SMED30027966

Overview
NameSMED30027966
Smed IDSMED30027966
Length (bp)435
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 SMED30027966 (SMED30027966) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30027966 (SMED30027966) 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.
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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



SMED30027966

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



PAGE Curations: 15

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30027966h1SMcG0020629 Contig2221GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30027966h1SMcG0020573 Contig2221GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30027966h1SMcG0020513 Contig2221GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30027966h1SMcG0020520 Contig2221GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30027966h1SMcG0020450 Contig2221GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30027966h1SMcG0020518 Contig2221GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30027966h1SMcG0020573 PL08004B1G06smed_ncbi_20240424PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
gutSMED30027966 Contig1674GPL15192PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30027966 Contig1674GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
prepharyngeal regionSMED30027966h1SMcG0020573 SmedASXL_073723SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30027966h1SMcG0020573 Contig31350newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30027966h1SMcG0020573 Contig31350uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30027966h1SMcG0020573 dd_Smed_v4_3945_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30027966h1SMcG0020573 dd_Smed_v4_8471_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30027966h1SMcG0020559 dd_Smed_v4_3945_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
SMED30027966 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006238:2330..2846 +2120
v31.002674:19787..20290 -1784
v31.002674:13108..13488 -667
Homology
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BLAST of SMED30027966 vs. Ensembl Zebrafish
Match: asb2a.1 (ankyrin repeat and SOCS box containing 2a, tandem duplicate 1 [Source:ZFIN;Acc:ZDB-GENE-030131-5355])

HSP 1 Score: 45.0542 bits (105), Expect = 9.301e-6
Identity = 29/85 (34.12%), Postives = 46/85 (54.12%), Query Frame = -1 
Query:  157 CISLLNAGAQVNSINNFGNSPLLEMFCETQLAVNDDNLNKLIDITNILIGNGADVNAQSSNGITAFQLAANIGSEKIMLALVSNN 411
            C  L+ AGA+V+  N +G +P+   F   Q        +  ++   +L+ NGAD+N+Q+S+G TA   A   G E I+  L+S N
Sbjct:  289 CEMLMKAGAKVSLPNKYGITPI---FVAAQ--------SGKVEALRMLLKNGADLNSQASDGATALYEACKNGHEDIVEFLLSQN 362
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BLAST of SMED30027966 vs. Ensembl Zebrafish
Match: asb2a.1 (ankyrin repeat and SOCS box containing 2a, tandem duplicate 1 [Source:ZFIN;Acc:ZDB-GENE-030131-5355])

HSP 1 Score: 45.0542 bits (105), Expect = 9.603e-6
Identity = 29/85 (34.12%), Postives = 46/85 (54.12%), Query Frame = -1 
Query:  157 CISLLNAGAQVNSINNFGNSPLLEMFCETQLAVNDDNLNKLIDITNILIGNGADVNAQSSNGITAFQLAANIGSEKIMLALVSNN 411
            C  L+ AGA+V+  N +G +P+   F   Q        +  ++   +L+ NGAD+N+Q+S+G TA   A   G E I+  L+S N
Sbjct:  289 CEMLMKAGAKVSLPNKYGITPI---FVAAQ--------SGKVEALRMLLKNGADLNSQASDGATALYEACKNGHEDIVEFLLSQN 362
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BLAST of SMED30027966 vs. Ensembl Cavefish
Match: asb15a (ankyrin repeat and SOCS box containing 15 [Source:NCBI gene;Acc:103036356])

