SMED30006202

Overview
NameSMED30006202
Smed IDSMED30006202
Length (bp)1651
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 SMED30006202 (SMED30006202) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30006202 (SMED30006202) 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 SMED30006202 (SMED30006202) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30006202 (SMED30006202) 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



SMED30006202

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
muscle cellSMED30006202 dd_Smed_v4_15845_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30006202 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000578:100878..102281 +5592
v31.005082:18237..19642 -5493
Homology
[Close]
BLAST of SMED30006202 vs. TrEMBL
Match: A0A0X9SRF7 (Putative BRCA2 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 68.1662 bits (165), Expect = 1.122e-11
Identity = 34/81 (41.98%), Postives = 52/81 (64.20%), Query Frame = -2 
Query: 1378 MLDFNVRKFDSRSTTEAEKRIKDITELLQIESQSLISAFYIL*KD*GAVLWKCYRDSCSTDEKAKNWFVDCFTIKKQLQDR 1620
            +L+FN+RKF+ R+  EAE+ +KDI + L I   SLI  F +L  +   + WK ++    TDE A++WFVD FT +K + D+
Sbjct:  347 ILNFNIRKFNGRNIFEAEQLLKDIDDWLGIRDLSLIGIFDLLLSEEAKIPWKDFKTIGLTDEDARSWFVDTFTSQKSIADK 427

HSP 2 Score: 31.9574 bits (71), Expect = 1.122e-11
Identity = 16/29 (55.17%), Postives = 22/29 (75.86%), Query Frame = -1 
Query: 1310 KTITRQIFDLNAVKQKANDRLATFEIRVR 1396
            K+I  +I+DL  VKQK N+  ATFE+RV+
Sbjct:  422 KSIADKIYDLAHVKQK-NEGFATFELRVK 449
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BLAST of SMED30006202 vs. Planmine SMEST
Match: SMESG000017400.1 (SMESG000017400.1)

HSP 1 Score: 169.088 bits (427), Expect = 2.283e-84
Identity = 94/122 (77.05%), Postives = 102/122 (83.61%), Query Frame = -2 
Query:  541 CIARKLYDESRGIKPRQPEILNPGNCFCCGESGHRSYQCPMKNKCLICDKENHTFGKCHLMGNHRSQMRRTVACIYXXXXXXXXXXXXNSYACEERTIEPERKHGKNTEDPIAFIS*VGLSN 906
             I RK+YD SR IK RQPEILNPGNCF C ES  R YQ PMKNKCLIC KENHTFG+CHL+G+HR Q RRTVACI+EEDNND+NFDDNNSYA  ERTIE +RKHGKN EDPI FIS VGL+N
Sbjct:  129 SITRKIYDGSRVIKQRQPEILNPGNCFYCEESALRRYQYPMKNKCLICGKENHTFGRCHLLGSHRPQRRRTVACIHEEDNNDKNFDDNNSYASGERTIEQKRKHGKNIEDPITFISSVGLNN 250

HSP 2 Score: 163.696 bits (413), Expect = 2.283e-84
Identity = 98/125 (78.40%), Postives = 112/125 (89.60%), Query Frame = -1 
Query:  905 MSAEDIVQDIIANKVWDDRVKEILLKKSSIQMEEVRSTAKIYENMTLSIS*SKNTNEIQVNSYAXXXXXXXXXXXXXXXXXKTYTNRYRQSNFLKRSQYVQSDNKYTAIANKYYNKNMPRKQPSV 1279
            MS EDIV+DII+NKV +DRVKEILL KS IQMEEVRSTAKIY+N+TLSIS  +NTNEIQVNSY+N VRRENK++N++D+K K Y NRY+QSNFLKRSQYVQ +NKYTAIANK Y KNMPRKQPSV
Sbjct:    1 MSEEDIVRDIISNKVREDRVKEILLTKSRIQMEEVRSTAKIYKNITLSISEIRNTNEIQVNSYSNAVRRENKSDNQEDIKLKNYINRYQQSNFLKRSQYVQDNNKYTAIANKNYYKNMPRKQPSV 125
[Close]
BLAST of SMED30006202 vs. Planmine SMEST
Match: SMESG000078154.1 (SMESG000078154.1)

HSP 1 Score: 223.787 bits (569), Expect = 5.080e-67
Identity = 131/158 (82.91%), Postives = 146/158 (92.41%), Query Frame = -1 
Query:  905 IFDLNAVKQKANDRLATFEIRVRNMVKTIFNSGMSAEDIVQDIIANKVWDDRVKEILLKKSSIQMEEVRSTAKIYENMTLSIS*SKNTNEIQVNSYAXXXXXXXXXXXXXXXXXKTYTNRYRQSNFLKRSQYVQSDNKYTAIANKYYNKNMPRKQPSV 1378
            IFDLN+VKQ+AN+R  TFEIRVRN+VKT+FNSGMS EDIV+DIIANKV DDRVKEILL KSSIQMEEVRSTAKIYEN+TLSI  S+NTN+IQVNSYANV+RRENKNNN++DVKSK YTNRY+Q+NFLK  QYVQ DNKYTAIAN+ YNKNMPRKQPSV
Sbjct:   46 IFDLNSVKQEANERFTTFEIRVRNLVKTVFNSGMSEEDIVRDIIANKVRDDRVKEILLTKSSIQMEEVRSTAKIYENLTLSIFESRNTNKIQVNSYANVIRRENKNNNQEDVKSKNYTNRYQQNNFLKCPQYVQDDNKYTAIANENYNKNMPRKQPSV 203
[Close]
BLAST of SMED30006202 vs. Planmine SMEST
Match: SMESG000051606.1 (SMESG000051606.1)

HSP 1 Score: 211.075 bits (536), Expect = 1.473e-64
Identity = 124/174 (71.26%), Postives = 134/174 (77.01%), Query Frame = -3 
Query:   27 YIKRD---ETIDRRKWSLMTVNGVDVEMLWDSGAVMSRSMCEKIGNPSVGESGITLR--------GVFSSGNEKPLGSTIVSVLWNGKVRKISIIIVEKI*PGFIKGVDIMELFGIKLLEINIIKVTLVNQNYTDLERIKKAMSSLNKGKNPKIERMLVKFGNIFMASKFDLGF 515
            +IKRD   ETI RRKWS MTVN VD+EMLW+S         E+I   +VG+S  T R        GVFSSG+EKPLGSTIVSVLWNG VRKISIII EKI P  I GVD MELFG+KLLEIN I+ TLVNQNYTDLERIKKAMS LNKGKNPKIER+LVKFGNIFMASKFDL F
Sbjct:   11 HIKRDVMYETIYRRKWSSMTVNEVDIEMLWESN--------EQI---NVGKSRETNRRREWNYSSGVFSSGSEKPLGSTIVSVLWNGIVRKISIIIGEKIKPELIGGVDTMELFGMKLLEINNIEETLVNQNYTDLERIKKAMSFLNKGKNPKIERILVKFGNIFMASKFDLRF 173
[Close]
BLAST of SMED30006202 vs. Planmine SMEST
Match: SMESG000012183.1 (SMESG000012183.1)

HSP 1 Score: 190.66 bits (483), Expect = 2.620e-58
Identity = 105/121 (86.78%), Postives = 113/121 (93.39%), Query Frame = -2 
Query:  541 IARKLYDESRGIKPRQPEILNPGNCFCCGESGHRSYQCPMKNKCLICDKENHTFGKCHLMGNHRSQMRRTVACIYXXXXXXXXXXXXNSYACEERTIEPERKHGKNTEDPIAFIS*VGLSN 903
            IARKLYD+SRGIKPR+P+ILNPGNCFCCGE+GHR YQCPMKNKCL+C KENHTF +CHL+GNHR QMRR VACIY EDNNDENFDDNNSYA EERTIEPERKHG+NTEDPIAFIS VGLSN
Sbjct:   13 IARKLYDKSRGIKPRKPKILNPGNCFCCGENGHRPYQCPMKNKCLVCGKENHTFERCHLLGNHRPQMRRPVACIY-EDNNDENFDDNNSYASEERTIEPERKHGENTEDPIAFISSVGLSN 132
[Close]
BLAST of SMED30006202 vs. Planmine SMEST
Match: SMESG000024723.1 (SMESG000024723.1)

