Reverse transcriptase domain-containing protein

Overview
NameReverse transcriptase domain-containing protein
Smed IDSMED30010644
Length (bp)632
Neoblast Clusters

Zeng et. al., 2018




 



 

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




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




SMED30010644

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30010644 Contig920GPL15192PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
ovarySMED30010644 Contig920GPL15192PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testisSMED30010644 Contig920GPL15192PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
ovarySMED30010644 PL030009A20C03ncbi_smed_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testisSMED30010644 PL030009A20C03ncbi_smed_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
reproductive organSMED30010644 Contig41757uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30010644 Contig41757newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Reverse transcriptase domain-containing protein vs. TrEMBL
Match: A0A0C2N2C4 (Retrovirus-related Pol polyprotein OS=Thelohanellus kitauei OX=669202 GN=RF11_14843 PE=4 SV=1)

HSP 1 Score: 56.9954 bits (136), Expect = 6.358e-6
Identity = 34/84 (40.48%), Postives = 44/84 (52.38%), Query Frame = 2
Query:  137 ATQLRSFLGTVNYFHLFIQRFPKFSHHCLVFVQIQRNL*LFGMKFCWTHLKKLKTCLANIQTLHYPKRILELRLTTDASNIAIG 388
            AT+L+ FLG   YF  FI+ F   +H CL +    +N        C     KLKT L+ +  LH+PK  + L L TDAS  AIG
Sbjct:  656 ATELKRFLGFCGYFQKFIKNFASIAH-CL-YSLTSKNTKFVRSPDCQEAFNKLKTSLSQLPLLHFPKPGIPLHLHTDASGKAIG 737          
BLAST of Reverse transcriptase domain-containing protein vs. Planmine SMEST
Match: SMESG000037560.1 (SMESG000037560.1)

HSP 1 Score: 177.948 bits (450), Expect = 7.278e-58
Identity = 87/87 (100.00%), Postives = 87/87 (100.00%), Query Frame = -2
Query:   23 MRPAKLHSKQLKISLDLNKDQTVVREFRKSLDKQMKVVYCSQKTSQLSCCLSASSYGHYTAVTCLTKLFIANTYLYCLNAFSIKFTI 283
            MRPAKLHSKQLKISLDLNKDQTVVREFRKSLDKQMKVVYCSQKTSQLSCCLSASSYGHYTAVTCLTKLFIANTYLYCLNAFSIKFTI
Sbjct:    1 MRPAKLHSKQLKISLDLNKDQTVVREFRKSLDKQMKVVYCSQKTSQLSCCLSASSYGHYTAVTCLTKLFIANTYLYCLNAFSIKFTI 87          
BLAST of Reverse transcriptase domain-containing protein vs. Planmine SMEST
Match: SMESG000022029.1 (SMESG000022029.1)

HSP 1 Score: 64.3142 bits (155), Expect = 6.163e-13
Identity = 31/40 (77.50%), Postives = 34/40 (85.00%), Query Frame = -1
Query:  399 TQISRELQRTKATWIEPSRVKSIYQRLTVAQRGWQEDKAL 518
             Q+S ELQRTKATWIE S VK IYQRLT AQRGW+E+KAL
Sbjct:   26 VQLSHELQRTKATWIETSGVKRIYQRLTAAQRGWKEEKAL 65          
BLAST of Reverse transcriptase domain-containing protein vs. Planmine SMEST
Match: SMESG000036641.1 (SMESG000036641.1)

HSP 1 Score: 62.7734 bits (151), Expect = 1.099e-11
Identity = 42/106 (39.62%), Postives = 62/106 (58.49%), Query Frame = -1
Query:  207 QISRELQRTKATWIEPSRVKSIYQRLTVAQRGWQEDKALKTHRQWLYSKHQLLNVTPKSF*GNVMFVY*LDMF---LAFSNASSKTSFQTTKDFFGFEQRPDSGER 515
            Q+SRE+Q+ +ATWIEP+R K+I QRLT AQRGW E+K L  +++   ++++ L V   +        Y L +    +A+ +ASS T   T K     +QRP   ER
Sbjct:  183 QMSREIQKIRATWIEPARAKAINQRLTAAQRGWAEEKQLVQNQR---TQNRSLEVALLACQEGNAVTYQLVIAPAQIAYRDASSTTKPVTAK---RPQQRPGKTER 282          
BLAST of Reverse transcriptase domain-containing protein vs. Planmine SMEST
Match: SMESG000042603.1 (SMESG000042603.1)

HSP 1 Score: 58.5362 bits (140), Expect = 7.611e-11
Identity = 26/59 (44.07%), Postives = 41/59 (69.49%), Query Frame = -1
Query:  396 ENNNCIYHWRITRVC*PWTQISRELQRTKATWIEPSRVKSIYQRLTVAQRGWQEDKALK 572
            +NN  +Y   +        Q+++E+Q+ K+TW++P+R+KSIYQRLT AQRGW E++ L 
Sbjct:   16 QNNQSLYGQIL--------QLTKEVQQVKSTWVDPARLKSIYQRLTAAQRGWAEERQLN 66          
BLAST of Reverse transcriptase domain-containing protein vs. Planmine SMEST
Match: SMESG000043233.1 (SMESG000043233.1)

HSP 1 Score: 58.151 bits (139), Expect = 9.106e-11
Identity = 25/39 (64.10%), Postives = 33/39 (84.62%), Query Frame = -1
Query:  399 QISRELQRTKATWIEPSRVKSIYQRLTVAQRGWQEDKAL 515
            Q++RE+Q+ KATWI+P +VKS+YQRLT AQ GW E+K L
Sbjct:   21 QLTREVQQVKATWIDPRKVKSLYQRLTTAQNGWAEEKQL 59          
The following BLAST results are available for this feature:
BLAST of Reverse transcriptase domain-containing protein 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 Reverse transcriptase domain-containing protein 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 Reverse transcriptase domain-containing protein 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 Reverse transcriptase domain-containing protein 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 Reverse transcriptase domain-containing protein 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 Reverse transcriptase domain-containing protein 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 Reverse transcriptase domain-containing protein 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 Reverse transcriptase domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A0C2N2C46.358e-640.48Retrovirus-related Pol polyprotein OS=Thelohanellu... [more]
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BLAST of Reverse transcriptase domain-containing protein 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 Reverse transcriptase domain-containing protein 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 Reverse transcriptase domain-containing protein 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 Reverse transcriptase domain-containing protein 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 Reverse transcriptase domain-containing protein 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 Reverse transcriptase domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000037560.17.278e-58100.00SMESG000037560.1[more]
SMESG000022029.16.163e-1377.50SMESG000022029.1[more]
SMESG000036641.11.099e-1139.62SMESG000036641.1[more]
SMESG000042603.17.611e-1144.07SMESG000042603.1[more]
SMESG000043233.19.106e-1164.10SMESG000043233.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010644 ID=SMED30010644|Name=Reverse transcriptase domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=632bp
TCGCATTTTTTTTTTTTTTTTTTATAGTGAATTTTATTGAAAAAGCATTT
AAGCAATACAGATAGGTGTTGGCAATGAATAATTTCGTCAGACACGTTAC
TGCAGTGTAGTGACCATACGAAGAAGCGCTAAGACAGCAACTCAATTGAG
AAGTTTTTTGGGAACAGTAAACTACTTTCATCTGTTTATCCAAAGATTTC
CGAAATTCTCTCACCACTGTCTGGTCTTTGTTCAAATCCAAAGAAATCTT
TAGTTGTTTGGAATGAAGTTTTGCTGGACGCATTTGAAAAAGCTAAAAAC
ATGTCTAGCTAATATACAAACATTACATTACCCTAAAAGGATTTTGGAGT
TACGTTTAACAACTGATGCTTCGAATATAGCCATTGGCGATGTGTTTTTA
AGGCTTTATCTTCTTGCCAACCCCTTTGAGCCACCGTGAGCCTTTGATAG
ATGCTTTTTACCCGCGAAGGCTCTATCCACGTGGCCTTAGTTCGTTGCAG
TTCCCGGCTGATTTGCGTCCATGGTTAGCAAACTCGAGTAATTCTCCAGT
GATAGATACAATTATTATTCTCATTAATTAATAATAGCGAATATTACTCC
TACTTAATTATTTTATTGTTTTTTTAATCATT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000204ovary
PLANA:0000208testis
PLANA:0002089reproductive organ