SMED30023123

Overview
NameSMED30023123
Smed IDSMED30023123
Length (bp)1961
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



SMED30023123

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30023123h1SMcG0004558 dd_Smed_v4_4432_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30023123h1SMcG0004558 dd_Smed_v4_4432_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30023123h1SMcG0004558 dd_Smed_v6_4432_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
photoreceptor neuronSMED30023123h1SMcG0004558 SMED30001672smed_20140614PMID:22884275
Lapan et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
head regionSMED30023123h1SMcG0004558 OX_Smed_1.0.19137ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30023123h1SMcG0004558 dd_Smed_v4_4432_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 SMED30023123 vs. TrEMBL
Match: A0A085N399 (Integrase catalytic domain-containing protein (Fragment) OS=Trichuris suis OX=68888 GN=M514_11630 PE=4 SV=1)

HSP 1 Score: 45.0542 bits (105), Expect = 4.996e-7
Identity = 35/90 (38.89%), Postives = 45/90 (50.00%), Query Frame = -1 
Query:  645 RDGRASFEATFDGSKCTVKWK-SSGGSP-MLRNQRGMYHVK*KVCPTYNNEI*TWI--GWLQEFN----G*YDGVIPILAVEQFNKGKVR 890
            RD   S+ A  D    T  WK S G  P +LRN    YH+       Y  E+ TWI  GWL  ++    G   G++P++AV Q NK KVR
Sbjct:  366 RDFAVSYSA--DTRSWTAVWKWSEGAEPGVLRNTAEEYHLADGARAPYKEELETWIRNGWLVPYDESKYGAAKGLVPLMAVVQRNKSKVR 453

HSP 2 Score: 39.6614 bits (91), Expect = 4.996e-7
Identity = 17/52 (32.69%), Postives = 30/52 (57.69%), Query Frame = -2 
Query:  530 DFRNINEWVECHIGDNDICSETIR-------------LIYA*LQIHVEKNLW 646
            DFR +N+++E H  D+D+C++ +R             L  A LQI ++++LW
Sbjct:  457 DFRELNDYIETHTADSDVCAQKLREWRRQGANVSVIDLNKAYLQIRIDESLW 508
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BLAST of SMED30023123 vs. TrEMBL
Match: A0A085MBY3 (Uncharacterized protein OS=Trichuris suis OX=68888 GN=M513_04429 PE=4 SV=1)

HSP 1 Score: 43.8986 bits (102), Expect = 6.778e-7
Identity = 34/90 (37.78%), Postives = 45/90 (50.00%), Query Frame = -1 
Query:  645 RDGRASFEATFDGSKCTVKWK-SSGGSP-MLRNQRGMYHVK*KVCPTYNNEI*TWI--GWLQEFN----G*YDGVIPILAVEQFNKGKVR 890
            RD   S+ A  D    T  WK S G  P +LRN    YH+       Y  ++ TWI  GWL  ++    G   G++P++AV Q NK KVR
Sbjct:  376 RDFAVSYSA--DTRSWTAVWKWSEGAEPGVLRNTAEEYHLADGARAPYEEDLETWIRNGWLVPYDESKHGAAKGLVPLMAVVQRNKSKVR 463

HSP 2 Score: 40.4318 bits (93), Expect = 6.778e-7
Identity = 18/59 (30.51%), Postives = 35/59 (59.32%), Query Frame = -2 
Query:  512 DFRNINEWVECHIGDNDICSETIR-------------LIYA*LQIHVEKNLW-WRNILF 646
            DFR +N+++E H  D+D+C++ +R             L  A LQI ++++LW ++ ++F
Sbjct:  467 DFRELNDYIETHTADSDVCAQKLREWRRQGANVSVIDLNKAYLQIRIDESLWPYQTVVF 525
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BLAST of SMED30023123 vs. TrEMBL
Match: A0A5S6QJ61 (Uncharacterized protein OS=Trichuris muris OX=70415 PE=4 SV=1)

HSP 1 Score: 45.8246 bits (107), Expect = 7.692e-7
Identity = 35/90 (38.89%), Postives = 46/90 (51.11%), Query Frame = -1 
Query:  645 RDGRASFEATFDGSKCTVKWK-SSGGSP-MLRNQRGMYHVK*KVCPTYNNEI*TWI--GWLQEFN----G*YDGVIPILAVEQFNKGKVR 890
            RD  AS+  + D    T  WK S G  P +LRN    YH+       Y  E+ TWI  GWL  ++    G   G++P++AV Q NK KVR
Sbjct:  376 RDFAASY--SVDTRSWTAVWKWSEGAEPGVLRNTAEEYHLADGARAPYEKELETWIQNGWLIPYDESKYGAAKGLVPLMAVVQRNKSKVR 463

