SMED30004807

Overview
NameSMED30004807
Smed IDSMED30004807
Length (bp)802
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 SMED30004807 (SMED30004807) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30004807 (SMED30004807) 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.
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



SMED30004807

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
head regionSMED30004807SMESG000011132.1 SMESG000011100.1 SmedASXL_063628SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30004807SMESG000011132.1 SMESG000011121.1 dd_Smed_v4_44724_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30004807SMESG000011132.1 SMESG000011121.1 dd_Smed_v4_44724_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30004807SMESG000011132.1 SMESG000011121.1 dd_Smed_v4_44724_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
SMED30004807 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006317:2839..3632 -3931
v31.013736:11656..12449 +3850
v31.065798:365..1158 -3769
v31.008237:18201..18991 -3164
v31.016461:7568..8349 +2848
Homology
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BLAST of SMED30004807 vs. Planmine SMEST
Match: SMESG000011121.1 (SMESG000011121.1)

HSP 1 Score: 488.419 bits (1256), Expect = 2.694e-177
Identity = 246/258 (95.35%), Postives = 251/258 (97.29%), Query Frame = 3 
Query:    3 MLLIFYXXXXXXXQVKNVLGNVVLSCGVSTCSTRRYFALVDNQCYVPQAASSFAGVNEVQRIYKKVQKSFILYRVISGTGQHPRYYFSNNTYTIQTGVETNNTDLINFRSVLLDEWNNLKPKMINLTLIDYDGTAVARLTFNVKVSDDIITWFQPLNLIYSFPWDVDYLRSLSYVFFMPFAITVNYGDCDTSLRIIGHAIIPDQCLNYWPNGTAYLPHQLIYVLNSARTAAEWSIYARPYQVLELYGQYDDNVDIYYS 776
            MLLIF+IIIII+SQVKNVLG VVLSCG STCSTRRYFALVDNQCYVPQAASSFAGVNEVQRIYKKVQKSFILYRVISGTGQHPRYYFSNNTYTIQT VET NTDLINFRSVLLDEWNNLKPKMINLTLIDYDGTAVARLTFNVKVSDDIITWFQPLNLIYSFPWDVDYLRSLSYVFF PF+ITVN+  C+TSLRIIGHAIIPDQCLNYWPNGTAYLPHQLIYVLNSARTAAEWSIYARPYQVLELYGQYDDNVDIYYS
Sbjct:    1 MLLIFFIIIIINSQVKNVLGKVVLSCGASTCSTRRYFALVDNQCYVPQAASSFAGVNEVQRIYKKVQKSFILYRVISGTGQHPRYYFSNNTYTIQTAVETKNTDLINFRSVLLDEWNNLKPKMINLTLIDYDGTAVARLTFNVKVSDDIITWFQPLNLIYSFPWDVDYLRSLSYVFFTPFSITVNHISCNTSLRIIGHAIIPDQCLNYWPNGTAYLPHQLIYVLNSARTAAEWSIYARPYQVLELYGQYDDNVDIYYS 258
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BLAST of SMED30004807 vs. Planmine SMEST
Match: SMESG000011132.1 (SMESG000011132.1)

HSP 1 Score: 483.026 bits (1242), Expect = 3.333e-173
Identity = 232/237 (97.89%), Postives = 234/237 (98.73%), Query Frame = 3 
Query:   66 VVLSCGVSTCSTRRYFALVDNQCYVPQAASSFAGVNEVQRIYKKVQKSFILYRVISGTGQHPRYYFSNNTYTIQTGVETNNTDLINFRSVLLDEWNNLKPKMINLTLIDYDGTAVARLTFNVKVSDDIITWFQPLNLIYSFPWDVDYLRSLSYVFFMPFAITVNYGDCDTSLRIIGHAIIPDQCLNYWPNGTAYLPHQLIYVLNSARTAAEWSIYARPYQVLELYGQYDDNVDIYYS 776
            VVLSCGVSTCSTRRYFALVDNQCYVPQAASSFAGVNEVQRIYKKVQKSFILYRVISGTGQHPRYYFSNNTYTIQT VET NTDLINFRSVLLDEWNNLKPKMINLTLIDYDGTAVARLTFNVKVSDDIITWFQPLNLIYSFPWDVDYLRSLSYVFFMPFAITVNYG+C+TSLRIIGHAIIPDQCLNYWPNGTAYLPHQL YVLNSARTAAEWSIYARPYQVLELYGQYDDNVDIYYS
Sbjct:  145 VVLSCGVSTCSTRRYFALVDNQCYVPQAASSFAGVNEVQRIYKKVQKSFILYRVISGTGQHPRYYFSNNTYTIQTAVETKNTDLINFRSVLLDEWNNLKPKMINLTLIDYDGTAVARLTFNVKVSDDIITWFQPLNLIYSFPWDVDYLRSLSYVFFMPFAITVNYGNCNTSLRIIGHAIIPDQCLNYWPNGTAYLPHQLFYVLNSARTAAEWSIYARPYQVLELYGQYDDNVDIYYS 381
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BLAST of SMED30004807 vs. Planmine SMEST
Match: SMESG000011122.1 (SMESG000011122.1)

HSP 1 Score: 414.846 bits (1065), Expect = 1.217e-148
Identity = 201/225 (89.33%), Postives = 211/225 (93.78%), Query Frame = 3 
Query:  102 RRYFALVDNQCYVPQAASSFAGVNEVQRIYKKVQKSFILYRVISGTGQHPRYYFSNNTYTIQTGVETNNTDLINFRSVLLDEWNNLKPKMINLTLIDYDGTAVARLTFNVKVSDDIITWFQPLNLIYSFPWDVDYLRSLSYVFFMPFAITVNYGDCDTSLRIIGHAIIPDQCLNYWPNGTAYLPHQLIYVLNSARTAAEWSIYARPYQVLELYGQYDDNVDIYYS 776
            RRYFALVDNQCYVPQAASSF GV E +RIY K+QKS IL+RVISGTGQ+P  YF    + IQT VE NNT+LINFRSVLLDEWNNLKPKMINLTLIDYDGTAVARLTFNVKVSDDIITWFQPLNLIYSFPWDVDYLRSLSYVFFMPFAITVNYG+C+TSLRIIGHAIIPDQCLNYWPNGTAYLPHQLIYVLNSARTAA+WSI+ARPYQVLELYGQYDDNVDIYYS
Sbjct:    2 RRYFALVDNQCYVPQAASSFEGVKEPKRIYNKMQKSTILFRVISGTGQNPIDYFLTADFAIQTIVEMNNTNLINFRSVLLDEWNNLKPKMINLTLIDYDGTAVARLTFNVKVSDDIITWFQPLNLIYSFPWDVDYLRSLSYVFFMPFAITVNYGNCNTSLRIIGHAIIPDQCLNYWPNGTAYLPHQLIYVLNSARTAAKWSIFARPYQVLELYGQYDDNVDIYYS 226
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BLAST of SMED30004807 vs. Planmine SMEST
Match: SMESG000011100.1 (SMESG000011100.1)

HSP 1 Score: 401.749 bits (1031), Expect = 7.187e-143
Identity = 204/258 (79.07%), Postives = 221/258 (85.66%), Query Frame = 3 
Query:    3 MLLIFYXXXXXXXQVKNVLGNVVLSCGVSTCSTRRYFALVDNQCYVPQAASSFAGVNEVQRIYKKVQKSFILYRVISGTGQHPRYYFSNNTYTIQTGVETNNTDLINFRSVLLDEWNNLKPKMINLTLIDYDGTAVARLTFNVKVSDDIITWFQPLNLIYSFPWDVDYLRSLSYVFFMPFAITVNYGDCDTSLRIIGHAIIPDQCLNYWPNGTAYLPHQLIYVLNSARTAAEWSIYARPYQVLELYGQYDDNVDIYYS 776
            MLL+FYIIII+ S   NVLG   + CGVSTC+TR YFALV+NQCYVPQAASS +G  E +RIYKK+QKS ILYRVISGTG++P  YF     TIQT  + +  +LINFRSVLLDEWNNLKPKMINLTLIDYDGTAVARLTFNVKVSDDIITWFQPLNLIYSFPWDVDYLRSLSYV F  F I VNY +CDTS RIIG    PDQCLNYWPNGTAYLP+QL+YVLNSARTAAEWSIYARPYQVLELYGQYDDN+DIYYS
Sbjct:    1 MLLVFYIIIILISLKGNVLGKGAVHCGVSTCNTRTYFALVNNQCYVPQAASSISGTKEPRRIYKKMQKSIILYRVISGTGKNPYNYFFTADSTIQTIFKMDYMNLINFRSVLLDEWNNLKPKMINLTLIDYDGTAVARLTFNVKVSDDIITWFQPLNLIYSFPWDVDYLRSLSYVLFTNFQIAVNYSNCDTSYRIIGWVNSPDQCLNYWPNGTAYLPYQLVYVLNSARTAAEWSIYARPYQVLELYGQYDDNIDIYYS 258
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BLAST of SMED30004807 vs. Planmine SMEST
Match: SMESG000065749.1 (SMESG000065749.1)

HSP 1 Score: 170.244 bits (430), Expect = 9.114e-52
Identity = 89/237 (37.55%), Postives = 135/237 (56.96%), Query Frame = 3 
Query:   63 NVVLSCGVSTCSTRRYFALVDNQCYVPQAASSFAGVNEVQRIYKKVQKSFILYRVISGTGQHPRYYFSNNTYTIQTGVETNNTDLINFRSVLLDEWNNLKPKMINLTLIDYDGTAVARLTFNVKVSDDIITWFQPLNLIYSFPWDVDYLRSLSYVFF--------MPFAITVNYGDCDTSLRIIGHAIIPDQCLNYWPNGTAYLPHQLIYVLNSARTAAEWSIYARPYQVLELYGQY 749
            N+ + CG+   + + YFA+++N CY PQ  SS      +QR Y K+  SF+++R++SG+G  P  Y+S    +I T  +  N  L+NFRS++LDEWNN+KP  + L   DY+      L FNV  +D I +WF   N  YSFPWD+++L++++Y +F        M F I      C     I G A  P+   + WPNGT++   Q++YVLN+ RT   W  + R  + LE+ G+Y
Sbjct:   20 NIAIECGLIALNGQMYFAVINNVCYFPQTPSSIINSKLLQRSYIKLNNSFVIFRLVSGSGVDPYGYWSTTNVSIHTVADDQN-KLMNFRSIILDEWNNIKPSRLTLVAFDYNDQVAVILGFNVFQTDSITSWFTKSNFNYSFPWDINFLQTINYTYFSLIGASFGMCFYINQINDVCIVDSGIFGIA-KPNMPCSMWPNGTSFTYPQIMYVLNNERTPDLWKNFERKLKYLEISGEY 254
The following BLAST results are available for this feature:
BLAST of SMED30004807 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 SMED30004807 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 SMED30004807 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 SMED30004807 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 SMED30004807 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 SMED30004807 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 SMED30004807 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 SMED30004807 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 SMED30004807 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 SMED30004807 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 SMED30004807 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 SMED30004807 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 SMED30004807 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 SMED30004807 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000011121.12.694e-17795.35SMESG000011121.1[more]
SMESG000011132.13.333e-17397.89SMESG000011132.1[more]
SMESG000011122.11.217e-14889.33SMESG000011122.1[more]
SMESG000011100.17.187e-14379.07SMESG000011100.1[more]
SMESG000065749.19.114e-5237.55SMESG000065749.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004807 ID=SMED30004807|Name=SMED30004807|organism=Schmidtea mediterranea sexual|type=transcript|length=802bp
CAATGTTATTGATATTTTATATAATTATCATTATTAGTTCTCAAGTAAAA
AATGTTCTAGGAAACGTTGTGCTGTCTTGCGGTGTGTCCACATGCAGCAC
GAGAAGATATTTTGCACTTGTGGACAACCAATGCTATGTGCCACAGGCGG
CATCATCATTTGCAGGTGTCAACGAGGTGCAAAGAATATATAAAAAAGTA
CAAAAATCATTTATTCTTTATCGAGTTATTTCTGGAACCGGACAGCACCC
GAGATATTATTTTTCAAATAATACTTATACAATTCAAACTGGTGTTGAAA
CGAACAACACGGATTTGATAAACTTTCGAAGTGTTCTCCTGGATGAATGG
AACAATTTGAAGCCGAAAATGATTAATCTAACTCTGATAGATTATGATGG
GACCGCGGTCGCCAGGCTCACATTCAATGTGAAAGTGTCTGATGACATTA
TAACATGGTTTCAACCGCTCAATCTGATCTATTCTTTTCCCTGGGACGTG
GACTACTTGAGAAGTCTTAGTTATGTGTTTTTTATGCCTTTTGCAATTAC
AGTTAATTATGGCGATTGTGATACTAGTCTTCGTATAATCGGGCATGCCA
TTATTCCTGACCAATGTCTGAACTATTGGCCAAATGGAACGGCTTACCTC
CCCCATCAATTAATCTATGTTCTGAATAGTGCAAGAACGGCTGCAGAGTG
GAGCATTTATGCGAGACCTTATCAAGTTTTGGAATTGTATGGACAATACG
ATGACAATGTTGATATTTATTATTCATAATCACAAACTAAGAGATCGGAA
GA
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protein sequence of SMED30004807-orf-1

>SMED30004807-orf-1 ID=SMED30004807-orf-1|Name=SMED30004807-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=259bp
MLLIFYIIIIISSQVKNVLGNVVLSCGVSTCSTRRYFALVDNQCYVPQAA
SSFAGVNEVQRIYKKVQKSFILYRVISGTGQHPRYYFSNNTYTIQTGVET
NNTDLINFRSVLLDEWNNLKPKMINLTLIDYDGTAVARLTFNVKVSDDII
TWFQPLNLIYSFPWDVDYLRSLSYVFFMPFAITVNYGDCDTSLRIIGHAI
IPDQCLNYWPNGTAYLPHQLIYVLNSARTAAEWSIYARPYQVLELYGQYD
DNVDIYYS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..20
score: 0.709