SMED30016946

Overview
NameSMED30016946
Smed IDSMED30016946
Length (bp)341
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.
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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30016946

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
X1 cellSMED30016946 SmedASXL_075355SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30016946 vs. TrEMBL
Match: A0A0L7QQ45 (SCAN domain-containing protein 3 OS=Habropoda laboriosa OX=597456 GN=WH47_06898 PE=4 SV=1)

HSP 1 Score: 98.5969 bits (244), Expect = 1.252e-21
Identity = 58/109 (53.21%), Postives = 74/109 (67.89%), Query Frame = -1 
Query:    3 KALSLQI-----------TSLLYFTEVSSNFFWISVKKEHPRISDKAI-----LTITYSCDKSYSTLVLIKNDKRSCLKDLDQEPWVALSIIKLNIELLCTLEQSQVLH 281
            +ALSLQI           T  L F+E+    FWISVKKE+P+ISDKAI      + TY C++S+STLVLIKNDKRSCLK LD E  VALS I+ NI+ +C+ +Q+Q+ H
Sbjct:  448 EALSLQIREEFIELRNDGTLKLNFSEMPLANFWISVKKEYPQISDKAIAILLPFSTTYLCEQSFSTLVLIKNDKRSCLKGLDHELRVALSNIEPNIKRICSSKQAQISH 556
[Close]
BLAST of SMED30016946 vs. TrEMBL
Match: J9M5D5 (DUF4371 domain-containing protein OS=Acyrthosiphon pisum OX=7029 PE=4 SV=2)

HSP 1 Score: 67.781 bits (164), Expect = 7.967e-11
Identity = 38/92 (41.30%), Postives = 57/92 (61.96%), Query Frame = -1 
Query:    3 ITSLLYFTEVSSNFFWISVKKEHPRISDKAI-----LTITYSCDKSYSTLVLIKNDKRSCLKDLDQEPWVALSIIKLNIELLCTLEQSQVLH 263
            + S  Y +E  S  FWIS++ E+P +S KA+      + +Y C+ ++S L + K  KRS LKD++ E  V+LS I+  IE LC++ QSQV H
Sbjct:  476 LKSKFYMSENDS--FWISLQNEYPEVSKKALQILLPFSTSYMCESAFSILEVTKTKKRSTLKDIESELRVSLSKIRPRIEDLCSIRQSQVSH 565
[Close]
BLAST of SMED30016946 vs. TrEMBL
Match: A0A2H6NA56 (Uncharacterized protein OS=Micrurus lemniscatus carvalhoi OX=129465 PE=4 SV=1)

HSP 1 Score: 64.6994 bits (156), Expect = 1.446e-10
Identity = 36/88 (40.91%), Postives = 54/88 (61.36%), Query Frame = -1 
Query:    3 LYFTEVSSNFFWISVKKEHPRISDKAILTI-----TYSCDKSYSTLVLIKNDKRSCLKDLDQEPWVALSIIKLNIELLCTLEQSQVLH 251
            L F ++  + FW+SV KE P +++KAILT+     TY C+  +S+L  IK   R  L+ +++E  V LS I   I LLC+ +Q+QV H
Sbjct:   79 LKFADLPLDSFWLSVAKEFPILANKAILTLLPFSTTYLCELGFSSLTAIKTKNRERLRTVEEELRVCLSTIPARISLLCSSKQAQVSH 166
[Close]
BLAST of SMED30016946 vs. TrEMBL
Match: A0A0L7QW41 (SCAN domain-containing protein 3 (Fragment) OS=Habropoda laboriosa OX=597456 GN=WH47_05031 PE=4 SV=1)

HSP 1 Score: 65.0846 bits (157), Expect = 1.850e-10
Identity = 40/78 (51.28%), Postives = 50/78 (64.10%), Query Frame = -1 
Query:   96 KALSLQI-----------TSLLYFTEVSSNFFWISVKKEHPRISDKAI-----LTITYSCDKSYSTLVLIKNDKRSCL 281
            +ALSLQI           T  L F+E+    FWISVKKE+P+IS K +      + TY C++S+STLVLIKNDKRSCL
Sbjct:  370 EALSLQIREEFIELRNDGTLKLNFSEMPLADFWISVKKEYPQISVKVVPILLPFSTTYLCEQSFSTLVLIKNDKRSCL 447

