SMED30030774

Overview
NameSMED30030774
Smed IDSMED30030774
Length (bp)2734
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30030774 (SMED30030774) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30030774 (SMED30030774) in cells (dots) of each of the 12 neoblast clusters.

 

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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

 

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Anatomical Expression

PAGE et. al., 2020



SMED30030774

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
testisSMED30030774SMESG000016039.1 HO005637.1ncbi_smed_estsPMID:22074376
Chong et al., 2011		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testis primordiumSMED30030774SMESG000016039.1 Contig4708_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism juvenile cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30030774 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.009403:10103..12836 +13661
Homology
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BLAST of SMED30030774 vs. Planmine SMEST
Match: SMESG000016039.1 (SMESG000016039.1)

HSP 1 Score: 1435.24 bits (3714), Expect = 0.000e+0
Identity = 869/869 (100.00%), Postives = 869/869 (100.00%), Query Frame = 3 
Query:   84 MIIITKFRRFFQHETSKEDSTKSINNSKLEDSSLKFKNEGDIECRSKSKYENIISNKFSNYEMSKRXXXXXXXXXXXXXXXXXXXXXXDTFQKYCNDTSESSFLDEFMKSNSEFSFQTSHLENSNFKSQLLNVTNLDPKERLSKVSKSNMGSLIPSNLKEIGSSKRKSLDLKNDEENISTNKKVKDNSELTSDTDNFEHESKDVKPKSRDKKSNPKRAGKKPKQKSKEGTSHRXXXXXXXXXXXXSSNEGLPTENSLNQVEVESKKTGKRHTKKDIGKKRVQNKKTKRIKQNXXXXXXXXXXXNDRNSLNTNETKHQISAFKDLDEVNSLSNADLSGGSTEDLSLGYKPSETTSKIQESDASSAVKEIPGITKTSSEELDNEQLMKIIESSNDSSTNEKPINKFPIISKQTEDKSLASDSSINSEQIEVIEKKEPKINIITPPESERRXXXXXXXXXXXXXXXXXXGQASKEKEIKDPQKEERKSDKVKKSKINGSKDANIDDLKKDSGKNSKTKEEKDQKNQPIXXXXXXXXXXXXXXXXXMADSDADSQLSIXXXXXXXXXXXXXXXXXXXXXXXNSTAGPNXXXXXXXXXPPDGDSVESSVDDIKDQEKVLESNRXXXXXXXXXXXXXXXMEDAKSKRKKETNITADTVRSSKSENTQDKLKYKEIGTDVQRFSENKGTQISKISLTIDPVEVHITQKNTSLDPQQGSQSTSQRKNITLDNLVNSPSDEEPKLDGKDNKKTLSNDDDLKYLFATNMQDLRNINLGTHCRICELIFDSCCNCGGLMDKNRIPVYSTVDCNYEPKKYNCNSLTKSRSVTFCKPKKSCDCNYPDRYSSCSDSLTLSYNCIFGDPLYNSACPQKVLCISR 2690
            MIIITKFRRFFQHETSKEDSTKSINNSKLEDSSLKFKNEGDIECRSKSKYENIISNKFSNYEMSKRKTPKVKISKSSKKKNKERSLKSDTFQKYCNDTSESSFLDEFMKSNSEFSFQTSHLENSNFKSQLLNVTNLDPKERLSKVSKSNMGSLIPSNLKEIGSSKRKSLDLKNDEENISTNKKVKDNSELTSDTDNFEHESKDVKPKSRDKKSNPKRAGKKPKQKSKEGTSHRKEKKTDVETKTESSNEGLPTENSLNQVEVESKKTGKRHTKKDIGKKRVQNKKTKRIKQNPESSPSSEETSNDRNSLNTNETKHQISAFKDLDEVNSLSNADLSGGSTEDLSLGYKPSETTSKIQESDASSAVKEIPGITKTSSEELDNEQLMKIIESSNDSSTNEKPINKFPIISKQTEDKSLASDSSINSEQIEVIEKKEPKINIITPPESERRNKKLKKTPEKKSKNNKDKGQASKEKEIKDPQKEERKSDKVKKSKINGSKDANIDDLKKDSGKNSKTKEEKDQKNQPIKNEKSGKKDKKNKKTKKMADSDADSQLSIESEKEPPTKEDEKKKSIKKSKAKNSTAGPNKKSKKQSKKPPDGDSVESSVDDIKDQEKVLESNRKSNLDKDRLNDDKKLMEDAKSKRKKETNITADTVRSSKSENTQDKLKYKEIGTDVQRFSENKGTQISKISLTIDPVEVHITQKNTSLDPQQGSQSTSQRKNITLDNLVNSPSDEEPKLDGKDNKKTLSNDDDLKYLFATNMQDLRNINLGTHCRICELIFDSCCNCGGLMDKNRIPVYSTVDCNYEPKKYNCNSLTKSRSVTFCKPKKSCDCNYPDRYSSCSDSLTLSYNCIFGDPLYNSACPQKVLCISR
