SMED30006685

Overview
NameSMED30006685
Smed IDSMED30006685
Length (bp)745
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




SMED30006685

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
intestinal phagocyteSMED30006685SMESG000039858.1 Contig1341newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30006685 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.019982:1683..2465 -3557
Homology
BLAST of SMED30006685 vs. Planmine SMEST
Match: SMESG000053151.1 (SMESG000053151.1)

HSP 1 Score: 51.6026 bits (122), Expect = 1.636e-14
Identity = 22/35 (62.86%), Postives = 29/35 (82.86%), Query Frame = -2
Query:  373 AFMSTKAAKLYKGVNE*INDYEERCRKVLKDSSKI 477
            +FMSTKAAKLY+GVN+ I+ YEERCRK  ++ S +
Sbjct:   56 SFMSTKAAKLYEGVNDEIDSYEERCRKAFEEPSNL 90          

HSP 2 Score: 36.965 bits (84), Expect = 1.636e-14
Identity = 16/31 (51.61%), Postives = 21/31 (67.74%), Query Frame = -3
Query:  531 LITNNQMNAFIPMTKIYMIGGSYEKFLTSYK 623
            L TNNQ+NAFIP  KI+ +G + E FL   +
Sbjct:    7 LTTNNQLNAFIPTPKIFTVGDNPEIFLEEIR 37          

HSP 3 Score: 28.1054 bits (61), Expect = 1.636e-14
Identity = 15/32 (46.88%), Postives = 19/32 (59.38%), Query Frame = -1
Query:  455 FLQVIR-FYNLTQTLIHLQDNFHRSIHVNQSG 547
            FL+ IR FY+LTQT   LQ  F RS    ++ 
Sbjct:   32 FLEEIRRFYDLTQTPTQLQKTFIRSFMSTKAA 63          
BLAST of SMED30006685 vs. Planmine SMEST
Match: SMESG000000197.1 (SMESG000000197.1)

HSP 1 Score: 47.3654 bits (111), Expect = 2.174e-13
Identity = 21/35 (60.00%), Postives = 28/35 (80.00%), Query Frame = -2
Query:  373 AFMSTKAAKLYKGVNE*INDYEERCRKVLKDSSKI 477
            +FMST+AAKL +GVNE I+ YEERCRK  ++ S +
Sbjct:   56 SFMSTEAAKLCEGVNEEIDSYEERCRKAFEEPSNL 90          

HSP 2 Score: 36.965 bits (84), Expect = 2.174e-13
Identity = 16/31 (51.61%), Postives = 21/31 (67.74%), Query Frame = -3
Query:  531 LITNNQMNAFIPMTKIYMIGGSYEKFLTSYK 623
            L TNNQ+NAFIP  KI+ +G + E FL   +
Sbjct:    7 LTTNNQLNAFIPTPKIFTVGDNLEIFLEEIR 37          

HSP 3 Score: 28.4906 bits (62), Expect = 2.174e-13
Identity = 15/32 (46.88%), Postives = 19/32 (59.38%), Query Frame = -1
Query:  455 FLQVIR-FYNLTQTLIHLQDNFHRSIHVNQSG 547
            FL+ IR FY+LTQT   LQ  F RS    ++ 
Sbjct:   32 FLEEIRRFYDLTQTPTQLQKTFIRSFMSTEAA 63          
BLAST of SMED30006685 vs. Planmine SMEST
Match: SMESG000049887.1 (SMESG000049887.1)

HSP 1 Score: 50.8322 bits (120), Expect = 5.407e-13
Identity = 22/36 (61.11%), Postives = 28/36 (77.78%), Query Frame = -2
Query:  373 GAFMSTKAAKLYKGVNE*INDYEERCRKVLKDSSKI 480
            GAFMS +AAKLY+GVN  I+ YEERCRK  ++ S +
Sbjct:   62 GAFMSAEAAKLYEGVNAEIDSYEERCRKTFEEPSNL 97          

HSP 2 Score: 31.5722 bits (70), Expect = 5.407e-13
Identity = 14/27 (51.85%), Postives = 19/27 (70.37%), Query Frame = -3
Query:  543 LITNNQMNAFIPMTKIYMIGGSYEKFL 623
            L TNN++NAFI   KI+ +G + E FL
Sbjct:   14 LTTNNKLNAFIRTPKIFTVGDNLEIFL 40          

HSP 3 Score: 29.261 bits (64), Expect = 5.407e-13
Identity = 14/22 (63.64%), Postives = 18/22 (81.82%), Query Frame = -1
Query:  485 FLQVIR-FYNLTQTLIHLQDNF 547
            FL+ IR FY+LTQTL H+Q +F
Sbjct:   39 FLEKIRRFYDLTQTLKHMQKSF 60          
BLAST of SMED30006685 vs. Planmine SMEST
Match: SMESG000018262.1 (SMESG000018262.1)

HSP 1 Score: 43.8986 bits (102), Expect = 4.538e-10
Identity = 21/35 (60.00%), Postives = 26/35 (74.29%), Query Frame = -2
Query:  373 AFMSTKAAKLYKGVNE*INDYEERCRKVLKDSSKI 477
            AFMST+ AKLY+ VNE I+ YEER RK  K+ S +
Sbjct:   63 AFMSTEVAKLYERVNEEIDSYEERRRKAFKEPSNL 97          

HSP 2 Score: 34.6538 bits (78), Expect = 4.538e-10
Identity = 15/27 (55.56%), Postives = 19/27 (70.37%), Query Frame = -3
Query:  543 LITNNQMNAFIPMTKIYMIGGSYEKFL 623
            L TNN +NAFIP  KI+ +G + E FL
Sbjct:   14 LTTNNHLNAFIPTPKIFNVGDNLEIFL 40          

HSP 3 Score: 22.7126 bits (47), Expect = 4.538e-10
Identity = 10/22 (45.45%), Postives = 14/22 (63.64%), Query Frame = -1
Query:  476 QVIRFYNLTQTLIHLQDNFHRS 541
            ++ RFY+LTQ    LQ  F R+
Sbjct:   42 KIRRFYDLTQASNQLQKTFIRA 63          
BLAST of SMED30006685 vs. Planmine SMEST
Match: SMESG000021617.1 (SMESG000021617.1)

HSP 1 Score: 47.3654 bits (111), Expect = 4.778e-10
Identity = 21/33 (63.64%), Postives = 26/33 (78.79%), Query Frame = -2
Query:  379 AFMSTKAAKLYKGVNE*INDYEERCRKVLKDSS 477
            AFMST+AAK Y+GVNE I+ YEE CRK  ++ S
Sbjct:   63 AFMSTEAAKFYEGVNEEIDSYEEICRKAFEEPS 95          

HSP 2 Score: 34.6538 bits (78), Expect = 4.778e-10
Identity = 15/31 (48.39%), Postives = 20/31 (64.52%), Query Frame = -3
Query:  531 LITNNQMNAFIPMTKIYMIGGSYEKFLTSYK 623
            L TNNQ+ AFIP  KI+ +G + E FL   +
Sbjct:   14 LTTNNQLTAFIPTPKIFTVGNNLEIFLDEIR 44          
The following BLAST results are available for this feature:
BLAST of SMED30006685 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 SMED30006685 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 SMED30006685 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 SMED30006685 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 SMED30006685 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 SMED30006685 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 SMED30006685 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 SMED30006685 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 SMED30006685 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 SMED30006685 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 SMED30006685 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 SMED30006685 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 SMED30006685 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 SMED30006685 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000053151.11.636e-1462.86SMESG000053151.1[more]
SMESG000000197.12.174e-1360.00SMESG000000197.1[more]
SMESG000049887.15.407e-1361.11SMESG000049887.1[more]
SMESG000018262.14.538e-1060.00SMESG000018262.1[more]
SMESG000021617.14.778e-1063.64SMESG000021617.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006685 ID=SMED30006685|Name=SMED30006685|organism=Schmidtea mediterranea sexual|type=transcript|length=745bp
ATTAATTTGATCACTATTTTTACATTTTTGGTTTTCTATCATCCAACATT
AAAATATTTTTTTTTCGTAGATTCAATACAAATTTTAGATTAAATTGATA
TATCATATTAATCCCTCCTATTAAACTTGGAGAAATTTCAATTGCAATTA
CGAAATCAACTTTTCCTAATATTTCTAAGGAGCTCTCATTTGCATACTTT
ACAATAAATTTGTATTTTCGACTTTTACATCTTCGAGTGTGTTCATTACT
TCTTTACTGATGAAACTTATTTTAATTCCCGTATTAAATAAACAATTAAA
TTTCTTATTATAATTCAATATATTAACCATTATTTAAAGTGTCTAACTGG
TTATTCATTCCTTTATTTACAGTATCTTTGAAGAATCTTTTAAGACTTTT
CGACATCTTTCTTCATAATCGTTAATTTATTCATTGACTCCTTTATATAA
TTTAGCCGCTTTGGTTGACATGAATGCTCCTATGAAAATTATCTTGCAAA
TGGATTAAAGTTTGAGTCAAATTATAAAATCTTATAACTTGTAAGAAATT
TTTCGTAACTGCCTCCAATCATATAGATTTTCGTCATTGGAATAAACGCA
TTCATTTGATTATTTGTTATGAGTCATTTTTGTTTAAAGATTTGTACCTG
ATATAAAAATTGTTAACAAAGCTCAGCTTTTACCCTCAATCAACGTTGGG
CCCTGTCCTTTAGTTTGAAAAACGACTGTCTCAATATATTGATAT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte