SMED30022588

Overview
NameSMED30022588
Smed IDSMED30022588
Length (bp)563
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ 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



 

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 SMED30022588 (SMED30022588) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30022588 (SMED30022588) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

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 SMED30022588 (SMED30022588) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30022588 (SMED30022588) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

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



SMED30022588

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30022588h1SMcG0022180 SmedASXL_010716SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30022588h1SMcG0012016 Contig40809newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022588h1SMcG0012016 Contig40809uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
protonephridiaSMED30022588h1SMcG0022180 dd_Smed_v4_3493_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30022588h1SMcG0022180 dd_Smed_v4_3493_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30022588h1SMcG0022180 dd_Smed_v4_3493_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30022588h1SMcG0022180 dd_Smed_v4_3493_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30022588h1SMcG0022180 dd_Smed_v4_3493_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30022588h1SMcG0022180 dd_Smed_v4_3493_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022588h1SMcG0022180 Contig40809newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022588h1SMcG0022180 Contig40809uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
zeta neoblastSMED30022588h1SMcG0022180 dd_Smed_v4_3493_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
SMED30022588 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001188:70191..70782 +2502
Homology
[Close]
BLAST of SMED30022588 vs. TrEMBL
Match: H2XY84 (HIG1 domain-containing protein OS=Ciona intestinalis OX=7719 PE=4 SV=1)

HSP 1 Score: 65.0846 bits (157), Expect = 3.689e-10
Identity = 36/89 (40.45%), Postives = 49/89 (55.06%), Query Frame = 1 
Query:  277 YKYLSAPKELEIMNDFKKPSMLNFMKDNFIVVIGIGVTVSALINGLRHLVKGNKMEQQYMMRLRVGGQAFAIFALIGTAAYKSLYEKKK 543
            YK ++ P++     +F     L   KDN  V +G+  TV  L NGLRH+  GN+ + Q MMR RV  Q F I AL   A Y+S ++ KK
Sbjct:   42 YKPITIPEKKSFGGNF-----LQHCKDNPFVPLGLSATVLFLFNGLRHMRLGNRQQSQVMMRGRVMAQGFTIIALTCGAVYQSAFKSKK 125
[Close]
BLAST of SMED30022588 vs. TrEMBL
Match: R7V5B2 (HIG1 domain-containing protein OS=Capitella teleta OX=283909 GN=CAPTEDRAFT_169190 PE=4 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 3.376e-8
Identity = 28/63 (44.44%), Postives = 42/63 (66.67%), Query Frame = 1 
Query:  352 KDNFIVVIGIGVTVSALINGLRHLVKGNKMEQQYMMRLRVGGQAFAIFALIGTAAYKSLYEKK 540
            K+N +V +G+GVTV AL+ G   +  G+  + Q MMRLRVG QAF +F+L+G   Y+   E++
Sbjct:   29 KENPLVPLGLGVTVFALVYGSLQMKSGDVRKSQLMMRLRVGAQAFTLFSLLGGVYYQGWKERR 91
[Close]
BLAST of SMED30022588 vs. TrEMBL
Match: A0A2T7P8H6 (HIG1 domain-containing protein OS=Pomacea canaliculata OX=400727 GN=C0Q70_08983 PE=4 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 3.773e-8
Identity = 34/95 (35.79%), Postives = 48/95 (50.53%), Query Frame = 1 
Query:  235 IMDDNNNKSKNVLKYKYLSAPKELEIMNDFKKPSMLNFMKDNFIVVIGIGVTVSALINGLRHLVKGNKMEQQYMMRLRVGGQAFAIFALIGTAAY 519
            I  + +       ++ YL  P+EL    +  K  +L   K+N  V IG+ VT  AL  GL  +  GNK   Q MMRLR+ GQ F + A++   AY
Sbjct:    6 IKKEESTTKPGEEEFGYLPPPRELLYREEGVKEKLLRKTKENPFVPIGVLVTTFALSYGLWQMKTGNKRMSQNMMRLRIVGQGFTVMAVLAGVAY 100
[Close]
BLAST of SMED30022588 vs. TrEMBL
Match: T2M6P8 (HIG1 domain family member 2A OS=Hydra vulgaris OX=6087 GN=HIGD2A PE=2 SV=1)

HSP 1 Score: 57.7658 bits (138), Expect = 1.072e-7
Identity = 36/95 (37.89%), Postives = 53/95 (55.79%), Query Frame = 1 
Query:  259 SKNVLKYKYLSAPKELEIMNDFKKPSMLNFMKDNFIVVIGIGVTVSALINGLRHLVKGNKMEQQYMMRLRVGGQAFAIFALIGTAAYKSLYEKKK 543
             KN +++ ++  PK  E  +D      +   K+N  V IG G+TV+AL+ GL +L +GN  +QQ MMR RV  Q   I A+I    Y   Y+KK+
Sbjct:    6 EKNEVEHDFVWYPKPAETQSD----KFIRKFKENPFVPIGAGLTVTALVIGLVNLKRGNSAKQQTMMRARVVAQGSTIVAIIAGFLYHQ-YKKKQ 95
[Close]
BLAST of SMED30022588 vs. TrEMBL
Match: A0A2P8Y9G4 (HIG1 domain family member 2A OS=Blattella germanica OX=6973 GN=HIGD2A PE=4 SV=1)

HSP 1 Score: 57.7658 bits (138), Expect = 1.321e-7
Identity = 31/91 (34.07%), Postives = 47/91 (51.65%), Query Frame = 1 
Query:  241 DDNNNKSKNVLKYKYLSAPKEL--EIMNDFKKPSMLNFMKDNFIVVIGIGVTVSALINGLRHLVKGNKMEQQYMMRLRVGGQAFAIFALIG 507
            DD  N++KN  ++ ++   +E+  +I  +  +   +   KDN  V +G   T  AL  GL    KG +   QYMMRLR+  Q F + ALI 
Sbjct:    4 DDKQNQTKNEPEFDWIQLRREIRKDIAIETTQDKFIRKFKDNPFVPLGCLATFGALAYGLWSFRKGRRQMSQYMMRLRIAAQGFTVVALIA 94
[Close]
BLAST of SMED30022588 vs. Ensembl Nematostella
Match: EDO42758 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S0L4])

HSP 1 Score: 43.8986 bits (102), Expect = 2.565e-6
Identity = 25/60 (41.67%), Postives = 32/60 (53.33%), Query Frame = 1 
Query:  349 MKDNFIVVIGIGVTVSALINGLRHLVKGNKMEQQYMMRLRVGGQAFAIFALIGTAAYKSL 528
            +K+N  V IG   T  AL+ GL    +GN+  QQ MMR RV  Q   + A+IG   Y  L
Sbjct:   33 VKENPFVPIGCFATAGALVYGLLSFKRGNQKVQQQMMRARVLAQGSTLIAVIGGLGYTML 92
[Close]
BLAST of SMED30022588 vs. Planmine SMEST
Match: SMESG000022886.1 (SMESG000022886.1)

