RNase H domain-containing protein

Overview
NameRNase H domain-containing protein
Smed IDSMED30030343
Length (bp)505
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




SMED30030343

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pigment cellSMED30030343 SmedASXL_073320SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017
whole organism asexual adult RNA-sequencing evidence
parenchymal cellSMED30030343 dd_Smed_v4_15487_0_2dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of RNase H domain-containing protein vs. TrEMBL
Match: A0A5S6QCD8 (Uncharacterized protein OS=Trichuris muris OX=70415 PE=4 SV=1)

HSP 1 Score: 82.8037 bits (203), Expect = 3.133e-15
Identity = 35/84 (41.67%), Postives = 63/84 (75.00%), Query Frame = 3
Query:    3 EGKIWCDVSNQRLGVCLENKETIVEEASWLRKKDDHLYINVAELDAVLQGINLTVGYNLQKL-VIIDTASVSKWIDNILSGKTK 251
            E ++W D S+  +GV LE   T++E+ +WLR  DD  +IN+AELDA+++G+NL + + ++++ ++ D+A+V +WID+ LSG+T+
Sbjct:  456 EARVWVDASSLAIGVALEVDGTVIEDGTWLR-PDDARHINMAELDAIIKGLNLAIAWQMKRIEIMTDSATVHRWIDDGLSGRTR 538          
BLAST of RNase H domain-containing protein vs. TrEMBL
Match: A0A5S6QC23 (Uncharacterized protein OS=Trichuris muris OX=70415 PE=4 SV=1)

HSP 1 Score: 82.4185 bits (202), Expect = 4.237e-15
Identity = 35/84 (41.67%), Postives = 63/84 (75.00%), Query Frame = 3
Query:    3 EGKIWCDVSNQRLGVCLENKETIVEEASWLRKKDDHLYINVAELDAVLQGINLTVGYNLQKL-VIIDTASVSKWIDNILSGKTK 251
            E ++W D S+  +GV LE   T++E+ +WLR  DD  +IN+AELDA+++G+NL + + ++++ ++ D+A+V +WID+ LSG+T+
Sbjct:  456 EARVWVDASSLAIGVALEVDGTVIEDGTWLR-PDDARHINMAELDAIIKGLNLAIAWQMKRIEIMTDSATVHRWIDDGLSGRTR 538          
BLAST of RNase H domain-containing protein vs. TrEMBL
Match: A0A5S6Q5E4 (Uncharacterized protein OS=Trichuris muris OX=70415 PE=4 SV=1)

HSP 1 Score: 81.6481 bits (200), Expect = 6.900e-15
Identity = 35/84 (41.67%), Postives = 63/84 (75.00%), Query Frame = 3
Query:    3 EGKIWCDVSNQRLGVCLENKETIVEEASWLRKKDDHLYINVAELDAVLQGINLTVGYNLQKL-VIIDTASVSKWIDNILSGKTK 251
            E ++W D S+  +GV LE   T++E+ +WLR  DD  +IN+AELDA+++G+NL + + ++++ ++ D+A+V +WID+ LSG+T+
Sbjct:  456 EARVWVDASSLAIGVALEVDGTVIEDGTWLR-PDDARHINMAELDAIIKGLNLAIAWQMKRIEIMTDSATVHRWIDDGLSGRTR 538          
BLAST of RNase H domain-containing protein vs. TrEMBL
Match: A0A085M3Y4 (Uncharacterized protein OS=Trichuris suis OX=68888 GN=M513_07259 PE=4 SV=1)

HSP 1 Score: 81.6481 bits (200), Expect = 7.139e-15
Identity = 38/84 (45.24%), Postives = 61/84 (72.62%), Query Frame = 3
Query:    3 EGKIWCDVSNQRLGVCLENKETIVEEASWLRKKDDHLYINVAELDAVLQGINLTVGYNLQKL-VIIDTASVSKWIDNILSGKTK 251
            E ++W D S+  +GV LE    IVE+ASWLR  D+  +IN+AELDAV++G+NL + + + K+ ++ D+++V +WI + LSGKT+
Sbjct:  539 EARVWVDASSLAIGVALEVDGAIVEDASWLR-SDEASHINMAELDAVVKGLNLAISWRMSKIQLVTDSSTVHRWITDGLSGKTR 621          
BLAST of RNase H domain-containing protein vs. TrEMBL
Match: A0A0V0Z4F8 (Integrase catalytic domain-containing protein OS=Trichinella patagoniensis OX=990121 GN=T12_2484 PE=4 SV=1)

