SMED30018626

Overview
NameSMED30018626
Smed IDSMED30018626
Length (bp)151
Neoblast Clusters

Zeng et. al., 2018




 



 

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




Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
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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




SMED30018626

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30018626SMESG000018264.1 dd_Smed_v4_41104_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30018626SMESG000018264.1 dd_Smed_v4_41104_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30018626SMESG000018264.1 dd_Smed_v4_41104_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
Alignments
SMED30018626 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004559:35230..36682 +708
Homology
BLAST of SMED30018626 vs. Ensembl Human
Match: ABHD12 (abhydrolase domain containing 12 [Source:HGNC Symbol;Acc:HGNC:15868])

HSP 1 Score: 43.1282 bits (100), Expect = 2.292e-6
Identity = 17/34 (50.00%), Postives = 23/34 (67.65%), Query Frame = 3
Query:    3 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 104
            Y HGN G+RG  +RV+ Y +L   G+HV+  DYR
Sbjct:  173 YLHGNAGTRGGDHRVELYKVLSSLGYHVVTFDYR 206          
BLAST of SMED30018626 vs. Ensembl Human
Match: ABHD12 (abhydrolase domain containing 12 [Source:HGNC Symbol;Acc:HGNC:15868])

HSP 1 Score: 42.743 bits (99), Expect = 3.819e-6
Identity = 17/34 (50.00%), Postives = 23/34 (67.65%), Query Frame = 3
Query:    3 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 104
            Y HGN G+RG  +RV+ Y +L   G+HV+  DYR
Sbjct:  173 YLHGNAGTRGGDHRVELYKVLSSLGYHVVTFDYR 206          
BLAST of SMED30018626 vs. Ensembl Human
Match: ABHD12 (abhydrolase domain containing 12 [Source:HGNC Symbol;Acc:HGNC:15868])

HSP 1 Score: 41.9726 bits (97), Expect = 5.251e-6
Identity = 17/34 (50.00%), Postives = 23/34 (67.65%), Query Frame = 3
Query:    3 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 104
            Y HGN G+RG  +RV+ Y +L   G+HV+  DYR
Sbjct:  128 YLHGNAGTRGGDHRVELYKVLSSLGYHVVTFDYR 161          
BLAST of SMED30018626 vs. Ensembl Mouse
Match: Abhd12 (abhydrolase domain containing 12 [Source:MGI Symbol;Acc:MGI:1923442])

HSP 1 Score: 43.8986 bits (102), Expect = 9.711e-7
Identity = 17/34 (50.00%), Postives = 23/34 (67.65%), Query Frame = 3
Query:    3 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 104
            Y HGN G+RG  +RV+ Y +L   G+HV+  DYR
Sbjct:  173 YLHGNAGTRGGDHRVELYKVLSSLGYHVVTFDYR 206          
BLAST of SMED30018626 vs. TrEMBL
Match: S4RKY2 (Hydrolase_4 domain-containing protein OS=Petromyzon marinus OX=7757 PE=4 SV=1)

HSP 1 Score: 50.447 bits (119), Expect = 8.937e-6
Identity = 19/34 (55.88%), Postives = 27/34 (79.41%), Query Frame = 3
Query:    3 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 104
            YFHGN G+RG ++RV+ Y +L  +GFHV+ +DYR
Sbjct:  105 YFHGNAGTRGGHHRVELYKVLSASGFHVVTLDYR 138          
BLAST of SMED30018626 vs. Ensembl Cavefish
Match: abhd12 (abhydrolase domain containing 12 [Source:NCBI gene;Acc:767657])

HSP 1 Score: 41.9726 bits (97), Expect = 3.542e-6
Identity = 17/34 (50.00%), Postives = 22/34 (64.71%), Query Frame = 3
Query:    3 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 104
            Y HGN G+RG  +RV  Y +L   G+HV+  DYR
Sbjct:  244 YLHGNAGTRGGDHRVQLYKVLSSLGYHVVTFDYR 277          
BLAST of SMED30018626 vs. Ensembl Sea Lamprey
Match: ENSPMAT00000005892.1 (pep scaffold:Pmarinus_7.0:GL476342:292888:300705:-1 gene:ENSPMAG00000005303.1 transcript:ENSPMAT00000005892.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 50.447 bits (119), Expect = 6.867e-10
Identity = 19/34 (55.88%), Postives = 27/34 (79.41%), Query Frame = 3
Query:    3 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 104
            YFHGN G+RG ++RV+ Y +L  +GFHV+ +DYR
Sbjct:  105 YFHGNAGTRGGHHRVELYKVLSASGFHVVTLDYR 138          
BLAST of SMED30018626 vs. Ensembl Medaka
Match: ENSORLT00000035678.1 (abhydrolase domain containing 12B [Source:NCBI gene;Acc:101159055])

HSP 1 Score: 42.743 bits (99), Expect = 2.098e-6
Identity = 18/34 (52.94%), Postives = 23/34 (67.65%), Query Frame = 3
Query:    3 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 104
            Y HGN G+R   +RV+   LL   GFHVL++DYR
Sbjct:  101 YLHGNVGTRALRHRVELVTLLSAAGFHVLSLDYR 134          
BLAST of SMED30018626 vs. Ensembl Medaka
Match: si:ch211-117n7.7 (monoacylglycerol lipase ABHD12 [Source:NCBI gene;Acc:101159289])

HSP 1 Score: 42.3578 bits (98), Expect = 2.712e-6
Identity = 19/34 (55.88%), Postives = 22/34 (64.71%), Query Frame = 3
Query:    3 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 104
            YFHGN G+R A +RV    LL   G+HVL  DYR
Sbjct:  119 YFHGNTGTRAAVHRVGVAKLLSALGYHVLVPDYR 152          
BLAST of SMED30018626 vs. Ensembl Medaka
Match: si:ch211-117n7.7 (monoacylglycerol lipase ABHD12 [Source:NCBI gene;Acc:101159289])

HSP 1 Score: 42.3578 bits (98), Expect = 2.769e-6
Identity = 19/34 (55.88%), Postives = 22/34 (64.71%), Query Frame = 3
Query:    3 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 104
            YFHGN G+R A +RV    LL   G+HVL  DYR
Sbjct:  135 YFHGNTGTRAAVHRVGVAKLLSALGYHVLVPDYR 168          
BLAST of SMED30018626 vs. Ensembl Medaka
Match: abhd12 (abhydrolase domain containing 12 [Source:NCBI gene;Acc:101170699])

HSP 1 Score: 41.9726 bits (97), Expect = 3.244e-6
Identity = 17/34 (50.00%), Postives = 22/34 (64.71%), Query Frame = 3
Query:    3 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 104
            Y HGN G+RG  +RV  Y +L   G+HV+  DYR
Sbjct:  150 YLHGNAGTRGGDHRVQLYKVLSSLGYHVVTFDYR 183          
BLAST of SMED30018626 vs. Planmine SMEST
Match: SMESG000018264.1 (SMESG000018264.1)

HSP 1 Score: 74.3294 bits (181), Expect = 7.552e-18
Identity = 34/34 (100.00%), Postives = 34/34 (100.00%), Query Frame = 3
Query:    3 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 104
            YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR
Sbjct:  146 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 179          
BLAST of SMED30018626 vs. Planmine SMEST
Match: SMESG000018264.1 (SMESG000018264.1)

HSP 1 Score: 73.559 bits (179), Expect = 8.586e-18
Identity = 34/34 (100.00%), Postives = 34/34 (100.00%), Query Frame = 3
Query:    3 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 104
            YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR
Sbjct:   78 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 111          
BLAST of SMED30018626 vs. Planmine SMEST
Match: SMESG000018264.1 (SMESG000018264.1)

HSP 1 Score: 73.559 bits (179), Expect = 9.406e-18
Identity = 34/34 (100.00%), Postives = 34/34 (100.00%), Query Frame = 3
Query:    3 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 104
            YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR
Sbjct:  103 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 136          
BLAST of SMED30018626 vs. Planmine SMEST
Match: SMESG000015331.1 (SMESG000015331.1)

HSP 1 Score: 48.521 bits (114), Expect = 1.318e-8
Identity = 18/34 (52.94%), Postives = 26/34 (76.47%), Query Frame = 3
Query:    3 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 104
            Y HGN   RG+ +R+  YH+LR++GFH+L +DYR
Sbjct:   71 YLHGNSMHRGSNHRLLLYHVLRESGFHILTIDYR 104          
BLAST of SMED30018626 vs. Planmine SMEST
Match: SMESG000015331.1 (SMESG000015331.1)

HSP 1 Score: 47.7506 bits (112), Expect = 2.231e-8
Identity = 18/34 (52.94%), Postives = 26/34 (76.47%), Query Frame = 3
Query:    3 YFHGNRGSRGAYYRVDFYHLLRKNGFHVLAVDYR 104
            Y HGN   RG+ +R+  YH+LR++GFH+L +DYR
Sbjct:   39 YLHGNSMHRGSNHRLLLYHVLRESGFHILTIDYR 72          
The following BLAST results are available for this feature:
BLAST of SMED30018626 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 3
Match NameE-valueIdentityDescription
ABHD122.292e-650.00abhydrolase domain containing 12 [Source:HGNC Symb... [more]
ABHD123.819e-650.00abhydrolase domain containing 12 [Source:HGNC Symb... [more]
ABHD125.251e-650.00abhydrolase domain containing 12 [Source:HGNC Symb... [more]
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BLAST of SMED30018626 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 SMED30018626 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 SMED30018626 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 SMED30018626 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 SMED30018626 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 1
Match NameE-valueIdentityDescription
Abhd129.711e-750.00abhydrolase domain containing 12 [Source:MGI Symbo... [more]
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BLAST of SMED30018626 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 SMED30018626 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
S4RKY28.937e-655.88Hydrolase_4 domain-containing protein OS=Petromyzo... [more]
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BLAST of SMED30018626 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
abhd123.542e-650.00abhydrolase domain containing 12 [Source:NCBI gene... [more]
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BLAST of SMED30018626 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ENSPMAT00000005892.16.867e-1055.88pep scaffold:Pmarinus_7.0:GL476342:292888:300705:-... [more]
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BLAST of SMED30018626 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 SMED30018626 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 SMED30018626 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 4
Match NameE-valueIdentityDescription
ENSORLT00000035678.12.098e-652.94abhydrolase domain containing 12B [Source:NCBI gen... [more]
si:ch211-117n7.72.712e-655.88monoacylglycerol lipase ABHD12 [Source:NCBI gene;A... [more]
si:ch211-117n7.72.769e-655.88monoacylglycerol lipase ABHD12 [Source:NCBI gene;A... [more]
abhd123.244e-650.00abhydrolase domain containing 12 [Source:NCBI gene... [more]
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BLAST of SMED30018626 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000018264.17.552e-18100.00SMESG000018264.1[more]
SMESG000018264.18.586e-18100.00SMESG000018264.1[more]
SMESG000018264.19.406e-18100.00SMESG000018264.1[more]
SMESG000015331.11.318e-852.94SMESG000015331.1[more]
SMESG000015331.12.231e-852.94SMESG000015331.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018626 ID=SMED30018626|Name=SMED30018626|organism=Schmidtea mediterranea sexual|type=transcript|length=151bp
TGTATTTTCATGGAAATAGAGGTAGCAGAGGAGCATACTATCGTGTTGAT
TTTTATCATCTTTTGAGAAAAAACGGATTCCATGTTTTAGCGGTTGATTA
TAGAGACTCTAGAGTGGGTTCAGCATTTTATCATACATACTACATTATCA
C
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR029058AB_hydrolase