Steroid dehydrogenase

Overview
NameSteroid dehydrogenase
Smed IDSMED30027222
Length (bp)649
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 Steroid dehydrogenase (SMED30027222) t-SNE clustered cells

Violin plots show distribution of expression levels for Steroid dehydrogenase (SMED30027222) in cells (dots) of each of the 12 neoblast clusters.

 

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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 Steroid dehydrogenase (SMED30027222) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Steroid dehydrogenase (SMED30027222) 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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Homology
BLAST of Steroid dehydrogenase vs. Ensembl Fly
Match: crim (gene:FBgn0036198 transcript:FBtr0076123)

HSP 1 Score: 45.0542 bits (105), Expect = 7.775e-6
Identity = 28/70 (40.00%), Postives = 36/70 (51.43%), Query Frame = 1
Query:  118 WCYRCQSAQSGCGGKIDIRIKHWM--YCLNTVAAKNMCVKVIERIAGQEYITRGCLDDLVRDTRHRFDMP 321
            WCYRC SA  GC  K + R   ++  +C       ++CVKV ER   +E ITR CL  L      R D+P
Sbjct:   24 WCYRCTSATPGCAEKFNWRGIGFLGEHCPE---PDDICVKVTERRGARETITRDCLSALS----FRKDIP 86          
BLAST of Steroid dehydrogenase vs. TrEMBL
Match: A0A5K3EPV6 (Uncharacterized protein OS=Mesocestoides corti OX=53468 PE=4 SV=1)

HSP 1 Score: 118.627 bits (296), Expect = 4.811e-30
Identity = 62/143 (43.36%), Postives = 80/143 (55.94%), Query Frame = 1
Query:   67 SLLFLCIATAHANMLVKWCYRCQSAQSGCGGKIDIRIKHWMYCLNTVAAKNMCVKVIERIAGQEYITRGCLDDLVRDTRHRFDMPNVIRHGYCEESKSTIAMKQSGYSGQD---------------NKVYCFCNDFDGCNSSD 450
            SL+FL ++   A+    WCY C SAQSGCG  IDIR +HW YC      + MCVK+IE++  Q  +TRGCL DL+  ++ R DMP V RHGYC  S S     Q    G +                K++CFC+D+ GCNS D
Sbjct:    7 SLIFLSLS-RFASCYNFWCYNCSSAQSGCGPPIDIRTEHWKYCSGAPVYEQMCVKIIEKVNDQVQVTRGCLSDLLLTSQIRLDMPKVRRHGYCLYSASNQRYLQKHLRGSELALWTMGVLRPDAEMYKLFCFCDDWPGCNSKD 148          
BLAST of Steroid dehydrogenase vs. TrEMBL
Match: A0A0R3TTX9 (Protein quiver OS=Rodentolepis nana OX=102285 GN=HNAJ_LOCUS11179 PE=4 SV=1)

HSP 1 Score: 117.857 bits (294), Expect = 1.053e-29
Identity = 56/126 (44.44%), Postives = 73/126 (57.94%), Query Frame = 1
Query:  118 WCYRCQSAQSGCGGKIDIRIKHWMYCLNTVAAKNMCVKVIERIAGQEYITRGCLDDLVRDTRHRFDMPNVIRHGYCEESKSTIAMKQSGYSGQD---------------NKVYCFCNDFDGCNSSD 450
            WCY C SAQSGCG  +D+R +HW YCL     + MCVK+IE++  Q  ITRGCL D++  T+ R D+P V RHGYC  S S     Q    G +                K++CFC+D+ GCNS+D
Sbjct:   24 WCYNCTSAQSGCGPPLDVRTQHWKYCLGAPVYEQMCVKIIEKVNDQVTITRGCLSDMLLTTQIRLDLPKVRRHGYCLYSASNQRYLQRILRGSELASWIMGVLRPETEMYKLFCFCDDWPGCNSND 149          
BLAST of Steroid dehydrogenase vs. TrEMBL
Match: A0A564YYV2 (Uncharacterized protein (Fragment) OS=Hymenolepis diminuta OX=6216 GN=WMSIL1_LOCUS10397 PE=4 SV=1)

HSP 1 Score: 117.087 bits (292), Expect = 2.273e-29
Identity = 59/144 (40.97%), Postives = 80/144 (55.56%), Query Frame = 1
Query:   73 LFLCIATAHANMLVK--WCYRCQSAQSGCGGKIDIRIKHWMYCLNTVAAKNMCVKVIERIAGQEYITRGCLDDLVRDTRHRFDMPNVIRHGYCEESKSTIAMKQSGYSGQD---------------NKVYCFCNDFDGCNSSDR 453
            + +C+ T  ++   K  WCY C SAQSGCG  +D+R +HW YC      + MCVK+IE++  Q  ITRGCL D++  T+ R D+P V RHGYC  S S     Q    G +                K++CFC+D+ GCNS DR
Sbjct:    6 VLICLFTLFSSGWSKGFWCYNCTSAQSGCGPPLDVRTQHWKYCSGAPVYEQMCVKIIEKVNDQVTITRGCLSDMLLTTQIRLDIPKVRRHGYCLYSTSNQRYLQRILRGSELATWTMGVLRPETEMYKLFCFCDDWPGCNSIDR 149          
BLAST of Steroid dehydrogenase vs. TrEMBL
Match: A0A0R3WW17 (Protein quiver OS=Hydatigena taeniaeformis OX=6205 PE=4 SV=1)

HSP 1 Score: 116.316 bits (290), Expect = 6.589e-29
Identity = 56/126 (44.44%), Postives = 73/126 (57.94%), Query Frame = 1
Query:  118 WCYRCQSAQSGCGGKIDIRIKHWMYCLNTVAAKNMCVKVIERIAGQEYITRGCLDDLVRDTRHRFDMPNVIRHGYCEESKST------------IAMKQSGYSGQDN---KVYCFCNDFDGCNSSD 450
            WCY C SAQSGCG  +D+R +HW YC      + MCVK+IE++  Q  ITRGCL DL+  T+ R D+P V RHGYC  S S             +A+   G    +    K+YCFC+D+ GCNS+ 
Sbjct:   35 WCYNCSSAQSGCGPPLDVRTQHWKYCSGVPVYEQMCVKIIEKVNDQITITRGCLSDLLLTTQIRLDIPRVRRHGYCLYSVSNQRYLHQHLRGSELALWAMGMLRPETEMYKLYCFCDDWPGCNSTS 160          
BLAST of Steroid dehydrogenase vs. TrEMBL
Match: A0A3P7ERL9 (Uncharacterized protein OS=Hydatigena taeniaeformis OX=6205 GN=TTAC_LOCUS4942 PE=4 SV=1)

HSP 1 Score: 116.316 bits (290), Expect = 6.953e-29
Identity = 56/126 (44.44%), Postives = 73/126 (57.94%), Query Frame = 1
Query:  118 WCYRCQSAQSGCGGKIDIRIKHWMYCLNTVAAKNMCVKVIERIAGQEYITRGCLDDLVRDTRHRFDMPNVIRHGYCEESKST------------IAMKQSGYSGQDN---KVYCFCNDFDGCNSSD 450
            WCY C SAQSGCG  +D+R +HW YC      + MCVK+IE++  Q  ITRGCL DL+  T+ R D+P V RHGYC  S S             +A+   G    +    K+YCFC+D+ GCNS+ 
Sbjct:   35 WCYNCSSAQSGCGPPLDVRTQHWKYCSGVPVYEQMCVKIIEKVNDQITITRGCLSDLLLTTQIRLDIPRVRRHGYCLYSVSNQRYLHQHLRGSELALWAMGMLRPETEMYKLYCFCDDWPGCNSTS 160          
BLAST of Steroid dehydrogenase vs. Planmine SMEST
Match: SMESG000041295.1 (SMESG000041295.1)

HSP 1 Score: 293.893 bits (751), Expect = 9.612e-103
Identity = 155/156 (99.36%), Postives = 156/156 (100.00%), Query Frame = 1
Query:   55 MKYFSLLFLCIATAHANMLVKWCYRCQSAQSGCGGKIDIRIKHWMYCLNTVAAKNMCVKVIERIAGQEYITRGCLDDLVRDTRHRFDMPNVIRHGYCEESKSTIAMKQSGYSGQDNKVYCFCNDFDGCNSSDRXXXXXXXXXXXXXXVVAAILANY 522
            MKYF+LLFLCIATAHANMLVKWCYRCQSAQSGCGGKIDIRIKHWMYCLNTVAAKNMCVKVIERIAGQEYITRGCLDDLVRDTRHRFDMPNVIRHGYCEESKSTIAMKQSGYSGQDNKVYCFCNDFDGCNSSDRLLSISSNILFLLFIVVAAILANY
Sbjct:    1 MKYFTLLFLCIATAHANMLVKWCYRCQSAQSGCGGKIDIRIKHWMYCLNTVAAKNMCVKVIERIAGQEYITRGCLDDLVRDTRHRFDMPNVIRHGYCEESKSTIAMKQSGYSGQDNKVYCFCNDFDGCNSSDRLLSISSNILFLLFIVVAAILANY 156          
The following BLAST results are available for this feature:
BLAST of Steroid dehydrogenase 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 Steroid dehydrogenase 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 Steroid dehydrogenase vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
crim7.775e-640.00gene:FBgn0036198 transcript:FBtr0076123[more]
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BLAST of Steroid dehydrogenase 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 Steroid dehydrogenase 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 Steroid dehydrogenase 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 Steroid dehydrogenase 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 Steroid dehydrogenase vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A5K3EPV64.811e-3043.36Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A0R3TTX91.053e-2944.44Protein quiver OS=Rodentolepis nana OX=102285 GN=H... [more]
A0A564YYV22.273e-2940.97Uncharacterized protein (Fragment) OS=Hymenolepis ... [more]
A0A0R3WW176.589e-2944.44Protein quiver OS=Hydatigena taeniaeformis OX=6205... [more]
A0A3P7ERL96.953e-2944.44Uncharacterized protein OS=Hydatigena taeniaeformi... [more]
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BLAST of Steroid dehydrogenase 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 Steroid dehydrogenase 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 Steroid dehydrogenase 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 Steroid dehydrogenase 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 Steroid dehydrogenase 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 Steroid dehydrogenase vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000041295.19.612e-10399.36SMESG000041295.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027222 ID=SMED30027222|Name=Steroid dehydrogenase|organism=Schmidtea mediterranea sexual|type=transcript|length=649bp
TTTAAATATTGCTTCTATAAACTGCTTAATATTTAAATTATATTATTTTC
CTCAATGAAATATTTCTCACTTTTATTTTTATGTATCGCAACAGCTCATG
CCAATATGTTGGTAAAATGGTGTTATCGCTGCCAAAGTGCTCAAAGTGGT
TGTGGTGGAAAAATTGATATTCGAATCAAACATTGGATGTATTGCTTGAA
TACTGTTGCAGCAAAAAACATGTGTGTTAAAGTAATTGAAAGAATTGCAG
GACAAGAATATATCACACGAGGTTGTCTAGATGATTTGGTTCGTGATACT
AGACATCGATTTGATATGCCGAATGTAATTCGGCATGGGTATTGTGAGGA
AAGCAAAAGTACCATTGCCATGAAACAATCGGGATACTCAGGACAGGATA
ATAAAGTTTATTGTTTTTGCAATGATTTTGATGGATGTAATTCAAGCGAT
CGTCTGTTGAGTATTTCCAGTAACATTTTGTTTCTTTTATTCATTGTGGT
AGCAGCTATTTTGGCAAATTATGATTTTTAAGTTTTTTAAATTAAATTTA
TATTTGACCTCCTTTTGCACTTTGTGCTTGGTTTACATAAGATTTCAGTT
AGTATTGTCATTATATATTTATATATCAATAAATATTCTTGTATTGAAA
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protein sequence of SMED30027222-orf-1

>SMED30027222-orf-1 ID=SMED30027222-orf-1|Name=SMED30027222-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=159bp
MKYFSLLFLCIATAHANMLVKWCYRCQSAQSGCGGKIDIRIKHWMYCLNT
VAAKNMCVKVIERIAGQEYITRGCLDDLVRDTRHRFDMPNVIRHGYCEES
KSTIAMKQSGYSGQDNKVYCFCNDFDGCNSSDRLLSISSNILFLLFIVVA
AILANYDF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: biological process
TermDefinition
GO:0030431sleep
GO:0032222regulation of synaptic transmission, cholinergic
GO:1903818positive regulation of voltage-gated potassium channel activity
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000074oocyte
PLANA:0000231vitelline gland
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
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..16
score: 0.874
NoneNo IPR availableTMHMMTMhelixcoord: 134..156