SJCHGC02540 protein

Overview
NameSJCHGC02540 protein
Smed IDSMED30011326
Length (bp)925
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 SJCHGC02540 protein (SMED30011326) t-SNE clustered cells

Violin plots show distribution of expression levels for SJCHGC02540 protein (SMED30011326) in cells (dots) of each of the 12 neoblast clusters.

 

back to top


 

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 SJCHGC02540 protein (SMED30011326) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SJCHGC02540 protein (SMED30011326) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top


 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020




SMED30011326

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30011326h1SMcG0006361 Contig49303uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011326h1SMcG0006361 Contig49303newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
protonephridiaSMED30011326h1SMcG0006361 dd_Smed_v4_16852_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30011326h1SMcG0006361 dd_Smed_v4_16852_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
BLAST of SJCHGC02540 protein vs. TrEMBL
Match: A0A075AI53 (Uncharacterized protein OS=Opisthorchis viverrini OX=6198 GN=T265_02707 PE=4 SV=1)

HSP 1 Score: 98.2117 bits (243), Expect = 1.173e-19
Identity = 72/254 (28.35%), Postives = 120/254 (47.24%), Query Frame = 3
Query:  111 TFVFPTFMIMVYVAGS-------WATNFRQETIN--GQKVEFSWWQNQTSIKTAADAVKFCHLKQAHLPYAENLKYFFKTLR------------------VGLFKRKDIRFYLYDVLESTLDYPNIESGEKMCIVVKKSLSNEIIIENTNASSSCSVKVDTVVCSTSPD--------------------------RLFDPNP-----VVRKSENTDNFLCLSRNLF----------IIVTGIITSLVAVQFIVI 668
            +FVF    +++Y+A S        A   R E I+  G++V FSW +++  I +  +A   C L+   LP A  ++YF+KTLR                  V L+    +RFYL D+LE+T+DYPN ESGE+MC++V+K  ++ + +   ++  SCS  V+ +VC  + D                          +L  P P     + +K+E  DN +C    +F          I +T I T L+A+++ ++
Sbjct:    8 SFVFFALSVLIYLASSEEPLRVERAEGSRVERISQTGRRVNFSWVRSE-QIGSWLEAEHQCSLRSGRLPQANEMRYFYKTLRSDDAQLPPLDPTDTHRTPVTLY---GVRFYLGDILEATMDYPNTESGERMCLIVEKRPNSPVQLVEVSSVRSCSTPVNLLVCRFALDGEEVYPIGASQSDENQLSNPCNIYSEQLSGPLPQWIVELKKKAELQDNHMCFRHEIFYATASLGCLVIFITTISTVLLAIRYYLL 257          
BLAST of SJCHGC02540 protein vs. TrEMBL
Match: A0A4S2LFC2 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_007597 PE=4 SV=1)

HSP 1 Score: 97.8265 bits (242), Expect = 1.781e-19
Identity = 73/254 (28.74%), Postives = 119/254 (46.85%), Query Frame = 3
Query:  111 TFVFPTFMIMVYVAGS-------WATNFRQETIN--GQKVEFSWWQNQTSIKTAADAVKFCHLKQAHLPYAENLKYFFKTLR------------------VGLFKRKDIRFYLYDVLESTLDYPNIESGEKMCIVVKKSLSNEIIIENTNASSSCSVKVDTVVCSTSPD--------------------------RLFDPNP-----VVRKSENTDNFLCLSRNLF----------IIVTGIITSLVAVQFIVI 668
            +FVF T + ++Y+A S        A   R E I+  G++V FSW +++  I +  +A   C L+   LP A  ++YF+KTLR                  V L+    +RFYL D+LE+T+DYPN ESGE+MC++V+K  +  + +    +  SCS  V+ +VC  + D                          +L  P P     + +K+E  DN +C    +F          I +T I T L+A+++ ++
Sbjct:    8 SFVFLTLIALIYLASSEEPLRVERAEGSRVERISQTGRRVNFSWVRSE-QIGSWLEAEHQCSLRSGRLPQANEMRYFYKTLRSDDAQLPPLDSADTHSTPVTLY---GVRFYLGDILEATMDYPNTESGERMCLIVEKRPNAPVQLVEVTSVRSCSTPVNLLVCRFALDGEEVYPIGASQSDGNQLSNPCNIYSEQLSGPLPQWIVELKKKAEFQDNHICFRYEIFYATASLGCLVIFITTISTVLLAIRYYLL 257          
BLAST of SJCHGC02540 protein vs. TrEMBL
Match: A0A183REG4 (Uncharacterized protein OS=Schistosoma rodhaini OX=6188 PE=4 SV=1)

HSP 1 Score: 95.1301 bits (235), Expect = 9.730e-19
Identity = 65/238 (27.31%), Postives = 116/238 (48.74%), Query Frame = 3
Query:  102 IIMTFVFPTFMIMVYVAGSWATNFRQETI--NGQKVEFSWWQNQTSIKTAADAVKFCHLKQAHLPYAENLKYFFKTLRV--------GLFKRK---DIRFYLYDVLESTLDYPNIESGEKMCIVVKKSLSNEIIIENTNASSSCSVKVDTVVCST---------------------SPDRLFDPNP-----VVRKSENTDNFLCLSRNLFIIVTGIITSLVAVQFIVIGVVCWKRKTC 698
            +I+ + F   +    +       +R E +  +G++V F+W++N T I++   A   C    + LP   +++YF+KTL+           F+ K    + FYL DVLE+T+DYPNIESGE+MC+ ++K   +++ +  ++A  SC    + +VC +                     + D+ F P P     + +K+E   + +CL + LF I T + + L+ V FI   ++   R  C
Sbjct:    9 LIVIYSFHLLLTESLLRTEQPEGYRVERVGLHGRRVNFTWYRNVT-IRSWVQAADKCSYLNSLLPKVNDMRYFYKTLQSDDIISSISNTFENKTHSGVVFYLGDVLEATMDYPNIESGERMCLTIEKVPGSQLHLAESSAVKSCLTHANLLVCKSEVDSSSVTNYDDDSYPHMCNFADDKWFGPLPKWILDLKQKAEFRQDHICLKKLLFYI-TAVCSGLIIVVFITSTLILAVRYKC 244          
BLAST of SJCHGC02540 protein vs. TrEMBL
Match: G7YC58 (Uncharacterized protein OS=Clonorchis sinensis OX=79923 GN=CLF_104702 PE=4 SV=1)

HSP 1 Score: 95.5153 bits (236), Expect = 1.098e-18
Identity = 71/251 (28.29%), Postives = 118/251 (47.01%), Query Frame = 3
Query:  111 TFVFPTFMIMVYVAGS-------WATNFRQETIN--GQKVEFSWWQNQTSIKTAADAVKFCHLKQAHLPYAENLKYFFKTLR-----VGLFKRKD----------IRFYLYDVLESTLDYPNIESGEKMCIVVKKSLSNEIIIENTNASSSCSVKVDTVVCSTSPD--------------------------RLFDPNP-----VVRKSENTDNFLCLSRNLF----------IIVTGIITSLVAVQFIVI 668
            +FVF     ++Y+A S        A   R E I+  G++V FSW +++  I +  +A   C L+   LP A  ++YF+KTLR     +      D          +RFYL D+LE+T+DYPN ESGE+MC++V+K  ++ + +   ++  SCS  V+ +VC  + D                          +L  P P     + +K+E  DN +C    +F          I +T I T L+A+++ ++
Sbjct:    8 SFVFLALTALIYLASSEEPLRVERAEGSRVERISQTGRRVNFSWVRSE-QIGSWLEAEHQCSLRSGRLPQANEMRYFYKTLRSDDAQLPPLDSADTHRTPATLYGVRFYLGDILEATMDYPNTESGERMCLIVEKRPNSPVQLVEVSSVRSCSTPVNLLVCRFALDGDEVYPIGAGQSDGNQLSNPCNIYSEQLSGPLPQWIVELKKKAEFQDNHMCFRYEIFYATASLGCLVIFMTTISTVLLAIRYYLL 257          
BLAST of SJCHGC02540 protein vs. TrEMBL
Match: A0A183M416 (Uncharacterized protein OS=Schistosoma margrebowiei OX=48269 GN=SMRZ_LOCUS10791 PE=4 SV=1)

HSP 1 Score: 94.7449 bits (234), Expect = 1.601e-18
Identity = 59/208 (28.37%), Postives = 104/208 (50.00%), Query Frame = 3
Query:  186 INGQKVEFSWWQNQTSIKTAADAVKFCHLKQAHLPYAENLKYFFKTLRVGLF-----------KRKDIRFYLYDVLESTLDYPNIESGEKMCIVVKKSLSNEIIIENTNASSSCSVKVDTVVCST---------------------SPDRLFDPNP-----VVRKSENTDNFLCLSRNLFIIVTGIITSLVAVQFIVIGVVCWKRKTC 698
            ++G++V F+W++N T I++   A   C    + LP   +++YF+KTL+                   + FYL DVLE+T+DYPNIESGE+MC+ V+K   +++ +  ++A  SC    + +VC +                     + D+ F P P     + +K+E   + +CL++ LF I T + + L+ V F+   ++   R  C
Sbjct:   59 LHGRRVNFTWYRNVT-IRSWVQAADKCSFLNSLLPKVTDMRYFYKTLQSDDVISPISKTSENKTHSGVVFYLGDVLEATMDYPNIESGERMCLTVEKVPGSQLHLAESSAVKSCLTHANLLVCKSEVDSSSVTNYDDDSYPHMCNFADDKWFGPLPKWILDLKQKAEFRQDHICLTKLLFCI-TAVCSGLIVVLFLTSTIILAVRYKC 264          
BLAST of SJCHGC02540 protein vs. Planmine SMEST
Match: SMESG000056369.1 (SMESG000056369.1)

HSP 1 Score: 482.256 bits (1240), Expect = 3.261e-174
Identity = 248/249 (99.60%), Postives = 248/249 (99.60%), Query Frame = 3
Query:  138 MVYVAGSWATNFRQETINGQKVEFSWWQNQTSIKTAADAVKFCHLKQAHLPYAENLKYFFKTLRVGLFKRKDIRFYLYDVLESTLDYPNIESGEKMCIVVKKSLSNEIIIENTNASSSCSVKVDTVVCSTSPDRLFDPNPVVRKSENTDNFLCLSRNLFIIVTGIITSLVAVQFIVIGVVCWKRKTCXXXXXXXXXXXXXXYEDDSYIQLISPKQFKNYPSFNSVDRKSTLKSRKRGYDEPKIVCRHIF 884
            MVYVAGSWATNFRQETINGQKVEFSWWQNQTSIKTAADAVKFCHLKQAHLPYAENLKYFFKTLRVGLFKRKDIRFYLYDVLESTLDYPNIESGEKMCIVVKKSLSNEIIIENTNASSSCSVKVDTVVCSTSPDRLFDPNPVVRKSENTDNFLCLSRNLFIIVTGIITSLVAVQFIVIGVVCWKRKTCKSPKLIPKLSKLSKYEDDSYIQLISPKQFKNYPSFNSVDRKSTLKSRKRGYDEPKIVCRH F
Sbjct:    1 MVYVAGSWATNFRQETINGQKVEFSWWQNQTSIKTAADAVKFCHLKQAHLPYAENLKYFFKTLRVGLFKRKDIRFYLYDVLESTLDYPNIESGEKMCIVVKKSLSNEIIIENTNASSSCSVKVDTVVCSTSPDRLFDPNPVVRKSENTDNFLCLSRNLFIIVTGIITSLVAVQFIVIGVVCWKRKTCKSPKLIPKLSKLSKYEDDSYIQLISPKQFKNYPSFNSVDRKSTLKSRKRGYDEPKIVCRHNF 249          
The following BLAST results are available for this feature:
BLAST of SJCHGC02540 protein vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SJCHGC02540 protein vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SJCHGC02540 protein vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SJCHGC02540 protein vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SJCHGC02540 protein vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SJCHGC02540 protein vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SJCHGC02540 protein vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SJCHGC02540 protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A075AI531.173e-1928.35Uncharacterized protein OS=Opisthorchis viverrini ... [more]
A0A4S2LFC21.781e-1928.74Uncharacterized protein OS=Opisthorchis felineus O... [more]
A0A183REG49.730e-1927.31Uncharacterized protein OS=Schistosoma rodhaini OX... [more]
G7YC581.098e-1828.29Uncharacterized protein OS=Clonorchis sinensis OX=... [more]
A0A183M4161.601e-1828.37Uncharacterized protein OS=Schistosoma margrebowie... [more]
back to top
BLAST of SJCHGC02540 protein vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SJCHGC02540 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
back to top
BLAST of SJCHGC02540 protein vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SJCHGC02540 protein vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SJCHGC02540 protein vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SJCHGC02540 protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000056369.13.261e-17499.60SMESG000056369.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011326 ID=SMED30011326|Name=SJCHGC02540 protein|organism=Schmidtea mediterranea sexual|type=transcript|length=925bp
TGATGATTAATATTTCTGTCAGCATAAAATTAGCAAGTCTAATTGGAAAG
TTGACTGTAAATTCATTGACAAATATTCTAATTTCGACAATTGAACGCAT
AATAATAATGACTTTTGTCTTTCCAACTTTTATGATAATGGTTTATGTTG
CTGGTTCTTGGGCAACGAATTTTCGACAAGAAACCATCAATGGACAGAAA
GTTGAGTTTTCCTGGTGGCAAAACCAGACCTCCATTAAAACCGCTGCTGA
TGCAGTAAAATTCTGCCACTTGAAACAAGCGCATTTGCCATACGCGGAAA
ATTTGAAATATTTCTTTAAAACACTTCGAGTAGGGTTGTTTAAAAGAAAA
GACATCCGGTTTTATTTGTATGATGTTCTTGAGTCTACTCTCGATTATCC
AAACATAGAAAGTGGAGAGAAAATGTGCATTGTGGTTAAAAAATCTCTGT
CAAATGAAATAATTATTGAAAATACGAATGCCAGCTCGAGCTGTTCTGTG
AAGGTTGACACTGTTGTTTGCTCAACGAGTCCAGATAGGTTATTTGATCC
AAACCCCGTTGTTCGCAAGAGTGAAAATACCGATAATTTCCTCTGTTTAA
GTCGGAATCTGTTTATTATTGTAACAGGTATTATAACTAGCTTGGTGGCT
GTCCAATTTATTGTCATAGGGGTAGTTTGTTGGAAACGTAAAACTTGCAA
ATCACCCAAACTGATTCCGAAATTATCTAAACTATCAAAATATGAGGACG
ACAGTTATATACAGTTAATTTCACCCAAGCAATTCAAGAATTATCCTAGT
TTCAACTCAGTGGACCGTAAATCTACTTTAAAAAGCAGAAAGCGAGGATA
TGATGAACCTAAAATTGTATGCCGACATATATTTTGAATAATAAATTAGC
TTTGAAATATTTTGTTTAGATCGGA
back to top

protein sequence of SMED30011326-orf-1

>SMED30011326-orf-1 ID=SMED30011326-orf-1|Name=SMED30011326-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=295bp
MINISVSIKLASLIGKLTVNSLTNILISTIERIIIMTFVFPTFMIMVYVA
GSWATNFRQETINGQKVEFSWWQNQTSIKTAADAVKFCHLKQAHLPYAEN
LKYFFKTLRVGLFKRKDIRFYLYDVLESTLDYPNIESGEKMCIVVKKSLS
NEIIIENTNASSSCSVKVDTVVCSTSPDRLFDPNPVVRKSENTDNFLCLS
RNLFIIVTGIITSLVAVQFIVIGVVCWKRKTCKSPKLIPKLSKLSKYEDD
SYIQLISPKQFKNYPSFNSVDRKSTLKSRKRGYDEPKIVCRHIF*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
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
NoneNo IPR availableTMHMMTMhelixcoord: 33..55
NoneNo IPR availableTMHMMTMhelixcoord: 205..227