HSP 1 Score: 210.305 bits (534), Expect = 7.887e-71
Identity = 104/104 (100.00%), Postives = 104/104 (100.00%), Query Frame = 1 
Query:  238 MDDNNNKSKNVLKYKYLSAPKELEIMNDFKKPSMLNFMKDNFIVVIGIGVTVSALINGLRHLVKGNKMEQQYMMRLRVGGQAFAIFALIGTAAYKSLYEKKKII 549
            MDDNNNKSKNVLKYKYLSAPKELEIMNDFKKPSMLNFMKDNFIVVIGIGVTVSALINGLRHLVKGNKMEQQYMMRLRVGGQAFAIFALIGTAAYKSLYEKKKII
Sbjct:    1 MDDNNNKSKNVLKYKYLSAPKELEIMNDFKKPSMLNFMKDNFIVVIGIGVTVSALINGLRHLVKGNKMEQQYMMRLRVGGQAFAIFALIGTAAYKSLYEKKKII 104
The following BLAST results are available for this feature:
BLAST of SMED30022588 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 SMED30022588 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 SMED30022588 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 SMED30022588 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 SMED30022588 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 SMED30022588 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 SMED30022588 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 SMED30022588 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
H2XY843.689e-1040.45HIG1 domain-containing protein OS=Ciona intestinal... [more]
R7V5B23.376e-844.44HIG1 domain-containing protein OS=Capitella teleta... [more]
A0A2T7P8H63.773e-835.79HIG1 domain-containing protein OS=Pomacea canalicu... [more]
T2M6P81.072e-737.89HIG1 domain family member 2A OS=Hydra vulgaris OX=... [more]
A0A2P8Y9G41.321e-734.07HIG1 domain family member 2A OS=Blattella germanic... [more]
back to top
BLAST of SMED30022588 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 SMED30022588 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 SMED30022588 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 SMED30022588 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO427582.565e-641.67Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
back to top
BLAST of SMED30022588 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 SMED30022588 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000022886.17.887e-71100.00SMESG000022886.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022588 ID=SMED30022588|Name=SMED30022588|organism=Schmidtea mediterranea sexual|type=transcript|length=563bp
ACAATATTAAGAAATTGAATAATTTTATGATATTGTTTGGTATCGCAAAT
TTAATGTTAAGGAAATGAATTTTATACATAAAACTTTTTTAATATTTTTA
AATATTTTAATTTTATTATGAATTTTTATGAAATATATGTAACTCATCTT
ATGAAGAAATAAATCCTTACATTATACATTTGATAATTGAAATTTAACGA
TAAACATTTTAAACATTTAAATAAAGTTGTTTATATAATGGATGATAATA
ATAATAAGTCAAAAAATGTTCTCAAATATAAATATTTGTCTGCACCTAAA
GAATTAGAAATCATGAATGATTTCAAGAAACCATCTATGTTGAATTTCAT
GAAAGATAATTTTATCGTGGTGATAGGTATTGGCGTTACTGTTTCAGCTC
TTATTAACGGATTACGTCATTTGGTAAAAGGGAACAAAATGGAACAGCAA
TATATGATGCGTTTGCGAGTAGGTGGTCAAGCTTTTGCGATTTTCGCATT
AATTGGAACCGCAGCTTATAAGAGTTTATACGAAAAGAAAAAAATAATTT
GATAAAATTTACG
back to top

protein sequence of SMED30022588-orf-1

>SMED30022588-orf-1 ID=SMED30022588-orf-1|Name=SMED30022588-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=105bp
MDDNNNKSKNVLKYKYLSAPKELEIMNDFKKPSMLNFMKDNFIVVIGIGV
TVSALINGLRHLVKGNKMEQQYMMRLRVGGQAFAIFALIGTAAYKSLYEK
KKII*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR007667Hypoxia_induced_domain
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR007667Hypoxia induced protein, domainPFAMPF04588HIG_1_Ncoord: 41..90
e-value: 3.6E-14
score: 52.7
IPR007667Hypoxia induced protein, domainPROSITEPS51503HIG1coord: 13..104
score: 16.776
NoneNo IPR availablePANTHERPTHR12297HYPOXIA-INDUCBILE GENE 1 HIG1 -RELATEDcoord: 32..99
NoneNo IPR availablePANTHERPTHR12297:SF3HIG1 DOMAIN FAMILY MEMBER 2Acoord: 32..99
NoneNo IPR availableTMHMMTMhelixcoord: 78..97
NoneNo IPR availableTMHMMTMhelixcoord: 41..63