SMED30028686

Overview
NameSMED30028686
Smed IDSMED30028686
Length (bp)512
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




SMED30028686

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30028686SMESG000069527.1 SmedASXL_001004SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
headSMED30028686SMESG000069527.1 dd_Smed_v6_77896_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30028686 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006139:26897..27450 -2504
Homology
BLAST of SMED30028686 vs. TrEMBL
Match: A0A1I8JLH1 (PBPe domain-containing protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 62.7734 bits (151), Expect = 1.668e-8
Identity = 23/71 (32.39%), Postives = 46/71 (64.79%), Query Frame = 2
Query:   74 ACITDTSLVVYVAKRHCSKMYTIPETFDSSSTSFIVQMDAPYKPILDMYIRKLVDTGQIEKWVTKYWSTSD 286
            AC+ D S ++ +A ++C++ Y   E F++ + +F+   DAPY  + + +++KL ++GQI++W   YWS  +
Sbjct:  155 ACVEDYSALLAIALKNCTQYYVANEQFNTGTIAFMFPEDAPYANLFNFHLQKLHESGQIQRWFDIYWSKDN 225          
BLAST of SMED30028686 vs. TrEMBL
Match: A0A1I8J176 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 7.549e-8
Identity = 30/96 (31.25%), Postives = 53/96 (55.21%), Query Frame = 2
Query:   74 ACITDTSLVVYVAKRHCSKMYTIPETFDSSSTSFIVQMDAPYKPILDMYIRKLVDTGQIEKWVTKYWSTSDINADXXXXXXXXXXXXXITLEDVAG 361
             C+ D S ++ +A ++CS+ Y   E F++++ +F+   DA Y    +  ++KL ++GQI++W   YWS+     D+      S  A +I LE V G
Sbjct:   24 GCMNDYSFLLAIAMKNCSEYYVADELFNTATLAFMFPEDAYYADSFNFQLQKLHESGQIQRWFEFYWSS-----DTVCTVGKSAEADAINLEGVGG 114          
BLAST of SMED30028686 vs. TrEMBL
Match: A0A1I8J1L9 (PBPe domain-containing protein OS=Macrostomum lignano OX=282301 PE=3 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 1.159e-7
Identity = 40/134 (29.85%), Postives = 78/134 (58.21%), Query Frame = 2
Query:   68 NLACITDTSLVVYVAKRHCSKMYTIPETFDSSSTSFIVQMDAPYKPILDMYIRKLVDTGQIEKWVTKYWSTSDINADXXXXXXXXXXXXXITLEDVAGXXXXXXXXXXXXXXXXXXXXFWYKVLKK-PLNSFCF 466
            N AC+TD + ++ +A+++C++ Y   E F ++  + ++  DA Y  + + +++KL +TGQ+++W   YWS+     DS     SS    +I+LE   G +I  +    + + +L+LE+ W K+ K+ PL+ F +
Sbjct:  260 NQACLTDYTYLLNIARKNCTQFYLAEELFLTAPIALMLPDDAFYAELFNFHMQKLHETGQLQRWFQLYWSS-----DSVCSVGSSAETDAISLESAGGCFIATLCFYGLGLLILLLELVWTKLAKRQPLDCFFY 388          
BLAST of SMED30028686 vs. TrEMBL
Match: A0A1I8H8P2 (PBPe domain-containing protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 2.064e-7
Identity = 47/140 (33.57%), Postives = 80/140 (57.14%), Query Frame = 2
Query:   38 IDQFYQDNGTNLACITDTSLVVYVAKRHCSKMYTIPETFDSSSTSFIVQMDAPYKPILDMYIRKLVDTGQIEKWVTKYWSTSDINADXXXXXXXXXXXXXITLEDVAGXXXXXXXXXXXXXXXXXXXXFWYKVLKK-PLN 454
            I+Q +Q      AC+TD + ++YVA+ +CSK+Y   E F++++ +F+   DA +   +D   +K+ +TG ++K    YWS+     D+   S SS  A SI LE   G +I  +A   + +  L++E+ W K LK+ PL+
Sbjct:   78 IEQTFQGKE---ACLTDYTALLYVARANCSKVYIADEIFNTATVAFMYPEDAYFGANIDFQFQKMHETGIMQKLFNTYWSS-----DAVCSSGSSTEADSINLEGSGGCFIVALAFYGLGLLTLLVELLWTKALKRHPLD 209          
BLAST of SMED30028686 vs. TrEMBL
Match: A0A1I8IYQ8 (PBPe domain-containing protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 4.429e-7
Identity = 30/96 (31.25%), Postives = 53/96 (55.21%), Query Frame = 2
Query:   74 ACITDTSLVVYVAKRHCSKMYTIPETFDSSSTSFIVQMDAPYKPILDMYIRKLVDTGQIEKWVTKYWSTSDINADXXXXXXXXXXXXXITLEDVAG 361
             C+ D S ++ +A ++CS+ Y   E F++++ +F+   DA Y    +  ++KL ++GQI++W   YWS+     D+      S  A +I LE V G
Sbjct:  119 GCMNDYSFLLAIAMKNCSEYYVADELFNTATLAFMFPEDAYYADSFNFQLQKLHESGQIQRWFEFYWSS-----DTVCTVGKSAEADAINLEGVGG 209          
BLAST of SMED30028686 vs. Planmine SMEST
Match: SMESG000069527.1 (SMESG000069527.1)

HSP 1 Score: 214.927 bits (546), Expect = 7.826e-70
Identity = 140/140 (100.00%), Postives = 140/140 (100.00%), Query Frame = 2
Query:   50 YQDNGTNLACITDTSLVVYVAKRHCSKMYTIPETFDSSSTSFIVQMDAPYKPILDMYIRKLVDTGQIEKWVTKYWSTSDINADXXXXXXXXXXXXXITLEDVAGXXXXXXXXXXXXXXXXXXXXFWYKVLKKPLNSFCFQ 469
            YQDNGTNLACITDTSLVVYVAKRHCSKMYTIPETFDSSSTSFIVQMDAPYKPILDMYIRKLVDTGQIEKWVTKYWSTSDINADSCMGSSSSDSAPSITLEDVAGIYIFIIALIIISISLLILEIFWYKVLKKPLNSFCFQ
Sbjct:   93 YQDNGTNLACITDTSLVVYVAKRHCSKMYTIPETFDSSSTSFIVQMDAPYKPILDMYIRKLVDTGQIEKWVTKYWSTSDINADSCMGSSSSDSAPSITLEDVAGIYIFIIALIIISISLLILEIFWYKVLKKPLNSFCFQ 232          
BLAST of SMED30028686 vs. Planmine SMEST
Match: SMESG000069544.1 (SMESG000069544.1)

HSP 1 Score: 125.946 bits (315), Expect = 1.338e-36
Identity = 73/145 (50.34%), Postives = 101/145 (69.66%), Query Frame = 2
Query:   38 IDQFYQDNGTNLACITDTSLVVYVAKRHCSKMYTIPETFDSSSTSFIVQMDAPYKPILDMYIRKLVDTGQIEKWVTKYWSTSDINADXXXXXXXXXXXXXITLEDVAGXXXXXXXXXXXXXXXXXXXXFWYKVLKKPLNSFCFQW 472
            I Q  QDN  NL CI+D+S   YV  R+CSK+Y IP+TF+ ++ +F VQ+DAPYKPILD YIRKL D+G IEKW+TKYWS +  + D+C  S++  +A  I LE++ G++I    LI +S+ +L  E+FW   L KPL+SF  Q+
Sbjct:   63 ILQILQDNANNLVCISDSSANQYVVNRNCSKIYMIPDTFNPANIAFGVQIDAPYKPILDSYIRKLTDSGDIEKWITKYWSINIGSVDTCDNSNTQGTALPIDLEELGGVFICTAILIGLSLLILCTEVFWTHSLDKPLDSFACQY 207          
BLAST of SMED30028686 vs. Planmine SMEST
Match: SMESG000069544.1 (SMESG000069544.1)

