hypothetical protein

Overview
Namehypothetical protein (AFJ24814.1)
Smed IDSMED30025384
Length (bp)1360
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 hypothetical protein (SMED30025384) t-SNE clustered cells

Violin plots show distribution of expression levels for hypothetical protein (SMED30025384) 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 hypothetical protein (SMED30025384) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for hypothetical protein (SMED30025384) 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




SMED30025384

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
protonephridiaSMED30025384SMESG000077040.1 dd_Smed_v4_7293_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30025384SMESG000077040.1 dd_Smed_v4_7293_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30025384SMESG000077040.1 dd_Smed_v4_7293_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30025384SMESG000077040.1 dd_Smed_v6_7293_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of hypothetical protein vs. TrEMBL
Match: I1ZIG0 (Uncharacterized protein OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 712.605 bits (1838), Expect = 0.000e+0
Identity = 360/376 (95.74%), Postives = 360/376 (95.74%), Query Frame = 2
Query:  128 MFIFKLGAEALTRLEEHLNDQTTQPSTCTQKTITSNNLYTYSSNMESSILYNLLSTEDGSMCKPKSLLHPNYQINLDQPMPPRANTISFSDLREDPISLSPRPYSAPQSDSSSNIRKRKHSIISEITELKTMNYIKNCRINGSRISDIVDSPTISCSTDSFSEEPMDLSKTGDQIQSHGENGRLIVNSWLIDIVEIINPNNEQSNKNLAELSLSVRLHLLQSTWHRIIVTFLFEHLMKTSSIHLEGITKFISSLSGINNRSVFNNKKISKMYKTQLEELNNILYQIKKLNLDEMSMHYLRIGLLLTGNHDEMNKKNLNLIEMFIHSKIGISELNILIIRETIENVLKLNSVIIETIFYSHLDESVENVIEQILNNS 1255
            MFIFKLGAEALTRLEEHLNDQTTQPSTCTQKTITSNNLYTYSSNMESSILYNLLSTEDGSM                QPMPPRANTISFSDLREDPISLSPRPYSAPQSDSSSNIRKRKHSIISEITELKTMNYIKNCRINGSRISDIVDSPTISCSTDSFSEEPMDLSKTGDQIQSHGENGRLIVNSWLIDIVEIINPNNEQSNKNLAELSLSVRLHLLQSTWHRIIVTFLFEHLMKTSSIHLEGITKFISSLSGINNRSVFNNKKISKMYKTQLEELNNILYQIKKLNLDEMSMHYLRIGLLLTGNHDEMNKKNLNLIEMFIHSKIGISELNILIIRETIENVLKLNSVIIETIFYSHLDESVENVIEQILNNS
Sbjct:    1 MFIFKLGAEALTRLEEHLNDQTTQPSTCTQKTITSNNLYTYSSNMESSILYNLLSTEDGSMY---------------QPMPPRANTISFSDLREDPISLSPRPYSAPQSDSSSNIRKRKHSIISEITELKTMNYIKNCRINGSRISDIVDSPTISCSTDSFSEEPMDLSKTGDQIQSHGENGRLIVNSWLIDIVEIINPNNEQSNKNLAELSLSVRLHLLQSTWHRIIVTFLFEHLMKTSSIHLEGITKFISSLSGINNRSVFNNKKISKMYKTQLEELNNILYQIKKLNLDEMSMHYLRIGLLLTGNHDEMNKKNLNLIEMFIHSKIGISELNILIIRETIENVLKLNSVIIETIFYSHLDESVENVIEQILNNS 361          
BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000077040.1 (SMESG000077040.1)

