SMED30023613

Overview
NameSMED30023613
Smed IDSMED30023613
Length (bp)1469
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 SMED30023613 (SMED30023613) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023613 (SMED30023613) 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.
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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




SMED30023613

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30023613 dd_Smed_v4_12778_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30023613 dd_Smed_v4_12778_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30023613 dd_Smed_v4_12778_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30023613 dd_Smed_v4_12778_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30023613 dd_Smed_v4_12778_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30023613 dd_Smed_v4_12778_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30023613 dd_Smed_v4_12778_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30023613 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000100:71509..72974 -5840
Homology
BLAST of SMED30023613 vs. TrEMBL
Match: A0A2C9JH44 (DDE_Tnp_IS1595 domain-containing protein OS=Biomphalaria glabrata OX=6526 GN=106059660 PE=4 SV=1)

HSP 1 Score: 77.7962 bits (190), Expect = 2.503e-17
Identity = 59/217 (27.19%), Postives = 98/217 (45.16%), Query Frame = -2
Query:  629 RLLRNC---CTCVTCNIPCTS-QAENRETEKYV*KCKA*KNVSCIIRNESFLFNSYLYLQSFIFLCFQ*SRETPIHLVCKDISVSRRVDVDWYNFIRGITCK*FENNTPXX--XXXXXXXXXXXXLPKESSEKADYKKPVWLFGGVQRGTKNCFLQVILNRQIQTLMPLIARHIFPGIHIMSDCLTIYQQLGNFRGL--------NNLQNFVHPGNA 1237
            R+LR     C    C    T   + +R+  KY  +C + K     +R +SFL  S L L+ FI+L +  S+ +   +V + +  S    VDW+N+ R I C+ +    P        ++++ +  + K       +  P W+FGG+   T N F+  + +R   TL+P+I ++I PG  I SD    Y  + +   L        N+  NFV P   
Sbjct:   41 RILRRTAPNCPLPECGREMTEINSADRKDGKYY-RCPSHKGKKLSLREDSFLSQSQLSLEEFIWLVYFWSKSSSNAMVMETLKFSSGTVVDWFNYFRNI-CRRYLTLHPIRIGGVGHVVEIDESVVAKRKYHVGRHVPPKWVFGGIDTTTDNGFMVFVEDRSANTLLPIIEQYIEPGTMIHSDAWAAYNGIAHLPVLPPYQHNVVNHSTNFVDPATG 255          

HSP 2 Score: 41.2022 bits (95), Expect = 2.503e-17
Identity = 18/38 (47.37%), Postives = 27/38 (71.05%), Query Frame = -3
Query:  514 SSTESVETMWFRLKRKFKRMNGTPYEMLNSYISEFICR 627
            ++T  VE MW  +K+K KRM+GT  ++L S+I EF+ R
Sbjct:  256 ATTNHVERMWKSMKQKLKRMSGTSDDLLQSHIDEFLWR 293          
BLAST of SMED30023613 vs. TrEMBL
Match: W4Z0I9 (DDE_Tnp_IS1595 domain-containing protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1)

