SMED30015387

Overview
NameSMED30015387
Smed IDSMED30015387
Length (bp)978
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 SMED30015387 (SMED30015387) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30015387 (SMED30015387) 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 SMED30015387 (SMED30015387) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30015387 (SMED30015387) 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




SMED30015387

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30015387SMESG000030085.1 SmedASXL_010468SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
neuronSMED30015387SMESG000030085.1 dd_Smed_v4_12792_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
headSMED30015387SMESG000030085.1 dd_Smed_v6_12792_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30015387SMESG000030085.1 dd_Smed_v4_12792_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30015387 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005730:33672..36669 +4816
v31.026723:2069..5239 -4804
Homology
BLAST of SMED30015387 vs. TrEMBL
Match: V3ZN59 (Uncharacterized protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_204592 PE=4 SV=1)

HSP 1 Score: 108.997 bits (271), Expect = 9.078e-24
Identity = 73/228 (32.02%), Postives = 134/228 (58.77%), Query Frame = 1
Query:  208 FAGMKKGFLANGFGDD-KPKTKN------NVPYLKANPSKVNSSLVFEELQENHK-------QKNWLSDDLLNKVTEDNELTTWLSDPKTNIILSDFQVNPQAAMEKYKDDINTQKMXXXXXXXXXXXXREL-ESAACAPSKNPKEVIISAYEPNVAPAIKSALDNKADEALATPGIKEALIDPRIQKIIDSMRSDPKTAQRLMQEADREVHQKLRLLVESGVLGIQQ 846
            F GMKKGFL +   D   P +KN       +PY+K   ++ N  L   E+Q+  K        K+W++DDLL ++ +++ L + LS+P+ +  +++FQ NP+ AM+KY D+   QK L +F  ++G HF +L E      ++  K  ++     +  P IKS  +N+ +E L++  +KE L+D +IQ +  +++++PK  +R++  AD +  +K+++L+++G+L I Q
Sbjct:   69 FGGMKKGFLFSSPKDKVTPVSKNKDSKCETMPYIKK--TETNDELRINEVQDAMKAGGNLLQNKDWVNDDLLKEIEKNDVLYSKLSNPQFSAAIAEFQHNPEGAMKKYADNAEMQKFLKEFCGVMGNHFSQLAEKNPSNKTEGGKGPVLITQNTDSEPHIKSEDENRLEEILSSEKVKEVLMDEKIQNLFHTLKNNPKAGERILHNADGDFKRKIKVLIDAGLLQIDQ 294          
BLAST of SMED30015387 vs. TrEMBL
Match: A0A267GCP8 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig001246g2 PE=4 SV=1)

HSP 1 Score: 98.5969 bits (244), Expect = 5.746e-20
Identity = 70/235 (29.79%), Postives = 121/235 (51.49%), Query Frame = 1
Query:  202 SEFAGMKKGFLANG-----------FGDDKPKTKNNVPYLKANPSKVNSSLVFEELQENHKQK----------NWLSDDLLNKVTEDNELTTWLSDPKTNIILSDFQVNPQAAMEKYKDDINTQKMXXXXXXXXXXXXRELESAACAPSKNPKEVIISAYEPNVAPAIKSALDNKADEALATPGIKEALIDPRIQKIIDSMRSDPKTAQRLMQEA-DREVHQKLRLLVESGVLGI 840
            S F GM++GFL  G               +     ++P+++++P+    SL  E++Q +  +            WL++DLL +V  D  L   L++P+ +  L+ FQ NP+ AME+YKDD   Q+ L KF  LLG HF +                I+  +       +   D +  E L+ PG++EAL +P +Q+ +  +R DP  AQ L++++ D E  +++RLL+E+G++G+
Sbjct:   75 SGFGGMRRGFLTAGPAKPAAASQKQQQQKQQPQAEDMPHIRSDPAAAARSLQLEDVQASLAEAASASAAAAPSGWLTEDLLARVESDETLLRGLANPRLSAALAKFQTNPRGAMEEYKDDTEVQEFLAKFSALLGEHFTQ----------------IADKQEQEQQQQQPPEDPEVAEVLSRPGVREALTNPDVQRWLSLLREDPDKAQGLLRQSRDGEFQRRIRLLMENGLIGV 293          
BLAST of SMED30015387 vs. TrEMBL
Match: A0A1S3JC95 (uncharacterized protein LOC106172003 OS=Lingula unguis OX=7574 GN=LOC106172003 PE=4 SV=1)

HSP 1 Score: 89.7373 bits (221), Expect = 1.074e-16
Identity = 72/214 (33.64%), Postives = 113/214 (52.80%), Query Frame = 1
Query:  265 TKNNVPYLKANPSK--------VNSSL-VFEELQENHKQKNWLSDDLLNKVTEDNELTTWLSDPKTNIILSDFQVNPQAAMEKYKDDINTQKMXXXXXXXXXXXXRELES-----------AACAPSKNPKEVIISAYEPNVAPAIKSALDNKADEALATPGIKEALIDPRIQKIIDSMRSDPKTAQRLMQEADREVHQKLRLLVESGVLGIQQ 846
            T +++PYLK   +K        V +++   E L +N   K+W++DDLL KV  +  L   LSDP     L++FQ NPQAAM KYKD+   Q+   +F  LLG HF  +             +   PS+     + S+  PN   A   A + K  E L+ P I+  L+DP IQ++ +++R DP+  QR++  A     +K++ LV++G+L  Q+
Sbjct:  118 TNDSIPYLKPKETKEKEYEIPEVQTAMKSAESLLQN---KDWITDDLLGKVENNEVLFKRLSDPSFTKALTEFQTNPQAAMLKYKDNQEVQQFFKEFCGLLGDHFSNMPDGQPQKPKTDTISTTMPSQGADISVRSSTNPNQPTA---ADEKKMQEILSDPEIRFVLLDPFIQQLFETLRKDPEKGQRMLSTAQPAQQEKIQKLVDAGLLAFQR 325          
BLAST of SMED30015387 vs. TrEMBL
Match: A0A1I8IZG1 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 90.8929 bits (224), Expect = 2.304e-16
Identity = 62/200 (31.00%), Postives = 110/200 (55.00%), Query Frame = 1
Query:  274 NVPYLKANPSKVNSSLVFEELQENHKQK----------NWLSDDLLNKVTEDNELTTWLSDPKTNIILSDFQVNPQAAMEKYKDDINTQKMXXXXXXXXXXXXRELESAACAPSKNPKEVIISAYEPNVAPAIKSALDNKADEALATPGIKEALIDPRIQKIIDSMRSDPKTAQRLMQEA-DREVHQKLRLLVESGVLGI 840
            ++P+++++P+    SL  E++Q +  +            WL++DLL +V  D  L   L++P+ +  L+ FQ NP+ AME+YKDD   Q+ L KF  LLG HF +                I+  +       +   D +  E L+ PG++EAL +P +Q+ +  +R DP  AQ L++++ D E  +++RLL+E+G++G+
Sbjct:  758 DMPHIRSDPAAAARSLQLEDVQASLAEAASASAAAAPSGWLTEDLLARVESDETLLRGLANPRLSAALAKFQTNPRGAMEEYKDDTEVQEFLAKFSALLGEHFTQ----------------IADKQEQEQQQQQPPEDPEVAEVLSRPGVREALTNPDVQRWLSLLREDPDKAQGLLRQSRDGEFQRRIRLLMENGLIGV 941          
BLAST of SMED30015387 vs. TrEMBL
Match: A0A2G8L9Q2 (STI1 domain-containing protein OS=Stichopus japonicus OX=307972 GN=BSL78_06080 PE=4 SV=1)

HSP 1 Score: 88.1965 bits (217), Expect = 4.362e-16
Identity = 76/239 (31.80%), Postives = 125/239 (52.30%), Query Frame = 1
Query:  208 FAGMKKGFLANGFGDDKPKTK---NNVPYLKANPSKVNSSLVFEELQENHKQ-------KNWLSDDLLNKVTEDNELTTWLSDPKTNIILSDFQVNPQAAMEKYKDDINTQKMXXXXXXXXXXXXRELESAACAP---------SKNPKEVIISAYEPNVAPAIKSALDNKA----DEA-----LATPGIKEALIDPRIQKIIDSMRSDPKTAQRLMQEADREVHQKLRLLVESGVLGI 840
            F G+KKGFL  GFGDDKPK K   NN+P +K    K   S   +E+Q+  ++       K+WLS DLL+KV +   L   +++P    +LS F+ +P+ A E+  ++   Q +   F  +LG HF  L     AP         S+ P   I +  E  +   ++S+ D K     DEA     L+ P +   L D +I+++++++R +P  AQ +++ A  ++ +K++ LVE G+L  
Sbjct:   83 FMGLKKGFLLGGFGDDKPKAKRKENNIPTIKPKLDKKEDSFKIKEVQDALQRASPLLQNKDWLSSDLLDKVEKHPYLAEVMANPDFTSVLSKFEKDPKGAAEQLHNNPQLQHIFRDFCAILGDHFTSLPGTPDAPQSTDHLGTSSQTPSPGIKTMDETGLDMKVRSSTDPKQPTADDEARMKQILSDPEVCNVLADEKIKQLMEALRCNPNEAQEIIRSATPDLKKKVKKLVEVGLLSF 321          
BLAST of SMED30015387 vs. Ensembl Nematostella
Match: EDO38750 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SC00])

HSP 1 Score: 53.9138 bits (128), Expect = 3.406e-8
Identity = 30/66 (45.45%), Postives = 43/66 (65.15%), Query Frame = 1
Query:  646 SALDNK-ADEALATPGIKEALIDPRIQKIIDSMRSDPKTAQRLMQEADREVHQKLRLLVESGVLGI 840
            SA D K   E L+ P +K  L D +IQ II  +RS+P+ A R +Q+A  EV  KLR+L+++G+L I
Sbjct:  283 SAADEKQMKEILSRPDVKLTLQDQQIQGIIGLLRSNPEAAHRQLQKASPEVQSKLRVLIDAGLLAI 348          
BLAST of SMED30015387 vs. Planmine SMEST
Match: SMESG000030085.1 (SMESG000030085.1)

HSP 1 Score: 428.713 bits (1101), Expect = 1.159e-152
Identity = 224/225 (99.56%), Postives = 225/225 (100.00%), Query Frame = 1
Query:  172 KTNNEKIVPKSEFAGMKKGFLANGFGDDKPKTKNNVPYLKANPSKVNSSLVFEELQENHKQKNWLSDDLLNKVTEDNELTTWLSDPKTNIILSDFQVNPQAAMEKYKDDINTQKMXXXXXXXXXXXXRELESAACAPSKNPKEVIISAYEPNVAPAIKSALDNKADEALATPGIKEALIDPRIQKIIDSMRSDPKTAQRLMQEADREVHQKLRLLVESGVLGIQQ 846
            KTNNEKIVPKSEFAGMKKGFLANGFGDDKPKTKNNVPYLKANPSKVNSSLVFEELQENHKQKNWLSDDLLNKVTEDNELTTWLSDPKTNIILSDFQVNPQAAMEKYKDDINTQKMLLKFGHLLGGHFRELESAACAPSKNPKEVIISAYEPNVAPAIKSALDNKADEALATPG+KEALIDPRIQKIIDSMRSDPKTAQRLMQEADREVHQKLRLLVESGVLGIQQ
Sbjct:   33 KTNNEKIVPKSEFAGMKKGFLANGFGDDKPKTKNNVPYLKANPSKVNSSLVFEELQENHKQKNWLSDDLLNKVTEDNELTTWLSDPKTNIILSDFQVNPQAAMEKYKDDINTQKMLLKFGHLLGGHFRELESAACAPSKNPKEVIISAYEPNVAPAIKSALDNKADEALATPGVKEALIDPRIQKIIDSMRSDPKTAQRLMQEADREVHQKLRLLVESGVLGIQQ 257          

HSP 2 Score: 69.3218 bits (168), Expect = 2.262e-13
Identity = 32/32 (100.00%), Postives = 32/32 (100.00%), Query Frame = 3
Query:   24 MYSDIPELEDFSDIINVSKEKQQTFKANNLHT 119
            MYSDIPELEDFSDIINVSKEKQQTFKANNLHT
Sbjct:    1 MYSDIPELEDFSDIINVSKEKQQTFKANNLHT 32          
The following BLAST results are available for this feature:
BLAST of SMED30015387 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 SMED30015387 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 SMED30015387 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 SMED30015387 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 SMED30015387 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 SMED30015387 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 SMED30015387 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 SMED30015387 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
V3ZN599.078e-2432.02Uncharacterized protein OS=Lottia gigantea OX=2251... [more]
A0A267GCP85.746e-2029.79Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A1S3JC951.074e-1633.64uncharacterized protein LOC106172003 OS=Lingula un... [more]
A0A1I8IZG12.304e-1631.00Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A2G8L9Q24.362e-1631.80STI1 domain-containing protein OS=Stichopus japoni... [more]
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BLAST of SMED30015387 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 SMED30015387 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 SMED30015387 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 SMED30015387 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO387503.406e-845.45Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30015387 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 SMED30015387 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000030085.11.159e-15299.56SMESG000030085.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015387 ID=SMED30015387|Name=SMED30015387|organism=Schmidtea mediterranea sexual|type=transcript|length=978bp
CTGCAGAGTGTTCATTTATTATCATGTATTCAGATATCCCGGAATTAGAA
GATTTTTCAGACATAATAAATGTTTCTAAAGAAAAACAACAAACATTTAA
AGCAAATAACTTACATACAGTTGATTTTGCAAATATTTCTTTAAATATTT
TATCGCATAATAACAATGTAGAAAACTAATAATGAAAAAATTGTCCCGAA
ATCCGAATTTGCTGGAATGAAAAAAGGATTTCTAGCAAATGGCTTTGGTG
ATGATAAACCGAAAACTAAAAATAATGTCCCATATTTGAAAGCAAATCCT
TCAAAAGTAAATTCAAGTTTGGTTTTTGAGGAACTACAAGAAAATCACAA
ACAAAAGAATTGGCTGTCGGATGATTTACTGAACAAAGTTACCGAAGACA
ACGAACTAACCACATGGTTAAGTGACCCGAAAACCAACATCATATTATCC
GATTTTCAAGTAAATCCGCAGGCTGCTATGGAAAAATACAAAGATGACAT
AAACACTCAGAAAATGCTTTTGAAATTTGGCCATTTACTCGGCGGGCATT
TTCGTGAATTAGAGTCGGCGGCATGTGCGCCGAGCAAGAATCCGAAAGAA
GTGATAATATCAGCGTATGAACCGAATGTTGCTCCAGCCATTAAATCAGC
ATTGGATAATAAAGCAGATGAAGCATTGGCTACTCCTGGAATTAAAGAAG
CTTTAATAGATCCGAGAATTCAGAAAATTATTGATTCAATGAGATCAGAT
CCTAAAACTGCCCAAAGATTAATGCAAGAAGCTGATAGAGAAGTTCATCA
AAAGTTGAGATTATTGGTCGAATCGGGCGTGCTTGGAATTCAGCAATAAT
TGAATGCAAATAAATGCCGACTGCATTTTTAGAACTCTTCAAGACATTCC
CAGATCCGGCTCTCAAATAAATGGTTTCAAATAGTTTTCCTATTTCATGT
TTTTAATTATAAAATACAAATTTTCACA
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protein sequence of SMED30015387-orf-1

>SMED30015387-orf-1 ID=SMED30015387-orf-1|Name=SMED30015387-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=211bp
MKKGFLANGFGDDKPKTKNNVPYLKANPSKVNSSLVFEELQENHKQKNWL
SDDLLNKVTEDNELTTWLSDPKTNIILSDFQVNPQAAMEKYKDDINTQKM
LLKFGHLLGGHFRELESAACAPSKNPKEVIISAYEPNVAPAIKSALDNKA
DEALATPGIKEALIDPRIQKIIDSMRSDPKTAQRLMQEADREVHQKLRLL
VESGVLGIQQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR041243STI1
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:1.10.260.100coord: 143..208
e-value: 1.1E-12
score: 49.7
NoneNo IPR availableGENE3DG3DSA:1.10.260.100coord: 52..111
e-value: 3.9E-8
score: 35.0
IPR041243STI1 domainPFAMPF17830STI1coord: 53..100
e-value: 3.7E-6
score: 26.8
coord: 155..200
e-value: 6.7E-6
score: 26.0