SMED30009021

Overview
NameSMED30009021
Smed IDSMED30009021
Length (bp)680
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



SMED30009021

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
Category 3 cellSMED30009021 dd_Smed_v4_31431_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30009021 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.014188:12270..12941 +2910
v31.000057:53006..53702 +2746
v31.000610:76146..76833 -2425
v31.003825:60998..61609 +2099
Homology
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BLAST of SMED30009021 vs. Planmine SMEST
Match: SMESG000003019.1 (SMESG000003019.1)

HSP 1 Score: 119.783 bits (299), Expect = 1.450e-52
Identity = 80/123 (65.04%), Postives = 91/123 (73.98%), Query Frame = -1 
Query:  243 TKQINIIPAHPLPINAENPSTNNDSSVPTDGISYAXXXXXXXXXXXXXXXRIAENTLLQENLRNDVHPELREISDRITMDHTAPRYDGDPDVIYAPIQPEFSHLTHTPAQITITANGHEPPIN 611
             +QI IIPAH   I AE  S N+DS  P D IS ANRR KPNRNRRRRQRR AEN LLQ NLR+D  PELR++ D + ++H+APRYD D D+IYAPIQPEFSHL   PAQ+TI A GHE PI 
Sbjct:  176 AQQIIIIPAHHQSIIAEKSSINHDSIAPVDRISQANRRHKPNRNRRRRQRRRAENALLQANLRSDGRPELRKVLDFVFIEHSAPRYDDDLDIIYAPIQPEFSHL--APAQLTINATGHELPIK 296

HSP 2 Score: 82.8037 bits (203), Expect = 1.450e-52
Identity = 45/69 (65.22%), Postives = 50/69 (72.46%), Query Frame = -2 
Query:   35 VTIHIATTSRTILDE*RPSIGRSSPLIISVVEPTASRGQGADSSRQMDPHPISRFQKRRCLPVDIDGEE 241
            + IHIATT R+ILDE   S GRSSP IISVVEPT  RGQ  DSS Q +PH I    KR+CL VDIDG+E
Sbjct:  295 IKIHIATTFRSILDEDVESSGRSSPQIISVVEPTTPRGQRVDSSPQAEPHTILLCPKRQCLSVDIDGDE 363

HSP 3 Score: 43.1282 bits (100), Expect = 1.450e-52
Identity = 20/24 (83.33%), Postives = 22/24 (91.67%), Query Frame = -2 
Query:  602 ISEQSAALRQIFTEKELQARIPSR 673
            IS+Q A LRQIFTEKELQAR+PSR
Sbjct:  150 ISKQIAVLRQIFTEKELQARLPSR 173
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BLAST of SMED30009021 vs. Planmine SMEST
Match: SMESG000075367.1 (SMESG000075367.1)

HSP 1 Score: 94.7449 bits (234), Expect = 2.502e-36
Identity = 64/107 (59.81%), Postives = 78/107 (72.90%), Query Frame = -1 
Query:  243 ENPSTNNDSSVPTDGISYAXXXXXXXXXXXXXXXRIAENTLLQENLRNDVHPELREISDRITMDHTAPRYDGDPDVIYAPIQPEFSHLTHTPAQITITANGHEPPIN 563
            EN S +N ++   DG S ANRR KPNRNR RRQ R AEN L+Q NLR D H ELRE+ + I+++H APR++ D  +IYAP+QP+FSH    PAQITI ANGHE PIN
Sbjct:  147 ENQSISNVNNTSADGTSQANRRHKPNRNRCRRQWRRAENALIQANLRTDGHSELREVPNPISLEHIAPRFEDDLGIIYAPVQPDFSH--PAPAQITINANGHESPIN 251

HSP 2 Score: 75.8702 bits (185), Expect = 2.502e-36
Identity = 46/75 (61.33%), Postives = 50/75 (66.67%), Query Frame = -2 
Query:   38 ATSLQSIVTIHIATTSRTILDE*RPSIGRSSPLIISVVEPTASRGQGADSSRQMDPHPISRFQKRRCLPVDIDGE 262
            A   +S + IHIATTSR +L+E   S GRSSPLIISVVE TA  GQ ADS  Q    PISR  KRR L VDID E
Sbjct:  243 ANGHESPINIHIATTSRVMLEEEGQSSGRSSPLIISVVESTAFHGQRADSCCQSTRRPISRCPKRRYLLVDIDEE 317
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BLAST of SMED30009021 vs. Planmine SMEST
Match: SMESG000055478.1 (SMESG000055478.1)

