SMED30027849

Overview
NameSMED30027849
Smed IDSMED30027849
Length (bp)2888
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 SMED30027849 (SMED30027849) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30027849 (SMED30027849) 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.
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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




SMED30027849

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
oocyteSMED30027849 Contig15165newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30027849 Contig15165uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30027849 Contig15165newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30027849 Contig15165uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30027849 vs. Planmine SMEST
Match: SMESG000026305.1 (SMESG000026305.1)

HSP 1 Score: 227.254 bits (578), Expect = 1.553e-67
Identity = 109/127 (85.83%), Postives = 116/127 (91.34%), Query Frame = 2
Query:  635 MSRPIDIGAFPFAYTNDNPGCDKCTNLQVSHMQFQHSDPYN-SRCDPYNTPTHCVRRFHLAKLVVTRISASSIDTPSYIRNIDGSGLTVKFRKIQMYRQSNPTNDDTTARIPYDDIVLNPRARPSGK 1012
            MSRPI+IG F FAYTNDNPGCD+CTNLQ+SHMQFQHSDP+N SRCDPYNTPTHCV RFHLA LVVTRI ASS+DTPSYIRNIDGSGLTVKFRKI+MYRQSNP N DTTARIP DDIVLNPRAR  G+
Sbjct:    1 MSRPINIGVFLFAYTNDNPGCDECTNLQISHMQFQHSDPHNDSRCDPYNTPTHCVPRFHLATLVVTRILASSVDTPSYIRNIDGSGLTVKFRKIKMYRQSNPANKDTTARIPDDDIVLNPRARLPGQ 127          

HSP 2 Score: 52.373 bits (124), Expect = 6.913e-7
Identity = 39/103 (37.86%), Postives = 50/103 (48.54%), Query Frame = 3
Query: 2532 VRFPAHAVNFCRQAMWDAGFT--VSQVREARAGSLQQAEDFELPFVTIKREPGRNPASEIRGQAEFLLARLGEHQRQTNE*VDRAKRYLGNVNDDIAAGRIAS 2834
            +  PAH V   RQA W+  +      V E         E+F   F  +  EP   P+ +I  QA+ LL  L +HQ Q    V RA  YL NV DD+ AGR+AS
Sbjct:  132 IELPAHIVEQWRQA-WNRVYQERYLDVPEEDQQDDISPEEFMGQFRKLSDEP--KPSQDILTQAQELLEGLLQHQGQVEADVARATEYLANVKDDLVAGRLAS 231          
BLAST of SMED30027849 vs. Planmine SMEST
Match: SMESG000042239.1 (SMESG000042239.1)

HSP 1 Score: 211.075 bits (536), Expect = 1.250e-62
Identity = 104/138 (75.36%), Postives = 116/138 (84.06%), Query Frame = 3
Query: 2475 NL*N*FLLDDSWIDESRITVRFPAHAVNFCRQAMWDAGFTVSQVREARAGSLQQAEDFELPFVTIKREPGRNPASEIRGQAEFLLARLGEHQRQTNE*VDRAKRYLGNVNDDIAAGRIASTDGYAPPYNTSYNLDDER 2888
            NL N    ++SWIDESR+TVRFPAHA N C QAM DAGFTVSQVRE+R+G+ QQ E+ EL FV IKREPGRNPA EIRGQAEFLLA L EHQRQT+  VDRA+RYL +VN+DIAAGRIA TD YAPPYNTS+NLDDER
Sbjct:   44 NLANQNRANESWIDESRVTVRFPAHAANRCLQAMCDAGFTVSQVRESRSGTPQQMEEVELRFVAIKREPGRNPAREIRGQAEFLLASLEEHQRQTDIQVDRARRYLASVNEDIAAGRIACTDCYAPPYNTSFNLDDER 181          
BLAST of SMED30027849 vs. Planmine SMEST
Match: SMESG000019398.1 (SMESG000019398.1)

HSP 1 Score: 226.483 bits (576), Expect = 8.938e-61
Identity = 102/132 (77.27%), Postives = 117/132 (88.64%), Query Frame = 3
Query: 2493 LLDDSWIDESRITVRFPAHAVNFCRQAMWDAGFTVSQVREARAGSLQQAEDFELPFVTIKREPGRNPASEIRGQAEFLLARLGEHQRQTNE*VDRAKRYLGNVNDDIAAGRIASTDGYAPPYNTSYNLDDER 2888
            L D+SW++ESR+T+RFPAHA N CRQAMWDAGFT+SQVRE+R+G+LQQ E+ ELPFV IKREPGRNPA EIRGQAEFLLARL EHQRQT+  V RA+ YL NVN+D AAGRIA T+GYAPPYNTS+NLDDER
Sbjct: 1107 LYDESWVNESRVTIRFPAHAANRCRQAMWDAGFTISQVRESRSGTLQQMEEVELPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQTDLQVARARLYLANVNEDKAAGRIACTEGYAPPYNTSFNLDDER 1238          
BLAST of SMED30027849 vs. Planmine SMEST
Match: SMESG000039041.1 (SMESG000039041.1)