HSP 2 Score: 38.5058 bits (88), Expect = 7.692e-7
Identity = 18/59 (30.51%), Postives = 35/59 (59.32%), Query Frame = -2 
Query:  512 DFRNINEWVECHIGDNDICSETIR-------------LIYA*LQIHVEKNLW-WRNILF 646
            DFR +N+++E H  D+D+C++ +R             L  A LQI ++++LW ++ ++F
Sbjct:  467 DFRELNDYIETHTADSDVCAQKLREWRRQGANVSVIDLNKAYLQIRIDESLWPYQTVVF 525
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BLAST of SMED30023123 vs. TrEMBL
Match: A0A085N030 (Uncharacterized protein (Fragment) OS=Trichuris suis OX=68888 GN=M514_05518 PE=4 SV=1)

HSP 1 Score: 43.1282 bits (100), Expect = 2.617e-6
Identity = 25/69 (36.23%), Postives = 38/69 (55.07%), Query Frame = -2 
Query:  509 TKEK----SDFRNINEWVECHIGDNDICSETIR-------------LIYA*LQIHVEKNLW-WRNILFD 661
            +KEK     DFR +N ++E    D D+C++ +R             L  A LQIHVEK+LW ++ ++FD
Sbjct: 1147 SKEKVRPVMDFRELNAFIETFTADADVCAQRLREWRRQGPNVSVIDLKAAYLQIHVEKSLWPFQTVIFD 1215

HSP 2 Score: 38.891 bits (89), Expect = 2.617e-6
Identity = 29/86 (33.72%), Postives = 41/86 (47.67%), Query Frame = -1 
Query:  645 FEATFDG-SKCTV---KWKSSGGSPMLRNQRGMYHVK*KVCPTYNNEI*TWI--GWLQEFN----G*YDGVIPILAVEQFNKGKVR 872
            F  TFD  ++C     +W    G  +LRN+   Y         Y  E+  WI  GWL  ++    G   G+IP++AV Q +K KVR
Sbjct: 1067 FALTFDPVARCWTAAWRWSDGRGPEVLRNKVKEYAPAAGAKTAYREELRNWIENGWLVPYDEKKYGPAKGLIPLMAVVQRSKEKVR 1152
[Close]
BLAST of SMED30023123 vs. TrEMBL
Match: A0A085LR73 (Integrase catalytic domain-containing protein OS=Trichuris suis OX=68888 GN=M513_11630 PE=4 SV=1)

HSP 1 Score: 43.5134 bits (101), Expect = 3.052e-6
Identity = 35/90 (38.89%), Postives = 44/90 (48.89%), Query Frame = -1 
Query:  645 RDGRASFEATFDGSKCTVKWK-SSGGSP-MLRNQRGMYHVK*KVCPTYNNEI*TWI--GWLQEFN----G*YDGVIPILAVEQFNKGKVR 890
            RD   S+ A  D    T  WK S G  P +LRN    YH+       Y  E+ TWI  GWL  ++    G   G++P+ AV Q NK KVR
Sbjct:  380 RDFAVSYSA--DTRSWTAVWKWSEGAEPGVLRNTAEEYHLADGARAPYKEELETWIRNGWLVPYDESKYGAAKGLVPLTAVVQRNKSKVR 467

HSP 2 Score: 38.5058 bits (88), Expect = 3.052e-6
Identity = 18/59 (30.51%), Postives = 35/59 (59.32%), Query Frame = -2 
Query:  512 DFRNINEWVECHIGDNDICSETIR-------------LIYA*LQIHVEKNLW-WRNILF 646
            DFR +N+++E H  D+D+C++ +R             L  A LQI ++++LW ++ ++F
Sbjct:  471 DFRELNDYIETHTADSDVCAQKLREWRRQGANVSVIDLNKAYLQIRIDESLWPYQTVVF 529
[Close]
BLAST of SMED30023123 vs. Planmine SMEST
Match: SMESG000040533.1 (SMESG000040533.1)

