SJCHGC05364 protein

Overview
NameSJCHGC05364 protein
Smed IDSMED30017354
Length (bp)673
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 SJCHGC05364 protein (SMED30017354) t-SNE clustered cells

Violin plots show distribution of expression levels for SJCHGC05364 protein (SMED30017354) 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 SJCHGC05364 protein (SMED30017354) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SJCHGC05364 protein (SMED30017354) 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



SMED30017354

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30017354SMESG000032293.1 dd_Smed_v4_7600_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30017354SMESG000032293.1 dd_Smed_v4_7600_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30017354SMESG000032293.1 dd_Smed_v4_7600_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30017354SMESG000032293.1 dd_Smed_v4_7600_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30017354SMESG000032293.1 dd_Smed_v4_7600_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30017354SMESG000035568.1 SMESG000032293.1 OX_Smed_1.0.03936ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SJCHGC05364 protein vs. Ensembl Xenopus
Match: drd1c (D(1C) dopamine receptor [Source:Xenbase;Acc:XB-GENE-5919679])

HSP 1 Score: 52.7582 bits (125), Expect = 2.303e-8
Identity = 27/70 (38.57%), Postives = 43/70 (61.43%), Query Frame = 2 
Query:  161 VVMGLLFIIPGMMK-TVKVNANLYKEMLKTFKNFTQVSPLQLIGVNPPPYVYMQSIGVIELVLGTTLIVG 367
            V++GL F + G++K T +++A++YK+M   F  F  V PL+  G  P P  Y+ ++G +ELV G  L  G
Sbjct:   10 VLLGLFFGLSGVVKLTDQISADVYKQMKTQFVQFADVFPLKDFGFKPDPEQYLLAVGWVELVAGVLLAFG 79
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BLAST of SJCHGC05364 protein vs. TrEMBL
Match: A0A2H1C2P9 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_12111 PE=4 SV=1)

HSP 1 Score: 161.384 bits (407), Expect = 7.242e-47
Identity = 76/133 (57.14%), Postives = 110/133 (82.71%), Query Frame = 2 
Query:  128 MSTKLGTRISSVVMGLLFIIPGMMKTVKVNANLYKEMLKTFKNFTQVSPLQLIGVNPPPYVYMQSIGVIELVLGTTLIVGGAASRKIACXXXXXXXXXTAASQFRLDDYMAMIVPSGYFALLSWVFISIEKLE 526
            M+++LGT++S+V++G+LFI+PG++KTV++N  LY+EMLKTFKNFT VSPL+ +G++P P +YMQS GV EL+ GTTL+VGG   +K+ACLG+M LML+T   Q  L D+ A+IVP GYF LL+W+++S+ KL+
Sbjct:    1 MASRLGTQVSTVILGILFILPGIVKTVRLNTTLYREMLKTFKNFTDVSPLRHLGIHPSPQIYMQSTGVFELIFGTTLVVGGRFFKKLACLGIMALMLMTTYCQLILRDFDAIIVPCGYFCLLTWIYLSLNKLD 133
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BLAST of SJCHGC05364 protein vs. TrEMBL
Match: A0A4E0RY84 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_007997 PE=4 SV=1)

HSP 1 Score: 161.384 bits (407), Expect = 9.348e-47
Identity = 76/133 (57.14%), Postives = 110/133 (82.71%), Query Frame = 2 
Query:  128 MSTKLGTRISSVVMGLLFIIPGMMKTVKVNANLYKEMLKTFKNFTQVSPLQLIGVNPPPYVYMQSIGVIELVLGTTLIVGGAASRKIACXXXXXXXXXTAASQFRLDDYMAMIVPSGYFALLSWVFISIEKLE 526
            M+++LGT++S+V++G+LFI+PG++KTV++N  LY+EMLKTFKNFT VSPL+ +G++P P +YMQS GV EL+ GTTL+VGG   +K+ACLG+M LML+T   Q  L D+ A+IVP GYF LL+W+++S+ KL+
Sbjct:   13 MASRLGTQVSTVILGILFILPGIVKTVRLNTTLYREMLKTFKNFTDVSPLRHLGIHPSPQIYMQSTGVFELIFGTTLVVGGRFFKKLACLGIMALMLMTTYCQLILRDFDAIIVPCGYFCLLTWIYLSLNKLD 145
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BLAST of SJCHGC05364 protein vs. TrEMBL
Match: A0A4S2L8S1 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_009006 PE=4 SV=1)

HSP 1 Score: 160.614 bits (405), Expect = 1.350e-46
Identity = 80/141 (56.74%), Postives = 111/141 (78.72%), Query Frame = 2 
Query:  128 MSTKLGTRISSVVMGLLFIIPGMMKTVKVNANLYKEMLKTFKNFTQVSPLQLIGVNPPPYVYMQSIGVIELVLGTTLIVGGAASRKIACXXXXXXXXXTAASQFRLDDYMAMIVPSGYFALLSWVFISIEKLERQSKGKTK 550
            M++ LGT++S+VV+G+LFI+PG++KTV++N  LY+EMLKTFKNFT+VSP + +GV   P VYMQS GV EL+LGTTL+VG    +K+ACLG+M LMLLT   Q  L DY A IVP GYF LL+W+++S+ ++E+Q++  T 
Sbjct:    1 MASYLGTQVSTVVLGILFILPGIVKTVRLNTTLYREMLKTFKNFTEVSPFRHLGVQLNPQVYMQSTGVFELMLGTTLVVGSKLFKKLACLGIMALMLLTTYCQLLLHDYDATIVPCGYFCLLAWIYVSLGRMEKQAQTATD 141
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BLAST of SJCHGC05364 protein vs. TrEMBL
Match: A0A094ZR86 (Uncharacterized protein (Fragment) OS=Schistosoma haematobium OX=6185 GN=MS3_04982 PE=4 SV=1)

HSP 1 Score: 159.844 bits (403), Expect = 2.261e-46
Identity = 82/135 (60.74%), Postives = 107/135 (79.26%), Query Frame = 2 
Query:  128 MSTKLGTRISSVVMGLLFIIPGMMKTVKVNANLYKEMLKTFKNFTQVSPLQLIGVNPPPYVYMQSIGVIELVLGTTLIVGGAASRKIACXXXXXXXXXTAASQFRLDDYMAMIVPSGYFALLSWVFISIEKLERQ 532
            M++ L T +S+VV+GLLFI+PG++KTV++N  LY+EMLKTFKNFT+VSPL+ IGV P P +YMQS+GV EL+LGTTL+VG  + +K ACLG+M LMLLT   Q  L DY A IVP GYF LLS ++ S++KLE +
Sbjct:    1 MASHLATHVSTVVLGLLFILPGIVKTVRLNTTLYREMLKTFKNFTEVSPLRHIGVIPSPQIYMQSMGVFELLLGTTLVVGHVSFKKFACLGIMALMLLTTYCQVALKDYSATIVPCGYFCLLSRLYFSLDKLEDR 135
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BLAST of SJCHGC05364 protein vs. TrEMBL
Match: A0A430Q3I7 (Uncharacterized protein OS=Schistosoma bovis OX=6184 GN=DC041_0006495 PE=4 SV=1)

HSP 1 Score: 159.844 bits (403), Expect = 2.261e-46
Identity = 82/135 (60.74%), Postives = 107/135 (79.26%), Query Frame = 2 
Query:  128 MSTKLGTRISSVVMGLLFIIPGMMKTVKVNANLYKEMLKTFKNFTQVSPLQLIGVNPPPYVYMQSIGVIELVLGTTLIVGGAASRKIACXXXXXXXXXTAASQFRLDDYMAMIVPSGYFALLSWVFISIEKLERQ 532
            M++ L T +S+VV+GLLFI+PG++KTV++N  LY+EMLKTFKNFT+VSPL+ IGV P P +YMQS+GV EL+LGTTL+VG  + +K ACLG+M LMLLT   Q  L DY A IVP GYF LLS ++ S++KLE +
Sbjct:    1 MASHLATHVSTVVLGLLFILPGIVKTVRLNTTLYREMLKTFKNFTEVSPLRHIGVIPSPQIYMQSMGVFELLLGTTLVVGHVSFKKFACLGIMALMLLTTYCQVALKDYSATIVPCGYFCLLSRLYFSLDKLEDR 135
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BLAST of SJCHGC05364 protein vs. Planmine SMEST
Match: SMESG000032293.1 (SMESG000032293.1)

