hypothetical protein

Overview
Namehypothetical protein (AFJ24787.1)
Smed IDSMED30021241
Length (bp)1275
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 hypothetical protein (SMED30021241) t-SNE clustered cells

Violin plots show distribution of expression levels for hypothetical protein (SMED30021241) 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 hypothetical protein (SMED30021241) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for hypothetical protein (SMED30021241) 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




SMED30021241

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30021241h1SMcG0006957 SmedASXL_010805SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30021241h1SMcG0006957 SmedASXL_010805SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30021241h1SMcG0006957 dd_Smed_v6_12310_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
neoblastSMED30021241h1SMcG0006957 SMED_04692_V2_1GPL14150PMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30021241h1SMcG0006957 SMED_04692_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
BLAST of hypothetical protein vs. TrEMBL
Match: I1ZID3 (Uncharacterized protein OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 732.635 bits (1890), Expect = 0.000e+0
Identity = 388/389 (99.74%), Postives = 389/389 (100.00%), Query Frame = 1
Query:  103 MDENLKNLIQELTSSQLVINWLELCGFETLEDIEYLNENVIADMESYIGSVCSSMSFDEREKYIHVNLXXXXXXXXXXTPCLKSRLLNVADAISRQFNKSSQINRSGPFLSKFVQKFNKDYLADNGYRLCSRDLYDSVSNSIRRSFQNIKYRFDLEFDLYQSDKDEKHETKNGFFACSINQHNEICGEFIKFYIDQDSLSIDIEPILVHIELHLDRKSESSSIKTKSRILSSVEIDLNKSSRSIDLADAKLSNNFIHNEIIKFAEQKFIDCHLVQDIDFNVYEIIDDDSSLTNRGCFLCYICLKTKSNESKIKXXXXXXXXXXXXNIVAHLRIHFQSVAPFATAAVSRKRTSTKTPKHSEKRLVLVNSATKNSASSLKLEALNDKENFI 1269
            MDENLKNLIQELTSSQLVINWLELCGFETLEDIEYLNENVIADMESYIGS+CSSMSFDEREKYIHVNLFKKFPQQFKFTPCLKSRLLNVADAISRQFNKSSQINRSGPFLSKFVQKFNKDYLADNGYRLCSRDLYDSVSNSIRRSFQNIKYRFDLEFDLYQSDKDEKHETKNGFFACSINQHNEICGEFIKFYIDQDSLSIDIEPILVHIELHLDRKSESSSIKTKSRILSSVEIDLNKSSRSIDLADAKLSNNFIHNEIIKFAEQKFIDCHLVQDIDFNVYEIIDDDSSLTNRGCFLCYICLKTKSNESKIKFFFTSTRSVVFTNIVAHLRIHFQSVAPFATAAVSRKRTSTKTPKHSEKRLVLVNSATKNSASSLKLEALNDKENFI
Sbjct:    1 MDENLKNLIQELTSSQLVINWLELCGFETLEDIEYLNENVIADMESYIGSICSSMSFDEREKYIHVNLFKKFPQQFKFTPCLKSRLLNVADAISRQFNKSSQINRSGPFLSKFVQKFNKDYLADNGYRLCSRDLYDSVSNSIRRSFQNIKYRFDLEFDLYQSDKDEKHETKNGFFACSINQHNEICGEFIKFYIDQDSLSIDIEPILVHIELHLDRKSESSSIKTKSRILSSVEIDLNKSSRSIDLADAKLSNNFIHNEIIKFAEQKFIDCHLVQDIDFNVYEIIDDDSSLTNRGCFLCYICLKTKSNESKIKFFFTSTRSVVFTNIVAHLRIHFQSVAPFATAAVSRKRTSTKTPKHSEKRLVLVNSATKNSASSLKLEALNDKENFI 389          
BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000044230.1 (SMESG000044230.1)

