SMED30035614

Overview
NameSMED30035614
Smed IDSMED30035614
Length (bp)600
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 SMED30035614 (SMED30035614) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30035614 (SMED30035614) 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 SMED30035614 (SMED30035614) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30035614 (SMED30035614) 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



SMED30035614

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30035614SMESG000023661.1 dd_Smed_v6_13154_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30035614SMESG000023661.1 dd_Smed_v4_13154_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30035614SMESG000023661.1 dd_Smed_v4_13154_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30035614SMESG000023661.1 dd_Smed_v4_13154_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult colorimetric in situ hybridization evidence
Category 4 cellSMED30035614SMESG000023661.1 dd_Smed_v4_13154_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
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BLAST of SMED30035614 vs. Ensembl Human
Match: CXorf65 (chromosome X open reading frame 65 [Source:HGNC Symbol;Acc:HGNC:33713])

HSP 1 Score: 48.1358 bits (113), Expect = 1.542e-6
Identity = 22/79 (27.85%), Postives = 44/79 (55.70%), Query Frame = 2 
Query:   86 FVWIHHGDNKKFIANTDCSALNFLDYIRKNCLIDESDIFDFTDING--KLLQISDQFHESWHTQF-ENRSIYIPVSIDK 313
            F++I HGDN++F+ NT+C+ +  L YIR    + +++  D  +  G  K+L +    H  + +++   RS Y    +++
Sbjct:    2 FIFIKHGDNQQFLVNTNCAVVVLLYYIRSKVKLPKTNTIDLCEQTGKMKMLFLMKPNHAEYASKYLTARSTYYVCKVER 80
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BLAST of SMED30035614 vs. Ensembl Zebrafish
Match: C14HXorf65 (si:ch211-191o15.6 [Source:ZFIN;Acc:ZDB-GENE-110228-3])

HSP 1 Score: 53.1434 bits (126), Expect = 1.335e-8
Identity = 30/116 (25.86%), Postives = 58/116 (50.00%), Query Frame = 2 
Query:   86 FVWIHHGDNKKFIANTDCSALNFLDYIRKNCLIDESDIFDFTDING--KLLQISDQFHESWHTQFENRSIYIPVSIDKDDHNEICDVRPLIEGI-NELYPSLQDKLQKYRKFKLQK 424
            F++I HGDN++F+ N++C  +  + Y+++   + ES++ D  D  G  K L       ES     + R  +I   +   +      VR L+ G+ + L  +LQ ++    K +L++
Sbjct:    2 FIYIRHGDNEQFLLNSNCPVVILVQYLKRMFGLAESELVDLCDERGVLKFLFQPQNLQESARELLKARESFIVCIVHCMNDGAFTSVRSLLAGVDSALLEALQSQIDHLEKARLKQ 117
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BLAST of SMED30035614 vs. Ensembl Mouse
Match: Gm614 (predicted gene 614 [Source:MGI Symbol;Acc:MGI:2685460])

HSP 1 Score: 50.8322 bits (120), Expect = 1.089e-7
Identity = 27/78 (34.62%), Postives = 43/78 (55.13%), Query Frame = 2 
Query:   86 FVWIHHGDNKKFIANTDCSALNFLDYIRKNCLIDESDIFDFTDING--KLLQISDQFHESWHTQFENRSIYIPVSIDK 313
            F+ I HGDN++F+ N++CS L  L YIRK   + ++D  D  D +G  KLL +S    +S       R+ Y    +++
Sbjct:    2 FIIIKHGDNQEFLVNSNCSVLLLLHYIRKKMKLRKTDTIDLCDESGTMKLLFLSKTPGDSASKFLTARNTYYVCKVER 79
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BLAST of SMED30035614 vs. UniProt/SwissProt
Match: sp|Q3V2K1|CX065_MOUSE (Uncharacterized protein CXorf65 homolog OS=Mus musculus OX=10090 GN=Gm614 PE=2 SV=1)

