SMED30005128

Overview
NameSMED30005128
Smed IDSMED30005128
Length (bp)1592
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 SMED30005128 (SMED30005128) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30005128 (SMED30005128) in cells (dots) of each of the 12 neoblast clusters.

 

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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 SMED30005128 (SMED30005128) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30005128 (SMED30005128) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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



SMED30005128

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
head regionSMED30005128h1SMcG0013068 dd_Smed_v6_13336_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
zeta neoblastSMED30005128h1SMcG0013068 dd_Smed_v4_13336_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30005128h1SMcG0013068 dd_Smed_v4_13336_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30005128 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000069:212715..216307 +7677
Homology
[Close]
BLAST of SMED30005128 vs. TrEMBL
Match: V3ZV41 (Uncharacterized protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_235459 PE=4 SV=1)

HSP 1 Score: 67.3958 bits (163), Expect = 3.896e-8
Identity = 56/189 (29.63%), Postives = 85/189 (44.97%), Query Frame = 1 
Query:  439 DDLDNLINEEFYSRSRTPSYAVRIIENSIENNPITESYLLQQNWISMTSKDRSTIPVRSARPFSSPSWVKG-FFKPDQSVVNKMHIYLSPTEVVKGNISQNDDRLGKPTRATLLRERMNSGG-----------QIAHSGRNTRMCSRSGNPTKYNEAVSSHAGIIQDVDYAFLIGARYNRVQILDCSSV 969
            +D+D +   E  +   +P++   I +    +    ES L  QN +S    D      +S RP S+ S V+G +++P     N+MH YLSPTE+      + D + GKPTR TLLR +  +G            QI +  +    C     P +     S       +  ++FL GARYN   ILD  S+
Sbjct:   67 EDIDTIYRNEILAAHGSPTWVAEISKQMTHSG---ESPLFLQNLLSPHKPDH-----KSKRPSSARSVVEGKYYRP-----NRMHQYLSPTELRDHWQGEIDVKYGKPTRTTLLRAQQRAGSVPVNAYDERRKQIENEKKLQASCQSLFTPKE-----SYDVDTDGESQHSFLTGARYNSAHILDSRSL 237
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BLAST of SMED30005128 vs. TrEMBL
Match: A0A210R778 (Uncharacterized protein OS=Mizuhopecten yessoensis OX=6573 GN=KP79_PYT20170 PE=4 SV=1)

HSP 1 Score: 63.1586 bits (152), Expect = 1.040e-6
Identity = 57/189 (30.16%), Postives = 89/189 (47.09%), Query Frame = 1 
Query:  463 EEFYSRSRTPSYAVRIIENSIENNPITESYLLQQNWISMTSKDRSTIPVRSARPFSSPSWVKG-----------FFKPDQSVVNKMHIYLSPTEVVKGNISQNDD----RLGKPTRATLLRERMNSGGQIAHSGRNTRMCSRSGNPTKYNEAVSSHAGI----IQDVDYAFLIGARYNRVQILDCSSVS 972
            E+F +  R+P++A   I  S E+N   ES L     +S +  D+    ++  RP SS   V+G           +++P     N  H YLS TE+ +   SQ+ D    + G+PTR TLLR R  S     ++    R  ++    T+Y+   +    I     ++  +AFL GARYNR  +LD   +S
Sbjct:   76 EKFAAGHRSPNWA---INTSRESNHSGESPLFVHGLLSSSKYDKEGQHLQEPRPRSS---VRGRSAPPKRSGTLYYRP-----NTTHQYLSATELHQ--TSQSSDATSIKYGRPTRTTLLRARQRSNSAPVNAYMQRRESAKKMESTQYSAMPTPREYIPARKKEESTHAFLTGARYNRAHLLDSKGLS 251
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BLAST of SMED30005128 vs. Planmine SMEST
Match: SMESG000039672.1 (SMESG000039672.1)

HSP 1 Score: 769.615 bits (1986), Expect = 0.000e+0
Identity = 374/378 (98.94%), Postives = 375/378 (99.21%), Query Frame = 1 
Query:  433 FKDDLDNLINEEFYSRSRTPSYAVRIIENSIENNPITESYLLQQNWISMTSKDRSTIPVRSARPFSSPSWVKGFFKPDQSVVNKMHIYLSPTEVVKGNISQNDDRLGKPTRATLLRERMNSGGQIAHSGRNTRMCSRSGNPTKYNEAVSSHAGIIQDVDYAFLIGARYNRVQILDCSSVSRKKANSVRKLLRDSQNNDSESSILIQSGPSPTNSPQPTNKIADIESDSQISPSKIENHIINQTETRQNLKKCSQIRPITLTKFAPSFIKSSPMGIKPSVLPIVVGEKYSVVEITGNFTQDSIPSHKWTRASLNLHIARQAKFLRNKRKDLMKNEPVKQPNFGFNQPQITSLSEHNPNEMNVKLKGKKTEVEVPTRSIQ 1566
            FKDDLDNLINEEFYSRSRTPSYAVRIIENSIENNPITESYLLQQNWISMTSKDRSTIPVRSARPFSSPSWVKGFFKPDQSVVNKMHIYLSPTEVV GNISQNDDRLGKPTRATLLRERMNSGGQIAHSGRNTRMCSRSGNPTKYNEAVSSHAGIIQDVDYAFLIGARYNRVQILDCSSVSRKKANSVRKLLRDSQNNDSESSILIQSGPSPTNSPQPTNKIADIESDSQISPSKIENHIINQTETRQNLKKCSQIRPITLTKFAPSFIKSSPMGIKPSVLPIVVGEKYSVVEITGNFTQDSIP HKWTRASLNLHIARQAKFLRNKRKDLMKNEPV+QPNFGFNQPQITSLSEHNPNEMNVKLK KKTEVEVPTRSIQ
Sbjct:   18 FKDDLDNLINEEFYSRSRTPSYAVRIIENSIENNPITESYLLQQNWISMTSKDRSTIPVRSARPFSSPSWVKGFFKPDQSVVNKMHIYLSPTEVVNGNISQNDDRLGKPTRATLLRERMNSGGQIAHSGRNTRMCSRSGNPTKYNEAVSSHAGIIQDVDYAFLIGARYNRVQILDCSSVSRKKANSVRKLLRDSQNNDSESSILIQSGPSPTNSPQPTNKIADIESDSQISPSKIENHIINQTETRQNLKKCSQIRPITLTKFAPSFIKSSPMGIKPSVLPIVVGEKYSVVEITGNFTQDSIPKHKWTRASLNLHIARQAKFLRNKRKDLMKNEPVQQPNFGFNQPQITSLSEHNPNEMNVKLKDKKTEVEVPTRSIQ 395
[Close]
BLAST of SMED30005128 vs. Planmine SMEST
Match: SMESG000039707.1 (SMESG000039707.1)

HSP 1 Score: 766.148 bits (1977), Expect = 0.000e+0
Identity = 371/378 (98.15%), Postives = 373/378 (98.68%), Query Frame = 1 
Query:  433 FKDDLDNLINEEFYSRSRTPSYAVRIIENSIENNPITESYLLQQNWISMTSKDRSTIPVRSARPFSSPSWVKGFFKPDQSVVNKMHIYLSPTEVVKGNISQNDDRLGKPTRATLLRERMNSGGQIAHSGRNTRMCSRSGNPTKYNEAVSSHAGIIQDVDYAFLIGARYNRVQILDCSSVSRKKANSVRKLLRDSQNNDSESSILIQSGPSPTNSPQPTNKIADIESDSQISPSKIENHIINQTETRQNLKKCSQIRPITLTKFAPSFIKSSPMGIKPSVLPIVVGEKYSVVEITGNFTQDSIPSHKWTRASLNLHIARQAKFLRNKRKDLMKNEPVKQPNFGFNQPQITSLSEHNPNEMNVKLKGKKTEVEVPTRSIQ 1566
            FKDDLDNLINEEFYSRSRTPSYAVRIIENSIENNPITESYLLQQNWISMTSKDRSTIPVRSARPFSSPSWVKGFFKPDQSVVNKMHIYLSPTEVV GNISQNDDRLGKPTRATLLRERMNSGGQIAHSGRNTR+CSRSGNPTKYNEAVSSHAGIIQDVDYAFLIGARYNRVQILDCSSVSRKKANSVRKLLRDSQNNDSESSILIQSGPSPTNSPQPTNKIADIESDSQISPSKIENHIINQTETRQNLKKCSQIRPITLTKFAPSFIKSSPM IKPSVLPIVVGEKYSVVEITGNFTQDSIP HKWTRASLNLHIARQAKFLRNKRKDLMKNE V+QPNFGFNQPQITSLSEHNPNEMNVKLK KKTEVEVPTRSIQ
Sbjct:  287 FKDDLDNLINEEFYSRSRTPSYAVRIIENSIENNPITESYLLQQNWISMTSKDRSTIPVRSARPFSSPSWVKGFFKPDQSVVNKMHIYLSPTEVVNGNISQNDDRLGKPTRATLLRERMNSGGQIAHSGRNTRICSRSGNPTKYNEAVSSHAGIIQDVDYAFLIGARYNRVQILDCSSVSRKKANSVRKLLRDSQNNDSESSILIQSGPSPTNSPQPTNKIADIESDSQISPSKIENHIINQTETRQNLKKCSQIRPITLTKFAPSFIKSSPMAIKPSVLPIVVGEKYSVVEITGNFTQDSIPKHKWTRASLNLHIARQAKFLRNKRKDLMKNERVQQPNFGFNQPQITSLSEHNPNEMNVKLKEKKTEVEVPTRSIQ 664
[Close]
BLAST of SMED30005128 vs. Planmine SMEST
Match: SMESG000039672.1 (SMESG000039672.1)

