SJCHGC04876 protein

Overview
NameSJCHGC04876 protein
Smed IDSMED30020043
Length (bp)610
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 SJCHGC04876 protein (SMED30020043) t-SNE clustered cells

Violin plots show distribution of expression levels for SJCHGC04876 protein (SMED30020043) 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 SJCHGC04876 protein (SMED30020043) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SJCHGC04876 protein (SMED30020043) 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



SMED30020043

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
neoblastSMED30020043SMESG000058578.1 dd_Smed_v4_7237_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30020043SMESG000058578.1 dd_Smed_v4_7237_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30020043SMESG000058578.1 dd_Smed_v4_7237_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
Homology
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BLAST of SJCHGC04876 protein vs. TrEMBL
Match: A0A5K3FPR7 (Uncharacterized protein OS=Mesocestoides corti OX=53468 PE=4 SV=1)

HSP 1 Score: 72.0182 bits (175), Expect = 1.207e-12
Identity = 45/119 (37.82%), Postives = 68/119 (57.14%), Query Frame = 1 
Query:  109 NPFRPDGDLCREADEILKNSTIYRDKVIISDPNSRINSLNRQSTPDGDINEIVIQKFTDEVLSEPS-ENVDIVKQENGEGPVVVEVTSKILTTK-EDPIQVEHVNIPGSKTKKGCCQII 459
            NPFRPDG+L REA+ ILKNSTI RDKVII+DP+ + +      +P+G    +  +  + +  + P+ E   I   E   G V +  T  +  ++ ++P+QVEHV I    T   CC ++
Sbjct:    8 NPFRPDGELSREAENILKNSTILRDKVIINDPSVKPSQNGISHSPNGSQPLLKSESISKDCSNPPTYEGSPIRTGEVVSGQVPLSATDGLAASEDQNPLQVEHVKIKSGPTN--CCSVL 124
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BLAST of SJCHGC04876 protein vs. TrEMBL
Match: A0A183VTN9 (Uncharacterized protein OS=Trichobilharzia regenti OX=157069 GN=TRE_LOCUS3846 PE=4 SV=1)

HSP 1 Score: 69.3218 bits (168), Expect = 1.314e-11
Identity = 50/123 (40.65%), Postives = 65/123 (52.85%), Query Frame = 1 
Query:  103 EENPFRPDGDLCREADEILKNSTIYRDKVIISDPNSRINSLNRQSTPDGDI-NEIVIQKFTDEVLSEPSENVDIVK-QENGEGPVVVEVTSKILTTKEDPI-----QVEHVNIPGSKTKKGCC 450
            E NPFRP G+L +E D+ILKNS I RD +II+DP  R  + N  S  DG + N I I+       S+ S   +I     +  GPV  EV S+ +   + P      QVEHVNI  S+    CC
Sbjct:    6 EINPFRPGGELSKEVDDILKNSYISRDTIIINDPALRRANGNPTSV-DGVVPNNIHIKSGDSSFKSQASNGPNIADISSHSSGPVTCEVMSQHVPPLQSPTTFQSEQVEHVNIKRSRKPTKCC 127
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BLAST of SJCHGC04876 protein vs. TrEMBL
Match: A0A183RWV7 (Uncharacterized protein OS=Schistosoma rodhaini OX=6188 PE=4 SV=1)

HSP 1 Score: 68.9366 bits (167), Expect = 1.873e-11
Identity = 48/122 (39.34%), Postives = 67/122 (54.92%), Query Frame = 1 
Query:  103 EENPFRPDGDLCREADEILKNSTIYRDKVIISDPNSRINSLNRQSTPDGDINEIVIQKFTDEVL-SEPSENVDIV-KQENGEGPVVVEVTSKILTTKEDPI----QVEHVNIPGSKTKKGCC 450
            E NPFRP G+L +E D+ILKNSTI RD +II+DP  R  + N  S  DG I+  V  K ++    S+ S  + +  +  +  G V  EV S+ +   + P     Q+EHVNI  S+    CC
Sbjct:    6 EINPFRPGGELSKEVDDILKNSTISRDTIIINDPALRRANGNATSV-DGIISNNVHTKCSESPFKSQTSNGLSVTDRSPHPSGLVTCEVVSQHIQPMQSPTFQSSQIEHVNIKSSRKPTKCC 126
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BLAST of SJCHGC04876 protein vs. TrEMBL
Match: G4M005 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 GN=Smp_133310 PE=4 SV=1)

HSP 1 Score: 68.9366 bits (167), Expect = 1.873e-11
Identity = 48/122 (39.34%), Postives = 67/122 (54.92%), Query Frame = 1 
Query:  103 EENPFRPDGDLCREADEILKNSTIYRDKVIISDPNSRINSLNRQSTPDGDINEIVIQKFTDEVL-SEPSENVDIV-KQENGEGPVVVEVTSKILTTKEDPI----QVEHVNIPGSKTKKGCC 450
            E NPFRP G+L +E D+ILKNSTI RD +II+DP  R  + N  S  DG I+  V  K ++    S+ S  + +  +  +  G V  EV S+ +   + P     Q+EHVNI  S+    CC
Sbjct:    6 EINPFRPGGELSKEVDDILKNSTISRDTIIINDPALRRANGNATSV-DGIISNNVHTKCSESPFKSQTSNGLSVTDRSPHPSGLVTCEVVSQHIQPMQSPTFQSSQIEHVNIKSSRKPTKCC 126
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BLAST of SJCHGC04876 protein vs. TrEMBL
Match: Q5DHA9 (SJCHGC04876 protein OS=Schistosoma japonicum OX=6182 GN=EWB00_004120 PE=2 SV=1)

HSP 1 Score: 68.9366 bits (167), Expect = 2.221e-11
Identity = 47/125 (37.60%), Postives = 67/125 (53.60%), Query Frame = 1 
Query:  103 EENPFRPDGDLCREADEILKNSTIYRDKVIISDPNSRINSLNRQSTPDGDINEIVIQKFTDEVL-SEPSENVDIV-KQENGEGPVVVEVTSKILTTKEDPI-----QVEHVNIPGSKTKKGCCQI 456
            E NPFRPDG+L +E D+ILKNSTI R+ +II+DP  R  +    S  +G ++  +  K+      S+ S  + +     +  GPV  EV S+ +   + P      QVEHVNI  S+    CC I
Sbjct:    6 EINPFRPDGELSKEVDDILKNSTISRNTIIINDPALRCPNGTAASV-EGIVSNNIHTKYAGSPFKSQTSNGLSVTDGPPHPPGPVTCEVVSQHIQPIQSPATFHSGQVEHVNIKSSRKPTKCCVI 129
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BLAST of SJCHGC04876 protein vs. Planmine SMEST
Match: SMESG000058578.1 (SMESG000058578.1)

HSP 1 Score: 241.121 bits (614), Expect = 1.195e-82
Identity = 121/121 (100.00%), Postives = 121/121 (100.00%), Query Frame = 1 
Query:   97 MNEENPFRPDGDLCREADEILKNSTIYRDKVIISDPNSRINSLNRQSTPDGDINEIVIQKFTDEVLSEPSENVDIVKQENGEGPVVVEVTSKILTTKEDPIQVEHVNIPGSKTKKGCCQII 459
            MNEENPFRPDGDLCREADEILKNSTIYRDKVIISDPNSRINSLNRQSTPDGDINEIVIQKFTDEVLSEPSENVDIVKQENGEGPVVVEVTSKILTTKEDPIQVEHVNIPGSKTKKGCCQII
Sbjct:    1 MNEENPFRPDGDLCREADEILKNSTIYRDKVIISDPNSRINSLNRQSTPDGDINEIVIQKFTDEVLSEPSENVDIVKQENGEGPVVVEVTSKILTTKEDPIQVEHVNIPGSKTKKGCCQII 121
The following BLAST results are available for this feature:
BLAST of SJCHGC04876 protein 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 SJCHGC04876 protein 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 SJCHGC04876 protein 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 SJCHGC04876 protein 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 SJCHGC04876 protein 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 SJCHGC04876 protein 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 SJCHGC04876 protein 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 SJCHGC04876 protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A5K3FPR71.207e-1237.82Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A183VTN91.314e-1140.65Uncharacterized protein OS=Trichobilharzia regenti... [more]
A0A183RWV71.873e-1139.34Uncharacterized protein OS=Schistosoma rodhaini OX... [more]
G4M0051.873e-1139.34Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
Q5DHA92.221e-1137.60SJCHGC04876 protein OS=Schistosoma japonicum OX=61... [more]
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BLAST of SJCHGC04876 protein 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 SJCHGC04876 protein 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 SJCHGC04876 protein 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 SJCHGC04876 protein 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 SJCHGC04876 protein 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 SJCHGC04876 protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000058578.11.195e-82100.00SMESG000058578.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020043 ID=SMED30020043|Name=SJCHGC04876 protein|organism=Schmidtea mediterranea sexual|type=transcript|length=610bp
ATTTGTTTTGTTTGCATAAATTCAAGGTTGACATCAATTTTGAATCTATT
CTGAATTTGAAATCTTTGTTTTTATTCTTTTTAAATTACACCTGCAATGA
ATGAAGAGAATCCATTTAGACCAGATGGTGACTTATGTCGAGAAGCTGAT
GAAATATTAAAAAATTCAACTATTTATCGAGATAAAGTTATTATATCAGA
TCCAAATTCAAGAATTAATTCACTAAATCGTCAATCAACTCCAGATGGGG
ATATCAATGAAATAGTTATTCAAAAATTTACTGACGAAGTATTATCTGAA
CCTTCGGAAAACGTTGACATTGTCAAACAAGAAAATGGTGAAGGCCCAGT
TGTAGTTGAAGTGACATCAAAAATTTTAACAACTAAAGAAGATCCAATTC
AAGTTGAGCATGTCAATATTCCAGGATCTAAAACCAAAAAAGGATGTTGT
CAAATAATTTAATTGTAATGAATTTGTCTAGTCTATTATTTTAAATGCGA
AAATTGGTTGTTTATATTTTAATTTTGGTAACTGGCAATTAGATATTAAA
TAATTTTTGGTTTTTTCAGATATGCTTATTGACTTTTTTGTTGCCATGTT
TCAGTGGGAA
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protein sequence of SMED30020043-orf-1

>SMED30020043-orf-1 ID=SMED30020043-orf-1|Name=SMED30020043-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=122bp
MNEENPFRPDGDLCREADEILKNSTIYRDKVIISDPNSRINSLNRQSTPD
GDINEIVIQKFTDEVLSEPSENVDIVKQENGEGPVVVEVTSKILTTKEDP
IQVEHVNIPGSKTKKGCCQII*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0000142posterior region of the whole animal
PLANA:0000429neoblast
PLANA:0002056medial muscle cell