HSP 2 Score: 28.1054 bits (61), Expect = 1.850e-10
Identity = 13/21 (61.90%), Postives = 16/21 (76.19%), Query Frame = -3 
Query:  277 TEQYD*IRNPFAINATNSTES 339
            TEQY+ IRN F  +A NSTE+
Sbjct:  351 TEQYNWIRNSFLADAENSTEA 371
[Close]
BLAST of SMED30016946 vs. TrEMBL
Match: A0A2H6NA63 (Uncharacterized protein OS=Micrurus lemniscatus carvalhoi OX=129465 PE=4 SV=1)

HSP 1 Score: 65.0846 bits (157), Expect = 1.925e-10
Identity = 36/88 (40.91%), Postives = 54/88 (61.36%), Query Frame = -1 
Query:    3 LYFTEVSSNFFWISVKKEHPRISDKAILTI-----TYSCDKSYSTLVLIKNDKRSCLKDLDQEPWVALSIIKLNIELLCTLEQSQVLH 251
            L F ++  + FW+SV KE P +++KAILT+     TY C+  +S+L  IK   R  L+ +++E  V LS I   I LLC+ +Q+QV H
Sbjct:  121 LKFADLPLDSFWLSVAKEFPILANKAILTLLPFSTTYLCELGFSSLTAIKTKNRERLRTVEEELRVCLSTIPARISLLCSSKQAQVSH 208
[Close]
BLAST of SMED30016946 vs. Ensembl Medaka
Match: ENSORLT00000040389.1 (pep primary_assembly:ASM223467v1:19:265767:268275:-1 gene:ENSORLG00000025045.1 transcript:ENSORLT00000040389.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 46.9802 bits (110), Expect = 6.479e-7
Identity = 26/88 (29.55%), Postives = 49/88 (55.68%), Query Frame = -1 
Query:    3 LYFTEVSSNFFWISVKKEHPRISDKAI-----LTITYSCDKSYSTLVLIKNDKRSCLKDLDQEPWVALSIIKLNIELLCTLEQSQVLH 251
            L FT  + + FW++V++++P +  +A+        +Y C+  +S +  +K   RS L +++QE  VA+S  K   E LCT +++   H
Sbjct:  526 LRFTSQTLSEFWLNVERQYPLLGQRAMGILLPFATSYLCETGFSAVAALKTKYRSQL-NIEQELRVAVSCFKPRFEKLCTAKRAHCSH 612
[Close]
BLAST of SMED30016946 vs. Ensembl Medaka
Match: ENSORLT00000035512.1 (pep primary_assembly:ASM223467v1:11:22712371:22714941:1 gene:ENSORLG00000026495.1 transcript:ENSORLT00000035512.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 46.9802 bits (110), Expect = 6.735e-7
Identity = 26/88 (29.55%), Postives = 49/88 (55.68%), Query Frame = -1 
Query:    3 LYFTEVSSNFFWISVKKEHPRISDKAI-----LTITYSCDKSYSTLVLIKNDKRSCLKDLDQEPWVALSIIKLNIELLCTLEQSQVLH 251
            L FT  + + FW++V++++P +  +A+        +Y C+  +S +  +K   RS L +++QE  VA+S  K   E LCT +++   H
Sbjct:  526 LRFTSQTLSEFWLNVERQYPLLGQRAMGILLPFATSYLCETGFSAVAALKTKYRSQL-NIEQELRVAVSCFKPRFEKLCTAKRAHCSH 612
[Close]
BLAST of SMED30016946 vs. Ensembl Medaka
Match: ENSORLT00000033301.1 (pep primary_assembly:ASM223467v1:24:1653567:1654763:-1 gene:ENSORLG00000025431.1 transcript:ENSORLT00000033301.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 45.0542 bits (105), Expect = 3.091e-6
Identity = 25/85 (29.41%), Postives = 48/85 (56.47%), Query Frame = -1 
Query:   12 LYFTEVSSNFFWISVKKEHPRISDKAI-----LTITYSCDKSYSTLVLIKNDKRSCLKDLDQEPWVALSIIKLNIELLCTLEQSQ 251
            L FT  + + FW++V++++P +  +A+        +Y C+  +S +  +K   RS L +++QE  VA+S  K   E LCT +++ 
Sbjct:  310 LRFTSQTLSEFWLNVERQYPLLGQRAMGILLPFATSYLCETGFSAVAALKTKYRSQL-NIEQELRVAVSCFKPRFEKLCTAKRAH 393
[Close]
BLAST of SMED30016946 vs. Ensembl Medaka
Match: ENSORLT00000030244.1 (pep primary_assembly:ASM223467v1:13:28104458:28106771:-1 gene:ENSORLG00000022768.1 transcript:ENSORLT00000030244.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 44.669 bits (104), Expect = 4.370e-6
Identity = 28/79 (35.44%), Postives = 44/79 (55.70%), Query Frame = -1 
Query:    3 FWISVKKEHPRISDKAI-----LTITYSCDKSYSTLVLIKNDKRSCLK-DLDQEPWVALSIIKLNIELLCTLEQSQVLH 221
            FWI V KE+P ++ +A+      T TY C+  +ST+   K   RS L+  L+    V+LS I   ++L+ +  Q+QV H
Sbjct:  391 FWIVVSKEYPLLALRAVKVLLPFTTTYLCESGFSTVATTKTKARSRLRASLEATLRVSLSPIPPRLDLIRSKRQAQVSH 469
[Close]
BLAST of SMED30016946 vs. Planmine SMEST
Match: SMESG000047974.1 (SMESG000047974.1)

HSP 1 Score: 70.8626 bits (172), Expect = 9.113e-16
Identity = 47/118 (39.83%), Postives = 69/118 (58.47%), Query Frame = -1 
Query:    3 TIEFEIPLQSMQRIQQKAL----SLQITSLLYFTEVSSNFFWISVKKEHPRISDKAI-----LTITYSCDKSYSTLVLIKNDKRSCLKDLDQEPWVALSIIKLNIELLCTLEQSQVLH 329
            T+ FE  LQ++   Q++ L    + +   L +   ++ + F +  KKE P IS KAI        TY C++S+S+LV IKN KRSC+K LDQE  V++S I+ NI  LC+  Q Q+ H
Sbjct:  163 TLPFEESLQNLSMKQKEELIDIKNDRTLELQFKDNITISQFRLIAKKEFPTISKKAIDILLPFATTYMCEQSFSSLVTIKNIKRSCIKSLDQELRVSISSIEPNISKLCSQHQGQISH 280
[Close]
BLAST of SMED30016946 vs. Planmine SMEST
Match: SMESG000073188.1 (SMESG000073188.1)

HSP 1 Score: 65.0846 bits (157), Expect = 9.271e-15
Identity = 33/88 (37.50%), Postives = 53/88 (60.23%), Query Frame = -1 
Query:    3 LYFTEVSSNFFWISVKKEHPRISDKAI-----LTITYSCDKSYSTLVLIKNDKRSCLKDLDQEPWVALSIIKLNIELLCTLEQSQVLH 251
            + FT++S+ +FWI V++E+P +S  AI        ++ C+  +STL  IK   R  L DL++E  VA+S I+ NI  +C   Q+Q+ H
Sbjct:   22 MEFTKMSNEYFWIFVQEEYPSLSKTAITILLQFATSFLCELGFSTLTNIKTKNRERLTDLEEEMRVAISYIRPNIGKICKTRQAQISH 109
[Close]
BLAST of SMED30016946 vs. Planmine SMEST
Match: SMESG000005074.1 (SMESG000005074.1)

HSP 1 Score: 51.6026 bits (122), Expect = 5.054e-9
Identity = 30/78 (38.46%), Postives = 45/78 (57.69%), Query Frame = -1 
Query:    3 FWISVKKEHPRISDKAI-----LTITYSCDKSYSTLVLIKNDKRSCLKDLDQEPWVALSIIKLNIELLCTLEQSQVLH 221
            FW+ + KE+P +S KAI      + +  C+  YS+L  IKN KR  L  ++ E  V LS I+  I +LC  +Q+Q+ H
Sbjct:   98 FWMQISKEYPNLSVKAIKILLPFSTSNLCELVYSSLTEIKNKKRERLLYVENELRVCLSTIRPRIMMLCEKQQAQISH 175
[Close]
BLAST of SMED30016946 vs. Planmine SMEST
Match: SMESG000028317.1 (SMESG000028317.1)