HSP 1 Score: 596.66 bits (1537), Expect = 0.000e+0
Identity = 290/294 (98.64%), Postives = 291/294 (98.98%), Query Frame = 1 
Query:  685 MHIYLSPTEVVKGNISQNDDRLGKPTRATLLRERMNSGGQIAHSGRNTRMCSRSGNPTKYNEAVSSHAGIIQDVDYAFLIGARYNRVQILDCSSVSRKKANSVRKLLRDSQNNDSESSILIQSGPSPTNSPQPTNKIADIESDSQISPSKIENHIINQTETRQNLKKCSQIRPITLTKFAPSFIKSSPMGIKPSVLPIVVGEKYSVVEITGNFTQDSIPSHKWTRASLNLHIARQAKFLRNKRKDLMKNEPVKQPNFGFNQPQITSLSEHNPNEMNVKLKGKKTEVEVPTRSIQ 1566
            MHIYLSPTEVV GNISQNDDRLGKPTRATLLRERMNSGGQIAHSGRNTRMCSRSGNPTKYNEAVSSHAGIIQDVDYAFLIGARYNRVQILDCSSVSRKKANSVRKLLRDSQNNDSESSILIQSGPSPTNSPQPTNKIADIESDSQISPSKIENHIINQTETRQNLKKCSQIRPITLTKFAPSFIKSSPMGIKPSVLPIVVGEKYSVVEITGNFTQDSIP HKWTRASLNLHIARQAKFLRNKRKDLMKNEPV+QPNFGFNQPQITSLSEHNPNEMNVKLK KKTEVEVPTRSIQ
Sbjct:    1 MHIYLSPTEVVNGNISQNDDRLGKPTRATLLRERMNSGGQIAHSGRNTRMCSRSGNPTKYNEAVSSHAGIIQDVDYAFLIGARYNRVQILDCSSVSRKKANSVRKLLRDSQNNDSESSILIQSGPSPTNSPQPTNKIADIESDSQISPSKIENHIINQTETRQNLKKCSQIRPITLTKFAPSFIKSSPMGIKPSVLPIVVGEKYSVVEITGNFTQDSIPKHKWTRASLNLHIARQAKFLRNKRKDLMKNEPVQQPNFGFNQPQITSLSEHNPNEMNVKLKDKKTEVEVPTRSIQ 294
The following BLAST results are available for this feature:
BLAST of SMED30005128 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 SMED30005128 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 SMED30005128 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 SMED30005128 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 SMED30005128 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 SMED30005128 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 SMED30005128 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 SMED30005128 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
V3ZV413.896e-829.63Uncharacterized protein OS=Lottia gigantea OX=2251... [more]
A0A210R7781.040e-630.16Uncharacterized protein OS=Mizuhopecten yessoensis... [more]
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BLAST of SMED30005128 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 SMED30005128 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 SMED30005128 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 SMED30005128 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 SMED30005128 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 SMED30005128 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000039672.10.000e+098.94SMESG000039672.1[more]
SMESG000039707.10.000e+098.15SMESG000039707.1[more]
