SMED30019546

Overview
NameSMED30019546
Smed IDSMED30019546
Length (bp)553
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




SMED30019546

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
parapharyngeal regionSMED30019546SMESG000018709.1 SmedASXL_004927SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30019546 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004817:21046..21598 -2756
Homology
BLAST of SMED30019546 vs. TrEMBL
Match: A0A1I8ICE9 (Ig-like domain-containing protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 8.965e-7
Identity = 39/132 (29.55%), Postives = 61/132 (46.21%), Query Frame = 2
Query:   38 VTFPVLVSAIYHQAQFYCSL-------HINSTELSRSVGEKLFVYYLSNLITIVPENTDYSISEIIQCSAEGRPTPKIQWTSVTPSTGIQITNNNLILSSAN--GEYQYKCSAEVQYKTELMSVSKTIKFRV 406
            VT  V +    H A + C L       H+N T   +S  + + V Y    I + P   +Y   + I C A+GRP PKIQWT +  +  +Q+  ++L L      G Y Y CSA  + +     + ++I F +
Sbjct:  117 VTHSVKIELGSHGAVYGCQLKPHPMFAHLNITYGVKS--DPIRVLYTVRRIELQPYRDNYFHGDRIDCLAKGRPAPKIQWTRIRGAGPLQVNGSSLYLQPGAKVGYYAYTCSASNRVRGHYHRLLQSIGFHL 246          
BLAST of SMED30019546 vs. TrEMBL
Match: A0A267FFZ8 (Ig-like domain-containing protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig032090g1 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 1.515e-6
Identity = 39/132 (29.55%), Postives = 61/132 (46.21%), Query Frame = 2
Query:   38 VTFPVLVSAIYHQAQFYCSL-------HINSTELSRSVGEKLFVYYLSNLITIVPENTDYSISEIIQCSAEGRPTPKIQWTSVTPSTGIQITNNNLILSSAN--GEYQYKCSAEVQYKTELMSVSKTIKFRV 406
            VT  V +    H A + C L       H+N T   +S  + + V Y    I + P   +Y   + I C A+GRP PKIQWT +  +  +Q+  ++L L      G Y Y CSA  + +     + ++I F +
Sbjct:  227 VTHSVKIELGSHGAVYGCQLKPHPMFAHLNITYGVKS--DPIRVLYTVRRIELQPYRDNYFHGDRIDCLAKGRPAPKIQWTRIRGAGPLQVNGSSLYLQPGAKVGYYAYTCSASNRVRGHYHRLLQSIGFHL 356          
BLAST of SMED30019546 vs. TrEMBL
Match: A0A267EK00 (Ig-like domain-containing protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig007081g1 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 1.544e-6
Identity = 39/132 (29.55%), Postives = 61/132 (46.21%), Query Frame = 2
Query:   38 VTFPVLVSAIYHQAQFYCSL-------HINSTELSRSVGEKLFVYYLSNLITIVPENTDYSISEIIQCSAEGRPTPKIQWTSVTPSTGIQITNNNLILSSAN--GEYQYKCSAEVQYKTELMSVSKTIKFRV 406
            VT  V +    H A + C L       H+N T   +S  + + V Y    I + P   +Y   + I C A+GRP PKIQWT +  +  +Q+  ++L L      G Y Y CSA  + +     + ++I F +
Sbjct:  227 VTHSVKIELGSHGAVYGCQLKPHPMFAHLNITYGVKS--DPIRVLYTVRRIELQPYRDNYFHGDRIDCLAKGRPAPKIQWTRIRGAGPLQVNGSSLYLQPGAKVGYYAYTCSASNRVRGHYHRLLQSIGFHL 356          
BLAST of SMED30019546 vs. TrEMBL
Match: A0A1I8IYL1 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 57.7658 bits (138), Expect = 1.745e-6
Identity = 39/132 (29.55%), Postives = 61/132 (46.21%), Query Frame = 2
Query:   38 VTFPVLVSAIYHQAQFYCSL-------HINSTELSRSVGEKLFVYYLSNLITIVPENTDYSISEIIQCSAEGRPTPKIQWTSVTPSTGIQITNNNLILSSAN--GEYQYKCSAEVQYKTELMSVSKTIKFRV 406
            VT  V +    H A + C L       H+N T   +S  + + V Y    I + P   +Y   + I C A+GRP PKIQWT +  +  +Q+  ++L L      G Y Y CSA  + +     + ++I F +
Sbjct:  225 VTHSVKIELGSHGAVYGCQLKPHPMFAHLNITYGVKS--DPIRVLYTVRRIELQPYRDNYFHGDRIDCLAKGRPAPKIQWTRIRGAGPLQVNGSSLYLQPGAKVGYYAYTCSASNRVRGHYHRLLQSIGFHL 354          
BLAST of SMED30019546 vs. Planmine SMEST
Match: SMESG000018709.1 (SMESG000018709.1)

