TPA_inf: pyrokinin prohormone like-1

Overview
NameTPA_inf: pyrokinin prohormone like-1 (DAA33896.1)
Smed IDSMED30026493
Length (bp)701
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 TPA_inf: pyrokinin prohormone like-1 (SMED30026493) t-SNE clustered cells

Violin plots show distribution of expression levels for TPA_inf: pyrokinin prohormone like-1 (SMED30026493) 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 TPA_inf: pyrokinin prohormone like-1 (SMED30026493) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for TPA_inf: pyrokinin prohormone like-1 (SMED30026493) 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.
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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




SMED30026493

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



PAGE Curations: 19

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30026493SMESG000013290.1 SmedASXL_007287SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30026493SMESG000013290.1 dd_Smed_v4_14095_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30026493SMESG000013290.1 dd_Smed_v4_14095_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30026493SMESG000013290.1 dd_Smed_v4_14095_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult fluorescence in situ hybridization evidence
head regionSMED30026493SMESG000013290.1 dd_Smed_v4_14095_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult fluorescence in situ hybridization evidence
pharynx tipSMED30026493SMESG000013290.1 dd_Smed_v4_14095_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult fluorescence in situ hybridization evidence
non-ciliated neuronSMED30026493SMESG000013290.1 dd_Smed_v4_14095_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30026493SMESG000013290.1 dd_Smed_v6_14095_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30026493SMESG000013290.1 OX_Smed_1.0.00937ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30026493SMESG000013290.1 BK007007smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism asexual adult colorimetric in situ hybridization evidence
pharynxSMED30026493SMESG000013290.1 BK007007smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism juvenile colorimetric in situ hybridization evidence
cephalic gangliaSMED30026493SMESG000013290.1 BK007007smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism juvenile colorimetric in situ hybridization evidence
cephalic gangliaSMED30026493SMESG000013290.1 BK007007smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism asexual adult colorimetric in situ hybridization evidence
ventral nerve cordSMED30026493SMESG000013290.1 BK007007smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism juvenile colorimetric in situ hybridization evidence
ventral nerve cordSMED30026493SMESG000013290.1 BK007007smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism asexual adult colorimetric in situ hybridization evidence
ventral nerve cordSMED30026493SMESG000013290.1 BK007007smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
copulatory apparatusSMED30026493SMESG000013290.1 BK007007smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
reproductive organSMED30026493SMESG000013290.1 Contig43965newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30026493SMESG000013290.1 Contig43965uc_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 TPA_inf: pyrokinin prohormone like-1 vs. TrEMBL
Match: E3CTI2 (Pyrokinin prohormone like-1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 223.016 bits (567), Expect = 1.654e-71
Identity = 110/110 (100.00%), Postives = 110/110 (100.00%), Query Frame = -1
Query:   78 MKFSRICFIILVSLELFVVNEAVHMSDQLVFSLLVLIANHEINSKNFIYIPDDSFINEMDRAIDKKIFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRLGK 407
            MKFSRICFIILVSLELFVVNEAVHMSDQLVFSLLVLIANHEINSKNFIYIPDDSFINEMDRAIDKKIFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRLGK
Sbjct:    1 MKFSRICFIILVSLELFVVNEAVHMSDQLVFSLLVLIANHEINSKNFIYIPDDSFINEMDRAIDKKIFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRLGK 110          
BLAST of TPA_inf: pyrokinin prohormone like-1 vs. TrEMBL
Match: A0A193PF67 (Neuropeptide-34 OS=Dugesia japonica OX=6161 GN=DjNp34 PE=2 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 2.027e-8
Identity = 32/46 (69.57%), Postives = 33/46 (71.74%), Query Frame = -1
Query:   78 KKIFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRLGK 215
            KK FSPRMGKRYFSPRMGKR  S  MG     P   KRYFSPR+GK
Sbjct:   12 KKYFSPRMGKRYFSPRMGKRDSSLTMGLSRIQPNWVKRYFSPRMGK 57          
BLAST of TPA_inf: pyrokinin prohormone like-1 vs. TrEMBL
Match: A0A381VRQ7 (Uncharacterized protein (Fragment) OS=marine metagenome OX=408172 GN=METZ01_LOCUS95864 PE=4 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 1.029e-6
Identity = 25/50 (50.00%), Postives = 26/50 (52.00%), Query Frame = -1
Query:   78 RAIDKKIFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRLGK 227
              I    FSP MG   FSP MG   FSP MG   FSP MG   FSP +G 
Sbjct:   35 TTIGSNPFSPNMGSNPFSPNMGSNPFSPNMGSNPFSPNMGSNPFSPNMGS 84          
BLAST of TPA_inf: pyrokinin prohormone like-1 vs. Ensembl Nematostella
Match: EDO46947 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7RNL3])