HSP 1 Score: 712.605 bits (1838), Expect = 0.000e+0
Identity = 360/376 (95.74%), Postives = 360/376 (95.74%), Query Frame = 2
Query:  128 MFIFKLGAEALTRLEEHLNDQTTQPSTCTQKTITSNNLYTYSSNMESSILYNLLSTEDGSMCKPKSLLHPNYQINLDQPMPPRANTISFSDLREDPISLSPRPYSAPQSDSSSNIRKRKHSIISEITELKTMNYIKNCRINGSRISDIVDSPTISCSTDSFSEEPMDLSKTGDQIQSHGENGRLIVNSWLIDIVEIINPNNEQSNKNLAELSLSVRLHLLQSTWHRIIVTFLFEHLMKTSSIHLEGITKFISSLSGINNRSVFNNKKISKMYKTQLEELNNILYQIKKLNLDEMSMHYLRIGLLLTGNHDEMNKKNLNLIEMFIHSKIGISELNILIIRETIENVLKLNSVIIETIFYSHLDESVENVIEQILNNS 1255
            MFIFKLGAEALTRLEEHLNDQTTQPSTCTQKTITSNNLYTYSSNMESSILYNLLSTEDGSM                QPMPPRANTISFSDLREDPISLSPRPYSAPQSDSSSNIRKRKHSIISEITELKTMNYIKNCRINGSRISDIVDSPTISCSTDSFSEEPMDLSKTGDQIQSHGENGRLIVNSWLIDIVEIINPNNEQSNKNLAELSLSVRLHLLQSTWHRIIVTFLFEHLMKTSSIHLEGITKFISSLSGINNRSVFNNKKISKMYKTQLEELNNILYQIKKLNLDEMSMHYLRIGLLLTGNHDEMNKKNLNLIEMFIHSKIGISELNILIIRETIENVLKLNSVIIETIFYSHLDESVENVIEQILNNS
Sbjct:    1 MFIFKLGAEALTRLEEHLNDQTTQPSTCTQKTITSNNLYTYSSNMESSILYNLLSTEDGSMY---------------QPMPPRANTISFSDLREDPISLSPRPYSAPQSDSSSNIRKRKHSIISEITELKTMNYIKNCRINGSRISDIVDSPTISCSTDSFSEEPMDLSKTGDQIQSHGENGRLIVNSWLIDIVEIINPNNEQSNKNLAELSLSVRLHLLQSTWHRIIVTFLFEHLMKTSSIHLEGITKFISSLSGINNRSVFNNKKISKMYKTQLEELNNILYQIKKLNLDEMSMHYLRIGLLLTGNHDEMNKKNLNLIEMFIHSKIGISELNILIIRETIENVLKLNSVIIETIFYSHLDESVENVIEQILNNS 361          
BLAST of hypothetical protein vs. Planmine SMEST
Match: SMESG000033675.1 (SMESG000033675.1)

HSP 1 Score: 71.2478 bits (173), Expect = 2.235e-13
Identity = 92/396 (23.23%), Postives = 172/396 (43.43%), Query Frame = 2
Query:  128 MFIFKLGAEALTRLEEHLND----QTTQPSTCTQKTITSNNLY------TYSSNMESSILYNLLSTEDGSMCKPKSLLHPNYQINLD----QPMPPRANTISFSDLREDPISLSP---RPYSAPQSDSSSNIRKRKHSIISEITELKTMNYIKNCRINGSRISDIVDSPTISCSTDSFSEEPMDLSKTGDQIQSHGENGRLIVNSWLIDIVEIINPNNEQSNK--NLAELSLSVRLHLLQSTWHRIIVTFLFEHLMKTSSIHLEGITKFISSLSGINNRSVFNNKKISKMYKTQLEELNNILYQIKKLNLDEMSMHYLRIGLLLTGNHDEMNKKNLNLIE--MFIHSKIGISELNILIIRETIENVLKLNSVIIETIFYSHLDESVENVIEQILNN 1252
            MFI ++GAEAL   +  L+        + S   +  I ++N Y           ++  ILYNLL+  +  + +    L  N  I ++      +  R N+ S   ++  P+ L P   RP SAPQ+       KRK  + +     +T+N   N                                             ++I+  WL + V ++ PN +  +   N+  L    R+ +L+ +WH I +T+L E + ++  I    ++ FI   +       F  KK+ ++ +    +L  ++ Q+  L L+      LRI +L T N +++ KKN+ L++  + I S     E + L   + ++N+ KL+  +IE++F+ HL  SV+ +I+++ +N
Sbjct:    1 MFILRIGAEALKNADHSLSGSFYTNNVKHSNHDKLKIINHNKYQIENYNKIDQPVDQGILYNLLNKNNQQIPQ----LDRNQHIEMNSLSRALINDRPNSSSLESVK--PVQLKPLSLRPSSAPQTIRFHPYTKRKQILNNNDNIEQTLNVYPN---------------------------------------------KMII-EWLRNTVLLMKPNKKTESMLLNVLRLPDRDRIRILKQSWHLIFITYLVEFIERSEKIK-SILSVFIKDYNKTEKNGNF--KKLFRLTRVFTNDLEIVITQMISLRLNHNLFELLRIAILFTDNQEDIKKKNIELLKPRLVIQS----DEYDKL-FDQLLDNLFKLDMSMIESVFFGHLSPSVDGIIDELYSN 336          
The following BLAST results are available for this feature:
BLAST of hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZIG00.000e+095.74Uncharacterized protein OS=Schmidtea mediterranea ... [more]
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BLAST of hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein 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 hypothetical protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000077040.10.000e+095.74SMESG000077040.1[more]
SMESG000033675.12.235e-1323.23SMESG000033675.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30025384
GenBankAFJ24814.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025384 ID=SMED30025384|Name=hypothetical protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1360bp
CAACGCTTATTTTGATAATTTTATTGATATTGTTTTATGTTTGGATAAAT
TTAGTCTCAACTGTAATATATATTGCTTAACTATATCCATTTATCGATAA
TTATTTATTTGAAATTTTGAATAATAAATGTTTATTTTTAAATTGGGCGC
CGAAGCACTTACTCGCTTAGAGGAGCATTTAAATGATCAAACAACCCAAC
CATCAACATGCACTCAGAAAACTATTACAAGCAATAACTTGTATACTTAT
AGTTCAAATATGGAGTCCAGTATACTTTATAATTTATTATCAACAGAAGA
TGGATCAATGTGTAAACCCAAAAGTCTTTTGCATCCAAATTATCAAATAA
ATTTAGATCAACCAATGCCTCCTAGAGCCAATACTATTTCTTTTTCTGAT
TTGCGCGAAGATCCAATCAGTCTCTCTCCCAGACCGTATTCAGCTCCCCA
ATCAGACAGTTCATCAAACATTCGTAAAAGAAAACATTCAATTATATCAG
AAATCACAGAGCTCAAAACTATGAATTATATAAAAAATTGTAGAATCAAT
GGTTCACGAATATCAGACATTGTTGATTCGCCGACTATTTCTTGTTCAAC
GGATTCTTTTAGTGAAGAACCGATGGATTTGTCAAAAACTGGAGATCAGA
TTCAAAGCCATGGAGAAAATGGAAGATTAATTGTAAATTCCTGGTTGATA
GACATCGTTGAAATTATCAATCCCAACAATGAGCAGTCAAATAAAAATCT
TGCCGAACTTTCACTCAGTGTAAGACTGCATTTGCTCCAGTCTACGTGGC
ATAGAATCATTGTTACGTTTCTATTTGAACATTTAATGAAAACATCTAGC
ATTCATCTGGAAGGTATCACAAAATTTATTAGTTCATTAAGTGGAATTAA
TAATAGATCGGTTTTCAATAATAAAAAGATTTCCAAAATGTATAAAACTC
AATTGGAAGAATTAAATAATATTTTATATCAAATCAAAAAGCTTAATCTT
GATGAAATGTCAATGCATTACTTGAGGATTGGATTGCTTTTGACGGGTAA
CCACGATGAAATGAATAAGAAAAATTTGAATCTCATTGAAATGTTTATTC
ATTCGAAAATCGGAATTAGCGAGCTGAATATTTTGATTATTAGGGAAACA
ATAGAAAATGTGTTGAAATTAAACTCGGTGATCATTGAAACGATTTTCTA
CAGTCATCTTGATGAGTCTGTGGAAAATGTTATTGAACAAATACTTAATA
ATTCATGAATTGTTATTTTTTTCATACCTCGATAATTTTTCTATGTTGCT
TTATACCAAATGTCAATGCATGTAAAAAAGATTTTTCAAATAATGTTATT
TTTAAAAAAA
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protein sequence of SMED30025384-orf-1

>SMED30025384-orf-1 ID=SMED30025384-orf-1|Name=SMED30025384-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=377bp
MFIFKLGAEALTRLEEHLNDQTTQPSTCTQKTITSNNLYTYSSNMESSIL
YNLLSTEDGSMCKPKSLLHPNYQINLDQPMPPRANTISFSDLREDPISLS
PRPYSAPQSDSSSNIRKRKHSIISEITELKTMNYIKNCRINGSRISDIVD
SPTISCSTDSFSEEPMDLSKTGDQIQSHGENGRLIVNSWLIDIVEIINPN
NEQSNKNLAELSLSVRLHLLQSTWHRIIVTFLFEHLMKTSSIHLEGITKF
ISSLSGINNRSVFNNKKISKMYKTQLEELNNILYQIKKLNLDEMSMHYLR
IGLLLTGNHDEMNKKNLNLIEMFIHSKIGISELNILIIRETIENVLKLNS
VIIETIFYSHLDESVENVIEQILNNS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000101muscle cell
PLANA:0003116parenchymal cell