SMED30014045

Overview
NameSMED30014045
Smed IDSMED30014045
Length (bp)1766
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 SMED30014045 (SMED30014045) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30014045 (SMED30014045) 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.
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

 

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Anatomical Expression

PAGE et. al., 2020



SMED30014045

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
X2 cellSMED30014045 SmedASXL_067960SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30014045 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000439:149008..150773 -8821
v31.011356:8913..10553 +5874
v31.007955:12126..14810 +5835
Homology
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BLAST of SMED30014045 vs. Planmine SMEST
Match: SMESG000028417.1 (SMESG000028417.1)

HSP 1 Score: 163.696 bits (413), Expect = 4.264e-46
Identity = 107/240 (44.58%), Postives = 136/240 (56.67%), Query Frame = -1 
Query:   21 FQNPKLAKSKRTDPIKSNAPKEKVLHLPCRKKYQKLWAEHERTLDTWFATEAVKDLH*QIHRLTRFRDDLITENRAQRVMNNDQSAVLIASFTEVELTKDLAGRDLTMILNLIPAK--PHARSITPVKKRR-----------------RAEGDILLANALKVFEEATAQVAEQYPEFIE---------------TRYLSDEM-ETSLDIGS-MIEMPQRRQQEVKETRHSSTSVGYWTDD 632
            ++ PKL+        K +A   ++ H  C++KY KL+AEHERTL TWFA EAVK L  +IHRL+R R+DLI ENRAQR++ NDQSA L+ASFTEVELTK LAGRDL + LNLIP    P      P +  R                 RAEG  LL+NA +V EEA   VAEQ+P+F++               T   +DE  E  + I + +I +P        E   SSTS+ YWTDD
Sbjct:    5 YKIPKLSS-------KPSAINTQMDHSSCQQKYNKLFAEHERTLGTWFAPEAVKILQDKIHRLSRCREDLIAENRAQRIIINDQSADLVASFTEVELTKRLAGRDLVVKLNLIPVNHLPEETQAGPAQTPRTSKKHHPSKNCRRRERRRAEGLTLLSNAAQVLEEAAMLVAEQHPQFVKSDENPQTTAKSEENATLISADETDELRIQINTPLISIPTSG---ADENLKSSTSISYWTDD 234
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BLAST of SMED30014045 vs. Planmine SMEST
Match: SMESG000057198.1 (SMESG000057198.1)

HSP 1 Score: 156.377 bits (394), Expect = 6.432e-45
Identity = 83/128 (64.84%), Postives = 91/128 (71.09%), Query Frame = -1 
Query:  255 FQNPKLAKSKRTDPIKSNAPKEKVLHLPCRKKYQKLWAEHERTLDTWFATEAVKDLH*QIHRLTRFRDDLITENRAQRVMNNDQSAVLIASFTEVELTKDLAGRDLTMILNLIPAK--PHARSITPVK 632
            ++ PK+ K+K  +P+K NA  E  LH  CR  YQKL+AEHERTL  WFA EAVK L  QIHRLTR R DLITENRAQRV+  D SAVLIASFTE ELT  LAGRDL M LNLIPA   P   SI P K
Sbjct:    4 YKIPKIVKAKEVNPVKLNAFTEDTLHRQCRSSYQKLYAEHERTLGMWFAPEAVKALQQQIHRLTRCRGDLITENRAQRVIITDYSAVLIASFTEAELTNYLAGRDLAMKLNLIPANHVPEKTSIGPDK 131
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BLAST of SMED30014045 vs. Planmine SMEST
Match: SMESG000077490.1 (SMESG000077490.1)

HSP 1 Score: 155.992 bits (393), Expect = 2.763e-44
Identity = 87/162 (53.70%), Postives = 105/162 (64.81%), Query Frame = -1 
Query:  204 FQNPKLAKSKRTDPIKSNAPKEKVLHLPCRKKYQKLWAEHERTLDTWFATEAVKDLH*QIHRLTRFRDDLITENRAQRVMNNDQSAVLIASFTEVELTKDLAGRDLTMILNLIPAK--PHARSITPV-----------------KKRRRAEGDILLANALKV 632
            ++ PKL+ +K     + N   E++ H+PC+++Y KL AEHERTL TWFA E VK LH QIHRLTR R+DLI ENRAQR++ NDQSAVLIASFTE ELTK LA RDL + LNLIPA   P    I P                  ++RRRAEG  LL NA +V
Sbjct:    5 YKIPKLSPAKPKLSTQPNTQNEQLDHIPCQQRYNKLLAEHERTLGTWFAPEVVKALHKQIHRLTRCREDLIAENRAQRIVINDQSAVLIASFTETELTKRLASRDLAVKLNLIPANDLPERNQIGPAQTPKTSKKHNPSKNRSGRERRRAEGVTLLNNAAQV 166
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BLAST of SMED30014045 vs. Planmine SMEST
Match: SMESG000059904.1 (SMESG000059904.1)

HSP 1 Score: 160.229 bits (404), Expect = 5.964e-44
Identity = 106/237 (44.73%), Postives = 134/237 (56.54%), Query Frame = -1 
Query:   21 KLAKSKRTDPIKSNAPKEKVLHLPCRKKYQKLWAEHERTLDTWFATEAVKDLH*QIHRLTRFRDDLITENRAQRVMNNDQSAVLIASFTEVELTKDLAGRDLTMILNLIPAK--PHARSITPVKKRR-----------------RAEGDILLANALKVFEEATAQVAEQYPEFIE----TRYL--------------SDEMETSLDIGSMIEMPQRRQQEVKETRHSSTSVGYWTDD 620
            ++ ++K   P+K+  P + + H  C++KY KL+AEHERTL TWFA EAVK L  +IH L+R R+DLI ENRAQR++ NDQSAVL+ASFTE EL K LAGRDL + LNLIPA   P      P +  R                 RAEG  +L NA +V EEA A VAEQ+PEF++    T  L              +DEM+  LDI S IE P    +E      S T    W D+
Sbjct:   84 EVGQAKPPKPVKNATPLQ-LNHDFCQQKYNKLFAEHERTLGTWFAPEAVKILQDKIHELSRCREDLIAENRAQRIIINDQSAVLVASFTEAELVKRLAGRDLALKLNLIPANHLPETTQAGPAQTPRTSKKHHPSKNRRRRERRRAEGLTILNNAAQVLEEAAALVAEQHPEFVKKDDTTLTLKRSKEHMLPIHVKETDEMQICLDI-SPIENPSTTTKE-----RSPTLASCWMDE 313

HSP 2 Score: 95.9005 bits (237), Expect = 2.637e-21
Identity = 47/64 (73.44%), Postives = 54/64 (84.38%), Query Frame = -1 
Query:  291 EAVKDLH*QIHRLTRFRDDLITENRAQRVMNNDQSAVLIASFTEVELTKDLAGRDLTMILNLIP 482
            E VK LH QIHRLTR+RDDLI+ENRAQR++ NDQ  VLIASFT+ ELTK +AGRDL + LNLIP
Sbjct:   12 EFVKALHQQIHRLTRYRDDLISENRAQRIIINDQIPVLIASFTKAELTKRIAGRDLAVKLNLIP 75
[Close]
BLAST of SMED30014045 vs. Planmine SMEST
Match: SMESG000051214.1 (SMESG000051214.1)

HSP 1 Score: 152.91 bits (385), Expect = 2.960e-43
Identity = 88/174 (50.57%), Postives = 107/174 (61.49%), Query Frame = -1 
Query:  177 VVEFQNPKLAKSKRTDPIKSNAPKEKVLHLPCRKKYQKLWAEHERTLDTWFATEAVKDLH*QIHRLTRFRDDLITENRAQRVMNNDQSAVLIASFTEVELTKDLAGRDLTMILNLIPAK--PHARSITPVKKRRRAEGD-----------------ILLANALKVFEEATAQVA 641
            +  ++ PKL + +    +KSN  KE   HL C++KY KL+AEHE TL TWF  EAVK LH QIHRLTR+ D LI+ENRAQRV+ NDQSAVLIA F E ELT  LAGRDL M LNLIP    P   SI   K  + ++ +                 + LAN+ KV EEAT +VA
Sbjct:    2 IPNYKFPKLLQLQPAHTVKSNTSKEDTSHLTCQQKYNKLYAEHECTLGTWFTPEAVKALHQQIHRLTRYCDGLISENRAQRVIINDQSAVLIAFFKEAELTNCLAGRDLAMKLNLIPPNHIPEKNSIGSDKTPKTSKKNNPRKNRRRRERRRANRAVFLANSAKVLEEATIRVA 175
The following BLAST results are available for this feature:
BLAST of SMED30014045 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 SMED30014045 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 SMED30014045 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 SMED30014045 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 SMED30014045 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 SMED30014045 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 SMED30014045 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 SMED30014045 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 SMED30014045 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 SMED30014045 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 SMED30014045 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 SMED30014045 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 SMED30014045 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 SMED30014045 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000028417.14.264e-4644.58SMESG000028417.1[more]
SMESG000057198.16.432e-4564.84SMESG000057198.1[more]
SMESG000077490.12.763e-4453.70SMESG000077490.1[more]
SMESG000059904.15.964e-4444.73SMESG000059904.1[more]
SMESG000051214.12.960e-4350.57SMESG000051214.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014045 ID=SMED30014045|Name=SMED30014045|organism=Schmidtea mediterranea sexual|type=transcript|length=1766bp
CTCAGAAACCCGTCACATTAGTCATCGGTCCAATACCCGACAGAAGTTGA
TGAATGTCGGGTCTCCTTGACCTCCTGCTGTCGGCGCTGTGGCATCTCTA
TCATTGATCCTATGTCCAAGCTAGTTTCCATCTCGTCACTGAGGTATCTC
GTTTCTATAAATTCTGGGTACTGTTCTGCGACCTGGGCTGTTGCCTCTTC
GAACACCTTTAAAGCATTTGCCAGAAGAATGTCCCCCTCAGCTCGACGAC
GTTTTTTTACTGGTGTGATGCTTCTTGCGTGGGGTTTTGCCGGGATTAAG
TTTAATATCATTGTCAAATCGCGGCCGGCTAGATCCTTGGTTAATTCGAC
CTCTGTGAATGAGGCTATTAATACGGCGCTCTGGTCATTATTCATGACTC
TTTGAGCTCGATTTTCAGTTATGAGGTCGTCGCGGAATCTCGTTAAGCGA
TGTATTTGCTAATGAAGGTCCTTCACCGCTTCTGTGGCGAACCACGTGTC
CAGCGTGCGTTCGTGTTCGGCCCATAGCTTTTGATATTTCTTTCGACATG
GGAGATGTAATACTTTTTCTTTCGGGGCATTGGATTTGATTGGATCGGTC
CTTTTTGATTTAGCGAGTTTTGGATTTTGAAATTCGACAACATTCTAGTG
ATTAACTTAGTACGGGAAAAATTCAACTCTTCTTTTGGTTTTAACTACTT
ATAATTATTCTAATGATAAGAAGGATAAATGAAGGTTAGAAAAAAGTTAT
TAATTAATTTACCAAAGTTGAATTAAGGGGCAAGATTAAAGAAAATGGTT
AATTAATCTATATATTACCCAGACTCAATTTAAAGTCTGCTAAGTAACAT
GCAAACACGCACATATACATACATATAAACAATCATTCGACCAATCGTTG
TGCAAATGCTAAAGATTGTTAATAATCAACATCTGTGTTTTATCTAATTA
CTGTAACGTGAAATGTCGGCATCTGGGGGAATTCAGTGTAGATAGTATGG
CTTCTAATGAGTGGTCAAGAATGGTGAATGAAGTGGTACCTTATCTATAA
GTTATATCATTGTGGTTTAAGTGGCATGGCAGAGTTAATGGTTTTCTTGA
TGTCTATATTGGGTTGATACTTACATGGCAGATCAGACTTACTACCGCCT
ATCAATAAGAAAACCAATTATAAAACGTCGCCGTAGCGTGGTGGAGTGTT
TCCATGAACTGTTGATTCTATGAGAATTTGACATTTTTAGCGATGCTCGA
GAGTTTCTTAATTTTGGAATTCAGTAAAGACATTTTTTTAAAAAATCATG
AATCTGTTCTCATTGGTAGTGGGCTATTAGAAGATACATATCTGAAATGA
GATGTCAAAATTTACTCCTGCGTCCTCTACAGTATTGATTGCTCACAAGA
TAAATACACACAAAAATTTTATTCCTGGTTCTCGTCGATATCTATTACTA
GTCGATCCCCTCATTAAATGTAAATATAGACAGGCCTGTTAAAAAATTTT
TTCCTACCTAAACATTTATTCAAATGTTAAATCACCTATAGTCAAAACGA
TCTTCCCGTGATTTCACTGCTGTTACCGCTCCGTCCACCATTCATAAACG
CTGCGGTGAAGTTCAGCGGACTCCTACTTTCGAGATCAGTACAGAGCTGA
CCTTTCCCAGCAGACACCGAGGGGTAAAAAACGATAATTGACACAACTGA
GGAAATTGAATACCAATTCAACATTTCCCACAGATTAATAAAATATATAA
ATATTTAAGGGGGACC
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protein sequence of SMED30014045-orf-1

>SMED30014045-orf-1 ID=SMED30014045-orf-1|Name=SMED30014045-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=126bp
MNNDQSAVLIASFTEVELTKDLAGRDLTMILNLIPAKPHARSITPVKKRR
RAEGDILLANALKVFEEATAQVAEQYPEFIETRYLSDEMETSLDIGSMIE
MPQRRQQEVKETRHSSTSVGYWTDD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 49..68
NoneNo IPR availableTMHMMTMhelixcoord: 7..29