SMED30022962

Overview
NameSMED30022962
Smed IDSMED30022962
Length (bp)358
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast Population

 



 

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




 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30022962 (SMED30022962) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30022962 (SMED30022962) in cells (dots) of each of the 12 neoblast clusters.

 

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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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Homology
BLAST of SMED30022962 vs. Ensembl Human
Match: SETMAR (SET domain and mariner transposase fusion gene [Source:HGNC Symbol;Acc:HGNC:10762])

HSP 1 Score: 91.6633 bits (226), Expect = 3.620e-22
Identity = 45/108 (41.67%), Postives = 67/108 (62.04%), Query Frame = -2
Query:    1 AFVNRNQALVQFDNASFHCARLTQQKIDELSGVEVLPHPPYSPDVAPSDYGLFHSMQHFLRGRKFTTLSEVDQACQQFFASKDQNWYFNQIQLLVDR*QLVIDNGGLY 324
            A VNR   ++  DNA  H A+ T QK++EL G EVLPHPPYSPD+ P++Y +F  + +FL+G++F    + + A Q+F  S+  ++Y   I  L+ R Q  +D  G Y
Sbjct:  576 ALVNRKGPILLHDNARPHVAQPTLQKLNEL-GYEVLPHPPYSPDLLPTNYHVFKHLNNFLQGKRFHNQQDAENAFQEFVESQSTDFYATGINQLISRWQKCVDCNGSY 682          
BLAST of SMED30022962 vs. Ensembl Human
Match: SETMAR (SET domain and mariner transposase fusion gene [Source:HGNC Symbol;Acc:HGNC:10762])

HSP 1 Score: 91.2781 bits (225), Expect = 4.165e-22
Identity = 45/108 (41.67%), Postives = 67/108 (62.04%), Query Frame = -2
Query:    1 AFVNRNQALVQFDNASFHCARLTQQKIDELSGVEVLPHPPYSPDVAPSDYGLFHSMQHFLRGRKFTTLSEVDQACQQFFASKDQNWYFNQIQLLVDR*QLVIDNGGLY 324
            A VNR   ++  DNA  H A+ T QK++EL G EVLPHPPYSPD+ P++Y +F  + +FL+G++F    + + A Q+F  S+  ++Y   I  L+ R Q  +D  G Y
Sbjct:  437 ALVNRKGPILLHDNARPHVAQPTLQKLNEL-GYEVLPHPPYSPDLLPTNYHVFKHLNNFLQGKRFHNQQDAENAFQEFVESQSTDFYATGINQLISRWQKCVDCNGSY 543          
BLAST of SMED30022962 vs. UniProt/SwissProt
Match: sp|Q53H47|SETMR_HUMAN (Histone-lysine N-methyltransferase SETMAR OS=Homo sapiens OX=9606 GN=SETMAR PE=1 SV=2)

HSP 1 Score: 91.6633 bits (226), Expect = 1.739e-21
Identity = 45/108 (41.67%), Postives = 67/108 (62.04%), Query Frame = -2
Query:    1 AFVNRNQALVQFDNASFHCARLTQQKIDELSGVEVLPHPPYSPDVAPSDYGLFHSMQHFLRGRKFTTLSEVDQACQQFFASKDQNWYFNQIQLLVDR*QLVIDNGGLY 324
            A VNR   ++  DNA  H A+ T QK++EL G EVLPHPPYSPD+ P++Y +F  + +FL+G++F    + + A Q+F  S+  ++Y   I  L+ R Q  +D  G Y
Sbjct:  576 ALVNRKGPILLHDNARPHVAQPTLQKLNEL-GYEVLPHPPYSPDLLPTNYHVFKHLNNFLQGKRFHNQQDAENAFQEFVESQSTDFYATGINQLISRWQKCVDCNGSY 682          
BLAST of SMED30022962 vs. UniProt/SwissProt
Match: sp|Q7JQ07|MOS1T_DROMA (Mariner Mos1 transposase OS=Drosophila mauritiana OX=7226 GN=mariner\T PE=1 SV=1)

HSP 1 Score: 77.0258 bits (188), Expect = 1.485e-16
Identity = 43/115 (37.39%), Postives = 65/115 (56.52%), Query Frame = -2
Query:    1 LKFKYPAFVNRNQALV-QFDNASFHCARLTQQKIDELSGVEVLPHPPYSPDVAPSDYGLFHSMQHFLRGRKFTTLSEVDQACQQFFASKDQNWYFNQIQLLVDR*QLVIDNGGLY 342
            L+ K P +  R   ++   DNA  H AR  +  ++ L+  EVLPH  YSPD+APSDY LF SM H L  ++F +   V +   ++FA+KD  +Y+  I  L +R +  + + G Y
Sbjct:  230 LQRKRPEYQKRQHRVIFLHDNAPSHTARAVRDTLETLNW-EVLPHAAYSPDLAPSDYHLFASMGHALAEQRFDSYESVKKWLDEWFAAKDDEFYWRGIHKLPERWEKCVASDGKY 343          
BLAST of SMED30022962 vs. TrEMBL
Match: A0A023F643 (Putative transposase (Fragment) OS=Triatoma infestans OX=30076 PE=2 SV=1)

HSP 1 Score: 134.42 bits (337), Expect = 9.281e-36
Identity = 64/119 (53.78%), Postives = 80/119 (67.23%), Query Frame = -2
Query:    1 RVYNILKFKYPAFVNRNQALVQFDNASFHCARLTQQKIDELSGVEVLPHPPYSPDVAPSDYGLFHSMQHFLRGRKFTTLSEVDQACQQFFASKDQNWYFNQIQLLVDR*QLVIDNGGLY 357
            RVY  L  +YPA VNR   L Q DNA  H +R T++K   L G+E+LPHPPYSPD+APSD+ LF SM HFL+G++F T  EV+ A Q+FF S  + WY   I+ L +R Q  IDN GLY
Sbjct:  216 RVYAKLSQRYPALVNRKGVLFQQDNARPHTSRQTKEKFKNLDGIELLPHPPYSPDLAPSDFYLFRSMAHFLKGKRFDTFQEVETAVQEFFDSHPKEWYQQGIKQLAERWQATIDNNGLY 334          
BLAST of SMED30022962 vs. TrEMBL
Match: A0A023F551 (Putative transposase (Fragment) OS=Triatoma infestans OX=30076 PE=2 SV=1)

HSP 1 Score: 134.42 bits (337), Expect = 9.349e-36
Identity = 64/119 (53.78%), Postives = 80/119 (67.23%), Query Frame = -2
Query:    1 RVYNILKFKYPAFVNRNQALVQFDNASFHCARLTQQKIDELSGVEVLPHPPYSPDVAPSDYGLFHSMQHFLRGRKFTTLSEVDQACQQFFASKDQNWYFNQIQLLVDR*QLVIDNGGLY 357
            RVY  L  +YPA VNR   L Q DNA  H +R T++K   L G+E+LPHPPYSPD+APSD+ LF SM HFL+G++F T  EV+ A Q+FF S  + WY   I+ L +R Q  IDN GLY
Sbjct:  221 RVYAKLSQRYPALVNRKGVLFQQDNARPHTSRQTKEKFKNLDGIELLPHPPYSPDLAPSDFYLFRSMAHFLKGKRFDTFQEVETAVQEFFDSHPKEWYQQGIKQLAERWQATIDNNGLY 339          
BLAST of SMED30022962 vs. TrEMBL
Match: A0A1I7RJP8 (Uncharacterized protein OS=Bursaphelenchus xylophilus OX=6326 PE=4 SV=1)