HSP 1 Score: 119.013 bits (297), Expect = 1.141e-32
Identity = 78/125 (62.40%), Postives = 89/125 (71.20%), Query Frame = -1 
Query:  237 TKQINIIPAHPLPINAENPSTNNDSSVPTDGISYAXXXXXXXXXXXXXXXRIAENTLLQENLRNDVHPELREISDRITMDHTAPRYDGDPDVIYAPIQPEFSHLTHTPAQITITANGHEPPINCY 611
             +QINII A+ LPINAEN   N DS++P DGI + NRR K NRNRR RQRR AEN LLQ NLRND  PELREI D ++     PR+D D D+IYAP QPEF H   TPAQITIT++GHE P   Y
Sbjct:  103 VQQINIIQAYHLPINAENSPINYDSNIPADGILHVNRRHKSNRNRRWRQRRRAENALLQANLRNDGLPELREIQDLVSTKQATPRHDDDLDIIYAPFQPEFFH--STPAQITITSHGHESPQLTY 225

HSP 2 Score: 53.5286 bits (127), Expect = 2.009e-8
Identity = 34/64 (53.12%), Postives = 42/64 (65.62%), Query Frame = -2 
Query:  494 ITISEQSAALRQIFTEKELQARIPSR-LI*SRHIPCQSMQKIHQPITTAAYP-QMESHMQIDGI 679
            ITISEQ+AA RQIFTEKELQAR+PSR L+   +I    +Q  H PI     P   +S++  DGI
Sbjct:   75 ITISEQTAAFRQIFTEKELQARLPSRNLVQQINI----IQAYHLPINAENSPINYDSNIPADGI 134
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BLAST of SMED30009021 vs. Planmine SMEST
Match: SMESG000056978.1 (SMESG000056978.1)

HSP 1 Score: 80.1073 bits (196), Expect = 1.127e-31
Identity = 65/119 (54.62%), Postives = 81/119 (68.07%), Query Frame = -1 
Query:  258 KQINIIPAHPLPINAENPSTNNDSSVPTDGISY--AXXXXXXXXXXXXXXXRIAENTLLQENLRNDVHPELREISDRITMDHTAPRYDGDPDVIYAPIQPEFSHLTHTPAQITITANGH 608
            ++++IIPAH LP NAE+   NN+++   +  SY  ANRR KPNRNRRRRQ+R AENTLL+ NLR    PEL E SD +T + T  R D +  VIYA  QP+F+H   TPAQITI  N H
Sbjct:    3 QRLDIIPAHHLPANAESSRVNNEANPLAERTSYSNANRRHKPNRNRRRRQKRRAENTLLKANLRGSDGPELIEFSDIMTAESTTFRNDDELSVIYASRQPDFTHPVPTPAQITIATNSH 121

HSP 2 Score: 74.3294 bits (181), Expect = 1.127e-31
Identity = 41/74 (55.41%), Postives = 51/74 (68.92%), Query Frame = -2 
Query:   35 SLQSIVTIHIATTSRTILDE*RPSIGRSSPLIISVVEPTASRGQGADSSRQMDPHPISRFQKRRCLPVDIDGEE 256
            S++ ++ I I+T+SRT LD   PS GRSSP IISVVEP  +R Q   +S Q  P+P SR  K R LPVDIDGE+
Sbjct:  122 SVEVLINIQISTSSRTTLDREIPSSGRSSPQIISVVEPRITRNQRVSNSHQTGPNPASRSPKCRYLPVDIDGED 195
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BLAST of SMED30009021 vs. Planmine SMEST
Match: SMESG000021151.1 (SMESG000021151.1)

HSP 1 Score: 78.9518 bits (193), Expect = 4.158e-31
Identity = 59/103 (57.28%), Postives = 75/103 (72.82%), Query Frame = -1 
Query:  300 KQINIIPAHPLPINAENPSTNNDSSVPTDGISYAXXXXXXXXXXXXXXXRIAENTLLQENLRNDVHPELREISDRITMDHTAPRYDGDPDVIYAPIQPEFSHL 608
            +QINIIPAH LP NAEN + N D+S P DGIS+ANRR KPNRNRR+RQRR AENTLL  NLR+D +P++ E+ D  T++     YD   ++IYAP+ P   H+
Sbjct:  104 QQINIIPAHHLPTNAENQAINQDNSTPEDGISHANRRHKPNRNRRQRQRRRAENTLLLANLRSDEYPDVTEVLDSTTIERAISGYDK--EIIYAPLNPSPIHI 204

HSP 2 Score: 73.9442 bits (180), Expect = 4.158e-31
Identity = 40/68 (58.82%), Postives = 49/68 (72.06%), Query Frame = -2 
Query:   38 VTIHIATTSRTILDE*RPSIGRSSPLIISVVEPTASRGQGADSSRQMDPHPISRFQKRRCLPVDIDGE 241
            + I+IATTSR +L+E   S GRSSPLII V EPTA + Q A   +Q + HP +R  KRRCLPVDIDG+
Sbjct:  202 IHINIATTSRAMLEEEGQSSGRSSPLIILVTEPTAPQEQMAGFPQQPESHPTARCPKRRCLPVDIDGD 269

HSP 3 Score: 52.373 bits (124), Expect = 5.166e-8
Identity = 31/55 (56.36%), Postives = 39/55 (70.91%), Query Frame = -2 
Query:  539 ITISEQSAALRQIFTEKELQARIPSR-------LI*SRHIPCQS-MQKIHQPITT 679
            +TISEQSAALRQIFTEKELQAR+PSR       +I + H+P  +  Q I+Q  +T
Sbjct:   75 VTISEQSAALRQIFTEKELQARLPSRNLAQQINIIPAHHLPTNAENQAINQDNST 129
The following BLAST results are available for this feature:
BLAST of SMED30009021 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 SMED30009021 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 SMED30009021 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 SMED30009021 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 SMED30009021 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 SMED30009021 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 SMED30009021 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 SMED30009021 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 SMED30009021 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 SMED30009021 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 SMED30009021 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 SMED30009021 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 SMED30009021 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 SMED30009021 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000003019.11.450e-5265.04SMESG000003019.1[more]
SMESG000075367.12.502e-3659.81SMESG000075367.1[more]
SMESG000055478.11.141e-3262.40SMESG000055478.1[more]
SMESG000056978.11.127e-3154.62SMESG000056978.1[more]
SMESG000021151.14.158e-3157.28SMESG000021151.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009021 ID=SMED30009021|Name=SMED30009021|organism=Schmidtea mediterranea sexual|type=transcript|length=680bp
CTTTGGTTCGTCGGTTTGAAGAACGTTTGATTTATTCTTCTCCGTCAATA
TCTACAGGTAAACATCGGCGTTTTTGGAATCGCGATATTGGGTGTGGATC
CATCTGACGAGAAGAATCTGCCCCCTGACCTCGAGATGCTGTCGGTTCTA
CGACTGAGATAATTAGCGGTGAGGATCGCCCGATGGAAGGCCTTTATTCA
TCCAGAATCGTACGAGATGTAGTGGCGATATGGATAGTAACAATTGATTG
GAGGCTCGTGGCCATTTGCGGTGATCGTGATCTGAGCCGGAGTGTGAGTG
AGATGGGAAAACTCTGGCTGGATAGGAGCATATATCACATCGGGATCGCC
ATCGTATCTAGGAGCGGTGTGGTCCATAGTTATCCGGTCTGAGATTTCTC
TCAGTTCCGGGTGTACATCGTTTCTCAAATTTTCCTGGAGCAGGGTGTTT
TCGGCTATACGCCTCTGCCGCCGGCGGCGATTTCGATTGGGTTTATCCCG
TCGATTTGCATATGAGATTCCATCTGTGGGTACGCTGCTGTCGTTATTGG
TTGATGGATTTTCTGCATTGATTGGCAGGGGATGTGCCGGGATTATATTA
ATCTGCTTGGTATGCGAGCTTGTAACTCCTTCTCCGTGAAAATCTGTCTG
AGAGCGGCACTTTGTTCGGATATTGTAATC
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protein sequence of SMED30009021-orf-1

>SMED30009021-orf-1 ID=SMED30009021-orf-1|Name=SMED30009021-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=161bp
DYNIRTKCRSQTDFHGEGVTSSHTKQINIIPAHPLPINAENPSTNNDSSV
PTDGISYANRRDKPNRNRRRRQRRIAENTLLQENLRNDVHPELREISDRI
TMDHTAPRYDGDPDVIYAPIQPEFSHLTHTPAQITITANGHEPPINCYYP
YRHYISYDSG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell