SMED30016677

Overview
NameSMED30016677
Smed IDSMED30016677
Length (bp)1060
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 SMED30016677 (SMED30016677) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016677 (SMED30016677) 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 SMED30016677 (SMED30016677) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30016677 (SMED30016677) 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




SMED30016677

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30016677SMESG000047677.1 SmedASXL_017395SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
neuronSMED30016677SMESG000047677.1 dd_Smed_v4_12168_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
headSMED30016677SMESG000047677.1 dd_Smed_v6_12168_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30016677SMESG000047677.1 dd_Smed_v4_12168_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30016677 vs. TrEMBL
Match: A0A3Q3BX92 (DUF4817 domain-containing protein OS=Haplochromis burtoni OX=8153 PE=4 SV=1)

HSP 1 Score: 79.337 bits (194), Expect = 8.921e-13
Identity = 36/67 (53.73%), Postives = 45/67 (67.16%), Query Frame = -3
Query:    6 PPFYAKEVRKWLDNRFAGKWIGCRGPIEWLTRSPDLTPPDLFRWVILKNIAYGDHYDKLEALKKIII 206
            PP Y ++VR +LD +F GKWIGCRGP+EW  RSPDLTP D + W  LK I YG     ++ LK  I+
Sbjct:  249 PPHYGRQVRAFLDEQFPGKWIGCRGPVEWAPRSPDLTPFDFYLWGHLKAIVYGVKIRDVQHLKLRIL 315          
BLAST of SMED30016677 vs. TrEMBL
Match: K9J026 (Putative mariner OS=Desmodus rotundus OX=9430 PE=2 SV=1)

HSP 1 Score: 78.1814 bits (191), Expect = 2.304e-12
Identity = 36/66 (54.55%), Postives = 44/66 (66.67%), Query Frame = -3
Query:    9 PPFYAKEVRKWLDNRFAGKWIGCRGPIEWLTRSPDLTPPDLFRWVILKNIAYGDHYDKLEALKKII 206
            PP YA  VR+WLD  F G+WIG RGP+EW  RSPDLTPPD F W +LK++ Y      ++ LK  I
Sbjct:  246 PPHYASCVREWLDVHFKGRWIGRRGPLEWPARSPDLTPPDFFLWGVLKDLVYKTEPRNIDELKDRI 311          
BLAST of SMED30016677 vs. TrEMBL
Match: A0A151XG18 (Uncharacterized protein (Fragment) OS=Trachymyrmex zeteki OX=64791 GN=ALC60_01634 PE=4 SV=1)

HSP 1 Score: 72.0182 bits (175), Expect = 8.990e-12
Identity = 35/68 (51.47%), Postives = 45/68 (66.18%), Query Frame = -3
Query:    3 PPFYAKEVRKWLDNRFAGKWIGCRGPIEWLTRSPDLTPPDLFRWVILKNIAYGDHYDKLEALKKIIIH 206
            PP YA+ VR++L+  F G+WIG RGPIEW  RSPDL+P D F W  LK+  Y      LE L++ II+
Sbjct:    4 PPHYARLVREYLNKTFPGRWIGRRGPIEWPPRSPDLSPLDFFLWGHLKSKIYATQPTSLEGLRQRIIN 71          
BLAST of SMED30016677 vs. TrEMBL
Match: A0A2J7QIB5 (DUF4817 domain-containing protein OS=Cryptotermes secundus OX=105785 GN=B7P43_G03473 PE=4 SV=1)

HSP 1 Score: 72.0182 bits (175), Expect = 5.086e-11
Identity = 32/68 (47.06%), Postives = 44/68 (64.71%), Query Frame = -3
Query:    3 PPFYAKEVRKWLDNRFAGKWIGCRGPIEWLTRSPDLTPPDLFRWVILKNIAYGDHYDKLEALKKIIIH 206
            PP +A  VR +L   F  +WIG RGP+EW  RSPD+TPPD F W  LK+  Y +  D ++ L+++II 
Sbjct:  102 PPHFANIVRAFLHQVFPQRWIGRRGPVEWPARSPDITPPDFFLWGYLKDKVYANLIDSVKHLREVIIQ 169          
BLAST of SMED30016677 vs. TrEMBL
Match: A0A026WGC9 (Uncharacterized protein (Fragment) OS=Ooceraea biroi OX=2015173 GN=X777_04497 PE=4 SV=1)

HSP 1 Score: 69.707 bits (169), Expect = 5.228e-11
Identity = 33/66 (50.00%), Postives = 40/66 (60.61%), Query Frame = -3
Query:    9 PPFYAKEVRKWLDNRFAGKWIGCRGPIEWLTRSPDLTPPDLFRWVILKNIAYGDHYDKLEALKKII 206
            P  YA++VR WLD  +A +WIG  GP+ W  RSPDLTP D + W  LKN  Y      LE LK+ I
Sbjct:   19 PSHYARQVRNWLDEHYAHRWIGRGGPVFWPPRSPDLTPLDFYLWATLKNKVYSTEVISLEDLKQRI 84          
BLAST of SMED30016677 vs. Ensembl Nematostella
Match: EDO42554 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S185])

HSP 1 Score: 58.151 bits (139), Expect = 2.092e-9
Identity = 40/168 (23.81%), Postives = 81/168 (48.21%), Query Frame = 1
Query:  229 ELSFTNFTDLIMEEIMQENGDPAPLLLTLDLFGFNEKCMIEEAFPFSMTFYVENSDYLAKCFGIHNKTILVESSLKNFVV----TQGEKLSGKVNWKDCNVYMSCRNGRILVAVENTNPASKQIPVRLTINMEKSKNLAVYKDKFQRNVSIDTGTKLLAVHGVPIEPK 720
            +++ + F +L + E    +GDP  L +T++  G+N+   +++A  F +  +V N +      G+   +  +E +L   V+    T  E + G    +D  +Y    N R  + +EN +       V++ ++  KSKN   ++D+    + I +G + +  H VP +PK
Sbjct:  425 QITLSGFLELNLMEAKDADGDPDDLWVTMESMGYNKSLELDQACSFYLDVFVRNCEPKLTVTGVGGDSEDLEKALMTSVMRSSATHRENVKG---MRDLILYRYDSNVRTTIMIENQS----YTDVKVRVDCGKSKNCVSHRDELDYVIDIKSGKRQVVHHIVPSDPK 585          
BLAST of SMED30016677 vs. Ensembl Medaka
Match: efcab7 (EF-hand calcium binding domain 7 [Source:NCBI gene;Acc:101154938])

HSP 1 Score: 51.2174 bits (121), Expect = 9.497e-7
Identity = 39/168 (23.21%), Postives = 76/168 (45.24%), Query Frame = 1
Query:  217 LHNGELSFTNFTDLIMEEIMQENGDPAPLLLTLDLFGFNEKCMIEEAFPFSMTFYVENSDYLAKCFGIHNKTILVESSLKNFVVTQGEKLSGKVNWKDCNVYMSCRNGRILVAVENTNPASKQIPVRLTINMEKSKNLAVYKDKFQRNVSIDTGTKLLAVHGVPIEPK 720
            +   +L+   F +L + E  +++GD A L +TL+  G+N    + EA PF +  Y E+S    +   + +   L+  +++  +     K   K      NV++    G   ++    N  ++++ V   +N E+S+N    +      V I   TK++  H +PI  K
Sbjct:  437 MRKNQLTRQGFMELNLMEATEKDGDSADLWVTLEAMGYNHMLELTEACPFQIDVYCESSQPSIQSLSLESGPKLLNQAVQKSITA---KSGAKALRGHDNVFIFTYRGEHRISSVIANKTNQKVTVH--VNNEQSRNCCSSRGMTVFAVEIPARTKMVCQHVMPINDK 599          
BLAST of SMED30016677 vs. Planmine SMEST
Match: SMESG000047677.1 (SMESG000047677.1)

HSP 1 Score: 387.882 bits (995), Expect = 3.796e-131
Identity = 183/184 (99.46%), Postives = 183/184 (99.46%), Query Frame = 1
Query:  205 GHVKLHNGELSFTNFTDLIMEEIMQENGDPAPLLLTLDLFGFNEKCMIEEAFPFSMTFYVENSDYLAKCFGIHNKTILVESSLKNFVVTQGEKLSGKVNWKDCNVYMSCRNGRILVAVENTNPASKQIPVRLTINMEKSKNLAVYKDKFQRNVSIDTGTKLLAVHGVPIEPKVPISCDCFIRRS 756
             HVKLHNGELSFTNFTDLIMEEIMQENGDPAPLLLTLDLFGFNEKCMIEEAFPFSMTFYVENSDYLAKCFGIHNKTILVESSLKNFVVTQGEKLSGKVNWKDCNVYMSCRNGRILVAVENTNPASKQIPVRLTINMEKSKNLAVYKDKFQRNVSIDTGTKLLAVHGVPIEPKVPISCDCFIRRS
Sbjct:  412 SHVKLHNGELSFTNFTDLIMEEIMQENGDPAPLLLTLDLFGFNEKCMIEEAFPFSMTFYVENSDYLAKCFGIHNKTILVESSLKNFVVTQGEKLSGKVNWKDCNVYMSCRNGRILVAVENTNPASKQIPVRLTINMEKSKNLAVYKDKFQRNVSIDTGTKLLAVHGVPIEPKVPISCDCFIRRS 595          
BLAST of SMED30016677 vs. Planmine SMEST
Match: SMESG000003879.1 (SMESG000003879.1)

