SMED30017887

Overview
NameSMED30017887
Smed IDSMED30017887
Length (bp)1513
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



SMED30017887

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
reproductive organSMED30017887SMESG000072874.1 SMESG000077611.1 SMESG000073729.1 Contig5399newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30017887SMESG000072874.1 SMESG000077611.1 SMESG000073729.1 Contig5399uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30017887SMESG000072403.1 Contig5399newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30017887SMESG000072403.1 Contig5399uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30017887 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001082:38833..40345 +7565
Homology
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BLAST of SMED30017887 vs. Planmine SMEST
Match: SMESG000072874.1 (SMESG000072874.1)

HSP 1 Score: 733.021 bits (1891), Expect = 0.000e+0
Identity = 472/472 (100.00%), Postives = 472/472 (100.00%), Query Frame = 2 
Query:   11 MFPEHWTYRPSERMKIVDPKVTKNIEDFKNRSEMKNFSNKIIREIRSTNILLQIXXXXXXXXXXXXXXXXXXAIAXXXXXXXXXXXXXXXXLKEYAMRIRYQKEIERKAEANEKYFQRDRLNDNEIRTAQRDIHFLEIIKDWXXXXXXXXXXXXXXXCESDFWAEKMKEERNKMLERENIEAAKLKIRSDEIMNQIKEREHQRALDREKQLEQIQFNFKNAKELQSKLEQEKIDRKANEKATKQNFRKSLDRHIQMKNRRLDEDKKRENAFDTIMMDENSLKMKESSYDAYKKKRETLKHLKNYIDRQNCIKEEKEADNKLIDQMVKKADIENNKKFRELQYLQRKKYADLIKSMNQSREDHLXXXXXXXXXXXXXXXXXXDAMNXXXXXXXXXXXXXXXXXXXXXNVYIDALSNQIKFNSHVAGMKKEEKIRELNSMKEAEQIYLKTLQEIKDKEELLFVHPWRSRVPGSK 1426
            MFPEHWTYRPSERMKIVDPKVTKNIEDFKNRSEMKNFSNKIIREIRSTNILLQINLEERRNRLRNLLDEEDRAIAEEHTTRIETIDRRRDRLKEYAMRIRYQKEIERKAEANEKYFQRDRLNDNEIRTAQRDIHFLEIIKDWEKLKDIKERIRKEERCESDFWAEKMKEERNKMLERENIEAAKLKIRSDEIMNQIKEREHQRALDREKQLEQIQFNFKNAKELQSKLEQEKIDRKANEKATKQNFRKSLDRHIQMKNRRLDEDKKRENAFDTIMMDENSLKMKESSYDAYKKKRETLKHLKNYIDRQNCIKEEKEADNKLIDQMVKKADIENNKKFRELQYLQRKKYADLIKSMNQSREDHLKKIEEKKVEKVIEIQKEKDAMNEFIKIEMEKERKKKEKEKEKINVYIDALSNQIKFNSHVAGMKKEEKIRELNSMKEAEQIYLKTLQEIKDKEELLFVHPWRSRVPGSK
Sbjct:    1 MFPEHWTYRPSERMKIVDPKVTKNIEDFKNRSEMKNFSNKIIREIRSTNILLQINLEERRNRLRNLLDEEDRAIAEEHTTRIETIDRRRDRLKEYAMRIRYQKEIERKAEANEKYFQRDRLNDNEIRTAQRDIHFLEIIKDWEKLKDIKERIRKEERCESDFWAEKMKEERNKMLERENIEAAKLKIRSDEIMNQIKEREHQRALDREKQLEQIQFNFKNAKELQSKLEQEKIDRKANEKATKQNFRKSLDRHIQMKNRRLDEDKKRENAFDTIMMDENSLKMKESSYDAYKKKRETLKHLKNYIDRQNCIKEEKEADNKLIDQMVKKADIENNKKFRELQYLQRKKYADLIKSMNQSREDHLKKIEEKKVEKVIEIQKEKDAMNEFIKIEMEKERKKKEKEKEKINVYIDALSNQIKFNSHVAGMKKEEKIRELNSMKEAEQIYLKTLQEIKDKEELLFVHPWRSRVPGSK 472
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BLAST of SMED30017887 vs. Planmine SMEST
Match: SMESG000071248.1 (SMESG000071248.1)

HSP 1 Score: 128.642 bits (322), Expect = 3.878e-32
Identity = 128/375 (34.13%), Postives = 213/375 (56.80%), Query Frame = 2 
Query:  284 LKEYAMRIRYQKEIERKAEANEKYFQRDRLNDNEIRTAQRDIHFLEIIKDWXXXXXXXXXXXXXXXCESDFWAEKMKEERNKMLERENIEAAKLKIRSDEIMNQIKEREHQRALDREKQLEQIQFNFKNAKELQSKLEQEKIDRKANEKATKQNFRKSLDRHIQMKNRRLDEDKKRENAFDTIMMDENSLKMKESSYDAYKKKRETLKHLKNYIDRQNCIKEEKEADNKLIDQMVKKADIENNKKFRELQYLQRKKYADLIKSMNQSREDHLXXXXXXXXXXXXXXXXXXDAMNXXXXXXXXXXXXXXXXXXXXXNVYIDALSNQIKFNSHVAGMKKEEKIRELNSMKEAEQIYLKTLQEIKDKEELLFVHPWRS 1408
            LKE A+RIR Q E+ER+  A+ K  Q  RLND++ R  QR  H   I +DW+KLK+I+ RI++EE CE  FW EK  E    ++ +ENI   K     ++   QI+ RE QR +++E++LE   F  + +KE+  ++ +E    K  +   + ++ K LD  I++K    D +K  E + + I+ DEN  K+K +     +  R   K   N++  Q+C+K+ +E + K I+  V K  I  ++K  E++  + KK+A LI  +  +++D L +  + K   V E  K+++ +N+  +  + +++ K EKE++K   +   L  Q+ FN  +    K EK RE  SM EAE+ Y+  ++EI+ KE+L F+HPWR+
Sbjct:   91 LKEQAVRIRKQTELERQLMADSKRTQAMRLNDDQTRYKQRLQHAKAIYEDWDKLKEIENRIKREENCEEKFWLEKNSERIEDLIRKENIVKNKNNAIKNDFKQQIEMREKQRQIEKEEKLENQAFLNEMSKEVDKQIAEEDALVKKKKAMKQSDYHKLLDNQIRIKKAINDRNKSTEESLELILKDENQQKIKSNQAKNQQAIRNNFKSFTNFMKYQDCLKKTREEEEKEINDNVMKTQIAIHRKNYEIEKEKVKKFAKLISEIKIAQKDQLVEASKLKNLIVEEKVKDRELVNKIYEEGLIQDKIKLEKERKKHESHFQLLKQQLVFNEEMRNFCKAEKDRERKSMNEAEKNYVVKIEEIRSKEQLQFIHPWRA 465
The following BLAST results are available for this feature:
BLAST of SMED30017887 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 SMED30017887 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 SMED30017887 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 SMED30017887 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 SMED30017887 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 SMED30017887 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 SMED30017887 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 SMED30017887 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 SMED30017887 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 SMED30017887 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 SMED30017887 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 SMED30017887 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 SMED30017887 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 SMED30017887 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000072874.10.000e+0100.00SMESG000072874.1[more]
SMESG000071248.13.878e-3234.13SMESG000071248.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017887 ID=SMED30017887|Name=SMED30017887|organism=Schmidtea mediterranea sexual|type=transcript|length=1513bp
ACAATTAATTATGTTTCCCGAGCATTGGACCTACAGGCCTAGTGAAAGAA
TGAAAATAGTTGACCCTAAGGTCACCAAAAATATTGAAGATTTCAAGAAC
AGAAGTGAAATGAAAAACTTCAGCAACAAGATAATTAGAGAAATTCGAAG
CACAAATATTTTGCTGCAAATTAATCTAGAAGAACGAAGAAATAGATTAC
GCAATTTATTGGACGAGGAAGACCGGGCTATTGCTGAAGAACATACCACA
AGAATAGAGACCATCGACAGAAGAAGAGATCGGTTGAAAGAATATGCAAT
GAGGATTCGCTACCAGAAAGAAATTGAAAGAAAAGCAGAAGCGAATGAGA
AATATTTTCAACGAGACAGACTAAACGACAACGAGATTCGAACTGCTCAA
AGAGACATTCATTTCCTTGAAATCATTAAAGACTGGGAAAAATTAAAAGA
TATAAAAGAAAGAATTCGTAAAGAAGAAAGGTGTGAATCAGATTTCTGGG
CAGAGAAGATGAAGGAAGAGAGAAATAAAATGCTTGAAAGAGAAAATATA
GAAGCTGCTAAATTGAAAATACGAAGTGATGAGATAATGAACCAAATCAA
GGAAAGAGAACATCAAAGAGCACTGGACCGAGAGAAGCAATTAGAACAAA
TACAATTCAACTTTAAAAATGCCAAAGAACTTCAAAGTAAATTGGAACAA
GAAAAGATTGATAGAAAAGCAAACGAGAAAGCAACAAAACAAAATTTCCG
GAAATCCTTAGATAGACATATTCAAATGAAAAACCGCAGATTAGACGAAG
ACAAAAAACGAGAAAATGCATTCGATACAATTATGATGGATGAGAATTCA
CTTAAGATGAAGGAAAGCAGCTACGACGCCTACAAGAAGAAGCGAGAAAC
TCTTAAGCATCTTAAAAATTACATAGATAGACAAAATTGTATCAAAGAAG
AAAAAGAAGCCGATAATAAATTAATTGATCAAATGGTGAAAAAGGCAGAT
ATAGAAAACAATAAAAAGTTCAGAGAGCTCCAATACCTTCAAAGAAAGAA
ATACGCGGATCTCATAAAATCTATGAATCAGTCTCGAGAGGACCATTTGA
AGAAAATCGAAGAAAAGAAAGTTGAGAAAGTCATTGAAATTCAAAAAGAA
AAAGATGCAATGAATGAGTTCATTAAAATCGAAATGGAAAAAGAAAGAAA
AAAGAAAGAAAAAGAAAAAGAAAAGATTAATGTTTATATTGACGCTTTAA
GCAATCAAATCAAATTTAATAGCCACGTTGCTGGTATGAAGAAGGAAGAA
AAGATACGCGAGTTGAATTCCATGAAAGAAGCTGAACAAATTTACTTGAA
AACCCTTCAAGAAATAAAAGACAAAGAGGAGTTATTATTTGTGCATCCTT
GGCGGTCCAGGGTTCCAGGGAGCAAATGATGAGGATGTCTTTTATGAGGA
GGGCGATTTGATTATTCTGTTGCTACAAATTGCAATTCTGTATAATTCAA
TGACAAATTCACG
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protein sequence of SMED30017887-orf-1

>SMED30017887-orf-1 ID=SMED30017887-orf-1|Name=SMED30017887-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=476bp
QLIMFPEHWTYRPSERMKIVDPKVTKNIEDFKNRSEMKNFSNKIIREIRS
TNILLQINLEERRNRLRNLLDEEDRAIAEEHTTRIETIDRRRDRLKEYAM
RIRYQKEIERKAEANEKYFQRDRLNDNEIRTAQRDIHFLEIIKDWEKLKD
IKERIRKEERCESDFWAEKMKEERNKMLERENIEAAKLKIRSDEIMNQIK
EREHQRALDREKQLEQIQFNFKNAKELQSKLEQEKIDRKANEKATKQNFR
KSLDRHIQMKNRRLDEDKKRENAFDTIMMDENSLKMKESSYDAYKKKRET
LKHLKNYIDRQNCIKEEKEADNKLIDQMVKKADIENNKKFRELQYLQRKK
YADLIKSMNQSREDHLKKIEEKKVEKVIEIQKEKDAMNEFIKIEMEKERK
KKEKEKEKINVYIDALSNQIKFNSHVAGMKKEEKIRELNSMKEAEQIYLK
TLQEIKDKEELLFVHPWRSRVPGSK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR033365CFAP53
Vocabulary: biological process
TermDefinition
GO:0060271cilium morphogenesis
GO:0003341cilium movement
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 441..461
NoneNo IPR availableCOILSCoilCoilcoord: 52..79
NoneNo IPR availableCOILSCoilCoilcoord: 355..386
NoneNo IPR availableCOILSCoilCoilcoord: 178..244
NoneNo IPR availableCOILSCoilCoilcoord: 388..419
NoneNo IPR availablePFAMPF13868TPHcoord: 125..458
e-value: 2.5E-7
score: 29.6
NoneNo IPR availablePANTHERPTHR31183FAMILY NOT NAMEDcoord: 29..472
IPR033365Cilia- and flagella-associated protein 53PANTHERPTHR31183:SF1CILIA- AND FLAGELLA-ASSOCIATED PROTEIN 53coord: 29..472