SMED30003231

Overview
NameSMED30003231
Smed IDSMED30003231
Length (bp)1216
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 SMED30003231 (SMED30003231) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30003231 (SMED30003231) 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 SMED30003231 (SMED30003231) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30003231 (SMED30003231) 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



SMED30003231

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
epidermisSMED30003231SMESG000011158.1 dd_Smed_v4_21640_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30003231SMESG000011158.1 Contig51857newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30003231SMESG000011158.1 Contig51857uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30003231 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003128:40325..45564 -5728
v31.007715:2332..7339 -4627
Homology
[Close]
BLAST of SMED30003231 vs. Planmine SMEST
Match: SMESG000046646.1 (SMESG000046646.1)

HSP 1 Score: 164.851 bits (416), Expect = 1.081e-47
Identity = 130/277 (46.93%), Postives = 169/277 (61.01%), Query Frame = 1 
Query:  361 KRKSYTKR-KICQIERYMVLPEATRELYEKKKR-GFLKPAMIW**RIRAKESQFQTS---AALRQIFTEKELQAQLPSRNMAQSLDIIPAHHLPTNSDNRMNNEDSNVTIEMRIPSNSXXXXXXXXXXXXXXXXXAENALLQPNLGTSENANPD--------------------VISFPRLPDFSQQTPM--HLK*TF*WTAA---TNVQISISTRTTPDNDKISSDRSSPQIISAVEPTPHSNPNRVAHNLPRTPSRFASKQPKRRCLPVDIDEKD 1101
            +R+++T R K  +++     PE TRE Y+K  R    +  +I    I  +  +   S   AA RQIFTEKE QA+LPSRNM Q LDIIP HHLPTN  N+ +N + NV  ++  PS  N+RH+PN+N RRRQ+R+AENALLQ NLG  ENA+ +                    VI  PR PDFSQ  P+   +  T    +A    N+QISI++RTTPD D ISS RSSPQIIS +EPT   N ++ + NLPR PS   ++ PKR+ LPVDIDE+D
Sbjct:   26 ERENFTLREKYNRLKVTWCSPEITRERYKKINRLSRARDDLI----IENRSQRIMISYECAAFRQIFTEKEKQARLPSRNMTQRLDIIPVHHLPTNPKNQRDNNNKNVPTKLTTPSTVNQRHRPNRNRRRRQRRKAENALLQSNLGVRENASLESITELFWPQPIALNDGEDLGVIDAPRQPDFSQPAPIPAQINITMDNYSAEMLINMQISIASRTTPDRDAISSGRSSPQIISVIEPT--INRSQRSDNLPRAPSSSTTRPPKRKYLPVDIDEED 296

HSP 2 Score: 74.7146 bits (182), Expect = 8.839e-15
Identity = 35/48 (72.92%), Postives = 38/48 (79.17%), Query Frame = 2 
Query:  284 MNLSGIPKISPAPSAVAAAQYLAKLESENHILREKYAKLKGTWCSQKL 427
            MNL  IPKISPAPSAVA AQYL KLE EN  LREKY +LK TWCS ++
Sbjct:    1 MNLPRIPKISPAPSAVAEAQYLEKLERENFTLREKYNRLKVTWCSPEI 48
[Close]
BLAST of SMED30003231 vs. Planmine SMEST
Match: SMESG000011158.1 (SMESG000011158.1)

HSP 1 Score: 126.716 bits (317), Expect = 1.799e-35
Identity = 90/113 (79.65%), Postives = 91/113 (80.53%), Query Frame = 1 
Query:  586 MAQSLDIIPAHHLPTNSDNRMNNEDSNVTIEMRIPSNSXXXXXXXXXXXXXXXXXAENALLQPNLGTSENANP--------------------DVISFPRLPDFSQQTPMHLK 864
            MAQSLDIIPAHHLPTNSDNRMNNEDSNVTIEM IPSNSNRRHKPNKNPRRRQKRRAENALLQ NLGTSENANP                    DVISFPRLP+FSQQTPMHLK
Sbjct:    1 MAQSLDIIPAHHLPTNSDNRMNNEDSNVTIEMPIPSNSNRRHKPNKNPRRRQKRRAENALLQLNLGTSENANPGRIAEIFPQEQLFMHNDKNLDVISFPRLPNFSQQTPMHLK 113
[Close]
BLAST of SMED30003231 vs. Planmine SMEST
Match: SMESG000021151.1 (SMESG000021151.1)

HSP 1 Score: 104.76 bits (260), Expect = 1.119e-33
Identity = 103/237 (43.46%), Postives = 137/237 (57.81%), Query Frame = 1 
Query:  418 PEATRELYEK-----KKRGFLKPAMIW**RIRAKESQF---QTSAALRQIFTEKELQAQLPSRNMAQSLDIIPAHHLPTNSDNRMNNEDSNVTIEMRIPSNSXXXXXXXXXXXXXXXXXAENALLQPNLGTSENANPDVISFPRLPDFSQQTPMHLK*TF*W---TAATNVQISISTRTTPDNDKISSDRSSPQIISAVEPTPHSNPNRVAHNLPRTP-SRFASKQPKRRCLPVDID 1092
            P+AT+EL++K     + R  L         I  +  Q    + SAALRQIFTEKELQA+LPSRN+AQ ++IIPAHHLPTN++N+  N+D N T E  I S++NRRHKPN+N R+RQ+RRAEN LL  NL + E   PDV          +    + K         +  ++ I+ ++R   + +  SS RSSP II   EPT    P       P+ P S   ++ PKRRCLPVDID
Sbjct:   46 PDATKELHKKITSLSRDRDDLV--------IETRSQQVTISEQSAALRQIFTEKELQARLPSRNLAQQINIIPAHHLPTNAENQAINQD-NSTPEDGI-SHANRRHKPNRNRRQRQRRRAENTLLLANLRSDE--YPDVTEVLDSTTIERAISGYDKEIIYAPLNPSPIHINIATTSRAMLEEEGQSSGRSSPLIILVTEPTA---PQEQMAGFPQQPESHPTARCPKRRCLPVDID 267

HSP 2 Score: 58.151 bits (139), Expect = 1.119e-33
Identity = 28/45 (62.22%), Postives = 31/45 (68.89%), Query Frame = 2 
Query:  284 MNLSGIPKISPAPSAVAAAQYLAKLESENHILREKYAKLKGTWCS 418
            MNL  I +I  AP AVA  Q L  LE EN I+REKY K+KGTWCS
Sbjct:    1 MNLPSIIRIVRAPYAVAMNQRLESLERENFIIREKYEKIKGTWCS 45
[Close]
BLAST of SMED30003231 vs. Planmine SMEST
Match: SMESG000054261.1 (SMESG000054261.1)

HSP 1 Score: 79.7221 bits (195), Expect = 7.281e-30
Identity = 92/215 (42.79%), Postives = 111/215 (51.63%), Query Frame = 1 
Query:  523 SAALRQIFTEKELQAQLPSRNMAQSLDIIPAHHLPTNSDNRMNNEDSNVTIEMRIPSNSXXXXXXXXXXXXXXXXXAENALLQPNLGTSE-----------------NANPDVISFPRLPDFSQQTPMHLK*TF*WTAATN-VQISISTRTTPD--NDKISSDRSSPQIISAVEPT--PHSNPNRVAHNLPRTPSRFASKQPKRRCLPVDIDEKD 1101
            SAAL QIFTE EL  +LPSR + Q LDIIPAHHLP  +  +M N  S       +  N   RH+PN+N RRRQ++RAENALLQ NL   E                  ++ DVI  P  P F  Q P   + T   T   +  +ISIST   P     + +S  SSP I+S VEPT      P R A N P        + PKRR LPVDID+ D
Sbjct:   83 SAALWQIFTEHELLTRLPSRRLTQELDIIPAHHLPLQTTIQMPNTLSYTNNPESVSGN--WRHRPNRNRRRRQRQRAENALLQANLRQEEPMKMSELQNTFDEEDRCASDLDVIYAPVPPFF--QHPSSTQITVNITRIKSPTRISISTMLNPPPIETETTSTHSSPVILSVVEPTISLQEEPRRSAPNPP-------VRCPKRRRLPVDIDDDD 286

HSP 2 Score: 51.6026 bits (122), Expect = 7.281e-30
Identity = 28/48 (58.33%), Postives = 31/48 (64.58%), Query Frame = 2 
Query:  275 STAMNLSGIPKISPAPSAVAAAQYLAKLESENHILREKYAKLKGTWCS 418
            ST   L  IPKISP  S  A  Q L KLE EN IL+EKY ++KGTW S
Sbjct:    2 STLSGLPRIPKISP--SVAATLQKLDKLERENAILQEKYQRVKGTWSS 47

HSP 3 Score: 38.891 bits (89), Expect = 7.281e-30
Identity = 18/24 (75.00%), Postives = 22/24 (91.67%), Query Frame = 3 
Query:  453 TRLSEARDDLVIENQSQRITISDQ 524
            +RLS ARDDL+IEN+S+RITIS Q
Sbjct:   59 SRLSRARDDLIIENRSRRITISKQ 82
[Close]
BLAST of SMED30003231 vs. Planmine SMEST
Match: SMESG000004294.1 (SMESG000004294.1)

HSP 1 Score: 73.1738 bits (178), Expect = 5.054e-27
Identity = 36/45 (80.00%), Postives = 36/45 (80.00%), Query Frame = 2 
Query:  284 MNLSGIPKISPAPSAVAAAQYLAKLESENHILREKYAKLKGTWCS 418
            MNL  IPKISP PSAVAAAQYL KLE EN  LREKY KLK TWCS
Sbjct:    1 MNLPRIPKISPPPSAVAAAQYLEKLERENFALREKYNKLKFTWCS 45

HSP 2 Score: 67.0106 bits (162), Expect = 5.054e-27
Identity = 54/131 (41.22%), Postives = 67/131 (51.15%), Query Frame = 1 
Query:  421 EATRELYEKKKR-GFLKPAMIW**RIRAKESQFQTS---AALRQIFTEKELQAQLPSRNMAQSLDIIPAHHLPTNSDNRMNNEDSNVTIEMRIPSNSXXXXXXXXXXXXXXXXXAENALLQPNLGTSENAN 801
            EATRELY+   R    +  +I    I  +  +   S   A LRQIFTEKELQA+LPSRNM Q LDII AHHL  N +N+ +    N                  +  +     RAEN L+Q NLG  ENA+
Sbjct:   47 EATRELYKMITRLSRARDDLI----IENRSQRITISDQNATLRQIFTEKELQARLPSRNMVQRLDIILAHHLSKNPENQRDYWPPNC-----------------RRCQPEIGVRAENTLIQANLGVRENAS 156
The following BLAST results are available for this feature:
BLAST of SMED30003231 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 SMED30003231 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 SMED30003231 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 SMED30003231 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 SMED30003231 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 SMED30003231 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 SMED30003231 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 SMED30003231 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 SMED30003231 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 SMED30003231 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 SMED30003231 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 SMED30003231 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 SMED30003231 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 SMED30003231 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000046646.11.081e-4746.93SMESG000046646.1[more]
SMESG000011158.11.799e-3579.65SMESG000011158.1[more]
SMESG000021151.11.119e-3343.46SMESG000021151.1[more]
SMESG000054261.17.281e-3042.79SMESG000054261.1[more]
SMESG000004294.15.054e-2780.00SMESG000004294.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003231 ID=SMED30003231|Name=SMED30003231|organism=Schmidtea mediterranea sexual|type=transcript|length=1216bp
CACGCCATCACGTGCACCTTAAGACGACACTTTAGACTGGCATGGTGATT
AGTTGGAACAAGTTTTAATATCTAGTTTTCATTTCAGTTTATTTTTTATC
ATTTCATTCATAAAATTAAAATACTGATATCGCATAAAGATTATTATGAA
TTGTACATATTTATCAGATTAATTGAATTAGTCAAAATTTATCAAAAAAG
AAAATATCACATTGTTTCCTAACTGGATAAGAAAAAAAAACATGCCCCTC
TCATATAGGCAGAAAATCAATTATTCAACCGCAATGAACCTTTCAGGGAT
TCCGAAGATATCTCCAGCACCATCTGCTGTCGCTGCAGCCCAATATCTGG
CAAAGTTAGAAAGCGAAAATCATATACTAAGAGAAAAATATGCCAAATTG
AAAGGTACATGGTGCTCCCAGAAGCTACGAGGGAGCTATACGAGAAGAAA
AAACGCGGCTTTCTGAAGCCCGCGATGATCTGGTGATAGAGAATCAGAGC
CAAAGAATCACAATTTCAGACCAGTGCCGCATTGAGGCAGATTTTTACTG
AAAAGGAATTACAGGCGCAGCTGCCAAGTCGGAATATGGCCCAAAGCCTC
GATATTATCCCGGCTCATCATCTGCCGACAAATTCTGATAATCGGATGAA
CAATGAAGATTCAAATGTGACCATCGAAATGCGAATACCGTCGAATTCTA
ATCGTCGTCATAAACCCAATAAGAACCCGAGAAGGCGACAGAAGAGGAGA
GCAGAAAATGCCCTACTGCAACCGAATCTGGGCACTAGTGAAAATGCAAA
TCCAGATGTAATTTCTTTTCCCCGACTACCGGATTTCTCGCAGCAAACTC
CAATGCATCTCAAATAAACATTTTAATGGACAGCCGCGACGAATGTGCAG
ATCTCCATCTCTACTCGGACAACCCCTGACAACGACAAAATTTCTAGTGA
TAGATCTTCGCCTCAAATTATCTCCGCCGTGGAACCAACGCCACACAGTA
ATCCGAACAGGGTGGCTCATAATCTCCCTCGAACACCTTCGAGATTCGCG
TCAAAGCAACCTAAGAGAAGATGCCTGCCAGTGGATATCGACGAAAAAGA
TTGGTAGAGAAGATTCGATGATTTTATGGAACTGTGTTTTCTTTGACAAA
ATTTTTGCACTTGTTTTAATTTTGCTCTATCAAAATATAAACCTTAGTTT
TAATCAAAAAAAAAGA
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protein sequence of SMED30003231-orf-1

>SMED30003231-orf-1 ID=SMED30003231-orf-1|Name=SMED30003231-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=108bp
MCRSPSLLGQPLTTTKFLVIDLRLKLSPPWNQRHTVIRTGWLIISLEHLR
DSRQSNLREDACQWISTKKIGREDSMILWNCVFFDKIFALVLILLYQNIN
LSFNQKKR
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002032epidermal cell