SMED30023907

Overview
NameSMED30023907
Smed IDSMED30023907
Length (bp)998
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




SMED30023907

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30023907SMESG000042253.1 SmedASXL_068812SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30023907SMESG000042253.1 SmedASXL_068812SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
muscle cellSMED30023907SMESG000042253.1 dd_Smed_v4_13413_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30023907SMESG000042253.1 dd_Smed_v4_13413_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30023907 vs. Planmine SMEST
Match: SMESG000042253.1 (SMESG000042253.1)

HSP 1 Score: 138.272 bits (347), Expect = 8.797e-41
Identity = 65/67 (97.01%), Postives = 65/67 (97.01%), Query Frame = -1
Query:  108 VCPNYGVSHKLDDPVLSDIKAPINVMLQRHLIRAPTFERIELQHWDGEHPYSIRRPTGEAGIQRSGY 308
            VCPNYGVSHKLDDPVLSDIKA INVMLQRHLIRAPTFERIELQHWDGEHPYSIRRPTGEA IQRSGY
Sbjct:   18 VCPNYGVSHKLDDPVLSDIKASINVMLQRHLIRAPTFERIELQHWDGEHPYSIRRPTGEAVIQRSGY 84          
BLAST of SMED30023907 vs. Planmine SMEST
Match: SMESG000057533.1 (SMESG000057533.1)

HSP 1 Score: 79.337 bits (194), Expect = 5.720e-16
Identity = 61/188 (32.45%), Postives = 89/188 (47.34%), Query Frame = -1
Query:  141 RDPRTMDGFWNDDSRVTVRFPTDATRRYEIQVI-------------S*QR*ESPDGQDENELPSVEIKRETGRNPAREARQHLGQAERSERQNQMENQHSTELTQLDKC*HRHRMHAQYRRVC-----------PNYGVSHKLDDPVLSDIKAPINVMLQRHLIRAPTFERIELQHWDGEHPYSIRRP 632
            RDP    G W+D+SRVT+  P+ +  RY  QV+             S  R  S    +E ELPS+ IKRE G NPAREARQ    A  + +  ++E ++  +         R R+    R +            P YGVS +LDDP L+ + AP  +++   L+++ T       H  G+H Y+ R P
Sbjct: 1640 RDPH---GSWSDNSRVTLEIPSASAARYR-QVLWDNGYLLSTYGDSSWPR-RSEYQAEEIELPSIAIKREPGHNPAREARQRAKYA--AMKMEELERKYHRKAVSA-----RQRLAQVNRDIASGSIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVQS-TLRNQLGSHQTGDHTYASRHP 1814          
BLAST of SMED30023907 vs. Planmine SMEST
Match: SMESG000044971.1 (SMESG000044971.1)

HSP 1 Score: 77.411 bits (189), Expect = 2.837e-15
Identity = 63/195 (32.31%), Postives = 94/195 (48.21%), Query Frame = -1
Query:  141 PFLDGTRDPRTMDGFWNDDSRVTVRFPTDATRRYEIQVI-------------S*QR*ESPDGQDENELPSVEIKRETGRNPAREARQHLGQAER-SERQNQMENQHSTELTQLDKC*HRHRMHAQYRRVC-----------PNYGVSHKLDDPVLSDIKAPINVMLQRHLIRAPTFERIELQHWDGEHPYSIRRP 650
            P  D  RDP    G W+D+SRVT++ P+ +  RY  QV+             S  R  S    +E ELPS+ IKRE G NPAREARQ   +AE  + +  ++E ++  +         R R+    R +            P YGVS +LDDP L  + AP  +++   L+++    R+  +   G+H Y+ R P
Sbjct: 1124 PSNDNRRDPH---GNWSDNSRVTLQIPSASAARYR-QVLWDNGYLLSTYGDSSWPR-RSEYQAEEIELPSIAIKREPGHNPAREARQ---RAEYVAMKMEELERKYHRKAVLA-----RQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRLGSRQ-TGDHTYASRHP 1304          
BLAST of SMED30023907 vs. Planmine SMEST
Match: SMESG000004883.1 (SMESG000004883.1)

HSP 1 Score: 72.0182 bits (175), Expect = 3.163e-14
Identity = 62/187 (33.16%), Postives = 87/187 (46.52%), Query Frame = -1
Query:  141 RDPRTMDGFWNDDSRVTVRFPTDATRRYEIQVI------------S*QR*ESPDGQDENELPSVEIKRETGRNPAREARQHLGQAERSERQNQMENQHSTELTQLDKC*HRHRMHAQYRRVC-----------PNYGVSHKLDDPVLSDIKAPINVMLQRHLIRAPTFERIELQHWDGEHPYSIRRP 632
            RDP    G W+D+SRVT++ P+ +  RY  QV+            S     S    +E ELPSV IKRE G NPAREARQ    A   + + + + Q    L        R R+    R +            P YGVS +LDDP L+ + AP  +++   L+R+    R+      G+H Y+ R P
Sbjct:   83 RDPH---GSWSDNSRVTLQIPSASAARYR-QVLWDNGYLLSTYGDSSWPRRSEYQAEEVELPSVAIKREPGHNPAREARQRAEYAAMKKEELERKYQRKAVLA-------RQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVRSTLRNRLGSSQ-TGDHTYASRHP 257          
BLAST of SMED30023907 vs. Planmine SMEST
Match: SMESG000014849.1 (SMESG000014849.1)

