SMED30021914

Overview
NameSMED30021914
Smed IDSMED30021914
Length (bp)1354
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 SMED30021914 (SMED30021914) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021914 (SMED30021914) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

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 SMED30021914 (SMED30021914) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021914 (SMED30021914) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30021914

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
ovarySMED30021914h1SMcG0014720 Contig4034GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
oocyteSMED30021914h1SMcG0022552 Contig18488uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30021914h1SMcG0022552 Contig18488newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30021914h1SMcG0022552 Contig18488uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30021914h1SMcG0022552 Contig18488newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
ovarySMED30021914h1SMcG0022552 Contig4034GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
ovarySMED30021914h1SMcG0022552 PL06005B1C05smed_ncbi_20240424PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30021914 vs. Ensembl Human
Match: CD164 (CD164 molecule [Source:HGNC Symbol;Acc:HGNC:1632])

HSP 1 Score: 48.9062 bits (115), Expect = 3.640e-6
Identity = 22/40 (55.00%), Postives = 28/40 (70.00%), Query Frame = 2 
Query:  293 RPRGFDGSSFVGGIVLCAGIFAIAFFTYKFCFSKKDQEYH 412
            R   FD +SF+GGIVL  G+ A+ FF YKFC S K++ YH
Sbjct:  138 RKSTFDAASFIGGIVLVLGVQAVIFFLYKFCKS-KERNYH 176
[Close]
BLAST of SMED30021914 vs. Ensembl Human
Match: CD164 (CD164 molecule [Source:HGNC Symbol;Acc:HGNC:1632])

HSP 1 Score: 48.9062 bits (115), Expect = 4.561e-6
Identity = 22/40 (55.00%), Postives = 28/40 (70.00%), Query Frame = 2 
Query:  293 RPRGFDGSSFVGGIVLCAGIFAIAFFTYKFCFSKKDQEYH 412
            R   FD +SF+GGIVL  G+ A+ FF YKFC S K++ YH
Sbjct:  157 RKSTFDAASFIGGIVLVLGVQAVIFFLYKFCKS-KERNYH 195
[Close]
BLAST of SMED30021914 vs. Ensembl Human
Match: CD164 (CD164 molecule [Source:HGNC Symbol;Acc:HGNC:1632])

HSP 1 Score: 48.521 bits (114), Expect = 5.108e-6
Identity = 22/40 (55.00%), Postives = 28/40 (70.00%), Query Frame = 2 
Query:  293 RPRGFDGSSFVGGIVLCAGIFAIAFFTYKFCFSKKDQEYH 412
            R   FD +SF+GGIVL  G+ A+ FF YKFC S K++ YH
Sbjct:  144 RKSTFDAASFIGGIVLVLGVQAVIFFLYKFCKS-KERNYH 182
[Close]
BLAST of SMED30021914 vs. Ensembl Human
Match: CD164 (CD164 molecule [Source:HGNC Symbol;Acc:HGNC:1632])

HSP 1 Score: 47.3654 bits (111), Expect = 8.973e-6
Identity = 22/40 (55.00%), Postives = 28/40 (70.00%), Query Frame = 2 
Query:  293 RPRGFDGSSFVGGIVLCAGIFAIAFFTYKFCFSKKDQEYH 412
            R   FD +SF+GGIVL  G+ A+ FF YKFC S K++ YH
Sbjct:  123 RKSTFDAASFIGGIVLVLGVQAVIFFLYKFCKS-KERNYH 161
[Close]
BLAST of SMED30021914 vs. Ensembl Zebrafish
Match: cd164 (CD164 molecule, sialomucin [Source:ZFIN;Acc:ZDB-GENE-030131-1598])