HSP 1 Score: 327.791 bits (839), Expect = 2.377e-107
Identity = 160/161 (99.38%), Postives = 161/161 (100.00%), Query Frame = 2
Query:    2 KSLQLISVLSEPVTFPVLVSAIYHQAQFYCSLHINSTELSRSVGEKLFVYYLSNLITIVPENTDYSISEIIQCSAEGRPTPKIQWTSVTPSTGIQITNNNLILSSANGEYQYKCSAEVQYKTELMSVSKTIKFRVGKASGYLRLCLMNFTLVLMAIAFPSF 484
            KSLQLISVLSEPVTFPVLVSAIYHQAQFYCSLH+NSTELSRSVGEKLFVYYLSNLITIVPENTDYSISEIIQCSAEGRPTPKIQWTSVTPSTGIQITNNNLILSSANGEYQYKCSAEVQYKTELMSVSKTIKFRVGKASGYLRLCLMNFTLVLMAIAFPSF
Sbjct:  748 KSLQLISVLSEPVTFPVLVSAIYHQAQFYCSLHMNSTELSRSVGEKLFVYYLSNLITIVPENTDYSISEIIQCSAEGRPTPKIQWTSVTPSTGIQITNNNLILSSANGEYQYKCSAEVQYKTELMSVSKTIKFRVGKASGYLRLCLMNFTLVLMAIAFPSF 908          
BLAST of SMED30019546 vs. Planmine SMEST
Match: SMESG000018952.1 (SMESG000018952.1)

HSP 1 Score: 256.529 bits (654), Expect = 4.615e-79
Identity = 126/161 (78.26%), Postives = 140/161 (86.96%), Query Frame = 2
Query:    2 KSLQLISVLSEPVTFPVLVSAIYHQAQFYCSLHINSTELSRSVGEKLFVYYLSNLITIVPENTDYSISEIIQCSAEGRPTPKIQWTSVTPSTGIQITNNNLILSSANGEYQYKCSAEVQYKTELMSVSKTIKFRVGKASGYLRLCLMNFTLVLMAIAFPSF 484
            KSLQLISVLSEPVTF VLVS  YHQ+ FYCSLH+NSTELSRSVGEKL VYYLSN+I I+PE TDY  SE IQCSAEGRP+P IQWTS++P TGI I NNNLILS+ANGEYQYKC AE+QY+TELMSVSKTIKFRVG+AS  L++C MN  LVL+AIAFP F
Sbjct: 1295 KSLQLISVLSEPVTFSVLVSVSYHQSPFYCSLHMNSTELSRSVGEKLIVYYLSNVIEIIPEKTDYLTSETIQCSAEGRPSPMIQWTSISPLTGILIANNNLILSTANGEYQYKCLAEIQYRTELMSVSKTIKFRVGQASC-LKVCWMNLALVLLAIAFPLF 1454          

HSP 2 Score: 46.9802 bits (110), Expect = 3.548e-6
Identity = 24/83 (28.92%), Postives = 42/83 (50.60%), Query Frame = 2
Query:  137 KLFVYYLSNLITIVPENTDYSISEIIQCSAEGRPTPKIQWTSVTPSTGIQITNNNLILSSANGEYQYKCSAEVQYKTELMSVS 385
            KL + Y    I I P    Y+ ++II+C +EG PTP ++W  +T      I  ++L + +  G     C A+  Y+ + + +S
Sbjct:  218 KLNISYKMKRIEIYPNRDVYNPTDIIRCYSEGNPTPTVEWELITTDFDDWINGSSLTIGNRLGNRTCNCRAQQNYRNQTILLS 300          
BLAST of SMED30019546 vs. Planmine SMEST
Match: SMESG000018945.1 (SMESG000018945.1)

