SMED30027761

Overview
NameSMED30027761
Smed IDSMED30027761
Length (bp)321
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



SMED30027761

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30027761 dd_Smed_v4_54604_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30027761 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.011523:6387..6704 -1247
Homology
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BLAST of SMED30027761 vs. Ensembl Zebrafish
Match: CABZ01072083.2 (dual specificity phosphatase 26 [Source:NCBI gene;Acc:570815])

HSP 1 Score: 58.9214 bits (141), Expect = 4.835e-11
Identity = 31/83 (37.35%), Postives = 44/83 (53.01%), Query Frame = -1 
Query:   10 RVVLDLARPLFNTNRNITLDNYFTSLLLANAFLKNGLTIVSTVRKNKTFIPASMFRRQNQPVESSLFLFQNNHTLVSYIPAMN 258
            RVVLD+   L     NIT D  FTS  L    L+  +T++ T R +   +P ++   + + + SS F F + HTLVSY P  N
Sbjct:  318 RVVLDMTSAL--EGHNITCDQSFTSYALGEELLRRNITMIGTTRLSNPELPPALLSVKGRAINSSKFAFTDTHTLVSYHPRKN 398
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BLAST of SMED30027761 vs. Ensembl Xenopus
Match: npffr2 (neuropeptide FF receptor 2 [Source:Xenbase;Acc:XB-GENE-994428])

HSP 1 Score: 46.2098 bits (108), Expect = 1.784e-6
Identity = 27/86 (31.40%), Postives = 45/86 (52.33%), Query Frame = -1 
Query:   10 LVQRVVLDLARPLFNTNRNITLDNYFTSLLLANAFLKNGLTIVSTVRKNKTFIPASMFRRQNQPVESSLFLFQNNHTLVSYIPAMN 267
            L + VV++L  P  +  RN+T DN+FTS  L++  L++  T++ TV K +  +P        + V S+  L   + +L  Y P  N
Sbjct:  149 LAENVVMNLMEPFLDEGRNVTTDNFFTS--LSHRLLQHKTTLLGTVNKVRRELPQLAKDTAQREVFSTSVLRSGSVSLTIYAPKKN 232
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BLAST of SMED30027761 vs. TrEMBL
Match: A0A4C1ZGA0 (PiggyBac transposable element-derived protein 4 OS=Eumeta variegata OX=151549 GN=PGBD4 PE=4 SV=1)

HSP 1 Score: 93.2041 bits (230), Expect = 7.468e-20
Identity = 48/106 (45.28%), Postives = 66/106 (62.26%), Query Frame = -1 
Query:    1 LQGQLYIAKESHSPEVGLVQRVVLDLARPLFNTNRNITLDNYFTSLLLANAFLKNGLTIVSTVRKNKTFIPASMFRRQNQPVESSLFLFQNNHTLVSYIPAMN*AI 318
            L G  Y+ KE  +    L   VV  L  P F +NRN+T DNYF S+ +A +  +NGLTIV T+RKNKT IP +   ++ + +ES++F F  N TLVSY+P  N A+
Sbjct:  201 LFGIPYLGKEGQNRAENLAYNVVNQLCEPYFRSNRNVTFDNYFMSIDVAKSLAQNGLTIVGTLRKNKTCIPPNFQPKKTRDIESNVFGFYKNMTLVSYVPKKNCAV 306
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BLAST of SMED30027761 vs. TrEMBL
Match: A0A4C1U7C2 (PiggyBac transposable element-derived protein 4 OS=Eumeta variegata OX=151549 GN=PGBD4 PE=4 SV=1)

HSP 1 Score: 91.2781 bits (225), Expect = 2.345e-19
Identity = 48/106 (45.28%), Postives = 66/106 (62.26%), Query Frame = -1 
Query:    1 LQGQLYIAKESHSPEVGLVQRVVLDLARPLFNTNRNITLDNYFTSLLLANAFLKNGLTIVSTVRKNKTFIPASMFRRQNQPVESSLFLFQNNHTLVSYIPAMN*AI 318
            L G  Y+ KE  +    L   VV  L +P F +NRN+T DNYFTS+ +A    +NGLT V T+RKNKT IP +   ++ + +ES++F F  N TLVSY+P  N A+
Sbjct:  291 LFGVPYLGKEGQNRAENLAYNVVNQLCQPYFRSNRNVTFDNYFTSIDVAKYLAQNGLTTVGTLRKNKTCIPPNFQPKKTRDIESNVFGFYKNMTLVSYVPKKNRAV 396
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BLAST of SMED30027761 vs. TrEMBL
Match: A0A1Y1MM34 (DDE_Tnp_1_7 domain-containing protein (Fragment) OS=Photinus pyralis OX=7054 PE=4 SV=1)

HSP 1 Score: 88.5817 bits (218), Expect = 3.515e-19
Identity = 47/107 (43.93%), Postives = 65/107 (60.75%), Query Frame = -1 
Query:    1 LQGQLYIAKESHSPEVGLVQRVVLDLARPLFNTNRNITLDNYFTSLLLANAFLKNGLTIVSTVRKNKTFIPASMFRRQNQPVESSLFLFQNNH-TLVSYIPAMN*AI 318
            L GQ+Y  K     E    +RVV DL     NT RNI +DN+FT+L LA   L  GL+IV T++KNK +IP+ M   +++P  SSLF F ++  T+VSY+P    A+
Sbjct:   57 LTGQIYTGKSPKGREQNQGERVVKDLCYRYKNTGRNIVVDNFFTTLPLARLLLSWGLSIVGTLKKNKPYIPSQMLAHKSRPTASSLFGFSDDKITMVSYVPKPKKAV 163
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BLAST of SMED30027761 vs. TrEMBL
Match: A0A4C1VNV0 (PiggyBac transposable element-derived protein 4 OS=Eumeta variegata OX=151549 GN=PGBD4 PE=4 SV=1)

HSP 1 Score: 88.9669 bits (219), Expect = 1.009e-18
Identity = 46/98 (46.94%), Postives = 61/98 (62.24%), Query Frame = -1 
Query:   10 YIAKESHSPEVGLVQRVVLDLARPLFNTNRNITLDNYFTSLLLANAFLKNGLTIVSTVRKNKTFIPASMFRRQNQPVESSLFLFQNNHTLVSYIPAMN 303
            Y  KE  +    L   VV  L  P F +NRN+T DNYFTS+ +A +  +NGLTIV T+RKNKT IP +   ++ + +ES++F F  N TLVSY P  N
Sbjct:   65 YRGKEGQNRAENLAYNVVNQLCEPYFRSNRNVTFDNYFTSIDVAKSLAQNGLTIVGTLRKNKTCIPPNFQPKKTRHIESNVFGFYENITLVSYGPKKN 162
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BLAST of SMED30027761 vs. TrEMBL
Match: A0A4C1UEE4 (PiggyBac transposable element-derived protein 4 OS=Eumeta variegata OX=151549 GN=PGBD4 PE=4 SV=1)

HSP 1 Score: 89.7373 bits (221), Expect = 1.576e-18
Identity = 46/104 (44.23%), Postives = 65/104 (62.50%), Query Frame = -1 
Query:    1 GQLYIAKESHSPEVGLVQRVVLDLARPLFNTNRNITLDNYFTSLLLANAFLKNGLTIVSTVRKNKTFIPASMFRRQNQPVESSLFLFQNNHTLVSYIPAMN*AI 312
            G  Y+ KE  +    L   V+  L  P   +NRN+T DNYFTS+ +A +  +NGLTIV T+RKNKT IP +   ++ + +ES++F F  N TLVSY+P  N A+
Sbjct:  293 GIPYLGKEGQNRAESLAYNVLNQLCEPNIRSNRNVTFDNYFTSIDVAKSLAQNGLTIVGTLRKNKTCIPPNFQPKKTRDIESNVFGFYKNMTLVSYVPKKNHAL 396
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BLAST of SMED30027761 vs. Ensembl Cavefish
Match: ENSAMXT00000039501.1 (pep primary_assembly:Astyanax_mexicanus-2.0:19:21564630:21575712:1 gene:ENSAMXG00000031759.1 transcript:ENSAMXT00000039501.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 45.0542 bits (105), Expect = 3.000e-6
Identity = 30/81 (37.04%), Postives = 38/81 (46.91%), Query Frame = -1 
Query:   25 VVLDLARPLFNTNRNITLDNYFTSLLLANAFLKNGLTIVSTVRKNKTFIPASMFRRQNQPVESSLF----LFQNNHTLVSY 255
            VV  L  P  +  RNIT   +F SL LA+  L N  T+V T+RK+K   P      Q    +S +F    L   N TL  Y
Sbjct:  758 VVTRLVEPFLDKGRNITTSGFFPSLALASHLLVNKTTVVGTIRKSKQETP------QCTQTQSEIFNTKVLRTGNTTLTIY 832
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BLAST of SMED30027761 vs. Ensembl Cavefish
Match: nsd3 (nuclear receptor binding SET domain protein 3 [Source:ZFIN;Acc:ZDB-GENE-050324-2])

HSP 1 Score: 44.2838 bits (103), Expect = 4.548e-6
Identity = 25/72 (34.72%), Postives = 39/72 (54.17%), Query Frame = -1 
Query:   97 QLYIAKESHSP-EVGLVQRVVLDLARPLFNTNRNITLDNYFTSLLLANAFLKNGLTIVSTVRKNKTFIPASM 309
            Q+Y  K +    E+G  +RV+LD+   L      +T DN+FTS  LA   L+  + +V T+R NK  +P  +
Sbjct:  499 QVYTGKPAGGALEMGQGKRVILDMTEGLKGVT--VTCDNFFTSYSLAQELLRKKVALVGTIRANKPELPPRL 568
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BLAST of SMED30027761 vs. Ensembl Medaka
Match: ENSORLT00000037833.1 (piggyBac transposable element-derived protein 4-like [Source:NCBI gene;Acc:101160710])

HSP 1 Score: 72.7886 bits (177), Expect = 5.432e-16
Identity = 40/101 (39.60%), Postives = 57/101 (56.44%), Query Frame = -1 
Query:   10 QLYIAKE-SHSPEVGLVQRVVLDLARPLFNTNRNITLDNYFTSLLLANAFLKNGLTIVSTVRKNKTFIPASMFRRQNQPVESSLFLFQNNHTLVSYIPAMN 309
            Q+Y  K    +PE     RVVL+++  L     NIT DN+FTS  L     K  LT++ TVR+NK  +P+ + + Q +P+ SS+F F    T+VSY P  N
Sbjct:  296 QVYTGKSPGGAPEKNQGMRVVLEMSEGL--QGHNITCDNFFTSYRLGEELQKRKLTMLGTVRRNKPELPSEILKIQGRPMHSSIFAFTEKATVVSYCPKRN 394
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BLAST of SMED30027761 vs. Ensembl Medaka
Match: ENSORLT00000027888.1 (pep primary_assembly:ASM223467v1:17:9217998:9219211:-1 gene:ENSORLG00000025878.1 transcript:ENSORLT00000027888.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 68.1662 bits (165), Expect = 1.901e-14
Identity = 39/101 (38.61%), Postives = 55/101 (54.46%), Query Frame = -1 
Query:   10 QLYIAK-ESHSPEVGLVQRVVLDLARPLFNTNRNITLDNYFTSLLLANAFLKNGLTIVSTVRKNKTFIPASMFRRQNQPVESSLFLFQNNHTLVSYIPAMN 309
            Q+Y  K    +PE     RVVL+++  L     NIT DN+FTS  L     K  L ++ TVR+NK  +P+ +   Q +P+ SS+F F    T+VSY P  N
Sbjct:   99 QVYTGKLPGGAPEKNQGMRVVLEMSEGL--QGHNITCDNFFTSYRLGEELQKRKLIMLGTVRRNKPELPSEILNIQGRPMHSSIFAFTEKATVVSYCPKRN 197
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BLAST of SMED30027761 vs. Ensembl Medaka
Match: ENSORLT00000029842.1 (piggyBac transposable element-derived protein 4 [Source:NCBI gene;Acc:101157644])

