SJCHGC07163 protein

Overview
NameSJCHGC07163 protein
Smed IDSMED30022337
Length (bp)1702
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 SJCHGC07163 protein (SMED30022337) t-SNE clustered cells

Violin plots show distribution of expression levels for SJCHGC07163 protein (SMED30022337) 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 SJCHGC07163 protein (SMED30022337) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SJCHGC07163 protein (SMED30022337) 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




SMED30022337

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30022337SMESG000034423.1 SmedASXL_013860SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30022337SMESG000034423.1 dd_Smed_v4_8079_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
neuronSMED30022337SMESG000034423.1 dd_Smed_v4_8079_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
epidermal cellSMED30022337SMESG000034423.1 dd_Smed_v4_8079_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
headSMED30022337SMESG000034423.1 dd_Smed_v6_8079_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
headSMED30022337SMESG000034423.1 OX_Smed_1.0.16318ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
reproductive organSMED30022337SMESG000034423.1 Contig35480newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30022337SMESG000034423.1 Contig35480uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
epidermisSMED30022337SMESG000034423.1 dd_Smed_v4_8079_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 SJCHGC07163 protein vs. TrEMBL
Match: A0A267GPP4 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig011189g1 PE=4 SV=1)

HSP 1 Score: 191.43 bits (485), Expect = 2.979e-54
Identity = 93/161 (57.76%), Postives = 115/161 (71.43%), Query Frame = 3
Query:  138 VSHYPMQFMPPPLYEIGSMWMPKLNHIDVYNSSGVDYCQGGWRKWNSA----GHWDMHAMSSTAVEPDWYHRKREYIRGADLKFMDWHYDQYAKPTQFQTYG-QVFPKNNRPVFREINNVTRKPESIKGNIEPVRYGIYHNPVYEEPVRVNRFPPVHDPKH 605
             S Y  QFM PPL+EIGSMWMP+  H++  +SSGVDYCQ GWRKWNS      HWDMHA S+ AVEPDWY R+ EY R AD KF++W YD+Y+KP+Q + +G +VFP   +P    +N+VTRKP +IKG+I PVRYG+ H   YEEP R    PP+HDP H
Sbjct:   14 ASRYKQQFMAPPLHEIGSMWMPRNGHVNTQHSSGVDYCQAGWRKWNSCQQWNTHWDMHARSAAAVEPDWYRRRLEYTRQADQKFLNWQYDRYSKPSQRRAFGEEVFPL--KPENTGVNDVTRKPGAIKGDIPPVRYGLCHPDHYEEPNRAQTLPPIHDPYH 172          
BLAST of SJCHGC07163 protein vs. TrEMBL
Match: A0A267E8T6 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig026143g1 PE=4 SV=1)

HSP 1 Score: 190.274 bits (482), Expect = 8.013e-54
Identity = 92/161 (57.14%), Postives = 115/161 (71.43%), Query Frame = 3
Query:  138 VSHYPMQFMPPPLYEIGSMWMPKLNHIDVYNSSGVDYCQGGWRKWNSA----GHWDMHAMSSTAVEPDWYHRKREYIRGADLKFMDWHYDQYAKPTQFQTYG-QVFPKNNRPVFREINNVTRKPESIKGNIEPVRYGIYHNPVYEEPVRVNRFPPVHDPKH 605
             S Y  QFM PPL+EIGSMWMP+  H++  +SSGVDYCQ GWRKWNS      HWDMHA S+ AVEPDWY R+ +Y R AD KF++W YD+Y+KP+Q + +G +VFP   +P    +N+VTRKP +IKG+I PVRYG+ H   YEEP R    PP+HDP H
Sbjct:   14 ASRYKQQFMAPPLHEIGSMWMPRNGHVNTQHSSGVDYCQAGWRKWNSCQQWNTHWDMHARSAAAVEPDWYRRRLDYTRQADQKFLNWQYDRYSKPSQRRAFGEEVFPL--KPENTGVNDVTRKPGAIKGDIPPVRYGLCHPDHYEEPNRAQTLPPIHDPYH 172          
BLAST of SJCHGC07163 protein vs. TrEMBL
Match: A0A4V3SGY5 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_001093 PE=4 SV=1)

HSP 1 Score: 113.235 bits (282), Expect = 2.980e-25
Identity = 59/149 (39.60%), Postives = 83/149 (55.70%), Query Frame = 3
Query:  171 PLYEIGSMWMPKLNHIDVYNSSGVDYCQGGWRKWNSAGHWDMHAMSSTAVEPDWYHRKREYIRGADLKFMDWHYDQYAKPTQFQTYGQVFPKNNRPV----FREINNVTRKPESIKGNIEPVRYGIYHNPVYEEPVRVNRFPPVHDPKH 605
            P++E+   W P+LN ++ Y+ +G++  + GW KWNSAGH D+ A S+TA EPDWY R+   IR +D     W YD++ KPT   T G        P      R I+  T KP  ++   +P+ YG      YE P+R   FPP+ DPKH
Sbjct:   30 PVHEMPHEWQPRLNRVNPYHWTGMEILKDGWTKWNSAGHPDIIAESATATEPDWYTRRVRDIRESDKHCEQWAYDRWGKPTSLSTLGLGHIAAQEPYRRYPHRGIDRTTVKPGILEHGEKPIHYGTTSGFNYEVPIRARTFPPIADPKH 178          
BLAST of SJCHGC07163 protein vs. TrEMBL
Match: A0A504YND2 (Uncharacterized protein OS=Fasciola gigantica OX=46835 GN=FGIG_02820 PE=4 SV=1)

