SMED30007770

Overview
NameSMED30007770
Smed IDSMED30007770
Length (bp)615
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



SMED30007770

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
Category 3 cellSMED30007770SMESG000059904.1 SMESG000042945.1 SMESG000007620.1 SMESG000072638.1 SMESG000039380.1 SMESG000042352.1 SMESG000028417.1 dd_Smed_v6_10138_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30007770 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000816:22588..23173 -2886
v31.000022:59474..60090 -2448
v31.000880:45149..45747 -2428
v31.010736:992..1600 +2119
v31.006344:1275..1884 -2070
v31.008283:20235..20844 +2052
v31.002339:24552..25156 +2004
v31.001205:14917..15537 +1987
v31.000565:22642..23260 -1659
Homology
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BLAST of SMED30007770 vs. Planmine SMEST
Match: SMESG000016136.1 (SMESG000016136.1)

HSP 1 Score: 245.358 bits (625), Expect = 1.187e-78
Identity = 126/167 (75.45%), Postives = 135/167 (80.84%), Query Frame = -3 
Query:   38 SFVRNFVNHLLVSNQEN----PQMNSIYRIPKLPQSKVNAATQPNVQNDDLTHLSCQQSYNKLFAEHERTLGTLFAPEVVKALHKHIHRLTRCREDLIAENRAQRIVINDQSAVLKASFTETELTKRLAGRDLAVKLNLIPANHIPEKTAIGPSQTPKHVRNTIPAK 526
            S  RN +NH L SN E      +MNS YRIP L Q K NA TQPNVQN DLTHLS QQSYNKL AEHERTLGT FAPEVVKALHK IH LTRC++DLIAENRAQRIVINDQSA+L ASFTETELTKRLAGRDLAVKLNLIP NH+P+KT IGPSQTPK  +   P+K
Sbjct:  318 SLFRNSINHSLASNPEILKHLSEMNSSYRIPNLSQPKANAVTQPNVQNGDLTHLSFQQSYNKLLAEHERTLGTWFAPEVVKALHKEIHPLTRCQDDLIAENRAQRIVINDQSAILIASFTETELTKRLAGRDLAVKLNLIPTNHLPKKTTIGPSQTPKTSKKHNPSK 484
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BLAST of SMED30007770 vs. Planmine SMEST
Match: SMESG000077490.1 (SMESG000077490.1)

HSP 1 Score: 220.705 bits (561), Expect = 1.493e-73
Identity = 109/144 (75.69%), Postives = 119/144 (82.64%), Query Frame = -3 
Query:   38 MNSIYRIPKLPQSKVNAATQPNVQNDDLTHLSCQQSYNKLFAEHERTLGTLFAPEVVKALHKHIHRLTRCREDLIAENRAQRIVINDQSAVLKASFTETELTKRLAGRDLAVKLNLIPANHIPEKTAIGPSQTPKHVRNTIPAK 469
            M S Y+IPKL  +K   +TQPN QN+ L H+ CQQ YNKL AEHERTLGT FAPEVVKALHK IHRLTRCREDLIAENRAQRIVINDQSAVL ASFTETELTKRLA RDLAVKLNLIPAN +PE+  IGP+QTPK  +   P+K
Sbjct:    1 MQSGYKIPKLSPAKPKLSTQPNTQNEQLDHIPCQQRYNKLLAEHERTLGTWFAPEVVKALHKQIHRLTRCREDLIAENRAQRIVINDQSAVLIASFTETELTKRLASRDLAVKLNLIPANDLPERNQIGPAQTPKTSKKHNPSK 144
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BLAST of SMED30007770 vs. Planmine SMEST
Match: SMESG000024721.1 (SMESG000024721.1)

HSP 1 Score: 195.282 bits (495), Expect = 8.742e-64
Identity = 93/144 (64.58%), Postives = 112/144 (77.78%), Query Frame = -3 
Query:   38 MNSIYRIPKLPQSKVNAATQPNVQNDDLTHLSCQQSYNKLFAEHERTLGTLFAPEVVKALHKHIHRLTRCREDLIAENRAQRIVINDQSAVLKASFTETELTKRLAGRDLAVKLNLIPANHIPEKTAIGPSQTPKHVRNTIPAK 469
            M S Y+IPK+   K   + Q   Q D L+H++CQQ Y+KLFAEHERTLGT FAPEVVKA+H+ IHRLTRCR+DLI+ENRAQRI+INDQSAVL  SFTE ELTKR+A RDLAV+LNLIP  HI EK  + P++TPK  +   P+K
Sbjct:    1 MQSGYKIPKISTPKSPHSVQSTTQKDSLSHITCQQKYDKLFAEHERTLGTWFAPEVVKAIHQQIHRLTRCRDDLISENRAQRIIINDQSAVLIVSFTEAELTKRIASRDLAVQLNLIPPRHILEKLEVCPAKTPKTSKRRNPSK 144
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BLAST of SMED30007770 vs. Planmine SMEST
Match: SMESG000028417.1 (SMESG000028417.1)