HSP 1 Score: 81.6481 bits (200), Expect = 7.675e-15
Identity = 38/84 (45.24%), Postives = 62/84 (73.81%), Query Frame = 3
Query:    3 EGKIWCDVSNQRLGVCLENKETIVEEASWLRKKDDHLYINVAELDAVLQGINLTVGYNLQKL-VIIDTASVSKWIDNILSGKTK 251
            E KIW D S+  +GV LE   +IVE+A+WLR  DD  +IN+AELDAV++G+NL + + ++++ ++ D+A+V +W+ + LSGK +
Sbjct:  221 EAKIWVDASSLAIGVALEVGGSIVEDAAWLR-PDDAQHINMAELDAVIKGLNLALSWQMRRIRLMTDSATVHRWVSDGLSGKAR 303          
BLAST of RNase H domain-containing protein vs. Planmine SMEST
Match: SMESG000002973.1 (SMESG000002973.1)

HSP 1 Score: 103.605 bits (257), Expect = 5.138e-26
Identity = 51/82 (62.20%), Postives = 65/82 (79.27%), Query Frame = 3
Query:    9 KIWCDVSNQRLGVCLENKETIVEEASWLRKKDDHLYINVAELDAVLQGINLTVGYNLQKLVII-DTASVSKWIDNILSGKTK 251
            KIWCD SN  L VCLE  E I+++ASWLRKK+DHLYINVAEL+AVL+GINL   + L+  +II D+A+V KW++N L+GK K
Sbjct:  633 KIWCDASNIALVVCLEINENIIDDASWLRKKNDHLYINVAELEAVLRGINLAGRWGLKDFIIIMDSATVFKWVNNFLTGKRK 714          
BLAST of RNase H domain-containing protein vs. Planmine SMEST
Match: SMESG000002973.1 (SMESG000002973.1)

HSP 1 Score: 80.8777 bits (198), Expect = 3.544e-18
Identity = 38/52 (73.08%), Postives = 44/52 (84.62%), Query Frame = 3
Query:    9 KIWCDVSNQRLGVCLENKETIVEEASWLRKKDDHLYINVAELDAVLQGINLT 164
            KIWCD SN  L VCLE  E I+++ASWLRKK+DHLYINVAEL+AVL+GINL 
Sbjct:  633 KIWCDASNIALVVCLEINENIIDDASWLRKKNDHLYINVAELEAVLRGINLA 684          
BLAST of RNase H domain-containing protein vs. Planmine SMEST
Match: SMESG000019677.1 (SMESG000019677.1)

HSP 1 Score: 73.1738 bits (178), Expect = 1.452e-15
Identity = 36/83 (43.37%), Postives = 57/83 (68.67%), Query Frame = 3
Query:    6 GKIWCDVSNQRLGVCLENKETIVEEASWLRKKDDHLYINVAELDAVLQGINLTVGYNLQKLVI-IDTASVSKWIDNILSGKTK 251
            G IWCD S+  +G+ LE ++ +VE+A WLRK DD  +IN+ EL+A+++G+NL +  NL+ + I  D+ SV  W++ +LS   K
Sbjct:  205 GIIWCDASSIAIGIVLEMEDAMVEDACWLRKPDDSRHINLVELEAIVKGVNLCIKRNLKYIKIKSDSKSVVCWVNKVLSNDRK 287          
BLAST of RNase H domain-containing protein vs. Planmine SMEST
Match: SMESG000076049.1 (SMESG000076049.1)

HSP 1 Score: 72.4034 bits (176), Expect = 3.847e-15
Identity = 36/88 (40.91%), Postives = 57/88 (64.77%), Query Frame = 3
Query:    6 GKIWCDVSNQRLGVCLENKETIVEEASWLRKKDDHLYINVAELDAVLQGINLTVGYNLQKLVI-IDTASVSKWIDNILSGKTKPFQFD 266
            G +WCD S+  +GV +E     VE+A+WLRK DD  +IN  EL+A L+GI + + +NLQ +++  D+A V +W   +LS  ++P + D
Sbjct:  269 GIVWCDASSLAIGVVVEIGTMSVEDATWLRKPDDATHINHVELEATLKGIEIVISWNLQAVLLKKDSAWVYRWFKEVLSDDSRPKRKD 356          
BLAST of RNase H domain-containing protein vs. Planmine SMEST
Match: SMESG000012165.1 (SMESG000012165.1)

