCWMMLIAMDSAMTFALKNMAHRRTTNSMNKFGIMLLFVSLTVMIFWIPGVINFACGYTCLYWLPVTYGRVPTCWLSGNISILFGVTGPAMATFGISLISLIVAIYGIYRSIQSTGSLTIAKSPNRNTKLIMLFSIKLGVITGMSLGIMQISILFDWKILNTISSAVNSCLGIFIGFVFICNGRIWRLYFK 834          
The following BLAST results are available for this feature:
BLAST of SMED30009927 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 SMED30009927 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 SMED30009927 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 SMED30009927 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 SMED30009927 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 SMED30009927 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 SMED30009927 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 SMED30009927 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A2G8LFR29.180e-627.16G_PROTEIN_RECEP_F2_4 domain-containing protein OS=... [more]
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BLAST of SMED30009927 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 SMED30009927 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 SMED30009927 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 SMED30009927 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 2
Match NameE-valueIdentityDescription
EDO312263.379e-627.59Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
EDO344204.440e-625.74Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30009927 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 SMED30009927 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000032093.16.837e-15399.61SMESG000032093.1[more]
SMESG000032103.11.249e-7058.82SMESG000032103.1[more]
SMESG000032100.11.718e-7059.24SMESG000032100.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009927 ID=SMED30009927|Name=SMED30009927|organism=Schmidtea mediterranea sexual|type=transcript|length=818bp
TTTCCCGGTTTGATGGTTTTGTCTATGAGCATTAGTCTATTGATTACATA
TTGTGGATTTCTGGCAATCGCATTCAGCGCCAATTACGCAATCGATTGCA
ATTGGATAGTTATGATTACTCATTTTGCATTGTTGTCGTGTCTATGTTGG
ATGATGCTGATTGCTGCCGACGCGGCAATGACCTTTTCCCGGCTGAAAGC
TGTCACCAACACAAAGGGTAAGTTGAAGAAAAAATTCATCATTGCACTAA
TTGAAGTCCATTTGATTGTTTTGATATTTTGGAGTCCTGGAGTTATTAAT
TATGCCTGTGGTTACCAATGCCTCGGATTATTGTCGGTAACGTATGGTCG
TATTCCGACTTGTTGGTTGAGTGGAAGTCTGTCAATTTTGTATGGTGTGA
CAAGTCCAGCAACACTAACGTTACTGATATCCATGATTTCGCTGGCTTCA
AGTGTTTTTGGAATTATTAGGTCCATTCGGAAAACGAGCAAAGTCATTCA
ATCCAAGCGCTCAAATAGGAATTCAAATCTTTTACTGTTATTTTCCATCA
AACTCGGCATATTAACCGGAGTGACAATAGGAATGATGCAATTGAGCATT
TTGTTTGAATGGAAATCAGTCAATTTAGTGTTCAGCGCCATCAATTCCAG
TTTGGGAGTTGCGATAATGGTTTTATTTACTTGTAACAATCGGGTGCTGA
ATTTGTACCGCAAACTTCTCAAATTCGGCTGCACTCCTCCACCTCATGGA
GTTCCTACTTCACAATCATAAGGAAATCAAAACTTTAAATGGCTTTCACG
AATGATTTATTGTAATCA
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protein sequence of SMED30009927-orf-1

>SMED30009927-orf-1 ID=SMED30009927-orf-1|Name=SMED30009927-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=257bp
FPGLMVLSMSISLLITYCGFLAIAFSANYAIDCNWIVMITHFALLSCLCW
MMLIAADAAMTFSRLKAVTNTKGKLKKKFIIALIEVHLIVLIFWSPGVIN
YACGYQCLGLLSVTYGRIPTCWLSGSLSILYGVTSPATLTLLISMISLAS
SVFGIIRSIRKTSKVIQSKRSNRNSNLLLLFSIKLGILTGVTIGMMQLSI
LFEWKSVNLVFSAINSSLGVAIMVLFTCNNRVLNLYRKLLKFGCTPPPHG
VPTSQS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR000832GPCR_2_secretin-like
Vocabulary: molecular function
TermDefinition
GO:0004930G-protein coupled receptor activity
Vocabulary: biological process
TermDefinition
GO:0007186G-protein coupled receptor signaling pathway
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:1.20.1070.10coord: 2..244
e-value: 4.2E-17
score: 64.0
NoneNo IPR availablePANTHERPTHR45902FAMILY NOT NAMEDcoord: 1..239
NoneNo IPR availableCDDcd150397tmB3_Methuselah-likecoord: 1..238
e-value: 5.55713E-22
score: 89.5908
NoneNo IPR availableTMHMMTMhelixcoord: 79..101
NoneNo IPR availableTMHMMTMhelixcoord: 209..228
NoneNo IPR availableTMHMMTMhelixcoord: 5..27
NoneNo IPR availableTMHMMTMhelixcoord: 134..156
NoneNo IPR availableTMHMMTMhelixcoord: 108..130
NoneNo IPR availableTMHMMTMhelixcoord: 34..56
NoneNo IPR availableTMHMMTMhelixcoord: 177..199