SMED30031753

Overview
NameSMED30031753
Smed IDSMED30031753
Length (bp)1113
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 SMED30031753 (SMED30031753) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031753 (SMED30031753) 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 SMED30031753 (SMED30031753) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30031753 (SMED30031753) 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




SMED30031753

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30031753SMESG000065762.1 SmedASXL_025080SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30031753SMESG000065762.1 dd_Smed_v4_21049_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30031753SMESG000065762.1 dd_Smed_v4_21049_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30031753SMESG000065762.1 dd_Smed_v4_21049_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30031753SMESG000065762.1 dd_Smed_v4_21049_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30031753SMESG000065762.1 dd_Smed_v6_21049_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
SMED30031753 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007271:22508..23850 -5458
v31.000627:180785..182126 -5261
Homology
BLAST of SMED30031753 vs. Planmine SMEST
Match: SMESG000065762.1 (SMESG000065762.1)

HSP 1 Score: 327.791 bits (839), Expect = 4.550e-113
Identity = 161/171 (94.15%), Postives = 167/171 (97.66%), Query Frame = 1
Query:  337 LVLLDALSVIRKISIYGRTDTNELFNANFSIYISIKQEQDFDVNSREFIKIQDNFLGVGSPSVLFQHFYFESTVARTIAISKLPDKLGDLTLCEVEIFGEEYDKYSSNIYTFSHIQNTLQNSENVVIVSTESLLECGILCYVSDFCMSFTLRDLSSCVLYDNNWGRFMNIQ 849
            LVLL+ALSVIRKISI+GRTDTNELFNANFSIYISI QEQ+F+VNSREFIKIQDNFL VGSPSVLFQHFYFESTVARTIAISK PD+LGDLTLCEVEIFGEEYDKYSSNIYTFSH +NTLQNSENVVIVSTESLLECGILCYVSDFCMSFTLRDLSSCVLYDNNWGRFMNIQ
Sbjct:   24 LVLLNALSVIRKISIFGRTDTNELFNANFSIYISINQEQNFNVNSREFIKIQDNFLDVGSPSVLFQHFYFESTVARTIAISKWPDELGDLTLCEVEIFGEEYDKYSSNIYTFSHNRNTLQNSENVVIVSTESLLECGILCYVSDFCMSFTLRDLSSCVLYDNNWGRFMNIQ 194          

HSP 2 Score: 52.7582 bits (125), Expect = 5.919e-8
Identity = 25/35 (71.43%), Postives = 26/35 (74.29%), Query Frame = 2
Query:  269 METAMEMFTMIIAFKALENQDGGLYFWTRFQSLEK 373
            METAMEMFTMIIAFKALENQDGGL        + K
Sbjct:    1 METAMEMFTMIIAFKALENQDGGLVLLNALSVIRK 35          
BLAST of SMED30031753 vs. Planmine SMEST
Match: SMESG000024886.1 (SMESG000024886.1)

HSP 1 Score: 112.079 bits (279), Expect = 1.540e-28
Identity = 81/245 (33.06%), Postives = 119/245 (48.57%), Query Frame = 1
Query:  112 YFKMKLEKIF-LMFYVDFVVSQKLLSLKRNTVSPNYFSGNIVKKRVWSSELAVDGNSDGNVYNDHCFQSSGKP--RWWLVLLDALSVIRKISIYGRTDTNELFNANFSIYISIKQEQDFDVNSREFIKIQDNFLGVGSPSVLFQHFYFESTVARTIAISKLPDKLGDLTLCEVEIFGEEYDKYSSNIYTFSHIQNTLQNSENVVIVSTESLLECGILCYVSDFCMSFTLRDLSSCVLYDNNWGRF 837
            YFK   E I+ L F +D ++S+      R T     F   I    VW  + AVDGN DGN +N  CF S G    +WWLV+LD+LSV+ K+ IY RTD      +  S Y+S K       N  +F  I   + G   P  +     F+   ART+AISK P     + LCE+E++G    K    ++ +    +   +  NV I +  S L+C + C +++ C SF+++    C  Y +  G F
Sbjct:   27 YFK---ETIYSLSFVLDLILSRG-----RPT-----FGTIIAGYSVWEPQKAVDGNYDGNQFNGSCFHSEGPNVNKWWLVILDSLSVVTKVVIYSRTDCCTNRTSFISFYVSYKNSTSLTNNMNDFFNIS-YYAGPPPPGEIITTLNFKRLYARTLAISK-PLAADHINLCELEVYGYPLIKSMFTLFKYFGTLSLYDSLGNVGIFTVVSNLDCALKCLLNEKCYSFSVQLKVYCFNYGHTGGDF 256          
BLAST of SMED30031753 vs. Planmine SMEST
Match: SMESG000046835.1 (SMESG000046835.1)

HSP 1 Score: 113.62 bits (283), Expect = 6.633e-28
Identity = 70/226 (30.97%), Postives = 114/226 (50.44%), Query Frame = 1
Query:  166 VSQKLLSLKRNTVSPNYFSGNIVKKRVWSSELAVDGNSDGNVYNDHCFQSS--GKPRWWLVLLDALSVIRKISIYGRTDTNELFNANFSIYISIKQEQDFDVNSREFIKIQDNFLGVGSPSVLFQHFYFESTVARTIAISKLPDKLGDLTLCEVEIFGEEYDKYSSNIYTFSHIQNTLQNSENVVIVSTESLLECGILCYVSDFCMSFTLRDLSSCVLYDNNWGRF 837
            +  +LLS  R T + N     I    +W+S+ AVDGN D N+++ +C+ S      +WWLV+LD+LSV+ ++ IY RT+      +  S Y+S         NS +F+ I   ++G   P        F     RT+AISK P     L +CE+E++G  + K  S I+ +   Q+   +  N      +S ++C I+C     C+SF+++   SC +Y +  G F
Sbjct:  187 IRNQLLSRSRPTFAANV----IANYPLWTSDKAVDGNYDCNMHHGYCYHSEELNSTKWWLVILDSLSVVTRVVIYSRTECCTQRTSLLSFYVSYTNSTSLSTNSNDFVNI-SYYVGPPPPGEFITTLNFTRLYMRTLAISK-PFGEQALNICELEVYGYTFIKKMSMIFKYFGRQSLYDSLGNFGTFPVQSNIDCAIICLQEAKCLSFSVQFGVSCFIYAHIGGEF 406          
BLAST of SMED30031753 vs. Planmine SMEST
Match: SMESG000046841.1 (SMESG000046841.1)

HSP 1 Score: 108.997 bits (271), Expect = 1.557e-27
Identity = 71/237 (29.96%), Postives = 113/237 (47.68%), Query Frame = 1
Query:  139 FLMFYVDFVVSQ-KLLSLKRNTVSPNYFSGNIV-KKRVWSSELAVDGNSDGNVYNDHCFQSS--GKPRWWLVLLDALSVIRKISIYGRTDTNELFNANFSIYISIKQEQDFDVNSREFIKIQDNFLGVGSPSVLFQHFYFESTVARTIAISKLPDKLGDLTLCEVEIFGEEYDKYSSNIYTFSHIQNTLQNSENVVIVSTESLLECGILCYVSDFCMSFTLRDLSSCVLYDNNWGRF 837
            FL+F      +Q  LLS  R T     F+ N++  +  WSS+ AVDGN DGN+ + HC+ S      +WWL++LD+LSV+ ++ IY RT+      +  S Y+S         NS +F  +   + G   P        F    ART+AISK P       LCE+E++G  + K     + +    +   +  N+      S L+  ++C     C+SF+++    C +Y +  G F
Sbjct:   11 FLLFVFQITTAQNALLSRGRPT-----FAANVIDNQPYWSSDKAVDGNYDGNMVDGHCYHSKELNSTKWWLIILDSLSVVTRVVIYSRTECCTQRTSLLSFYVSYTNSTSLSTNSNDFTNV-SYYPGSPPPGEFITTLNFTRLYARTLAISK-PFAEQPFNLCELEVYGYPFIKTMPMTFKYLRALSIYDSLGNIGTFPVLSNLDSAMICLQEAKCISFSVQFSVKCFIYAHIGGEF 240          
BLAST of SMED30031753 vs. Planmine SMEST
Match: SMESG000024705.1 (SMESG000024705.1)