HSP 1 Score: 46.2098 bits (108), Expect = 2.976e-6
Identity = 34/114 (29.82%), Postives = 58/114 (50.88%), Query Frame = -1 
Query:   67 LLNAGAQVNSINNFGNSPLLEMFCETQLAVNDDNLNKLIDITNILIGNGADVNAQSSNGITAFQLAANIGSEKIMLALVSN--NPKLINFASIDFQIPFTNQWFEYGEILIKLL 402
            LL  G Q++  +  G +P+  +  E   A          ++ ++LI NGADVNAQ+ NG +    AA  G+   +  L+ N  NP L+N +S   Q+P     +E   +++++L
Sbjct:  153 LLQHGGQISDTDQSGVTPM-GIAAEYAQA----------EVLDLLIHNGADVNAQAPNGDSVLYDAAGAGNPDCIDLLLQNGANPNLLNLSS---QLPIHRAAYEGHYLVLRML 252
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BLAST of SMED30027966 vs. Ensembl Cavefish
Match: asb15a (ankyrin repeat and SOCS box containing 15 [Source:NCBI gene;Acc:103036356])

HSP 1 Score: 46.2098 bits (108), Expect = 3.009e-6
Identity = 34/114 (29.82%), Postives = 58/114 (50.88%), Query Frame = -1 
Query:   67 LLNAGAQVNSINNFGNSPLLEMFCETQLAVNDDNLNKLIDITNILIGNGADVNAQSSNGITAFQLAANIGSEKIMLALVSN--NPKLINFASIDFQIPFTNQWFEYGEILIKLL 402
            LL  G Q++  +  G +P+  +  E   A          ++ ++LI NGADVNAQ+ NG +    AA  G+   +  L+ N  NP L+N +S   Q+P     +E   +++++L
Sbjct:  188 LLQHGGQISDTDQSGVTPM-GIAAEYAQA----------EVLDLLIHNGADVNAQAPNGDSVLYDAAGAGNPDCIDLLLQNGANPNLLNLSS---QLPIHRAAYEGHYLVLRML 287
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BLAST of SMED30027966 vs. Planmine SMEST
Match: SMESG000010604.1 (SMESG000010604.1)

HSP 1 Score: 285.419 bits (729), Expect = 5.610e-96
Identity = 144/145 (99.31%), Postives = 144/145 (99.31%), Query Frame = -1 
Query:    1 VKSLQSNTCISLLNAGAQVNSINNFGNSPLLEMFCETQLAVNDDNLNKLIDITNILIGNGADVNAQSSNGITAFQLAANIGSEKIMLALVSNNPKLINFASIDFQIPFTNQWFEYGEILIKLLPDNFLSSTISNETFQSCESAGT 435
            VKSLQSNTCISLLNAGAQVNSINNFGNSPLLEMFCETQLAVNDDNLNKLIDITNILIGNGADVNAQSSNGITAFQLAANIGSEKIMLALVSNNPKLINFAS DFQIPFTNQWFEYGEILIKLLPDNFLSSTISNETFQSCESAGT
Sbjct:   35 VKSLQSNTCISLLNAGAQVNSINNFGNSPLLEMFCETQLAVNDDNLNKLIDITNILIGNGADVNAQSSNGITAFQLAANIGSEKIMLALVSNNPKLINFASTDFQIPFTNQWFEYGEILIKLLPDNFLSSTISNETFQSCESAGT 179
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BLAST of SMED30027966 vs. Planmine SMEST
Match: SMESG000010464.1 (SMESG000010464.1)

HSP 1 Score: 255.373 bits (651), Expect = 2.276e-80
Identity = 125/142 (88.03%), Postives = 133/142 (93.66%), Query Frame = -1 
Query:   10 VKSLQSNTCISLLNAGAQVNSINNFGNSPLLEMFCETQLAVNDDNLNKLIDITNILIGNGADVNAQSSNGITAFQLAANIGSEKIMLALVSNNPKLINFASIDFQIPFTNQWFEYGEILIKLLPDNFLSSTISNETFQSCES 435
            VKSLQSNTCISLLNAGAQVNSINNFGNSPLL+MFCE QLAVNDDNLNK I+ITNILIGNGAD NAQSSNGITAFQLA+NIGSEK+MLALVSNNPKLINFASIDFQIPFTNQWFEYGEILIKLLPDNFLS+ I+   F  C++
Sbjct:  599 VKSLQSNTCISLLNAGAQVNSINNFGNSPLLDMFCEAQLAVNDDNLNKSIEITNILIGNGADTNAQSSNGITAFQLASNIGSEKLMLALVSNNPKLINFASIDFQIPFTNQWFEYGEILIKLLPDNFLSANITRNIFHLCKA 740
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BLAST of SMED30027966 vs. Planmine SMEST
Match: SMESG000010464.1 (SMESG000010464.1)

HSP 1 Score: 254.988 bits (650), Expect = 3.113e-80
Identity = 125/142 (88.03%), Postives = 133/142 (93.66%), Query Frame = -1 
Query:   10 VKSLQSNTCISLLNAGAQVNSINNFGNSPLLEMFCETQLAVNDDNLNKLIDITNILIGNGADVNAQSSNGITAFQLAANIGSEKIMLALVSNNPKLINFASIDFQIPFTNQWFEYGEILIKLLPDNFLSSTISNETFQSCES 435
            VKSLQSNTCISLLNAGAQVNSINNFGNSPLL+MFCE QLAVNDDNLNK I+ITNILIGNGAD NAQSSNGITAFQLA+NIGSEK+MLALVSNNPKLINFASIDFQIPFTNQWFEYGEILIKLLPDNFLS+ I+   F  C++
Sbjct:  599 VKSLQSNTCISLLNAGAQVNSINNFGNSPLLDMFCEAQLAVNDDNLNKSIEITNILIGNGADTNAQSSNGITAFQLASNIGSEKLMLALVSNNPKLINFASIDFQIPFTNQWFEYGEILIKLLPDNFLSANITRNIFHLCKA 740
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BLAST of SMED30027966 vs. Planmine SMEST
Match: SMESG000010217.1 (SMESG000010217.1)

HSP 1 Score: 201.06 bits (510), Expect = 3.629e-66
Identity = 100/142 (70.42%), Postives = 115/142 (80.99%), Query Frame = -1 
Query:   10 VKSLQSNTCISLLNAGAQVNSINNFGNSPLLEMFCETQLAVNDDNLNKLIDITNILIGNGADVNAQSSNGITAFQLAANIGSEKIMLALVSNNPKLINFASIDFQIPFTNQWFEYGEILIKLLPDNFLSSTISNETFQSCES 435
            VK L+ + C SLLNAGA VN+INNFGNSPLLEM  + QL  N++NLNK I+IT ILIG+GADV+AQ SNG+TAFQLA N GSE++MLALVSNNPKLINF SIDFQ+PF NQWF Y E LIKLLPDNFLSS I+   F  C +
Sbjct:   35 VKCLKPDICSSLLNAGAHVNNINNFGNSPLLEMLNDAQLVANENNLNKSIEITKILIGSGADVSAQLSNGVTAFQLATNFGSEELMLALVSNNPKLINFISIDFQLPFQNQWFAYAEALIKLLPDNFLSSNITRNIFYLCRA 176
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BLAST of SMED30027966 vs. Planmine SMEST
Match: SMESG000010218.1 (SMESG000010218.1)