HSP 1 Score: 189.119 bits (479), Expect = 1.294e-55
Identity = 91/117 (77.78%), Postives = 101/117 (86.32%), Query Frame = 2
Query:    2 KSLQLISVLSEPVTFPVLVSAIYHQAQFYCSLHINSTELSRSVGEKLFVYYLSNLITIVPENTDYSISEIIQCSAEGRPTPKIQWTSVTPSTGIQITNNNLILSSANGEYQYKCSAE 352
            KSLQLISVLSEPVTF VLVS  YHQ+ FYC+LH+NSTELSRSVG KL VYYLSN+I I+PE TDY  SE IQCSAEGRP+P IQWTS++P TGI I NNNLILS+ANGEYQYKC A+
Sbjct: 1322 KSLQLISVLSEPVTFSVLVSVSYHQSPFYCALHMNSTELSRSVGGKLIVYYLSNVIEIIPEKTDYLTSETIQCSAEGRPSPMIQWTSISPLTGILIANNNLILSTANGEYQYKCLAK 1438          
The following BLAST results are available for this feature:
BLAST of SMED30019546 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 SMED30019546 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 SMED30019546 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 SMED30019546 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 SMED30019546 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 SMED30019546 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 SMED30019546 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 SMED30019546 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
A0A1I8ICE98.965e-729.55Ig-like domain-containing protein OS=Macrostomum l... [more]
A0A267FFZ81.515e-629.55Ig-like domain-containing protein OS=Macrostomum l... [more]
A0A267EK001.544e-629.55Ig-like domain-containing protein OS=Macrostomum l... [more]
A0A1I8IYL11.745e-629.55Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of SMED30019546 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 SMED30019546 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 SMED30019546 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 SMED30019546 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 SMED30019546 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 SMED30019546 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000018709.12.377e-10799.38SMESG000018709.1[more]
SMESG000018952.14.615e-7978.26SMESG000018952.1[more]
SMESG000018945.11.294e-5577.78SMESG000018945.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30019546 ID=SMED30019546|Name=SMED30019546|organism=Schmidtea mediterranea sexual|type=transcript|length=553bp
GAAGTCATTGCAATTAATATCAGTATTGTCGGAGCCTGTGACATTTCCGG
TTCTGGTGAGTGCAATTTATCACCAGGCACAATTTTATTGTTCATTGCAC
ATTAATTCAACTGAACTGTCTCGATCAGTCGGTGAGAAATTATTTGTCTA
TTATCTGTCCAATCTCATCACAATTGTTCCGGAGAACACTGATTATTCAA
TATCCGAAATCATTCAATGTTCAGCTGAAGGAAGACCTACTCCAAAGATT
CAATGGACATCCGTTACGCCTTCAACTGGTATTCAAATAACAAATAATAA
TTTGATTTTATCAAGCGCAAATGGAGAATATCAGTACAAATGTTCGGCGG
AAGTTCAATATAAAACGGAATTAATGTCAGTTAGTAAAACGATAAAATTT
CGAGTTGGAAAGGCCTCTGGTTATTTGAGATTGTGCTTGATGAATTTTAC
ATTGGTTCTAATGGCCATCGCCTTTCCTTCCTTTTGATCAGATCATACAC
TATTTTCATTTTTGGCTTGATTTTATCTCACATTCATATTTATATTATCT
AAC
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protein sequence of SMED30019546-orf-1

>SMED30019546-orf-1 ID=SMED30019546-orf-1|Name=SMED30019546-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=162bp
KSLQLISVLSEPVTFPVLVSAIYHQAQFYCSLHINSTELSRSVGEKLFVY
YLSNLITIVPENTDYSISEIIQCSAEGRPTPKIQWTSVTPSTGIQITNNN
LILSSANGEYQYKCSAEVQYKTELMSVSKTIKFRVGKASGYLRLCLMNFT
LVLMAIAFPSF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000420parapharyngeal region
Vocabulary: INTERPRO
TermDefinition
IPR013783Ig-like_fold
IPR007110Ig-like_dom
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR013783Immunoglobulin-like foldGENE3DG3DSA:2.60.40.10coord: 53..139
e-value: 1.9E-7
score: 33.1
IPR007110Immunoglobulin-like domainPROSITEPS50835IG_LIKEcoord: 71..132
score: 6.814
NoneNo IPR availableTMHMMTMhelixcoord: 139..158