Sbjct:    1 MIIITKFRRFFQHETSKEDSTKSINNSKLEDSSLKFKNEGDIECRSKSKYENIISNKFSNYEMSKRKTPKVKISKSSKKKNKERSLKSDTFQKYCNDTSESSFLDEFMKSNSEFSFQTSHLENSNFKSQLLNVTNLDPKERLSKVSKSNMGSLIPSNLKEIGSSKRKSLDLKNDEENISTNKKVKDNSELTSDTDNFEHESKDVKPKSRDKKSNPKRAGKKPKQKSKEGTSHRKEKKTDVETKTESSNEGLPTENSLNQVEVESKKTGKRHTKKDIGKKRVQNKKTKRIKQNPESSPSSEETSNDRNSLNTNETKHQISAFKDLDEVNSLSNADLSGGSTEDLSLGYKPSETTSKIQESDASSAVKEIPGITKTSSEELDNEQLMKIIESSNDSSTNEKPINKFPIISKQTEDKSLASDSSINSEQIEVIEKKEPKINIITPPESERRNKKLKKTPEKKSKNNKDKGQASKEKEIKDPQKEERKSDKVKKSKINGSKDANIDDLKKDSGKNSKTKEEKDQKNQPIKNEKSGKKDKKNKKTKKMADSDADSQLSIESEKEPPTKEDEKKKSIKKSKAKNSTAGPNKKSKKQSKKPPDGDSVESSVDDIKDQEKVLESNRKSNLDKDRLNDDKKLMEDAKSKRKKETNITADTVRSSKSENTQDKLKYKEIGTDVQRFSENKGTQISKISLTIDPVEVHITQKNTSLDPQQGSQSTSQRKNITLDNLVNSPSDEEPKLDGKDNKKTLSNDDDLKYLFATNMQDLRNINLGTHCRICELIFDSCCNCGGLMDKNRIPVYSTVDCNYEPKKYNCNSLTKSRSVTFCKPKKSCDCNYPDRYSSCSDSLTLSYNCIFGDPLYNSACPQKVLCISR 869
The following BLAST results are available for this feature:
BLAST of SMED30030774 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 SMED30030774 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 SMED30030774 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 SMED30030774 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 SMED30030774 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 SMED30030774 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 SMED30030774 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 SMED30030774 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 SMED30030774 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 SMED30030774 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 SMED30030774 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 SMED30030774 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 SMED30030774 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 SMED30030774 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000016039.10.000e+0100.00SMESG000016039.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030774 ID=SMED30030774|Name=SMED30030774|organism=Schmidtea mediterranea sexual|type=transcript|length=2734bp
GTTGCGAAAGGTTGTTTAATTAAATAATTAATTGACATCAATAAATATAT
TTATTAATATTAATCAGCTTTTATTTAAAGTCAATGATTATTATCACAAA
ATTTCGAAGGTTTTTTCAGCATGAAACCTCAAAGGAAGATTCAACTAAGA
GCATAAATAATTCAAAACTCGAAGATTCAAGTTTAAAGTTCAAAAACGAG