HSP 1 Score: 91.6633 bits (226), Expect = 1.138e-16
Identity = 73/289 (25.26%), Postives = 124/289 (42.91%), Query Frame = -2
Query:  560 AGRPSAPTLIVSAEGILSHEAIQNEVWATLIIVPLIVEPLQCIK*LITHRLLRNCCTCVTCNIPCTSQAENRETEKYV*KCKA*KNVSCIIRNESFLFNSYLYLQSFIFLCFQ*SRETPIHLVCKDISVSRRV-DVDWYNFIRGITCK*FENNTPXXXXXXXXXXXXXXLPKESS------EKADYKKPVWLFGGVQRGTKNCFLQVILNRQIQTLMPLIARHIFPGIHIMSDCLTIYQQLGNFRG---LNNL----QNFVHPGNAFVHRVCRNYVVST*TKIQENEWN 1384
            AGRP APT I+  + I+    I          +P +      ++ L +  L+ N   C  C+ PC   A     + +  KC   +    + R+ SF   S++ L+  +   +  + + P++ + +   +S  V  V+W N +R +  +    N  +                ES        +  Y++  W+FG V+R T  C L+++ NR   TL P+I+R + PG HI+SD    YQQL    G   L+++     NFV P + ++H           T   E +WN
Sbjct:    2 AGRPRAPTRIIPIQNIMPIAEIIAADILLRDFMPGLATVEDTLRWLASRSLIANSHLCAWCHEPCGLVAHQGIDKVW--KCLQCRRRKSV-RHGSFFSRSHICLRDLLIFIYLWAEDLPLNFIARQSGLSTDVTSVNWANMLREVCGQELMANFRQLGGFDENGQATVVEIDESKYFHRKYHRGAYREGFWVFGAVERATGRCQLEIVPNRTRATLEPIISRWLLPGTHILSDGWRSYQQLDQLDGGVYLHDVVIHEDNFVDPVHEWLH-----------TNTIEGKWN 276          
BLAST of SMED30023613 vs. TrEMBL
Match: A0A0L8G5T0 (DDE_Tnp_IS1595 domain-containing protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22039914mg PE=4 SV=1)

HSP 1 Score: 91.2781 bits (225), Expect = 1.674e-16
Identity = 71/250 (28.40%), Postives = 107/250 (42.80%), Query Frame = -2
Query:  683 MPAGRPSAPTLIVSAEGILSHEAIQNEVWATLIIVPLIVEPLQCIK*LITHRLLRNCCTCVTCNIPCTSQAENRETEKYV*KCKA*KNVSCIIRNESFLFNSYLYLQSFIFLCFQ*SRETPIHLVCKDISVSRRVDVDWYNFIRGITCK*FE-------NNTPXXXXXXXXXXXXXXLP-------KESSEKADYKKPVWLFGGVQRGTKNCFLQVILNRQIQTLMPLIARHIFPGIHIMSDCLTIYQQL 1390
            MP GRPS P  I +   I+  E I+ E W    +   I      I  L  ++L+ N   C  C  PCT     R  +    +C    N S  IR  SF   S+L L +FI+L +  SR+     +  + +V++    D +  IR +  +  E       ++ P+     L     + +        K    +  +KK  W+FGG++RGT  CFL  I  +  +     I R I PG HI+SD    Y Q+
Sbjct:    5 MPRGRPSNPKTICA--DIVDDEKIRQESWTFYDLFKQISTNDIAITWLAKYKLISNSVICSVCGNPCTINVIKRSIDGIRWRCPQ-HNFSRSIRKGSFFEKSHLSLTTFIWLMYMWSRDYQHTEMTHETNVNKNSTTDMFRLIRELLERFLEDHPTELGDDPPEIGGFDLQTGEPKVVEIDVTKCVKSKRNEKKHKKEFWIFGGIERGTDKCFLVPIEYQNKEAFEAAIIRWILPGTHIVSDIWAEYLQI 251          
BLAST of SMED30023613 vs. TrEMBL
Match: A0A0L8FW94 (DDE_Tnp_IS1595 domain-containing protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22006020mg PE=4 SV=1)

