SJCHGC08494 protein

Overview
NameSJCHGC08494 protein
Smed IDSMED30022057
Length (bp)605
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 SJCHGC08494 protein (SMED30022057) t-SNE clustered cells

Violin plots show distribution of expression levels for SJCHGC08494 protein (SMED30022057) 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 SJCHGC08494 protein (SMED30022057) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SJCHGC08494 protein (SMED30022057) 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




SMED30022057

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30022057SMESG000027083.1 dd_Smed_v4_2196_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30022057SMESG000027083.1 dd_Smed_v4_2196_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30022057SMESG000027083.1 dd_Smed_v4_2196_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30022057SMESG000027083.1 dd_Smed_v4_2196_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30022057SMESG000027083.1 dd_Smed_v4_2196_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30022057SMESG000027083.1 dd_Smed_v4_2196_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30022057SMESG000027083.1 dd_Smed_v4_2196_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022057SMESG000027083.1 Contig50735newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022057SMESG000027083.1 Contig50735uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022057SMESG000027094.1 SMESG000027083.1 Contig55900newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022057SMESG000027094.1 SMESG000027083.1 Contig55900uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Category 4 cellSMED30022057SMESG000027083.1 dd_Smed_v4_2196_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30022057SMESG000027083.1 dd_Smed_v4_2196_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 SJCHGC08494 protein vs. Ensembl Fly
Match: CG6583 (gene:FBgn0032420 transcript:FBtr0080358)

HSP 1 Score: 74.3294 bits (181), Expect = 8.335e-17
Identity = 44/120 (36.67%), Postives = 67/120 (55.83%), Query Frame = 2
Query:   62 FLFSCNLIFYTEAIRCYQCDSKED----GSCPAYRFFDTRLNALVDCNSVQSHNPGVFCLKIYRESTG---WN-RWIKITRQCAARTSGGIAWGCVYTFEDRGMYKEVCYCQDRDGCNSA 397
            FL     I  + AIRCYQC S +D     SC AY+ F+   +  ++CNS +SH PG FC+K+ ++      W+ RW ++ R+CA+ +  G+   C +   + G+Y E CYC   D CN +
Sbjct:    9 FLLLTLAICGSWAIRCYQCSSDQDRKGHDSCGAYKRFNRTEHISIECNSDESHMPGSFCMKVVQQGPRGFIWDGRWRQVIRRCASVSDTGVVGVCNWGVYENGVYWEECYCSS-DSCNGS 127          
BLAST of SJCHGC08494 protein vs. Ensembl Fly
Match: crok (gene:FBgn0032421 transcript:FBtr0080342)

HSP 1 Score: 55.8398 bits (133), Expect = 7.137e-10
Identity = 50/151 (33.11%), Postives = 66/151 (43.71%), Query Frame = 2
Query:   47 EKIWLF-LFSCNLIFYTEAIRCYQCDSKEDGSCPAYRFFDTRLNALVDCNSVQS--HNPGV---FCLKIYRESTGWNRWIKITRQCAARTSGGIAWG---CVYTFEDRGMYKEVCYCQDRDGCNSALGIKGKSLIGVVMSIALSVIFKDFI 472
            EK  LF +  C L+   +AI+C+ C S  D  C     FD    A+ DC       H  GV    C KI ++  G  R+    R CA     GI      C+       ++ E C C  +DGCNSA GI    L+GV+    LSVI    +
Sbjct:    5 EKYILFAIVLCCLLQLGQAIKCWDCRSDNDPKCGDP--FDNSTLAITDCQQAPELEHLKGVRPTMCRKIRQKVHGEWRYF---RSCAYMGEPGIEGDERFCLMRTGSYNIFMEFCTCNSKDGCNSA-GIHRLGLMGVLTGTLLSVIVAHLL 149          
BLAST of SJCHGC08494 protein vs. TrEMBL
Match: A0A4S2KL33 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_010897 PE=4 SV=1)