HSP 1 Score: 193.356 bits (490), Expect = 1.039e-61
Identity = 95/144 (65.97%), Postives = 109/144 (75.69%), Query Frame = -3 
Query:   38 MNSIYRIPKLPQSKVNAATQPNVQNDDLTHLSCQQSYNKLFAEHERTLGTLFAPEVVKALHKHIHRLTRCREDLIAENRAQRIVINDQSAVLKASFTETELTKRLAGRDLAVKLNLIPANHIPEKTAIGPSQTPKHVRNTIPAK 469
            M   Y+IPKL       +++P+  N  + H SCQQ YNKLFAEHERTLGT FAPE VK L   IHRL+RCREDLIAENRAQRI+INDQSA L ASFTE ELTKRLAGRDL VKLNLIP NH+PE+T  GP+QTP+  +   P+K
Sbjct:    1 MQPGYKIPKL-------SSKPSAINTQMDHSSCQQKYNKLFAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSADLVASFTEVELTKRLAGRDLVVKLNLIPVNHLPEETQAGPAQTPRTSKKHHPSK 137
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BLAST of SMED30007770 vs. Planmine SMEST
Match: SMESG000003594.1 (SMESG000003594.1)

HSP 1 Score: 187.578 bits (475), Expect = 2.556e-59
Identity = 90/144 (62.50%), Postives = 105/144 (72.92%), Query Frame = -3 
Query:   38 MNSIYRIPKLPQSKVNAATQPNVQNDDLTHLSCQQSYNKLFAEHERTLGTLFAPEVVKALHKHIHRLTRCREDLIAENRAQRIVINDQSAVLKASFTETELTKRLAGRDLAVKLNLIPANHIPEKTAIGPSQTPKHVRNTIPAK 469
            M   Y+IPKL   +   +    + NDD +H  C++ Y++L  EHERTL T FAPE VKALHK IHRLTRCREDLIAENRAQRIVIN+QSAVL ASF ETEL KRLAGRDLA+KLN+IPA H+PE    GP Q PK  +   P+K
Sbjct:    1 MQPGYKIPKLTSQRSEKSNLSILNNDDKSHQECRRKYDQLVVEHERTLSTWFAPEAVKALHKQIHRLTRCREDLIAENRAQRIVINNQSAVLTASFNETELKKRLAGRDLAIKLNIIPAEHVPETATTGPPQMPKTSKKHNPSK 144
The following BLAST results are available for this feature:
BLAST of SMED30007770 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 SMED30007770 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 SMED30007770 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 SMED30007770 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 SMED30007770 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 SMED30007770 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 SMED30007770 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 SMED30007770 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 SMED30007770 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 SMED30007770 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 SMED30007770 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 SMED30007770 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 SMED30007770 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 SMED30007770 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000016136.11.187e-7875.45SMESG000016136.1[more]
SMESG000077490.11.493e-7375.69SMESG000077490.1[more]
SMESG000024721.18.742e-6464.58SMESG000024721.1[more]
SMESG000028417.11.039e-6165.97SMESG000028417.1[more]
SMESG000003594.12.556e-5962.50SMESG000003594.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007770 ID=SMED30007770|Name=SMED30007770|organism=Schmidtea mediterranea sexual|type=transcript|length=615bp
GGCTTATTCAGCTCGGCGTCGTTCACGGCAACGCCGGTTTTGCTGGGATT
GTGTTTCTTACATGTTTTGGGGTCTGCGAAGGGCCAATTGCGGTTTTTTC
CGGAATGTGATTAGCGGGGATTAGGTTCAGTTTTACTGCCAGGTCACGGC
CGGCTAATCGCTTGGTTAACTCGGTTTCAGTGAACGATGCTTTCAGTACA
GCGCTCTGATCGTTGATGACGATCCTTTGAGCCCGATTTTCGGCGATCAG
ATCTTCTCGGCATCTAGTCAGTCGATGTATATGCTTGTGTAACGCCTTCA
CTACTTCGGGAGCGAACAACGTACCGAGCGTGCGTTCGTGCTCCGCGAAC
AATTTATTATAACTTTGTTGACAGGACAAGTGAGTGAGATCGTCGTTCTG
GACGTTGGGTTGGGTAGCTGCATTTACCTTAGACTGCGGTAATTTTGGAA
TGCGATAGATGGAATTCATTTGAGGATTTTCTTGATTGGAGACGAGAAGG
TGATTTACAAAGTTTCGGACAAAAGAAAACTAAATGGGGAAAAATCTCTT
ATTATGAATTTATATAATGATAATAATAAATATAATAAAGAATAATAATT
AATTAAAATTTTCAA
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protein sequence of SMED30007770-orf-1

>SMED30007770-orf-1 ID=SMED30007770-orf-1|Name=SMED30007770-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=149bp
MNSIYRIPKLPQSKVNAATQPNVQNDDLTHLSCQQSYNKLFAEHERTLGT
LFAPEVVKALHKHIHRLTRCREDLIAENRAQRIVINDQSAVLKASFTETE
LTKRLAGRDLAVKLNLIPANHIPEKTAIGPSQTPKHVRNTIPAKPALP*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell