SMED30017632

Overview
NameSMED30017632
Smed IDSMED30017632
Length (bp)2866
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 SMED30017632 (SMED30017632) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30017632 (SMED30017632) 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 SMED30017632 (SMED30017632) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30017632 (SMED30017632) 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




SMED30017632

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30017632 SmedASXL_017030SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30017632 SmedASXL_017030SmedAsxl_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
SMED30017632 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000838:83747..86600 +14152
Homology
BLAST of SMED30017632 vs. Planmine SMEST
Match: SMESG000032225.1 (SMESG000032225.1)

HSP 1 Score: 189.504 bits (480), Expect = 4.872e-55
Identity = 125/206 (60.68%), Postives = 142/206 (68.93%), Query Frame = 3
Query: 1206 MHLPRIPKISPAPSVLAASQXXXXXXXXXXXXRKKYEKMKGTWHSPRATKKLYKKISRISRARDVLIVENRAQRLTIAEQSAMLRKIFTEKELQARLPGWSMAQQINIISANHLLGPSSNRIGRDDINTVVNREVPQTTNRNIKHKPNKXXXXXXXXXXXXXXXQANLNITGSTTSTEVSKTPRNSTSFHPILKPADSDLEVIYAP 1823
            M LP+IP ISPA SVLA                 KYEKMKGTW SP ATK+LYK I+RISRARD LIVENR QR+TI ++S  LR++FTEKELQARLPG S AQQ+NIIS +HL   SSNRI RD  N V+ R V    NR  KHKPNKN+RRRE RR ENALLQANLN   +  S  +S+T    T + PI  PADSDL +IYAP
Sbjct:    1 MPLPKIPNISPALSVLAPLNTWQIWRIV------KYEKMKGTWCSPEATKELYKNITRISRARDDLIVENRTQRITIVDKSPALRQLFTEKELQARLPGRSTAQQLNIISVHHLPVYSSNRIERDVTNAVMTRPVLPICNR--KHKPNKNQRRREKRRTENALLQANLNAIENVISIGISET----TPYEPISMPADSDLAIIYAP 194          
BLAST of SMED30017632 vs. Planmine SMEST
Match: SMESG000047293.1 (SMESG000047293.1)

HSP 1 Score: 193.356 bits (490), Expect = 6.000e-55
Identity = 123/229 (53.71%), Postives = 158/229 (69.00%), Query Frame = 3
Query: 1305 KKYEKMKGTWHSPRATKKLYKKISRISRARDVLIVENRAQRLTIAEQSAMLRKIFTEKELQARLPGWSMAQQINIISANHLLGPSSNRIGRDDINTVVNREVPQTTNRNIKHKPNKXXXXXXXXXXXXXXXQANLNITGSTTSTEVSKTPRNSTSFHPILKPADSDLEVIYAPQLVNFSQSAPESLQFNISIESLTTDTPANVQLAISTR--TVRDERFAISSERYTPQ 1985
            +KY+++KGTW SP ATK   +K      + + LI+ENRAQRLTIAEQSA LR+IF EKELQARLP  S+AQ+I+II A+HLLG SS RIG +DI      E PQT+   IKHKPNKNRRRRE RRAENALLQANLN T + TS E +K  +   +   IL+ +DSDL+ IYAP+++NF     E +  N+S E+L    P+N+QL ++     +RDER  ++S   TPQ
Sbjct:   36 QKYKRVKGTWCSPEATKSSTRK------SLEGLIIENRAQRLTIAEQSATLRQIFAEKELQARLPSRSIAQKIDIIPAHHLLGSSSGRIGHNDIKATAIGEAPQTSKPTIKHKPNKNRRRREKRRAENALLQANLNTTRNETSNETTKISKIPAALDLILRTSDSDLDAIYAPRMINFFTQNSEPMHINVSKENLMVSLPSNLQLVVTAEPSNIRDERSTVTSGGSTPQ 258          
BLAST of SMED30017632 vs. Planmine SMEST
Match: SMESG000033974.1 (SMESG000033974.1)

HSP 1 Score: 185.652 bits (470), Expect = 8.204e-53
Identity = 126/224 (56.25%), Postives = 153/224 (68.30%), Query Frame = 3
Query: 1320 MKGTWHSPRATKKLYKKISRISRARDVLIVENRAQRLTIAEQSAMLRKIFTEKELQARLPGWSMAQQINIISANHLLGPSSNRIGRDDINTVVNREVPQTTNRNIKHKPNKXXXXXXXXXXXXXXXQANLNITGSTTSTEVSKTPRNSTSFHPILKPADSDLEVIYAPQLVNFSQSAPESLQFNISIESLTTDTPANVQLAISTRT--VRDERFAISSERYTPQ 1985
            MKGTW SP ATKKLYKKI+R+SRARD LIV+NR+QR+TIA+Q A LR+IFTEKELQARLP  S+ QQ+N+I   HL    SN +  D  N      VP   NR  KHKPNKNRRR+E RR ENALLQ NL    +  +  V K P   TS+     PA+SDLE+I  P+L++F QSAP   QFNIS+E+L+TD   N Q+ IS R+  +R+ER   SS R TPQ
Sbjct:    1 MKGTWCSPEATKKLYKKITRVSRARDDLIVKNRSQRITIADQCATLRQIFTEKELQARLPDRSITQQLNMIPVQHLPVNLSNCVEWDATNVFTLAPVPSIPNR--KHKPNKNRRRKEKRRTENALLQVNL---ITIENPNVIKIPE-VTSYESNEMPANSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQ 218          
BLAST of SMED30017632 vs. Planmine SMEST
Match: SMESG000046646.1 (SMESG000046646.1)

HSP 1 Score: 155.606 bits (392), Expect = 7.349e-42
Identity = 121/262 (46.18%), Postives = 175/262 (66.79%), Query Frame = 3
Query: 1206 MHLPRIPKISPAPSVLAASQXXXXXXXXXXXXRKKYEKMKGTWHSPRATKKLYKKISRISRARDVLIVENRAQRLTIAEQSAMLRKIFTEKELQARLPGWSMAQQINIISANHLLGPSSNRIGRDDINTVVNREVPQTTNRNIKHKPNKXXXXXXXXXXXXXXXQANLNITGSTTSTEVSKTPRNSTSF--HPILKPADSDLEVIYAPQLVNFSQSAPESLQFNISIESLTTDTPANVQLAISTRTVRDERFAISSERYTPQ 1985
            M+LPRIPKISPAPS +A +QYL  LE     LR+KY ++K TW SP  T++ YKKI+R+SRARD LI+ENR+QR+ I+ + A  R+IFTEKE QARLP  +M Q+++II  +HL  P++ +  RD+ N  V  ++   +  N +H+PN+NRRRR+ R+AENALLQ+NL +  + +   +++       F   PI      DL VI AP+  +FSQ AP   Q NI++++ + +   N+Q++I++RT  D R AISS R +PQ
Sbjct:    1 MNLPRIPKISPAPSAVAEAQYLEKLERENFTLREKYNRLKVTWCSPEITRERYKKINRLSRARDDLIIENRSQRIMISYECAAFRQIFTEKEKQARLPSRNMTQRLDIIPVHHL--PTNPKNQRDNNNKNVPTKLTTPSTVNQRHRPNRNRRRRQRRKAENALLQSNLGVRENASLESITEL------FWPQPIALNDGEDLGVIDAPRQPDFSQPAPIPAQINITMDNYSAEMLINMQISIASRTTPD-RDAISSGRSSPQ 253          
BLAST of SMED30017632 vs. Planmine SMEST
Match: SMESG000055478.1 (SMESG000055478.1)

HSP 1 Score: 146.362 bits (368), Expect = 3.721e-39
Identity = 109/218 (50.00%), Postives = 138/218 (63.30%), Query Frame = 3
Query: 1206 MHLPRIPKISPAPSVLAASQXXXXXXXXXXXXRKKYEKMKGTWHSPRATKKLYKKISRISRARDVLIVENRAQRLTIAEQSAMLRKIFTEKELQARLPGWSMAQQINIISANHLLGPSSNRIGRDDINTVVNREVPQTTNRNIKHKPNKXXXXXXXXXXXXXXXQANLNITGSTTSTEVSK--TPRNSTSFHPILKPADSDLEVIYAPQLVNFSQSAP 1853
            M+LP IP+I  APS +A +Q L  L+     LR+KYEK+KGTW SP ATK+ YKKI+R+SRARD LI+E R+QR+TI+EQ+A  R+IFTEKELQARLP  ++ QQINII A HL   + N      IN   N       + N +HK N+NRR R+ RRAENALLQANL   G     E+    + + +T  H      D DL++IYAP    F  S P
Sbjct:    1 MNLPSIPRIVLAPSAVAMTQRLEKLKWENFVLREKYEKLKGTWCSPEATKEQYKKITRLSRARDDLIIETRSQRITISEQTAAFRQIFTEKELQARLPSRNLVQQINIIQAYHLPINAEN----SPINYDSNIPADGILHVNRRHKSNRNRRWRQRRRAENALLQANLRNDGLPELREIQDLVSTKQATPRH------DDDLDIIYAPFQPEFFHSTP 208          
The following BLAST results are available for this feature:
BLAST of SMED30017632 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 SMED30017632 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 SMED30017632 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 SMED30017632 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 SMED30017632 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 SMED30017632 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 SMED30017632 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 SMED30017632 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 SMED30017632 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 SMED30017632 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 SMED30017632 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 SMED30017632 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 SMED30017632 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 SMED30017632 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000032225.14.872e-5560.68SMESG000032225.1[more]
SMESG000047293.16.000e-5553.71SMESG000047293.1[more]
SMESG000033974.18.204e-5356.25SMESG000033974.1[more]
SMESG000046646.17.349e-4246.18SMESG000046646.1[more]
SMESG000055478.13.721e-3950.00SMESG000055478.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017632 ID=SMED30017632|Name=SMED30017632|organism=Schmidtea mediterranea sexual|type=transcript|length=2866bp
GAGGAAATTATTATATGAATATTGAAAATAAACTCTAAATAAAATAATTC
CAAGCATTTAAAACATGTAAAATTTGTTTATCTACATTTATGTTGGGCTT
AAAGCCAAAATTTAAACCAAATTGTATATTGATTCTAAGTCGATTAAAAA
CTACTCTGGATGGTCGTGGGATTTTTGATACCACTGACGAATCCCCATTT
AAACTTTATATATTTATGCATGGTAATAGCATTTCCGGAGTGCAGACTGG
CGGTCCGGCTAACGAGTTCACTTTCGTTAGCTGTGACTACTATTCATGCT
ATTCCTGATACTTCGGCTGTCCGCGACGAGTTCTGGTCAAAAGACGCAGA
ACGTTACCCACAGAGCGTTGTTGTAAAACCCATGGTGGGTGATGGAAACG
TCGGTTGAAATGGGCAGAGAAAAATCACCGGGAAGAGCGAAATGACTTAG
GGAACTAAGAAATGATTCTCTACGGATCATTTAGGCTGAATTTTTCTAAA
AACTCGTCAAGACGTTAATTAATATGGGGTAGCTAGAGATAGGATAGTTG
TTACGATCATAAATAAAATCTAATGATTAGGCAAAGAAACCTTTGCCAGA
ATTGAAACGCATAATATAAAAATATATTCTCGCATTAAGGAAAATAGCAA
GAATCTGACCGCGGTAAAAGCATCATCCACTTAACTATTTTGCAACATTG
ACTAAGTACAATAGGAAGACCCTCTTTTTTGCAAATTAATGATCTTGAGA
ATCGAATAGTGAAGTAATTAATTTAATAACAACACCCTGAGAAAAATATC
GATGTCCACGATAAATTAAATGCTACCATCAAAAACTTCTAATTAATTTA
AAATTAGTGTGATTGAATTTTCGATGGTTTTTGCATGGTGAGATTTTAAT
TTTGTCGACTGGATGATCAAAGCGTCCTGTAAATATGACTAGTATGCTAT
AGACTTCCGGATGCACCCATAACCATTCACATCAAAGAGAACCTTGATCA
GGCTTCCAGTATATTGTAAACCAGTAAGCCAGAAATACATTAAATTTTAA
ACCGAATCAAACCTTCAATCCAATTTAAATAACAATACCAACTTCAACGC
GTTCTACGTTGAGTTATAGACGGCCACTATTCTAAATTTTTCTTTTAATC
AGTATATAATTCTATATAATCGTCATCATTAAGTAAACTAAACGATATCT
TTGAAATGCACTTGCCAAGAATTCCAAAAATATCGCCGGCTCCTTCAGTT
TTGGCTGCTTCCCAATATCTAGCCAATCTGGAAAATAATTATCTCGAGCT
CAGAAAAAAATACGAAAAAATGAAAGGAACATGGCATTCCCCTAGAGCTA
CCAAGAAATTATATAAGAAAATCTCCAGGATCTCGCGGGCACGAGATGTT
CTAATCGTAGAGAATCGTGCTCAACGACTGACTATCGCCGAGCAGAGTGC
CATGCTGCGAAAAATCTTCACCGAGAAAGAACTGCAAGCGCGATTACCGG
GTTGGAGCATGGCCCAGCAAATCAACATCATTTCGGCTAACCATCTGCTG
GGTCCCTCGTCTAATCGCATCGGACGCGATGATATTAATACTGTCGTAAA
CCGGGAAGTCCCACAAACTACCAATCGAAACATCAAACACAAGCCAAACA
AGAATCGGAGGCGCAGAGAAATGCGAAGAGCGGAAAACGCCTTATTGCAG
GCAAATTTGAATATCACGGGAAGCACTACTTCAACTGAGGTATCTAAGAC
CCCTAGAAATTCGACGTCATTTCACCCTATCTTGAAGCCGGCCGATTCCG
ATTTAGAAGTAATATATGCGCCCCAATTAGTGAATTTCTCCCAGTCAGCT
CCGGAATCATTACAGTTCAATATCTCGATAGAAAGCCTCACTACTGACAC
TCCAGCTAATGTGCAGTTAGCCATCTCTACGAGAACTGTTAGGGACGAGA
GGTTTGCAATCTCTAGTGAGAGATATACTCCACAATAGTCTCGGTCCGGG
AAGGTCCACACGACCGCGCTGGCGTCAACTCGATTTCCGAGGATACTTTT
AGGCGGAATCTAGATCAAAACCCGCAAAGACGTTACCTTCAGGTGGATAT
TGACGCCGAAGACGATTAGGGACAAAAACTTGATTGAGATTTAATGCAAT
TTTCGTGCTAACATGCTCCTAGTGATTGTCTGAAAGTCCTTAAAAACATA
ATAAATTTAGTTCTAGTTGATTGTTTCTTTTAGTACGAGTGACGAATAAC
GCTAGTTTTGTGTTAAATTTATGTAATTTTTACCATTGTATAATTAAAAG
TTTTTTTTACTTAATGATTCTAAATCTAGCGATTAATAAATAAATAAACT
ACCAACATAAATGTGAGAAAATCTCATTAGGTAACTTTCTATCGAATTGG
TCAGGGAAATAAAAATTGTTTTTAGAGTTAATAAGTTTCAACCGTAATTT
TGTTCCTCAATAACAACATAGGATTGTTCCCGGTTGACGATTTAAAGGCT
TGGATTGACGAGAGTTGAGTTCAAATGAATAAAGCGTAAGTCATTCTAAT
TGGCCGCATTGTACCCGAATCGAAGGTTATTCAGGGAATAGTGTTGGTAA
CGACGCTCACTGGCTTGAATAGCATTCGGTTGTCATGCACAGTACCAACA
TGGGTTCGATCATGGGTGCATGATGGTAAGGCTTAAATTGTGTGATGTGC
GCGGGAAGGTGTGACCCTACTGGTAAAGAGACATCGAGAGAAAATTGTCG
ATAGAATTTAATAATTAATTGTTTAAGTGTTCCCCGTACACCAGAATTTA
TAATAAAATAAAAAATATTGAGATTGATACTGGTGAATTTGGAAATCGAA
TTCAGACTGGTGTAAC
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protein sequence of SMED30017632-orf-1

>SMED30017632-orf-1 ID=SMED30017632-orf-1|Name=SMED30017632-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=261bp
MHLPRIPKISPAPSVLAASQYLANLENNYLELRKKYEKMKGTWHSPRATK
KLYKKISRISRARDVLIVENRAQRLTIAEQSAMLRKIFTEKELQARLPGW
SMAQQINIISANHLLGPSSNRIGRDDINTVVNREVPQTTNRNIKHKPNKN
RRRREMRRAENALLQANLNITGSTTSTEVSKTPRNSTSFHPILKPADSDL
EVIYAPQLVNFSQSAPESLQFNISIESLTTDTPANVQLAISTRTVRDERF
AISSERYTPQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
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 availableCOILSCoilCoilcoord: 15..42
NoneNo IPR availableCOILSCoilCoilcoord: 149..169