HSP 1 Score: 123.25 bits (308), Expect = 7.897e-34
Identity = 57/113 (50.44%), Postives = 75/113 (66.37%), Query Frame = -2
Query:    1 KFKYPAFVNRNQALVQFDNASFHCARLTQQKIDELSGVEVLPHPPYSPDVAPSDYGLFHSMQHFLRGRKFTTLSEVDQACQQFFASKDQNWYFNQIQLLVDR*QLVIDNGGLY 339
            K K PA +NR   L+Q DNA  H A+ T++ I  L  +E+ PHP Y+PD+APSD+ LF SM HFLRGR F  L +V+  C++FFASK++ WY + I  L DR    ID+ GLY
Sbjct:    8 KEKCPALINRKCVLLQQDNAKPHTAKQTKENIKTLDAIELFPHPAYNPDLAPSDFHLFRSMAHFLRGRSFNDLDDVENGCREFFASKNKEWYRSAIAQLADRWVQAIDSNGLY 120          
BLAST of SMED30022962 vs. TrEMBL
Match: A0A154PTB0 (Histone-lysine N-methyltransferase SETMAR (Fragment) OS=Dufourea novaeangliae OX=178035 GN=WN55_07281 PE=4 SV=1)

HSP 1 Score: 113.235 bits (282), Expect = 5.435e-30
Identity = 57/107 (53.27%), Postives = 73/107 (68.22%), Query Frame = -2
Query:    1 FVNRNQALVQFDNASFHCARLTQQKIDELSGVEVLPHPPYSPDVAPSDYGLFHSMQHFLRGRKFTTLSEVDQACQQFFASKDQNWYFNQIQLLVDR*QLVIDNGGLY 321
             VNR   ++Q DNA  HCAR T +KI+EL G EVLPHPPYSPD+APSD+ LF S+QHFL G+KF  L +V  A  ++F  K  ++Y + I+ L  R Q V+DN G Y
Sbjct:    1 IVNRKGVILQHDNARPHCARRTLEKINEL-GWEVLPHPPYSPDIAPSDFNLFRSLQHFLSGKKFENLDDVQNAISRYFTQKPIDFYRSGIENLHTRWQKVVDNEGDY 106          
BLAST of SMED30022962 vs. TrEMBL
Match: A0A1I7S7K6 (HTH_48 domain-containing protein OS=Bursaphelenchus xylophilus OX=6326 PE=4 SV=1)

HSP 1 Score: 115.161 bits (287), Expect = 1.334e-29
Identity = 54/119 (45.38%), Postives = 75/119 (63.03%), Query Frame = -2
Query:    1 RVYNILKFKYPAFVNRNQALVQFDNASFHCARLTQQKIDELSGVEVLPHPPYSPDVAPSDYGLFHSMQHFLRGRKFTTLSEVDQACQQFFASKDQNWYFNQIQLLVDR*QLVIDNGGLY 357
            R+Y  +  KYPA +NR +  +Q DNA    A+ T++KI  L  +E+LP P  S  +   DY LF SM HFLRGR F  L +V+  C++FFASK++ WY ++I+ L DR    ID+ GLY
Sbjct:   90 RMYAAIGKKYPALINRTRTPLQQDNAKPRTAKQTKEKIKTLDAIELLPDPANSLHIVSHDYHLFRSMAHFLRGRSFNDLDDVENGCREFFASKNKEWYRSEIEQLADRWVQAIDSNGLY 208          
BLAST of SMED30022962 vs. Planmine SMEST
Match: SMESG000005372.1 (SMESG000005372.1)

HSP 1 Score: 93.9745 bits (232), Expect = 3.545e-34
Identity = 43/54 (79.63%), Postives = 48/54 (88.89%), Query Frame = -2
Query:  196 RVYNILKFKYPAFVNRNQALVQFDNASFHCARLTQQKIDELSGVEVLPHPPYSP 357
            RVYNILK KYPA VNRN+ L++FDN+  H +RLTQQKIDELSGVEVLPHPPYSP
Sbjct:   30 RVYNILKVKYPALVNRNRVLIKFDNSPCHRSRLTQQKIDELSGVEVLPHPPYSP 83          

