SJCHGC08351 protein

Overview
NameSJCHGC08351 protein
Smed IDSMED30017795
Length (bp)838
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 SJCHGC08351 protein (SMED30017795) t-SNE clustered cells

Violin plots show distribution of expression levels for SJCHGC08351 protein (SMED30017795) 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 SJCHGC08351 protein (SMED30017795) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SJCHGC08351 protein (SMED30017795) 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



SMED30017795

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30017795SMESG000005753.1 SmedASXL_010378SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30017795SMESG000005753.1 dd_Smed_v4_8141_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30017795SMESG000005753.1 dd_Smed_v4_8141_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30017795SMESG000005753.1 dd_Smed_v4_8141_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30017795SMESG000005753.1 dd_Smed_v4_8141_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30017795SMESG000005753.1 dd_Smed_v4_8141_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017795SMESG000005753.1 Contig48800newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017795SMESG000005753.1 Contig48800uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30017795SMESG000005753.1 dd_Smed_v6_8141_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30017795SMESG000005753.1 dd_Smed_v4_8141_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
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BLAST of SJCHGC08351 protein vs. TrEMBL
Match: A0A1I8GGY4 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig011092g2 PE=4 SV=1)

HSP 1 Score: 94.7449 bits (234), Expect = 1.033e-20
Identity = 47/119 (39.50%), Postives = 73/119 (61.34%), Query Frame = 3 
Query:   63 ESSPSKNKKETGILTESSLLCLGKELNANNFRFFMNLGIPTIQIAIMKSENDEKGLTYQNLCQKILLYWLNMRKNANDKDKVFNLERALRSSNQMRLADIVIERYRLNMDLVPAVFKEA 419
            ++   + +KE  +LTE+SLL LGK +   + + +M L IPT++I   K  N+E  +      QK+LLYW  MRK A + D + +L+ ALR S Q  +ADIV +R R++ ++VP +F  A
Sbjct:    4 QTEQPEEQKEARVLTETSLLNLGKAVKQGDMKLYMLLNIPTVEIVRQKVRNEELKMPEYGAAQKLLLYWKKMRKGAKENDIIRDLDNALRESGQEEIADIVSDRNRIDQEIVPELFVSA 122
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BLAST of SJCHGC08351 protein vs. TrEMBL
Match: A0A267DMV2 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig011092g1 PE=4 SV=1)

HSP 1 Score: 94.3597 bits (233), Expect = 1.510e-20
Identity = 47/119 (39.50%), Postives = 73/119 (61.34%), Query Frame = 3 
Query:   63 ESSPSKNKKETGILTESSLLCLGKELNANNFRFFMNLGIPTIQIAIMKSENDEKGLTYQNLCQKILLYWLNMRKNANDKDKVFNLERALRSSNQMRLADIVIERYRLNMDLVPAVFKEA 419
            ++   + +KE  +LTE+SLL LGK +   + + +M L IPT++I   K  N+E  +      QK+LLYW  MRK A + D + +L+ ALR S Q  +ADIV +R R++ ++VP +F  A
Sbjct:    4 QTEQPEEQKEARVLTETSLLNLGKAVKQGDMKLYMLLNIPTVEIVRQKVRNEEFKMPEYGAAQKLLLYWKKMRKGAKENDIIRDLDNALRESGQEEIADIVSDRNRIDQEIVPELFVSA 122
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BLAST of SJCHGC08351 protein vs. TrEMBL
Match: A0A1I8IG32 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 94.3597 bits (233), Expect = 2.381e-18
Identity = 47/114 (41.23%), Postives = 72/114 (63.16%), Query Frame = 3 
Query:   78 KNKKETGILTESSLLCLGKELNANNFRFFMNLGIPTIQIAIMKSENDEKGLTYQNLCQKILLYWLNMRKNANDKDKVFNLERALRSSNQMRLADIVIERYRLNMDLVPAVFKEA 419
            + +KE  +LTE+SLL LGK +   + + +M L IPT++I   K  N+E  +      QK+LLYW  MRK A + D + +L+ ALR S Q  +ADIV +R R++ ++VP +F+ A
Sbjct:   94 EEQKEARVLTETSLLNLGKAVKQGDMKLYMLLNIPTVEIVRQKVRNEELKMPEYGAAQKLLLYWKKMRKGAKENDIIRDLDNALRESGQEEIADIVSDRNRIDQEIVPELFRTA 207
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BLAST of SJCHGC08351 protein vs. TrEMBL
Match: A0A267EVN1 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig022750g1 PE=4 SV=1)

HSP 1 Score: 88.5817 bits (218), Expect = 2.416e-18
Identity = 44/111 (39.64%), Postives = 69/111 (62.16%), Query Frame = 3 
Query:   87 KETGILTESSLLCLGKELNANNFRFFMNLGIPTIQIAIMKSENDEKGLTYQNLCQKILLYWLNMRKNANDKDKVFNLERALRSSNQMRLADIVIERYRLNMDLVPAVFKEA 419
            KE  +LT+ SL+ L + +   + + +M L IPT++I  +K +NDE+  T   L QK+LLYW  MR  A + + +  LE AL  S Q  +ADIV +R+++N ++VP +F  A
Sbjct:   11 KEAKVLTDVSLINLSRAVKQGDLQLYMLLNIPTVEIIRLKFKNDEQQQTETGLSQKLLLYWKAMRNGAKEGELIRELEAALGDSGQQDIADIVSQRHQINQEIVPELFVSA 121
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BLAST of SJCHGC08351 protein vs. TrEMBL
Match: A0A267EAF7 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig013760g1 PE=4 SV=1)

