SMED30014801

Overview
NameSMED30014801
Smed IDSMED30014801
Length (bp)754
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




SMED30014801

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
cilated neuronSMED30014801h1SMcG0008800 dd_Smed_v4_48558_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
tail regionSMED30014801h1SMcG0008800 dd_Smed_v6_48558_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
SMED30014801 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.011082:2386..3126 -3642
Homology
BLAST of SMED30014801 vs. TrEMBL
Match: C3YAE7 (Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_72548 PE=4 SV=1)

HSP 1 Score: 67.781 bits (164), Expect = 2.726e-9
Identity = 45/154 (29.22%), Postives = 74/154 (48.05%), Query Frame = 2
Query:  119 LFRVVSGSGINAYNFYMNMEKQMQSSTFIDNSSDKSGNFRSILLDEWMFIRPISINITLRSEDHHLRGWLSFRVRKSDSSVSWFDKKNLLDCFPWESDKISKDDYRYFSLRGDNTFDERSFLIYLSYIGCSNDRGILAIFQKRDTCKYGNRKNS 580
            +F++V+G+  ++Y  + +          +  S     ++RS  LD W  +    + +TL ++  H R  + F     D   +WF K  LL   PW   K +    ++FS+RGDN ++ R F I+ SY GC+NDRG L +      C +  R  S
Sbjct:  290 VFKIVAGAPGSSYGIWKSRGGHGDQ---VHPSLTGHSHYRSPDLDRWSSLHVTKVKVTLVAQHQHTRD-IIFNAHGCDMD-NWFTKDRLLSS-PWTDLKTAPT--KFFSIRGDNQYNRR-FFIHRSYGGCANDRGWLIVLDPGAECPWEKRVKS 434          
BLAST of SMED30014801 vs. TrEMBL
Match: A0A2B4SQ68 (Uncharacterized protein OS=Stylophora pistillata OX=50429 GN=AWC38_SpisGene4451 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 2.789e-6
Identity = 45/171 (26.32%), Postives = 78/171 (45.61%), Query Frame = 2
Query:  119 LFRVVSGSGINAYNFYMNMEKQMQSSTFIDNSSDKSGNFRSILLDEWMFIRPISINITLRSEDHHLRGWLSFRVRKSDSSVSWFDKKNLLDCFPWESDKISKDDYRYFSLRGDNTFDERSFLIYLSYIGCSNDRGILAIFQKRDTCKYGNRKNSYPFIAMAVSNGTSGNWN 631
            +F+ VSG+  NA+N Y + E   ++     + + K+G+++S ++  W         + L   +  ++  L F  + SD  ++WF    L + +PW    +   +   FS++G      R+F I  SY GC ND G +AI      C + NR      + +     T  NWN
Sbjct:  120 IFKAVSGAKENAFNAYNSGETLAENDMSALDVTTKTGDYKSRIILNWAEFSISEAKVVLYEGNSAVKE-LFFNAQGSD-KLNWFSNDKLKEPYPWTD--VKNGEQNSFSIQG---LSGRNFFINKSYGGCPNDNGWMAITSTH--CSWENRFGEEKNVVLYSKLETYTNWN 281          
BLAST of SMED30014801 vs. Planmine SMEST
Match: SMESG000076329.1 (SMESG000076329.1)