HSP 1 Score: 104.76 bits (260), Expect = 2.997e-22
Identity = 61/162 (37.65%), Postives = 86/162 (53.09%), Query Frame = 3
Query:  132 GYVSHYPMQFMPPPLYEIGSMWMPKLNHIDVYNSSGVDYCQGGWRKWNSAGHWDMHAMSSTAVEPDWYHRKREYIRGADLKFMD-WHYDQYAKPTQFQTYG--QVFPKNNR--PVFREINNVTRKPESIKGNIEPVRYGIYHNPVYEEPVRVNRFPPVHDPK 602
            G+    P +++ P L+E+   W P LN I   +  G +   GGW KWNSAGH DM   SS +V PDWY R+ + +R AD KF + + YD+++KPT     G  + FP  +   P  R     T KP SI      + YGI  + +Y  P R +  P +HDP+
Sbjct:   17 GHTRWAPTRYLKP-LHEMPHDWAPVLNKISPSHWKGSELLMGGWTKWNSAGHADMVTQSSASVLPDWYSRRLDDVRNADTKFCEHFPYDRWSKPTSIVPLGDERTFPDADHELPFARGRQKCTGKPASIPKTKNDIFYGIGSHTLYGSPTRASSLPTLHDPR 177          
BLAST of SJCHGC07163 protein vs. TrEMBL
Match: A0A183T1X4 (Uncharacterized protein OS=Schistocephalus solidus OX=70667 GN=SSLN_LOCUS10472 PE=4 SV=1)

HSP 1 Score: 102.064 bits (253), Expect = 6.014e-22
Identity = 57/125 (45.60%), Postives = 71/125 (56.80%), Query Frame = 3
Query:  252 QGGWRKWNSAGHWDMHAMSSTAVEPDWYHRKREYIRGADLKFMD-WHYDQYAKPTQFQTYGQVFP------KNNRPVFREINNVTRKPESIKGNIEPVRYGIYHNPVYEEPVRVNRFPPVHDPKH 605
            Q  W KWNS GH D+HA SS A  PDWY R+   IR ADLKF   W YD++ KP  F   G V P      K+ R   R+    TRKP+ +  +I  VRYG  H P YE+P+R   FPP+ D ++
Sbjct:    3 QKCWVKWNSQGHLDLHAKSSAANYPDWYARRIADIRAADLKFTQKWAYDRWGKPNSFNALGFVGPEAAAETKDTRFFMRDCG--TRKPQKVAADIPTVRYGQLHPPHYEQPMRSELFPPLVDAEN 125          
BLAST of SJCHGC07163 protein vs. Planmine SMEST
Match: SMESG000034423.1 (SMESG000034423.1)