HSP 1 Score: 66.6254 bits (161), Expect = 1.872e-13
Identity = 34/81 (41.98%), Postives = 54/81 (66.67%), Query Frame = 3
Query:   12 IWCDVSNQRLGVCLENKETIVEEASWLRKKDDHLYINVAELDAVLQGINLTVGYNLQKLVII-DTASVSKWIDNILSGKTK 251
            +WCD S+  +G  LE    I+E+A WLRK+ D  +IN+ EL+A+++GINL + +NL+ + I+ D  SV  W+ N L+ + K
Sbjct:  191 LWCDASSIAIGAALEIDGNIMEDACWLRKEKDVRHINLCELEAIVKGINLCIKWNLKFVKIMSDNKSVVSWVHNSLTSERK 271          
The following BLAST results are available for this feature:
BLAST of RNase H 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 RNase H 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 RNase H 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 RNase H 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 RNase H 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 RNase H 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 RNase H 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 RNase H domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A5S6QCD83.133e-1541.67Uncharacterized protein OS=Trichuris muris OX=7041... [more]
A0A5S6QC234.237e-1541.67Uncharacterized protein OS=Trichuris muris OX=7041... [more]
A0A5S6Q5E46.900e-1541.67Uncharacterized protein OS=Trichuris muris OX=7041... [more]
A0A085M3Y47.139e-1545.24Uncharacterized protein OS=Trichuris suis OX=68888... [more]
A0A0V0Z4F87.675e-1545.24Integrase catalytic domain-containing protein OS=T... [more]
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BLAST of RNase H 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 RNase H 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 RNase H 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 RNase H 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 RNase H 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 RNase H domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000002973.15.138e-2662.20SMESG000002973.1[more]
SMESG000002973.13.544e-1873.08SMESG000002973.1[more]
SMESG000019677.11.452e-1543.37SMESG000019677.1[more]
SMESG000076049.13.847e-1540.91SMESG000076049.1[more]
SMESG000012165.11.872e-1341.98SMESG000012165.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030343 ID=SMED30030343|Name=RNase H domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=505bp
ATGAAGGTAAAATTTGGTGCGACGTAAGTAATCAACGCCTTGGAGTCTGC
TTGGAAAATAAGGAAACAATTGTTGAAGAAGCGTCATGGTTGAGGAAGAA
AGATGATCATTTATACATTAATGTCGCAGAATTAGATGCGGTTTTACAAG
GCATCAATCTTACGGTTGGATATAACCTCCAAAAATTAGTCATCATAGAT
ACTGCCTCGGTGTCTAAATGGATCGACAATATCTTGTCAGGAAAAACGAA
ACCTTTTCAATTTGATAAGAAAATGAAATTAATGTATTATATCAAAATTT
TAATTCTAACATAACCTAAAACAGATATATAATTATTCCAAATTCAATCA
GATTTAAAGCAGATAAACATACTTATTAGAGGTTATTTGAGCGTTGGCAT
ATTGCCGATTCTTATTGAGCCACAAAAATGTCAAATGAGTGTGACATACA
AATTGGGTTTAATTTTGAAATGGTGCAAACTTTTGGTTGCTTTTTCCAAA
AGCAG
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protein sequence of SMED30030343-orf-1

>SMED30030343-orf-1 ID=SMED30030343-orf-1|Name=SMED30030343-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=104bp
EGKIWCDVSNQRLGVCLENKETIVEEASWLRKKDDHLYINVAELDAVLQG
INLTVGYNLQKLVIIDTASVSKWIDNILSGKTKPFQFDKKMKLMYYIKIL
ILT*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0004523RNA-DNA hybrid ribonuclease activity
GO:0003676nucleic acid binding
Vocabulary: biological process
TermDefinition
GO:0090502RNA phosphodiester bond hydrolysis, endonucleolytic
GO:0015074DNA integration
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002075pigment cell
PLANA:0003116parenchymal cell