HSP 1 Score: 47.3654 bits (111), Expect = 5.367e-6
Identity = 22/36 (61.11%), Postives = 27/36 (75.00%), Query Frame = 2 
Query:  305 FDGSSFVGGIVLCAGIFAIAFFTYKFCFSKKDQEYH 412
            FD +SF+GGIVL  G+ A+ FF YKFC S KD+ YH
Sbjct:  131 FDAASFIGGIVLVLGLQAVIFFLYKFCKS-KDRNYH 165
[Close]
BLAST of SMED30021914 vs. Ensembl Xenopus
Match: CD164 (CD164 molecule [Source:NCBI gene;Acc:100496645])

HSP 1 Score: 48.521 bits (114), Expect = 3.593e-6
Identity = 22/36 (61.11%), Postives = 27/36 (75.00%), Query Frame = 2 
Query:  305 FDGSSFVGGIVLCAGIFAIAFFTYKFCFSKKDQEYH 412
            FD +SF+GGIVL  GI A+ FF YKFC + KD+ YH
Sbjct:  142 FDAASFIGGIVLVLGIQAVIFFLYKFCKA-KDRNYH 176
[Close]
BLAST of SMED30021914 vs. Ensembl Mouse
Match: Cd164 (CD164 antigen [Source:MGI Symbol;Acc:MGI:1859568])

HSP 1 Score: 48.521 bits (114), Expect = 3.570e-6
Identity = 22/40 (55.00%), Postives = 28/40 (70.00%), Query Frame = 2 
Query:  293 RPRGFDGSSFVGGIVLCAGIFAIAFFTYKFCFSKKDQEYH 412
            R   FD +SF+GGIVL  G+ A+ FF YKFC S K++ YH
Sbjct:  157 RKSTFDAASFIGGIVLVLGVQAVIFFLYKFCKS-KERNYH 195
[Close]
BLAST of SMED30021914 vs. Ensembl Mouse
Match: Cd164 (CD164 antigen [Source:MGI Symbol;Acc:MGI:1859568])

HSP 1 Score: 46.9802 bits (110), Expect = 7.334e-6
Identity = 22/40 (55.00%), Postives = 28/40 (70.00%), Query Frame = 2 
Query:  293 RPRGFDGSSFVGGIVLCAGIFAIAFFTYKFCFSKKDQEYH 412
            R   FD +SF+GGIVL  G+ A+ FF YKFC S K++ YH
Sbjct:  122 RKSTFDAASFIGGIVLVLGVQAVIFFLYKFCKS-KERNYH 160
[Close]
BLAST of SMED30021914 vs. Ensembl Cavefish
Match: cd164 (CD164 molecule [Source:NCBI gene;Acc:103046498])

HSP 1 Score: 47.3654 bits (111), Expect = 4.155e-6
Identity = 22/36 (61.11%), Postives = 27/36 (75.00%), Query Frame = 2 
Query:  305 FDGSSFVGGIVLCAGIFAIAFFTYKFCFSKKDQEYH 412
            FD +SF+GGIVL  G+ A+ FF YKFC S KD+ YH
Sbjct:  127 FDAASFIGGIVLVLGLQAVIFFLYKFCKS-KDRNYH 161
[Close]
BLAST of SMED30021914 vs. Ensembl Medaka
Match: ENSORLT00000038037.1 (CD164 molecule [Source:NCBI gene;Acc:111947061])

HSP 1 Score: 46.9802 bits (110), Expect = 6.722e-6
Identity = 22/36 (61.11%), Postives = 27/36 (75.00%), Query Frame = 2 
Query:  305 FDGSSFVGGIVLCAGIFAIAFFTYKFCFSKKDQEYH 412
            FD +SF+GGIVL  G+ A+ FF YKFC S KD+ YH
Sbjct:  140 FDAASFIGGIVLVLGLQAVIFFLYKFCKS-KDRNYH 174
[Close]
BLAST of SMED30021914 vs. Planmine SMEST
Match: SMESG000012307.1 (SMESG000012307.1)