HSP 1 Score: 71.633 bits (174), Expect = 1.847e-15
Identity = 70/265 (26.42%), Postives = 103/265 (38.87%), Query Frame = -2
Query:  623 MPAGRPSAPTLIVSAEGILSHEAIQNEVWATLIIVPLIVEPLQCIK*LITHRLLRNCCTCVTCNIPC---TSQAENRETEKYV*KCKA*KNVSCIIRNESFLFNSYLYLQSFIFLCFQ*SRETPIHLVCKDISVSRRVDVDWYNFIRGITCK*FENNTPXXXXXXXXXXXXXXLPKESS------EKADYKKPVWLFGGVQRGTKNCFLQVILNRQIQTLMPLIARHIFPGIHIMSDCLTIYQQLGNFRGLNNLQNFVHPGNAFV 1390
            MP GRP+A  LIV+   IL+ + I  E W    +       +  ++     RL+RN  TC  C +PC   T        E Y   C+  K+V    R  SF   S++ L   + L +   +E     +  + S+S    VDW NF R +  +    N  +                ES        +  ++   W+FGGV+R +  CFL  IL                PG HI+SD    Y  + N  G       +  G+ FV
Sbjct:    1 MPRGRPAAQHLIVAENEILNRQLILEEKWNIRELCSSSRHRM--LEWCARRRLIRNKFTCDDCLVPCGLVTRGDRIDGKEWYCKHCEKKKSV----RYSSFFERSHIPLYHLVLLIYCWCKEIMQKYIVDESSLSHTSVVDWNNFCREVCDEWLRQNPMEIGGVDNNGQPLVVEIDESKFFHRTYHRGLWRPGHWVFGGVERDSGKCFLVEIL----------------PGTHIISDRWASYANITNLGGCIYTHEVIVHGDHFV 243          

HSP 2 Score: 41.2022 bits (95), Expect = 1.847e-15
Identity = 20/51 (39.22%), Postives = 33/51 (64.71%), Query Frame = -3
Query:  484 EMHSSTESVETMWFRLKRKFKRMNGTPYEMLNSYISEFICRNNFVRQILYV 636
            E+H  T+++E +W RLKRK +   GT  E+  SY+ EF+ RN+  ++  +V
Sbjct:  249 EIH--TQNIENLWMRLKRKLRWQYGTSDELFLSYLHEFLWRNSIPKEKTFV 297          
BLAST of SMED30023613 vs. TrEMBL
Match: A0A1X7SZA3 (DDE_Tnp_IS1595 domain-containing protein OS=Amphimedon queenslandica OX=400682 GN=109590640 PE=4 SV=1)

HSP 1 Score: 85.1149 bits (209), Expect = 1.381e-14
Identity = 56/187 (29.95%), Postives = 91/187 (48.66%), Query Frame = -2
Query:  692 LITHRLLRNCCTCVTCNIPCTSQAENRETEKYV*KCKA*KNVSCIIRNESFLFNSYLYLQSFIFLCFQ*SRETPIHLVCKDISVSRRVDVDWYNFIRGITCK*FENN-TPXXXXXXXXXXXXXXLPKESSEKADYKKPVWLFGGVQRGTKNCFLQVILNRQIQTLMPLIARHIFPGIHIMSDCLTIY 1249
            L +  L+ N   C  C   C      ++T+ +    K  ++V   IRNESF   S+L L   + L +  S ++ +H    +   S    VDW+NF+R I    F +N T       ++++ K    K    +  Y    W+FGG++RGT NCF+  + +R   TL+P+I +++ PG  I+SD    Y
Sbjct:   21 LRSKHLIANYMDCKKCGSSC-RLVTKKDTKVWRCPLKGCQSV-ISIRNESFFSGSHLKLNEIVDLIYWWSCKSTVHATMHETGHSEHTIVDWFNFLRDICADYFLSNPTVIGGPGSVIEIDKSKFGKRKYNRGRYVDGHWVFGGIERGTSNCFMVAVADRSAATLLPIIYKYVRPGSTIISDQWRAY 205          
The following BLAST results are available for this feature:
BLAST of SMED30023613 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 SMED30023613 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 SMED30023613 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 SMED30023613 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 SMED30023613 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 SMED30023613 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 SMED30023613 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 SMED30023613 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A2C9JH442.503e-1727.19DDE_Tnp_IS1595 domain-containing protein OS=Biomph... [more]
W4Z0I91.138e-1625.26DDE_Tnp_IS1595 domain-containing protein OS=Strong... [more]
A0A0L8G5T01.674e-1628.40DDE_Tnp_IS1595 domain-containing protein OS=Octopu... [more]
A0A0L8FW941.847e-1526.42DDE_Tnp_IS1595 domain-containing protein OS=Octopu... [more]
A0A1X7SZA31.381e-1429.95DDE_Tnp_IS1595 domain-containing protein OS=Amphim... [more]
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BLAST of SMED30023613 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 SMED30023613 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 SMED30023613 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 SMED30023613 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 SMED30023613 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 SMED30023613 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023613 ID=SMED30023613|Name=SMED30023613|organism=Schmidtea mediterranea sexual|type=transcript|length=1469bp
ATTTATATTAAATATATCGTGATTTTAATTGTTAATTTAAAGTTTGAATA
ATGATTGTTACTGATAATAAATATAACACATGAGGGAAATCAAGTCTTTA
AAACATGAGTAGAGTGCAACTAATAATATTATAATTCTAAGTTTCCTAAT
GATTATGATTTACATGTTAGAACTTGCATTTATAACAAATGCGATGACAT
GATTTATAAGTTGAAACAAAATATTTTATCAATAATGATAGTTAAACGGA
TTAAGCTACACCTGGTGCTAAACCTTCAAAATTGCCAAATAAAAATTTAG
TTTAATTTTGAATAAAGTTGCTATTTGTAAGATATAATATATTTGTTGAT
TTTGATCTTGAATACTCGTGTTTAGTGAACAGTCACATCGTTAATTGTTT
AGACACGTAAATTCCCCTAATTACTTTTACAAGTAAATCCTAAAAATAAC
CATATATTTATCATAATGGATAGTATTAATACAGACATACAATATTTGTC
TTACAAAATTATTACGGCATATAAACTCAGAAATATAAGAGTTTAGCATT
TCATAAGGAGTTCCATTCATTCTCTTGAATTTTCGTTTAAGTCGAAACCA
CATAGTTTCGACAGACTCTGTGGACGAATGCATTTCCTGGATGAACAAAG
TTCTGTAAATTATTGAGACCTCTGAAATTTCCAAGTTGTTGATAAATGGT
TAAACAATCTGACATGATGTGAATGCCAGGAAAAATATGTCTAGCAATAA
GTGGCATAAGTGTTTGAATCTGTCGGTTTAGGATTACTTGTAGGAAACAG
TTTTTCGTGCCACGTTGGACACCACCAAATAGCCACACAGGTTTTTTGTA
ATCTGCCTTTTCTGAACTTTCTTTTGGCAATGACTGTTTCATCAATTTCA
ACAACAATTGACTCAAACTTTTTGGAGTATTATTCTCAAATCACTTGCAA
GTAATGCCTCTAATGAAATTATACCAATCAACATCAACACGACGTGAGAC
TGAGATATCTTTACACACAAGGTGAATAGGCGTTTCTCGACTTCATTGAA
AGCATAAAAATATAAAGGATTGTAGATAGAGGTAAGAGTTAAATAAAAAC
GATTCGTTGCGAATGATGCAGGAAACGTTTTTTCAAGCTTTGCACTTCTA
AACATACTTTTCGGTTTCCCTGTTCTCAGCCTGAGAAGTGCACGGAATAT
TACATGTAACGCAGGTGCAGCAATTTCGGAGAAGTCTATGAGTGATGAGT
CATTTGATACATTGAAGTGGTTCAACGATCAAAGGGACGATGATAAGTGT
TGCCCATACTTCATTCTGAATAGCTTCATGGCTTAAAATACCTTCTGCTG
ATACAATTAAAGTTGGTGCAGAAGGACGTCCAGCAGGCATGTTAACAACA
ATATTAAGGGAATTTTCGTGTTTAAAGATTACAAATACCGTCATATCCGG
TACAAACATCATTCACGGC
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protein sequence of SMED30023613-orf-1

>SMED30023613-orf-1 ID=SMED30023613-orf-1|Name=SMED30023613-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
MKQSLPKESSEKADYKKPVWLFGGVQRGTKNCFLQVILNRQIQTLMPLIA
RHIFPGIHIMSDCLTIYQQLGNFRGLNNLQNFVHPGNAFVHRVCRNYVVS
T*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR024445Tnp_ISXO2-like