GGGGACATCGAATGTCGAAGTAAATCAAAATATGAAAACATAATTTCTAA
TAAATTTTCAAATTATGAAATGTCAAAAAGAAAAACTCCAAAGGTTAAAA
TCTCAAAATCGAGCAAGAAGAAAAATAAAGAAAGGTCTTTAAAATCAGAT
ACCTTTCAAAAATACTGTAATGATACTTCTGAGTCAAGTTTCCTTGATGA
ATTTATGAAAAGTAACAGCGAATTCTCTTTTCAGACGAGCCATTTGGAAA
ATTCTAATTTTAAAAGTCAACTATTAAATGTGACTAACTTAGATCCGAAA
GAAAGATTATCAAAAGTTTCTAAAAGTAATATGGGAAGCCTAATTCCGTC
TAATTTGAAAGAAATTGGATCATCAAAGAGAAAGAGCTTGGATTTAAAGA
ATGACGAAGAAAACATCTCAACGAATAAGAAAGTAAAAGATAACAGCGAG
CTGACAAGTGACACGGATAATTTTGAACATGAAAGCAAAGATGTCAAACC
TAAATCTAGGGATAAAAAATCTAATCCAAAAAGAGCTGGAAAGAAACCTA
AACAGAAATCAAAAGAAGGCACTTCACATCGAAAGGAAAAGAAAACGGAT
GTTGAAACTAAAACAGAATCCAGTAATGAAGGTCTTCCGACGGAAAATTC
ATTAAACCAAGTTGAAGTTGAATCGAAGAAAACTGGTAAAAGACATACTA
AAAAAGATATCGGAAAGAAAAGAGTTCAAAATAAGAAAACAAAAAGAATA
AAGCAAAATCCTGAATCAAGCCCTTCTAGCGAGGAAACTTCAAATGACCG
GAATTCATTGAATACAAATGAAACAAAACATCAAATATCTGCTTTCAAAG
ATTTAGATGAAGTAAATAGTTTAAGCAATGCAGACTTGTCAGGAGGCTCG
ACAGAAGATTTGTCTTTAGGTTATAAGCCATCTGAAACTACCAGTAAAAT
CCAAGAATCGGACGCTTCGTCAGCTGTGAAAGAAATTCCGGGGATTACTA
AAACTAGTTCAGAGGAACTGGATAATGAACAACTTATGAAAATAATTGAA
TCTTCAAATGATTCAAGTACTAATGAAAAACCTATAAATAAATTTCCTAT
AATATCAAAGCAAACTGAAGATAAATCTTTGGCATCAGATTCTTCCATAA
ATTCTGAACAAATCGAAGTCATTGAAAAGAAGGAACCGAAAATAAATATC
ATAACACCACCTGAGAGTGAAAGAAGAAACAAAAAATTAAAAAAGACGCC
TGAAAAAAAATCAAAAAATAACAAAGATAAAGGTCAGGCATCAAAAGAAA
AAGAAATTAAAGATCCACAAAAAGAAGAAAGAAAATCAGATAAAGTAAAG
AAATCTAAAATAAATGGAAGCAAAGATGCAAACATAGATGATTTAAAAAA
GGATTCTGGTAAAAATTCCAAAACTAAAGAAGAAAAAGATCAAAAGAATC
AGCCAATTAAAAATGAAAAATCGGGGAAAAAAGACAAAAAAAATAAAAAA
ACAAAAAAAATGGCTGACAGTGATGCAGATTCACAGCTTTCTATTGAATC
AGAGAAAGAACCACCGACTAAAGAAGACGAAAAAAAGAAAAGTATAAAAA
AGTCAAAAGCGAAAAATAGCACAGCTGGTCCAAATAAGAAAAGCAAAAAA
CAGTCAAAGAAACCGCCAGATGGCGATAGTGTTGAGTCTTCCGTTGACGA
TATCAAGGATCAAGAAAAGGTTTTGGAATCAAATAGAAAAAGTAATTTGG
ATAAGGATCGTTTAAACGATGATAAAAAATTAATGGAAGACGCAAAGTCA
AAGAGAAAAAAAGAAACAAATATTACCGCAGATACTGTTCGTTCTTCTAA
ATCTGAAAATACTCAAGACAAATTGAAATATAAAGAGATTGGTACAGATG
TACAGAGATTTTCTGAAAATAAAGGAACTCAAATCAGTAAGATCTCTTTA
ACCATAGATCCTGTGGAGGTTCACATCACACAGAAAAATACTAGCTTGGA
TCCCCAACAAGGAAGTCAATCAACTTCTCAACGTAAAAATATTACATTGG
ATAATCTCGTGAATAGTCCTTCAGACGAAGAGCCAAAACTAGATGGCAAA
GATAACAAGAAAACATTGAGCAATGATGATGATTTGAAATATTTATTTGC
TACAAACATGCAAGACTTAAGGAACATAAACCTTGGGACTCACTGCCGGA
TTTGTGAATTAATATTTGATTCGTGTTGCAATTGTGGTGGTTTAATGGAT
AAAAACAGGATTCCCGTCTATTCAACCGTCGACTGCAATTACGAGCCAAA
GAAATATAACTGCAACTCGTTGACAAAGAGCCGATCTGTGACATTTTGTA
AACCTAAAAAGTCCTGTGACTGTAATTATCCAGATCGTTATTCTTCTTGT
TCCGATAGCTTGACTCTTTCATATAATTGCATTTTCGGCGACCCCTTATA
CAATAGTGCTTGTCCACAAAAGGTGCTCTGTATTTCCAGATAAAAATATA
GATATTTTTACTCAATTTTTTTTTGTGAATTTTG
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protein sequence of SMED30030774-orf-1