HSP 1 Score: 176.792 bits (447), Expect = 2.733e-53
Identity = 86/139 (61.87%), Postives = 103/139 (74.10%), Query Frame = 2
Query:   50 KIWLFLFSCNLI-FYTEAIRCYQCDSKEDGSCPAYRFFDTRLNALVDCNSVQSHNPGVFCLKIYRESTGWNRWIKITRQCAARTSGGIAWGCVYTFEDRGMYKEVCYCQDRDGCNSALGIKGKSLIGVVMSIALSVIFK 463
             I+  L  CN I   + AIRCYQCDS ED SCPA RFFDTRLNA+VDC S  SH+PG FC+KIY+ESTGWN WIKITR+C ART  G+AWGC Y FE +G+YKEVCYCQDRDGCNS+  +  + L   ++++ L  I K
Sbjct:    2 SIFPVLLICNFIVLVSNAIRCYQCDSNEDDSCPARRFFDTRLNAMVDCGSFLSHSPGTFCVKIYQESTGWNSWIKITRRCGARTDYGLAWGCRYWFEAQGIYKEVCYCQDRDGCNSSSRLSFRKLNYTMVALCLIWILK 140          
BLAST of SJCHGC08494 protein vs. TrEMBL
Match: A0A075AHH9 (Uncharacterized protein OS=Opisthorchis viverrini OX=6198 GN=T265_13293 PE=4 SV=1)

HSP 1 Score: 174.866 bits (442), Expect = 1.375e-52
Identity = 85/142 (59.86%), Postives = 105/142 (73.94%), Query Frame = 2
Query:   50 KIWLFLFSCNLI-FYTEAIRCYQCDSKEDGSCPAYRFFDTRLNALVDCNSVQSHNPGVFCLKIYRESTGWNRWIKITRQCAARTSGGIAWGCVYTFEDRGMYKEVCYCQDRDGCNSALGIKGKSLIGVVMSIALSVIFKDFI 472
             I+  +  CN I   + AIRCYQCDS ED SCPA RFFDTRLNA+VDC S  SH+PG FC+KIY+ESTGWN WIKITR+C ART  G+AWGC Y FE +G+YKEVCYCQD+DGCNS+  +  ++L   ++++ L  I K  I
Sbjct:    2 SIFPVVLICNFIVLVSNAIRCYQCDSNEDDSCPARRFFDTRLNAMVDCGSFLSHSPGTFCVKIYQESTGWNSWIKITRRCGARTDYGLAWGCRYWFEAQGVYKEVCYCQDQDGCNSSSRLSFRTLNYTLVALCLIWILKPRI 143          
BLAST of SJCHGC08494 protein vs. TrEMBL
Match: Q5C1I6 (SJCHGC08494 protein (Fragment) OS=Schistosoma japonicum OX=6182 PE=2 SV=2)

HSP 1 Score: 172.17 bits (435), Expect = 2.175e-51
Identity = 81/138 (58.70%), Postives = 98/138 (71.01%), Query Frame = 2
Query:   53 IWLFLFSCNLIFYTE---AIRCYQCDSKEDGSCPAYRFFDTRLNALVDCNSVQSHNPGVFCLKIYRESTGWNRWIKITRQCAARTSGGIAWGCVYTFEDRGMYKEVCYCQDRDGCNSALGIKGKSLIGVVMSIALSVI 457
            ++LF     L+ Y     AIRCYQCDS ED SCPA RFFDTRLNA++DC S  SH+PG FC+KIY+ESTGWN WIK+TR C ART  G+AW C Y FE +G+YKEVCYCQDRDGCN A  +   +L+  +    L V+
Sbjct:    9 VYLFPVFILLLLYESEILAIRCYQCDSNEDDSCPARRFFDTRLNAMIDCGSFLSHSPGTFCVKIYQESTGWNSWIKVTRTCGARTDYGLAWSCRYWFEAQGVYKEVCYCQDRDGCNKATKLMNNTLVSRLTLFFLQVL 146          
BLAST of SJCHGC08494 protein vs. TrEMBL
Match: A0A094ZWX6 (Uncharacterized protein (Fragment) OS=Schistosoma haematobium OX=6185 GN=MS3_06012 PE=4 SV=1)

HSP 1 Score: 166.392 bits (420), Expect = 3.998e-49
Identity = 80/139 (57.55%), Postives = 99/139 (71.22%), Query Frame = 2
Query:   53 IWLFLFSCNLIFYTE---AIRCYQCDSKEDGSCPAYRFFDTRLNALVDCNSVQSHNPGVFCLKIYRESTGWNRWIKITRQCAARTSGGIAWGCVYTFEDRGMYKEVCYCQDRDGCNSALGIKGKSLIGVVMSIALSVIF 460
            + LF     L+FY     AIRCYQCDS ED SCPA RFFDTRLNA++DC S  SH+PG FC+KIY+ESTGW+ WIK+TR C ART  G+AW C Y FE +G+YKEVCYCQDRDGCN A  +   + + ++ ++ L  I 
Sbjct:   11 VLLFPVYILLLFYENEVLAIRCYQCDSNEDDSCPAGRFFDTRLNAMIDCGSFLSHSPGTFCVKIYQESTGWHSWIKVTRTCGARTDYGLAWSCRYWFEAQGVYKEVCYCQDRDGCNKATTLFMNNKVILLFTLFLCFIL 149          
BLAST of SJCHGC08494 protein vs. TrEMBL
Match: A0A4E0RHN7 (Crooked OS=Fasciola hepatica OX=6192 GN=D915_008235 PE=4 SV=1)

HSP 1 Score: 165.622 bits (418), Expect = 4.816e-49
Identity = 77/116 (66.38%), Postives = 91/116 (78.45%), Query Frame = 2
Query:   50 KIWLFLFSCNLIFYTEAIRCYQCDSKEDGSCPAYRFFDTRLNALVDCNSVQSHNPGVFCLKIYRESTGWNRWIKITRQCAARTSGGIAWGCVYTFEDRGMYKEVCYCQDRDGCNSA 397
             +W+  F   L+  T AIRCYQCDS ED SCPA R+FD R+NA++DC S  SH+PG FC+KIY+ESTGWNRWIKITR+C ART  G+AW C Y FE +G+YKEVCYCQDRDGCN A
Sbjct:    3 PVWIIYF---LLPATAAIRCYQCDSNEDDSCPARRYFDRRMNAMIDCGSFLSHSPGTFCVKIYQESTGWNRWIKITRRCGARTDYGLAWSCRYWFEAQGVYKEVCYCQDRDGCNGA 115          
BLAST of SJCHGC08494 protein vs. Planmine SMEST
Match: SMESG000027083.1 (SMESG000027083.1)

HSP 1 Score: 298.13 bits (762), Expect = 9.356e-105
Identity = 143/144 (99.31%), Postives = 143/144 (99.31%), Query Frame = 2
Query:   41 MQEKIWLFLFSCNLIFYTEAIRCYQCDSKEDGSCPAYRFFDTRLNALVDCNSVQSHNPGVFCLKIYRESTGWNRWIKITRQCAARTSGGIAWGCVYTFEDRGMYKEVCYCQDRDGCNSALGIKGKSLIGVVMSIALSVIFKDFI 472
            MQEKIWLFLFSCNLIFYTEAIRCYQCDSKEDGSCPAYRFFDTRLNALVDCNSVQSHNPGVFCLKIYRESTGWNRWIKITRQCAARTSGGIAWGCVYTFEDRGMYKEVCYCQDRDGCNSALGIKGKSLIGVVMSIALSVI KDFI
Sbjct:    1 MQEKIWLFLFSCNLIFYTEAIRCYQCDSKEDGSCPAYRFFDTRLNALVDCNSVQSHNPGVFCLKIYRESTGWNRWIKITRQCAARTSGGIAWGCVYTFEDRGMYKEVCYCQDRDGCNSALGIKGKSLIGVVMSIALSVILKDFI 144          
The following BLAST results are available for this feature:
BLAST of SJCHGC08494 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 SJCHGC08494 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 SJCHGC08494 protein vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 2
Match NameE-valueIdentityDescription
CG65838.335e-1736.67gene:FBgn0032420 transcript:FBtr0080358[more]
crok7.137e-1033.11gene:FBgn0032421 transcript:FBtr0080342[more]
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BLAST of SJCHGC08494 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 SJCHGC08494 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 SJCHGC08494 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 SJCHGC08494 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 SJCHGC08494 protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4S2KL332.733e-5361.87Uncharacterized protein OS=Opisthorchis felineus O... [more]
A0A075AHH91.375e-5259.86Uncharacterized protein OS=Opisthorchis viverrini ... [more]
Q5C1I62.175e-5158.70SJCHGC08494 protein (Fragment) OS=Schistosoma japo... [more]
A0A094ZWX63.998e-4957.55Uncharacterized protein (Fragment) OS=Schistosoma ... [more]
A0A4E0RHN74.816e-4966.38Crooked OS=Fasciola hepatica OX=6192 GN=D915_00823... [more]
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BLAST of SJCHGC08494 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 SJCHGC08494 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 SJCHGC08494 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 SJCHGC08494 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 SJCHGC08494 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 SJCHGC08494 protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000027083.19.356e-10599.31SMESG000027083.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022057 ID=SMED30022057|Name=SJCHGC08494 protein|organism=Schmidtea mediterranea sexual|type=transcript|length=605bp
AAATAATCCAAAATGTTTATGAACATTATTTAAAATCTAAATGCAGGAAA
AAATTTGGCTATTTCTTTTTAGTTGTAATTTGATATTTTACACCGAAGCC
ATTAGATGTTATCAATGTGATAGTAAAGAAGATGGTTCTTGCCCTGCTTA
TCGATTTTTTGATACACGTTTAAATGCTCTTGTTGATTGTAATAGTGTCC
AAAGTCACAATCCAGGAGTGTTTTGTTTGAAAATTTATCGAGAGAGTACC
GGATGGAATAGATGGATTAAAATTACTCGCCAATGTGCAGCAAGAACATC
TGGAGGTATTGCGTGGGGTTGTGTATATACTTTTGAGGATAGAGGTATGT
ACAAGGAGGTTTGTTATTGCCAGGACAGAGACGGGTGTAATTCAGCACTT
GGTATTAAAGGGAAATCTCTAATAGGCGTTGTGATGAGCATTGCTTTGTC
AGTTATTTTTAAAGACTTCATTTGAATTTATTGCAGTTTATATTAATTTA
TTTTTATTGTACCGTTTAGAATCATTTACAGTGATATATAAACTTACCTA
CATATCATGATAATTTTGTACATAAAATAATAAATATTTTTGTTTTGAAA
AAAAA
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protein sequence of SMED30022057-orf-1

>SMED30022057-orf-1 ID=SMED30022057-orf-1|Name=SMED30022057-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=145bp
MQEKIWLFLFSCNLIFYTEAIRCYQCDSKEDGSCPAYRFFDTRLNALVDC
NSVQSHNPGVFCLKIYRESTGWNRWIKITRQCAARTSGGIAWGCVYTFED
RGMYKEVCYCQDRDGCNSALGIKGKSLIGVVMSIALSVIFKDFI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000018Category 4 cell
PLANA:0000020protonephridia
PLANA:0000026gut
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR031424QVR
Vocabulary: biological process
TermDefinition
GO:1903818positive regulation of voltage-gated potassium channel activity
GO:0030431sleep
GO:0032222regulation of synaptic transmission, cholinergic
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
IPR031424Protein quiverPFAMPF17064QVRcoord: 19..119
e-value: 6.5E-6
score: 26.3
NoneNo IPR availablePANTHERPTHR33562FAMILY NOT NAMEDcoord: 14..138
NoneNo IPR availablePANTHERPTHR33562:SF1coord: 14..138
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..20
score: 0.712