HSP 1 Score: 48.521 bits (114), Expect = 1.523e-7
Identity = 28/88 (31.82%), Postives = 49/88 (55.68%), Query Frame = -1 
Query:    3 LYFTEVSSNFFWISVKKEHPRISDKAILTI-----TYSCDKSYSTLVLIKNDKRSCLKDLDQEPWVALSIIKLNIELLCTLEQSQVLH 251
            L F E   + FW+S++ E+P IS+  + T+     TY C+  +S L+ IK   R+ L  ++    ++ S I L  ++LC+++Q Q  H
Sbjct: 1095 LMFQEKDLDEFWLSIQNEYPTISNYVMNTLLPFASTYLCEAGFSALLYIKPQYRTRLTTVENALRISWSQIVLRFDMLCSMKQQQKSH 1182
[Close]
BLAST of SMED30016946 vs. Planmine SMEST
Match: SMESG000009617.1 (SMESG000009617.1)

HSP 1 Score: 43.8986 bits (102), Expect = 3.177e-6
Identity = 29/87 (33.33%), Postives = 48/87 (55.17%), Query Frame = -1 
Query:    6 FTEVSSNFFWISVKKEHPRISDKAI-----LTITYSCDKSYSTLVLI--KNDKRSCLKDLDQEPWVALSIIKLNIELLCTLEQSQVL 245
            F   +   FW+ + KE+P +S KAI      + +Y C+ +YS+L  I  K +++ C++D   E  V  S I+  I +LC  +Q+Q L
Sbjct:   90 FDGTNPTEFWMQISKEYPNLSVKAIKILLPFSTSYLCELAYSSLTEIKKKRERQLCVED---ELRVCSSTIRPRIMMLCEKQQAQTL 173
The following BLAST results are available for this feature:
BLAST of SMED30016946 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016946 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016946 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016946 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016946 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016946 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016946 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016946 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A0L7QQ451.252e-2153.21SCAN domain-containing protein 3 OS=Habropoda labo... [more]
J9M5D57.967e-1141.30DUF4371 domain-containing protein OS=Acyrthosiphon... [more]
A0A2H6NA561.446e-1040.91Uncharacterized protein OS=Micrurus lemniscatus ca... [more]
A0A0L7QW411.850e-1051.28SCAN domain-containing protein 3 (Fragment) OS=Hab... [more]
A0A2H6NA631.925e-1040.91Uncharacterized protein OS=Micrurus lemniscatus ca... [more]
back to top
BLAST of SMED30016946 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016946 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016946 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016946 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30016946 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 4
Match NameE-valueIdentityDescription
ENSORLT00000040389.16.479e-729.55pep primary_assembly:ASM223467v1:19:265767:268275:... [more]
ENSORLT00000035512.16.735e-729.55pep primary_assembly:ASM223467v1:11:22712371:22714... [more]
ENSORLT00000033301.13.091e-629.41pep primary_assembly:ASM223467v1:24:1653567:165476... [more]
ENSORLT00000030244.14.370e-635.44pep primary_assembly:ASM223467v1:13:28104458:28106... [more]
back to top
BLAST of SMED30016946 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000047974.19.113e-1639.83SMESG000047974.1[more]
SMESG000073188.19.271e-1537.50SMESG000073188.1[more]
SMESG000005074.15.054e-938.46SMESG000005074.1[more]
SMESG000028317.11.523e-731.82SMESG000028317.1[more]
SMESG000009617.13.177e-633.33SMESG000009617.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016946 ID=SMED30016946|Name=SMED30016946|organism=Schmidtea mediterranea sexual|type=transcript|length=341bp
TAATGTAATACCTGCGATTGTTCCAATGTACACAAAAGTTCTATATTCAG
CTTAATAATTGACAGCGCAACCCAAGGTTCTTGATCAAGATCTTTTAGGC
ATGACCGCTTATCGTTTTTGATCAATACAAGAGTTGAATAACTTTTATCA
CATGAATATGTTATCGTTAGGATGGCTTTATCGGAGATGCGAGGATGTTC
TTTCTTAACGGATATCCAGAAAAAATTTGATGAAACTTCAGTGAAGTAAA
GTAGTGAAGTAATCTGTAAAGAGAGCGCTTTCTGTTGAATTCGTTGCATT
GATTGCAAAGGGATTTCGAATTCAATCGTATTGTTCCGTAA
back to top

protein sequence of SMED30016946-orf-1

>SMED30016946-orf-1 ID=SMED30016946-orf-1|Name=SMED30016946-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=113bp
LRNNTIEFEIPLQSMQRIQQKALSLQITSLLYFTEVSSNFFWISVKKEHP
RISDKAILTITYSCDKSYSTLVLIKNDKRSCLKDLDQEPWVALSIIKLNI
ELLCTLEQSQVLH
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell