SMED30012151

Overview
NameSMED30012151
Smed IDSMED30012151
Length (bp)2025
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 SMED30012151 (SMED30012151) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30012151 (SMED30012151) 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 SMED30012151 (SMED30012151) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30012151 (SMED30012151) 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



SMED30012151

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
head regionSMED30012151 SmedASXL_025936SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
X1 cellSMED30012151 SmedASXL_025936SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30012151 SmedASXL_025936SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30012151 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000793:83608..85611 -9806
Homology
[Close]
BLAST of SMED30012151 vs. Planmine SMEST
Match: SMESG000021151.1 (SMESG000021151.1)

HSP 1 Score: 145.591 bits (366), Expect = 2.783e-60
Identity = 102/163 (62.58%), Postives = 127/163 (77.91%), Query Frame = -1 
Query: 1144 EKIKAT*CSSEATEEQFKKIT*LSRARDDLIIETRSQQITISDQSAALQQIFMKKKFQARLPSRSLAQQINIIPANHLPGNAKNQSISNVNNTFTAGISXXXXXXXXXXXXXXXXXXXXXNALLQENLRTYGHSEQQEIPDSISLEHTAHRFDDDLYII*APV 1632
            EKIK T CS +AT+E  KKIT LSR RDDL+IETRSQQ+TIS+QSAAL+QIF +K+ QARLPSR+LAQQINIIPA+HLP NA+NQ+I+  N+T   GIS ANRRHK NRNRR+RQRRRA+N LL  NLR+  + +  E+ DS ++E     +D +  II AP+
Sbjct:   37 EKIKGTWCSPDATKELHKKITSLSRDRDDLVIETRSQQVTISEQSAALRQIFTEKELQARLPSRNLAQQINIIPAHHLPTNAENQAINQDNSTPEDGISHANRRHKPNRNRRQRQRRRAENTLLLANLRSDEYPDVTEVLDSTTIERAISGYDKE--IIYAPL 197

HSP 2 Score: 72.4034 bits (176), Expect = 2.783e-60
Identity = 41/68 (60.29%), Postives = 50/68 (73.53%), Query Frame = -3 
Query:  908 SPINIHIATTARAMLEE-GQSSGQSSPLIISVVKPDSRR--------QSTPRPLSRCPQRRCLPVDID 1084
            SPI+I+IATT+RAMLEE GQSSG+SSPLII V +P + +        Q    P +RCP+RRCLPVDID
Sbjct:  200 SPIHINIATTSRAMLEEEGQSSGRSSPLIILVTEPTAPQEQMAGFPQQPESHPTARCPKRRCLPVDID 267

HSP 3 Score: 55.8398 bits (133), Expect = 2.783e-60
Identity = 26/34 (76.47%), Postives = 29/34 (85.29%), Query Frame = -3 
Query: 1628 INLPRILRIVPAPYAVAMNQRLSKLERENFIPRK 1729
            +NLP I+RIV APYAVAMNQRL  LERENFI R+
Sbjct:    1 MNLPSIIRIVRAPYAVAMNQRLESLERENFIIRE 34
[Close]
BLAST of SMED30012151 vs. Planmine SMEST
Match: SMESG000011251.1 (SMESG000011251.1)

HSP 1 Score: 177.948 bits (450), Expect = 2.526e-51
Identity = 117/171 (68.42%), Postives = 137/171 (80.12%), Query Frame = -1 
Query: 1120 EKIKAT*CSSEATEEQFKKIT*LSRARDDLIIETRSQQITISDQSAALQQIFMKKKFQARLPSRSLAQQINIIPANHLPGNAKNQSISNVNNTFTAGISXXXXXXXXXXXXXXXXXXXXXNALLQENLRTYGHSEQQEIPDSISLEHTAHRFDDDLYII*APVQLEFSHPA 1632
            EKIK T CS EAT+E +KKIT LSRARDDLIIETRSQ+ITIS+++AAL+QIF  K+ QARLPSR+LAQQINIIPA+HLPGNA+NQS SNVN+T   GISQANRRHK NRNRRRRQ+RRA+  LLQ NLR+ G+ E  EI DS+ +E     FD++  II AP Q  F HPA
Sbjct:   37 EKIKGTWCSPEATKELYKKITRLSRARDDLIIETRSQRITISEKNAALRQIFTVKELQARLPSRTLAQQINIIPAHHLPGNAENQSFSNVNSTSADGISQANRRHKPNRNRRRRQKRRAEKPLLQANLRSDGYRESAEILDSMPMERAFPHFDEE--IIYAPTQPIFLHPA 205

HSP 2 Score: 45.0542 bits (105), Expect = 2.526e-51
Identity = 22/31 (70.97%), Postives = 24/31 (77.42%), Query Frame = -3 
Query: 1637 INLPRILRIVPAPYAVAMNQRLSKLERENFI 1729
            + +PRI RIV AP AVAMNQRL  LEREN I
Sbjct:    1 MTMPRIPRIVLAPSAVAMNQRLENLERENLI 31
[Close]
BLAST of SMED30012151 vs. Planmine SMEST
Match: SMESG000011251.1 (SMESG000011251.1)

HSP 1 Score: 177.563 bits (449), Expect = 3.208e-51
Identity = 117/171 (68.42%), Postives = 137/171 (80.12%), Query Frame = -1 
Query: 1120 EKIKAT*CSSEATEEQFKKIT*LSRARDDLIIETRSQQITISDQSAALQQIFMKKKFQARLPSRSLAQQINIIPANHLPGNAKNQSISNVNNTFTAGISXXXXXXXXXXXXXXXXXXXXXNALLQENLRTYGHSEQQEIPDSISLEHTAHRFDDDLYII*APVQLEFSHPA 1632
            EKIK T CS EAT+E +KKIT LSRARDDLIIETRSQ+ITIS+++AAL+QIF  K+ QARLPSR+LAQQINIIPA+HLPGNA+NQS SNVN+T   GISQANRRHK NRNRRRRQ+RRA+  LLQ NLR+ G+ E  EI DS+ +E     FD++  II AP Q  F HPA
Sbjct:   35 EKIKGTWCSPEATKELYKKITRLSRARDDLIIETRSQRITISEKNAALRQIFTVKELQARLPSRTLAQQINIIPAHHLPGNAENQSFSNVNSTSADGISQANRRHKPNRNRRRRQKRRAEKPLLQANLRSDGYRESAEILDSMPMERAFPHFDEE--IIYAPTQPIFLHPA 203
[Close]
BLAST of SMED30012151 vs. Planmine SMEST
Match: SMESG000055478.1 (SMESG000055478.1)

HSP 1 Score: 162.155 bits (409), Expect = 3.956e-46
Identity = 122/202 (60.40%), Postives = 140/202 (69.31%), Query Frame = -1 
Query: 1033 EKIKAT*CSSEATEEQFKKIT*LSRARDDLIIETRSQQITISDQSAALQQIFMKKKFQARLPSRSLAQQINIIPANHLPGNAKNQSISNVNNTFTAGISXXXXXXXXXXXXXXXXXXXXXNALLQENLRTYGHSEQQEIPDSISLEHTAHRFDDDLYII*APVQLEFSH--PAQPKLRSMQMPMSRQSTSTSRLLPVLCWRK 1632
            EK+K T CS EAT+EQ+KKIT LSRARDDLIIETRSQ+ITIS+Q+AA +QIF +K+ QARLPSR+L QQINII A HLP NA+N  I+  +N    GI   NRRHK NRNRR RQRRRA+NALLQ NLR  G  E +EI D +S +    R DDDL II AP Q EF H  PAQ  + S     S Q T TS LL    W K
Sbjct:   37 EKLKGTWCSPEATKEQYKKITRLSRARDDLIIETRSQRITISEQTAAFRQIFTEKELQARLPSRNLVQQINIIQAYHLPINAENSPINYDSNIPADGILHVNRRHKSNRNRRWRQRRRAENALLQANLRNDGLPELREIQDLVSTKQATPRHDDDLDIIYAPFQPEFFHSTPAQITITSHGH-ESPQLTYTSPLLLERFWMK 237

HSP 2 Score: 43.1282 bits (100), Expect = 3.956e-46
Identity = 22/34 (64.71%), Postives = 26/34 (76.47%), Query Frame = -3 
Query: 1628 INLPRILRIVPAPYAVAMNQRLSKLERENFIPRK 1729
            +NLP I RIV AP AVAM QRL KL+ ENF+ R+
Sbjct:    1 MNLPSIPRIVLAPSAVAMTQRLEKLKWENFVLRE 34
[Close]
BLAST of SMED30012151 vs. Planmine SMEST
Match: SMESG000046646.1 (SMESG000046646.1)