HSP 1 Score: 201.83 bits (512), Expect = 1.524e-57
Identity = 97/133 (72.93%), Postives = 109/133 (81.95%), Query Frame = 3
Query: 2490 FLLDDSWIDESRITVRFPAHAVNFCRQAMWDAGFTVSQVREARAGSLQQAEDFELPFVTIKREPGRNPASEIRGQAEFLLARLGEHQRQTNE*VDRAKRYLGNVNDDIAAGRIASTDGYAPPYNTSYNLDDER 2888
            F LDDSWID SRITVRFPAHA N CRQA+WDAGFTVSQ +E+R G  + +E+ +LPFV IKREPGRN A EIRG AEFL+A L EHQRQT+  V+ A+RYL NVNDDIA GRI STDGYAP YNTS+NLDD R
Sbjct:   13 FGLDDSWIDSSRITVRFPAHAANRCRQALWDAGFTVSQAKESRFGQQRPSEEIKLPFVAIKREPGRNSAREIRGHAEFLIAPLEEHQRQTDAHVESARRYLANVNDDIAKGRILSTDGYAPSYNTSFNLDDRR 145          
BLAST of SMED30027849 vs. Planmine SMEST
Match: SMESG000011208.1 (SMESG000011208.1)

HSP 1 Score: 206.068 bits (523), Expect = 7.256e-57
Identity = 100/129 (77.52%), Postives = 111/129 (86.05%), Query Frame = 3
Query: 2502 DSWIDESRITVRFPAHAVNFCRQAMWDAGFTVSQVREARAGSLQQAEDFELPFVTIKREPGRNPASEIRGQAEFLLARLGEHQRQTNE*VDRAKRYLGNVNDDIAAGRIASTDGYAPPYNTSYNLDDER 2888
            DSWIDESRITVRFP HA N CRQAM DAGFTVSQV+E+R G+LQQ ++ EL FV IKR+PG NPA  IR QAEFLLARL EHQRQT+  VD+A+RYL NVNDDIAAGRIASTDGY+PPYNTS+NL DER
Sbjct:   68 DSWIDESRITVRFPPHAANRCRQAMLDAGFTVSQVKESRFGTLQQTKEVELLFVAIKRKPGHNPARGIRSQAEFLLARLEEHQRQTDIHVDQARRYLDNVNDDIAAGRIASTDGYSPPYNTSFNLHDER 196          
The following BLAST results are available for this feature:
BLAST of SMED30027849 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 SMED30027849 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 SMED30027849 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 SMED30027849 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 SMED30027849 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 SMED30027849 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 SMED30027849 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 SMED30027849 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 SMED30027849 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 SMED30027849 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 SMED30027849 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 SMED30027849 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 SMED30027849 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 SMED30027849 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000026305.11.553e-6785.83SMESG000026305.1[more]
SMESG000042239.11.250e-6275.36SMESG000042239.1[more]
SMESG000019398.18.938e-6177.27SMESG000019398.1[more]
SMESG000039041.11.524e-5772.93SMESG000039041.1[more]
SMESG000011208.17.256e-5777.52SMESG000011208.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027849 ID=SMED30027849|Name=SMED30027849|organism=Schmidtea mediterranea sexual|type=transcript|length=2888bp
CTAACAAATAAACTTGAACCGTATCCGTAACAACCGCAATAGAAAATTTC
TTACAACCTAAACTCCAATAATTAATGAATGACCATAGAGTGAGGGTTAG
TAAAAATCGGGAAAACGTAGCGATAGGTCAATAGATAAGGATCAATAAAA
ATCTATACCTAAGGAAAGGTGGCACGCCAAACATCGAGTCTGTCATTGGT
TAAGTAATAATGTTCATCGACACAGAGAGACACTAACAGATAGACCCCGG
TCTCTATTAATACTCATCACTACAACTAACTTCCACCTCAAGTGAGTATT
CGGATTAACCAGTCATTTAACCCCAGTTTACTCCCTTTCTAAACCCAATA
