SMED30019990

Overview
NameSMED30019990
Smed IDSMED30019990
Length (bp)1307
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell 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




Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30019990 (SMED30019990) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30019990 (SMED30019990) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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




SMED30019990

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
tailSMED30019990SMESG000079521.1 SmedASXL_068958SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30019990SMESG000079521.1 dd_Smed_v4_19657_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30019990SMESG000079521.1 dd_Smed_v4_19657_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30019990 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.009135:3604..4891 -5150
v31.003409:9479..10765 +4640
Homology
BLAST of SMED30019990 vs. Ensembl Zebrafish
Match: adora4a (adenosine A4 receptor a [Source:ZFIN;Acc:ZDB-GENE-131127-239])

HSP 1 Score: 50.447 bits (119), Expect = 2.210e-6
Identity = 62/258 (24.03%), Postives = 114/258 (44.19%), Query Frame = 1
Query:  457 PLLCLSVGEVVYVLITTVTA--FAVLGDMNVVYNIRRLNMCHVLGTVNLILVQFDLTTHGLLGVIRYLAICQPLKYRKYINLKNSIIITLFNGLYAIIMGYIPSIIVFDNEFILSYTLDPSALNCMMKLGKMASSYICIFYFG----PPMALAGFSYILCFYKLGNPGSSTVIVTK--SQRRLVITLSTSFVVIFIQSCFYPL----SIILFEGKEHLCHLTRRHFTWLILHNSLVNPVAFLSMYAY-----KRKYFR 1179
            P  CL V   V  L+    A   A++ DM+V  +    + C  +    ++ +Q  + T   + V R L +C P +Y+  +  K S II     + A ++G++P    ++++ +  +  + ++++C   +  ++ SY+  F F     PP+A+    Y   FYK+       +  T   +Q+   +  S   V+     C+ PL    SI+ +    ++  +       L   NS VNPV    +YAY     KR+Y R
Sbjct:   46 PTFCLIVSLSVADLLVGAVAVPLALIVDMHVKMS---FHACLFISCFLIVPLQASVLTLLAIAVDRCLRVCIPFRYKSTVTKKRSWIIAAVCWMLAFMLGFLPMFGWYNHDTLAQH--NSTSIDCEF-VAVISISYLVHFIFEGCFLPPLAVMTALYYYVFYKIRRQSRGALGETGPYTQKEQKLASSLVLVLALFAVCWLPLHIIQSIMFYNHSVYVPSIALYSGILLSHANSAVNPV----VYAYKVPKMKREYMR 293          
BLAST of SMED30019990 vs. Ensembl Nematostella
Match: EDO45454 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7RSP6])

HSP 1 Score: 54.299 bits (129), Expect = 4.014e-8
Identity = 65/274 (23.72%), Postives = 120/274 (43.80%), Query Frame = 1
Query:  400 NIFMIAISLKDANLKGGMLPLLCLSVGEVVYVLITTVTAFAVLGDMNVVYNIRRLNMCHVLGTVNLILVQFDLTTHGLLGVIRYLAICQPLKYRKYINLKNSIIITLFNGLYAI-IMGYIPSIIVFDNEFILSYTLDPSALNCMMKLGK--MASSYICIFYFGPPMALAGFSYILCFYKL--------GNPGSSTVIVTKSQRRLVITLSTSFVVIFIQSCFYPLSII----LFEGKEHLCHLTRRHFTWLILHNSLVNPVAF-LSMYAYKRKY 1173
            N+F++A+++ D ++      +LC+      +   T V+   V G           + C+V G   + L    + T  L+ V RY  I +P KY++    + +++  L  G++ I  +G IP   + D+E    Y   P    C+ K       + +I   Y   P+ L G+ Y   F ++         NP S+  +    Q    IT + + V +    C+ P SII     F G+          +T+L + +SL+NPV + ++  A++++Y
Sbjct:   62 NMFVVALAVSDTSMG-----VLCMP-----FTFGTLVSGGWVFGK----------SFCYVHGFTGMTLALASIYTMSLISVNRYFCIVKPAKYQELFKKRRTVLYIL--GVWTIAFIGSIPPFFL-DDE---GYGFQPGKAMCLYKFETNLTFTIFIECVYIACPILLIGYCYSSVFREVYRTNKVFAPNPQSTDQLRAHIQ-ETKITKTLAIVFLGFSLCWVPASIIDTLGSFSGEPPFERPVYLAYTYLAMISSLINPVIYGVTSRAFRQEY 308          
BLAST of SMED30019990 vs. Planmine SMEST
Match: SMESG000079521.1 (SMESG000079521.1)

HSP 1 Score: 617.461 bits (1591), Expect = 0.000e+0
Identity = 311/312 (99.68%), Postives = 311/312 (99.68%), Query Frame = 1
Query:  286 VQSSTLSTDSIYLDFPRCGDVGAEVAYXXXXXXXSISGNIFMIAISLKDANLKGGMLPLLCLSVGEVVYVLITTVTAFAVLGDMNVVYNIRRLNMCHVLGTVNLILVQFDLTTHGLLGVIRYLAICQPLKYRKYINLKNSIIITLFNGLYAIIMGYIPSIIVFDNEFILSYTLDPSALNCMMKLGKMASSYICIFYFGPPMALAGFSYILCFYKLGNPGSSTVIVTKSQRRLVITLSTSFVVIFIQSCFYPLSIILFEGKEHLCHLTRRHFTWLILHNSLVNPVAFLSMYAYKRKYFRSGVVSSTFNETRAT 1221
            VQSSTLSTDSIYLDFPRCGDVGAEVAYLVLVLVLSISGNIFMIAISLKDANLKGGMLPLLCLSVGEVVYVLITTVTAFAVLGDMNVVYNIRRLNMCHVLGTVNLILVQFDLTTHGLLGVIRYLAICQPLKYRKYINLKNSIIITLFNGLYAIIMGYIPSIIVFDNEFILSYTLDPSALNCMMKLGKMASSYICIFYFGPPM LAGFSYILCFYKLGNPGSSTVIVTKSQRRLVITLSTSFVVIFIQSCFYPLSIILFEGKEHLCHLTRRHFTWLILHNSLVNPVAFLSMYAYKRKYFRSGVVSSTFNETRAT
Sbjct:    7 VQSSTLSTDSIYLDFPRCGDVGAEVAYLVLVLVLSISGNIFMIAISLKDANLKGGMLPLLCLSVGEVVYVLITTVTAFAVLGDMNVVYNIRRLNMCHVLGTVNLILVQFDLTTHGLLGVIRYLAICQPLKYRKYINLKNSIIITLFNGLYAIIMGYIPSIIVFDNEFILSYTLDPSALNCMMKLGKMASSYICIFYFGPPMVLAGFSYILCFYKLGNPGSSTVIVTKSQRRLVITLSTSFVVIFIQSCFYPLSIILFEGKEHLCHLTRRHFTWLILHNSLVNPVAFLSMYAYKRKYFRSGVVSSTFNETRAT 318          
BLAST of SMED30019990 vs. Planmine SMEST
Match: SMESG000002315.1 (SMESG000002315.1)