>SMED30030774-orf-1 ID=SMED30030774-orf-1|Name=SMED30030774-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=870bp
MIIITKFRRFFQHETSKEDSTKSINNSKLEDSSLKFKNEGDIECRSKSKY
ENIISNKFSNYEMSKRKTPKVKISKSSKKKNKERSLKSDTFQKYCNDTSE
SSFLDEFMKSNSEFSFQTSHLENSNFKSQLLNVTNLDPKERLSKVSKSNM
GSLIPSNLKEIGSSKRKSLDLKNDEENISTNKKVKDNSELTSDTDNFEHE
SKDVKPKSRDKKSNPKRAGKKPKQKSKEGTSHRKEKKTDVETKTESSNEG
LPTENSLNQVEVESKKTGKRHTKKDIGKKRVQNKKTKRIKQNPESSPSSE
ETSNDRNSLNTNETKHQISAFKDLDEVNSLSNADLSGGSTEDLSLGYKPS
ETTSKIQESDASSAVKEIPGITKTSSEELDNEQLMKIIESSNDSSTNEKP
INKFPIISKQTEDKSLASDSSINSEQIEVIEKKEPKINIITPPESERRNK
KLKKTPEKKSKNNKDKGQASKEKEIKDPQKEERKSDKVKKSKINGSKDAN
IDDLKKDSGKNSKTKEEKDQKNQPIKNEKSGKKDKKNKKTKKMADSDADS
QLSIESEKEPPTKEDEKKKSIKKSKAKNSTAGPNKKSKKQSKKPPDGDSV
ESSVDDIKDQEKVLESNRKSNLDKDRLNDDKKLMEDAKSKRKKETNITAD
TVRSSKSENTQDKLKYKEIGTDVQRFSENKGTQISKISLTIDPVEVHITQ
KNTSLDPQQGSQSTSQRKNITLDNLVNSPSDEEPKLDGKDNKKTLSNDDD
LKYLFATNMQDLRNINLGTHCRICELIFDSCCNCGGLMDKNRIPVYSTVD
CNYEPKKYNCNSLTKSRSVTFCKPKKSCDCNYPDRYSSCSDSLTLSYNCI
FGDPLYNSACPQKVLCISR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
PLANA:0003304testis primordium
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 224..244
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 324..361
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 426..451
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 540..572
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 164..660
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 245..262
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 385..425
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 164..210
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 589..649
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 458..531
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 65..87
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 292..317
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 701..728
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 701..743
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 271..286