HSP 1 Score: 269.626 bits (688), Expect = 3.585e-93
Identity = 143/143 (100.00%), Postives = 143/143 (100.00%), Query Frame = 2 
Query:  128 MSTKLGTRISSVVMGLLFIIPGMMKTVKVNANLYKEMLKTFKNFTQVSPLQLIGVNPPPYVYMQSIGVIELVLGTTLIVGGAASRKIACXXXXXXXXXTAASQFRLDDYMAMIVPSGYFALLSWVFISIEKLERQSKGKTKFE 556
            MSTKLGTRISSVVMGLLFIIPGMMKTVKVNANLYKEMLKTFKNFTQVSPLQLIGVNPPPYVYMQSIGVIELVLGTTLIVGGAASRKIACLGLMLLMLLTAASQFRLDDYMAMIVPSGYFALLSWVFISIEKLERQSKGKTKFE
Sbjct:    1 MSTKLGTRISSVVMGLLFIIPGMMKTVKVNANLYKEMLKTFKNFTQVSPLQLIGVNPPPYVYMQSIGVIELVLGTTLIVGGAASRKIACLGLMLLMLLTAASQFRLDDYMAMIVPSGYFALLSWVFISIEKLERQSKGKTKFE 143
The following BLAST results are available for this feature:
BLAST of SJCHGC05364 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 SJCHGC05364 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 SJCHGC05364 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 SJCHGC05364 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 SJCHGC05364 protein vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
drd1c2.303e-838.57D(1C) dopamine receptor [Source:Xenbase;Acc:XB-GEN... [more]
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BLAST of SJCHGC05364 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 SJCHGC05364 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 SJCHGC05364 protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A2H1C2P97.242e-4757.14Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
A0A4E0RY849.348e-4757.14Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
A0A4S2L8S11.350e-4656.74Uncharacterized protein OS=Opisthorchis felineus O... [more]
A0A094ZR862.261e-4660.74Uncharacterized protein (Fragment) OS=Schistosoma ... [more]
A0A430Q3I72.261e-4660.74Uncharacterized protein OS=Schistosoma bovis OX=61... [more]
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BLAST of SJCHGC05364 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 SJCHGC05364 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 SJCHGC05364 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 SJCHGC05364 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 SJCHGC05364 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 SJCHGC05364 protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000032293.13.585e-93100.00SMESG000032293.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017354 ID=SMED30017354|Name=SJCHGC05364 protein|organism=Schmidtea mediterranea sexual|type=transcript|length=673bp
CCGATCTATTTGTTTAACTTTATAAATTAGAAATACACATTATTTTACAA
ATTTGAATATTATATTTTATAATTTTTACTTATATTTTACAATTAAAAGA
AAATTTAAAATTTTAATACTCAAAACAATGTCTACGAAATTAGGTACTAG
GATATCTTCAGTTGTTATGGGTTTATTATTTATCATACCTGGTATGATGA
AAACAGTAAAAGTGAATGCTAACTTGTATAAAGAAATGTTAAAAACTTTC
AAAAATTTTACTCAAGTTTCACCCCTTCAACTTATTGGTGTAAATCCTCC
TCCATATGTTTATATGCAAAGTATCGGTGTCATTGAACTGGTTTTAGGCA
CTACCCTTATTGTCGGTGGTGCGGCATCGCGAAAAATTGCCTGTCTCGGT
TTGATGTTGCTAATGCTATTAACTGCAGCCAGTCAGTTTCGGCTTGATGA
CTATATGGCGATGATTGTACCATCAGGATATTTCGCTTTATTGAGTTGGG
TATTTATCAGTATCGAAAAGCTGGAAAGACAAAGTAAAGGCAAAACCAAA
TTTGAATAATGCCTATTATAATCAATGTTTTCTCTATTTTATTTGTCTTA
TAAATCTTTAGCATTTGATCTCACCTTAAAGTTAAGTTATGAAAATTGTA
CAATTTAATATATTTCACATTCG
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protein sequence of SMED30017354-orf-1

>SMED30017354-orf-1 ID=SMED30017354-orf-1|Name=SMED30017354-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=144bp
MSTKLGTRISSVVMGLLFIIPGMMKTVKVNANLYKEMLKTFKNFTQVSPL
QLIGVNPPPYVYMQSIGVIELVLGTTLIVGGAASRKIACLGLMLLMLLTA
ASQFRLDDYMAMIVPSGYFALLSWVFISIEKLERQSKGKTKFE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000142posterior region of the whole animal
PLANA:0000418head
PLANA:0002056medial muscle cell
Vocabulary: INTERPRO
TermDefinition
IPR040399TM35A/B
IPR032808DoxX
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR032808DoxX familyPFAMPF13564DoxX_2coord: 9..122
e-value: 1.6E-9
score: 37.8
IPR040399Transmembrane protein 35A/BPANTHERPTHR13163SPINAL CORD EXPRESSION PROTEIN 4coord: 8..127
NoneNo IPR availableTMHMMTMhelixcoord: 60..82
NoneNo IPR availableTMHMMTMhelixcoord: 5..24
NoneNo IPR availableTMHMMTMhelixcoord: 109..128
NoneNo IPR availableTMHMMTMhelixcoord: 87..104