SMED30035470

Overview
NameSMED30035470
Smed IDSMED30035470
Length (bp)1537
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 SMED30035470 (SMED30035470) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30035470 (SMED30035470) 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.
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




SMED30035470

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



PAGE Curations: 14

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30035470h1SMcG0008880 dd_Smed_v4_1097_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30035470h1SMcG0008880 dd_Smed_v4_1097_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30035470h1SMcG0008880 dd_Smed_v4_1097_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30035470h1SMcG0008880 dd_Smed_v4_1097_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30035470h1SMcG0008880 dd_Smed_v4_1097_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30035470h1SMcG0008880 dd_Smed_v4_1097_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynxSMED30035470h1SMcG0020636 dd_Smed_v4_1097_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30035470h1SMcG0020636 dd_Smed_v4_1097_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30035470h1SMcG0020636 dd_Smed_v4_1097_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30035470h1SMcG0020636 dd_Smed_v4_1097_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30035470h1SMcG0020636 dd_Smed_v4_1097_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30035470h1SMcG0020636 dd_Smed_v4_1097_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30035470h1SMcG0008880 dd_Smed_v4_1097_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30035470h1SMcG0020636 dd_Smed_v4_1097_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
Alignments
SMED30035470 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003088:25235..26769 +7325
v31.001708:102074..103573 +5697
v31.013430:13356..14840 -4897
v31.013111:5180..7139 +4640
v31.003255:28683..30535 -4601
Homology
BLAST of SMED30035470 vs. Planmine SMEST
Match: SMESG000028747.1 (SMESG000028747.1)

HSP 1 Score: 132.494 bits (332), Expect = 2.345e-48
Identity = 61/79 (77.22%), Postives = 67/79 (84.81%), Query Frame = -3
Query:  189 MKHKFPLFPDIFFLLENSWIDASRVIARFPAHSAARCRQAMWDAGFSISPVRETRSGMQRDPDQVELPYVAI*REPGQG 425
            MKH F L P++ FLLENSWIDASRVIARFPAHSAARCRQAMWDA FSISPVRE RS  QR+ D+V+LPYV I REPG+ 
Sbjct:    1 MKHNFQLLPNVSFLLENSWIDASRVIARFPAHSAARCRQAMWDARFSISPVREARSDKQRNSDEVDLPYVVIKREPGRN 79          

HSP 2 Score: 78.5666 bits (192), Expect = 2.345e-48
Identity = 36/46 (78.26%), Postives = 43/46 (93.48%), Query Frame = -1
Query:   65 NPAREIQGQAEFLLARLEEHQKETDRQVEKARQYLNQVNVDIAAGK 202
            NPARE++GQAE+LLARLE+HQKET++QVEK RQYL Q+N DIAAGK
Sbjct:   79 NPAREMRGQAEYLLARLEKHQKETNKQVEKPRQYLRQINADIAAGK 124          

HSP 3 Score: 21.9422 bits (45), Expect = 2.345e-48
Identity = 10/19 (52.63%), Postives = 13/19 (68.42%), Query Frame = -2
Query:   13 GKKTSTDWEAPPPQLSYQV 69
            GK  STD  APP  +SY++
Sbjct:  123 GKIPSTDGYAPPYNISYEL 141          
BLAST of SMED30035470 vs. Planmine SMEST
Match: SMESG000003962.1 (SMESG000003962.1)

HSP 1 Score: 103.605 bits (257), Expect = 1.330e-38
Identity = 42/62 (67.74%), Postives = 54/62 (87.10%), Query Frame = -3
Query:  192 NSWIDASRVIARFPAHSAARCRQAMWDAGFSISPVRETRSGMQRDPDQVELPYVAI*REPGQ 377
            +SWIDASRV  RFPA SA RC+Q++WDAGFS+SPVRE R+G+QRD  +++LP+VAI REPG+
Sbjct:    8 HSWIDASRVTVRFPARSATRCQQSLWDAGFSVSPVREFRAGIQRDDGEIDLPFVAIKREPGR 69          

HSP 2 Score: 73.1738 bits (178), Expect = 1.330e-38
Identity = 31/45 (68.89%), Postives = 41/45 (91.11%), Query Frame = -1
Query:   68 NPAREIQGQAEFLLARLEEHQKETDRQVEKARQYLNQVNVDIAAG 202
            NPAREI+GQAEFLLARLEEHQ++T+RQV++AR++L ++N  IA G
Sbjct:   70 NPAREIRGQAEFLLARLEEHQRQTNRQVDRARRHLAEINKAIATG 114          