HSP 1 Score: 63.5438 bits (153), Expect = 2.144e-11
Identity = 51/90 (56.67%), Postives = 58/90 (64.44%), Query Frame = 1 
Query: 1702 NIP*YLMST-LNDF--TIDDLKNGSSLK*FKDFKLLARFIPRFKEXX-XXXXXXXXXXXXXXXXXXXXXXPILLF*CLRILIDFIQ*IEK 1959
            N+P YLMST + D   TIDDLK+GSSL   KDFKLLARFIPR KEN+  N+            LHN  N+PILLF CLR LI  I+  EK
Sbjct:   52 NVPRYLMSTSVKDLRRTIDDLKDGSSLNKLKDFKLLARFIPRLKENIFSNFNIETIIKTIHRELHNPENSPILLFECLRTLIGLIESCEK 141
[Close]
BLAST of SMED30023123 vs. Planmine SMEST
Match: SMESG000069076.1 (SMESG000069076.1)

HSP 1 Score: 43.1282 bits (100), Expect = 5.182e-7
Identity = 28/79 (35.44%), Postives = 38/79 (48.10%), Query Frame = -1 
Query:  645 SFEATFDGSKCTVKWKSSGGSPMLRNQRGMYHVK*KVCPTYNNEI*TWIG--WLQEFNG*YDGVIPILAVEQFNKGKVR 875
             F A+FD  K T  WK      +L+N    Y VK ++   Y  E+  WI    L   N    G++P+LA  Q  KGKV+
Sbjct:   15 DFTASFDREKWTASWKWRDKPALLKNHVAEYAVKQEIRQEYEQEVERWIKEYLLIPANDNDHGILPLLATGQEIKGKVQ 93

HSP 2 Score: 30.0314 bits (66), Expect = 5.182e-7
Identity = 10/24 (41.67%), Postives = 16/24 (66.67%), Query Frame = -2 
Query:  575 DFRNINEWVECHIGDNDICSETIR 646
            DFR +N +V+ H  D+++C E  R
Sbjct:   97 DFREVNNYVKSHTADSNVCGEIAR 120
[Close]
BLAST of SMED30023123 vs. Planmine SMEST
Match: SMESG000020506.1 (SMESG000020506.1)

HSP 1 Score: 48.521 bits (114), Expect = 6.997e-6
Identity = 27/66 (40.91%), Postives = 37/66 (56.06%), Query Frame = -2 
Query: 1394 ARSRSNPRDSVSWYNVAPRLKCDKTS---KQIFNYDWLLCTGFSLKLLICIIKKNCHSAYFVFYDF 1582
            +RSRS+PRD + WYNVA +LK DK+S    ++FNY W    G  L +      + C S +   Y F
Sbjct:  111 SRSRSDPRDDIFWYNVALKLKGDKSSAPANRLFNYGWRFNIGNFLNVPHNSGFEECQSGFVKPYPF 176
The following BLAST results are available for this feature:
BLAST of SMED30023123 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 SMED30023123 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 SMED30023123 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 SMED30023123 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 SMED30023123 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 SMED30023123 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 SMED30023123 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 SMED30023123 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A085N3994.996e-738.89Integrase catalytic domain-containing protein (Fra... [more]
A0A085MBY36.778e-737.78Uncharacterized protein OS=Trichuris suis OX=68888... [more]
A0A5S6QJ617.692e-738.89Uncharacterized protein OS=Trichuris muris OX=7041... [more]
A0A085N0302.617e-636.23Uncharacterized protein (Fragment) OS=Trichuris su... [more]
A0A085LR733.052e-638.89Integrase catalytic domain-containing protein OS=T... [more]
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BLAST of SMED30023123 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 SMED30023123 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 SMED30023123 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 SMED30023123 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 SMED30023123 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 SMED30023123 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000040533.12.144e-1156.67SMESG000040533.1[more]
SMESG000069076.15.182e-735.44SMESG000069076.1[more]
SMESG000020506.16.997e-640.91SMESG000020506.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023123 ID=SMED30023123|Name=SMED30023123|organism=Schmidtea mediterranea sexual|type=transcript|length=1961bp
TGAATATAATTTATGCTGGGTATCTGATAGGGATGAAAAGTATAAATATG
AGCACCTTCCAGGGATTCTTATCAAATACTAATTAGATAATGTTACCATT
ACACACCCGCCACGACTTTTAAATGTGTTCCAATTGGCGGTTACTAGTAG
GTGTACTATATCACCATGATTGCAAATACCTGGTATACTTATGAGTTCAA
GAGCTATCATAGAATGCTTCATGTTTATTTTATACAACTCATAATTTACA
AAAAAGATTAAAATATATATTCAATAAATATATTTTAAATCAATTTTTCA
GCAGCGTTGACTTTATCCAATAACCTGGCCGTCCTTAACCTTTTCGTTTA
CGTTCAGCTTTTCCTGGACGTGATTGCTGGGCGTTATTAATTTATAGTAG
ATATTTCTAGCAATCGGCAACTTATACCGACATTATTGCTATAAATATTG
TATCTCGTTTATCCTTCGTTAGGTTTATCATTGATTTTTGGAAAAAACCC
CAAAACAAGTCAAATAGTATGTTTCTCCACCACAAGTTCTTTTCAACATG
GATCTGCAATTAAGCGTAAATAAGACGAATCGTTTCTGAGCAGATATCAT
TATCTCCGATGTGGCACTCAACCCATTCATTTATGTTTCGGAAGTCGGAC
TTTTCCTTTGTTAAATTGTTCTACTGCCAAAATAGGTATGACCCCATCAT
ATCATCCATTGAATTCTTGCAGCCAACCAATCCAGGTTTAAATTTCGTTG
TTATAGGTGGGACAAACTTTCTATTTCACATGGTACATTCCACGTTGGTT
TCGGAGCATTGGTGACCCTCCAGACGATTTCCATTTCACCGTACATTTAG
ATCCGTCAAATGTTGCTTCAAATGAAGCTCGTCCATCACGAGGCACGACG
AAGTAACTAATTTATCCTGAATCATGAACTCGATAGTAGATGATTCGCGA
CACTTAAGCTTTCTGCCATCAACTGTATCTATCCACTTGTCCGAAATACA
CATTCCCGAGTGCCATATCCTTGGTCGAATCGATCGAGAACTACCTGATT
TTGAAACTCCAGTTTGAATGCTATTGAGATTACTTCTTTTCCGATTTTCA
GAGAGATTAACTAGAATTCGACTGATTCGCCCTGTTTCCATTTTCGCAAA
AGGCCGTAAATCGACCTAAACCAAAACAGATTTGGACGATGAATAATTGC
GCCTTACAGCTTCTGATTGGTGTCTCTTTATATCTAGTCGTATGGAAGTA
TCTATTGAATGAAATCGAAGGCTCCTTTTAATTGGTTTTTCAATTCGAAT
TACTCGGCCCAATGGAGACATCTCCGTCTCAAGAATATTTTGGGAAAAGG
TCCAAATTCTTCACTAAAGTGGCGAAAGCTTATTATTCCATCAGAAATCG
TAGAAGACAAAGTAAGCTGAGTGACAATTTTTTTTAATAATACAAATTAA
TAATTTTAATGAAAATCCCGTACACAAAAGCCAATCGTAATTAAAAATCT
GTTTGCTGGTTTTGTCACATTTAAGCCTAGGAGCCACGTTGTACCAGGAT
ACAGAATCTCGAGGATTGCTGCGACTCCTTGCATTGATATGTATCCCAAA
TTATCACAGTTCCAACATCATAAGCGCAGGCGGCCAGGTGTCTCACATTT
TAAGCATTTAAACGTTTTCTGACCTCGATTGACTACCTGACTTCCACAGA
CAACATTCCTTGATATTTAATGTCAACTTTGAATGATTTTACTATTGACG
ATCTTAAAAACGGTTCTTCTCTAAAATAGTTTAAAGATTTCAAACTCTTG
GCCAGATTCATTCCTAGATTTAAGGAAAATGTTTTCAATTATCAACATTA
GAACAATAATTCAAACAATTCTTCCGTATTACATAATACATAAAATAATC
CAATCTTATTGTTTTAGTGTCTAAGAATATTAATTGACTTTATTCAATAA
ATTGAGAAGTC
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protein sequence of SMED30023123-orf-1

>SMED30023123-orf-1 ID=SMED30023123-orf-1|Name=SMED30023123-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
METGRISRILVNLSENRKRSNLNSIQTGVSKSGSSRSIRPRIWHSGMCIS
DKWIDTVDGRKLKCRESSTIEFMIQDKLVTSSCLVMDELHLKQHLTDLNV
R*
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