HSP 1 Score: 464.922 bits (1195), Expect = 3.925e-168
Identity = 225/228 (98.68%), Postives = 226/228 (99.12%), Query Frame = 2
Query:   17 KYFIFFKNLCYMPKSAASGNHSKQIYKKIFNEITLFRVVSGSGINAYNFYMNMEKQMQSSTFIDNSSDKSGNFRSILLDEWMFIRPISINITLRSEDHHLRGWLSFRVRKSDSSVSWFDKKNLLDCFPWESDKISKDDYRYFSLRGDNTFDERSFLIYLSYIGCSNDRGILAIFQKRDTCKYGNRKNSYPFIAMAVSNGTSGNWNLDSLPLMSLELIGIYDSKIHFYV 700
            KYFIFFKNLCYMPKSAASGNHSKQIYKKIFNEITL RVVSGSGINAYNFYMNMEKQMQS TFIDNSSDKSGNFRSILLDEWMFIRPISINITLRSEDHHLRGWLSFRVRKSDSSVSWFDKKNLLDCFPWESDKISKDDYRYFSLRGDNTFDERSFLIYLSYIGCSNDRGILAIFQKRDTC+YGNRKNSYPFIAMAVSNGTSGNWNLDSLPLMSLELIGIYDSKIHFYV
Sbjct:   31 KYFIFFKNLCYMPKSAASGNHSKQIYKKIFNEITLLRVVSGSGINAYNFYMNMEKQMQSPTFIDNSSDKSGNFRSILLDEWMFIRPISINITLRSEDHHLRGWLSFRVRKSDSSVSWFDKKNLLDCFPWESDKISKDDYRYFSLRGDNTFDERSFLIYLSYIGCSNDRGILAIFQKRDTCEYGNRKNSYPFIAMAVSNGTSGNWNLDSLPLMSLELIGIYDSKIHFYV 258          
BLAST of SMED30014801 vs. Planmine SMEST
Match: SMESG000034452.1 (SMESG000034452.1)

HSP 1 Score: 173.326 bits (438), Expect = 1.683e-53
Identity = 92/230 (40.00%), Postives = 132/230 (57.39%), Query Frame = 2
Query:   20 YFIFFKNLCYMPKSAASG--NHSKQIYKKIFNEITLFRVVSGSGINAYNFYMNMEKQMQSSTFI-DNSSDKSGNFRSILLDEWMFIRPISINITLRSEDHHLRGWLSFRVRKSDSSVSWFDKKNLLDCFPWESDKISKDDYRYFSLRGD-NTFDERSFLIYLSYIGCSNDRGILAIFQKRDTCKYGNRKNSYPFIAMAVSNGTSGNWNLDSLPLMSLELIGIYDSKIHFY 697
            Y +     CY P++  S     + Q Y +I N +T+FR+++GS +N   F+  M+  +    F+ D       NFRS +LDEW  I+PI +N+T++  +  + GWL F+V ++DS +SWF K NLL+ FPW+ DK+  ++YR+FS+ GD N   +R+F I + Y GC ND GIL IF   D C Y      YP I   ++NG  G WN  SL   SLE+I  YD  I  Y
Sbjct:   17 YLVIANETCYHPQNMTSQPFQTNSQFYVRIPNLLTVFRILTGSEVNPVTFF-TMQMVLNDIMFVEDKRRINPSNFRSPILDEWNNIKPIFMNVTIKDSNDLVVGWLFFKVGQADSLLSWFTKANLLNSFPWDIDKLLSNNYRFFSVIGDINLNKQRNFFISILYYGCPNDTGILCIFGLSDPCSYSQSTAGYPLIKYVINNGNGGLWNTSSLA-KSLEIIATYDQLIAIY 244          
BLAST of SMED30014801 vs. Planmine SMEST
Match: SMESG000034404.1 (SMESG000034404.1)

HSP 1 Score: 166.777 bits (421), Expect = 1.266e-50
Identity = 93/232 (40.09%), Postives = 129/232 (55.60%), Query Frame = 2
Query:   20 YFIFFKNLCYMPKSAASG--NHSKQIYKKIFNEITLFRVVSGSGINAYNFYMNMEKQMQSSTFI---DNSSDKSGNFRSILLDEWMFIRPISINITLRSEDHHLRGWLSFRVRKSDSSVSWFDKKNLLDCFPWESDKISKDDYRYFSLRGDNTFD-ERSFLIYLSYIGCSNDRGILAIFQKRDTCKYGNRKNSYPFIAMAVSNGTSGNWNLDSLPLMSLELIGIYDSKIHFY 697
            Y +     CY P++  S     + QIY +I N +T+FR+++GSG+N   F+    KQM  S  +   D       NFRS +LDEW  I+PI +N+T++  +  + GWL F+V ++DS +SWF K NLL  FPW+ DK+    Y  FS+ GD   + +R+F I + Y GCS D GIL IF   D C YG     YP I  A++ G  G W   +L   SLE+I  YD  I  Y
Sbjct:   36 YMVIANETCYHPQNMTSQPFQTNSQIYARIPNLLTVFRILTGSGVNPVTFF---TKQMVLSDVMFAEDKRRINPSNFRSPILDEWNNIKPIFMNVTIKDSNDLVVGWLFFKVGQADSLLSWFTKANLLKSFPWDIDKLLSSYYPVFSVIGDTQPNVQRNFFISILYNGCSYDSGILCIFGLSDPCSYGQSTAGYPLIRYAINYGNGGPWTTSNL-AKSLEIIATYDQLIAIY 263          
BLAST of SMED30014801 vs. Planmine SMEST
Match: SMESG000032522.1 (SMESG000032522.1)

