SMED30005384

Overview
NameSMED30005384
Smed IDSMED30005384
Length (bp)411
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



SMED30005384

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
parenchymaSMED30005384 dd_Smed_v4_45827_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30005384 vs. Planmine SMEST
Match: SMESG000028853.1 (SMESG000028853.1)

HSP 1 Score: 125.561 bits (314), Expect = 2.115e-36
Identity = 76/136 (55.88%), Postives = 92/136 (67.65%), Query Frame = 3 
Query:    3 ERRRADHALLMAHLEQAKKVVVNPVPAESINTNNISFPAENSHFVRAPVVQDSMALNIPVSVDQFNLNFPEKFKLAIAAGQRKKRAPEIIHLXXXXXXXXXXXXXYTNVVTRQAFKSDISRLRGSPKRRYLPGDID 410
            E+R+A+ ALL+A LEQAK+++ NP P+ S   NN S   EN H V A   +D MAL I V+VDQ N+NF +KFK AIAAGQRK    EII LS  P    P SSPYTNV+T +  K D+ +LR SPKRRY P DID
Sbjct:  120 EQRQAEQALLIAQLEQAKEIISNPAPSTSAIENNRSPGMENLHLVNALATRDDMALIIRVTVDQLNVNFSDKFKFAIAAGQRKS---EIIDLSGLPGLITPASSPYTNVLTGRTTKEDVVKLRLSPKRRYFPVDID 252
[Close]
BLAST of SMED30005384 vs. Planmine SMEST
Match: SMESG000047477.1 (SMESG000047477.1)

HSP 1 Score: 119.013 bits (297), Expect = 1.562e-35
Identity = 69/112 (61.61%), Postives = 81/112 (72.32%), Query Frame = 3 
Query:   33 MAHLEQAKKVVVNPVPAESINTNNISFPAENSHFVRAPVVQDSMALNIPVSVDQFNLNFPEKFKLAIAAGQRKKRAPEIIHLXXXXXXXXXXXXXYTNVVTRQAFKSDISRL 368
            MAHLEQAK+V+ NP P  S   + IS    NSH + APV  D MALNI V+VDQ NLNF EKFKLAIAAGQRKKR PEII  S+ P  S  T+SPYTN+VT +A K D+++L
Sbjct:    1 MAHLEQAKEVIGNPAPTTSTTESIISPVTGNSHHINAPVAPDDMALNIRVTVDQLNLNFLEKFKLAIAAGQRKKRVPEIIDPSSLPGLSALTASPYTNLVTGRATKEDVTKL 112
[Close]
BLAST of SMED30005384 vs. Planmine SMEST
Match: SMESG000059356.1 (SMESG000059356.1)

HSP 1 Score: 88.1965 bits (217), Expect = 1.015e-23
Identity = 43/89 (48.31%), Postives = 61/89 (68.54%), Query Frame = 3 
Query:  144 PVVQDSMALNIPVSVDQFNLNFPEKFKLAIAAGQRKKRAPEIIHLXXXXXXXXXXXXXYTNVVTRQAFKSDISRLRGSPKRRYLPGDID 410
            P   D M LNI +++DQ N+NFPE+FKL IA GQR+++ PE+I LS     ++P+   YT + T++  KS + +LR +PKRRY P DID
Sbjct:    2 PADHDDMVLNIRLTMDQSNVNFPERFKLVIAEGQRRQKKPEVIDLSELLELTIPSVRSYTKLATKRIVKSGMDKLRQTPKRRYFPVDID 90
[Close]
BLAST of SMED30005384 vs. Planmine SMEST
Match: SMESG000054550.1 (SMESG000054550.1)

HSP 1 Score: 85.5001 bits (210), Expect = 6.524e-22
Identity = 52/127 (40.94%), Postives = 76/127 (59.84%), Query Frame = 3 
Query:   33 MAHLEQAKKVVVNPVPAES-INTNNISFPAENSHFVRAPVVQDSMALNIPVSVDQFNLNFPEKFKLAIAAGQRKKRAPEIIHLXXXXXXXXXXXXXYTNVVTRQAFKSDISRLRGSPKRRYLPGDID 410
            +AHLE+A   V  P+P+ S I  + +S   E+  F   P   D MALNI +++DQ N+NFPE+FKLAIA GQ +++  E+I L   P  ++  +  Y+ V T    K  + + R + KRRYLP D+D
Sbjct:   27 LAHLEKANVNVPAPIPSISPIEHHQVSR-EEDPCFATMPA-HDDMALNIRLTMDQLNVNFPERFKLAIATGQWRQKKLEVIDLRELPGLTIALARSYSKVATESILKKGMEQPRQTSKRRYLPVDMD 151
[Close]
BLAST of SMED30005384 vs. Planmine SMEST
Match: SMESG000019166.1 (SMESG000019166.1)

HSP 1 Score: 58.151 bits (139), Expect = 3.018e-12
Identity = 29/47 (61.70%), Postives = 32/47 (68.09%), Query Frame = -3 
Query:  155 ETGELLRCIISGARFFRCPAAMANLNFSGKFRLNWSTDTGIFRAILS 295
              G  LR I SG R  RCPAAM NLNFSGKF+ +WST   +FRAI S
Sbjct:    3 NPGNPLRSITSGMRCLRCPAAMTNLNFSGKFKFSWSTVNRMFRAISS 49
The following BLAST results are available for this feature:
BLAST of SMED30005384 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 SMED30005384 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 SMED30005384 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 SMED30005384 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 SMED30005384 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 SMED30005384 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 SMED30005384 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 SMED30005384 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30005384 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 SMED30005384 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 SMED30005384 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 SMED30005384 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 SMED30005384 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30005384 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000028853.12.115e-3655.88SMESG000028853.1[more]
SMESG000047477.11.562e-3561.61SMESG000047477.1[more]
SMESG000059356.11.015e-2348.31SMESG000059356.1[more]
SMESG000054550.16.524e-2240.94SMESG000054550.1[more]
SMESG000019166.13.018e-1261.70SMESG000019166.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005384 ID=SMED30005384|Name=SMED30005384|organism=Schmidtea mediterranea sexual|type=transcript|length=411bp
TCGAACGACGGCGGGCTGACCACGCTCTATTAATGGCTCATCTGGAACAG
GCGAAAAAAGTAGTCGTGAACCCCGTTCCAGCAGAATCCATCAACACAAA
TAATATTTCATTCCCAGCGGAAAATTCTCACTTCGTAAGGGCACCTGTTG
TTCAAGATAGTATGGCCCTGAATATTCCAGTGTCGGTCGACCAGTTCAAT
CTGAATTTCCCGGAGAAATTCAAGTTAGCCATAGCTGCCGGACAGCGAAA
GAAGCGAGCACCCGAAATTATACATCTAAGCAACTCCCCCGTCTCATCAA
TGCCAACATCCAGTCCCTATACCAATGTGGTGACAAGACAAGCCTTCAAG
TCTGACATCTCGAGATTGAGAGGATCACCCAAACGCCGCTACCTTCCGGG
AGATATTGACG
back to top

protein sequence of SMED30005384-orf-1

>SMED30005384-orf-1 ID=SMED30005384-orf-1|Name=SMED30005384-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=136bp
ERRRADHALLMAHLEQAKKVVVNPVPAESINTNNISFPAENSHFVRAPVV
QDSMALNIPVSVDQFNLNFPEKFKLAIAAGQRKKRAPEIIHLSNSPVSSM
PTSSPYTNVVTRQAFKSDISRLRGSPKRRYLPGDID
back to top