HSP 1 Score: 73.1738 bits (178), Expect = 6.121e-14
Identity = 54/166 (32.53%), Postives = 81/166 (48.80%), Query Frame = -1
Query:  207 RDPRTMDGFWNDDSRVTVRFPTDATRRYEIQVI-------------S*QR*ESPDGQDENELPSVEIKRETGRNPAREARQHLGQAERSERQNQMENQHSTELTQLDKC*HRHRMHAQYRRVC-----------PNYGVSHKLDDPVLSDIKAPINVMLQRHLIRA 632
            RDP    G W+D+SRVT++ P+ +  RY  QV+             S  R  S    +E ELPS+ IKRE G NPAREARQ    A  + +  ++E ++  +         R R+    R +            P YGVS +LDDP L+ + AP  +++   L+++
Sbjct:  877 RDPH---GNWSDNSRVTLQIPSASAARYR-QVLWDNGYLLSTYGDSSWPR-RSEYRAEEIELPSIAIKREPGHNPAREARQRAEYA--AMKMEELERKYHRKAVLA-----RQRLAQVNRDIASGVIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVQS 1030          
The following BLAST results are available for this feature:
BLAST of SMED30023907 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 SMED30023907 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 SMED30023907 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 SMED30023907 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 SMED30023907 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 SMED30023907 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 SMED30023907 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 SMED30023907 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 SMED30023907 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 SMED30023907 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 SMED30023907 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 SMED30023907 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 SMED30023907 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 SMED30023907 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000042253.18.797e-4197.01SMESG000042253.1[more]
SMESG000057533.15.720e-1632.45SMESG000057533.1[more]
SMESG000044971.12.837e-1532.31SMESG000044971.1[more]
SMESG000004883.13.163e-1433.16SMESG000004883.1[more]
SMESG000014849.16.121e-1432.53SMESG000014849.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023907 ID=SMED30023907|Name=SMED30023907|organism=Schmidtea mediterranea sexual|type=transcript|length=998bp
GGCCGCCCTTTTTTTTTTTTTTTTTTTTTTTTCTTGAAAATATAATTTAT
TCAACTAATTACAACGAATTCCATGTCTTCCATTCAACTACGTCTACTGT
TATTTCGATAGCCAGATCGTTGGATCCCCGCCTCTCCAGTTGGCCGTCGT
ATAGAATATGGGTGTTCTCCGTCCCAGTGTTGGAGTTCAATTCTCTCAAA
AGTTGGTGCCCGAATGAGATGCCGTTGTAGCATCACATTGATTGGCGCTT
TTATATCTGATAACACTGGGTCGTCCAGTTTATGTGAGACTCCATAGTTT
GGACATACCCGTCGGTACTGGGCATGCATCCTATGTCGATGTCAGCATTT
ATCCAATTGAGTTAGTTCCGTGCTATGTTGATTTTCCATTTGATTTTGCC
GCTCAGATCTTTCAGCTTGGCCAAGGTGTTGACGAGCTTCCCGCGCCGGG
TTTCGACCCGTTTCCCGTTTTATCTCCACACTTGGTAACTCATTCTCATC
CTGGCCATCCGGACTCTCCTACCGTTGCTAAGATATAACCTGAATCTCAT
AACGCCTGGTGGCATCGGTCGGAAATCTAACCGTAACTCTGGAGTCATCG
TTCCAGAATCCATCCATCGTTCGTGGGTCTCTCGTGCCATCTAAAAATGG
AAATATAATAACGCTACTATCATACCCAACGAGAGATAATAATGGCACTA
GAGGATAGACATCATTGTTATAACCACACTCCTGAGGCTGAGTAATACAT
TAATTGCTAAAATGTGGCAGATCAACAATATATTATTGCAATGATCTCGG
TGACTTTCCTTTGGGACATTTATTTAACTTCATACAATATTGAAGATTCC
TGTTATTCCTCACCTTGCTGATTAGAACACTCGCCCCTCACTACATTGGG
TCCTCTTCTCGTTGGATCCTCGTCCATTAGGCATATTTCGCAGGTGTGTC
ATCTCTAATCACACTCTCGACATATGAGTGTCGTCAACTTGGGTAGAG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0002109X1 cell
PLANA:0002111X2 cell
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..16
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..26