HSP 1 Score: 166.777 bits (421), Expect = 1.453e-50
Identity = 84/237 (35.44%), Postives = 131/237 (55.27%), Query Frame = 2
Query:   20 YFIFFKNLCYMPKSAASGNHSKQI---YKKIFNEITLFRVVSGSGINAYNFYM-----NMEKQMQSSTFIDNSSDKSGNFRSILLDEWMFIRPISINITLRSEDHHLRGWLSFRVRKSDSSVSWFDKKNLLDCFPWESDKISKDDYRYFSLRGDNTFDE---RSFLIYLSYIGCSNDRGILAIFQKRDTCKYGNRKNSYPFIAMAVSNGTSGNWNLDSLPLMSLELIGIYDSKIHFY 697
            YF+  K +C  P+  AS +    +   ++ +   +T+FR+V+GSG+++  F+          Q ++   ID   + S NFRS++LDEW  I+PI++N+T++  +     WL F+V K+D+ +SWF K+NLL   PW    +  + Y YF++ G    D+   R F I LSY GC ND G+  +F + D C +G     YP I  A+ NG   NWN  S    S+E++  YD  I+FY
Sbjct:   37 YFVIPKPICNPPQEVASQSFQMNLQIRFESLPKPMTVFRLVTGSGVSSLKFFSEKNGGTQAGQSETKYVIDKKRNYSQNFRSLILDEWNSIKPINMNVTIKDSNDFTVAWLFFKVDKTDTLISWFKKENLLSSHPWNIKMLLGNLYNYFNISGHAPPDQPVIRLFFINLSYGGCPNDVGVFCVFDRADPCPFGKSTCGYPLIKYAIHNGNGANWNHYSTAAKSMEIVATYDEMIYFY 273          
BLAST of SMED30014801 vs. Planmine SMEST
Match: SMESG000076260.1 (SMESG000076260.1)

HSP 1 Score: 162.54 bits (410), Expect = 7.642e-49
Identity = 84/235 (35.74%), Postives = 132/235 (56.17%), Query Frame = 2
Query:   20 YFIFFKNLCYMPKSAASGNHSKQI---YKKIFNEITLFRVVSGSGINAYNFYM--NMEKQMQSS---TFIDNSSDKSGNFRSILLDEWMFIRPISINITLRSEDHHLRGWLSFRVRKSDSSVSWFDKKNLLDCFPWESDKISKDDYRYFSLRGDNTFD-ERSFLIYLSYIGCSNDRGILAIFQKRDTCKYGNRKNSYPFIAMAVSNGTSGNWNLDSLPLMSLELIGIYDSKIHFY 697
            YFI     C+ P+S +S +   ++   ++K+ N++ + R+VSGSG+N   F +  N+  Q+ +S   + +D  S+ S NFRSILLDEW  ++P+ +N+T++      + WL F+V  +DS  SWF K NLL  FPW  + + +++Y YF + G  T   +R+F I + Y  C  D G+L +F   D C YG   + YP I   + NG  GNW   S+   ++E+  IYD     Y
Sbjct:   39 YFIMLNQTCFNPQSTSSLSFQIKLQFMFQKLPNQLVVLRIVSGSGVNPPYFLIGQNISSQIDTSDIFSVVDKMSNYSNNFRSILLDEWSNVKPMFMNVTIKDSSAITKAWLFFKVDPNDSLSSWFRKTNLLKSFPWNVEILLRNNYNYFDITGHTTDQLKRNFFINIYYNYCPGDVGVLCVFGIADGCSYGQTNSGYPLIKYVIKNGNGGNWTSYSVTAQAMEITAIYDDSTLIY 273          
The following BLAST results are available for this feature:
BLAST of SMED30014801 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 SMED30014801 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 SMED30014801 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 SMED30014801 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 SMED30014801 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 SMED30014801 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 SMED30014801 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 SMED30014801 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
C3YAE72.726e-929.22Uncharacterized protein OS=Branchiostoma floridae ... [more]
A0A2B4SQ682.789e-626.32Uncharacterized protein OS=Stylophora pistillata O... [more]
back to top
BLAST of SMED30014801 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 SMED30014801 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 SMED30014801 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 SMED30014801 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 SMED30014801 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 SMED30014801 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000076329.13.925e-16898.68SMESG000076329.1[more]
SMESG000034452.11.683e-5340.00SMESG000034452.1[more]
SMESG000034404.11.266e-5040.09SMESG000034404.1[more]
SMESG000032522.11.453e-5035.44SMESG000032522.1[more]
SMESG000076260.17.642e-4935.74SMESG000076260.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014801 ID=SMED30014801|Name=SMED30014801|organism=Schmidtea mediterranea sexual|type=transcript|length=754bp
TAATAAAATAAGCAGTAAATATTTTATATTTTTTAAAAATCTTTGCTACA
TGCCCAAGTCGGCCGCATCAGGGAACCATTCAAAGCAGATCTACAAGAAA
ATATTCAACGAAATCACGTTATTTAGAGTGGTAAGCGGCAGCGGAATAAA
TGCCTACAACTTTTATATGAATATGGAGAAGCAAATGCAATCTTCAACTT
TTATCGACAATTCGAGTGATAAGTCAGGGAATTTCAGGAGTATTCTACTT
GATGAATGGATGTTTATACGCCCAATATCTATAAATATCACTCTCAGGAG
TGAGGATCATCACCTCAGAGGGTGGCTTTCCTTTAGGGTCAGGAAAAGCG
ATTCGTCTGTTTCGTGGTTTGATAAGAAAAATTTATTAGATTGTTTTCCC
TGGGAGTCAGATAAGATTTCCAAAGATGATTACAGATATTTTTCCCTTCG
TGGAGATAACACATTTGATGAAAGATCATTCTTGATATATCTGAGTTATA
TCGGATGCAGCAATGACAGAGGAATTTTGGCTATTTTTCAGAAGCGAGAT
ACATGCAAATATGGAAATAGAAAGAACTCATACCCTTTTATAGCTATGGC
AGTTTCAAATGGAACGTCAGGTAATTGGAACTTGGATTCTTTGCCTTTGA
TGTCACTAGAATTAATTGGAATTTATGATTCAAAGATTCATTTTTATGTA
TGATGTAATGTAACTGCAAATTTTGTGATTATTAATCAAATTATTCGTTT
TGGG
back to top

protein sequence of SMED30014801-orf-1

>SMED30014801-orf-1 ID=SMED30014801-orf-1|Name=SMED30014801-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=234bp
NKISSKYFIFFKNLCYMPKSAASGNHSKQIYKKIFNEITLFRVVSGSGIN
AYNFYMNMEKQMQSSTFIDNSSDKSGNFRSILLDEWMFIRPISINITLRS
EDHHLRGWLSFRVRKSDSSVSWFDKKNLLDCFPWESDKISKDDYRYFSLR
GDNTFDERSFLIYLSYIGCSNDRGILAIFQKRDTCKYGNRKNSYPFIAMA
VSNGTSGNWNLDSLPLMSLELIGIYDSKIHFYV*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000421tail