HSP 3 Score: 23.483 bits (49), Expect = 1.330e-38
Identity = 10/22 (45.45%), Postives = 13/22 (59.09%), Query Frame = -2
Query:    4 GKKTSTDWEAPPPQLSYQVAHP 69
            G   STD  APP  +SY + +P
Sbjct:  114 GAIPSTDGYAPPYNVSYDLNNP 135          
BLAST of SMED30035470 vs. Planmine SMEST
Match: SMESG000003962.1 (SMESG000003962.1)

HSP 1 Score: 103.605 bits (257), Expect = 1.330e-38
Identity = 42/62 (67.74%), Postives = 54/62 (87.10%), Query Frame = -3
Query:  192 NSWIDASRVIARFPAHSAARCRQAMWDAGFSISPVRETRSGMQRDPDQVELPYVAI*REPGQ 377
            +SWIDASRV  RFPA SA RC+Q++WDAGFS+SPVRE R+G+QRD  +++LP+VAI REPG+
Sbjct:    8 HSWIDASRVTVRFPARSATRCQQSLWDAGFSVSPVREFRAGIQRDDGEIDLPFVAIKREPGR 69          

HSP 2 Score: 73.1738 bits (178), Expect = 1.330e-38
Identity = 31/45 (68.89%), Postives = 41/45 (91.11%), Query Frame = -1
Query:   68 NPAREIQGQAEFLLARLEEHQKETDRQVEKARQYLNQVNVDIAAG 202
            NPAREI+GQAEFLLARLEEHQ++T+RQV++AR++L ++N  IA G
Sbjct:   70 NPAREIRGQAEFLLARLEEHQRQTNRQVDRARRHLAEINKAIATG 114          

HSP 3 Score: 23.483 bits (49), Expect = 1.330e-38
Identity = 10/22 (45.45%), Postives = 13/22 (59.09%), Query Frame = -2
Query:    4 GKKTSTDWEAPPPQLSYQVAHP 69
            G   STD  APP  +SY + +P
Sbjct:  114 GAIPSTDGYAPPYNVSYDLNNP 135          
BLAST of SMED30035470 vs. Planmine SMEST
Match: SMESG000065931.1 (SMESG000065931.1)

HSP 1 Score: 106.686 bits (265), Expect = 1.515e-38
Identity = 52/67 (77.61%), Postives = 56/67 (83.58%), Query Frame = -3
Query:  195 IFFLLENSWIDASRVIARFPAHSAARCRQAMWDAGFSISPVRETRSGMQRDPDQVELPYVAI*REPG 395
            I + LE+SWIDA RVIARFPAH+AARCRQAMWDAGFSIS VRETR G Q   + VELPYVAI REPG
Sbjct:    7 IHYNLEDSWIDAPRVIARFPAHAAARCRQAMWDAGFSISTVRETRFGNQGSSEDVELPYVAIKREPG 73          

HSP 2 Score: 72.7886 bits (177), Expect = 1.515e-38
Identity = 36/47 (76.60%), Postives = 41/47 (87.23%), Query Frame = -1
Query:   65 GNPAREIQGQAEFLLARLEEHQKETDRQVEKARQYLNQVNVDIAAGK 205
            GN AREI+GQAEFLL RLEEHQKET+RQ+ KAR+YL QVN DIA G+
Sbjct:   74 GNLAREIRGQAEFLLGRLEEHQKETERQIIKARRYLAQVNKDIAEGR 120          
BLAST of SMED30035470 vs. Planmine SMEST
Match: SMESG000013157.1 (SMESG000013157.1)

HSP 1 Score: 106.301 bits (264), Expect = 3.471e-38
Identity = 50/64 (78.12%), Postives = 55/64 (85.94%), Query Frame = -3
Query:  189 ENSWIDASRVIARFPAHSAARCRQAMWDAGFSISPVRETRSGMQRDPDQVELPYVAI*REPGQG 380
             +SWIDASRVIARFPAHSAARCRQAMWDAGFSI PVRETR G Q D ++V+L YVAI REPG+ 
Sbjct:   89 HDSWIDASRVIARFPAHSAARCRQAMWDAGFSIFPVRETRGGTQGDSNEVDLSYVAIKREPGRS 152          

HSP 2 Score: 71.633 bits (174), Expect = 3.471e-38
Identity = 34/46 (73.91%), Postives = 42/46 (91.30%), Query Frame = -1
Query:   65 NPAREIQGQAEFLLARLEEHQKETDRQVEKARQYLNQVNVDIAAGK 202
            +PARE++GQAE+LLARLE HQ ET+RQVE+ARQYL +VN DIAAG+
Sbjct:  152 SPAREMRGQAEYLLARLERHQAETNRQVEQARQYLRRVNEDIAAGR 197          
The following BLAST results are available for this feature:
BLAST of SMED30035470 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 SMED30035470 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 SMED30035470 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 SMED30035470 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 SMED30035470 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 SMED30035470 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 SMED30035470 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 SMED30035470 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30035470 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 SMED30035470 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 SMED30035470 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 SMED30035470 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 SMED30035470 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 SMED30035470 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000028747.12.345e-4877.22SMESG000028747.1[more]
SMESG000003962.11.330e-3867.74SMESG000003962.1[more]
SMESG000003962.11.330e-3867.74SMESG000003962.1[more]
SMESG000065931.11.515e-3877.61SMESG000065931.1[more]
SMESG000013157.13.471e-3878.13SMESG000013157.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035470 ID=SMED30035470|Name=SMED30035470|organism=Schmidtea mediterranea sexual|type=transcript|length=1537bp
TTGTGGGTGTGCCACCTGGTAGGATAATTGGGGGGGGGGGGCTTCCCAAT
CCGTACTGGTTTTTTTTCCCCGCCGCTATATCTACGTTGACCTGATTCAA
ATATTGTCTGGCCTTCTCCACTTGTCTGTCAGTTTCCTTCTGGTGTTCTT
CGAGGCGAGCCAACAGAAACTCAGCTTGGCCTTGAATCTCCCTGGCCGGG
TTCCCTTTATATCGCCACATAAGGGAGTTCGACCTGATCCGGATCCCTTT
GCATGCCCGATCTGGTCTCTCGCACCGGGGAAATGGAAAATCCCGCGTCC
CACATCGCCTGCCTACATCTGGCAGCCGAGTGAGCGGGGAACCGTGCAAT
AACACGGGATGCATCAATCCACGAGTTTTCTAAAAGAAAAAAAATATCAG
GAAATAATGGGAACTTGTGCTTCATTTTTGCGGACTGATAATCTTCGGAC
TTAGTGTTTGTCAATTTCATTTACCAGATTGCGGGCTGTCTCCTCCATTT
ATAGGGCTCGTGTACTTGTAAATCTCAATATTGTGGGGCGTGTGTGGGTA
CAGCATATACGCCTGGATCAAGATTGAGTTGTCGGGTCCTGTAGTATAAG
CGTAGTCAATTTGGTTCGTTTAAAGGAACCGTCAGGGTTGCCGTCGTGGT
AGTGGTGGTATGCTAGTTTTATGTTGCTAAATGTATCCTAACAGTGGGTC
GTCCTCGAGTAATGATTCCCAATTCTCGCATATCGCCGGCAGTGTGATTA
GAGGTTTAATTTTTAATACCATTTACTTACGCCAATCCACCCTAATTAGT
TATGATAGTTTAAAAATTACTTTTATAATCGATGAGTTTTCTTCATAATC
AATAAATTCTCCTAGAAAACGTTACGAATCGTTTTTTATTCGTACTAATA
AAATTTCAAACGACATTAAAATTATTTAAATTTTTAGATAAACGTTATGC
TGATAAATTACAGATGATGATAAAGATTAATTATTATGTAGATAAACTTT
ATACCAATAAATTACAAATGAGGATAAAGATTAATTATTATTTAGATACA
CTTTTGGGTCTTTCCAAGGTCAAATTAACGCACGCAAGATTCAAATTATA
ATTCCAATTTTACGAATAAAACTATCGCCGACGTTTAGATTAACTAGGAT
GGCAATACCAAATGCCATGACTATCGAGAACTCAATTAACTTATAATTTT
CAAATTCAATCAGTTAAAGATTCCAATCAAATATATTACTAAATTAACTT
ACACATCATTGTCATTATTGGGGTTCAATAGAAAGGTAGTAAAAGTTATA
TAATGTAAAAGCAAATATTGTAACTTGTCTTTTGTTCTTTGAACTCCTTA
CGTCTGCCAACACGATCTGCGAAAATTGGATTCATATCCTTACGCTTATG
ACGGTACTTAGTCGGGTGTTGGGTATTGGTCATTTGAAGCGACTTGAATG
GCTCATCTGTTTTAAATGTACATAATATTTATTCTTTTAGGGAACTGTTT
GAGGAACTCAAAGGAAAATCAGTCGAACGAGCATATT
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protein sequence of SMED30035470-orf-1

>SMED30035470-orf-1 ID=SMED30035470-orf-1|Name=SMED30035470-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=121bp
MHPVLLHGSPLTRLPDVGRRCGTRDFPFPRCERPDRACKGIRIRSNSLMW
RYKGNPAREIQGQAEFLLARLEEHQKETDRQVEKARQYLNQVNVDIAAGK
KNQYGLGSPPPPIILPGGTPT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0002032epidermal cell
PLANA:0003116parenchymal cell