HSP 1 Score: 124.02 bits (310), Expect = 9.351e-36
Identity = 71/140 (50.71%), Postives = 99/140 (70.71%), Query Frame = 2
Query:   53 QDNGTNLACITDTSLVVYVAKRHCSKMYTIPETFDSSSTSFIVQMDAPYKPILDMYIRKLVDTGQIEKWVTKYWSTSDINADXXXXXXXXXXXXXITLEDVAGXXXXXXXXXXXXXXXXXXXXFWYKVLKKPLNSFCFQW 472
            QDN  NL CI+D+S   YV  R+CSK+Y IP+TF+ ++ +F VQ+DAPYKPILD YIRKL D+G IEKW+TKYWS +  + D+C  S++  +A  I LE++ G++I    LI +S+ +L  E+FW   L KPL+SF  Q+
Sbjct:   70 QDNANNLVCISDSSANQYVVNRNCSKIYMIPDTFNPANIAFGVQIDAPYKPILDSYIRKLTDSGDIEKWITKYWSINIGSVDTCDNSNTQGTALPIDLEELGGVFICTAILIGLSLLILCTEVFWTHSLDKPLDSFACQY 209          
BLAST of SMED30028686 vs. Planmine SMEST
Match: SMESG000018611.1 (SMESG000018611.1)

HSP 1 Score: 83.5741 bits (205), Expect = 5.007e-19
Identity = 43/100 (43.00%), Postives = 67/100 (67.00%), Query Frame = 2
Query:   62 GTNLACITDTSLVVYVAKRHCSKMYTIPETFDSSSTSFIVQMDAPYKPILDMYIRKLVDTGQIEKWVTKYWSTSDINADXXXXXXXXXXXXXITLEDVAG 361
             T+L CITDTS+VVY   ++CS +YT+PETF+++   F+   DAP+K  +D  I+ LV+TG I +W+  YW T+  ++ +C   S+++SA  I L+ V G
Sbjct:  829 STDLVCITDTSVVVYTVNKYCSVIYTVPETFNTAPLGFLTPKDAPFKKKIDQIIQSLVETGIISRWIEFYWKTNQSDSQNCEAGSNNNSADPIDLDGVLG 928          

HSP 2 Score: 77.411 bits (189), Expect = 6.725e-17
Identity = 32/76 (42.11%), Postives = 50/76 (65.79%), Query Frame = 2
Query:   62 GTNLACITDTSLVVYVAKRHCSKMYTIPETFDSSSTSFIVQMDAPYKPILDMYIRKLVDTGQIEKWVTKYWSTSDI 289
             TNL CI+D S + YV   +C  +Y +PE F+ ++  F+++ D+PYK ++D YI+ LV+ G I KWV KYW   ++
Sbjct:  270 STNLVCISDRSGMRYVTNMNCKDVYMVPEIFNIAALGFVLEKDSPYKNMIDSYIQILVENGLITKWVRKYWEDDEV 345          
BLAST of SMED30028686 vs. Planmine SMEST
Match: SMESG000018611.1 (SMESG000018611.1)

HSP 1 Score: 82.8037 bits (203), Expect = 9.995e-19
Identity = 35/74 (47.30%), Postives = 52/74 (70.27%), Query Frame = 2
Query:   62 GTNLACITDTSLVVYVAKRHCSKMYTIPETFDSSSTSFIVQMDAPYKPILDMYIRKLVDTGQIEKWVTKYWSTS 283
             T+L CITDTS+VVY   ++CS +YT+PETF+++   F+   DAP+K  +D  I+ LV+TG I +W+  YW T+
Sbjct:  829 STDLVCITDTSVVVYTVNKYCSVIYTVPETFNTAPLGFLTPKDAPFKKKIDQIIQSLVETGIISRWIEFYWKTN 902          

HSP 2 Score: 77.411 bits (189), Expect = 7.317e-17
Identity = 32/76 (42.11%), Postives = 50/76 (65.79%), Query Frame = 2
Query:   62 GTNLACITDTSLVVYVAKRHCSKMYTIPETFDSSSTSFIVQMDAPYKPILDMYIRKLVDTGQIEKWVTKYWSTSDI 289
             TNL CI+D S + YV   +C  +Y +PE F+ ++  F+++ D+PYK ++D YI+ LV+ G I KWV KYW   ++
Sbjct:  270 STNLVCISDRSGMRYVTNMNCKDVYMVPEIFNIAALGFVLEKDSPYKNMIDSYIQILVENGLITKWVRKYWEDDEV 345          
The following BLAST results are available for this feature:
BLAST of SMED30028686 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 SMED30028686 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 SMED30028686 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 SMED30028686 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 SMED30028686 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 SMED30028686 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 SMED30028686 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 SMED30028686 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1I8JLH11.668e-832.39PBPe domain-containing protein OS=Macrostomum lign... [more]
A0A1I8J1767.549e-831.25Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8J1L91.159e-729.85PBPe domain-containing protein OS=Macrostomum lign... [more]
A0A1I8H8P22.064e-733.57PBPe domain-containing protein OS=Macrostomum lign... [more]
A0A1I8IYQ84.429e-731.25PBPe domain-containing protein OS=Macrostomum lign... [more]
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BLAST of SMED30028686 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 SMED30028686 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 SMED30028686 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 SMED30028686 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 SMED30028686 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 SMED30028686 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000069527.17.826e-70100.00SMESG000069527.1[more]
SMESG000069544.11.338e-3650.34SMESG000069544.1[more]
SMESG000069544.19.351e-3650.71SMESG000069544.1[more]
SMESG000018611.15.007e-1943.00SMESG000018611.1[more]
SMESG000018611.19.995e-1947.30SMESG000018611.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028686 ID=SMED30028686|Name=SMED30028686|organism=Schmidtea mediterranea sexual|type=transcript|length=512bp
CTTTTTGATGTCTATTAACCTATATTTTTAATTGTATATTGACCAGTTTT
ATCAAGACAATGGAACTAATCTTGCATGTATAACAGATACATCTCTTGTT
GTATACGTTGCAAAGCGCCACTGTTCAAAGATGTACACTATTCCAGAGAC
TTTTGACTCTTCAAGTACGAGTTTCATTGTTCAAATGGACGCACCTTATA
AACCGATTTTGGACATGTATATACGTAAACTTGTAGATACCGGACAAATT
GAAAAATGGGTGACAAAATATTGGTCAACTAGTGACATTAATGCAGACTC
CTGTATGGGATCCTCGAGTTCCGATTCAGCCCCGTCTATAACATTAGAAG
ATGTTGCAGGAATTTATATTTTCATTATTGCTTTGATTATCATTTCAATA
AGCTTGTTAATTCTAGAAATCTTTTGGTACAAAGTATTAAAAAAACCTTT
AAATTCATTTTGTTTTCAATGGTAAGAACATTTACTTTGAATCAAAAATT
GTTGTCACAAAG
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protein sequence of SMED30028686-orf-1

>SMED30028686-orf-1 ID=SMED30028686-orf-1|Name=SMED30028686-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=115bp
MYTIPETFDSSSTSFIVQMDAPYKPILDMYIRKLVDTGQIEKWVTKYWST
SDINADSCMGSSSSDSAPSITLEDVAGIYIFIIALIIISISLLILEIFWY
KVLKKPLNSFCFQW*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head