SMED30030884

Overview
NameSMED30030884
Smed IDSMED30030884
Length (bp)511
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




SMED30030884

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
testis primordiumSMED30030884 Contig1497_WUSTLGPL10652PMID:20844018
Wang et al., 2010
whole organism juvenile cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30030884 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003416:26188..26742 -2517
v31.054620:652..1176 +1860
v31.003359:9487..10011 -1851
v31.000061:1737..2277 -1814
Homology
BLAST of SMED30030884 vs. Planmine SMEST
Match: SMESG000077847.1 (SMESG000077847.1)

HSP 1 Score: 59.6918 bits (143), Expect = 2.396e-21
Identity = 29/61 (47.54%), Postives = 38/61 (62.30%), Query Frame = -1
Query:  293 ISEMAVAQGRQIFWDYGYLVSTMETATWPTRL-HTIGGIDFLGIAIKRELGRNPAKEAHQR 472
            I   + A+ RQ+ WD GYL+ST   ++WP R  +    I+   IAIKRE G NPA+EA QR
Sbjct:  689 IPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHNPAREARQR 749          

HSP 2 Score: 59.6918 bits (143), Expect = 2.396e-21
Identity = 27/62 (43.55%), Postives = 41/62 (66.13%), Query Frame = -2
Query:   88 ARMELNKINCEIVAGRISGSDGYTPEYDVSFEPSDPIPRTLTAPTQVMIPDELIHPSMLERL 273
            AR  L ++N +I +G I  +DG+ PEY VSFE  DP    +TAPT+++IP+ L+  ++  RL
Sbjct:  771 ARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPENLVQSTLRNRL 832          
BLAST of SMED30030884 vs. Planmine SMEST
Match: SMESG000014849.1 (SMESG000014849.1)

HSP 1 Score: 59.6918 bits (143), Expect = 2.551e-21
Identity = 25/58 (43.10%), Postives = 40/58 (68.97%), Query Frame = -2
Query:  100 ARMELNKINCEIVAGRISGSDGYTPEYDVSFEPSDPIPRTLTAPTQVMIPDELIHPSM 273
            AR  L ++N +I +G I  +DG+ PEY VSFE  DP    +TAPT+++IP++L+  ++
Sbjct:  975 ARQRLAQVNRDIASGVIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVQSTL 1032          

HSP 2 Score: 59.3066 bits (142), Expect = 2.551e-21
Identity = 29/61 (47.54%), Postives = 38/61 (62.30%), Query Frame = -1
Query:  293 ISEMAVAQGRQIFWDYGYLVSTMETATWPTRL-HTIGGIDFLGIAIKRELGRNPAKEAHQR 472
            I   + A+ RQ+ WD GYL+ST   ++WP R  +    I+   IAIKRE G NPA+EA QR
Sbjct:  893 IPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYRAEEIELPSIAIKREPGHNPAREARQR 953          
BLAST of SMED30030884 vs. Planmine SMEST
Match: SMESG000031842.1 (SMESG000031842.1)

HSP 1 Score: 59.6918 bits (143), Expect = 2.728e-21
Identity = 29/61 (47.54%), Postives = 38/61 (62.30%), Query Frame = -1
Query:  293 ISEMAVAQGRQIFWDYGYLVSTMETATWPTRL-HTIGGIDFLGIAIKRELGRNPAKEAHQR 472
            I   + A+ RQ+ WD GYL+ST   ++WP R  +    I+   IAIKRE G NPA+EA QR
Sbjct:  784 IPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHNPAREARQR 844          

HSP 2 Score: 59.3066 bits (142), Expect = 2.728e-21
Identity = 27/62 (43.55%), Postives = 42/62 (67.74%), Query Frame = -2
Query:   88 ARMELNKINCEIVAGRISGSDGYTPEYDVSFEPSDPIPRTLTAPTQVMIPDELIHPSMLERL 273
            AR  L ++N +I +G I  +DG+ PEY VSFE  DP    +TAPT+++IP++L+  ++  RL
Sbjct:  866 ARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRL 927          
BLAST of SMED30030884 vs. Planmine SMEST
Match: SMESG000031842.1 (SMESG000031842.1)

HSP 1 Score: 59.6918 bits (143), Expect = 2.846e-21
Identity = 29/61 (47.54%), Postives = 38/61 (62.30%), Query Frame = -1
Query:  293 ISEMAVAQGRQIFWDYGYLVSTMETATWPTRL-HTIGGIDFLGIAIKRELGRNPAKEAHQR 472
            I   + A+ RQ+ WD GYL+ST   ++WP R  +    I+   IAIKRE G NPA+EA QR
Sbjct:  710 IPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHNPAREARQR 770          

HSP 2 Score: 59.3066 bits (142), Expect = 2.846e-21
Identity = 27/62 (43.55%), Postives = 42/62 (67.74%), Query Frame = -2
Query:   88 ARMELNKINCEIVAGRISGSDGYTPEYDVSFEPSDPIPRTLTAPTQVMIPDELIHPSMLERL 273
            AR  L ++N +I +G I  +DG+ PEY VSFE  DP    +TAPT+++IP++L+  ++  RL
Sbjct:  792 ARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRL 853          
BLAST of SMED30030884 vs. Planmine SMEST
Match: SMESG000042475.1 (SMESG000042475.1)

HSP 1 Score: 62.3882 bits (150), Expect = 2.986e-21
Identity = 30/61 (49.18%), Postives = 39/61 (63.93%), Query Frame = -1
Query:  293 ISEMAVAQGRQIFWDYGYLVSTMETATWPTRL-HTIGGIDFLGIAIKRELGRNPAKEAHQR 472
            I   + A+ RQ+ WD GYL+ST   ++WP R  +    I+   IAIKRE G NPA+EAHQR
Sbjct: 1341 IPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHNPAREAHQR 1401          

HSP 2 Score: 56.225 bits (134), Expect = 2.986e-21
Identity = 26/62 (41.94%), Postives = 41/62 (66.13%), Query Frame = -2
Query:   88 ARMELNKINCEIVAGRISGSDGYTPEYDVSFEPSDPIPRTLTAPTQVMIPDELIHPSMLERL 273
            AR  L ++N +I +G I  +DG+  EY VSFE  DP    +TAPT++++P++LI  ++  RL
Sbjct: 1423 ARQRLAQVNRDIASGAIPSTDGFPQEYGVSFELDDPRLMQMTAPTKLVLPEKLIQSTLRNRL 1484          
The following BLAST results are available for this feature:
BLAST of SMED30030884 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 SMED30030884 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 SMED30030884 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 SMED30030884 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 SMED30030884 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 SMED30030884 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 SMED30030884 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 SMED30030884 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030884 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 SMED30030884 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 SMED30030884 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 SMED30030884 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 SMED30030884 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 SMED30030884 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000077847.12.396e-2147.54SMESG000077847.1[more]
SMESG000014849.12.551e-2143.10SMESG000014849.1[more]
SMESG000031842.12.728e-2147.54SMESG000031842.1[more]
SMESG000031842.12.846e-2147.54SMESG000031842.1[more]
SMESG000042475.12.986e-2149.18SMESG000042475.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030884 ID=SMED30030884|Name=SMED30030884|organism=Schmidtea mediterranea sexual|type=transcript|length=511bp
TTTTTTCTCCAGTTATGATTTGGCAAAACGAGATCTTGCCCCACGGAAAT
CTCTACCATTCGGATTTCTTCGTTTTTGTACTAATTCTAGCCGTTCCAGC
ATGCTTGGGTGTATCAGTTCATCTGGAATCATCACCTGGGTTGGGGCGGT
TAAAGTCCTCGGAATAGGGTCACTGGGTTCAAATGAAACATCATATTCTG
GAGTATAGCCATCTGAACCTGAAATTCTACCGGCCACTATCTCACAGTTT
ATCTTATTCAGCTCCATTCGAGCGGAGTAATAAGGATTATACTCTTTGGT
GGGCTTCTTTGGCTGGGTTCCGTCCAAGCTCTCTTTTGATGGCGATGCCG
AGGAAATCAATGCCTCCGATCGTATGTAGTCGAGTTGGCCACGTGGCAGT
TTCCATTGTGGAGACGAGGTACCCATAGTCCCAAAAGATCTGGCGACCTT
GTGCTACCGCCATTTCGCTGATTCAAATTATTTGTCAACCCTGCGCCGGT
CTTCCTGAAGA
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protein sequence of SMED30030884-orf-1

>SMED30030884-orf-1 ID=SMED30030884-orf-1|Name=SMED30030884-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=138bp
MGTSSPQWKLPRGQLDYIRSEALISSASPSKESLDGTQPKKPTKEYNPYY
SARMELNKINCEIVAGRISGSDGYTPEYDVSFEPSDPIPRTLTAPTQVMI
PDELIHPSMLERLELVQKRRNPNGRDFRGARSRFAKS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003304testis primordium