HSP 1 Score: 105.145 bits (261), Expect = 2.448e-25
Identity = 51/68 (75.00%), Postives = 52/68 (76.47%), Query Frame = -3
Query:    3 PPFYAKEVRKWLDNRFAGKWIGCRGPIEWLTRSPDLTPPDLFRWVILKNIAYGDHYDKLEALKKIIIH 206
            PP YAKEVRKWLD RFA KWI  RGP EW  RSPDLT PD F W+ILKNI  G HYD LE LKKIIIH
Sbjct:   27 PPNYAKEVRKWLDIRFAVKWIDHRGPTEWPARSPDLTTPDFFLWIILKNIFNGKHYDNLEDLKKIIIH 94          
The following BLAST results are available for this feature:
BLAST of SMED30016677 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 SMED30016677 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 SMED30016677 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 SMED30016677 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 SMED30016677 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 SMED30016677 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 SMED30016677 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 SMED30016677 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A3Q3BX928.921e-1353.73DUF4817 domain-containing protein OS=Haplochromis ... [more]
K9J0262.304e-1254.55Putative mariner OS=Desmodus rotundus OX=9430 PE=2... [more]
A0A151XG188.990e-1251.47Uncharacterized protein (Fragment) OS=Trachymyrmex... [more]
A0A2J7QIB55.086e-1147.06DUF4817 domain-containing protein OS=Cryptotermes ... [more]
A0A026WGC95.228e-1150.00Uncharacterized protein (Fragment) OS=Ooceraea bir... [more]
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BLAST of SMED30016677 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 SMED30016677 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 SMED30016677 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 SMED30016677 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO425542.092e-923.81Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30016677 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
efcab79.497e-723.21EF-hand calcium binding domain 7 [Source:NCBI gene... [more]
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BLAST of SMED30016677 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000047677.13.796e-13199.46SMESG000047677.1[more]
SMESG000003879.12.448e-2575.00SMESG000003879.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016677 ID=SMED30016677|Name=SMED30016677|organism=Schmidtea mediterranea sexual|type=transcript|length=1060bp
GAATGAATTATTATTTTCTTTAGAGCTTCCAATTTGTCATAATGATCACC
ATAGGCAATATTCTTAAGAATGACCCAACGGAATAAATCTGGTGGTGTTA
GATCAGGTGATCGAGTAAGCCATTCTATCGGTCCACGACAGCCAATCCAT
TTTCCTGCAAATCTGTTGTCCAACCATTTCCTCACTTCTTTCGCATAAAA
AGGAGGCCACGTAAAACTACATAATGGTGAATTGAGCTTCACTAATTTCA
CCGACTTAATTATGGAAGAAATTATGCAAGAAAACGGCGATCCTGCTCCA
CTTCTGCTTACGTTGGATTTGTTTGGATTCAATGAGAAATGCATGATAGA
AGAAGCGTTTCCATTTTCTATGACGTTTTATGTGGAAAATTCAGATTATT
TAGCTAAATGTTTCGGTATCCATAATAAGACAATTCTGGTAGAATCTTCA
TTGAAAAATTTTGTCGTTACTCAGGGAGAAAAACTTTCGGGAAAAGTCAA
TTGGAAAGATTGTAACGTGTATATGTCTTGCAGAAACGGCCGTATTCTAG
TTGCTGTTGAAAATACTAATCCAGCTTCTAAACAGATTCCTGTTCGACTT
ACAATTAACATGGAAAAAAGTAAAAATTTGGCTGTTTATAAAGATAAATT
TCAAAGAAATGTTTCAATTGACACGGGAACGAAATTACTAGCCGTGCACG
GTGTGCCCATAGAACCTAAAGTCCCAATTTCCTGTGACTGTTTTATAAGA
AGAAGTTGAAATTCTTAACCGGATATCTATAAAACGTCTCGCGAAAATCC
CGTGATTAAAATTTTGTTCCCAACTATCTGTCTAATCATGATATTGTATG
AGTTTGATGGCAGTGTGGGATTCACTGTGTTGCGTTTGGGCTTTTCCTGC
TCCGAATATATTTCGTATTTTGCCTGTGAATGTGTATGTGAATGAGTTAC
AAATTTTCTATTTCTACACCAATTTATCCCACTGCTACACTGAAGAGTAC
TGGGAAAATATTCTCGATATTTTATATCTTTGTTTCATATATCTTTGATT
TTAATAATAA
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protein sequence of SMED30016677-orf-1

>SMED30016677-orf-1 ID=SMED30016677-orf-1|Name=SMED30016677-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=114bp
MHFSLNPNKSNVSRSGAGSPFSCIISSIIKSVKLVKLNSPLCSFTWPPFY
AKEVRKWLDNRFAGKWIGCRGPIEWLTRSPDLTPPDLFRWVILKNIAYGD
HYDKLEALKKIIIH
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protein sequence of SMED30016677-orf-2

>SMED30016677-orf-2 ID=SMED30016677-orf-2|Name=SMED30016677-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=166bp
MEEIMQENGDPAPLLLTLDLFGFNEKCMIEEAFPFSMTFYVENSDYLAKC
FGIHNKTILVESSLKNFVVTQGEKLSGKVNWKDCNVYMSCRNGRILVAVE
NTNPASKQIPVRLTINMEKSKNLAVYKDKFQRNVSIDTGTKLLAVHGVPI
EPKVPISCDCFIRRS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000418head
Vocabulary: molecular function
TermDefinition
GO:0005509calcium ion binding
GO:0046872metal ion binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availablePANTHERPTHR46819FAMILY NOT NAMEDcoord: 3..153