SMED30006141

Overview
NameSMED30006141
Smed IDSMED30006141
Length (bp)747
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 SMED30006141 (SMED30006141) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30006141 (SMED30006141) in cells (dots) of each of the 12 neoblast clusters.

 

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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




SMED30006141

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
parenchymal cellSMED30006141SMESG000014679.1 dd_Smed_v4_17222_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30006141 vs. TrEMBL
Match: A0A2B4RC04 (Uncharacterized protein OS=Stylophora pistillata OX=50429 GN=AWC38_SpisGene20623 PE=4 SV=1)

HSP 1 Score: 94.7449 bits (234), Expect = 2.409e-18
Identity = 44/111 (39.64%), Postives = 71/111 (63.96%), Query Frame = -1
Query:    1 KEIENAKVQVIDGKQREYETWKAAFCACVDSSYGDDDEKILHLWSYLSGESLRLIENLGFSSAGYTVAKQKLGRRYGGDERNYLAIVDQIDNFRPVRDGDLRELEALISVL 333
            K+++   + + +G +  YE+WKAAF AC+D +    + K+L L  YLSGE+L+ IENLG S++ Y  AK +L  +YGG  R     ++++DNF+PVR G  +++E    +L
Sbjct:  286 KQLKGVSIPLFNGDKTNYESWKAAFEACIDKA----EYKLLQLRQYLSGEALKAIENLGHSASAYEAAKSRLEGKYGGRRRQIALHLEELDNFKPVRPGHPKDIERFADIL 392          
BLAST of SMED30006141 vs. TrEMBL
Match: A0A2B4T023 (Uncharacterized protein OS=Stylophora pistillata OX=50429 GN=AWC38_SpisGene666 PE=4 SV=1)

HSP 1 Score: 93.5893 bits (231), Expect = 4.067e-18
Identity = 43/118 (36.44%), Postives = 75/118 (63.56%), Query Frame = -1
Query:    1 KIEALMQKEIENAKVQVIDGKQREYETWKAAFCACVDSSYGDDDEKILHLWSYLSGESLRLIENLGFSSAGYTVAKQKLGRRYGGDERNYLAIVDQIDNFRPVRDGDLRELEALISVL 354
            +++A M  +++   + V +G +R YE WK AF A VD +    + K+L L  YLSGE+L+++E LG+S+  Y  A ++L R++GG  R     +++++NF+P+R G+ R+LE L  + 
Sbjct:  173 EVKADMWNQLKRVSIPVFNGDER-YEGWKMAFMAFVDKAPATPEYKLLQLRQYLSGEALKVVEPLGYSATAYETATERLERKFGGKRRQVALHLEELENFKPLRPGNARDLERLADLF 289          
BLAST of SMED30006141 vs. TrEMBL
Match: A0A2B4R783 (Uncharacterized protein OS=Stylophora pistillata OX=50429 GN=AWC38_SpisGene23326 PE=4 SV=1)

HSP 1 Score: 83.5741 bits (205), Expect = 1.814e-15
Identity = 38/99 (38.38%), Postives = 61/99 (61.62%), Query Frame = -1
Query:    1 GKQREYETWKAAFCACVDSSYGDDDEKILHLWSYLSGESLRLIENLGFSSAGYTVAKQKLGRRYGGDERNYLAIVDQIDNFRPVRDGDLRELEALISVL 297
            G ++   +WKAAFC+CVD        K+L L   L GE+LR+IENLG S+  Y  A+ +L R+YGG+ R     +++++ F+ +R+G  ++LE    +L
Sbjct:  101 GYKKHCASWKAAFCSCVDQVKAAPQYKLLRLRECLQGEALRVIENLGHSTTAYEAARSRLERKYGGEGRALTLRLEELEAFKQLREGSKKDLEKFAELL 199          
BLAST of SMED30006141 vs. TrEMBL
Match: A0A2B4RR18 (Integrase catalytic domain-containing protein OS=Stylophora pistillata OX=50429 GN=AWC38_SpisGene16829 PE=4 SV=1)

HSP 1 Score: 77.411 bits (189), Expect = 2.331e-12
Identity = 38/105 (36.19%), Postives = 58/105 (55.24%), Query Frame = -1
Query:   19 KEIENAKVQVIDGKQREYETWKAAFCACVDSSYGDDDEKILHLWSYLSGESLRLIENLGFSSAGYTVAKQKLGRRYGGDERNYLAIVDQIDNFRPVRDGDLRELE 333
            K++E  ++    G + +Y  W AAF +CVD +      KIL L   L GE+   +  LG+SS  Y  AK +L R+YGG+ R   A +D++   +P+   + RELE
Sbjct: 1093 KQLERIRIPKFSGDKMKYSAWWAAFSSCVDETSLSPQFKILRLKGCLEGEAAATVRGLGYSSEAYKAAKARLNRKYGGNRRQVQAHIDELRRMKPLNAENPRELE 1197          
BLAST of SMED30006141 vs. TrEMBL
Match: A0A2B4RG26 (Dual specificity protein kinase shkC OS=Stylophora pistillata OX=50429 GN=shkC PE=4 SV=1)

HSP 1 Score: 73.559 bits (179), Expect = 3.455e-11
Identity = 31/73 (42.47%), Postives = 52/73 (71.23%), Query Frame = -1
Query:    1 KILHLWSYLSGESLRLIENLGFSSAGYTVAKQKLGRRYGGDERNYLAIVDQIDNFRPVRDGDLRELEALISVL 219
            K+L L  YLSG++L+++E LG+S+  Y  AK++L R++GG  R     +++++NFRP+R G+ R+LE L  +L
Sbjct:  154 KLLQLRQYLSGKALKVVEPLGYSATAYETAKERLERKFGGKRRQVALHLEELENFRPLRPGNARDLERLADLL 226          
BLAST of SMED30006141 vs. Planmine SMEST
Match: SMESG000014679.1 (SMESG000014679.1)

HSP 1 Score: 207.994 bits (528), Expect = 7.957e-64
Identity = 98/99 (98.99%), Postives = 98/99 (98.99%), Query Frame = -1
Query:    1 GKQREYETWKAAFCACVDSSYGDDDEKILHLWSYLSGESLRLIENLGFSSAGYTVAKQKLGRRYGGDERNYLAIVDQIDNFRPVRDGDLRELEALISVL 297
             KQREYETWKAAFCACVDSSYGDDDEKILHLWSYLSGESLRLIENLGFSSAGYTVAKQKLGRRYGGDERNYLAIVDQIDNFRPVRDGDLRELEALISVL
Sbjct:  293 AKQREYETWKAAFCACVDSSYGDDDEKILHLWSYLSGESLRLIENLGFSSAGYTVAKQKLGRRYGGDERNYLAIVDQIDNFRPVRDGDLRELEALISVL 391          
BLAST of SMED30006141 vs. Planmine SMEST
Match: SMESG000000863.1 (SMESG000000863.1)

HSP 1 Score: 148.673 bits (374), Expect = 8.717e-41
Identity = 69/104 (66.35%), Postives = 84/104 (80.77%), Query Frame = -1
Query:    1 VQVIDGKQREYETWKAAFCACVDSSYGDDDEKILHLWSYLSGESLRLIENLGFSSAGYTVAKQKLGRRYGGDERNYLAIVDQIDNFRPVRDGDLRELEALISVL 312
            +    G+Q +YE+WKAAF AC+D +  +D EK LHL SYL+GE L+LIENLG+S+  Y  AK+KL RRYGGDERNYLAI+DQ DNFR VRDGDL++LEALISVL
Sbjct:   67 IPTFSGRQSDYESWKAAFNACLDDTEAEDKEKKLHLKSYLNGEPLKLIENLGYSAEAYKTAKEKLERRYGGDERNYLAIMDQNDNFRHVRDGDLKDLEALISVL 170          
BLAST of SMED30006141 vs. Planmine SMEST
Match: SMESG000074922.1 (SMESG000074922.1)

HSP 1 Score: 138.658 bits (348), Expect = 3.690e-39
Identity = 65/115 (56.52%), Postives = 86/115 (74.78%), Query Frame = -1
Query:    1 QKEIENAK---VQVIDGKQREYETWKAAFCACVDSSYGDDDEKILHLWSYLSGESLRLIENLGFSSAGYTVAKQKLGRRYGGDERNYLAIVDQIDNFRPVRDGDLRELEALISVL 336
            QK++ + K   +     ++ +Y++WKAAF  C+D +  +D+EK+LHL SYL+ E L+LIENLG+S+  Y  AK KL R YGGDERNYLAI+D IDN RPV DGDL++LEALISVL
Sbjct:  150 QKKLNHVKPLTIPTFSRRESDYDSWKAAFNVCIDETEAEDEEKMLHLKSYLNWEPLKLIENLGYSTEAYKTAKVKLERHYGGDERNYLAIMDHIDNLRPVHDGDLKDLEALISVL 264          
BLAST of SMED30006141 vs. Planmine SMEST
Match: SMESG000043147.1 (SMESG000043147.1)

HSP 1 Score: 134.42 bits (337), Expect = 5.191e-38
Identity = 65/118 (55.08%), Postives = 87/118 (73.73%), Query Frame = -1
Query:    1 ALMQKEIENAK---VQVIDGKQREYETWKAAFCACVDSSYGDDDEKILHLWSYLSGESLRLIENLGFSSAGYTVAKQKLGRRYGGDERNYLAIVDQIDNFRPVRDGDLRELEALISVL 345
            A  +K++ N K   ++  +G+Q +YE+WKAA   C D +  +D++K+LHL S  +GE L+ I+NLG+S+  Y   K KL RRYGGDERNYLAI+D ID+FRPVRDGDLR+LE LISVL
Sbjct:  130 AKQKKKLNNVKPLPIETFNGRQSDYESWKAASNVCFDET-AEDEKKMLHLKSCFNGEPLKFIQNLGYSAEAYRTYKVKLERRYGGDERNYLAIIDHIDSFRPVRDGDLRDLEVLISVL 246          
BLAST of SMED30006141 vs. Planmine SMEST
Match: SMESG000042514.1 (SMESG000042514.1)

HSP 1 Score: 110.153 bits (274), Expect = 1.385e-30
Identity = 51/72 (70.83%), Postives = 63/72 (87.50%), Query Frame = -1
Query:    1 ILHLWSYLSGESLRLIENLGFSSAGYTVAKQKLGRRYGGDERNYLAIVDQIDNFRPVRDGDLRELEALISVL 216
            +LHL S+L+GE L+LIENLG+ +  Y +AK+KL R YGGDERNYLAI++QIDNFRP RDGDL++LEALISVL
Sbjct:    1 MLHLKSFLNGEQLKLIENLGYLAEVYKIAKEKLERSYGGDERNYLAIMNQIDNFRPFRDGDLKDLEALISVL 72          
The following BLAST results are available for this feature:
BLAST of SMED30006141 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 SMED30006141 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 SMED30006141 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 SMED30006141 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 SMED30006141 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 SMED30006141 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 SMED30006141 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 SMED30006141 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A2B4RC042.409e-1839.64Uncharacterized protein OS=Stylophora pistillata O... [more]
A0A2B4T0234.067e-1836.44Uncharacterized protein OS=Stylophora pistillata O... [more]
A0A2B4R7831.814e-1538.38Uncharacterized protein OS=Stylophora pistillata O... [more]
A0A2B4RR182.331e-1236.19Integrase catalytic domain-containing protein OS=S... [more]
A0A2B4RG263.455e-1142.47Dual specificity protein kinase shkC OS=Stylophora... [more]
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BLAST of SMED30006141 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 SMED30006141 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 SMED30006141 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 SMED30006141 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 SMED30006141 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 SMED30006141 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000014679.17.957e-6498.99SMESG000014679.1[more]
SMESG000000863.18.717e-4166.35SMESG000000863.1[more]
SMESG000074922.13.690e-3956.52SMESG000074922.1[more]
SMESG000043147.15.191e-3855.08SMESG000043147.1[more]
SMESG000042514.11.385e-3070.83SMESG000042514.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006141 ID=SMED30006141|Name=SMED30006141|organism=Schmidtea mediterranea sexual|type=transcript|length=747bp
TAAAACGCTTATCAAGGCTTCCAATTCTCTTAGATCTCCATCACGAACTG
GTCGGAAGTTATCGATCTGATCCACGATCGCCAGGTAATTGCGTTCATCT
CCGCCATATCTTCTACCGAGCTTCTGCTTCGCCACTGTGTAACCCGCGGA
TGAAAATCCCAAGTTCTCGATCAACCTTAGGGATTCTCCACTCAGATATG
ACCAAAGGTGTAAAATCTTTTCATCATCATCACCGTAGGAACTATCCACA
CACGCACAAAAAGCAGCTTTCCAAGTTTCATATTCTCTTTGTTTCCCGTC
AATCACCTGAACTTTTGCATTTTCAATCTCTTTCTGCATTAATGCCTCAA
TTTTAGACAGATTCCTCATTTTCACTTGCAGATTCTTCGTCTTGATTGAA
ATTGCGATATATAATCTGATCGGATTTACGTGAATTTTGATAAAAATTTT
TTAATATTTTTAAGTAGTGGGCTCGCAAAATTGTACAAAAAAAATTTTTT
TCTAATGAAAAATATGAGACAATTGTCTCATTTTAAAAGGAAAGGATGCA
AAATAAGGAAATTCAATTATCGATAAATTTCCAAATCTCGAGTTGACCGA
CATTGAAGTATAAAATTCAATTAACTATGCAATTTTTCTCAACACAACGA
CTTGATATTAGAGAGGTTCCTAAAATGAATGTCACGATTGCTGAGAAAAA
AAAGAAGCTAGACGGTTCAGGTATTTAGAAATTATTATTATTATTAT
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protein sequence of SMED30006141-orf-1

>SMED30006141-orf-1 ID=SMED30006141-orf-1|Name=SMED30006141-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=123bp
MRNLSKIEALMQKEIENAKVQVIDGKQREYETWKAAFCACVDSSYGDDDE
KILHLWSYLSGESLRLIENLGFSSAGYTVAKQKLGRRYGGDERNYLAIVD
QIDNFRPVRDGDLRELEALISVL
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 70..88
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 69..88