SJCHGC05108 protein

Overview
NameSJCHGC05108 protein
Smed IDSMED30000974
Length (bp)798
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 SJCHGC05108 protein (SMED30000974) t-SNE clustered cells

Violin plots show distribution of expression levels for SJCHGC05108 protein (SMED30000974) 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 SJCHGC05108 protein (SMED30000974) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SJCHGC05108 protein (SMED30000974) 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




SMED30000974

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
intestinal phagocyteSMED30000974SMESG000012748.1 Contig2765GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30000974SMESG000000375.1 Contig2765GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
epidermisSMED30000974SMESG000000375.1 dd_Smed_v4_6676_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
Homology
BLAST of SJCHGC05108 protein vs. TrEMBL
Match: A0A3P7LY79 (Uncharacterized protein OS=Dibothriocephalus latus OX=60516 GN=DILT_LOCUS6942 PE=4 SV=1)

HSP 1 Score: 65.4698 bits (158), Expect = 4.388e-9
Identity = 46/155 (29.68%), Postives = 76/155 (49.03%), Query Frame = 1
Query:   73 FCVNEIIHFLKHLKETDNESIMITGNYESILQVLADLQFEGYGNY---FKNIIIATDNVSECVNRYFSSTCLFIVEWLESVDEVYLKNRVLQKRS--NIKMAIDFNPSLRRLHRIYEIIDINSVVFLKQLPSLWKQQFPVLFVAFKEKNSNVVNF 522
            F   +II  L   KE   + +++ G    +   LA L     GN     ++II+AT+N++   N   +     IVEW ESV E YL  RV       +I +AIDF+P+LRR+ RI ++++ + V+ +      W+   P L  +F     +++  
Sbjct:   18 FVCEKIISCLSENKE-HTKKVLLCGRLRELEPCLASL-----GNRPELLEHIIVATNNITRLYNDKTTVKKPLIVEWDESVYEEYLIERVKTSSDHFSISLAIDFSPTLRRIERIRKLLEKDGVLIITAENPGWRMAKPQLLSSFSANGGSLIKL 166          
BLAST of SJCHGC05108 protein vs. TrEMBL
Match: A0A4Z2DIM7 (Uncharacterized protein OS=Schistosoma japonicum OX=6182 GN=EWB00_000471 PE=4 SV=1)

HSP 1 Score: 64.6994 bits (156), Expect = 7.331e-9
Identity = 47/174 (27.01%), Postives = 85/174 (48.85%), Query Frame = 1
Query:   91 IHFLKHLKETDNESIMITGNYESILQVL--ADLQFEGYGNYFKNIIIATDNVSECVNRYFSSTCLFIVEWLESVDEVYLKNRVLQKRSN--IKMAIDFNPSLRRLHRIYEIIDINSVVFLKQLPSLWKQQFPVLFVAFKEKNSNVVNFE---LACGPSRQNENYNGAKMVLHAR 591
            IH   H  +   + I+I G  + I   L  A +   G  +Y  ++IIA+ ++ E +  YF  T + +V W E+  E  L  RV  +  N  I + I+F P++RR+ RI E+++ N  + +      W+ ++  L  +F E N  ++         G +RQ ++  G +  +H+R
Sbjct:    3 IHSYSHFADYPRQKILICGLPDDISPCLDYAMIAKPGVIDY-SSLIIASTDIDELIVNYFGKTKIHLVNWDETDYEEMLIERVRPRSDNFTIPLVIEFQPTIRRMKRIRELLEKNGTLVIPSENPEWRIRYTNLMNSFTENNGTLIKLAENVFDAGFTRQIDHLLGRRH-MHSR 174          
BLAST of SJCHGC05108 protein vs. TrEMBL
Match: A0A0X3PHU1 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=TR116247 PE=4 SV=1)

HSP 1 Score: 62.3882 bits (150), Expect = 3.344e-8
Identity = 37/132 (28.03%), Postives = 68/132 (51.52%), Query Frame = 1
Query:  133 IMITGNYESILQVLADLQFEGYGNYFKNIIIATDNVSECVNRYFSSTCLFIVEWLESVDEVYLKNRVLQKRS--NIKMAIDFNPSLRRLHRIYEIIDINSVVFLKQLPSLWKQQFPVLFVAFKEKNSNVVNF 522
            +++ G    +   LA L  +      ++II+AT N++   +   +S+   +VEW ESV E YL  RV  +    +I +AIDF+P+LRR+ RI ++++   V+ +      W+   P L  +F     +++  
Sbjct:    2 VLLCGRLGELEPCLASLSNQP--EVLEHIIVATSNITRLYSDKATSSKPHMVEWDESVYEEYLIERVKTRNDQFSISLAIDFSPTLRRIERIRKLLEKEGVLIITAENPGWRMAKPELISSFSANGGSLIKL 131          
BLAST of SJCHGC05108 protein vs. TrEMBL
Match: A0A0X3PY18 (Uncharacterized protein (Fragment) OS=Schistocephalus solidus OX=70667 GN=TR116247 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 1.222e-7
Identity = 37/132 (28.03%), Postives = 68/132 (51.52%), Query Frame = 1
Query:  133 IMITGNYESILQVLADLQFEGYGNYFKNIIIATDNVSECVNRYFSSTCLFIVEWLESVDEVYLKNRVLQKRS--NIKMAIDFNPSLRRLHRIYEIIDINSVVFLKQLPSLWKQQFPVLFVAFKEKNSNVVNF 522
            +++ G    +   LA L  +      ++II+AT N++   +   +S+   +VEW ESV E YL  RV  +    +I +AIDF+P+LRR+ RI ++++   V+ +      W+   P L  +F     +++  
Sbjct:   76 VLLCGRLGELEPCLASLSNQP--EVLEHIIVATSNITRLYSDKATSSKPHMVEWDESVYEEYLIERVKTRNDQFSISLAIDFSPTLRRIERIRKLLEKEGVLIITAENPGWRMAKPELISSFSANGGSLIKL 205          
BLAST of SJCHGC05108 protein vs. TrEMBL
Match: A0A4Z2DIN4 (Uncharacterized protein OS=Schistosoma japonicum OX=6182 GN=EWB00_000471 PE=4 SV=1)

HSP 1 Score: 60.077 bits (144), Expect = 5.533e-7
Identity = 36/133 (27.07%), Postives = 69/133 (51.88%), Query Frame = 1
Query:  208 FKNIIIATDNVSECVNRYFSSTCLFIVEWLESVDEVYLKNRVLQKRSN--IKMAIDFNPSLRRLHRIYEIIDINSVVFLKQLPSLWKQQFPVLFVAFKEKNSNVVNFE---LACGPSRQNENYNGAKMVLHAR 591
            + ++IIA+ ++ E +  YF  T + +V W E+  E  L  RV  +  N  I + I+F P++RR+ RI E+++ N  + +      W+ ++  L  +F E N  ++         G +RQ ++  G +  +H+R
Sbjct:   92 YSSLIIASTDIDELIVNYFGKTKIHLVNWDETDYEEMLIERVRPRSDNFTIPLVIEFQPTIRRMKRIRELLEKNGTLVIPSENPEWRIRYTNLMNSFTENNGTLIKLAENVFDAGFTRQIDHLLGRRH-MHSR 223          
BLAST of SJCHGC05108 protein vs. Planmine SMEST
Match: SMESG000000375.1 (SMESG000000375.1)

HSP 1 Score: 362.844 bits (930), Expect = 7.038e-129
Identity = 176/176 (100.00%), Postives = 176/176 (100.00%), Query Frame = 1
Query:   64 MEEFCVNEIIHFLKHLKETDNESIMITGNYESILQVLADLQFEGYGNYFKNIIIATDNVSECVNRYFSSTCLFIVEWLESVDEVYLKNRVLQKRSNIKMAIDFNPSLRRLHRIYEIIDINSVVFLKQLPSLWKQQFPVLFVAFKEKNSNVVNFELACGPSRQNENYNGAKMVLHAR 591
            MEEFCVNEIIHFLKHLKETDNESIMITGNYESILQVLADLQFEGYGNYFKNIIIATDNVSECVNRYFSSTCLFIVEWLESVDEVYLKNRVLQKRSNIKMAIDFNPSLRRLHRIYEIIDINSVVFLKQLPSLWKQQFPVLFVAFKEKNSNVVNFELACGPSRQNENYNGAKMVLHAR
Sbjct:    1 MEEFCVNEIIHFLKHLKETDNESIMITGNYESILQVLADLQFEGYGNYFKNIIIATDNVSECVNRYFSSTCLFIVEWLESVDEVYLKNRVLQKRSNIKMAIDFNPSLRRLHRIYEIIDINSVVFLKQLPSLWKQQFPVLFVAFKEKNSNVVNFELACGPSRQNENYNGAKMVLHAR 176          
BLAST of SJCHGC05108 protein vs. Planmine SMEST
Match: SMESG000000375.1 (SMESG000000375.1)

HSP 1 Score: 313.538 bits (802), Expect = 1.028e-109
Identity = 152/152 (100.00%), Postives = 152/152 (100.00%), Query Frame = 1
Query:  136 MITGNYESILQVLADLQFEGYGNYFKNIIIATDNVSECVNRYFSSTCLFIVEWLESVDEVYLKNRVLQKRSNIKMAIDFNPSLRRLHRIYEIIDINSVVFLKQLPSLWKQQFPVLFVAFKEKNSNVVNFELACGPSRQNENYNGAKMVLHAR 591
            MITGNYESILQVLADLQFEGYGNYFKNIIIATDNVSECVNRYFSSTCLFIVEWLESVDEVYLKNRVLQKRSNIKMAIDFNPSLRRLHRIYEIIDINSVVFLKQLPSLWKQQFPVLFVAFKEKNSNVVNFELACGPSRQNENYNGAKMVLHAR
Sbjct:    1 MITGNYESILQVLADLQFEGYGNYFKNIIIATDNVSECVNRYFSSTCLFIVEWLESVDEVYLKNRVLQKRSNIKMAIDFNPSLRRLHRIYEIIDINSVVFLKQLPSLWKQQFPVLFVAFKEKNSNVVNFELACGPSRQNENYNGAKMVLHAR 152          
The following BLAST results are available for this feature:
BLAST of SJCHGC05108 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 SJCHGC05108 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 SJCHGC05108 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 SJCHGC05108 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 SJCHGC05108 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 SJCHGC05108 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 SJCHGC05108 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 SJCHGC05108 protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A3P7LY794.388e-929.68Uncharacterized protein OS=Dibothriocephalus latus... [more]
A0A4Z2DIM77.331e-927.01Uncharacterized protein OS=Schistosoma japonicum O... [more]
A0A0X3PHU13.344e-828.03Uncharacterized protein OS=Schistocephalus solidus... [more]
A0A0X3PY181.222e-728.03Uncharacterized protein (Fragment) OS=Schistocepha... [more]
A0A4Z2DIN45.533e-727.07Uncharacterized protein OS=Schistosoma japonicum O... [more]
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BLAST of SJCHGC05108 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 SJCHGC05108 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 SJCHGC05108 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 SJCHGC05108 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 SJCHGC05108 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 SJCHGC05108 protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000000375.17.038e-129100.00SMESG000000375.1[more]
SMESG000000375.11.028e-109100.00SMESG000000375.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000974 ID=SMED30000974|Name=SJCHGC05108 protein|organism=Schmidtea mediterranea sexual|type=transcript|length=798bp
AAAAAATGTTAATATTAAATCGATATATACTTTATGCATTATTTTAAAGT
GTATTTTATTTAAATGGAGGAATTTTGTGTAAATGAAATTATTCATTTTT
TGAAACATTTAAAAGAAACTGACAATGAATCTATTATGATCACTGGAAAT
TATGAAAGCATTCTACAAGTTCTAGCGGATCTTCAATTTGAAGGCTACGG
AAATTATTTCAAAAATATTATAATAGCCACAGATAATGTAAGTGAATGTG
TAAATCGATATTTTTCATCGACCTGTTTATTTATCGTAGAATGGCTCGAA
AGCGTCGATGAAGTCTATCTAAAAAACCGGGTGCTACAGAAACGCTCAAA
CATCAAAATGGCTATCGATTTTAACCCATCTCTGCGGCGCCTCCATAGAA
TCTATGAAATCATAGACATAAATTCCGTTGTCTTTCTCAAACAGCTGCCT
TCCCTATGGAAACAGCAATTTCCCGTGTTATTTGTGGCGTTCAAGGAGAA
GAATTCTAATGTTGTGAATTTTGAATTAGCTTGCGGTCCAAGTCGACAAA
ATGAGAATTACAATGGTGCCAAAATGGTGCTTCATGCAAGATGAACCGTT
GCGCACGCTCATCTGATGCTGGGGTCTAGCAGGAGACCAAATACTTATAA
TATTTTCAAGTGCCTAACTGCAATTTTGTTCTTTCTCTTCTGTCATTCAA
ATGTAGGTATTCGGATTTCTATGACAAATGTCCGTTGAATTCACTGTTAG
TGAATTATGTAAATGAAATGTAAATATTTAATAAATGCCTGTCTAATG
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protein sequence of SMED30000974-orf-1

>SMED30000974-orf-1 ID=SMED30000974-orf-1|Name=SMED30000974-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=177bp
MEEFCVNEIIHFLKHLKETDNESIMITGNYESILQVLADLQFEGYGNYFK
NIIIATDNVSECVNRYFSSTCLFIVEWLESVDEVYLKNRVLQKRSNIKMA
IDFNPSLRRLHRIYEIIDINSVVFLKQLPSLWKQQFPVLFVAFKEKNSNV
VNFELACGPSRQNENYNGAKMVLHAR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000070intestinal phagocyte