ACAAACAATGTTTCGGAGAAATTTTTTTATTAAACAAAATATATTATAAT
CACAATTGTAAGCTTGCTACGGAGAATCCCATTTTGACATAATCGCCCAG
AAAATAACGCCCTAAAAGCCCAAAAAAATCAATAATTCAAAAGAGAAAAA
TCATACCAAATACCTGTTATGAAAGTAATTACGATCCACGAGTATCAATC
AACCTAAGGATAGCCGGAAAAATCAAGAAGGCGAATGACACAAACCAAAT
AGTATTCTGTATATAAACTGTCGATTTGATATTTATGTCTCGGCCGATCG
ATATTGGTGCTTTTCCTTTTGCATACACTAACGACAATCCAGGATGCGAT
AAGTGCACCAATTTACAAGTGTCCCACATGCAATTTCAGCACAGTGATCC
ATATAACAGTCGATGTGACCCATACAACACACCCACTCACTGTGTCCGCC
GATTCCATTTAGCAAAGCTGGTAGTCACACGCATTTCCGCTTCTTCGATT
GACACCCCGAGCTATATAAGAAATATCGATGGGTCGGGGCTAACAGTTAA
ATTTCGGAAAATTCAAATGTATCGCCAATCGAACCCAACAAACGACGACA
CAACGGCCAGGATTCCGTATGATGACATAGTTCTAAACCCAAGAGCTCGA
CCTTCAGGTAAATTTTATTTCTACGAATTTCATTGTTAATCTGTACAAGC
CCTAGATAGAGATCTCGCAGTACCAGCCCCAATGCTAATTTTTGAACTAG
AAATGCCAATAACAAAAAACGATTTAAAAAATTATAAAATACAATACTGG
AAAGACCGGTGTTTTATCTTGATCATTTTTATGCCAAAACCCCAATCAGT
AAAGATTATGCACACTAGTACCCGTTCAAGAGAATAAATGAGGCCATATC
CGTTTCCGACTACCATAGCCCATATTCCAAAAATTACAAGGGGACATATA
GATTTCACGTTATCCGTTAACCAAGGAGAGACTATCCGAATGTTAAGACG
ATTTTAAAAAATATTTTTCCCATGGATATAATTAATTGAGATGCCGAAAA
CCTACCAATTTCAAATGATGAAGTATTCCGTTGTTTTTGATGTTTTTGAT
GTTTGTGCCCAAATTTCAGGTTATCGCTAAATTTAATAACTAAAATATAT
TGAATAACTCGATTTATTTTTTTGTGAATATTATGTATTTGATAGAAGTA
ATTTTGATTTAATTTATTTTTATTTAATAAGTTCTGTGTTAATGACAGAT
GGCCATAACGTACTTTAGACCCTATCCGGTAAATAAGGTCACATAAGTAT
TGATAAATCGATATCATTATCAAATACAAATAGGTATATTTTTAACTTTA
TATATGTAGGTAATATTAAGTAGTAGGGTTGTAGAATAATTGTAAATAAA
ATAATTTAATAAATAAAATACCCGTGTCAAGTCAACGTAAGTAGCCAAAT
TCTTATTTCGTAATACTAAAGAATACTAAAGAATATAGATAATTTTAAAA
TGGAATATCATTATCAAGTTGAAATAAGTCCTCTAATATTAACAGGAGAA
GTTCCGTTCCCGTACACGATAAAAATACATTCTAAATGAAATATAACTAG
GAAGTGATATGATAATTAAATGTATAAAATATACTTAATATTACTTACGA
TTAGTAATATCAATAAAGATTAATTACCAAGTAACTAATGATAGGGTTGA
ATTTTTCTCAGCTTTTGTGACAGTAACTTCGTTACTTAGGATATGGAAAA
CTAACTAACTAGTTAATTTAAACAAAACTGAAGAGGTTTAATGCAAAGAA
TCTTACATTTATTAGCCCAGAGAAAAACATACTAAACATCATCCCACGAG
ATTACCATTTAGTTCTAGTTTGATTTTAATTAAGTTAATTCATAATTACA
TTGTTAATTTAGTTATTTATTTTATAATTAGTTATACGTGGAGGTGTCCG
AAAAATGAATTAAATTACAAATATCGTATTACAAATTAATGCAACGAAAA
TAATCATGTTTGAAAAGCCTACAAAGTTTTGATTCTTTTAGGTCAACGTA
TCAACCTTTTCGACGAAATTATAGCGAATAGGAAATAATTTCTTCTCCAT
AGAGTGTGCGTAGAGTGTATTAAAAATTTGTAAAATTAGTTTCTTTTAGA
CGATTCGTGGATTGATGAATCCCGGATCACAGTACGTTTTCCAGCGCATG
CGGTAAACTTTTGCCGCCAGGCAATGTGGGATGCGGGATTTACCGTATCC
CAAGTCAGAGAGGCCAGAGCCGGTAGCCTACAACAAGCGGAAGATTTCGA
GCTCCCGTTCGTCACGATAAAGCGGGAGCCGGGTCGGAATCCTGCCAGTG
AGATCCGTGGCCAAGCTGAGTTCCTCCTTGCGCGTCTTGGGGAACATCAG
CGACAGACCAATGAGTAAGTGGATCGTGCAAAACGCTACCTCGGCAATGT
AAACGACGACATTGCCGCGGGCCGGATCGCCAGTACGGACGGGTACGCCC
CGCCGTACAATACGTCGTACAATCTCGACGACGAAAGG
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protein sequence of SMED30027849-orf-1

>SMED30027849-orf-1 ID=SMED30027849-orf-1|Name=SMED30027849-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=135bp
MSRPIDIGAFPFAYTNDNPGCDKCTNLQVSHMQFQHSDPYNSRCDPYNTP
THCVRRFHLAKLVVTRISASSIDTPSYIRNIDGSGLTVKFRKIQMYRQSN
PTNDDTTARIPYDDIVLNPRARPSGKFYFYEFHC*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland