SMED30004496

Overview
NameSMED30004496
Smed IDSMED30004496
Length (bp)1839
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 SMED30004496 (SMED30004496) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30004496 (SMED30004496) 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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Anatomical Expression

PAGE et. al., 2020



SMED30004496

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pigment cellSMED30004496 SmedASXL_075972SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017		whole organism asexual adult RNA-sequencing evidence
X1 cellSMED30004496 SmedASXL_075972SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30004496 SmedASXL_075972SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30004496 vs. Planmine SMEST
Match: SMESG000024721.1 (SMESG000024721.1)

HSP 1 Score: 181.8 bits (460), Expect = 5.777e-54
Identity = 93/145 (64.14%), Postives = 108/145 (74.48%), Query Frame = -3 
Query:  836 IQAGYKIPKVTPPKPGQSAQSNFKDDSLSHLECQQKYNKLPA*YERTLGTWFAPMAVKALHQQIHRLTRCRDDLISENRAQRIIINDQS---------AELIKRIAGRNLAVQMNLIPLTHITEKPGVGPTKPHKRAKSITPART 1243
            +Q+GYKIPK++ PK   S QS  + DSLSH+ CQQKY+KL A +ERTLGTWFAP  VKA+HQQIHRLTRCRDDLISENRAQRIIINDQS         AEL KRIA R+LAVQ+NLIP  HI EK  V P K  K +K   P+++
Sbjct:    1 MQSGYKIPKISTPKSPHSVQSTTQKDSLSHITCQQKYDKLFAEHERTLGTWFAPEVVKAIHQQIHRLTRCRDDLISENRAQRIIINDQSAVLIVSFTEAELTKRIASRDLAVQLNLIPPRHILEKLEVCPAKTPKTSKRRNPSKS 145
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BLAST of SMED30004496 vs. Planmine SMEST
Match: SMESG000077490.1 (SMESG000077490.1)

HSP 1 Score: 171.014 bits (432), Expect = 9.332e-50
Identity = 84/152 (55.26%), Postives = 109/152 (71.71%), Query Frame = -3 
Query:  815 IQAGYKIPKVTPPKPGQSAQSNFKDDSLSHLECQQKYNKLPA*YERTLGTWFAPMAVKALHQQIHRLTRCRDDLISENRAQRIIINDQSA---------ELIKRIAGRNLAVQMNLIPLTHITEKPGVGPTKPHKRAKSITPARTGDAVELR 1243
            +Q+GYKIPK++P KP  S Q N +++ L H+ CQQ+YNKL A +ERTLGTWFAP  VKALH+QIHRLTRCR+DLI+ENRAQRI+INDQSA         EL KR+A R+LAV++NLIP   + E+  +GP +  K +K   P++     E R
Sbjct:    1 MQSGYKIPKLSPAKPKLSTQPNTQNEQLDHIPCQQRYNKLLAEHERTLGTWFAPEVVKALHKQIHRLTRCREDLIAENRAQRIVINDQSAVLIASFTETELTKRLASRDLAVKLNLIPANDLPERNQIGPAQTPKTSKKHNPSKNRSGRERR 152
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BLAST of SMED30004496 vs. Planmine SMEST
Match: SMESG000003594.1 (SMESG000003594.1)

HSP 1 Score: 154.066 bits (388), Expect = 2.444e-42
Identity = 76/144 (52.78%), Postives = 102/144 (70.83%), Query Frame = -3 
Query:  839 IQAGYKIPKVTPPKPGQSAQSNFKDDSLSHLECQQKYNKLPA*YERTLGTWFAPMAVKALHQQIHRLTRCRDDLISENRAQRIIINDQSA---------ELIKRIAGRNLAVQMNLIPLTHITEKPGVGPTKPHKRAKSITPAR 1243
            +Q GYKIPK+T  +  +S  S   +D  SH EC++KY++L   +ERTL TWFAP AVKALH+QIHRLTRCR+DLI+ENRAQRI+IN+QSA         EL KR+AGR+LA+++N+IP  H+ E    GP +  K +K   P++
Sbjct:    1 MQPGYKIPKLTSQRSEKSNLSILNNDDKSHQECRRKYDQLVVEHERTLSTWFAPEAVKALHKQIHRLTRCREDLIAENRAQRIVINNQSAVLTASFNETELKKRLAGRDLAIKLNIIPAEHVPETATTGPPQMPKTSKKHNPSK 144

HSP 2 Score: 80.1073 bits (196), Expect = 7.171e-23
Identity = 35/45 (77.78%), Postives = 38/45 (84.44%), Query Frame = -1 
Query:  481 NRNSSTSVGYWTDDFGDELCHSVPQVGSNKLNLGRKRKIPVDIDE 615
            NR SSTS+GYWTDD GDELCHSVPQVGSN+L + RKR   VDIDE
Sbjct:  228 NRKSSTSIGYWTDDVGDELCHSVPQVGSNELKISRKRIFSVDIDE 272

HSP 3 Score: 46.9802 bits (110), Expect = 7.171e-23
Identity = 30/53 (56.60%), Postives = 38/53 (71.70%), Query Frame = -2 
Query:  720 QTSKKHNPSKNXXXXR---AEGATRLANADRVIEEATIRVAEQYPEFVKSDEK 869
            +TSKKHNPSKNRRRR    AEG ++L NA + +EEA + VAEQ  +  K+ EK
Sbjct:  135 KTSKKHNPSKNRRRRERRRAEGVSQLKNAAQTLEEAAMLVAEQQSQLAKAAEK 187
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BLAST of SMED30004496 vs. Planmine SMEST
Match: SMESG000016136.1 (SMESG000016136.1)

HSP 1 Score: 160.229 bits (404), Expect = 4.310e-42
Identity = 79/148 (53.38%), Postives = 106/148 (71.62%), Query Frame = -3 
Query:  839 NLSEIQAGYKIPKVTPPKPGQSAQSNFKDDSLSHLECQQKYNKLPA*YERTLGTWFAPMAVKALHQQIHRLTRCRDDLISENRAQRIIINDQSA---------ELIKRIAGRNLAVQMNLIPLTHITEKPGVGPTKPHKRAKSITPAR 1255
            +LSE+ + Y+IP ++ PK     Q N ++  L+HL  QQ YNKL A +ERTLGTWFAP  VKALH++IH LTRC+DDLI+ENRAQRI+INDQSA         EL KR+AGR+LAV++NLIP  H+ +K  +GP++  K +K   P++
Sbjct:  337 HLSEMNSSYRIPNLSQPKANAVTQPNVQNGDLTHLSFQQSYNKLLAEHERTLGTWFAPEVVKALHKEIHPLTRCQDDLIAENRAQRIVINDQSAILIASFTETELTKRLAGRDLAVKLNLIPTNHLPKKTTIGPSQTPKTSKKHNPSK 484

HSP 2 Score: 64.3142 bits (155), Expect = 1.696e-10
Identity = 41/70 (58.57%), Postives = 48/70 (68.57%), Query Frame = -2 
Query:  702 RKTRSWPHKTSQTSKKHNPSKNXXXXR---AEGATRLANADRVIEEATIRVAEQYPEFVKSDEKLPEPAK 902
            +KT   P +T +TSKKHNPSKNR RR    A G T L NA +V+EEA   VAEQ+PEFVK+DE   E AK
Sbjct:  464 KKTTIGPSQTPKTSKKHNPSKNRCRRERRRAVGVTILNNAAKVLEEAAALVAEQHPEFVKTDENPQESAK 533
[Close]
BLAST of SMED30004496 vs. Planmine SMEST
Match: SMESG000051214.1 (SMESG000051214.1)

HSP 1 Score: 144.436 bits (363), Expect = 4.715e-40
Identity = 75/129 (58.14%), Postives = 88/129 (68.22%), Query Frame = -3 
Query:  875 GYKIPKVTPPKPGQSAQSNFKDDSLSHLECQQKYNKLPA*YERTLGTWFAPMAVKALHQQIHRLTRCRDDLISENRAQRIIINDQS---------AELIKRIAGRNLAVQMNLIPLTHITEKPGVGPTK 1234
             YK PK+   +P  + +SN   +  SHL CQQKYNKL A +E TLGTWF P AVKALHQQIHRLTR  D LISENRAQR+IINDQS         AEL   +AGR+LA+++NLIP  HI EK  +G  K
Sbjct:    4 NYKFPKLLQLQPAHTVKSNTSKEDTSHLTCQQKYNKLYAEHECTLGTWFTPEAVKALHQQIHRLTRYCDGLISENRAQRVIINDQSAVLIAFFKEAELTNCLAGRDLAMKLNLIPPNHIPEKNSIGSDK 132
The following BLAST results are available for this feature:
BLAST of SMED30004496 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 SMED30004496 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 SMED30004496 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 SMED30004496 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 SMED30004496 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 SMED30004496 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 SMED30004496 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 SMED30004496 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 SMED30004496 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 SMED30004496 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 SMED30004496 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 SMED30004496 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 SMED30004496 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 SMED30004496 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000024721.15.777e-5464.14SMESG000024721.1[more]
SMESG000077490.19.332e-5055.26SMESG000077490.1[more]
SMESG000003594.12.444e-4252.78SMESG000003594.1[more]
SMESG000016136.14.310e-4253.38SMESG000016136.1[more]
SMESG000051214.14.715e-4058.14SMESG000051214.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004496 ID=SMED30004496|Name=SMED30004496|organism=Schmidtea mediterranea sexual|type=transcript|length=1839bp
CTTGGTTAATAAGGTTAATAAGGTTATCTGTTCGATCAGCTGTTTTTAAT
TTTAAGAAATTTTTATTTCTAATTTAAGGGGAAATAAGGTTGTCTTAAGG
TTCGCATCATATCTTTGACTAAACTATATTCTTTTTCTTTTAAAAAGTCC
TCACTCAAATGTTAAAAATTAATTTATCGAGAGCTATGATTTCTCTTAAT
TTAACTTTCTCAGTTGAATTCTCCCTTCTAATGATATTATTTGCATTATT
TAGGCGCTCACTACCTGCAGGTCATACCTGGTCACGGTCTTTGACATAAA
TTACACATTAATTATAGAGGTAAACTGAAAATTTCAGCAAACAAAAAAAA
TAAGGCTAATTACAAAATTTAATTGCTAATAAAACTAGTAACAATAAGAT
AAAAAAATATGTACAAATAACACATAAATTTATAATAAGTCTCAGAAAAT
GCATCGATTAGCATTGTCGTCCCTGTTATATTCGTCAATATCAACTGGAA
TTTTCCGTTTTCGGCCGAGATTTAGTTTATTAGACCCGACTTGGGGAACT
GAGTGACAGAGCTCGTCCCCGAAGTCATCGGTCCAGTATCCGACGGAAGT
TGACGAATTTCTGTTTTCTTCGACTGCCGACGAGGTTGTTGTAACCGAGG
ATAACGTCCAAACGAATTTGCATTTCGTTCTCTTTGCGTTAATTCTACGG
GTTTCGCCGGTTCAGGCAATTTTTCATCTGACTTGACAAACTCTGGGTAT
TGTTCGGCGACTCGAATGGTGGCTTCCTCTATCACCCTGTCCGCATTTGC
CAGTCTTGTGGCCCCCTCAGCTCGACGGCGTCGCCGGTTCTTGCTGGGGT
TATGCTTTTTGCTCGTTTGTGAGGTTTTGTGGGGCCAACTCCGGGTTTTT
CTGTGATATGGGTTAGGGGAATCAGATTCATCTGCACAGCCAGATTGCGG
CCGGCTATCCTTTTGATTAATTCGGCGCTCTGATCATTTATAATGATCCT
TTGAGCCCGGTTTTCGGAGATCAGATCATCGCGACATCTCGTCAAGCGAT
GGATCTGTTGGTGCAATGCTTTGACGGCCATTGGAGCGAACCAAGTACCT
AATGTGCGTTCGTACTACGCGGGCAATTTGTTATACTTCTGTTGGCATTC
TAGGTGGGAAAGGCTGTCATCTTTGAAATTGGATTGAGCAGATTGTCCTG
GTTTTGGCGGCGTTACTTTTGGGATTTTGTAACCGGCTTGAATTTCTGAC
AAATTTGAGGATTTCGCGAATGGTTTCGAAAACAGAAAATACTTATCGGC
GTTTTCGGAACAGAGAAAGCTAAATGGGGAAAATTTCGTAATATGAATTT
ATTTACTTAAAATAATGATTATAATAGAGATAATAATTAATTAATATTTT
CAAACAATTGGATTCTTCATAAACAATACAGTTGTTATTAGCTACTGTGG
TATTTTGTTTAATGTAAAAATTGGTCGCTAGCTAATAATGGTAAAAAGTT
AAAAAATATAGAACTGACTATACCTAATTCATTAAAATTATTTTCAAATT
TAATATTACATTTTTATTCTTTACAGGATAAGATCTAAATAAGTATATGT
AGAAATAAATTCTGTTGTCAATTCTTTGGTTATTATTCTTAACCCTAGTC
GGTCCCCTCAATATATCTTTTTGCGACAGGAATTTTAAAAATAAAAAATT
CATTATTCTACCTAAACATTTACACAATTGTTATTACCCCTCTTACTATA
GCGATATTCCCGTATATTACCCTCTTACCGCTCCGTCCACGCGAATGCCA
ACGGTGTCCTGCTATGTGATCAGTGCAAACGAGGCCTGA
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protein sequence of SMED30004496-orf-1

>SMED30004496-orf-1 ID=SMED30004496-orf-1|Name=SMED30004496-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=100bp
MAVKALHQQIHRLTRCRDDLISENRAQRIIINDQSAELIKRIAGRNLAVQ
MNLIPLTHITEKPGVGPTKPHKRAKSITPARTGDAVELRGPQDWQMRTG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002075pigment cell
PLANA:0002109X1 cell
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 25..42