SMED30006223

Overview
NameSMED30006223
Smed IDSMED30006223
Length (bp)1495
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 SMED30006223 (SMED30006223) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30006223 (SMED30006223) 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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Alignments
SMED30006223 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.011634:1940..11592 +7355
Homology
BLAST of SMED30006223 vs. Planmine SMEST
Match: SMESG000003494.1 (SMESG000003494.1)

HSP 1 Score: 258.455 bits (659), Expect = 8.798e-80
Identity = 148/401 (36.91%), Postives = 233/401 (58.10%), Query Frame = 1
Query:    1 VIIQLIGKFSCGLIGEFKYKFENHLKFEIFIDF---LPIADKNLVQLIDSDQNRLLIQTSRSFAHDNKLIINFNGFTYNWISYQSFSLFYYKCC*FLTPDRRYQDIFFLDIKMKLINNKLYKLGSSSYVLLFPD--VFNGNGSKRMTEND------SIRQRNLAKVWLGHERNFINYSNSDWPTNQIIGCVHRFRLNNKKINFAKYGSNFFANCILQQSERICQDSECRNGT-SFLHILDCSLAKVNTGRHCFPGLYNNVNKFYSYAPIINEPIRIKLAWIPKLSISQCLLEIGAKNDSIISIYVGPTGKIVLNIKHNKLTEVPKFILHRMTSNDIYVILIKFTVRKWEIQVSDGIFIRAQEVLDLQGVHFINIGWNTNVNFCQPLNDKFEIQHNINVKSG 1167
            +++ ++G  S  LIGE + +F N L   I I +      +DK  +  IDS++N+L I+TS+ FA+D+KLIINFNG T    +Y+                 RY  +F+L IK+    N LY    S   L+  D  +   + S+   END        +  N  K+WLG++ ++I  S+SDWPTNQIIGC +R  +N K +    +G+NF+++C  + +E IC+ S+CRN T ++ HILDC L++++T  HC+P + +N    +SY PI +E + +KL WIP+LSISQCL+ I   N+SII IY+    +I+L +   K  +  K+  ++++S DI+ + I F      I++S+G FI+ + + + + +  I IGWN N   C P+ +KF IQ N N+KS 
Sbjct:   10 ILVSILGILSSYLIGEIEEEFRNDLIIWIKIRYGIRSQTSDKYFLHAIDSNRNKLSIKTSKLFANDSKLIINFNGQTGTRTAYKYI---------------RYVGVFYLHIKLTFKANNLYAGKWSPDELIISDELISYSSSSRAAMENDWPSAGDVSKLTNRMKIWLGYDHDWIGKSHSDWPTNQIIGCGYRIDVNKKSVILVNHGNNFYSDCFNEVTESICEQSQCRNETDNYQHILDCRLSRMSTAPHCYPDVTDNTEGLHSYQPIKDEHVTVKLGWIPQLSISQCLMHIITSNESIIDIYINSANQIILEMTIKKSIK-SKYNSYQISSIDIHALSIGFIDHNLTIRISNGSFIKTRMLPNQERIKTIYIGWNPNPCLCHPIRNKFGIQLNSNLKSA 394          
BLAST of SMED30006223 vs. Planmine SMEST
Match: SMESG000003492.1 (SMESG000003492.1)

HSP 1 Score: 252.292 bits (643), Expect = 1.168e-77
Identity = 146/394 (37.06%), Postives = 230/394 (58.38%), Query Frame = 1
Query:    1 VIIQLIGKFSCGLIGEFKYKFENHLKFEIFIDFLPIADKNLVQLIDSDQNRLLIQTSRSFAHDNKLIINFNGFTYNWISYQSFSLFYYKCC*FLTPDRRYQDIFFLDIKMKLINNKLYKLGSSSYVLLFPDVFNGNGSKR-MTEND---SIRQRNLAKVWLGHERNFINYSNSDWPTNQIIGCVHRFRLNNKKINFAKYGSNFFANCILQQSERICQDSECRNGT-SFLHILDCSLAKVNTGRHCFPGLYNNVNKFYSYAPIINEPIRIKLAWIPKLSISQCLLEIGAKNDSIISIYVGPTGKIVLNIKHNKLTEVPKFILHRMTSNDIYVILIKFTVRKWEIQVSDGIFIRAQEVLDLQGVHFINIGWNTNVNFCQPLNDKFEIQHNINVKSG 1167
            +++ + G  S  LIGE + +F N +   I I F  I+DK L+  ID++QN+L I+TS+SFA D+KLI+NFNG T             +KC                      + N LY     S  L+  ++   + + R +TEND   +    N  K+WLG++ ++I+ S+S+WPTNQIIGCV    +N K I F K+G++F+ +C  + +E IC+ S+CRN T +  +IL+C L  ++T  HC+P + +N    +SY PI +  + +K+AWIP+LSI QCL++I  +NDSII IY+    +I++ I  NK  +  K+  ++++S D++ + + F   K  I++S+G FI+ + + +   V  INIGWN+N   CQP+  KF IQ N N+KS 
Sbjct:   10 ILVSIFGISSSYLIGEIEGEFRNDVTIGIRIGFSRISDKYLLHAIDANQNKLSIKTSKSFASDSKLILNFNGATR-----------AFKC----------------------LENSLYAAKWPSDELIISNISYSSINSRSVTENDWPAAGDMSNRMKIWLGYDHDWISKSHSNWPTNQIIGCVELIDVNGKSIIFVKHGNDFYMDCYNRVTESICEKSQCRNETDNHQYILNCRLPGLSTSPHCYPDITDNTGGLHSYQPITHGHVAVKIAWIPQLSIRQCLIQIITRNDSIIDIYINSANQIMIEITDNKSIKSSKYNSYQISSTDVHALSMGFIDHKLTIRISNGYFIKTRMLPNHFRVETINIGWNSNPYLCQPIRGKFGIQLNSNLKSA 370          
BLAST of SMED30006223 vs. Planmine SMEST
Match: SMESG000003492.1 (SMESG000003492.1)

HSP 1 Score: 252.292 bits (643), Expect = 1.448e-77
Identity = 147/394 (37.31%), Postives = 230/394 (58.38%), Query Frame = 1
Query:    1 VIIQLIGKFSCGLIGEFKYKFENHLKFEIFIDFLPIADKNLVQLIDSDQNRLLIQTSRSFAHDNKLIINFNGFTYNWISYQSFSLFYYKCC*FLTPDRRYQDIFFLDIKMKLINNKLYKLGSSSYVLLFPDVFNGNGSKR-MTEND---SIRQRNLAKVWLGHERNFINYSNSDWPTNQIIGCVHRFRLNNKKINFAKYGSNFFANCILQQSERICQDSECRNGT-SFLHILDCSLAKVNTGRHCFPGLYNNVNKFYSYAPIINEPIRIKLAWIPKLSISQCLLEIGAKNDSIISIYVGPTGKIVLNIKHNKLTEVPKFILHRMTSNDIYVILIKFTVRKWEIQVSDGIFIRAQEVLDLQGVHFINIGWNTNVNFCQPLNDKFEIQHNINVKSG 1167
            V++ + G  S  LIGE + +F N +   I I F  I+DK L+  ID++QN+L I+TS+SFA D+KLI+NFNG T             +KC                      + N LY     S  L+  ++   + + R +TEND   +    N  K+WLG++ ++I+ S+S+WPTNQIIGCV    +N K I F K+G++F+ +C  + +E IC+ S+CRN T +  +IL+C L  ++T  HC+P + +N    +SY PI +  + +K+AWIP+LSI QCL++I  +NDSII IY+    +I++ I  NK  +  K+  ++++S D++ + + F   K  I++S+G FI+ + + +   V  INIGWN+N   CQP+  KF IQ N N+KS 
Sbjct:   23 VLVSIFGISSSYLIGEIEGEFRNDVTIGIRIGFSRISDKYLLHAIDANQNKLSIKTSKSFASDSKLILNFNGATR-----------AFKC----------------------LENSLYAAKWPSDELIISNISYSSINSRSVTENDWPAAGDMSNRMKIWLGYDHDWISKSHSNWPTNQIIGCVELIDVNGKSIIFVKHGNDFYMDCYNRVTESICEKSQCRNETDNHQYILNCRLPGLSTSPHCYPDITDNTGGLHSYQPITHGHVAVKIAWIPQLSIRQCLIQIITRNDSIIDIYINSANQIMIEITDNKSIKSSKYNSYQISSTDVHALSMGFIDHKLTIRISNGYFIKTRMLPNHFRVETINIGWNSNPYLCQPIRGKFGIQLNSNLKSA 383          
BLAST of SMED30006223 vs. Planmine SMEST
Match: SMESG000003551.1 (SMESG000003551.1)

HSP 1 Score: 251.136 bits (640), Expect = 6.980e-77
Identity = 148/415 (35.66%), Postives = 235/415 (56.63%), Query Frame = 1
Query:    4 IIQLIGKFSCGLIGEFKYKFENHLKFEIFIDFLPIADKNLVQLIDSDQNRLLIQTSRSFAHDNKLIINFNGFTYNWISYQSFSLFYYKCC*FLTPDRRYQDIFFLDIKMKLINNKLY------------KLGSSSYVLLFPDVFNGNGSKRMTENDSIRQRNLAK------VWLGHERNFINYSNSDWPTNQIIGCVHRFR--------LNNKKINFAKYGSNFFANCILQQSERICQDSECRNGT-SFLHILDCSLAKVNTGRHCFPGLYNNVNKFYSYAPIINEPIRIKLAWIPKLSISQCLLEIGAKNDSIISIYVGPTGKIVLNIKHNKLTEVPKFILHRMTSNDIYVILIKFTVRKWEIQVSDGIFIRAQEVLDLQGVHFINIGWNTNVNFCQPLNDKFEIQHNINVKSG 1167
            ++ ++G  S  LIGE + +F N LK  I I+F  I+DK L+Q IDS+ N+L I+TS+SFA+DN++IINFNG T    +Y+   + +           RY  +F+L +++    N LY            KL      L+  ++   + S+   END     +L+K      +W+G + ++I  S+SDWPTNQI GCVHR          +N   + F K+G+NF+++C  + +E IC+ S+CRN T  +  IL C L++++T  HC+P + +N    +SY PI +  + +KL WIP+LSISQCL+ I   N+SII IY+    +I+L     K  +  K+  ++++S DI+ + I F      I++S+G FI+ + + +   +  + IGWN N   C P+ +KF IQ N N+KS 
Sbjct:   11 LVSILGISSSYLIGEIEGEFRNDLKIGIGIEFSQISDKYLLQAIDSNWNKLSIKTSKSFANDNQIIINFNGQTCTRTAYEDLDMIF-----------RYVAVFYLYVRLTFKANNLYASIWPSDELINIKLIPKYPKLIISNISYRSISRAAIENDWPSAGDLSKLTNRIKIWIGFDHDWIGKSHSDWPTNQIFGCVHRIDSIDVNRIDVNWNSVIFDKHGNNFYSDCYNKVTESICEQSQCRNETYKYQFILGCRLSRMSTAPHCYPDVTDNTEGLHSYQPITDGNVTLKLGWIPQLSISQCLMHIITSNESIIDIYINSANQIILETMIKKSIK-SKYNSYQISSVDIHALSIGFIDHNLTIRISNGSFIKTRMLPNQDRIKTVYIGWNPNRCLCHPIRNKFGIQLNSNLKSA 413          
BLAST of SMED30006223 vs. Planmine SMEST
Match: SMESG000024557.1 (SMESG000024557.1)

HSP 1 Score: 248.44 bits (633), Expect = 7.837e-76
Identity = 143/396 (36.11%), Postives = 225/396 (56.82%), Query Frame = 1
Query:    4 IIQLIGKFSCGLIGEFKYKFENHLKFEIFIDFLPIADKNLVQLIDSDQNRLLIQTSRSFAHDNKLIINFNGFTYNWISYQSFSLFYYKCC*FLTPDRRYQDIFFLDIKMKLINNKLYKLGSSSYVLLFPDVF--NGNGSKRMTEND------SIRQRNLAKVWLGHERNFINYSNSDWPTNQIIGCVHRFRLNNKKINFAKYGSNFFANCILQQSERICQDSECRNGTSFLHILDCSLAKVNTGRHCFPGLYNNVNKFYSYAPIINEPIRIKLAWIPKLSISQCLLEIGAKNDSIISIYVGPTGKIVLNIKHNKLTEVPKFILHRMTSNDIYVILIKFTVRKWEIQVSDGIFIRAQEVLDLQGVHFINIGWNTNVNFCQPLNDKFEIQHNINVKSG 1167
            ++ ++G  S  LIGE + +F N L   I I F  I+DK L+Q IDS++N+L I+TS+SFA+D+KLIINFNG T    +Y+   + +           RY    +L I +    N +Y      Y L+  ++   + N S+   END       I+  N  K+W+G++ ++I+ S+SDWPTNQIIGCV+R  +N   +                 +E IC+ S+CRN T + HILDC +++++T  +C+P + +N    +SY PI +  + +KL WIP+LSISQCL+ I   N+SII IY+    +I+L +   K  +  K+  ++++S DI+ + I F      I++S+G FI+ + + +   +  I IGWN N   C P+ +KF IQ N N+KS 
Sbjct:   11 LVSILGISSSYLIGEIEGEFRNDLIIVITIRFSQISDKYLLQPIDSNRNKLSIKTSKSFANDSKLIINFNGQTCTRTAYEDLDMIF-----------RYMGALYLYIVLAFKANNVYAGKWPPYELIISNISYRSSNSSRAAIENDWPSAGDLIKLTNRIKIWIGYDHDWISKSHSDWPTNQIIGCVYRIHVNGNSV-----------------TESICEQSQCRNETDYQHILDCRISRMSTAPNCYPDVTDNTEGLHSYQPITDGHVTLKLGWIPQLSISQCLIHIITSNESIIDIYINSANQIILEMTIKKSIK-SKYNSYQISSVDIHALSIGFIDHNLTIRISNGSFIKTRMLPNQDRIKTIYIGWNPNPCLCYPIRNKFGIQLNSNLKSA 377          
The following BLAST results are available for this feature:
BLAST of SMED30006223 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 SMED30006223 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 SMED30006223 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 SMED30006223 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 SMED30006223 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 SMED30006223 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 SMED30006223 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 SMED30006223 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 SMED30006223 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 SMED30006223 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 SMED30006223 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 SMED30006223 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 SMED30006223 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 SMED30006223 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000003494.18.798e-8036.91SMESG000003494.1[more]
SMESG000003492.11.168e-7737.06SMESG000003492.1[more]
SMESG000003492.11.448e-7737.31SMESG000003492.1[more]
SMESG000003551.16.980e-7735.66SMESG000003551.1[more]
SMESG000024557.17.837e-7636.11SMESG000024557.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006223 ID=SMED30006223|Name=SMED30006223|organism=Schmidtea mediterranea sexual|type=transcript|length=1495bp
GTGATTATTCAGTTAATTGGAAAATTTTCATGCGGTTTGATTGGTGAATT
CAAATACAAATTCGAAAACCATTTGAAATTTGAAATATTTATCGATTTTC
TACCGATTGCCGATAAAAATTTGGTGCAATTGATCGATTCGGATCAAAAT
CGATTATTGATCCAAACCAGTAGATCATTTGCACATGACAATAAATTAAT
AATAAATTTCAATGGATTCACGTATAACTGGATCAGTTATCAAAGTTTCT
CTTTGTTTTATTATAAATGCTGTTGATTCCTTACTCCAGACCGACGATAT
CAGGACATCTTTTTTCTAGATATTAAAATGAAATTAATAAATAATAAATT
ATATAAGCTTGGCTCCTCATCATACGTTTTACTATTTCCAGACGTTTTTA
ATGGAAACGGCAGTAAAAGAATGACAGAAAATGATTCCATCAGACAAAGA
AATTTGGCAAAGGTCTGGTTAGGACATGAGCGTAATTTTATTAATTATTC
AAATTCTGATTGGCCGACCAATCAAATCATTGGCTGCGTTCATCGTTTCC
GGCTGAATAATAAAAAAATTAATTTTGCAAAGTACGGAAGTAATTTTTTT
GCGAACTGCATTTTGCAACAATCAGAACGAATTTGTCAAGATTCAGAATG
CAGAAATGGAACATCCTTTCTGCACATTCTGGACTGCTCTTTGGCAAAGG
TCAACACGGGCAGGCATTGCTTTCCAGGTTTATATAATAATGTTAATAAA
TTTTATTCCTACGCGCCGATAATTAATGAGCCAATTAGAATCAAATTGGC
ATGGATTCCGAAATTGTCAATTAGCCAATGTCTGCTGGAGATCGGCGCAA
AAAATGATTCAATTATTAGTATTTATGTCGGTCCGACCGGTAAAATTGTT
CTAAATATCAAGCATAACAAATTGACAGAAGTGCCAAAATTTATTTTACA
TCGAATGACATCGAATGACATTTATGTCATATTAATAAAGTTTACAGTAC
GCAAATGGGAAATTCAGGTATCAGATGGGATTTTCATTCGGGCTCAGGAA
GTGCTGGATTTACAGGGAGTACATTTCATAAATATCGGTTGGAATACTAA
TGTGAATTTTTGTCAGCCCCTTAATGATAAATTTGAAATTCAGCACAACA
TCAATGTTAAATCTGGTCAAATTATAAAGGCTTACTCTTCGTTGATAAAA
ATAATAATAATAATCAATATTTTATTTTTTTTATTTTTATTATTCTTTAT
TGGGAAATATGTTTTTGGTAATCATTGGAGAGATATTGACAGGCCGTTGT
CAAATGTCTACGAAGACCCTCAACAAATTGACGACGCCGATAATCTCAAG
TCAAATGCTATTAAACATTCAGAAACAAATGTTTATGACGAGTGCCTTTT
TTGATTTATTGAACATTATTTGGTTTTTATATAGATTTTTAAAAGATAAA
CAAAAATTTAGTTTTCACAAACTTACATTGAAATTACATAAAGCA
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protein sequence of SMED30006223-orf-1

>SMED30006223-orf-1 ID=SMED30006223-orf-1|Name=SMED30006223-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=359bp
MKLINNKLYKLGSSSYVLLFPDVFNGNGSKRMTENDSIRQRNLAKVWLGH
ERNFINYSNSDWPTNQIIGCVHRFRLNNKKINFAKYGSNFFANCILQQSE
RICQDSECRNGTSFLHILDCSLAKVNTGRHCFPGLYNNVNKFYSYAPIIN
EPIRIKLAWIPKLSISQCLLEIGAKNDSIISIYVGPTGKIVLNIKHNKLT
EVPKFILHRMTSNDIYVILIKFTVRKWEIQVSDGIFIRAQEVLDLQGVHF
INIGWNTNVNFCQPLNDKFEIQHNINVKSGQIIKAYSSLIKIIIIINILF
FLFLLFFIGKYVFGNHWRDIDRPLSNVYEDPQQIDDADNLKSNAIKHSET
NVYDECLF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0003116parenchymal cell