HSP 1 Score: 183.341 bits (464), Expect = 1.439e-54
Identity = 114/159 (71.70%), Postives = 126/159 (79.25%), Query Frame = -1 
Query:  959 KSKKLVCRLFYH*KTITRQIFDLNAVKQKANDRLATFEIRVRNMVKTIFNSGMSAEDIVQDIIANKVWDDRVKEILLKKSSIQMEEVRSTAKIYENMTLSIS*SKNTNEIQVNSYAXXXXXXXXXXXXXXXXXKTYTNRYRQSNFLKRSQYVQSDNKYT 1435
            K K      F   KTITRQIFDLN VKQ+  +R ATF+IRVRN+VKT+FNS MS EDIV  IIANKV DDRVKEILL KSSI++EEVRSTAKIY+N+TLSIS S+NTNEIQVNSYA  V R    NN +DVKSK YTNRY+QSNFLKR  YVQ DNKYT
Sbjct:   26 KPKNWFVDCFTIKKTITRQIFDLNVVKQEEIERFATFKIRVRNLVKTLFNSVMSEEDIVLVIIANKVRDDRVKEILLTKSSIRIEEVRSTAKIYKNLTLSISESRNTNEIQVNSYA-NVVRRENKNNIQDVKSKIYTNRYQQSNFLKRLLYVQDDNKYT 183
The following BLAST results are available for this feature:
BLAST of SMED30006202 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 SMED30006202 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 SMED30006202 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 SMED30006202 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 SMED30006202 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 SMED30006202 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 SMED30006202 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 SMED30006202 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A0X9SRF71.122e-1141.98Putative BRCA2 OS=Schmidtea mediterranea OX=79327 ... [more]
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BLAST of SMED30006202 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 SMED30006202 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 SMED30006202 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 SMED30006202 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 SMED30006202 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 SMED30006202 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000017400.12.283e-8477.05SMESG000017400.1[more]
SMESG000078154.15.080e-6782.91SMESG000078154.1[more]
SMESG000051606.11.473e-6471.26SMESG000051606.1[more]
SMESG000012183.12.620e-5886.78SMESG000012183.1[more]
SMESG000024723.11.439e-5471.70SMESG000024723.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006202 ID=SMED30006202|Name=SMED30006202|organism=Schmidtea mediterranea sexual|type=transcript|length=1651bp
TTTTCATTTCATGACTAACTAGGTTTGAACCCGAGATCAAATTTTGACGC
CATAAATATATTCCCAAATTTTACTAACATCCTTTCAATCTTTGGATTCT
TTCCTTTGTTTAGAGACGACATTGCTTTCTTTATCCTTTCCAAATCGGTA
TAATTTTGATTAACTAAAGTTACTTTAATAATATTTATTTCTAAAAGTTT
GATTCCAAATAGCTCCATTATGTCCACACCCTTAATAAACCCTGGTTAAA
TTTTTTCAACTATGATTATGCTAATTTTACGTACTTTTCCATTCCATAAA
ACACTGACAATAGTACTTCCTAGTGGCTTTTCGTTTCCAGATGAAAATAC
TCCACGAAGAGTAATACCACTCTCACCGACGCTTGGGTTCCCTATTTTTT
CACACATTGATCTGCTCATTACTGCACCTGAATCCCACAACATTTCAACA
TCCACTCCATTTACGGTCATTAAACTCCATTTTCTTCTATCTATAGTCTC
ATCCCTCTTTATATATCATTTCGTTTTCTTTCTAAATTCAATTGCTCAAT
CCCACTTACGAAATGAAAGCAATGGGATCCTCCGTGTTTTTTCCATGTTT
TCTTTCCGGCTCAATTGTTCTCTCTTCACAAGCATATGAATTATTATCAT
CAAAATTTTCATCATTGTTATCTTCTTCATAAATACATGCAACAGTTCGT
CTCATTTGCGATCTGTGGTTACCCATCAGATGACATTTTCCAAAGGTATG
GTTTTCCTTATCACAAATTAAACATTTATTTTTCATTGGGCACTGATAAC
TTCTATGTCCACTTTCTCCACAACAAAAACAATTACCTGGGTTTAGAATC
TCTGGTTGGCGTGGTTTTATTCCTCGGCTTTCATCATAAAGTTTTCTAGC
TATACACGCTTGGTTGCTTTCTTGGCATATTTTTATTATAATATTTGTTA
GCGATCGCTGTATATTTATTGTCGCTTTGAACATATTGGGAACGTTTCAA
GAAATTACTCTGTCGATACCTGTTTGTATAAGTTTTTGACTTGACATCTT
TTTTATTATTATTTTTATTTTCTCTTCTTACCACATTAGCGTAACTGTTT
ACTTGGATTTCATTCGTATTTTTACTCTAGGATATTGATAGTGTCATATT
TTCATATATTTTAGCAGTTGATCTAACTTCCTCCATCTGTATGCTTGACT
TTTTCAATAGAATTTCTTTGACTCGATCATCCCATACTTTATTCGCAATA
ATATCTTGAACAATGTCTTCTGCGCTCATTCCTGAATTAAATATGGTTTT
AACCATATTTCGGACTCTAATCTCAAATGTTGCCAATCTGTCATTTGCTT
TTTGTTTCACGGCATTTAAATCAAAGATCTGTCTTGTAATTGTTTTTTAA
TGGTAAAACAATCTACAAACCAGTTTTTTGCTTTTTCATCTGTTGAACAG
CTGTCTCTATAACACTTCCATAACACTGCACCTTAATCTTTCTATAATAT
ATAGAAAGCACTAATTAAACTTTGACTTTCGATTTGCAGCAATTCGGTAA
TATCTTTTATCCGTTTTTCAGCTTCCGTCGTGCTTCGACTATCGAACTTC
CGTACATTAAAATCAAGCATGCTGTGAGCCTGCTTTGATAACGATTCCAA
G
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protein sequence of SMED30006202-orf-1

>SMED30006202-orf-1 ID=SMED30006202-orf-1|Name=SMED30006202-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=143bp
MFKATINIQRSLTNIIIKICQESNQACIARKLYDESRGIKPRQPEILNPG
NCFCCGESGHRSYQCPMKNKCLICDKENHTFGKCHLMGNHRSQMRRTVAC
IYEEDNNDENFDDNNSYACEERTIEPERKHGKNTEDPIAFIS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
Vocabulary: INTERPRO
TermDefinition
IPR001878Znf_CCHC
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0008270zinc ion binding