HSP 1 Score: 162.54 bits (410), Expect = 8.070e-48
Identity = 93/93 (100.00%), Postives = 93/93 (100.00%), Query Frame = 2 
Query:  140 PIFTPGTTPALNISASSTNNVISTTGTTILNVDXXXXXXXXXXXXXIVSTYRPRGFDGSSFVGGIVLCAGIFAIAFFTYKFCFSKKDQEYHEV 418
            PIFTPGTTPALNISASSTNNVISTTGTTILNVDTTTTAKATTQSSTIVSTYRPRGFDGSSFVGGIVLCAGIFAIAFFTYKFCFSKKDQEYHEV
Sbjct:   86 PIFTPGTTPALNISASSTNNVISTTGTTILNVDTTTTAKATTQSSTIVSTYRPRGFDGSSFVGGIVLCAGIFAIAFFTYKFCFSKKDQEYHEV 178
The following BLAST results are available for this feature:
BLAST of SMED30021914 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 4
Match NameE-valueIdentityDescription
CD1643.640e-655.00CD164 molecule [Source:HGNC Symbol;Acc:HGNC:1632][more]
CD1644.561e-655.00CD164 molecule [Source:HGNC Symbol;Acc:HGNC:1632][more]
CD1645.108e-655.00CD164 molecule [Source:HGNC Symbol;Acc:HGNC:1632][more]
CD1648.973e-655.00CD164 molecule [Source:HGNC Symbol;Acc:HGNC:1632][more]
back to top
BLAST of SMED30021914 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021914 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021914 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
cd1645.367e-661.11CD164 molecule, sialomucin [Source:ZFIN;Acc:ZDB-GE... [more]
back to top
BLAST of SMED30021914 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
CD1643.593e-661.11CD164 molecule [Source:NCBI gene;Acc:100496645][more]
back to top
BLAST of SMED30021914 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 2
Match NameE-valueIdentityDescription
Cd1643.570e-655.00CD164 antigen [Source:MGI Symbol;Acc:MGI:1859568][more]
Cd1647.334e-655.00CD164 antigen [Source:MGI Symbol;Acc:MGI:1859568][more]
back to top
BLAST of SMED30021914 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021914 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021914 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
cd1644.155e-661.11CD164 molecule [Source:NCBI gene;Acc:103046498][more]
back to top
BLAST of SMED30021914 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021914 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021914 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021914 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ENSORLT00000038037.16.722e-661.11CD164 molecule [Source:NCBI gene;Acc:111947061][more]
back to top
BLAST of SMED30021914 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000012307.18.070e-48100.00SMESG000012307.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021914 ID=SMED30021914|Name=SMED30021914|organism=Schmidtea mediterranea sexual|type=transcript|length=1354bp
CGAAATGCTGTTAATAAGTTTAACCTTTACAATTTGTTTTCTTTTATTGA
ATTATTCTACATCAGCTTATGAGTCGTCAGCCAACTTTAGCAGCTTTTCA
AATTCAACGTTAAGCAATGATACATCAAATAGTAGCACGCCAATATTTAC
ACCAGGCACAACTCCTGCCTTGAACATTTCGGCCAGTTCAACTAATAATG
TGATATCTACTACCGGTACTACTATCCTTAACGTCGATACTACTACAACT
GCAAAAGCTACCACTCAATCATCGACCATCGTTTCAACATATCGACCAAG
AGGATTCGATGGTAGCTCTTTCGTAGGTGGGATAGTTTTGTGCGCAGGAA
TATTCGCAATCGCATTCTTTACTTATAAATTCTGCTTCAGTAAAAAAGAT
CAAGAATACCATGAAGTGTGACATCCCATTGAAACTAATTGACATAATTG
GTGTTGGATTTAATTGTTATGATGAGATTTTGTTAATAATTTCTGTGTAA
TCCTTGAAATTATCGGCTTACAAATACGCAAGCCGATGAAATATTTATTG
TTTTCTCTCTCTCTCTCTCTCTCTCTTGTCTATCCAATCACGATTTCACC
GAACGCTACTCAATGCGTGCCGCGGTTTTTCTCTTCTGTAGTTCAATGTG
CAATTTATTTCTCTTTGATTTTTATGCCGCTATTATTTATTTTGACAGTG
AATAATAATTCTGTCACACCGATATATGTTCGGATTTTTTATTTGTCATT
TCTACAGCTGGAACTTTGGATACCTGTGCCATTCGCTGCCAGATATCCAT
CCAATCATGTGCAACTTGTCCATGGGTTTCATGGAATTGTGAAATCGATT
TATAAATGCCAATACATTTGTGTTTTTGGTTCGATTTGCAATGTCTAATA
TGATGGATCTCTCTCCCTTCCTTCCTCACTCCCTCCCTCCTTTTCTTTCT
CCATCGATTTCTTCCCACTCCTTCTCATTTCCTCTCCATACCACTCACTC
CATATCATTCTTCATTTTTCTCTCCATATCTCCCTTTTCTTTTTTTTCCT
CTCCATCTCTCTCCGTAGCTTTAAACTTAATAAATTTAATACTGAATTTA
CTACATTTATGACAGAAGTTCCTCCTGTTAACTCTCGTTAATTAAGTTGC
GATCAACGATATTCAACAAAAGCAGCGAAGGTTTGAAACACAAGACATAA
AATTGTCATCTAGATTAGTTTCCCTGGGACTTGTGGAACATAATTATGAA
TATTATATACTACTTATTAGCTAGTAGTAACAATATCCAATATAAAAGTT
ACCTTGGTATGTATGTATCTATGACCATCTGTTACAATCATGGCCTGAAA
CAGG
back to top

protein sequence of SMED30021914-orf-1

>SMED30021914-orf-1 ID=SMED30021914-orf-1|Name=SMED30021914-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=140bp
EMLLISLTFTICFLLLNYSTSAYESSANFSSFSNSTLSNDTSNSSTPIFT
PGTTPALNISASSTNNVISTTGTTILNVDTTTTAKATTQSSTIVSTYRPR
GFDGSSFVGGIVLCAGIFAIAFFTYKFCFSKKDQEYHEV*
back to top

protein sequence of SMED30021914-orf-2

>SMED30021914-orf-2 ID=SMED30021914-orf-2|Name=SMED30021914-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=121bp
MKYLLFSLSLSLSLVYPITISPNATQCVPRFFSSVVQCAIYFSLIFMPLL
FILTVNNNSVTPIYVRIFYLSFLQLELWIPVPFAARYPSNHVQLVHGFHG
IVKSIYKCQYICVFGSICNV*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000418head
PLANA:0000419prepharyngeal region
PLANA:0003116parenchymal cell
PLANA:0003117parapharyngeal cell
Vocabulary: INTERPRO
TermDefinition
IPR007947CD164_MGC24
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
Vocabulary: cellular component
TermDefinition
GO:0005576extracellular region
GO:0005764lysosome
GO:0005765lysosomal membrane
GO:0005768endosome
GO:0005886plasma membrane
GO:0005887integral component of plasma membrane
GO:0010008endosome membrane
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: biological process
TermDefinition
GO:0006955immune response
GO:0007155cell adhesion
GO:0007157heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0007162negative regulation of cell adhesion
GO:0007165signal transduction
GO:0007275multicellular organism development
GO:0007517muscle organ development
GO:0008285negative regulation of cell proliferation
GO:0030097hemopoiesis
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR007947CD164-related proteinPFAMPF05283MGC-24coord: 28..137
e-value: 4.6E-16
score: 59.5
IPR007947CD164-related proteinPANTHERPTHR11337MUCIN/PORIMINcoord: 31..137
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..22
score: 0.794
NoneNo IPR availableTMHMMTMhelixcoord: 107..129