SMESG000039672.10.000e+098.64SMESG000039672.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005128 ID=SMED30005128|Name=SMED30005128|organism=Schmidtea mediterranea sexual|type=transcript|length=1592bp
TGCGTTTTAGCGTTTTTAACTATTTATATTTATTTTATTAATAATTAATT
GTTTCTATTTTGATTTTTTACAAGATTTTAGCATGTCTGGATCTGATTAC
TAGCAGATTCATGGTCCCAAAAAACGACTAGCATATTTAAAATATAGAGA
ATCGGATACTATTCATTCTGTCTTTCAATCACATTTATAAGAATTTATAC
TAAAGATTATTGACGACATCTACCTGACGAATAATATTATTAATAATAAA
TAATATACTGAGGTTTTCGATTCATATTAATATATGAATAATTAATGATA
TTAAAAAGCGCATGTTTACCAAATTATTTCTTTTTATAATCATTTTTAAT
ATTTATATTTTTAAATTTATACTATTGAAATATAAAAAATTTTCTACAGG
CTTCCATAAGTAGCAGTTCAAATATATCTTCATTTAAAGATGATTTAGAC
AATCTCATAAACGAAGAATTCTATAGCCGATCTAGAACTCCATCATATGC
CGTTCGAATAATCGAGAATTCTATTGAAAATAATCCTATTACAGAATCAT
ATCTTCTTCAACAGAATTGGATTTCAATGACATCGAAAGACCGTTCAACA
ATTCCAGTAAGATCCGCTAGGCCTTTTTCTTCTCCGAGTTGGGTAAAAGG
CTTCTTTAAACCAGATCAATCAGTTGTGAATAAAATGCATATTTATCTTT
CACCGACTGAAGTCGTAAAAGGAAACATTTCACAAAATGACGACAGATTA
GGAAAACCGACACGCGCAACTCTATTGAGAGAAAGGATGAACTCAGGAGG
TCAAATTGCCCACAGTGGTAGAAATACTAGAATGTGTTCTAGAAGTGGAA
ATCCTACTAAATATAACGAAGCAGTCAGCTCACACGCTGGCATCATTCAA
GACGTGGATTACGCATTTCTGATTGGTGCTCGCTATAATAGAGTTCAAAT
ACTTGATTGCAGTTCTGTCTCCCGGAAGAAGGCTAATTCAGTAAGGAAGT
TGTTGCGGGACAGTCAAAATAATGACTCTGAATCTTCAATACTGATTCAG
TCGGGTCCTTCTCCCACAAATTCTCCACAACCGACAAACAAAATTGCTGA
CATCGAATCAGATTCTCAAATCTCACCGTCGAAAATTGAAAATCATATAA
TTAACCAAACAGAGACTCGTCAGAATTTGAAAAAGTGTTCCCAAATCCGG
CCTATCACACTGACAAAATTTGCACCTTCATTCATTAAATCTTCTCCTAT
GGGAATAAAACCTTCAGTTTTACCAATTGTTGTCGGTGAAAAATATTCTG
TTGTAGAAATCACCGGAAATTTCACCCAGGACTCAATTCCGTCACACAAA
TGGACAAGGGCTTCACTAAATTTGCATATCGCTAGACAAGCAAAATTCCT
CAGGAATAAAAGAAAAGACCTCATGAAAAATGAGCCAGTCAAGCAGCCAA
ATTTCGGATTTAATCAGCCGCAAATAACAAGCCTTTCCGAACACAACCCA
AATGAAATGAATGTTAAACTGAAAGGTAAGAAAACGGAAGTGGAAGTTCC
TACAAGATCTATTCAATGATTTAATTCTAAATTGGATAGTAT
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protein sequence of SMED30005128-orf-1

>SMED30005128-orf-1 ID=SMED30005128-orf-1|Name=SMED30005128-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=331bp
MTSKDRSTIPVRSARPFSSPSWVKGFFKPDQSVVNKMHIYLSPTEVVKGN
ISQNDDRLGKPTRATLLRERMNSGGQIAHSGRNTRMCSRSGNPTKYNEAV
SSHAGIIQDVDYAFLIGARYNRVQILDCSSVSRKKANSVRKLLRDSQNND
SESSILIQSGPSPTNSPQPTNKIADIESDSQISPSKIENHIINQTETRQN
LKKCSQIRPITLTKFAPSFIKSSPMGIKPSVLPIVVGEKYSVVEITGNFT
QDSIPSHKWTRASLNLHIARQAKFLRNKRKDLMKNEPVKQPNFGFNQPQI
TSLSEHNPNEMNVKLKGKKTEVEVPTRSIQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000034epidermis
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 143..168
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 148..168