SMED30001668

Overview
NameSMED30001668
Smed IDSMED30001668
Length (bp)2628
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 SMED30001668 (SMED30001668) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30001668 (SMED30001668) 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 SMED30001668 (SMED30001668) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30001668 (SMED30001668) 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




SMED30001668

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
pharynxSMED30001668SMESG000033527.1 Contig2307GPL15192PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30001668SMESG000033527.1 Contig2307GPL15192PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30001668SMESG000033527.1 Contig2307GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
epidermisSMED30001668SMESG000033527.1 dd_Smed_v4_5061_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
Homology
BLAST of SMED30001668 vs. Ensembl Human
Match: SVEP1 (sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1 [Source:HGNC Symbol;Acc:HGNC:15985])

HSP 1 Score: 36.1946 bits (82), Expect = 9.090e-6
Identity = 16/59 (27.12%), Postives = 28/59 (47.46%), Query Frame = 1
Query:  442 DKFFVGSEAAIRCERGYRILGNNRMVCQIQTKRKPAWSSPVPKCVLIEASELSDIDQDH 618
            D F+ GS    +C  GY +LG++RM C        +W+   P C+ ++   +     +H
Sbjct: 1704 DDFYAGSTVTYQCNNGYYLLGDSRMFC----TDNGSWNGVSPSCLDVDECAVGSDCSEH 1758          

HSP 2 Score: 34.2686 bits (77), Expect = 9.090e-6
Identity = 13/35 (37.14%), Postives = 22/35 (62.86%), Query Frame = 2
Query:  278 KIIVTCESNYTLSGNPINQCKN-GKWMKPFPFCQK 379
            K+ + C+  + L GNP+  C N G+W +P P C++
Sbjct: 1653 KVNLFCDPGFQLVGNPVQYCLNQGQWTQPLPHCER 1687          
BLAST of SMED30001668 vs. Ensembl Human
Match: SVEP1 (sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1 [Source:HGNC Symbol;Acc:HGNC:15985])

HSP 1 Score: 36.1946 bits (82), Expect = 9.163e-6
Identity = 16/59 (27.12%), Postives = 28/59 (47.46%), Query Frame = 1
Query:  442 DKFFVGSEAAIRCERGYRILGNNRMVCQIQTKRKPAWSSPVPKCVLIEASELSDIDQDH 618
            D F+ GS    +C  GY +LG++RM C        +W+   P C+ ++   +     +H
Sbjct: 1707 DDFYAGSTVTYQCNNGYYLLGDSRMFC----TDNGSWNGVSPSCLDVDECAVGSDCSEH 1761          

HSP 2 Score: 34.2686 bits (77), Expect = 9.163e-6
Identity = 13/35 (37.14%), Postives = 22/35 (62.86%), Query Frame = 2
Query:  278 KIIVTCESNYTLSGNPINQCKN-GKWMKPFPFCQK 379
            K+ + C+  + L GNP+  C N G+W +P P C++
Sbjct: 1656 KVNLFCDPGFQLVGNPVQYCLNQGQWTQPLPHCER 1690          
BLAST of SMED30001668 vs. Ensembl Medaka
Match: CSMD1 (CUB and Sushi multiple domains 1 [Source:NCBI gene;Acc:101164142])

HSP 1 Score: 38.891 bits (89), Expect = 2.157e-7
Identity = 16/49 (32.65%), Postives = 25/49 (51.02%), Query Frame = 1
Query:  448 FFVGSEAAIRCERGYRILGNNRMVCQIQTKRKPAWSSPVPKCVLIEASE 594
            F  G   AI C+RG+ +LG+  + CQ        W  P+P+C+ I   +
Sbjct: 2681 FSYGVTVAIHCKRGFYLLGSAILTCQ----HDGLWDRPMPRCLAISCGD 2725          

HSP 2 Score: 36.5798 bits (83), Expect = 2.157e-7
Identity = 15/30 (50.00%), Postives = 19/30 (63.33%), Query Frame = 2
Query:  290 TCESNYTLSGNPINQCK-NGKWMKPFPFCQ 376
            TC   Y LSG+P  QC+ NG+W  P P C+
Sbjct: 2627 TCNKGYILSGSPRAQCRLNGQWSSPLPVCK 2656          
BLAST of SMED30001668 vs. Planmine SMEST
Match: SMESG000033527.1 (SMESG000033527.1)

HSP 1 Score: 920.998 bits (2379), Expect = 0.000e+0
Identity = 484/486 (99.59%), Postives = 484/486 (99.59%), Query Frame = 1
Query:  367 FLPKKLECIKPKVRKGWIECLTFRCDKFFVGSEAAIRCERGYRILGNNRMVCQIQTKRKPAWSSPVPKCVLIEASELSDIDQDHQPFNLFYPENSSXXXXXXXLSVLAGGXXXXXXXXXXNXXXXXXXXXXXXXSENNSIQPVISTIENVDIERNNQSFSATREISGSPMIWNCFRSLMFRNSRYQHMDTQTVEPQTNFEADFNPTDNFEIFNTIYSDDQTSLIQPPCYEEAVKCSQYSIVAPKNASEHQKYKGNHNKSKSNITARSTDKDVRQSNLRDINSSSLNNDPPENINQSITSIPNTSMQSNFPGFQNPKDQNNVANRSNDMDNVSRRSARVHCPRVTNNLASDSNVSFRSGSIETMAISDGTSVTVHTLDSRGSNPSLGSMRPQTGSIGDPTNCPNNFTTHYRYPLTQERSATPFTETDFAANETRYSPPPSYECSLNNPPVIRSSRYNHSNTTSPSSNLNVALFVDNMACIEDANDNS 1824
            F  KKLECIKPKVRKGWIECLTFRCDKFFVGSEAAIRCERGYRILGNNRMVCQIQTKRKPAWSSPVPKCVLIEASELSDIDQDHQPFNLFYPENSSIMIIIIILSVLAGGLMLLMSIMLMNRLFQRRRLLRVQRSENNSIQPVISTIENVDIERNNQSFSATREISGSPMIWNCFRSLMFRNSRYQHMDTQTVEPQTNFEADFNPTDNFEIFNTIYSDDQTSLIQPPCYEEAVKCSQYSIVAPKNASEHQKYKGNHNKSKSNITARSTDKDVRQSNLRDINSSSLNNDPPENINQSITSIPNTSMQSNFPGFQNPKDQNNVANRSNDMDNVSRRSARVHCPRVTNNLASDSNVSFRSGSIETMAISDGTSVTVHTLDSRGSNPSLGSMRPQTGSIGDPTNCPNNFTTHYRYPLTQERSATPFTETDFAANETRYSPPPSYECSLNNPPVIRSSRYNHSNTTSPSSNLNVALFVDNMACIEDANDNS
Sbjct:   79 FCQKKLECIKPKVRKGWIECLTFRCDKFFVGSEAAIRCERGYRILGNNRMVCQIQTKRKPAWSSPVPKCVLIEASELSDIDQDHQPFNLFYPENSSIMIIIIILSVLAGGLMLLMSIMLMNRLFQRRRLLRVQRSENNSIQPVISTIENVDIERNNQSFSATREISGSPMIWNCFRSLMFRNSRYQHMDTQTVEPQTNFEADFNPTDNFEIFNTIYSDDQTSLIQPPCYEEAVKCSQYSIVAPKNASEHQKYKGNHNKSKSNITARSTDKDVRQSNLRDINSSSLNNDPPENINQSITSIPNTSMQSNFPGFQNPKDQNNVANRSNDMDNVSRRSARVHCPRVTNNLASDSNVSFRSGSIETMAISDGTSVTVHTLDSRGSNPSLGSMRPQTGSIGDPTNCPNNFTTHYRYPLTQERSATPFTETDFAANETRYSPPPSYECSLNNPPVIRSSRYNHSNTTSPSSNLNVALFVDNMACIEDANDNS 564          

