SMED30025371

Overview
NameSMED30025371
Smed IDSMED30025371
Length (bp)1623
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 SMED30025371 (SMED30025371) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30025371 (SMED30025371) 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



SMED30025371

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
reproductive organSMED30025371SMESG000061985.1 Contig20014newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30025371SMESG000061985.1 Contig20014uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30025371 vs. Ensembl Human
Match: FBXL12 (F-box and leucine rich repeat protein 12 [Source:HGNC Symbol;Acc:HGNC:13611])

HSP 1 Score: 53.5286 bits (127), Expect = 4.618e-7
Identity = 49/217 (22.58%), Postives = 97/217 (44.70%), Query Frame = 2 
Query:   17 LPDSIIENIFSFLKVKHILTANKVCRKWNTIINSSLSWTNVDFS------EVSIHFNQENLK-RIRSLIGPLTGVLRFNDNTSNEVN------------NIIKICVHVE-----------------EMHLCNVR---LYSEIDILLWPRCLTVLEIIDTYIND--GKFYEQYQLNGTPFPQLRSLVVNNPYIMSENDMKALLSSKT-VESLKIKVCS 541
            LPDS++  IFS+L V+  +  ++VC +W  +++    W +VD +      +V  H  +  +  R+ SL     G   F+ + + +++            N+ ++C+HV                  E+H C +    L+ + D        TVL +++  + D    F +++    T F  LRSLV+   Y ++E  + A L   + ++ L++  C+
Sbjct:    7 LPDSVLLEIFSYLPVRDRIRISRVCHRWKRLVDDRWLWRHVDLTLYTMRPKVMWHLLRRYMASRLHSL---RMGGYLFSGSQAPQLSPALLRALGQKCPNLKRLCLHVADLSMVPITSLPSTLRTLELHSCEISMAWLHKQQDP-------TVLPLLECIVLDRVPAFRDEHLQGLTRFRALRSLVLGGTYRVTETGLDAGLQELSYLQRLEVLGCT 213
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BLAST of SMED30025371 vs. Ensembl Nematostella
Match: EDO40897 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S602])

HSP 1 Score: 46.595 bits (109), Expect = 1.166e-6
Identity = 27/101 (26.73%), Postives = 51/101 (50.50%), Query Frame = 2 
Query:   14 SLPDSIIENIFSFLKVKHILTANKVCRKWNTIINSSLSWTNVDFSEVSIHFNQENLKRIRSL-IGPLTGVLRFNDNTSNEVNNIIKICV--HVEEMHLCNV 307
            ++ D +I  +F FL ++++L+A+ VCR+W  +   S  WT++D ++ S       + R+ S    PL   L      +  VN+   +CV      +H+ N+
Sbjct:    3 TIADDVIIAVFRFLDMRNLLSASLVCRRWYRLTQDSSLWTDLDLAQYSTKLQPAAIHRLLSQSFAPLGRRLSL---ATCAVNSETLVCVRQRCHSLHILNL 100
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BLAST of SMED30025371 vs. Planmine SMEST
Match: SMESG000061985.1 (SMESG000061985.1)