HSP 1 Score: 732.635 bits (1890), Expect = 0.000e+0
Identity = 388/389 (99.74%), Postives = 389/389 (100.00%), Query Frame = 1
Query:  103 MDENLKNLIQELTSSQLVINWLELCGFETLEDIEYLNENVIADMESYIGSVCSSMSFDEREKYIHVNLXXXXXXXXXXTPCLKSRLLNVADAISRQFNKSSQINRSGPFLSKFVQKFNKDYLADNGYRLCSRDLYDSVSNSIRRSFQNIKYRFDLEFDLYQSDKDEKHETKNGFFACSINQHNEICGEFIKFYIDQDSLSIDIEPILVHIELHLDRKSESSSIKTKSRILSSVEIDLNKSSRSIDLADAKLSNNFIHNEIIKFAEQKFIDCHLVQDIDFNVYEIIDDDSSLTNRGCFLCYICLKTKSNESKIKXXXXXXXXXXXXNIVAHLRIHFQSVAPFATAAVSRKRTSTKTPKHSEKRLVLVNSATKNSASSLKLEALNDKENFI 1269
            MDENLKNLIQELTSSQLVINWLELCGFETLEDIEYLNENVIADMESYIGS+CSSMSFDEREKYIHVNLFKKFPQQFKFTPCLKSRLLNVADAISRQFNKSSQINRSGPFLSKFVQKFNKDYLADNGYRLCSRDLYDSVSNSIRRSFQNIKYRFDLEFDLYQSDKDEKHETKNGFFACSINQHNEICGEFIKFYIDQDSLSIDIEPILVHIELHLDRKSESSSIKTKSRILSSVEIDLNKSSRSIDLADAKLSNNFIHNEIIKFAEQKFIDCHLVQDIDFNVYEIIDDDSSLTNRGCFLCYICLKTKSNESKIKFFFTSTRSVVFTNIVAHLRIHFQSVAPFATAAVSRKRTSTKTPKHSEKRLVLVNSATKNSASSLKLEALNDKENFI
Sbjct:    1 MDENLKNLIQELTSSQLVINWLELCGFETLEDIEYLNENVIADMESYIGSICSSMSFDEREKYIHVNLFKKFPQQFKFTPCLKSRLLNVADAISRQFNKSSQINRSGPFLSKFVQKFNKDYLADNGYRLCSRDLYDSVSNSIRRSFQNIKYRFDLEFDLYQSDKDEKHETKNGFFACSINQHNEICGEFIKFYIDQDSLSIDIEPILVHIELHLDRKSESSSIKTKSRILSSVEIDLNKSSRSIDLADAKLSNNFIHNEIIKFAEQKFIDCHLVQDIDFNVYEIIDDDSSLTNRGCFLCYICLKTKSNESKIKFFFTSTRSVVFTNIVAHLRIHFQSVAPFATAAVSRKRTSTKTPKHSEKRLVLVNSATKNSASSLKLEALNDKENFI 389          
BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000071865.1 (SMESG000071865.1)

HSP 1 Score: 52.7582 bits (125), Expect = 1.507e-7
Identity = 57/197 (28.93%), Postives = 90/197 (45.69%), Query Frame = 1
Query:  607 ETKNGFFACSI-NQHNE---ICG-EFIKFYIDQDSLSIDIEPILVHIELHLDRKSESSSIKTKSRILSSVEIDLNKSSRSIDLADAKLSNNFIHNEIIKFAEQKFIDCHLVQDIDFNVYEIIDDDSSLTNRGCFLCYICLKTKSNESKIKXXXXXXXXXXXXNIVAHLRIHFQSVAPFATAAVSRKRTSTKTPKHSE 1182
            +T  G + C I  +HN+   IC   F K+       SI    ILVH++ H      +   + + + L     + +K  + I+  D  L +   H  +   A +KF  C L  + DF++Y+    DS     G ++C +C +T  N ++ KF FT   S+ FTNI  HL  HF       + A SR+    +  KHS+
Sbjct:   64 DTTLGIYQCKICPKHNDDYRICKFRFTKYG------SIQFMNILVHLKKHFSLAESAPLRRGRRKTLFKTTKNTSKPEKVIEFTDLNLCDEKYHQYVSDMALEKFDSCRLKMNKDFSLYK----DSEDPLLGYYVCKLCAETAQNRNQCKFRFTKYHSLNFTNIQFHLLSHF-------SMADSRRTKRGRKGKHSK 243          
BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000072330.1 (SMESG000072330.1)