HSP 1 Score: 204.527 bits (519), Expect = 3.158e-65
Identity = 102/142 (71.83%), Postives = 117/142 (82.39%), Query Frame = -1 
Query:   10 VKSLQSNTCISLLNAGAQVNSINNFGNSPLLEMFCETQLAVNDDNLNKLIDITNILIGNGADVNAQSSNGITAFQLAANIGSEKIMLALVSNNPKLINFASIDFQIPFTNQWFEYGEILIKLLPDNFLSSTISNETFQSCES 435
            VK L+ + C SLLNAGA VN+INNFGNSP+LEM  + QL  N++NLNK I+IT ILIG+GADV+AQ SNGITAFQLAANIGSE++MLALVSNNPKLINF SIDFQ+PF NQWF Y E LIKLLPDNFLSS I+   F  C +
Sbjct:   35 VKCLKPDICSSLLNAGAHVNNINNFGNSPMLEMLNDAQLVANENNLNKSIEITKILIGSGADVSAQLSNGITAFQLAANIGSEELMLALVSNNPKLINFISIDFQLPFQNQWFAYAEALIKLLPDNFLSSNITRNIFYLCRA 176
The following BLAST results are available for this feature:
BLAST of SMED30027966 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 SMED30027966 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 SMED30027966 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 SMED30027966 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 2
Match NameE-valueIdentityDescription
asb2a.19.301e-634.12ankyrin repeat and SOCS box containing 2a, tandem ... [more]
asb2a.19.603e-634.12ankyrin repeat and SOCS box containing 2a, tandem ... [more]
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BLAST of SMED30027966 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 SMED30027966 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 SMED30027966 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 SMED30027966 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 SMED30027966 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 2
Match NameE-valueIdentityDescription
asb15a2.976e-629.82ankyrin repeat and SOCS box containing 15 [Source:... [more]
asb15a3.009e-629.82ankyrin repeat and SOCS box containing 15 [Source:... [more]
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BLAST of SMED30027966 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 SMED30027966 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 SMED30027966 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 SMED30027966 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 SMED30027966 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000010604.15.610e-9699.31SMESG000010604.1[more]
SMESG000010464.12.276e-8088.03SMESG000010464.1[more]
SMESG000010464.13.113e-8088.03SMESG000010464.1[more]
SMESG000010217.13.629e-6670.42SMESG000010217.1[more]
SMESG000010218.13.158e-6571.83SMESG000010218.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027966 ID=SMED30027966|Name=SMED30027966|organism=Schmidtea mediterranea sexual|type=transcript|length=435bp
AGTTCCAGCACTCTCGCATGATTGAAAGGTCTCATTTGATATAGTGGAGG
ACAAAAAATTGTCAGGCAAAAGCTTTATCAATATTTCCCCATATTCAAAC
CATTGATTGGTGAAAGGAATTTGGAAATCGATAGAGGCAAAATTGATCAA
TTTAGGATTATTGGACACGAGTGCAAGCATTATTTTTTCACTTCCGATAT
TCGCAGCCAATTGAAATGCAGTGATTCCATTGGATGATTGCGCATTGACA
TCAGCTCCATTTCCAATCAATATATTTGTGATATCGATTAATTTATTTAA
GTTGTCATCATTAACAGCTAGTTGTGTCTCACAAAACATCTCAAGCAATG
GAGAGTTACCGAAATTGTTGATACTGTTGACCTGTGCTCCAGCGTTAAGC
AGTGAAATGCATGTATTTGATTGGAGGGATTTCAC
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protein sequence of SMED30027966-orf-1

>SMED30027966-orf-1 ID=SMED30027966-orf-1|Name=SMED30027966-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=145bp
VKSLQSNTCISLLNAGAQVNSINNFGNSPLLEMFCETQLAVNDDNLNKLI
DITNILIGNGADVNAQSSNGITAFQLAANIGSEKIMLALVSNNPKLINFA
SIDFQIPFTNQWFEYGEILIKLLPDNFLSSTISNETFQSCESAGT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
Vocabulary: INTERPRO
TermDefinition
IPR036770Ankyrin_rpt-contain_sf
IPR020683Ankyrin_rpt-contain_dom
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR036770Ankyrin repeat-containing domain superfamilyGENE3DG3DSA:1.25.40.20coord: 2..111
e-value: 4.2E-13
score: 51.1
IPR036770Ankyrin repeat-containing domain superfamilySUPERFAMILYSSF48403Ankyrin repeatcoord: 8..94
IPR020683Ankyrin repeat-containing domainPROSITEPS50297ANK_REP_REGIONcoord: 12..93
score: 13.177