HSP 2 Score: 128.642 bits (322), Expect = 8.540e-31
Identity = 74/74 (100.00%), Postives = 74/74 (100.00%), Query Frame = 2
Query:  158 KVFILMIFNLYLSDSYCAIPVIVHGSXXXXXXXXXXXXXYKIIVTCESNYTLSGNPINQCKNGKWMKPFPFCQK 379
            KVFILMIFNLYLSDSYCAIPVIVHGSTVNVHNNTVNLNTYKIIVTCESNYTLSGNPINQCKNGKWMKPFPFCQK
Sbjct:    9 KVFILMIFNLYLSDSYCAIPVIVHGSTVNVHNNTVNLNTYKIIVTCESNYTLSGNPINQCKNGKWMKPFPFCQK 82          
The following BLAST results are available for this feature:
BLAST of SMED30001668 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 2
Match NameE-valueIdentityDescription
SVEP19.090e-627.12sushi, von Willebrand factor type A, EGF and pentr... [more]
SVEP19.163e-627.12sushi, von Willebrand factor type A, EGF and pentr... [more]
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BLAST of SMED30001668 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 SMED30001668 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 SMED30001668 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 SMED30001668 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 SMED30001668 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 SMED30001668 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 SMED30001668 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 SMED30001668 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 SMED30001668 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 SMED30001668 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 SMED30001668 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 SMED30001668 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
CSMD12.157e-732.65CUB and Sushi multiple domains 1 [Source:NCBI gene... [more]
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BLAST of SMED30001668 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000033527.18.540e-3199.59SMESG000033527.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001668 ID=SMED30001668|Name=SMED30001668|organism=Schmidtea mediterranea sexual|type=transcript|length=2628bp
ATTTTATTGTAAATGTAACAATTTGTAAAATTACTACGCAATATATTATG
AAATATGTTTTAATAATCTTTAATTTATCACAATAAACAATTATAATTTA
TATAACCTTAATAGATTGAAAATTTTATACTTAATGTACTATATTTATAT
ATGCTTAAAAGTTTTCATTTTAATGATTTTTAATTTATATTTATCTGATT
CATATTGTGCGATTCCAGTTATTGTCCACGGAAGTACAGTAAATGTTCAT
AATAATACAGTAAATCTTAATACATATAAAATTATTGTAACGTGTGAATC
AAATTATACATTGTCTGGGAATCCTATTAATCAATGCAAGAACGGGAAAT
GGATGAAACCATTTCCTTTTTGCCAAAAAAATTAGAATGTATTAAACCTA
AAGTGCGAAAAGGATGGATAGAATGTTTGACTTTTCGCTGTGATAAATTT
TTTGTTGGGAGTGAAGCTGCTATTCGATGTGAACGTGGCTATAGAATATT
AGGTAACAATCGAATGGTTTGTCAAATACAAACGAAAAGAAAGCCTGCAT
GGAGTTCACCTGTTCCAAAATGTGTATTAATTGAAGCCTCTGAATTGTCG
GACATTGATCAAGATCATCAGCCATTTAATTTATTTTACCCCGAAAATAG
CAGTATCATGATTATAATAATAATATTATCTGTTCTTGCGGGTGGTCTCA
TGTTACTAATGAGTATAATGCTTATGAATCGTTTATTTCAACGCCGTCGA
CTTTTGCGTGTTCAAAGATCTGAAAATAACTCCATTCAACCAGTAATTTC
AACCATAGAAAATGTTGACATAGAAAGAAATAATCAAAGTTTTTCTGCAA
CTCGCGAGATTTCTGGTTCACCAATGATATGGAATTGTTTCAGGTCTTTG
ATGTTTAGAAATTCTCGTTACCAGCATATGGATACTCAAACAGTAGAACC
GCAAACTAATTTCGAAGCGGATTTCAACCCAACAGACAATTTTGAGATAT
TCAATACTATTTATAGTGATGACCAAACATCATTAATTCAACCTCCATGT
TATGAGGAGGCTGTAAAGTGTTCTCAATACAGTATTGTTGCTCCTAAGAA
TGCAAGTGAGCATCAAAAGTATAAAGGAAATCACAATAAATCAAAATCAA
ATATAACTGCACGGTCTACAGATAAAGATGTGAGACAAAGTAACCTCAGG
GATATAAATTCCAGTTCACTGAATAATGATCCCCCTGAAAATATTAATCA
ATCCATTACCTCAATCCCCAATACGTCAATGCAATCTAATTTTCCTGGAT
TTCAGAATCCTAAAGATCAAAATAATGTCGCTAATAGGTCAAATGATATG
GATAACGTGAGTAGGCGCTCTGCAAGAGTCCATTGTCCTAGAGTTACTAA
CAATCTTGCATCAGATTCAAATGTTTCTTTTCGATCTGGTAGTATTGAAA
CAATGGCGATATCAGATGGCACATCAGTTACAGTTCATACACTTGATAGT
CGAGGCAGTAATCCCAGTCTGGGATCAATGCGTCCACAGACTGGATCAAT
CGGTGATCCAACAAACTGTCCTAATAATTTCACAACACATTACAGATATC
CCTTAACACAGGAAAGATCTGCTACTCCTTTTACTGAAACTGATTTTGCA
GCAAATGAGACACGATATTCACCACCTCCTTCATATGAATGCTCATTAAA
CAATCCACCAGTAATCAGGAGCTCTAGATATAATCACTCAAACACAACTT
CTCCAAGCTCAAATTTAAACGTAGCTTTATTTGTAGACAACATGGCTTGT
ATAGAGGATGCCAATGATAATTCTTAATTGTGATTTTAAAATGTAGTAAC
TATTTTAACCTGATAAAGAAAATGATTTTTACAAAATATTTTCCAAAGTG
TTAATATTTTTAATACCTTTGAAAGATTGGACTAAATTTTCTTTATGTGC
AAATTTTAAAATCAATAAGTTTAATAATTTTATATTAAAATATTTTTCTC
TATTAAACTTTAAATTTGCAGCATTTCCATCTAAATTATTTCACTAATAA
ACTATAGAAATGGATTTCGAAGGTTGGACGCGGAATGTTCATCGAAAACC
CAAAGAAAATGTACAAGGTAGCAAAACTCCATTGATCGCTGTGATTTGAC
TGTGTAGCAAGAGCTGGGAAAATCTCGGTTTTTCAGGAAAGGTGGCGAAT
ATGATAGATGGAAAGCATTATTAATGACTTGTGTAGATGAATATAATTTT
TAAATTATAATAAAAATTTGATTTTTTTAGAGGGTCACCTTTTTGAGTAC
TAACGAAACCTTAGGGAGCGCCCGTTAGGTACGCCCCCAAAAAGTAAATT
TTGACCCCTTCCATTGGCCCTATACTTGAGTCTCAAGTTCTCTTTCTAAA
GACTTCCTCTTTCTAGAGTACGTCTTTAATAGATGTTCCAATTAGTCTGT
TAGCGAGTCTAAGAGAAATAAAGTTATCAAAGCTCACTGAATATGGCGAT
TAAGTCTCTACGAAAACTATAGATACGAAAATCCTTTAAGTGCGTCCATC
TAAGAAAGGGGAGGAAGGGGTCTTCGCAAAAGTGACAAATGGGGAAACTA
GGAAGGGTCTCTAAGTGCTTATTACATC
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protein sequence of SMED30001668-orf-1

>SMED30001668-orf-1 ID=SMED30001668-orf-1|Name=SMED30001668-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=498bp
MQEREMDETISFLPKKLECIKPKVRKGWIECLTFRCDKFFVGSEAAIRCE
RGYRILGNNRMVCQIQTKRKPAWSSPVPKCVLIEASELSDIDQDHQPFNL
FYPENSSIMIIIIILSVLAGGLMLLMSIMLMNRLFQRRRLLRVQRSENNS
IQPVISTIENVDIERNNQSFSATREISGSPMIWNCFRSLMFRNSRYQHMD
TQTVEPQTNFEADFNPTDNFEIFNTIYSDDQTSLIQPPCYEEAVKCSQYS
IVAPKNASEHQKYKGNHNKSKSNITARSTDKDVRQSNLRDINSSSLNNDP
PENINQSITSIPNTSMQSNFPGFQNPKDQNNVANRSNDMDNVSRRSARVH
CPRVTNNLASDSNVSFRSGSIETMAISDGTSVTVHTLDSRGSNPSLGSMR
PQTGSIGDPTNCPNNFTTHYRYPLTQERSATPFTETDFAANETRYSPPPS
YECSLNNPPVIRSSRYNHSNTTSPSSNLNVALFVDNMACIEDANDNS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000026gut
PLANA:0000034epidermis
PLANA:0000070intestinal phagocyte
Vocabulary: INTERPRO
TermDefinition
IPR035976Sushi/SCR/CCP_sf
IPR000436Sushi_SCR_CCP_dom
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR000436Sushi/SCR/CCP domainSMARTSM00032CCP_2coord: 25..80
e-value: 1.2E-4
score: 31.5
IPR000436Sushi/SCR/CCP domainPFAMPF00084Sushicoord: 25..80
e-value: 6.1E-7
score: 29.9
IPR000436Sushi/SCR/CCP domainPROSITEPS50923SUSHIcoord: 23..82
score: 8.582
IPR000436Sushi/SCR/CCP domainCDDcd00033CCPcoord: 25..81
e-value: 2.06781E-6
score: 38.9832
NoneNo IPR availableGENE3DG3DSA:2.10.70.10coord: 24..82
e-value: 5.5E-9
score: 38.3
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..25
score: 0.672
NoneNo IPR availableTMHMMTMhelixcoord: 10..32
IPR035976Sushi/SCR/CCP superfamilySUPERFAMILYSSF57535Complement control module/SCR domaincoord: 24..81