HSP 1 Score: 117.857 bits (294), Expect = 8.208e-41
Identity = 91/178 (51.12%), Postives = 118/178 (66.29%), Query Frame = -1 
Query: 1120 FREK---IKAT*CSSEATEEQFKKIT*LSRARDDLIIETRSQQITISDQSAALQQIFMKKKFQARLPSRSLAQQINIIPANHLPGNAKNQSISNVNNTFT--AGISXXXXXXXXXXXXXXXXXXXXXNALLQENLRTYGHSEQQEIPDSISLEHTAHRFDDDLYII*APVQLEFSHPA 1638
             REK   +K T CS E T E++KKI  LSRARDDLIIE RSQ+I IS + AA +QIF +K+ QARLPSR++ Q+++IIP +HLP N KNQ  +N  N  T     S  N+RH+ NRNRRRRQRR+A+NALLQ NL    ++  + I +    +  A    +DL +I AP Q +FS PA
Sbjct:   32 LREKYNRLKVTWCSPEITRERYKKINRLSRARDDLIIENRSQRIMISYECAAFRQIFTEKEKQARLPSRNMTQRLDIIPVHHLPTNPKNQRDNNNKNVPTKLTTPSTVNQRHRPNRNRRRRQRRKAENALLQSNLGVRENASLESITELFWPQPIALNDGEDLGVIDAPRQPDFSQPA 209

HSP 2 Score: 45.8246 bits (107), Expect = 8.208e-41
Identity = 34/85 (40.00%), Postives = 49/85 (57.65%), Query Frame = -3 
Query:  902 CPAQITINANAH--ESPINIHIATTARAMLE-EGQSSGQSSPLIISVVKP----DSRRQSTPRP----LSRCPQRRCLPVDIDKE 1123
             PAQI I  + +  E  IN+ I+  +R   + +  SSG+SSP IISV++P      R  + PR      +R P+R+ LPVDID+E
Sbjct:  211 IPAQINITMDNYSAEMLINMQISIASRTTPDRDAISSGRSSPQIISVIEPTINRSQRSDNLPRAPSSSTTRPPKRKYLPVDIDEE 295

HSP 3 Score: 44.2838 bits (103), Expect = 8.208e-41
Identity = 23/39 (58.97%), Postives = 27/39 (69.23%), Query Frame = -3 
Query: 1613 INLPRILRIVPAPYAVAMNQRLSKLERENFIPRKNQSHL 1729
            +NLPRI +I PAP AVA  Q L KLERENF  R+  + L
Sbjct:    1 MNLPRIPKISPAPSAVAEAQYLEKLERENFTLREKYNRL 39
The following BLAST results are available for this feature:
BLAST of SMED30012151 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 SMED30012151 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 SMED30012151 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 SMED30012151 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 SMED30012151 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 SMED30012151 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 SMED30012151 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 SMED30012151 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 SMED30012151 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 SMED30012151 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 SMED30012151 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 SMED30012151 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 SMED30012151 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 SMED30012151 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000021151.12.783e-6062.58SMESG000021151.1[more]
SMESG000011251.12.526e-5168.42SMESG000011251.1[more]
SMESG000011251.13.208e-5168.42SMESG000011251.1[more]
SMESG000055478.13.956e-4660.40SMESG000055478.1[more]
SMESG000046646.18.208e-4151.12SMESG000046646.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012151 ID=SMED30012151|Name=SMED30012151|organism=Schmidtea mediterranea sexual|type=transcript|length=2025bp
ACTTTGGTTTTCTTGAGTTTCTATAAAGTTATTGCTAGTCGATGCTGTAT
CTTCAATATTGGGGTTTATTTGTGAAATTTCAATTTCATCTTCTATAAAT
TTTTTTTTGTTTTCATAATATATTGTGTCTTATGAATTACTTCCATTATC
ATCTGTATTCATTTCATCATTATCTGTTAAATCTTTGTCAGATAATTCAG
TATCATTACTTTCATCCTTTTTTTATTTTGTTTTCACTTTCACTTATTTT
AATTTAATTATAATAAATTAATTTTTATTTCGAGTATTAAATAAAAAAAT
ACTTATTTTCCGAATTCTTAATTTTAAACTTCCACATCCAAATTTTATTA
TTTACAACTCTTAAAACAAAAACACATTTCAACATAACATGAAACCGATC
ATTTTCTTATTTCAAAATGTTTGATCCTTTGTTTGAAGTGGATGAGGCGA
GTTAGGTTGACCCGTTAGAATTCTGTGTTATGGTTACTCATACTATGACT
AGCTATTATATTTACTCCTGACTAGCAGCCAAATTCACTTTTTCCATAGT
TATTTAATATAAAACCGAAAAAAATGTAAACAATTAATTTATTCTACCAT
TATGAGTAAATCGCTTTTATGCAATAATTGCATGAATTCCAAATTGACTA
TTTAATAATAACAAAATAAAAGTATAATACACATTATTATTTTTCAATTA
TATATATAAATACAAATTTTAACTAGTATCAAAATGTTTGTCACAAGGCA
AGATAAACGAAGAAGAAACATAAAATGAAGCACAAGTTTTTCGGGTAAAC
AGCAAATGAGATTCCACGCTATTAATACTTCGGCTCACTGCCGGTACCAA
TTCTGGGGTGACGGTTTCGAATAGTTGGTTCAAGCGAGACTTGATTTAGT
GTTCCTTGTCGATGTCTACCGGCAAACATCGACGTTGGGGACATCGCGAT
AATGGGCGCGGAGTCGATTGGCGGCGAGAATCTGGTTTTACCACCGAGAT
AATCAGGGGCGACGATTGCCCGCTAGATTGTCCTTCCTCCAGCATAGCAC
GGGCAGTAGTCGCGATGTGGATGTTGATTGGCGACTCATGGGCATTTGCA
TTGATCGTAATTTGGGCTGGGCAGGATGAGAAAACTCCAGTTGGACTGGT
GCTTAGATTATATACAGGTCGTCATCGAACCTGTGAGCGGTATGCTCTAA
AGATATTGAATCTGGGATTTCTTGCTGCTCCGAGTGGCCGTAGGTCCTCA
AATTTTCCTGCAGCAGGGCGTTTTTGGCTCTACGCCTCTGCCGCCGGCGA
CGATTTCTATTGTGCTTATGCCTGCGATTAGCCTGTGAGATCCCAGCTGT
GAACGTGTTGTTGACATTACTGATTGATTGATTTTTCGCATTTCCCGGCA
GATGATTGGCCGGAATTATGTTAATTTGCTGGGCTAAGCTTCTACTCGGC
AGACGGGCTTGGAACTTCTTTTTCATAAAAATCTGTTGGAGAGCTGCGCT
TTGATCGGATATGGTAATCTGCTGACTTCTTGTCTCTATGATAAGATCAT
CACGGGCACGAGAAAGTCACGTGATTTTCTTAAATTGCTCCTCGGTGGCT
TCAGACGAGCACTAAGTGGCTTTGATTTTTTCTCGGAATAAAATTCTCCC
GTTCGAGCTTTGAGAGCCGTTGGTTCATAGCCACCGCATAAGGAGCGGGA
ACAATCCTGAGAATGCGCGGCAAGTTTATTTTTATAGAATAATTGTAATA
ACTGCCGAGAGAAATTTGGAGTGAATTGTGGGCAAAAGAAAATCCGAAAA
TTTCGAACAGTTATTGGGATGATATGATTATGTATTCCAGAAATTTGCGT
AGGACTGACGATTTGGTCGGTTTTAGATTGAGTTAAAATACTTCCAATTC
ACGGGAAATTTTCGATGGAGGCTACAGATGGATACAAACTTCGGTTTCTC
GCAAAATAGAAGGAGAGAATAAGCTCATACAATAAATGCATGATTTAAGA
CTCAATACCAATTAAATTTTAATTA
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protein sequence of SMED30012151-orf-1

>SMED30012151-orf-1 ID=SMED30012151-orf-1|Name=SMED30012151-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=108bp
MKKKFQARLPSRSLAQQINIIPANHLPGNAKNQSISNVNNTFTAGISQAN
RRHKHNRNRRRRQRRRAKNALLQENLRTYGHSEQQEIPDSISLEHTAHRF
DDDLYII*
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protein sequence of SMED30012151-orf-2

>SMED30012151-orf-2 ID=SMED30012151-orf-2|Name=SMED30012151-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=140bp
MSTGKHRRWGHRDNGRGVDWRRESGFTTEIIRGDDCPLDCPSSSIARAVV
AMWMLIGDSWAFALIVIWAGQDEKTPVGLVLRLYTGRHRTCERYALKILN
LGFLAAPSGRRSSNFPAAGRFWLYASAAGDDFYCAYACD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0002109X1 cell
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 41..67
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 50..67