SMED30026900

Overview
NameSMED30026900
Smed IDSMED30026900
Length (bp)930
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



SMED30026900

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
reproductive organSMED30026900SMESG000032267.1 Contig37936newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30026900SMESG000032267.1 Contig37936uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
cement glandSMED30026900SMESG000032267.1 GDAG01008672.1SmedSxl_ww_GDAG01.fsa_ntPMID:279364
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30026900 vs. Planmine SMEST
Match: SMESG000032267.1 (SMESG000032267.1)

HSP 1 Score: 553.903 bits (1426), Expect = 0.000e+0
Identity = 271/271 (100.00%), Postives = 271/271 (100.00%), Query Frame = 2 
Query:    2 NYIILLLCLFNVISINTIKLAEAKQRLSNNNCVRNRKYCHLGFTTLHSLCLAWSEVNEDHKIPRILEKTTICVKSYDLYICHTKEYSLDNRIRNWDYCEQQICDPYDLCRDGIKWETFDKSIKLNIPKKFDTLIILEKSKFDCVISAQCQNCESAKRTIENDFSQCKILEINNDKNKWISFDNLQPKRRYLFYVLPLKNNDLIGSVFEVILDTLPLNKGKPVQLTTKKRSYMIKEMKAAQWNNIIRSTKKMLEPVKEYNIFAFEPAGVVYI 814
            NYIILLLCLFNVISINTIKLAEAKQRLSNNNCVRNRKYCHLGFTTLHSLCLAWSEVNEDHKIPRILEKTTICVKSYDLYICHTKEYSLDNRIRNWDYCEQQICDPYDLCRDGIKWETFDKSIKLNIPKKFDTLIILEKSKFDCVISAQCQNCESAKRTIENDFSQCKILEINNDKNKWISFDNLQPKRRYLFYVLPLKNNDLIGSVFEVILDTLPLNKGKPVQLTTKKRSYMIKEMKAAQWNNIIRSTKKMLEPVKEYNIFAFEPAGVVYI
Sbjct:    5 NYIILLLCLFNVISINTIKLAEAKQRLSNNNCVRNRKYCHLGFTTLHSLCLAWSEVNEDHKIPRILEKTTICVKSYDLYICHTKEYSLDNRIRNWDYCEQQICDPYDLCRDGIKWETFDKSIKLNIPKKFDTLIILEKSKFDCVISAQCQNCESAKRTIENDFSQCKILEINNDKNKWISFDNLQPKRRYLFYVLPLKNNDLIGSVFEVILDTLPLNKGKPVQLTTKKRSYMIKEMKAAQWNNIIRSTKKMLEPVKEYNIFAFEPAGVVYI 275
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BLAST of SMED30026900 vs. Planmine SMEST
Match: SMESG000032278.1 (SMESG000032278.1)

HSP 1 Score: 151.754 bits (382), Expect = 3.186e-44
Identity = 77/186 (41.40%), Postives = 119/186 (63.98%), Query Frame = 2 
Query:   83 SNNNCVRNRKYCHLGFTTLHSLCLAWSEVNEDHKIPRILEKTTICVKSYDLYICHTKEYSLDNRIRNWDYCEQQICDPYDLCRDGIKWETFDKSIKLNIPKKFDTLIILEKSKFDCVISAQCQNCESAKRTIENDFSQCKILEINNDKNKWISFDNLQPKRRYLFYVLPLKNNDLIGSVFEVILDT 640
            SN  C R+ ++C+L   +  S C+ W ++++  KI +I E TT+C K  + Y+C +     D + +++  C  Q CD Y+LC+ G+K+ET  KSIK N+ + +DT+II +KSK +C+ISA C +CES K  I+ +FS CK+L+  N   +   FDNL+P   ++FY+LP+KN  L GSVF V  +T
Sbjct:   32 SNLECARDLRFCNLAIMSPTSNCIPW-KLSKSFKIMKIFENTTLCQKGKEGYLCASNVLPSDKQKKDFTLCPNQKCDTYNLCKHGMKYETTYKSIKFNLSQDYDTVIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFDNLKPNTNHVFYLLPIKNRRLKGSVFTVSFNT 216
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BLAST of SMED30026900 vs. Planmine SMEST
Match: SMESG000032278.1 (SMESG000032278.1)

HSP 1 Score: 151.754 bits (382), Expect = 3.784e-44
Identity = 77/186 (41.40%), Postives = 119/186 (63.98%), Query Frame = 2 
Query:   83 SNNNCVRNRKYCHLGFTTLHSLCLAWSEVNEDHKIPRILEKTTICVKSYDLYICHTKEYSLDNRIRNWDYCEQQICDPYDLCRDGIKWETFDKSIKLNIPKKFDTLIILEKSKFDCVISAQCQNCESAKRTIENDFSQCKILEINNDKNKWISFDNLQPKRRYLFYVLPLKNNDLIGSVFEVILDT 640
            SN  C R+ ++C+L   +  S C+ W ++++  KI +I E TT+C K  + Y+C +     D + +++  C  Q CD Y+LC+ G+K+ET  KSIK N+ + +DT+II +KSK +C+ISA C +CES K  I+ +FS CK+L+  N   +   FDNL+P   ++FY+LP+KN  L GSVF V  +T
Sbjct:   36 SNLECARDLRFCNLAIMSPTSNCIPW-KLSKSFKIMKIFENTTLCQKGKEGYLCASNVLPSDKQKKDFTLCPNQKCDTYNLCKHGMKYETTYKSIKFNLSQDYDTVIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFDNLKPNTNHVFYLLPIKNRRLKGSVFTVSFNT 220
[Close]
BLAST of SMED30026900 vs. Planmine SMEST
Match: SMESG000032278.1 (SMESG000032278.1)

HSP 1 Score: 151.754 bits (382), Expect = 5.351e-44
Identity = 77/186 (41.40%), Postives = 119/186 (63.98%), Query Frame = 2 
Query:   83 SNNNCVRNRKYCHLGFTTLHSLCLAWSEVNEDHKIPRILEKTTICVKSYDLYICHTKEYSLDNRIRNWDYCEQQICDPYDLCRDGIKWETFDKSIKLNIPKKFDTLIILEKSKFDCVISAQCQNCESAKRTIENDFSQCKILEINNDKNKWISFDNLQPKRRYLFYVLPLKNNDLIGSVFEVILDT 640
            SN  C R+ ++C+L   +  S C+ W ++++  KI +I E TT+C K  + Y+C +     D + +++  C  Q CD Y+LC+ G+K+ET  KSIK N+ + +DT+II +KSK +C+ISA C +CES K  I+ +FS CK+L+  N   +   FDNL+P   ++FY+LP+KN  L GSVF V  +T
Sbjct:   47 SNLECARDLRFCNLAIMSPTSNCIPW-KLSKSFKIMKIFENTTLCQKGKEGYLCASNVLPSDKQKKDFTLCPNQKCDTYNLCKHGMKYETTYKSIKFNLSQDYDTVIIWQKSKSECIISALCHDCESVKNIIKINFSGCKLLKGTNITPEPTLFDNLKPNTNHVFYLLPIKNRRLKGSVFTVSFNT 231
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BLAST of SMED30026900 vs. Planmine SMEST
Match: SMESG000032456.1 (SMESG000032456.1)

HSP 1 Score: 149.058 bits (375), Expect = 1.683e-40
Identity = 80/202 (39.60%), Postives = 122/202 (60.40%), Query Frame = 2 
Query:   86 NNNCVRNRKYCHLGFTTLHSLCLAWSEVNEDHKIPRILEKTTICVKSYDLYICHTKEYSLDNRIRNWDYCEQQICD-PYDLCRDGIKWETFDKSIKLNIPKKFDTLIILEKSKFDCVISAQCQNCESAKRTIENDFSQCKILEINNDKNKWISFDNLQPKRRYLFYVLPLKNNDLIGSVFEVILDTLPLNKGKPVQLTTKKR 688
            ++ CV ++ YC  G ++  S C+ W++  + +K   I  KTT+C K  + Y C T          +W+YC+   C+  Y+LC DGI WETF+KS+KL IP KFDT+ IL+KS+ +C ISAQC+ C S ++ I N F+ C++LE++ D  + ISF NL    +Y FY+LP++   L+G VF++ L T       P  + + KR
Sbjct:   10 DSECVHDKAYCINGESSWKSPCIPWAQSTK-YKSVNIFLKTTLCKKENNDYWCATS--------VSWNYCQPSRCELSYNLCEDGISWETFEKSVKLKIPNKFDTVTILQKSESECAISAQCRMCRSVEQMIGNLFNGCQLLEVSRDHTRSISFPNLLHSTKYHFYILPIQEGRLMGFVFKLYLLTKISKPCLPYSIKSVKR 202
The following BLAST results are available for this feature:
BLAST of SMED30026900 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 SMED30026900 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 SMED30026900 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 SMED30026900 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 SMED30026900 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 SMED30026900 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 SMED30026900 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 SMED30026900 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 SMED30026900 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 SMED30026900 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 SMED30026900 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 SMED30026900 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 SMED30026900 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 SMED30026900 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000032267.10.000e+0100.00SMESG000032267.1[more]
SMESG000032278.13.186e-4441.40SMESG000032278.1[more]
SMESG000032278.13.784e-4441.40SMESG000032278.1[more]
SMESG000032278.15.351e-4441.40SMESG000032278.1[more]
SMESG000032456.11.683e-4039.60SMESG000032456.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026900 ID=SMED30026900|Name=SMED30026900|organism=Schmidtea mediterranea sexual|type=transcript|length=930bp
TAATTATATAATTTTGTTATTATGTCTTTTCAATGTAATATCAATAAATA
CAATAAAGTTGGCAGAAGCAAAACAAAGGTTATCAAATAACAATTGCGTT
CGAAACCGTAAATACTGTCATTTGGGGTTCACTACCCTTCATTCTTTGTG
TTTAGCGTGGTCAGAAGTAAATGAAGACCACAAAATTCCAAGAATATTAG
AAAAGACAACAATTTGTGTAAAGTCTTATGATTTATACATTTGTCACACT
AAAGAGTATTCATTAGACAATAGAATACGTAATTGGGATTACTGTGAACA
ACAGATCTGTGACCCCTACGATTTGTGTAGAGATGGAATAAAATGGGAAA
CTTTTGACAAATCCATCAAGCTGAATATTCCAAAGAAATTCGACACTTTG
ATTATTTTGGAAAAATCCAAGTTTGATTGCGTAATATCTGCCCAATGCCA
AAATTGTGAATCGGCAAAAAGAACAATTGAAAATGATTTCAGTCAGTGTA
AAATATTGGAAATAAATAATGATAAAAATAAATGGATATCATTTGACAAT
CTCCAACCAAAAAGAAGGTACTTATTTTATGTGCTTCCATTGAAGAACAA
TGATTTGATCGGATCTGTGTTTGAGGTAATCTTGGATACATTACCCTTAA
ATAAAGGGAAACCTGTTCAACTGACTACTAAAAAACGATCATACATGATA
AAAGAAATGAAAGCTGCTCAATGGAATAATATCATACGAAGTACCAAAAA
AATGTTAGAACCTGTCAAAGAATATAATATTTTCGCATTTGAACCTGCCG
GTGTTGTTTATATATAATATAAATGTTTTGTTCAGATGTAAAACTATAAA
TTGTAATACCTATTTATTCAAATGATCACAATATGTTTGATTTGTTCAAT
TATTTACGTGCATTAAAAACTGAAACACAG
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protein sequence of SMED30026900-orf-1

>SMED30026900-orf-1 ID=SMED30026900-orf-1|Name=SMED30026900-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=272bp
NYIILLLCLFNVISINTIKLAEAKQRLSNNNCVRNRKYCHLGFTTLHSLC
LAWSEVNEDHKIPRILEKTTICVKSYDLYICHTKEYSLDNRIRNWDYCEQ
QICDPYDLCRDGIKWETFDKSIKLNIPKKFDTLIILEKSKFDCVISAQCQ
NCESAKRTIENDFSQCKILEINNDKNKWISFDNLQPKRRYLFYVLPLKNN
DLIGSVFEVILDTLPLNKGKPVQLTTKKRSYMIKEMKAAQWNNIIRSTKK
MLEPVKEYNIFAFEPAGVVYI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000224cement gland
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR023795Serpin_CS
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..23
score: 0.696