HSP 1 Score: 108.612 bits (270), Expect = 4.211e-27
Identity = 76/256 (29.69%), Postives = 124/256 (48.44%), Query Frame = 1
Query:   76 DSPIKPISRKKSYFKMKLEKIFLMFYVDFVVSQKLLSLKRNTVSPNYFSGNIVKKRVWSSELAVDGNSDGNVYNDHCFQSS--GKPRWWLVLLDALSVIRKISIYGRTDTNELFNANFSIYISIKQEQDFDVNSREFIKIQDNFLGVGSPSVLFQHFYFESTVARTIAISKLPDKLGDLTLCEVEIFGEEYDKYSSNIYTFSHIQNTLQNSENVVIVSTESLLECGILCYVSDFCMSFTLRDLSSCVLYDNNWGRF 837
            ++P++P+S  K    + +E I        V    LLS+ R T     F+ N +    W+S+ AVDGN +GN+    C+ S      +WWLV+LD+LSV+ K+ IY RTD      +  S Y+S K       N+ +F+ +   + G   P        F    ART+AISK P     + LCE+E++G  + K  S  + +    +   +  N      +S L+C ++C +   C+SF+++    C +Y +  G F
Sbjct:   38 EAPLRPLSSDKGLKVIIVEII--------VAEDSLLSIGRPT-----FANNAMFP--WTSDKAVDGNYNGNMSKGSCYHSETFNYDKWWLVILDSLSVVTKVVIYSRTDCCTQRTSLLSFYVSYKSSTSLSNNNNDFVNVS-YYAGPPPPGEFITTLNFTRLYARTLAISK-PSLEDAINLCELEVYGYPFTKTMSMTFKYFGALSIYDSLGNFGTFPVQSNLDCAMICLLEAKCLSFSVQFGVKCFIYFHTGGDF 276          
The following BLAST results are available for this feature:
BLAST of SMED30031753 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 SMED30031753 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 SMED30031753 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 SMED30031753 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 SMED30031753 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 SMED30031753 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 SMED30031753 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 SMED30031753 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 SMED30031753 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 SMED30031753 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 SMED30031753 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 SMED30031753 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 SMED30031753 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 SMED30031753 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000065762.14.550e-11394.15SMESG000065762.1[more]
SMESG000024886.11.540e-2833.06SMESG000024886.1[more]
SMESG000046835.16.633e-2830.97SMESG000046835.1[more]
SMESG000046841.11.557e-2729.96SMESG000046841.1[more]
SMESG000024705.14.211e-2729.69SMESG000024705.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031753 ID=SMED30031753|Name=SMED30031753|organism=Schmidtea mediterranea sexual|type=transcript|length=1113bp
CTTCAATTTCATCAAATATTTGATTTAGTTCCTGGGTAAACACTGCTTTC
GTGACTTGAAACGCAATTGGTTAAGGATTCCCCAATAAAGCCAATTAGTA
GGAAAAAAAGTTATTTCAAAATGAAATTAGAAAAGATTTTCTTGATGTTT
TATGTCGATTTTGTAGTTTCTCAAAAATTACTCTCTCTGAAAAGGAATAC
AGTTTCCCCAAACTATTTTAGTGGGAACATTGTGAAGAAAAGAGTTTGGA
GTTCGGAGCTAGCAGTAGATGGAAACAGCGATGGAAATGTTTACAATGAT
CATTGCTTTCAAAGCTCTGGAAAACCAAGATGGTGGCTTGTACTTTTGGA
CGCGCTTTCAGTCATTAGAAAAATATCTATTTACGGACGAACTGACACCA
ATGAACTCTTCAATGCAAATTTCTCAATCTATATCAGCATCAAACAGGAA
CAAGATTTTGATGTTAATTCAAGGGAATTCATAAAAATTCAAGATAATTT
TCTAGGTGTAGGGTCACCATCAGTTTTGTTTCAACATTTTTATTTCGAAT
CTACGGTTGCGCGTACAATCGCAATTTCAAAATTGCCTGACAAACTGGGG
GACTTGACGCTATGTGAGGTGGAAATCTTTGGGGAAGAATATGACAAATA
TAGTTCAAACATTTATACATTTTCACATATTCAAAATACGTTGCAGAATT
CAGAAAATGTTGTAATTGTTTCAACGGAATCTTTATTGGAATGCGGAATT
TTGTGTTATGTATCAGATTTCTGCATGTCATTCACGTTGAGAGATCTCAG
TTCTTGTGTATTATATGACAATAATTGGGGCCGTTTTATGAATATCCAAT
GATTCCTCTCCTTTACGTTACGGTTGTGGTGAATATTACGTAATTTTAGT
TTGTTTGTTCATGTGATCATTTTAATGAAAAATTTATGAATAAAGTTTTT
ATCGGAATAGATGAAAGGAATCAAATTAGAGCTTAAAATTAAGGGGTTTC
AATTTTTAACCAATATATGCGTGAGCAATTACTTGCGACCATTTCCTACT
TTTCAAGAAACACGAATCCTCAAAATATTTACTTTTTAAAAGGATTTAGG
AATTACAAAAATA
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protein sequence of SMED30031753-orf-1

>SMED30031753-orf-1 ID=SMED30031753-orf-1|Name=SMED30031753-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=244bp
MKLEKIFLMFYVDFVVSQKLLSLKRNTVSPNYFSGNIVKKRVWSSELAVD
GNSDGNVYNDHCFQSSGKPRWWLVLLDALSVIRKISIYGRTDTNELFNAN
FSIYISIKQEQDFDVNSREFIKIQDNFLGVGSPSVLFQHFYFESTVARTI
AISKLPDKLGDLTLCEVEIFGEEYDKYSSNIYTFSHIQNTLQNSENVVIV
STESLLECGILCYVSDFCMSFTLRDLSSCVLYDNNWGRFMNIQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
PLANA:0000420parapharyngeal region
Vocabulary: INTERPRO
TermDefinition
IPR008979Galactose-bd-like_sf
IPR003609Pan_app