HSP 1 Score: 1041.18 bits (2691), Expect = 0.000e+0
Identity = 536/536 (100.00%), Postives = 536/536 (100.00%), Query Frame = 2 
Query:    2 MNVNSLPDSIIENIFSFLKVKHILTANKVCRKWNTIINSSLSWTNVDFSEVSIHFNQENLKRIRSLIGPLTGVLRFNDNTSNEVNNIIKICVHVEEMHLCNVRLYSEIDILLWPRCLTVLEIIDTYINDGKFYEQYQLNGTPFPQLRSLVVNNPYIMSENDMKALLSSKTVESLKIKVCSTFVINSVIELCPNLISIILQWGNIEIDDNKLIMYLWPKSLKVIKFNSFPNTTAIARINKSKSKNIETDFAKLRVLHLKNCIGFSSRSLNIMIKYGNITHINLDNLTAATINQIVEHSKYLMSISLKLIFKPQEKEKLNLLLWPPTLKVIILKHIDIESFHSPEPFYSKMKKEKAKKVFPLLEELHCVSCSGFTSRDLLAIGPSNCLYSLTPMASMINDQINLLEMFPQLIRINLRCLPNISCSNLLKWLDQSHVTQFEILDQEFADFTLADLILKLIRSRLNETKRKMLPVSWVRLSLVXXXXXXXXXXXXXXXMTDETPPLTLIIDIFDEESNSAWNLERNCVLKKNTSLDIIID 1609
            MNVNSLPDSIIENIFSFLKVKHILTANKVCRKWNTIINSSLSWTNVDFSEVSIHFNQENLKRIRSLIGPLTGVLRFNDNTSNEVNNIIKICVHVEEMHLCNVRLYSEIDILLWPRCLTVLEIIDTYINDGKFYEQYQLNGTPFPQLRSLVVNNPYIMSENDMKALLSSKTVESLKIKVCSTFVINSVIELCPNLISIILQWGNIEIDDNKLIMYLWPKSLKVIKFNSFPNTTAIARINKSKSKNIETDFAKLRVLHLKNCIGFSSRSLNIMIKYGNITHINLDNLTAATINQIVEHSKYLMSISLKLIFKPQEKEKLNLLLWPPTLKVIILKHIDIESFHSPEPFYSKMKKEKAKKVFPLLEELHCVSCSGFTSRDLLAIGPSNCLYSLTPMASMINDQINLLEMFPQLIRINLRCLPNISCSNLLKWLDQSHVTQFEILDQEFADFTLADLILKLIRSRLNETKRKMLPVSWVRLSLVHNLLPSHLLPELSELMTDETPPLTLIIDIFDEESNSAWNLERNCVLKKNTSLDIIID
Sbjct:    1 MNVNSLPDSIIENIFSFLKVKHILTANKVCRKWNTIINSSLSWTNVDFSEVSIHFNQENLKRIRSLIGPLTGVLRFNDNTSNEVNNIIKICVHVEEMHLCNVRLYSEIDILLWPRCLTVLEIIDTYINDGKFYEQYQLNGTPFPQLRSLVVNNPYIMSENDMKALLSSKTVESLKIKVCSTFVINSVIELCPNLISIILQWGNIEIDDNKLIMYLWPKSLKVIKFNSFPNTTAIARINKSKSKNIETDFAKLRVLHLKNCIGFSSRSLNIMIKYGNITHINLDNLTAATINQIVEHSKYLMSISLKLIFKPQEKEKLNLLLWPPTLKVIILKHIDIESFHSPEPFYSKMKKEKAKKVFPLLEELHCVSCSGFTSRDLLAIGPSNCLYSLTPMASMINDQINLLEMFPQLIRINLRCLPNISCSNLLKWLDQSHVTQFEILDQEFADFTLADLILKLIRSRLNETKRKMLPVSWVRLSLVHNLLPSHLLPELSELMTDETPPLTLIIDIFDEESNSAWNLERNCVLKKNTSLDIIID 536
The following BLAST results are available for this feature:
BLAST of SMED30025371 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 1
Match NameE-valueIdentityDescription
FBXL124.618e-722.58F-box and leucine rich repeat protein 12 [Source:H... [more]
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BLAST of SMED30025371 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 SMED30025371 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 SMED30025371 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 SMED30025371 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 SMED30025371 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 SMED30025371 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 SMED30025371 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 SMED30025371 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 SMED30025371 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 SMED30025371 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 SMED30025371 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO408971.166e-626.73Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30025371 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 SMED30025371 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000061985.10.000e+0100.00SMESG000061985.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025371 ID=SMED30025371|Name=SMED30025371|organism=Schmidtea mediterranea sexual|type=transcript|length=1623bp
GATGAACGTAAATTCTCTCCCAGATAGTATAATAGAGAATATTTTTTCAT
TTTTAAAGGTGAAGCATATTCTCACTGCAAATAAAGTCTGCAGAAAATGG
AATACAATAATTAACAGTTCTCTTTCTTGGACCAATGTTGATTTTTCAGA
AGTTTCAATTCATTTTAATCAAGAAAATCTAAAGAGGATCCGATCTTTGA
TAGGACCACTTACCGGAGTTCTTCGATTTAATGACAATACTTCTAATGAA
GTAAATAATATAATTAAGATCTGTGTCCATGTTGAAGAAATGCATTTATG
CAATGTGAGACTGTATTCTGAAATAGATATATTATTATGGCCCAGATGTC
TAACTGTATTAGAGATCATTGACACATACATTAATGACGGAAAGTTTTAC
GAGCAATATCAATTGAATGGAACTCCCTTTCCACAACTTAGGTCATTAGT
TGTTAATAATCCTTATATAATGTCAGAAAACGATATGAAGGCTCTTTTAT
CATCAAAAACCGTCGAATCTCTCAAAATAAAAGTTTGTTCGACATTTGTT
ATCAATTCCGTAATTGAGCTCTGTCCTAACTTGATTTCAATAATTCTTCA
ATGGGGTAACATAGAAATTGATGATAATAAACTGATAATGTATTTGTGGC
CAAAATCTTTAAAGGTGATAAAATTTAACAGCTTTCCTAATACTACAGCT
ATAGCCAGGATAAATAAATCGAAATCAAAAAACATCGAAACTGACTTTGC
AAAACTTCGAGTGCTTCATTTGAAAAATTGCATCGGTTTCAGTTCCCGTT
CATTAAACATCATGATAAAATATGGCAATATTACGCACATAAATCTTGAT
AATTTAACTGCAGCGACTATAAACCAAATAGTTGAACATTCAAAATATTT
GATGAGTATTTCGTTGAAATTAATTTTTAAACCCCAAGAAAAAGAGAAAC
TAAATTTATTGCTATGGCCTCCTACATTAAAAGTTATTATTCTTAAACAT
ATTGATATTGAGAGTTTTCATTCACCAGAGCCATTTTACAGCAAAATGAA
AAAAGAAAAAGCGAAAAAGGTTTTCCCTCTACTAGAAGAACTTCATTGTG
TTTCATGCTCAGGATTTACTTCTAGAGATTTACTAGCCATCGGTCCGAGC
AACTGCCTCTATTCTCTGACACCAATGGCTTCTATGATAAATGATCAGAT
CAATCTGCTAGAAATGTTTCCTCAACTGATTCGTATCAATCTCAGGTGTT
TACCAAACATTTCGTGCTCAAATTTATTAAAATGGCTTGACCAGTCTCAT
GTAACCCAATTCGAAATATTAGATCAGGAGTTTGCCGATTTTACGTTGGC
TGATCTTATTCTTAAATTGATACGCTCAAGACTTAATGAAACGAAACGAA
AAATGCTTCCGGTCAGTTGGGTACGACTTTCTTTGGTTCACAACTTACTA
CCAAGCCATTTGTTACCGGAATTGTCTGAATTGATGACTGATGAAACGCC
ACCATTGACGCTGATCATTGACATCTTTGACGAAGAGTCAAACAGTGCTT
GGAATCTAGAAAGAAATTGTGTTTTAAAGAAGAATACTTCATTGGACATC
ATAATCGACTGAGGAATTTCCAC
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protein sequence of SMED30025371-orf-1

>SMED30025371-orf-1 ID=SMED30025371-orf-1|Name=SMED30025371-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=537bp
MNVNSLPDSIIENIFSFLKVKHILTANKVCRKWNTIINSSLSWTNVDFSE
VSIHFNQENLKRIRSLIGPLTGVLRFNDNTSNEVNNIIKICVHVEEMHLC
NVRLYSEIDILLWPRCLTVLEIIDTYINDGKFYEQYQLNGTPFPQLRSLV
VNNPYIMSENDMKALLSSKTVESLKIKVCSTFVINSVIELCPNLISIILQ
WGNIEIDDNKLIMYLWPKSLKVIKFNSFPNTTAIARINKSKSKNIETDFA
KLRVLHLKNCIGFSSRSLNIMIKYGNITHINLDNLTAATINQIVEHSKYL
MSISLKLIFKPQEKEKLNLLLWPPTLKVIILKHIDIESFHSPEPFYSKMK
KEKAKKVFPLLEELHCVSCSGFTSRDLLAIGPSNCLYSLTPMASMINDQI
NLLEMFPQLIRINLRCLPNISCSNLLKWLDQSHVTQFEILDQEFADFTLA
DLILKLIRSRLNETKRKMLPVSWVRLSLVHNLLPSHLLPELSELMTDETP
PLTLIIDIFDEESNSAWNLERNCVLKKNTSLDIIID*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR036047F-box-like_dom_sf
IPR032675LRR_dom_sf
IPR001810F-box_dom
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
GO:0004842ubiquitin-protein transferase activity
Vocabulary: cellular component
TermDefinition
GO:0000151ubiquitin ligase complex
GO:0005737cytoplasm
GO:0005829cytosol
Vocabulary: biological process
TermDefinition
GO:0000209protein polyubiquitination
GO:0006511ubiquitin-dependent protein catabolic process
GO:0016567protein ubiquitination
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001810F-box domainSMARTSM00256fbox_2coord: 6..46
e-value: 9.5E-9
score: 45.1
IPR001810F-box domainPFAMPF12937F-box-likecoord: 4..48
e-value: 3.8E-9
score: 36.3
IPR001810F-box domainPROSITEPS50181FBOXcoord: 1..46
score: 14.955
IPR032675Leucine-rich repeat domain superfamilyGENE3DG3DSA:3.80.10.10coord: 1..311
e-value: 1.3E-21
score: 78.9
NoneNo IPR availablePANTHERPTHR16134:SF3F-BOX/LRR-REPEAT PROTEIN 12coord: 3..182
NoneNo IPR availablePANTHERPTHR16134FAMILY NOT NAMEDcoord: 3..182
NoneNo IPR availableSUPERFAMILYSSF52047RNI-likecoord: 27..285
IPR036047F-box-like domain superfamilySUPERFAMILYSSF81383F-box domaincoord: 3..52