HSP 1 Score: 49.2914 bits (116), Expect = 7.183e-7
Identity = 29/76 (38.16%), Postives = 40/76 (52.63%), Query Frame = -1
Query:   78 VLIANHEINSKNFIYIPDDSFINEMDRAIDKKIFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRLGK 305
            V++ ++E ++ +  Y+P+      +    DK+  S   GKRY S   GKRY S   GKRY S   GKRY S   GK
Sbjct:  652 VVVKDNEDHTYSCRYVPNTPGKRYVSNTPDKRYLSNTPGKRYVSNTPGKRYVSNTPGKRYVSNTPGKRYVSNTPGK 727          
BLAST of TPA_inf: pyrokinin prohormone like-1 vs. Planmine SMEST
Match: SMESG000013290.1 (SMESG000013290.1)

HSP 1 Score: 223.016 bits (567), Expect = 4.601e-75
Identity = 110/110 (100.00%), Postives = 110/110 (100.00%), Query Frame = -1
Query:   78 MKFSRICFIILVSLELFVVNEAVHMSDQLVFSLLVLIANHEINSKNFIYIPDDSFINEMDRAIDKKIFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRLGK 407
            MKFSRICFIILVSLELFVVNEAVHMSDQLVFSLLVLIANHEINSKNFIYIPDDSFINEMDRAIDKKIFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRLGK
Sbjct:    1 MKFSRICFIILVSLELFVVNEAVHMSDQLVFSLLVLIANHEINSKNFIYIPDDSFINEMDRAIDKKIFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRLGK 110          
The following BLAST results are available for this feature:
BLAST of TPA_inf: pyrokinin prohormone like-1 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 TPA_inf: pyrokinin prohormone like-1 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 TPA_inf: pyrokinin prohormone like-1 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 TPA_inf: pyrokinin prohormone like-1 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 TPA_inf: pyrokinin prohormone like-1 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 TPA_inf: pyrokinin prohormone like-1 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 TPA_inf: pyrokinin prohormone like-1 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 TPA_inf: pyrokinin prohormone like-1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
E3CTI21.654e-71100.00Pyrokinin prohormone like-1 OS=Schmidtea mediterra... [more]
A0A193PF672.027e-869.57Neuropeptide-34 OS=Dugesia japonica OX=6161 GN=DjN... [more]
A0A381VRQ71.029e-650.00Uncharacterized protein (Fragment) OS=marine metag... [more]
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BLAST of TPA_inf: pyrokinin prohormone like-1 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 TPA_inf: pyrokinin prohormone like-1 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 TPA_inf: pyrokinin prohormone like-1 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 TPA_inf: pyrokinin prohormone like-1 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO469477.183e-738.16Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of TPA_inf: pyrokinin prohormone like-1 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 TPA_inf: pyrokinin prohormone like-1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000013290.14.601e-75100.00SMESG000013290.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30026493
GenBankDAA33896.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026493 ID=SMED30026493|Name=TPA_inf: pyrokinin prohormone like-1|organism=Schmidtea mediterranea sexual|type=transcript|length=701bp
TTTTTTTAAGTCACTTTGAAAATGTTTTTATTAAAATAAAACAATAATAT
AAATATTTATGAAGCACTTTATGTTCATTTACCTAATCTTGGAGAAAAGT
ACCGCTTGCCCATTCTCGGAGAAAAATACCTTTTTCCCATTCTCGGAGAA
AAATATCTTTTTCCCATTCTCGGAGAAAAATACCGTTTTCCCATTCTTGG
TGAAAAGATCTTCTTGTCAATCGCTCGATCCATTTCATTGATGAAACTAT
CATCAGGAATATAAATGAAGTTTTTCGAATTTATTTCATGGTTGGCAATC
AAAACCAAAAGACTGAAAACCAACTGGTCACTCATGTGAACAGCTTCATT
GACAACAAACAGTTCAAGTGACACCAAAATAATGAAACAAATCCTGCTGA
ATTTCATCACTGAATGCCTTTATTATTACATTTAGCGCATTTATAGAAAA
TGGCAAGAATTGTCCATTAGCCAATGAAATCGAGGCGGAAATTTGGTTCA
TTTATAAGTCGTCAGGAAAAAGTAACAAATAATATTTTCTAATCATTCAA
CGAAAGTAGTAAAATCGTGAAAAATGTCCTTCAGAAATTTTCGGTTATTT
TAGACAAGAAATGAATAGTATAATTTATTTTAATGATAATTTATTGAGAA
ATAATAATTTAATAAAAATAACTAATTCAATTAGGCCGACTTTGATAATT
T
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protein sequence of SMED30026493-orf-1

>SMED30026493-orf-1 ID=SMED30026493-orf-1|Name=SMED30026493-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=111bp
MKFSRICFIILVSLELFVVNEAVHMSDQLVFSLLVLIANHEINSKNFIYI
PDDSFINEMDRAIDKKIFSPRMGKRYFSPRMGKRYFSPRMGKRYFSPRMG
KRYFSPRLGK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000044cephalic ganglia
PLANA:0000097ventral nerve cord
PLANA:0000099neuron
PLANA:0000232copulatory apparatus
PLANA:0000418head
PLANA:0002074pharynx tip
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR001484Pyrokinin_CS
Vocabulary: biological process
TermDefinition
GO:0007218neuropeptide signaling pathway
Vocabulary: molecular function
TermDefinition
GO:0005184neuropeptide hormone activity
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001484Pyrokinin, conserved sitePROSITEPS00539PYROKININcoord: 104..109
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..22
score: 0.806