Glutamate receptor NMDA

Overview
NameGlutamate receptor NMDA
Smed IDSMED30022329
Length (bp)627
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 Glutamate receptor NMDA (SMED30022329) t-SNE clustered cells

Violin plots show distribution of expression levels for Glutamate receptor NMDA (SMED30022329) 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 Glutamate receptor NMDA (SMED30022329) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Glutamate receptor NMDA (SMED30022329) 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




SMED30022329

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
intestinal phagocyteSMED30022329SMESG000008774.1 Contig1558GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
gutSMED30022329SMESG000008774.1 dd_Smed_v4_10043_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022329SMESG000008774.1 SMESG000008785.1 Contig20962newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022329SMESG000008774.1 SMESG000008785.1 Contig20962uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Glutamate receptor NMDA vs. TrEMBL
Match: A0A0R3UN72 (Uncharacterized protein OS=Mesocestoides corti OX=53468 GN=MCOS_LOCUS9232 PE=4 SV=1)

HSP 1 Score: 60.077 bits (144), Expect = 3.087e-8
Identity = 31/96 (32.29%), Postives = 53/96 (55.21%), Query Frame = 2
Query:   23 MLLCGGDQLLFALYSSSLILLLVGGCLWGQATETYNESKEEFGIFLFVSGGVLISIAILINIYKCIKQNRRKR------IAQKSTAKASQGVKNER 292
            MLL  G+  LF L+S+S++  L+GGCLWG   +  N++K   GI +F  G        ++  YK IK+ RR++      +  ++   A++G +N+ 
Sbjct:    1 MLLFEGEPALFLLFSASILSFLIGGCLWGSGEDAGNQAKRTVGIVIFFCGVTCCVAFFMLFTYKTIKRKRREKQDFEELMRMQNEFAANEGFQNDE 96          
BLAST of Glutamate receptor NMDA vs. TrEMBL
Match: A0A3P6PVJ9 (Uncharacterized protein OS=Dibothriocephalus latus OX=60516 GN=DILT_LOCUS1233 PE=4 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 7.203e-7
Identity = 33/90 (36.67%), Postives = 51/90 (56.67%), Query Frame = 2
Query:   23 MLLCGGDQLLFALYSSSLILLLVGGCLWGQATETYNESKEEFGIFLFVSGGVLISIAILINIYKCIKQNR-RKRIAQKSTAKASQGVKNE 289
            MLL  G+ LLF L+  S++ LL+GGC+WG  T+T +  +   GI +F  G       I++ +YK IK+ R RKR   +     ++  +NE
Sbjct:    1 MLLFEGEPLLFTLFGLSVLSLLIGGCMWGVGTDTNDHPRYVAGISVFFFGTGCCVCFIIVFVYKHIKKMRIRKRDLAEVVRLQNEFAENE 90          
BLAST of Glutamate receptor NMDA vs. TrEMBL
Match: A0A0R3XAL7 (Uncharacterized protein OS=Hydatigena taeniaeformis OX=6205 GN=TTAC_LOCUS10577 PE=4 SV=1)

HSP 1 Score: 55.4546 bits (132), Expect = 1.094e-6
Identity = 26/73 (35.62%), Postives = 43/73 (58.90%), Query Frame = 2
Query:   23 MLLCGGDQLLFALYSSSLILLLVGGCLWGQATETYNESKEEFGIFLFVSGGVLISIAILINIYKCIKQNRRKR 241
            MLL  G+ +LF L++  ++  L+GGC+WG   E  + +K   GI +F  G     +  ++ IYK I+Q RR++
Sbjct:    1 MLLFEGEPILFILFALFILSFLIGGCMWGSGEEANDRTKHIVGIIIFFFGVTCCVLFFILFIYKKIRQRRREK 73          
BLAST of Glutamate receptor NMDA vs. TrEMBL
Match: A0A0R3SPF6 (Uncharacterized protein OS=Hymenolepis diminuta OX=6216 GN=HDID_LOCUS6841 PE=4 SV=1)

HSP 1 Score: 53.5286 bits (127), Expect = 6.496e-6
Identity = 26/73 (35.62%), Postives = 41/73 (56.16%), Query Frame = 2
Query:   23 MLLCGGDQLLFALYSSSLILLLVGGCLWGQATETYNESKEEFGIFLFVSGGVLISIAILINIYKCIKQNRRKR 241
            MLL  G+ +LF L++  ++  L+GGC+WG   E  +E K   GI +F  G     +  ++  YK I+Q RR+ 
Sbjct:    1 MLLFEGEPVLFILFALFILSFLIGGCMWGSGEEAQDEPKYIVGIIIFFFGVTCCVLFFVLFTYKKIRQKRREE 73          
BLAST of Glutamate receptor NMDA vs. TrEMBL
Match: A0A068Y7W1 (Glutamate receptor NMDA OS=Echinococcus multilocularis OX=6211 PE=4 SV=1)

HSP 1 Score: 53.5286 bits (127), Expect = 8.922e-6
Identity = 26/73 (35.62%), Postives = 43/73 (58.90%), Query Frame = 2
Query:   23 MLLCGGDQLLFALYSSSLILLLVGGCLWGQATETYNESKEEFGIFLFVSGGVLISIAILINIYKCIKQNRRKR 241
            MLL  G+  LF L++  ++  L+GGC+WG   E  +++K   GI +F  G     I  ++ IYK ++Q RR++
Sbjct:    1 MLLFEGEPALFILFALFILSFLIGGCMWGSGEEENDQAKLTVGIVIFFLGVTCCIIFFILFIYKKVRQRRREK 73          
BLAST of Glutamate receptor NMDA vs. Planmine SMEST
Match: SMESG000008774.1 (SMESG000008774.1)

HSP 1 Score: 263.848 bits (673), Expect = 2.245e-90
Identity = 181/191 (94.76%), Postives = 181/191 (94.76%), Query Frame = 2
Query:   23 MLLCGGDQLLFALYSSSLILLLVGGCLWGQATETYNESKEEFGIFLFVSGGVLISIAILINIYKCIKQNRRKRIAQKSTAKASQGVKNERKLIDNDLLNLSEKDFYFXXXXXXXXXXXXXXXXXXXXXXXXAMASMTSGISNMVPXXXXXXXXXXXGSLNFRDSVLQLSTTSSNKTQITYLNPDDTNIKTL 595
            MLLCGGDQLLF LYSSSLILLLVGGCLWGQATETYNESKEEFGIFLFV GGVLISIAIL NIYKCIKQ RRKRIAQK TAKASQGVKNERK IDNDLLNLSEKDFYFNNNQNINKLSNSSSNNSQIISSSIAMA MTSGISNMV INKKKSKN  IGSLNFRDSVLQLSTTSSNKTQITYLNPDDTNIKTL
Sbjct:    1 MLLCGGDQLLFGLYSSSLILLLVGGCLWGQATETYNESKEEFGIFLFVCGGVLISIAILTNIYKCIKQKRRKRIAQKPTAKASQGVKNERKPIDNDLLNLSEKDFYFNNNQNINKLSNSSSNNSQIISSSIAMAPMTSGISNMVRINKKKSKNNYIGSLNFRDSVLQLSTTSSNKTQITYLNPDDTNIKTL 191          
BLAST of Glutamate receptor NMDA vs. Planmine SMEST
Match: SMESG000008768.1 (SMESG000008768.1)

HSP 1 Score: 73.9442 bits (180), Expect = 4.910e-16
Identity = 42/83 (50.60%), Postives = 61/83 (73.49%), Query Frame = 2
Query:   23 MLLCGGDQLLFALYSSSLILLLVGGCLWGQATETYNESKEEFGIFLFVSGGVLISIAILINIYKCIKQ-NRRKRIAQKSTAKA 268
            MLLCGGDQLLF LYS ++I LL+GGCLWGQ  +  + +K   GI +F+ GG +  IA+++NI+K +K+ N+R++IA+ S  K 
Sbjct:    1 MLLCGGDQLLFGLYSVAIICLLIGGCLWGQGQDKNDSAKLTAGIVVFIIGGSIAIIAVIVNIFKSLKKMNKRRKIARMSKEKP 83          
BLAST of Glutamate receptor NMDA vs. Planmine SMEST
Match: SMESG000061766.1 (SMESG000061766.1)

HSP 1 Score: 52.373 bits (124), Expect = 5.660e-9
Identity = 35/105 (33.33%), Postives = 55/105 (52.38%), Query Frame = 2
Query:   23 MLLCGGDQLLFALYSSSLILLLVGGCLWGQATETYNESKEEFGIFLFVSGGVLISIAILINIYKCIKQNRRKRIAQ-KSTAKASQGVKNERKLI---DNDLLNLS 325
            ML C GD LLF  ++S++I  L+GG L+G   +     K   G+ L +SG VL +I  +  I K     +RK + + K+     Q + N+ K     DN+ LN++
Sbjct:    1 MLFCNGDPLLFGFFASAMISTLIGGMLYGSGVDNNILEKTVIGLILLISGCVLFAIGFVFLIIK-----KRKTLKESKAIELQKQEMFNKNKTTQSYDNEALNVT 100          
The following BLAST results are available for this feature:
BLAST of Glutamate receptor NMDA 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 Glutamate receptor NMDA 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 Glutamate receptor NMDA 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 Glutamate receptor NMDA 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 Glutamate receptor NMDA 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 Glutamate receptor NMDA 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 Glutamate receptor NMDA 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 Glutamate receptor NMDA vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A0R3UN723.087e-832.29Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A3P6PVJ97.203e-736.67Uncharacterized protein OS=Dibothriocephalus latus... [more]
A0A0R3XAL71.094e-635.62Uncharacterized protein OS=Hydatigena taeniaeformi... [more]
A0A0R3SPF66.496e-635.62Uncharacterized protein OS=Hymenolepis diminuta OX... [more]
A0A068Y7W18.922e-635.62Glutamate receptor NMDA OS=Echinococcus multilocul... [more]
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BLAST of Glutamate receptor NMDA 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 Glutamate receptor NMDA 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 Glutamate receptor NMDA 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 Glutamate receptor NMDA 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 Glutamate receptor NMDA 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 Glutamate receptor NMDA vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000008774.12.245e-9094.76SMESG000008774.1[more]
SMESG000008768.14.910e-1650.60SMESG000008768.1[more]
SMESG000061766.15.660e-933.33SMESG000061766.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022329 ID=SMED30022329|Name=Glutamate receptor NMDA|organism=Schmidtea mediterranea sexual|type=transcript|length=627bp
TAATTATTAAAAAAAAAACTAAATGCTATTATGTGGTGGAGATCAGTTAT
TGTTCGCATTATACTCTTCGAGTCTCATTCTTCTGCTTGTCGGAGGATGC
TTATGGGGACAAGCTACAGAGACTTATAACGAATCCAAAGAAGAATTCGG
AATATTTCTGTTCGTTAGTGGAGGTGTTCTGATATCAATAGCTATTTTGA
TCAACATTTATAAGTGTATAAAACAAAATAGGAGAAAGAGAATTGCTCAA
AAGTCAACCGCGAAAGCTTCACAAGGTGTCAAAAATGAAAGGAAACTGAT
TGATAATGATTTATTAAATCTATCAGAAAAAGATTTCTATTTTAATAATA
ATCAAAACATTAATAAATTGTCTAATAGCAGTTCTAACAATTCCCAAATC
ATTTCATCGTCTATTGCAATGGCTTCAATGACTTCGGGCATTTCCAATAT
GGTTCCAATTAACAAGAAAAAATCAAAAAATAAAAGCATTGGTTCCTTAA
ATTTTAGAGATTCTGTTCTTCAACTTTCAACAACATCTTCTAACAAAACT
CAAATTACATACTTAAATCCGGACGATACCAATATTAAAACTCTTTGAAA
TAATAGAATATATGTTTTAAAATGTTA
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protein sequence of SMED30022329-orf-1

>SMED30022329-orf-1 ID=SMED30022329-orf-1|Name=SMED30022329-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=192bp
MLLCGGDQLLFALYSSSLILLLVGGCLWGQATETYNESKEEFGIFLFVSG
GVLISIAILINIYKCIKQNRRKRIAQKSTAKASQGVKNERKLIDNDLLNL
SEKDFYFNNNQNINKLSNSSSNNSQIISSSIAMASMTSGISNMVPINKKK
SKNKSIGSLNFRDSVLQLSTTSSNKTQITYLNPDDTNIKTL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 41..63
NoneNo IPR availableTMHMMTMhelixcoord: 9..31