HSP 2 Score: 67.0106 bits (162), Expect = 3.545e-34
Identity = 34/40 (85.00%), Postives = 34/40 (85.00%), Query Frame = -3
Query:   33 ISYEDENLQLYLRLIRLVSNSLPVKIKIGILIRFSCLLID 152
            ISYEDENLQLYLRL RLVSNS PVKIKIGILI F CL  D
Sbjct:   87 ISYEDENLQLYLRLNRLVSNSFPVKIKIGILITFGCLWRD 126          
BLAST of SMED30022962 vs. Planmine SMEST
Match: SMESG000049199.1 (SMESG000049199.1)

HSP 1 Score: 60.8474 bits (146), Expect = 1.092e-12
Identity = 35/95 (36.84%), Postives = 55/95 (57.89%), Query Frame = -2
Query:    1 NASFHCARLTQQKIDELSGVEVLPHPPYSPDVAPSDYGLFHSMQHFLRGRKFTTLSEVDQACQQFFASKDQNWYFNQIQLLVDR*QLVIDNGGLY 285
            NA  H A  + QK+ ++ G  VL HPPYSPD+A SD+ LF  ++  +RGR F   +E+       F SK ++++ + I+ L DR +  + + G Y
Sbjct:   47 NARPHTAAKSVQKLIDI-GFTVLLHPPYSPDLATSDFYLFSPLKSSIRGRDFNGDNEIQVVLDAGFNSKPRSFFADGIRKLPDRWRRCVLHSGAY 140          
BLAST of SMED30022962 vs. Planmine SMEST
Match: SMESG000070487.1 (SMESG000070487.1)

HSP 1 Score: 50.0618 bits (118), Expect = 4.876e-8
Identity = 22/32 (68.75%), Postives = 24/32 (75.00%), Query Frame = -2
Query:  262 RVYNILKFKYPAFVNRNQALVQFDNASFHCAR 357
            R YNILK KYPA VNRN+ L+QFDNA  H  R
Sbjct:  705 RAYNILKVKYPALVNRNRVLMQFDNAPCHHTR 736          

HSP 2 Score: 46.595 bits (109), Expect = 7.271e-7
Identity = 20/25 (80.00%), Postives = 23/25 (92.00%), Query Frame = -2
Query:    1 QNWYFNQIQLLVDR*QLVIDNGGLY 75
            QNWYF+QI+LLV+  QLVIDNGGLY
Sbjct:  737 QNWYFSQIRLLVESWQLVIDNGGLY 761          
BLAST of SMED30022962 vs. Planmine SMEST
Match: SMESG000030262.1 (SMESG000030262.1)

HSP 1 Score: 45.4394 bits (106), Expect = 7.095e-7
Identity = 32/94 (34.04%), Postives = 51/94 (54.26%), Query Frame = -2
Query:   73 KFKYPAFVNRNQALVQFDNASFHCARLTQQKIDELSGVEVLP---HPPYSPDVAPSDYGLFHSMQH--FLRGRKFTTLSEVDQACQQFFASKDQ 339
            KFKY  +   +  ++Q D A  H AR T   I   SG+EV+     PP SPD+ P DY ++ ++Q   +LR R FT++  + Q   + + + +Q
Sbjct:   20 KFKYLKY-GEDSWILQQDGAPAHTARNTINFIHN-SGIEVIEPDKWPPNSPDLNPVDYAIWGALQEKVYLR-RTFTSIEHLKQVIIEEWNNIEQ 110          
BLAST of SMED30022962 vs. Planmine SMEST
Match: SMESG000002061.1 (SMESG000002061.1)

HSP 1 Score: 45.4394 bits (106), Expect = 7.095e-7
Identity = 32/94 (34.04%), Postives = 51/94 (54.26%), Query Frame = -2
Query:   73 KFKYPAFVNRNQALVQFDNASFHCARLTQQKIDELSGVEVLP---HPPYSPDVAPSDYGLFHSMQH--FLRGRKFTTLSEVDQACQQFFASKDQ 339
            KFKY  +   +  ++Q D A  H AR T   I   SG+EV+     PP SPD+ P DY ++ ++Q   +LR R FT++  + Q   + + + +Q
Sbjct:   20 KFKYLKY-GEDSWILQQDGAPAHTARNTINFIHN-SGIEVIEPDKWPPNSPDLNPVDYAIWGALQEKVYLR-RTFTSIEHLKQVIIEEWNNIEQ 110          
The following BLAST results are available for this feature:
BLAST of SMED30022962 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 2
Match NameE-valueIdentityDescription
SETMAR3.620e-2241.67SET domain and mariner transposase fusion gene [So... [more]
SETMAR4.165e-2241.67SET domain and mariner transposase fusion gene [So... [more]
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BLAST of SMED30022962 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 SMED30022962 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 SMED30022962 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 SMED30022962 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 SMED30022962 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 SMED30022962 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 2
Match NameE-valueIdentityDescription
sp|Q53H47|SETMR_HUMAN1.739e-2141.67Histone-lysine N-methyltransferase SETMAR OS=Homo ... [more]
sp|Q7JQ07|MOS1T_DROMA1.485e-1637.39Mariner Mos1 transposase OS=Drosophila mauritiana ... [more]
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BLAST of SMED30022962 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A023F6439.281e-3653.78Putative transposase (Fragment) OS=Triatoma infest... [more]
A0A023F5519.349e-3653.78Putative transposase (Fragment) OS=Triatoma infest... [more]
A0A1I7RJP87.897e-3450.44Uncharacterized protein OS=Bursaphelenchus xylophi... [more]
A0A154PTB05.435e-3053.27Histone-lysine N-methyltransferase SETMAR (Fragmen... [more]
A0A1I7S7K61.334e-2945.38HTH_48 domain-containing protein OS=Bursaphelenchu... [more]
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BLAST of SMED30022962 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 SMED30022962 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 SMED30022962 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 SMED30022962 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 SMED30022962 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 SMED30022962 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000005372.13.545e-3479.63SMESG000005372.1[more]
SMESG000049199.11.092e-1236.84SMESG000049199.1[more]
SMESG000070487.14.876e-868.75SMESG000070487.1[more]
SMESG000030262.17.095e-734.04SMESG000030262.1[more]
SMESG000002061.17.095e-734.04SMESG000002061.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022962 ID=SMED30022962|Name=SMED30022962|organism=Schmidtea mediterranea sexual|type=transcript|length=358bp
GTAAAGTCCTCCATTGTCTATAACGAGCTGTCATCTATCAACAAGCAGCT
GAATCTGATTAAAATACCAATTTTGATCTTTACTGGCAAAGAATTGCTGA
CAAGCCTGATCAACCTCAGATAAAGTTGTAAATTTTCGTCCTCGTAAGAA
ATGTTGCATTGAATGGAACAATCCGTAATCAGATGGAGCAACATCTGGGC
TGTATGGAGGATGGGGTAAAACTTCAACACCAGACAATTCATCAATCTTC
TGCTGAGTTAGACGAGCGCAATGGAAGGAGGCATTGTCAAATTGCACGAG
AGCCTGATTTCGATTGACAAATGCTGGGTATTTAAATTTTAAAATGTTGT
ATACACGA
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protein sequence of SMED30022962-orf-1

>SMED30022962-orf-1 ID=SMED30022962-orf-1|Name=SMED30022962-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=109bp
RVYNILKFKYPAFVNRNQALVQFDNASFHCARLTQQKIDELSGVEVLPHP
PYSPDVAPSDYGLFHSMQHFLRGRKFTTLSEVDQACQQFFASKDQNWYFN
QIQLLVDR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