spermatid elongation defective 1

Overview
Namespermatid elongation defective 1 (ADG08185.1)
Smed IDSMED30009122
Length (bp)874
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 spermatid elongation defective 1 (SMED30009122) t-SNE clustered cells

Violin plots show distribution of expression levels for spermatid elongation defective 1 (SMED30009122) 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



SMED30009122

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
neoblastSMED30009122SMESG000010125.1 SMESG000001454.1 dd_Smed_v4_31167_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
testisSMED30009122SMESG000010125.1 SMESG000001454.1 Contig4559_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
early male germ cellSMED30009122SMESG000010125.1 SMESG000001454.1 Contig4559_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism asexual adult cDNA to DNA expression microarray evidence
testis primordiumSMED30009122SMESG000010125.1 SMESG000001454.1 Contig4559_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism juvenile cDNA to DNA expression microarray evidence
neoblastSMED30009122SMESG000010125.1 SMESG000001454.1 SMED_03087_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30009122SMESG000010125.1 SMESG000001454.1 SMED_03087_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of spermatid elongation defective 1 vs. TrEMBL
Match: E2FB13 (Spermatid elongation defective 1 OS=Schmidtea mediterranea OX=79327 GN=Sped-1 PE=2 SV=1)

HSP 1 Score: 403.675 bits (1036), Expect = 9.713e-141
Identity = 198/198 (100.00%), Postives = 198/198 (100.00%), Query Frame = 3 
Query:  186 MILLVTGLLPLMVELCLGSSQPSNLVLDKPVQYGSIKEGVKESWGNDGHINKNCFVSKDNGEKYWEVGLPYLSLISHIEIYSENEPNELRLITVSKPQKETKTVLAGKSCVDGCKIPINKELIKIRIEKLGPSALNLCEVAAYGKVNKVQENSVPSGGASTDASGTTADGKKRANSIEMCMFTHIFIISLMILITRCM 779
            MILLVTGLLPLMVELCLGSSQPSNLVLDKPVQYGSIKEGVKESWGNDGHINKNCFVSKDNGEKYWEVGLPYLSLISHIEIYSENEPNELRLITVSKPQKETKTVLAGKSCVDGCKIPINKELIKIRIEKLGPSALNLCEVAAYGKVNKVQENSVPSGGASTDASGTTADGKKRANSIEMCMFTHIFIISLMILITRCM
Sbjct:    1 MILLVTGLLPLMVELCLGSSQPSNLVLDKPVQYGSIKEGVKESWGNDGHINKNCFVSKDNGEKYWEVGLPYLSLISHIEIYSENEPNELRLITVSKPQKETKTVLAGKSCVDGCKIPINKELIKIRIEKLGPSALNLCEVAAYGKVNKVQENSVPSGGASTDASGTTADGKKRANSIEMCMFTHIFIISLMILITRCM 198
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BLAST of spermatid elongation defective 1 vs. Planmine SMEST
Match: SMESG000010125.1 (SMESG000010125.1)

HSP 1 Score: 383.259 bits (983), Expect = 2.106e-136
Identity = 187/187 (100.00%), Postives = 187/187 (100.00%), Query Frame = 3 
Query:  219 MVELCLGSSQPSNLVLDKPVQYGSIKEGVKESWGNDGHINKNCFVSKDNGEKYWEVGLPYLSLISHIEIYSENEPNELRLITVSKPQKETKTVLAGKSCVDGCKIPINKELIKIRIEKLGPSALNLCEVAAYGKVNKVQENSVPSGGASTDASGTTADGKKRANSIEMCMFTHIFIISLMILITRCM 779
            MVELCLGSSQPSNLVLDKPVQYGSIKEGVKESWGNDGHINKNCFVSKDNGEKYWEVGLPYLSLISHIEIYSENEPNELRLITVSKPQKETKTVLAGKSCVDGCKIPINKELIKIRIEKLGPSALNLCEVAAYGKVNKVQENSVPSGGASTDASGTTADGKKRANSIEMCMFTHIFIISLMILITRCM
Sbjct:    1 MVELCLGSSQPSNLVLDKPVQYGSIKEGVKESWGNDGHINKNCFVSKDNGEKYWEVGLPYLSLISHIEIYSENEPNELRLITVSKPQKETKTVLAGKSCVDGCKIPINKELIKIRIEKLGPSALNLCEVAAYGKVNKVQENSVPSGGASTDASGTTADGKKRANSIEMCMFTHIFIISLMILITRCM 187
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BLAST of spermatid elongation defective 1 vs. Planmine SMEST
Match: SMESG000001454.1 (SMESG000001454.1)

HSP 1 Score: 253.062 bits (645), Expect = 1.398e-85
Identity = 124/124 (100.00%), Postives = 124/124 (100.00%), Query Frame = 3 
Query:  186 MILLVTGLLPLMVELCLGSSQPSNLVLDKPVQYGSIKEGVKESWGNDGHINKNCFVSKDNGEKYWEVGLPYLSLISHIEIYSENEPNELRLITVSKPQKETKTVLAGKSCVDGCKIPINKELIK 557
            MILLVTGLLPLMVELCLGSSQPSNLVLDKPVQYGSIKEGVKESWGNDGHINKNCFVSKDNGEKYWEVGLPYLSLISHIEIYSENEPNELRLITVSKPQKETKTVLAGKSCVDGCKIPINKELIK
Sbjct:    1 MILLVTGLLPLMVELCLGSSQPSNLVLDKPVQYGSIKEGVKESWGNDGHINKNCFVSKDNGEKYWEVGLPYLSLISHIEIYSENEPNELRLITVSKPQKETKTVLAGKSCVDGCKIPINKELIK 124

HSP 2 Score: 47.3654 bits (111), Expect = 1.635e-6
Identity = 22/22 (100.00%), Postives = 22/22 (100.00%), Query Frame = 1 
Query:  556 KSELKNWVHRLLIFVKWQLMVK 621
            KSELKNWVHRLLIFVKWQLMVK
Sbjct:  124 KSELKNWVHRLLIFVKWQLMVK 145
[Close]
BLAST of spermatid elongation defective 1 vs. Planmine SMEST
Match: SMESG000074065.1 (SMESG000074065.1)

HSP 1 Score: 127.102 bits (318), Expect = 1.087e-35
Identity = 71/175 (40.57%), Postives = 101/175 (57.71%), Query Frame = 3 
Query:  255 NLVLDKPVQYGSIKEGVKESWGNDGHINKNCFVSKDNGEKYWEVGLPYLSLISHIEIYSENEPNELRLITVSKPQKETKTVLAGKSCVDGCKIPINKELIKIRIEKLGPSALNLCEVAAYGKVNKVQENSVPSGGASTDASGTTADGKKRANSIEMCMFTHIFIISLMILITRCM 779
            N+  DKPV YGSI+   +++W NDG  N NCF S + G+K+WEV L   + +  +EI S+N  NEL +    K   ETK  L G +C  GCK+ I +E+ K++I   G +AL LCEV AYG   +VQ      G +S    GTT    K +N +E+   T+  IIS + L+T+ +
Sbjct:   25 NVAKDKPVSYGSIENINQKNWANDGSENSNCFKSTETGDKFWEVDLINPTFVVELEIKSDNLANELLITIYDKKFVETKKSLTGTNCSKGCKLSIKQEVRKVKISLTGKTALQLCEVKAYGLAKEVQ------GLSSLSPGGTT----KNSNLVELNKITYFLIISSLALLTKSI 189
The following BLAST results are available for this feature:
BLAST of spermatid elongation defective 1 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 spermatid elongation defective 1 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 spermatid elongation defective 1 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 spermatid elongation defective 1 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 spermatid elongation defective 1 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 spermatid elongation defective 1 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 spermatid elongation defective 1 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 spermatid elongation defective 1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
E2FB139.713e-141100.00Spermatid elongation defective 1 OS=Schmidtea medi... [more]
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BLAST of spermatid elongation defective 1 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 spermatid elongation defective 1 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 spermatid elongation defective 1 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 spermatid elongation defective 1 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 spermatid elongation defective 1 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 spermatid elongation defective 1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000010125.12.106e-136100.00SMESG000010125.1[more]
SMESG000001454.11.398e-85100.00SMESG000001454.1[more]
SMESG000074065.11.087e-3540.57SMESG000074065.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30009122
GenBankADG08185.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009122 ID=SMED30009122|Name=spermatid elongation defective 1|organism=Schmidtea mediterranea sexual|type=transcript|length=874bp
AGTCGCTAGCTAAAAAAATGGGGAAGTCTGCTATAGATTATTAAATTCTT
TTATCAAAATTTTATGAAATTCTTAAATCAACAAACAAATAAATGAAATA
AAATCAATTGTTGTCTAGATATGATGGATTCAAATATGCTTATTGAATAT
TATTATTAATTCATTTATATTTTGAATTTATCACTATGATATTGTTGGTT
ACCGGCTTACTACCTTTGATGGTAGAGCTTTGTCTGGGCAGCAGCCAACC
AAGCAATCTAGTTCTAGATAAGCCAGTGCAATACGGAAGCATCAAAGAAG
GTGTTAAAGAATCATGGGGAAATGATGGCCATATCAATAAAAATTGCTTT
GTAAGTAAAGACAACGGAGAAAAGTATTGGGAAGTAGGTTTGCCATATCT
ATCCTTGATTTCCCATATAGAAATATATTCTGAAAATGAGCCAAATGAAT
TGCGGCTCATTACAGTATCAAAACCACAAAAAGAAACAAAAACCGTTTTG
GCCGGAAAATCTTGTGTTGACGGTTGTAAAATCCCTATAAATAAAGAACT
GATAAAAATCAGAATTGAAAAATTGGGTCCATCGGCTCTTAATCTTTGTG
AAGTGGCAGCTTATGGTAAAGTGAATAAAGTTCAAGAGAATTCTGTTCCA
AGTGGAGGCGCATCAACGGACGCGTCAGGAACAACTGCTGATGGAAAGAA
AAGAGCAAATTCAATTGAAATGTGCATGTTTACTCACATTTTCATTATTT
CCTTAATGATTCTGATAACCAGATGTATGTGAATCGCTTGATTGAACAAA
TTTCTTTTTTCGAACCAATAGGGTAAAACTCAAAATAAGTTAGTTATTAA
ATTTAAGTTGCATAGTTGTAAGGA
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protein sequence of SMED30009122-orf-1

>SMED30009122-orf-1 ID=SMED30009122-orf-1|Name=SMED30009122-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=199bp
MILLVTGLLPLMVELCLGSSQPSNLVLDKPVQYGSIKEGVKESWGNDGHI
NKNCFVSKDNGEKYWEVGLPYLSLISHIEIYSENEPNELRLITVSKPQKE
TKTVLAGKSCVDGCKIPINKELIKIRIEKLGPSALNLCEVAAYGKVNKVQ
ENSVPSGGASTDASGTTADGKKRANSIEMCMFTHIFIISLMILITRCM*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
PLANA:0000429neoblast
PLANA:0002030early male germ cell
PLANA:0003304testis primordium
Vocabulary: INTERPRO
TermDefinition
IPR008979Galactose-bd-like_sf
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR008979Galactose-binding-like domain superfamilyGENE3DG3DSA:2.60.120.260coord: 16..144
e-value: 1.1E-6
score: 30.6
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..18
score: 0.793