HSP 1 Score: 354.755 bits (909), Expect = 3.513e-121
Identity = 168/171 (98.25%), Postives = 169/171 (98.83%), Query Frame = 3
Query:   96 MTSNSTRMNYHRGYVSHYPMQFMPPPLYEIGSMWMPKLNHIDVYNSSGVDYCQGGWRKWNSAGHWDMHAMSSTAVEPDWYHRKREYIRGADLKFMDWHYDQYAKPTQFQTYGQVFPKNNRPVFREINNVTRKPESIKGNIEPVRYGIYHNPVYEEPVRVNRFPPVHDPKHK 608
            MTSNSTRMNYHRGYVSHYPMQFMPPPLYEIGSMW PKLNHIDVYNSSGVDYCQGGWRKWNSAGHWDMHAMSSTAVEPDWYHRKREYIRGADLKFMDWHYDQYAKPTQFQTYGQVFPKNNRPVFREINNVTRKPESIKGNIEPVRYGIYHNPVYEEP RVNRFPP+HDPKHK
Sbjct:    1 MTSNSTRMNYHRGYVSHYPMQFMPPPLYEIGSMWTPKLNHIDVYNSSGVDYCQGGWRKWNSAGHWDMHAMSSTAVEPDWYHRKREYIRGADLKFMDWHYDQYAKPTQFQTYGQVFPKNNRPVFREINNVTRKPESIKGNIEPVRYGIYHNPVYEEPFRVNRFPPLHDPKHK 171          
The following BLAST results are available for this feature:
BLAST of SJCHGC07163 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 SJCHGC07163 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 SJCHGC07163 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 SJCHGC07163 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 SJCHGC07163 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 SJCHGC07163 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 SJCHGC07163 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 SJCHGC07163 protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A267GPP42.979e-5457.76Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A267E8T68.013e-5457.14Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A4V3SGY52.980e-2539.60Uncharacterized protein OS=Opisthorchis felineus O... [more]
A0A504YND22.997e-2237.65Uncharacterized protein OS=Fasciola gigantica OX=4... [more]
A0A183T1X46.014e-2245.60Uncharacterized protein OS=Schistocephalus solidus... [more]
back to top
BLAST of SJCHGC07163 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 SJCHGC07163 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 SJCHGC07163 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 SJCHGC07163 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 SJCHGC07163 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 SJCHGC07163 protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000034423.13.513e-12198.25SMESG000034423.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022337 ID=SMED30022337|Name=SJCHGC07163 protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1702bp
TTTAAATAATATTTTAAAACAGTCAATTATAAATAAAATTTTGAAAGCTA
AATTTAAAAGTTTTAATTTACAAAAGCTCATCAGAATTAAAAATTATGAC
TTCAAATTCAACAAGAATGAATTACCACCGTGGCTACGTGTCTCACTATC
CGATGCAATTTATGCCCCCTCCACTCTATGAGATCGGCAGCATGTGGATG
CCGAAATTGAACCACATCGACGTCTACAATTCAAGCGGAGTGGATTATTG
TCAGGGTGGTTGGCGAAAATGGAACAGTGCAGGTCACTGGGATATGCACG
CCATGAGTAGTACCGCTGTTGAACCCGACTGGTACCATCGGAAAAGGGAA
TATATTAGAGGAGCCGATCTGAAATTTATGGATTGGCATTATGATCAGTA
TGCAAAACCGACCCAGTTTCAAACATACGGTCAAGTGTTTCCTAAAAATA
ATCGTCCAGTGTTTAGGGAAATCAACAATGTAACTCGCAAGCCAGAATCG
ATAAAGGGAAACATAGAACCGGTAAGATACGGAATCTACCACAACCCGGT
TTATGAGGAACCGGTTCGAGTGAACCGTTTTCCTCCTGTTCATGACCCAA
AACACAAATAAATATACAATAAATTTTATTTTCTGCAAGAATTAACTATT
GTAAGGCTGTTATGAAATACACTTACTGTCCTTAATTTGTAATTTGCTGC
GGCAATGACATGCATACACCTAAGGTACAATAGGAAGGACTTTGTCGAGG
ATAGCTAAATAATGAAATTGTTGGGGTTGATATAAAATGAATGGAATAAA
ATGAGAGCATGGAAAATCAAAAATCAACAAAAATATCAAAAATAATTAAA
GTACAAAAATTAATTAAAAATTTATAAAATTTGAAAATTAATATTGATCG
GGGAAACGGCTATGGTTGAATGCCAAATCATAAGACGAGTTCAGTAATAA
TAATTGTATTTTAATTAAATTAACGTGCCAGACAAGGTGATTTCCCATTG
GGACATCTGACTTCAGGTTTGTAAATCGATATCTGATAGAAAAGTGCAAT
TCGTGGGACAAATTGTAAATTTTGTGATCGAAATTAATAAAAGTATTGTT
GGGTTTTCGTTATTTGATATAATAAAAGAAACACGAGGAGTCAGATATTT
GACCGATTTGAAAATAATAACCCAACATTTATGTCATTGCAAAATAAAAA
GCAATCAGAGGTAAAAGCTAGAAAAAGTTCTTTTAATATATGATAAACTT
TTTATAATTAAATAAGTTTAATGCAAATAAATTTATTTATGAATTTATGT
TAAAAACAATTTTTAAAAATAATCTTCTCTGCTTTATCTTTTTGTGGGGT
TAATCAATTTGTCAAATTGGCTGTTCATATGAGTCGCAAAGTCCAATTTC
TCACTAGGAATTTTAAATTAAAATTTTAAAATAAAAATTATAGAATAATT
TTGCATATTTTAAAATTTAGTGTCAAAATATGAGGAGTATATTTATATAT
TTTATACATTTAAGCAAATCAAACGAATTAATATTATTATAAATTAATAC
ATTTTGATTATTAGTAATATTTACTTTAAAAGTTTGGAGTTTTGCGCATT
TTTAACCATTTGCGGTTCGTAAAAAAAGAAGTTACACACCAGGCCACAAT
TGTTTTAATGATTTTTTGTATATATAATTTTCTTGAACTAAATTGGGTTT
TT
back to top

protein sequence of SMED30022337-orf-1

>SMED30022337-orf-1 ID=SMED30022337-orf-1|Name=SMED30022337-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=172bp
MTSNSTRMNYHRGYVSHYPMQFMPPPLYEIGSMWMPKLNHIDVYNSSGVD
YCQGGWRKWNSAGHWDMHAMSSTAVEPDWYHRKREYIRGADLKFMDWHYD
QYAKPTQFQTYGQVFPKNNRPVFREINNVTRKPESIKGNIEPVRYGIYHN
PVYEEPVRVNRFPPVHDPKHK*
back to top
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
PLANA:0002089reproductive organ