HSP 1 Score: 108.612 bits (270), Expect = 2.846e-26
Identity = 78/286 (27.27%), Postives = 146/286 (51.05%), Query Frame = 1
Query:  337 CGDVGAEVAYXXXXXXXSISGNIFMIAISLKDANL-KGGMLPLLCLSVGEVVYVLITTVTAFAVLGDMNVVYNIRRLNMCHVLGTVNLILVQFDLTTHGLLGVIRYLAICQPLKYRKYINLKNS----IIITLFNGLYAIIMGYIPSIIVFDNEFILSYTLDPSALNCMMKLGKMASSYICIFYFGPPMALAGFSYILCFYKL---GNPGSSTVIVTKSQRRLVITLSTSFVVIFIQSCFYPLSIILFEGKEHLCHLTRRHFTWLILHNSLVNPVAFLSMYAYKRK 1170
            CG     + YL +V ++++ GN  ++ ++  ++   KGGMLP+  L++ ++++  +  +T   +L  ++ VY    L+ C +   +   +  + +  H +L V R++AIC P +Y+  +  K +      + LF  +  I+   +PS     N F+  Y  +PS L C+         YI +  +GPP  +A F YI C Y L   G   S+   V K Q RL   +  ++V++ I  C YP +I +      +C+L +R  ++ IL+NS+V+P+ ++S+    R+
Sbjct:   11 CGAQTITLIYLSIVYIVALGGNTIILTVAWFNSEFRKGGMLPMFTLAICDMIFAHMAILTF--ILNMISEVYLKYTLHNCSLNSMIGSAVSAYVVYHHAILAVTRFIAICHPTRYKTILTTKTTGLFIFFVILFVTIITILTYLLPSPW---NSFMHPY-YNPSMLCCIYGSNWGIVLYIVLVVYGPPFHIATFCYIRCLYILKIKGKSSSTNSAVDKKQTRLAYIMLINYVIVNINCCLYPAAIYIETDDPMVCNLWKRFLSYCILNNSVVSPIVYISLNKKIRQ 290          
The following BLAST results are available for this feature:
BLAST of SMED30019990 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 SMED30019990 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 SMED30019990 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 SMED30019990 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
adora4a2.210e-624.03adenosine A4 receptor a [Source:ZFIN;Acc:ZDB-GENE-... [more]
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BLAST of SMED30019990 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 SMED30019990 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 SMED30019990 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 SMED30019990 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 SMED30019990 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 SMED30019990 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 SMED30019990 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 SMED30019990 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO454544.014e-823.72Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30019990 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 SMED30019990 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000079521.10.000e+099.68SMESG000079521.1[more]
SMESG000002315.12.846e-2627.27SMESG000002315.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30019990 ID=SMED30019990|Name=SMED30019990|organism=Schmidtea mediterranea sexual|type=transcript|length=1307bp
TTATTGGGATATATAAATGGTTACAACTGAATTTCGAAAGTGACTAAAGG
AATCAGTGAAATTTTTAGAAAAAATTTTAGTAAAACTTTGGCTAAAAGGG
GTTTGGATAAAATTTTGAAAAAAATTCATGTCAAAATCTATGTATTTTCA
AAAAATTTCAAAGATTCGATTAAATGTCCTGTCCACAAACACACTGCGGT
CGAAAATTTCTTCATTTTTCAGAAAAATGATCAAGAAAAATGTTCGAAGT
GGGAAGAAAAAACTAAAAATAAAATAGTGAAATAAGTACAATCTTCGACT
CTCTCTACCGATTCCATTTACCTTGACTTTCCTCGTTGCGGTGATGTTGG
CGCCGAAGTTGCCTATTTGGTGTTGGTTCTTGTTTTATCAATTTCTGGAA
ATATATTTATGATCGCCATCAGTTTGAAGGACGCAAATCTCAAAGGGGGG
ATGTTGCCATTATTGTGTTTATCAGTCGGAGAAGTTGTTTATGTTCTCAT
AACTACAGTCACAGCATTTGCGGTACTTGGAGACATGAATGTGGTTTACA
ATATTAGAAGACTAAATATGTGTCATGTACTAGGGACAGTCAACTTAATC
TTAGTCCAGTTCGACCTTACAACTCATGGACTGTTGGGAGTTATCCGGTA
TTTGGCCATTTGCCAGCCTTTGAAATATCGCAAGTACATAAATTTGAAAA
ACAGTATCATTATAACACTATTCAACGGACTATACGCAATCATTATGGGC
TACATTCCGTCAATAATCGTTTTTGACAACGAATTCATCCTTTCTTACAC
ATTAGATCCATCTGCTCTGAATTGTATGATGAAACTTGGTAAAATGGCGT
CTAGTTATATTTGCATATTTTATTTTGGTCCTCCAATGGCGCTAGCAGGG
TTCAGTTATATTTTGTGTTTTTACAAACTAGGGAATCCAGGTTCTTCAAC
TGTCATTGTGACAAAGAGCCAGAGGCGACTCGTAATCACTTTATCGACTT
CTTTCGTCGTTATTTTTATTCAATCATGTTTTTATCCTTTGAGTATCATC
TTATTTGAAGGCAAAGAACATTTATGTCACTTAACACGAAGACATTTTAC
TTGGTTAATTCTTCACAATTCCTTGGTGAATCCGGTAGCGTTTCTATCAA
TGTATGCGTATAAGCGAAAGTATTTCCGATCCGGAGTCGTCTCGTCCACG
TTCAATGAAACTAGAGCAACTTAAAATTTTACAACTTGAAATGACATAAT
AAAAAAGGTTAATAATTAGTTACAGAAATTATTTGTGTTACTTTGTTTGA
CTTATTC
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protein sequence of SMED30019990-orf-1