HSP 1 Score: 50.8322 bits (120), Expect = 7.615e-7
Identity = 27/78 (34.62%), Postives = 43/78 (55.13%), Query Frame = 2 
Query:   86 FVWIHHGDNKKFIANTDCSALNFLDYIRKNCLIDESDIFDFTDING--KLLQISDQFHESWHTQFENRSIYIPVSIDK 313
            F+ I HGDN++F+ N++CS L  L YIRK   + ++D  D  D +G  KLL +S    +S       R+ Y    +++
Sbjct:    2 FIIIKHGDNQEFLVNSNCSVLLLLHYIRKKMKLRKTDTIDLCDESGTMKLLFLSKTPGDSASKFLTARNTYYVCKVER 79
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BLAST of SMED30035614 vs. TrEMBL
Match: A0A3Q0KSY5 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 PE=4 SV=1)

HSP 1 Score: 75.8702 bits (185), Expect = 5.586e-14
Identity = 43/132 (32.58%), Postives = 71/132 (53.79%), Query Frame = 2 
Query:   68 NAVNCKFVWIHHGDNKKFIANTDCSALNFLDYIRKNCLIDESDIFDFTDINGKLLQISD-QFHESWHTQFENRSIYIPVSIDKDDHNEICDVRPLIEGINELYPSLQDKL--------QKYRKFKLQKKINL 436
            ++ +  F+WI  G+NKK + N  CS    L+YI   C ID    FD  D +G+LL +SD Q ++      E   +YI V+I+ D  ++  ++RP++E   + YP+L D++        ++Y K K  K+  L
Sbjct:    2 SSTSRSFIWIRFGENKKVLVNMWCSFEILLNYIVTVCDIDPEITFDLCDTSGRLLGLSDSQNYQQTVQSIEGGGVYILVAIEGDKSDQQMNIRPMLENFEQYYPNLTDQILQNLHDKSERYSKKKHMKRTPL 133
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BLAST of SMED30035614 vs. TrEMBL
Match: C1LEX5 (Hypotheticial protein OS=Schistosoma japonicum OX=6182 PE=2 SV=1)

HSP 1 Score: 65.0846 bits (157), Expect = 6.799e-10
Identity = 36/109 (33.03%), Postives = 59/109 (54.13%), Query Frame = 2 
Query:   71 AVNCKFVWIHHGDNKKFIANTDCSALNFLDYIRKNCLIDESDIFDFTDINGKLLQISD-QFHESWHTQFENRSIYIPVSIDKDDHNEICDVRPLIEGINELYPSLQDKL 394
              N  F+WI  G+N K + N  CS+   L++I   C ID    FD  D +G+LL +S+ Q  +      E  ++YI V I+ D  ++  +VRP++    + YP+L D++
Sbjct:    3 TTNRPFIWIRFGENNKVLVNMWCSSEILLNHIISVCDIDPEITFDLCDTSGRLLGLSEAQTFQQTIQSLEGGAVYILVIIE-DKSDQQVNVRPMLTNFEQYYPNLTDQI 110
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BLAST of SMED30035614 vs. TrEMBL
Match: A0A4Z2DEA6 (Uncharacterized protein OS=Schistosoma japonicum OX=6182 GN=EWB00_001977 PE=4 SV=1)

HSP 1 Score: 65.0846 bits (157), Expect = 7.015e-10
Identity = 36/109 (33.03%), Postives = 59/109 (54.13%), Query Frame = 2 
Query:   71 AVNCKFVWIHHGDNKKFIANTDCSALNFLDYIRKNCLIDESDIFDFTDINGKLLQISD-QFHESWHTQFENRSIYIPVSIDKDDHNEICDVRPLIEGINELYPSLQDKL 394
              N  F+WI  G+N K + N  CS+   L++I   C ID    FD  D +G+LL +S+ Q  +      E  ++YI V I+ D  ++  +VRP++    + YP+L D++
Sbjct:    3 TTNRPFIWIRFGENNKVLVNMWCSSEILLNHIISVCDIDPEITFDLCDTSGRLLGLSEAQTFQQTIQSLEGGAVYILVIIE-DKSDQQVNVRPMLTNFEQYYPNLTDQI 110
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BLAST of SMED30035614 vs. TrEMBL
Match: A0A2D0RGJ6 (uncharacterized protein CXorf65 homolog isoform X1 OS=Ictalurus punctatus OX=7998 GN=c8hxorf65 PE=4 SV=1)

HSP 1 Score: 62.3882 bits (150), Expect = 6.164e-9
Identity = 31/104 (29.81%), Postives = 51/104 (49.04%), Query Frame = 2 
Query:   86 FVWIHHGDNKKFIANTDCSALNFLDYIRKNCLIDESDIFDFTDINGKLLQISDQFHESWHTQFENRSIYIPVSIDKDDHNEICDVRPLIEGINELYPSLQDKLQ 397
            FV+I HGDN++F+ NT+CS +  L Y+R    + ++D+ D  D  G LL +S             R  YI  +I++        + P +  ++ +   LQ  LQ
Sbjct:    2 FVYIKHGDNEQFLVNTNCSIICLLQYVRSKLKLTDTDLVDLCDERGALLSLSGHRQGYASQILTPRKTYIICTINRSSEGAYVSITPHVANLDSV---LQGVLQ 102
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BLAST of SMED30035614 vs. TrEMBL
Match: A0A4E0QXZ9 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_010902 PE=4 SV=1)

HSP 1 Score: 62.7734 bits (151), Expect = 6.406e-9
Identity = 34/107 (31.78%), Postives = 62/107 (57.94%), Query Frame = 2 
Query:   86 FVWIHHGDNKKFIANTDCSALNFLDYIRKNCLIDESDIFDFTDINGKLLQISDQFHESWHTQ-FENRSIYIPVSIDKDDHNEICDVRPLIEGINELYPSLQDKLQKY 403
            F+W+++GD ++ + N +C+     +Y+   C IDE  +FD  D +GKLL I+D    +   Q  +    YI VSI+ D  +   DV+PL+E  +  +P+L +++ ++
Sbjct:   26 FIWVNYGDTQRILINVNCAYEILNNYLVTQCDIDEDVVFDLCDSSGKLLNINDPLSYTQVIQSIDGGGEYILVSIEGDRAS---DVKPLLENYDAKFPNLIEQIAQH 129
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BLAST of SMED30035614 vs. Planmine SMEST
Match: SMESG000023661.1 (SMESG000023661.1)

HSP 1 Score: 279.641 bits (714), Expect = 2.078e-97
Identity = 152/152 (100.00%), Postives = 152/152 (100.00%), Query Frame = 2 
Query:   56 MIVDNAVNCKFVWIHHGDNKKFIANTDCSALNFLDYIRKNCLIDESDIFDFTDINGKLLQISDQFHESWHTQFENRSIYIPVSIDKDDHNEICDVRPLIEGINELYPSLQDKLQKYRKFKLQKKINLKNGNGXXXXXXXXXXXXXXKVKKIG 511
            MIVDNAVNCKFVWIHHGDNKKFIANTDCSALNFLDYIRKNCLIDESDIFDFTDINGKLLQISDQFHESWHTQFENRSIYIPVSIDKDDHNEICDVRPLIEGINELYPSLQDKLQKYRKFKLQKKINLKNGNGSGSISARSDSRSFRKVKKIG
Sbjct:    1 MIVDNAVNCKFVWIHHGDNKKFIANTDCSALNFLDYIRKNCLIDESDIFDFTDINGKLLQISDQFHESWHTQFENRSIYIPVSIDKDDHNEICDVRPLIEGINELYPSLQDKLQKYRKFKLQKKINLKNGNGSGSISARSDSRSFRKVKKIG 152
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BLAST of SMED30035614 vs. Planmine SMEST
Match: SMESG000033459.1 (SMESG000033459.1)

HSP 1 Score: 57.3806 bits (137), Expect = 6.031e-11
Identity = 27/84 (32.14%), Postives = 46/84 (54.76%), Query Frame = 2 
Query:   86 FVWIHHGDNKKFIANTDCSALNFLDYIRKNCL----IDESDIFDFTDINGKLLQISDQFHESWHTQFENRSIYIPVSIDKDDHN 325
            FV++H+G+ +K I N DC  +  +DY+++NCL    I E+ +FD  D+NG +  I +   +S   +   R   + V +  D  N
Sbjct:    3 FVFVHYGNQQKMILNADCRLVCLMDYLKRNCLQNYKITENMLFDLVDVNGGIKNIRNITDQSGLEELHTREELLIVQVTNDAAN 86
The following BLAST results are available for this feature:
BLAST of SMED30035614 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 1
Match NameE-valueIdentityDescription
CXorf651.542e-627.85chromosome X open reading frame 65 [Source:HGNC Sy... [more]
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BLAST of SMED30035614 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 SMED30035614 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 SMED30035614 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
C14HXorf651.335e-825.86si:ch211-191o15.6 [Source:ZFIN;Acc:ZDB-GENE-110228... [more]
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BLAST of SMED30035614 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 SMED30035614 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 1
Match NameE-valueIdentityDescription
Gm6141.089e-734.62predicted gene 614 [Source:MGI Symbol;Acc:MGI:2685... [more]
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BLAST of SMED30035614 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|Q3V2K1|CX065_MOUSE7.615e-734.62Uncharacterized protein CXorf65 homolog OS=Mus mus... [more]
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BLAST of SMED30035614 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A3Q0KSY55.586e-1432.58Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
C1LEX56.799e-1033.03Hypotheticial protein OS=Schistosoma japonicum OX=... [more]
A0A4Z2DEA67.015e-1033.03Uncharacterized protein OS=Schistosoma japonicum O... [more]
A0A2D0RGJ66.164e-929.81uncharacterized protein CXorf65 homolog isoform X1... [more]
A0A4E0QXZ96.406e-931.78Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
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BLAST of SMED30035614 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 SMED30035614 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 SMED30035614 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 SMED30035614 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 SMED30035614 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 SMED30035614 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000023661.12.078e-97100.00SMESG000023661.1[more]
SMESG000033459.16.031e-1132.14SMESG000033459.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035614 ID=SMED30035614|Name=SMED30035614|organism=Schmidtea mediterranea sexual|type=transcript|length=600bp
AAAACTTTTATTTTAATACATTTATTTGATAAATTAGAATATTAGTAATA
TTCGAATGATTGTAGATAACGCCGTTAATTGTAAATTTGTCTGGATTCAT
CACGGAGATAATAAAAAATTTATTGCTAACACGGATTGCAGTGCTTTGAA
TTTTCTTGATTACATTCGAAAAAATTGTTTAATCGATGAATCAGATATTT
TTGATTTTACCGATATAAATGGTAAACTTCTTCAAATATCAGATCAATTT
CATGAGTCTTGGCATACTCAATTTGAAAACAGATCGATCTATATCCCTGT
TTCTATTGATAAAGACGATCATAATGAAATTTGCGATGTTCGCCCTTTAA
TTGAGGGCATCAATGAGTTGTACCCGAGTTTGCAAGATAAACTTCAGAAA
TATCGAAAATTCAAGCTCCAGAAAAAAATTAACCTAAAGAACGGAAACGG
AAGCGGAAGCATAAGTGCTCGATCCGATTCAAGAAGTTTCAGAAAAGTAA
AAAAAATCGGATAAAATTATTTTACGTTATTTTTTTCATACAAATATTTG
TTTTCATTATTGAATGTATTTTTTCTTAATAAAATTCATTGACTTCTGAA
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protein sequence of SMED30035614-orf-1

>SMED30035614-orf-1 ID=SMED30035614-orf-1|Name=SMED30035614-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=153bp
MIVDNAVNCKFVWIHHGDNKKFIANTDCSALNFLDYIRKNCLIDESDIFD
FTDINGKLLQISDQFHESWHTQFENRSIYIPVSIDKDDHNEICDVRPLIE
GINELYPSLQDKLQKYRKFKLQKKINLKNGNGSGSISARSDSRSFRKVKK
IG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000034epidermis
PLANA:0000096ventral epidermis
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR039471CXorf65-like
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR039471Uncharacterized protein CXorf65-likePFAMPF15874Il2rgcoord: 16..101
e-value: 5.2E-15
score: 55.5
IPR039471Uncharacterized protein CXorf65-likePANTHERPTHR33887FAMILY NOT NAMEDcoord: 11..134
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 132..152