SMED30000712

Overview
NameSMED30000712
Smed IDSMED30000712
Length (bp)923
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 SMED30000712 (SMED30000712) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30000712 (SMED30000712) 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 SMED30000712 (SMED30000712) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30000712 (SMED30000712) 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




SMED30000712

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymal cellSMED30000712SMESG000059672.1 dd_Smed_v4_5681_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
SMED30000712 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004946:22719..23640 +4511
Homology
BLAST of SMED30000712 vs. Ensembl Fly
Match: CG9286 (gene:FBgn0038183 transcript:FBtr0082830)

HSP 1 Score: 48.9062 bits (115), Expect = 2.066e-6
Identity = 50/198 (25.25%), Postives = 100/198 (50.51%), Query Frame = 2
Query:  281 EDSTLLSLTTVINLKKHQNAISIMQLLSSI--KANI-ANDTIGLEIIKILEDPVNNIGFVINERNIN-NSSLTLRVLETVFEDIIKFQSTDEELKYSHYCILLTLSKNCSTGDLEFYHEEMKK------VY-----------GKFTYKSLFKIESETSDKGSSVSIQG------YRAFVLFPSNELDKFLSYIK*IIN 793
            ED T+  +T+V+NL   ++  SI QL + I  +A   A+  +  ++ +IL+    ++GF+INER IN  + +++ +L+++ ++I   ++  +++KY    +LL          ++FY +E KK      VY            KF+++  + + SET    S   ++G      YR  ++  + +L + +  I+  IN
Sbjct:  111 EDGTIFGITSVLNLTAKKDQPSIAQLRTYILDRAKTHASPEVQQQLKEILDSEQRHVGFLINERFINIPAQISVPLLQSLQQEIEAAKA--KKMKYDFGTLLLL---------VKFYRKESKKGKPGEDVYTNAEDELLSDRAKFSFE--YSMASETDSGMSGDWLEGDAVMTPYRKLLVLEAKKLPQLIDDIQRFIN 295          
BLAST of SMED30000712 vs. UniProt/SwissProt
Match: sp|Q5AXW5|BCP1_EMENI (Protein bcp1 OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) OX=227321 GN=bcp1 PE=3 SV=1)

HSP 1 Score: 56.6102 bits (135), Expect = 5.725e-8
Identity = 52/192 (27.08%), Postives = 91/192 (47.40%), Query Frame = 2
Query:   41 MSKRSKVVD-NVEIYNCDFICDYVMNEDFDMIMTIFQNFIPKEFNLDFKNITEIV-------LSDTDLALCMRNCLSEDDP---NNLDVDPEDSTLLSLTTVINLKKHQNAISIMQLLSSIKANIANDTIGLEIIKIL--EDPVNNIGFVINERNINNSSLTLRVLETVFEDIIKFQSTDEE-LKYSHYCIL 574
            M KR ++ D +V +   D       +ED DM+   F+ F P+E  +DF  I  ++         D DL+      L++  P   + +  D +DS   +  TV+NL++H +   I  L + IK   A+ T  L  +  L  + P+  IG ++ ER IN  S  +  +  + ++ I +   ++E   +SHY I+
Sbjct:    1 MGKRKQIKDGDVSMGGTDPATGDSSDEDIDMVNVDFEWFDPQE--IDFHGIKHLIRQLFDVDAQDLDLSGLTDMILAQ--PLLGSTVKTDGKDSDPYAFLTVLNLQEHADKPPIKSLTTYIKRK-ASGTPSLSPLAQLFSQTPIPPIGLILTERLINMPSEVVPPMYAMLQEEITWAIEEKEPYNFSHYLIV 187          
BLAST of SMED30000712 vs. UniProt/SwissProt
Match: sp|Q2U600|BCP1_ASPOR (Protein bcp1 OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) OX=510516 GN=bcp1 PE=3 SV=1)

HSP 1 Score: 54.6842 bits (130), Expect = 2.529e-7
Identity = 54/194 (27.84%), Postives = 97/194 (50.00%), Query Frame = 2
Query:   41 MSKRSKVVDN-VEIYNCDFICDY-VMNEDFDMIMTIFQNFIPKEFNLDFKNITEIVLSDTDLALCMRNCLSE---DDP---NNLDVDPEDSTLLSLTTVINLKKHQNAISIMQLLSSIKANIANDTIGLEIIKIL-EDPVNNIGFVINERNINNSSLTLRVLETVFEDIIKFQSTDEE-LKYSHYCILLTLSKN 592
            M KR ++ DN VE+   D   D    +ED D++   F+ F P+  +     I    L D+D  +   + LS+     P   + + VD  +S   +  TV+NL++H++   I  L+S ++   +++     + ++L + PV  IG ++ ER IN  +  +  + T+  + I +   D+E  K+SHY I   +SKN
Sbjct:    1 MGKRKEIKDNDVEMGGTDPRVDGDESDEDMDIVNVDFEWFDPQPIDFHGLKILLRQLFDSDAQIFDMSALSDMILAQPLLGSTVKVDGNESDPYAFLTVLNLQEHKDKPVIKDLISYLQRKASSNPDLAPLSQLLSQTPVPPIGLILTERLINMPAEVVPPMYTMLMEEIAWAIQDKEPYKFSHYLI---VSKN 191          
BLAST of SMED30000712 vs. TrEMBL
Match: A0A4Y7LU90 (Protein BCCIP homolog OS=Ceriodaphnia reticulata OX=302197 GN=EOG090X0C3Y PE=2 SV=1)

HSP 1 Score: 57.7658 bits (138), Expect = 8.047e-6
Identity = 42/174 (24.14%), Postives = 85/174 (48.85%), Query Frame = 2
Query:   83 NCDFICDYVMNEDFDMIMTI-FQNFIPKEFNLDFKNITEIVLSDTDLALCMRNCLSEDDPNNLDVD--PEDSTLLSLTTVINLKKHQNAISIMQLLSSIKANIANDTIGLEIIKILEDPVNNIGFVINERNIN-NSSLTLRVLETVFEDIIKFQSTDEELKYSHYCILLTLSKN 592
              +F       EDF  I  + +Q F+    NL    +TE+++  + +   ++ C+ EDDP+N D +  P D  +  +T+VINL  H++   + ++   +         GL      ED  N +G + NER IN    +++ +LE + ++I + +   +   ++H+ ++  L ++
Sbjct:   47 QVEFAGQSPAPEDFHGIKALMYQLFLKAHINL--SGLTELIIEQSYIGSILQQCVDEDDPDNSDEEGAPADE-VFGITSVINLTHHKDVECVKEVKKYLLEKTQKKLTGL-----FEDSSNQVGLLFNERFINIPPQVSVPLLENLCKEIEEAKKGGKPFDFTHFILISKLHES 212          
BLAST of SMED30000712 vs. TrEMBL
Match: A0A4Y7MV34 (Protein BCCIP homolog OS=Daphnia pulex OX=6669 GN=EOG090X0C3Y PE=2 SV=1)

HSP 1 Score: 57.3806 bits (137), Expect = 9.752e-6
Identity = 47/206 (22.82%), Postives = 96/206 (46.60%), Query Frame = 2
Query:   41 MSKRSKVVDNVEIYNCDFICDYVMNEDFDMIMTIFQNFIPKEFNLDFKNITEIVLSDTDLALCMRNCLSEDDPNNLDVDPEDSTLLSLTTVINLKKHQNAISIMQLLSSIKANIANDTIGLEIIKILEDPVNNIGFVINERNIN-NSSLTLRVLETVFEDIIKFQSTDEELKYSHYCILLTLSKNCSTGDLEFYHEEMKKVYGKFT 655
            M +  ++ +N      DF+    + EDF  I ++      K  +++   +TE+++    +   ++ C+  D+P++ D       +  +T+VINL  H++   I ++   +         GL      +DP N IG + NER IN    +++ +LE + ++I + + + +   ++H+ IL++     +  D E      KKV G  T
Sbjct:   32 MGEDEQLGENDREIQVDFVGQSPIAEDFHGIKSLMHQLFLKA-HINLSGLTELIIQQNYIGSILQQCVDNDEPDSDDEGNSLDEVFGITSVINLTHHKDVECIKEVKKYLLEKTQKKLSGL-----FDDPSNQIGLLFNERFINIPPQVSVPLLENLCKEIDEAKKSGKPFDFTHF-ILISKLHESTRKDPE---SRKKKVKGGAT 227          
BLAST of SMED30000712 vs. Planmine SMEST
Match: SMESG000059672.1 (SMESG000059672.1)

HSP 1 Score: 488.804 bits (1257), Expect = 8.196e-177
Identity = 244/247 (98.79%), Postives = 245/247 (99.19%), Query Frame = 2
Query:   41 MSKRSKVVDNVEIYNCDFICDYVMNEDFDMIMTIFQNFIPKEFNLDFKNITEIVLSDTDLALCMRNCLSEDDPNNLDVDPEDSTLLSLTTVINLKKHQNAISIMQLLSSIKANIANDTIGLEIIKILEDPVNNIGFVINERNINNSSLTLRVLETVFEDIIKFQSTDEELKYSHYCILLTLSKNCSTGDLEFYHEEMKKVYGKFTYKSLFKIESETSDKGSSVSIQGYRAFVLFPSNELDKFLSYIK 781
            MSKRSKVVDNVEIYNCDFICDYVMNEDFDMIMTIFQNFIPKEFNLDFKNITEIVLSDTDLALCMRNCLSEDDPNNLDVDPEDSTLLSLTTVINLKKHQN ISI+QLLSSIKANIANDTIGLEIIKILEDPVNNIGFVINERNINNSSLTLRVLETVFEDIIKFQSTDEELKYSHYCILLTLSKNCSTGDLEFYHEEMKKVYGK TYKSLFKIESETSDKGSSVSIQGYRAFVLFPSNELDKFLSYIK
Sbjct:    1 MSKRSKVVDNVEIYNCDFICDYVMNEDFDMIMTIFQNFIPKEFNLDFKNITEIVLSDTDLALCMRNCLSEDDPNNLDVDPEDSTLLSLTTVINLKKHQNEISIVQLLSSIKANIANDTIGLEIIKILEDPVNNIGFVINERNINNSSLTLRVLETVFEDIIKFQSTDEELKYSHYCILLTLSKNCSTGDLEFYHEEMKKVYGKLTYKSLFKIESETSDKGSSVSIQGYRAFVLFPSNELDKFLSYIK 247          
The following BLAST results are available for this feature:
BLAST of SMED30000712 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 SMED30000712 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 SMED30000712 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
CG92862.066e-625.25gene:FBgn0038183 transcript:FBtr0082830[more]
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BLAST of SMED30000712 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 SMED30000712 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 SMED30000712 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 SMED30000712 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 2
Match NameE-valueIdentityDescription
sp|Q5AXW5|BCP1_EMENI5.725e-827.08Protein bcp1 OS=Emericella nidulans (strain FGSC A... [more]
sp|Q2U600|BCP1_ASPOR2.529e-727.84Protein bcp1 OS=Aspergillus oryzae (strain ATCC 42... [more]
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BLAST of SMED30000712 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A4Y7LU908.047e-624.14Protein BCCIP homolog OS=Ceriodaphnia reticulata O... [more]
A0A4Y7MV349.752e-622.82Protein BCCIP homolog OS=Daphnia pulex OX=6669 GN=... [more]
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BLAST of SMED30000712 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 SMED30000712 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 SMED30000712 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 SMED30000712 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 SMED30000712 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 SMED30000712 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000059672.18.196e-17798.79SMESG000059672.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000712 ID=SMED30000712|Name=SMED30000712|organism=Schmidtea mediterranea sexual|type=transcript|length=923bp
TAATAATTAATTTTAACGCTTTATATTTTTTATTTATCCAATGTCCAAAA
GAAGTAAAGTTGTAGATAACGTTGAAATTTATAATTGTGATTTTATTTGT
GATTATGTCATGAATGAAGATTTTGATATGATCATGACTATTTTTCAAAA
TTTTATACCCAAAGAATTCAATCTTGATTTTAAAAATATTACAGAAATAG
TCTTAAGTGATACTGATCTAGCACTTTGTATGCGTAATTGTCTGTCGGAA
GATGACCCTAATAATCTTGATGTTGATCCTGAAGATTCTACTCTTTTGAG
TTTGACAACTGTAATCAATCTTAAAAAACATCAAAATGCAATATCTATTA
TGCAGTTACTTTCCTCGATTAAAGCAAATATTGCTAATGATACTATTGGT
TTAGAAATTATTAAAATTCTAGAAGACCCAGTTAATAACATTGGATTTGT
TATTAACGAAAGGAACATAAACAATTCCTCTCTAACGTTAAGAGTCTTAG
AAACTGTTTTCGAAGATATAATAAAATTTCAATCTACGGACGAAGAATTA
AAATATTCGCATTATTGTATCCTGTTGACTTTATCCAAAAATTGCTCCAC
TGGTGACTTGGAATTTTATCACGAGGAAATGAAAAAGGTTTATGGTAAAT
TTACATATAAATCTTTGTTCAAAATCGAAAGTGAAACTAGTGACAAGGGG
AGCTCAGTTTCAATTCAAGGCTATCGAGCATTTGTGTTATTTCCTTCTAA
TGAATTAGATAAATTTCTATCTTATATAAAATAAATTATAAATCTTTGGA
TTTTACGCGTTTATTGGATTATTTTAATGCTTATGTATTTTATATCTAGG
TTGTAACGGGATGAGTCAAATACTTTTAAAAAGATTGTTTTACTAATCAT
TATTAATGTGATTAACACAGGCG
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protein sequence of SMED30000712-orf-1

>SMED30000712-orf-1 ID=SMED30000712-orf-1|Name=SMED30000712-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=248bp
MSKRSKVVDNVEIYNCDFICDYVMNEDFDMIMTIFQNFIPKEFNLDFKNI
TEIVLSDTDLALCMRNCLSEDDPNNLDVDPEDSTLLSLTTVINLKKHQNA
ISIMQLLSSIKANIANDTIGLEIIKILEDPVNNIGFVINERNINNSSLTL
RVLETVFEDIIKFQSTDEELKYSHYCILLTLSKNCSTGDLEFYHEEMKKV
YGKFTYKSLFKIESETSDKGSSVSIQGYRAFVLFPSNELDKFLSYIK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR025602BCP1_family
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR025602BCP1 familyPFAMPF13862BCIPcoord: 16..186
e-value: 3.5E-14
score: 53.1
IPR025602BCP1 familyPANTHERPTHR13261BRCA2 AND CDKN1A INTERACTING PROTEINcoord: 13..244
NoneNo IPR availablePANTHERPTHR13261:SF0BRCA2 AND CDKN1A-INTERACTING PROTEINcoord: 13..244