>SMED30019990-orf-1 ID=SMED30019990-orf-1|Name=SMED30019990-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=272bp
MIAISLKDANLKGGMLPLLCLSVGEVVYVLITTVTAFAVLGDMNVVYNIR
RLNMCHVLGTVNLILVQFDLTTHGLLGVIRYLAICQPLKYRKYINLKNSI
IITLFNGLYAIIMGYIPSIIVFDNEFILSYTLDPSALNCMMKLGKMASSY
ICIFYFGPPMALAGFSYILCFYKLGNPGSSTVIVTKSQRRLVITLSTSFV
VIFIQSCFYPLSIILFEGKEHLCHLTRRHFTWLILHNSLVNPVAFLSMYA
YKRKYFRSGVVSSTFNETRAT*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0000421tail
Vocabulary: INTERPRO
TermDefinition
IPR000276GPCR_Rhodpsn
IPR017452GPCR_Rhodpsn_7TM
Vocabulary: biological process
TermDefinition
GO:0007186G-protein coupled receptor signaling pathway
Vocabulary: molecular function
TermDefinition
GO:0004930G-protein coupled receptor activity
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR000276G protein-coupled receptor, rhodopsin-likePFAMPF000017tm_1coord: 32..243
e-value: 1.1E-7
score: 31.4
NoneNo IPR availableGENE3DG3DSA:1.20.1070.10coord: 15..270
e-value: 1.3E-15
score: 59.2
NoneNo IPR availablePANTHERPTHR24228B2 BRADYKININ RECEPTOR/ANGIOTENSIN II RECEPTORcoord: 16..258
NoneNo IPR availableCDDcd006377tm_classA_rhodopsin-likecoord: 54..243
e-value: 1.34336E-8
score: 52.2798
NoneNo IPR availableSUPERFAMILYSSF81321Family A G protein-coupled receptor-likecoord: 18..257
NoneNo IPR availableTMHMMTMhelixcoord: 57..79
NoneNo IPR availableTMHMMTMhelixcoord: 13..35
NoneNo IPR availableTMHMMTMhelixcoord: 192..214
NoneNo IPR availableTMHMMTMhelixcoord: 150..172
NoneNo IPR availableTMHMMTMhelixcoord: 100..122
NoneNo IPR availableTMHMMTMhelixcoord: 229..251
IPR017452GPCR, rhodopsin-like, 7TMPROSITEPS50262G_PROTEIN_RECEP_F1_2coord: 1..245
score: 14.995