HSP 1 Score: 87.4261 bits (215), Expect = 6.749e-18
Identity = 44/111 (39.64%), Postives = 69/111 (62.16%), Query Frame = 3 
Query:   87 KETGILTESSLLCLGKELNANNFRFFMNLGIPTIQIAIMKSENDEKGLTYQNLCQKILLYWLNMRKNANDKDKVFNLERALRSSNQMRLADIVIERYRLNMDLVPAVFKEA 419
            KE  +LT+ SL+ L + +   + + +M L IPT++I  +K +NDE+  T   L QK+LLYW  MR  A + + +  LE AL  S Q  +ADIV +R+++N ++VP +F  A
Sbjct:   11 KEAKVLTDVSLINLSRAVKQGDLQLYMLLNIPTVEIIRLKFKNDEQQQTETGLSQKLLLYWKAMRNVAKEGELIRELEAALGDSGQQDIADIVSQRHQINQEIVPELFVSA 121
[Close]
BLAST of SJCHGC08351 protein vs. Planmine SMEST
Match: SMESG000005753.1 (SMESG000005753.1)

HSP 1 Score: 251.521 bits (641), Expect = 1.752e-85
Identity = 123/123 (100.00%), Postives = 123/123 (100.00%), Query Frame = 3 
Query:   51 MSFEESSPSKNKKETGILTESSLLCLGKELNANNFRFFMNLGIPTIQIAIMKSENDEKGLTYQNLCQKILLYWLNMRKNANDKDKVFNLERALRSSNQMRLADIVIERYRLNMDLVPAVFKEA 419
            MSFEESSPSKNKKETGILTESSLLCLGKELNANNFRFFMNLGIPTIQIAIMKSENDEKGLTYQNLCQKILLYWLNMRKNANDKDKVFNLERALRSSNQMRLADIVIERYRLNMDLVPAVFKEA
Sbjct:    1 MSFEESSPSKNKKETGILTESSLLCLGKELNANNFRFFMNLGIPTIQIAIMKSENDEKGLTYQNLCQKILLYWLNMRKNANDKDKVFNLERALRSSNQMRLADIVIERYRLNMDLVPAVFKEA 123
The following BLAST results are available for this feature:
BLAST of SJCHGC08351 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 SJCHGC08351 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 SJCHGC08351 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 SJCHGC08351 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 SJCHGC08351 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 SJCHGC08351 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 SJCHGC08351 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 SJCHGC08351 protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1I8GGY41.033e-2039.50Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267DMV21.510e-2039.50Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8IG322.381e-1841.23Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267EVN12.416e-1839.64Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267EAF76.749e-1839.64Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of SJCHGC08351 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 SJCHGC08351 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 SJCHGC08351 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 SJCHGC08351 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 SJCHGC08351 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 SJCHGC08351 protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000005753.11.752e-85100.00SMESG000005753.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017795 ID=SMED30017795|Name=SJCHGC08351 protein|organism=Schmidtea mediterranea sexual|type=transcript|length=838bp
TTTTATTTTAATTTGTTTAACTTTTTGATGTCATAGCAATATTCTTGGAA
ATGTCTTTTGAAGAGTCAAGTCCTTCCAAAAATAAGAAAGAAACCGGTAT
TCTCACAGAATCTAGTTTATTGTGCTTGGGAAAAGAACTAAACGCAAATA
ATTTTAGATTTTTTATGAATTTAGGTATTCCAACTATACAAATTGCCATA
ATGAAGAGTGAAAATGATGAAAAGGGATTAACATATCAAAATTTATGTCA
AAAAATTTTACTTTACTGGTTGAATATGAGAAAAAATGCCAACGATAAAG
ATAAAGTATTTAATTTAGAACGAGCTCTTAGAAGCTCAAATCAAATGCGC
CTAGCTGATATTGTTATTGAGCGCTATAGACTGAACATGGATTTAGTTCC
CGCAGTATTTAAAGAAGCTTGATGTGAATATTTTTCTAAGTTGTAACGGA
TTTTTTGAGTATTGATTTTATAATATTTTTCTCTTTTCTTAGACTTTCCT
TTGATTACTCTATTTAATTATTGTTTTTTTATTTATTTTAAATCACAAAT
AAATTATTGTTTGACGTTGACAACTTTTTTATGTTTTTATTTAGGAATAT
ATCTAGAATTTGTCTGTCGTGAAGGGGAAAGGGGGTTGTTGGAGATATTT
GCTGAAAATCCATGATTATTGCTGACTGGATCCATGTAAGCATTATAAAA
TCATAGCAAAGAAATCAGTGGCGTAGCCAAGGGGTGGGTTTAAGGTGTCA
ACCTCCCCCCCCACCATTGGATTTTTCATCTAAAGATTTTTGACGTCAAG
TACCTAAAAGGTCATCCACCTAAATAAGAAAAAAAACA
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protein sequence of SMED30017795-orf-1

>SMED30017795-orf-1 ID=SMED30017795-orf-1|Name=SMED30017795-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=124bp
MSFEESSPSKNKKETGILTESSLLCLGKELNANNFRFFMNLGIPTIQIAI
MKSENDEKGLTYQNLCQKILLYWLNMRKNANDKDKVFNLERALRSSNQMR
LADIVIERYRLNMDLVPAVFKEA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000418head
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR011029DEATH-like_dom_sf
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:1.10.533.10coord: 9..108
e-value: 1.1E-8
score: 37.0