HSP 1 Score: 66.2402 bits (160), Expect = 9.975e-14
Identity = 38/101 (37.62%), Postives = 55/101 (54.46%), Query Frame = -1 
Query:   10 QLYIAK-ESHSPEVGLVQRVVLDLARPLFNTNRNITLDNYFTSLLLANAFLKNGLTIVSTVRKNKTFIPASMFRRQNQPVESSLFLFQNNHTLVSYIPAMN 309
            Q Y+ K  S + E  L  RVV DL R L   +RN+T DN+FTS  LA   LK  +T++ T++ NK  +P  +   + +   SS F F +    +SY+P  N
Sbjct:  547 QPYMGKLASGARETNLASRVVSDLTRGL--EHRNVTCDNFFTSYALATELLKRNITLLGTIKSNKPELPPELASARGREALSSRFAFTDCAAALSYVPKKN 645
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BLAST of SMED30027761 vs. Planmine SMEST
Match: SMESG000081807.1 (SMESG000081807.1)

HSP 1 Score: 75.0998 bits (183), Expect = 5.343e-17
Identity = 39/100 (39.00%), Postives = 56/100 (56.00%), Query Frame = -1 
Query:   10 QLYIAKESHSPEVGLVQRVVLDLARPLFNTNRNITLDNYFTSLLLANAFLKNGLTIVSTVRKNKTFIPASMFRRQNQPVESSLFLFQNNHTLVSYIPAMN 309
            Q+Y+ K+  SP+     RVV  L  PL+N+ RN+T DN+FTS  L    L   +T++ T+RK++T IP     +  +  ES  F F  +  LVSY P  N
Sbjct:  172 QVYLGKKGQSPKHQQGTRVVKQLMLPLYNSGRNVTTDNFFTSYDLGQFLLSQNITLLGTMRKSRTEIPPEFLSKSREEFESK-FAFTKDTALVSYAPPKN 270
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BLAST of SMED30027761 vs. Planmine SMEST
Match: SMESG000070813.1 (SMESG000070813.1)

HSP 1 Score: 47.7506 bits (112), Expect = 2.155e-7
Identity = 29/68 (42.65%), Postives = 39/68 (57.35%), Query Frame = -1 
Query:   19 TNRNITLDNYFTSLLLANAFLKNGLTIVSTVRKNKTFIPASMFRRQNQPVESSLFLFQNNHTLVSYIP 222
            T  ++T DN+FTS+ LA   L N + +  T+R NK  IP   F+   +   SS F +  N TLVSYIP
Sbjct:  150 TGFSVTTDNFFTSVPLALKLLNNKIYLTGTLRTNKREIPVQ-FQVSRRSELSSNFGYNINLTLVSYIP 216
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BLAST of SMED30027761 vs. Planmine SMEST
Match: SMESG000080622.1 (SMESG000080622.1)

HSP 1 Score: 43.1282 bits (100), Expect = 9.292e-6
Identity = 19/58 (32.76%), Postives = 36/58 (62.07%), Query Frame = -1 
Query:  139 QLYIAKES-HSPEVGLVQRVVLDLARPLFNTNRNITLDNYFTSLLLANAFLKNGLTIV 309
            + Y+ KE     +V   + + +D+ + L+ + RN+T DN+FTSL L+    +NG+T++
Sbjct:  232 RFYMGKEDDRDMQVSCGEYITMDMLQGLYGSGRNVTCDNFFTSLNLSKRLFQNGITML 289
The following BLAST results are available for this feature:
BLAST of SMED30027761 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 SMED30027761 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 SMED30027761 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 SMED30027761 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
CABZ01072083.24.835e-1137.35dual specificity phosphatase 26 [Source:NCBI gene;... [more]
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BLAST of SMED30027761 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
npffr21.784e-631.40neuropeptide FF receptor 2 [Source:Xenbase;Acc:XB-... [more]
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BLAST of SMED30027761 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 SMED30027761 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 SMED30027761 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4C1ZGA07.468e-2045.28PiggyBac transposable element-derived protein 4 OS... [more]
A0A4C1U7C22.345e-1945.28PiggyBac transposable element-derived protein 4 OS... [more]
A0A1Y1MM343.515e-1943.93DDE_Tnp_1_7 domain-containing protein (Fragment) O... [more]
A0A4C1VNV01.009e-1846.94PiggyBac transposable element-derived protein 4 OS... [more]
A0A4C1UEE41.576e-1844.23PiggyBac transposable element-derived protein 4 OS... [more]
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BLAST of SMED30027761 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 2
Match NameE-valueIdentityDescription
ENSAMXT00000039501.13.000e-637.04pep primary_assembly:Astyanax_mexicanus-2.0:19:215... [more]
nsd34.548e-634.72nuclear receptor binding SET domain protein 3 [Sou... [more]
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BLAST of SMED30027761 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 SMED30027761 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 SMED30027761 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 SMED30027761 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 3
Match NameE-valueIdentityDescription
ENSORLT00000037833.15.432e-1639.60piggyBac transposable element-derived protein 4-li... [more]
ENSORLT00000027888.11.901e-1438.61pep primary_assembly:ASM223467v1:17:9217998:921921... [more]
ENSORLT00000029842.19.975e-1437.62piggyBac transposable element-derived protein 4 [S... [more]
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BLAST of SMED30027761 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000081807.15.343e-1739.00SMESG000081807.1[more]
SMESG000070813.12.155e-742.65SMESG000070813.1[more]
SMESG000080622.19.292e-632.76SMESG000080622.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027761 ID=SMED30027761|Name=SMED30027761|organism=Schmidtea mediterranea sexual|type=transcript|length=321bp
AATAGCTCAATTCATTGCTGGAATATACGACACCAATGTATGGTTGTTCT
GGAAAAGAAAGAGGCTGGACTCTACTGGCTGATTTTGTCTGCGAAACATT
GACGCTGGAATGAAAGTTTTGTTTTTTCGAACAGTACTAACAATAGTGAG
GCCATTCTTAAGGAAAGCATTTGCCAGTAACAGACTTGTAAAGTAATTGT
CCAAAGTAATATTCCTATTGGTATTGAATAAAGGTCTTGCCAAATCCAAA
ACTACACGTTGAACAAGGCCAACTTCTGGTGAATGAGACTCCTTGGCAAT
ATATAGTTGACCTTGCAGAAG
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protein sequence of SMED30027761-orf-1

>SMED30027761-orf-1 ID=SMED30027761-orf-1|Name=SMED30027761-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=105bp
LLQGQLYIAKESHSPEVGLVQRVVLDLARPLFNTNRNITLDNYFTSLLLA
NAFLKNGLTIVSTVRKNKTFIPASMFRRQNQPVESSLFLFQNNHTLVSYI
PAMN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
Vocabulary: INTERPRO
TermDefinition
IPR029526PGBD
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR029526PiggyBac transposable element-derived proteinPFAMPF13843DDE_Tnp_1_7coord: 10..95
e-value: 4.2E-12
score: 46.1