Si:dkey-90a13.10

Overview
NameSi:dkey-90a13.10
Smed IDSMED30020205
Length (bp)619
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 Si:dkey-90a13.10 (SMED30020205) t-SNE clustered cells

Violin plots show distribution of expression levels for Si:dkey-90a13.10 (SMED30020205) 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 Si:dkey-90a13.10 (SMED30020205) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Si:dkey-90a13.10 (SMED30020205) 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




SMED30020205

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30020205SMESG000035648.1 SmedASXL_050224SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30020205SMESG000035648.1 dd_Smed_v4_5452_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30020205SMESG000035648.1 dd_Smed_v4_5452_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30020205SMESG000035648.1 dd_Smed_v4_5452_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30020205SMESG000035648.1 dd_Smed_v4_5452_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30020205SMESG000035648.1 dd_Smed_v6_5452_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30020205SMESG000035648.1 dd_Smed_v4_5452_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 Si:dkey-90a13.10 vs. Ensembl Zebrafish
Match: si:dkey-90a13.10 (si:dkey-90a13.10 [Source:ZFIN;Acc:ZDB-GENE-131121-317])

HSP 1 Score: 48.9062 bits (115), Expect = 1.661e-7
Identity = 38/122 (31.15%), Postives = 58/122 (47.54%), Query Frame = 1
Query:   85 MAFFGNTQLGYQNTIREYVREPIDHSKTYLPKL---SSDHLSKERKPELSWYDYTNKKNFKCSNLPNPITVYRRPLTTNQDIGFFHEYNPLLKNLPWMYVKRYPAVQGETTRFVNQILLTNP 441
            MAFFG T LGYQN   + +     HS    P     S  HL  + +    + D+   ++ + S    P  +YR P+T NQ  G++     +    PW   + +P    E T+FVN++ +TNP
Sbjct:    1 MAFFGITYLGYQNPFGDRML----HSTQNKPDARDPSDLHLVSQNR----YKDHLITRHAQRS----PKDLYRVPVTENQRYGWWIPTGGMKNQEPWTQTRHFPRKNSEMTKFVNEMSVTNP 110          
BLAST of Si:dkey-90a13.10 vs. TrEMBL
Match: A0A210PVS6 (Uncharacterized protein OS=Mizuhopecten yessoensis OX=6573 GN=KP79_PYT04470 PE=4 SV=1)

HSP 1 Score: 77.0258 bits (188), Expect = 2.807e-14
Identity = 54/140 (38.57%), Postives = 70/140 (50.00%), Query Frame = 1
Query:   85 MAFFGNTQLGYQNTIRE-YVREPID----HSKT-----YLPKLSSDHLSKER------------KPELSWYDYTNKKNFKCSNLPNPITVYRRPLTTNQDIGFFHEYNPLLKNLPWMYVKRYPAVQGETTRFVNQILLTN 438
            MAFFG +QLGYQNTIRE   R   D     +KT      LP L   +  +               PE S  ++T  +     N   PI +YR PLTT+  +G++    PL +  PW YVKR  +V  E TRFVN++ LTN
Sbjct:    1 MAFFGLSQLGYQNTIREGSARAKADPQSLRAKTQLGFVALPPLQDKNPPRRSIVPINQVSGYGPGPEGSHVEHTRMRTKHIRNPREPIELYRIPLTTSSQLGWWRTDEPLRERQPWTYVKRNVSVNSEMTRFVNEMSLTN 140          
BLAST of Si:dkey-90a13.10 vs. TrEMBL
Match: K1R1W7 (Uncharacterized protein OS=Crassostrea gigas OX=29159 GN=CGI_10015117 PE=4 SV=1)

HSP 1 Score: 75.0998 bits (183), Expect = 1.100e-13
Identity = 49/138 (35.51%), Postives = 69/138 (50.00%), Query Frame = 1
Query:   85 MAFFGNTQLGYQNTIREY--------VREPIDHSKTYLPKLSS-----------DHLSK-ERKPELSWYDYTNKKNFKCSNLPNPITVYRRPLTTNQDIGFFHEYNPLLKNLPWMYVKRYPAVQGETTRFVNQILLTN 438
            M+FFG +QLGYQNT+RE         VR         LP L+            D +S     P+ S  +YT  +     +   P  +YR P+ T++ +G++ +  PL KN PW YV R+  V  E TRFVN++ LTN
Sbjct:    1 MSFFGISQLGYQNTLREATIQAKMDPVRSKTQIGFVALPPLAEKNPPRRSIVPIDQVSGYGPGPQGSHVEYTRMRTKHIRSPKEPFEIYRFPVQTSRQVGWWSKEEPLRKNQPWTYVPRHVHVNSEMTRFVNEMSLTN 138          
BLAST of Si:dkey-90a13.10 vs. TrEMBL
Match: A0A1S3GZY9 (testis-expressed protein 49 OS=Lingula unguis OX=7574 GN=LOC106150797 PE=4 SV=1)

HSP 1 Score: 75.0998 bits (183), Expect = 1.292e-13
Identity = 48/137 (35.04%), Postives = 73/137 (53.28%), Query Frame = 1
Query:   85 MAFFGNTQLGYQNTIREYVREP---------------IDHSKTYLPKLSSDHLSK----ERKPELSWYDYTNKKNFKCSNLPNPITVYRRPLTTNQDIGFFHEYNPLLKNLPWMYVKRYPAVQGETTRFVNQILLTN 438
            MAFFG T++GYQ+TIRE V  P               +D  K  LP+ S   +++       P+ S+ +YT ++     N   P+ +YR    T+ D G++++  PL +  PW +VKR+  V  E TRFVN++ LTN
Sbjct:    1 MAFFGLTEMGYQDTIREKVVNPTFNPQYDPMDKLPPIVDREK--LPRPSIIPINQVSAYGAGPQGSYVEYTRQRTKHIRNPKGPLAIYRDKTITSHDYGWWNKDAPLKQKEPWTHVKRHVFVNSEMTRFVNEMSLTN 135          
BLAST of Si:dkey-90a13.10 vs. TrEMBL
Match: A0A2C9L0H4 (Uncharacterized protein OS=Biomphalaria glabrata OX=6526 GN=106066387 PE=4 SV=1)

HSP 1 Score: 72.7886 bits (177), Expect = 1.014e-12
Identity = 49/139 (35.25%), Postives = 73/139 (52.52%), Query Frame = 1
Query:   85 MAFFGNTQLGYQNTIREYV----REPIDHSKTYLPKLS----------------SDHLSK-ERKPELSWYDYTNKKNFKCSNLPNPITVYRRPLTTNQDIGFFHEYNPLLKNLPWMYVKRYPAVQGETTRFVNQILLTN 438
            M+FFG T +GYQNTI+E      ++PI  SKT L  L+                 D +S+  R P+ S+ +Y   +     N  +P  +Y RP TT Q+IG++ +  PL   LPW  V+R P +  E ++FV+ + LTN
Sbjct:    1 MSFFGLTHVGYQNTIKEISIASQKDPI-RSKTQLGYLALPPLKDFNSPPRSIVPVDDISQYGRGPDRSYNEYCRLRMKHVRNPRDPQNIYLRPATTAQNIGWWKKDEPLRTMLPWTCVQRKPVIHSEMSKFVDDMKLTN 138          
BLAST of Si:dkey-90a13.10 vs. TrEMBL
Match: A0A151MUF7 (Uncharacterized protein OS=Alligator mississippiensis OX=8496 GN=Y1Q_0012955 PE=4 SV=1)

HSP 1 Score: 69.3218 bits (168), Expect = 1.374e-11
Identity = 47/134 (35.07%), Postives = 62/134 (46.27%), Query Frame = 1
Query:   85 MAFFGNTQLGYQNTIREYVREPIDHSKT------YLPKL------SSDHLSKERKPELSWYDYTNKKNFKCSNLPNPITVYRRPLTTNQDIGFFHEYNPLLKN---LPWMYVKRYPAVQGETTRFVNQILLTNP 441
            MAFFG T LGYQ   R + RE     K       +LPKL       + H  +E        D   +   +      P  VYR PLT  QD+G++   +P L+    +PWM V R P V    TRFV+ + L+NP
Sbjct:    1 MAFFGLTLLGYQEPFRAWRRELAADRKEPAGAGPFLPKLLPLRPGGTVHQGRE--------DVCGQPTRRVRRATPPNQVYRVPLTCGQDLGWWLPRDPALRPEEMMPWMVVPRRPLVWSPVTRFVDSMSLSNP 126          
BLAST of Si:dkey-90a13.10 vs. Ensembl Nematostella
Match: EDO42881 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S008])

HSP 1 Score: 49.2914 bits (116), Expect = 5.158e-8
Identity = 37/128 (28.91%), Postives = 64/128 (50.00%), Query Frame = 1
Query:   85 MAFFGNTQLGYQNTIREYVREPIDHSKTYLPKLSSDHLSKERKPEL--------SWYDYTNK--KNFKCSNLPNPITVYRRPLTTNQDIGFFHEYNPLLKNLPWMYVKRYPAVQGETTRFVNQILLTN 438
            M+FF  TQLG Q+ +   V++P         +  +     ER+ ++        S+  YT +  K+ +  N PN I  Y R ++TN + G++      +++  W   K +P V+ E TRFV+++ LTN
Sbjct:    1 MSFFNLTQLGVQDPVNHAVKKPGSSPLNRPTETRTAQQPTERRKQVHPNSEADGSYVKYTERLHKHIRPENGPNEI--YDRKISTNYEYGWWMRDG--VQDEAWTKNKNHPVVKSEMTRFVDEMTLTN 124          
BLAST of Si:dkey-90a13.10 vs. Planmine SMEST
Match: SMESG000035648.1 (SMESG000035648.1)

HSP 1 Score: 250.751 bits (639), Expect = 2.549e-86
Identity = 120/120 (100.00%), Postives = 120/120 (100.00%), Query Frame = 1
Query:   85 MAFFGNTQLGYQNTIREYVREPIDHSKTYLPKLSSDHLSKERKPELSWYDYTNKKNFKCSNLPNPITVYRRPLTTNQDIGFFHEYNPLLKNLPWMYVKRYPAVQGETTRFVNQILLTNPT 444
            MAFFGNTQLGYQNTIREYVREPIDHSKTYLPKLSSDHLSKERKPELSWYDYTNKKNFKCSNLPNPITVYRRPLTTNQDIGFFHEYNPLLKNLPWMYVKRYPAVQGETTRFVNQILLTNPT
Sbjct:    1 MAFFGNTQLGYQNTIREYVREPIDHSKTYLPKLSSDHLSKERKPELSWYDYTNKKNFKCSNLPNPITVYRRPLTTNQDIGFFHEYNPLLKNLPWMYVKRYPAVQGETTRFVNQILLTNPT 120          
The following BLAST results are available for this feature:
BLAST of Si:dkey-90a13.10 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 Si:dkey-90a13.10 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 Si:dkey-90a13.10 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 Si:dkey-90a13.10 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
si:dkey-90a13.101.661e-731.15si:dkey-90a13.10 [Source:ZFIN;Acc:ZDB-GENE-131121-... [more]
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BLAST of Si:dkey-90a13.10 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 Si:dkey-90a13.10 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 Si:dkey-90a13.10 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 Si:dkey-90a13.10 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A210PVS62.807e-1438.57Uncharacterized protein OS=Mizuhopecten yessoensis... [more]
K1R1W71.100e-1335.51Uncharacterized protein OS=Crassostrea gigas OX=29... [more]
A0A1S3GZY91.292e-1335.04testis-expressed protein 49 OS=Lingula unguis OX=7... [more]
A0A2C9L0H41.014e-1235.25Uncharacterized protein OS=Biomphalaria glabrata O... [more]
A0A151MUF71.374e-1135.07Uncharacterized protein OS=Alligator mississippien... [more]
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BLAST of Si:dkey-90a13.10 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 Si:dkey-90a13.10 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 Si:dkey-90a13.10 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 Si:dkey-90a13.10 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO428815.158e-828.91Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of Si:dkey-90a13.10 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 Si:dkey-90a13.10 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000035648.12.549e-86100.00SMESG000035648.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020205 ID=SMED30020205|Name=Si:dkey-90a13.10|organism=Schmidtea mediterranea sexual|type=transcript|length=619bp
CATTTTTTACAGAAAATGACCTTTAAATAATTCAAATTTTTTTCTGTGTT
ATAATGAATGTTGTTATAGTAACATATTTTTTAAATGGCATTTTTTGGTA
ATACTCAACTTGGTTATCAAAATACCATTCGGGAATATGTTAGAGAGCCT
ATAGATCATTCAAAAACTTATCTTCCAAAATTATCAAGTGACCACTTAAG
TAAAGAAAGAAAACCAGAATTGTCGTGGTACGATTATACAAATAAGAAAA
ATTTTAAATGCTCAAATCTGCCAAATCCAATAACTGTTTATAGAAGACCA
TTAACGACAAATCAAGATATTGGTTTCTTTCATGAATATAATCCGCTATT
AAAAAATTTGCCTTGGATGTATGTAAAACGATACCCAGCAGTTCAGGGAG
AAACTACTAGATTTGTCAATCAAATTTTATTAACGAATCCTACTTTTTTC
TTGTTTTAATTTTACTGTCAATTTAACATTTGATTTATTACTTTAACAAA
ATTATTGCATGACTGATACATTAGTTATTTTAGAGTTCCTTATATGTAAA
AATTGTTTTTAAAATGCAGTTTGATAGAGTTGTATGGTTTTTGATAAAAA
CACCTGATTTAACTTGAAT
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protein sequence of SMED30020205-orf-1

>SMED30020205-orf-1 ID=SMED30020205-orf-1|Name=SMED30020205-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=125bp
MAFFGNTQLGYQNTIREYVREPIDHSKTYLPKLSSDHLSKERKPELSWYD
YTNKKNFKCSNLPNPITVYRRPLTTNQDIGFFHEYNPLLKNLPWMYVKRY
PAVQGETTRFVNQILLTNPTFFLF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000418head
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR038775TEX49
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR038775Testis-expressed protein 49PANTHERPTHR35263FAMILY NOT NAMEDcoord: 1..124