HSP 1 Score: 51.6026 bits (122), Expect = 3.587e-7
Identity = 33/97 (34.02%), Postives = 50/97 (51.55%), Query Frame = 1
Query:  103 MDENLKNLIQELTSSQLVINWLELCGFETLEDIEYLNENVIADMESYIGSVCSSMSFDEREKYIHVNLXXXXXXXXXXTPCLKSRLLNVADAISRQF 393
            M+ ++ N I  L     V NWLELC FE ++D    N N +  +E YI   CS M  + R+ Y++ +     P +F  +P L++RLL   D +   F
Sbjct:    1 MNIDIPNAIAYLCEFPKVANWLELCKFELMDDFLNFNNNTVDKIEKYIQIQCSLMPINVRQLYLNES-DLLSPTKFLISPGLRNRLLKAVDILVSYF 96          
BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000047524.1 (SMESG000047524.1)

HSP 1 Score: 50.447 bits (119), Expect = 9.447e-7
Identity = 36/105 (34.29%), Postives = 62/105 (59.05%), Query Frame = 1
Query:  802 EIDLNKSSRSIDLADAKLSNNFIHNEIIKFAEQKFIDCHLVQDIDFNVYEIIDDDSSLTNRGCFLCYICLKTKSNESKIKXXXXXXXXXXXXNIVAHLRIHFQSV 1116
            E+D+N+S    ++          +N+I+K A + FI+C L+ D+DF++    +D + L   G + C++C   K   +KIKF F+   SV++TNI +HL+ H+Q V
Sbjct:  159 ELDMNRSRHLQNMEK-------YYNDIVKNAAKNFIECSLIPDVDFHLSIPENDSTDLI--GYYHCHLCTDRKKAMTKIKFRFSKYNSVIYTNINSHLKTHYQYV 254          
BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000047524.1 (SMESG000047524.1)

HSP 1 Score: 50.447 bits (119), Expect = 1.145e-6
Identity = 36/105 (34.29%), Postives = 62/105 (59.05%), Query Frame = 1
Query:  802 EIDLNKSSRSIDLADAKLSNNFIHNEIIKFAEQKFIDCHLVQDIDFNVYEIIDDDSSLTNRGCFLCYICLKTKSNESKIKXXXXXXXXXXXXNIVAHLRIHFQSV 1116
            E+D+N+S    ++          +N+I+K A + FI+C L+ D+DF++    +D + L   G + C++C   K   +KIKF F+   SV++TNI +HL+ H+Q V
Sbjct:  171 ELDMNRSRHLQNMEK-------YYNDIVKNAAKNFIECSLIPDVDFHLSIPENDSTDLI--GYYHCHLCTDRKKAMTKIKFRFSKYNSVIYTNINSHLKTHYQYV 266          
The following BLAST results are available for this feature:
BLAST of hypothetical 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 hypothetical 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 hypothetical 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 hypothetical 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 hypothetical 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 hypothetical 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 hypothetical 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 hypothetical protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZID30.000e+099.74Uncharacterized protein OS=Schmidtea mediterranea ... [more]
back to top
BLAST of hypothetical 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 hypothetical 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 hypothetical 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 hypothetical 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 hypothetical 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 hypothetical protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000044230.10.000e+099.74SMESG000044230.1[more]
SMESG000071865.11.507e-728.93SMESG000071865.1[more]
SMESG000072330.13.587e-734.02SMESG000072330.1[more]
SMESG000047524.19.447e-734.29SMESG000047524.1[more]
SMESG000047524.11.145e-634.29SMESG000047524.1[more]
back to top
Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30021241
GenBankAFJ24787.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021241 ID=SMED30021241|Name=hypothetical protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1275bp
ATAACGTTGTTTATATAACATCCTTTTTGATAAGGTTTACCATTTAAATT
TTTATAACCGTTATTTGAATTATTATTTTCTACTTTTTTGGATTTTTTAA
GGATGGATGAGAATTTAAAAAATCTTATCCAAGAATTGACTTCATCTCAA
TTGGTAATAAACTGGCTGGAATTATGCGGATTTGAAACACTGGAAGACAT
TGAATATTTAAATGAAAACGTCATCGCCGACATGGAGAGCTATATCGGAT
CTGTTTGTAGCTCCATGTCTTTCGATGAAAGAGAAAAATATATCCATGTA
AATTTATTTAAAAAATTTCCACAACAATTCAAATTTACTCCATGCTTAAA
AAGTCGTTTACTGAATGTCGCTGACGCTATTTCGAGACAATTCAACAAAA
GTTCCCAGATTAATCGCAGCGGTCCATTTTTATCGAAATTTGTTCAGAAG
TTCAATAAGGATTATTTAGCGGATAACGGCTATCGGTTATGTTCCCGTGA
TTTGTATGATAGCGTTTCGAATAGTATTAGAAGATCCTTTCAAAATATCA
AGTATCGATTCGACCTTGAATTTGATTTATATCAGTCAGATAAAGATGAA
AAACATGAAACGAAAAACGGTTTTTTTGCATGTTCCATCAATCAACACAA
TGAAATTTGTGGGGAATTCATCAAGTTCTATATCGATCAAGACAGCTTGT
CGATCGATATTGAACCGATCCTCGTGCACATTGAGCTACACTTAGATCGG
AAATCAGAGTCGTCGTCGATCAAGACAAAATCTCGAATTTTGTCTTCCGT
TGAAATCGATCTAAATAAATCTTCACGCTCTATTGATCTCGCCGATGCAA
AATTGTCCAACAATTTTATTCACAACGAAATAATAAAATTCGCAGAGCAA
AAATTTATCGATTGTCATTTGGTGCAGGATATCGATTTCAATGTGTATGA
AATTATCGATGACGACTCTTCCTTGACAAATCGTGGCTGTTTTCTCTGCT
ATATTTGCTTGAAAACGAAATCGAATGAATCGAAAATCAAATTCTTTTTC
ACTAGCACTCGCTCGGTTGTGTTCACGAATATCGTTGCCCATTTACGGAT
TCATTTCCAGTCGGTTGCGCCGTTTGCAACCGCTGCGGTTTCCAGGAAAC
GGACTTCCACTAAAACTCCAAAACATTCTGAAAAACGACTCGTACTTGTT
AATTCAGCAACGAAAAATAGCGCGTCTAGTTTGAAATTAGAGGCTTTAAA
TGATAAAGAAAATTTTATATGAACC
back to top

protein sequence of SMED30021241-orf-1

>SMED30021241-orf-1 ID=SMED30021241-orf-1|Name=SMED30021241-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=390bp
MDENLKNLIQELTSSQLVINWLELCGFETLEDIEYLNENVIADMESYIGS
VCSSMSFDEREKYIHVNLFKKFPQQFKFTPCLKSRLLNVADAISRQFNKS
SQINRSGPFLSKFVQKFNKDYLADNGYRLCSRDLYDSVSNSIRRSFQNIK
YRFDLEFDLYQSDKDEKHETKNGFFACSINQHNEICGEFIKFYIDQDSLS
IDIEPILVHIELHLDRKSESSSIKTKSRILSSVEIDLNKSSRSIDLADAK
LSNNFIHNEIIKFAEQKFIDCHLVQDIDFNVYEIIDDDSSLTNRGCFLCY
ICLKTKSNESKIKFFFTSTRSVVFTNIVAHLRIHFQSVAPFATAAVSRKR
TSTKTPKHSEKRLVLVNSATKNSASSLKLEALNDKENFI*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000420parapharyngeal region
PLANA:0000429neoblast
PLANA:0002109X1 cell
PLANA:0002111X2 cell