Integrase catalytic domain-containing protein

Overview
NameIntegrase catalytic domain-containing protein
Smed IDSMED30035832
Length (bp)659
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 Integrase catalytic domain-containing protein (SMED30035832) t-SNE clustered cells

Violin plots show distribution of expression levels for Integrase catalytic domain-containing protein (SMED30035832) 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



SMED30035832

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
nervous systemSMED30035832 dd_Smed_v4_91690_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30035832 dd_Smed_v4_91690_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of Integrase catalytic domain-containing protein vs. TrEMBL
Match: A0A2G8LCX9 (Uncharacterized protein OS=Stichopus japonicus OX=307972 GN=BSL78_04959 PE=4 SV=1)

HSP 1 Score: 85.1149 bits (209), Expect = 5.468e-16
Identity = 45/110 (40.91%), Postives = 66/110 (60.00%), Query Frame = 1 
Query:  310 TWKA----FGF---DVNLPIEKMWMKRKVLIMVARIFGPLGIIGSFIILGETIIQSIWLEGLHWDLELLKEISNKVEKWIREVEELRKIRIARCFIIEKHPTQLHAFMDA 618
            +WKA    F F   DV  P EK   KRKVL  +A +F PLG +   +I G+ ++Q IW +GL WD  +  E++++V KW+ +++ LRKI I RC    +   +LH F+DA
Sbjct:   42 SWKADEDVFTFIEPDVTNP-EKKLTKRKVLSKIASVFDPLGFLSPVVIAGKVLMQKIWADGLQWDEVMEGELADEVIKWLEDLQNLRKISIQRCLCTNEGAVELHTFVDA 150
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BLAST of Integrase catalytic domain-containing protein vs. TrEMBL
Match: A0A4Y2NEC5 (Uncharacterized protein OS=Araneus ventricosus OX=182803 GN=AVEN_172648_1 PE=4 SV=1)

HSP 1 Score: 70.4774 bits (171), Expect = 2.165e-11
Identity = 37/103 (35.92%), Postives = 57/103 (55.34%), Query Frame = 1 
Query:  319 AFGFDVNLPIEKMWMKRKVLIMVARIFGPLGIIGSFIILGETIIQSIWLEGLHWDLELLKEISNKVEKWIREVEELRKIRIARCFI-IEKHPTQLHAFMDALS 624
             F +  N+ I + + KR VL  +ARI+ P+G++G  I   +  +Q +WL  L W   L  +IS + E +I+ + +L KI+I RCF+        LH F DA S
Sbjct:    9 TFTYKANVNINQSYTKRDVLSQIARIYDPVGLLGPVISKAKIFMQHLWLLKLDWYETLPPDISQQWENFIKTLPDLEKIKIPRCFLKTNAIRVILHGFADAFS 111
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BLAST of Integrase catalytic domain-containing protein vs. TrEMBL
Match: A0A2D0QLQ6 (uncharacterized protein LOC108262813 OS=Ictalurus punctatus OX=7998 GN=LOC108262813 PE=4 SV=1)

HSP 1 Score: 72.7886 bits (177), Expect = 3.982e-11
Identity = 39/104 (37.50%), Postives = 60/104 (57.69%), Query Frame = 1 
Query:  319 AFGFDVNLPIEKMWMKRKVLIMVARIFGPLGIIGSFIILGETIIQSIWLEGLHWDLELLKEISNKVEKWIREVEELRKIRIARCFIIEKHPT----QLHAFMDA 618
            AF F+V L  EK   +R +L  VA ++ PLG +  +I+ G+ ++Q +   G+ WD  +  E+  K E W+ ++E L KI+I RCFI +   T    +LH F DA
Sbjct:  749 AFSFNVVLN-EKAATRRGILSTVASVYDPLGFLSPYILTGKRVLQEMCKRGVGWDEHVPLELKPKWETWLHDLENLEKIQIPRCFIPDHLSTIRKIELHHFSDA 851
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BLAST of Integrase catalytic domain-containing protein vs. TrEMBL
Match: A0A4Y2RKT2 (Uncharacterized protein OS=Araneus ventricosus OX=182803 GN=AVEN_244035_1 PE=4 SV=1)

HSP 1 Score: 68.5514 bits (166), Expect = 5.422e-11
Identity = 36/93 (38.71%), Postives = 58/93 (62.37%), Query Frame = 1 
Query:  352 KMWMKRKVLIMVARIFGPLGIIGSFIILGETIIQSIWLEGLHWDLELLKEISNKVEKWIREVEELRKIRIARCFIIEKHPT----QLHAFMDA 618
            K+  KR +L +V RIF P+GI+G F+I  + ++Q +W  G+ WD ELL ++ +K ++W  E E+L +IRI R ++ E        ++H F DA
Sbjct:    4 KIESKRFILSVVGRIFDPIGILGPFVIKLKCLLQDLWTLGVDWDSELLPKLRHKWQQWSSEAEDLTEIRIPRYYLGELDQEISIFEIHCFSDA 96
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BLAST of Integrase catalytic domain-containing protein vs. TrEMBL
Match: A0A1B6KU24 (Uncharacterized protein (Fragment) OS=Graphocephala atropunctata OX=36148 GN=g.40856 PE=4 SV=1)

HSP 1 Score: 71.2478 bits (173), Expect = 5.666e-11
Identity = 33/101 (32.67%), Postives = 54/101 (53.47%), Query Frame = 1 
Query:  319 AFGFDVNLPIEKMWMKRKVLIMVARIFGPLGIIGSFIILGETIIQSIWLEGLHWDLELLKEISNKVEKWIREVEELRKIRIARCFIIE-KHPTQLHAFMDA 618
             F + +N+P++    KR VL ++A+I+ P G +  FI+  +  +Q +W  GL WD  L  + +NK   +I + + L  I I R F     +  +LH F DA
Sbjct:   97 CFSYRLNVPLDDRPTKRSVLSLIAKIYDPCGFLAPFIMQAKCFMQFLWTTGLSWDAPLPSDCANKWCNFITDAQALSYISIPRSFQFSLSYVIELHGFADA 197
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BLAST of Integrase catalytic domain-containing protein vs. Planmine SMEST
Match: SMESG000081491.1 (SMESG000081491.1)

HSP 1 Score: 144.05 bits (362), Expect = 2.715e-42
Identity = 75/104 (72.12%), Postives = 82/104 (78.85%), Query Frame = 1 
Query:  322 FGFDVNLPIEKMWMKRKVLI--MVARIFGPLGIIGSFIILGETIIQSIWLEGLHWDLELLKEISNKVEKWIREVEELRKIRIARCFIIE-KHPTQLHAFMDALS 624
            F F VN P+EKMW KRKVL   +V RIF PLGIIG FIILG+ IIQSIWLEGL  D+EL KE+SNKVE+WI+EVEELRKIRIARC I E KHP QLH F D  S
Sbjct:  127 FSFHVNFPVEKMWTKRKVLARSVVDRIFDPLGIIGPFIILGKMIIQSIWLEGLDGDIELPKEMSNKVEQWIQEVEELRKIRIARCLITEKKHPIQLHVFTDVSS 230
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BLAST of Integrase catalytic domain-containing protein vs. Planmine SMEST
Match: SMESG000042733.1 (SMESG000042733.1)

HSP 1 Score: 86.6557 bits (213), Expect = 1.015e-19
Identity = 50/126 (39.68%), Postives = 70/126 (55.56%), Query Frame = 1 
Query:  262 QKLKIPIFDGKVLE--FETWKA----FGFDVNLPIEKMWMKRKVLIMVARIFGPLGIIGSFIILGETIIQSIWLEGLHWDLELLKEISNKVEKWIREVEELRKIRIARCFI-IEKHPTQLHAFMDA 618
            +KL I   D ++L+  +  W+A    F F +N P E    KR +L ++ARIF PLG  G F+I G  IIQ IW+ GL W      EI+ K   W+ E++ L++I + RC I   +   QLH F DA
Sbjct:   24 EKLHINETDCRMLKRLWVQWQADTDEFVFKMNTPTENKLTKRNLLSLIARIFDPLGFFGVFVIRGTMIIQEIWMFGLEWVQNTPMEIACKTGAWVNEIDRLKEINVGRCIIKTNEENIQLHVFTDA 149
[Close]
BLAST of Integrase catalytic domain-containing protein vs. Planmine SMEST
Match: SMESG000016652.1 (SMESG000016652.1)

HSP 1 Score: 68.5514 bits (166), Expect = 2.695e-13
Identity = 31/60 (51.67%), Postives = 42/60 (70.00%), Query Frame = 1 
Query:  304 FETWKAFGFDVNLPIEKMWMKRKVLIMVARIFGPLGIIGSFIILGETIIQSIWLEGLHWD 483
            + +   F FD NLP ++   KRKVL ++ARIF PLG+IG FII G+ I+Q +W+ GL WD
Sbjct:  577 YSSSDKFRFDENLPKDQYPTKRKVLSIMARIFDPLGLIGPFIIRGKMIVQKLWVLGLDWD 636
[Close]
BLAST of Integrase catalytic domain-containing protein vs. Planmine SMEST
Match: SMESG000058405.1 (SMESG000058405.1)

HSP 1 Score: 65.855 bits (159), Expect = 1.676e-12
Identity = 33/86 (38.37%), Postives = 49/86 (56.98%), Query Frame = 1 
Query:  364 KRKVLIMVARIFGPLGIIGSFIILGETIIQSIWLEGLHWDLELLKEISNKVEKWIREVEELRKIRIARCFI-IEKHPTQLHAFMDA 618
            KR +L  +ARIF PLG + +F+++GE I+QSIW+ G  WD  L   I  +   W+ E  E+  +R+ R  +  E     +H F DA
Sbjct:  309 KRLLLSWIARIFDPLGFLTAFVVIGEMIMQSIWITGADWDECLPLNIDQEARLWVNEAREIMSMRVPRNLLESESDDWTIHVFSDA 394
[Close]
BLAST of Integrase catalytic domain-containing protein vs. Planmine SMEST
Match: SMESG000022805.1 (SMESG000022805.1)

HSP 1 Score: 65.0846 bits (157), Expect = 3.938e-12
Identity = 43/136 (31.62%), Postives = 66/136 (48.53%), Query Frame = 1 
Query:  214 ISEYGSPMEKKSLNMLQKLKIPIFDGKVLEFETWKAFGFDVNLPIEKMWMKRKVLIMVARIFGPLGIIGSFIILGETIIQSIWLEGLHWDLELLKEISNKVEKWIREVEELRKIRIARCFI-IEKHPTQLHAFMDA 618
            I E GS M  K+L +     + +F+  V  FE+             +   KR +L  +ARIF PLG + +F++ G+ I+QSIW+ G  WD  L   I  +   W+ E  E+  +R+ R  +  E     +H F DA
Sbjct:  200 IKEEGS-MTMKTLGLRWVANLDVFEFSVKAFES-------------ETLTKRLLLSWIARIFDPLGFLAAFVVRGKMIMQSIWITGADWDECLPLNIDQEARLWVNEAREIVSMRVPRNLLESESDDWTIHVFSDA 321
The following BLAST results are available for this feature:
BLAST of Integrase catalytic 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 Integrase catalytic 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 Integrase catalytic 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 Integrase catalytic 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 Integrase catalytic 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 Integrase catalytic 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 Integrase catalytic 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 Integrase catalytic domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A2G8LCX95.468e-1640.91Uncharacterized protein OS=Stichopus japonicus OX=... [more]
A0A4Y2NEC52.165e-1135.92Uncharacterized protein OS=Araneus ventricosus OX=... [more]
A0A2D0QLQ63.982e-1137.50uncharacterized protein LOC108262813 OS=Ictalurus ... [more]
A0A4Y2RKT25.422e-1138.71Uncharacterized protein OS=Araneus ventricosus OX=... [more]
A0A1B6KU245.666e-1132.67Uncharacterized protein (Fragment) OS=Graphocephal... [more]
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BLAST of Integrase catalytic 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 Integrase catalytic 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 Integrase catalytic 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 Integrase catalytic 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 Integrase catalytic 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 Integrase catalytic domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000081491.12.715e-4272.12SMESG000081491.1[more]
SMESG000042733.11.015e-1939.68SMESG000042733.1[more]
SMESG000016652.12.695e-1351.67SMESG000016652.1[more]
SMESG000058405.11.676e-1238.37SMESG000058405.1[more]
SMESG000022805.13.938e-1231.62SMESG000022805.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035832 ID=SMED30035832|Name=Integrase catalytic domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=659bp
AAAGGCTTGACGAATTAGCAGAAAATTATTTGTAATTAATAAATTGAATT
CAAATATCAAGAACCAATGCATTGCTACTGTCAGATGTAATTTTACTTCA
CTTTTAACAATTTAATGTCTGCGGAAGCTACATTGGCATCTTTAAAGACA
TGAGACATATTGATTTAAAAGTAATATTATTCTTAGTTCAAAATTTAATC
CATACATGACTATATATCGGAATATGGATCTCCTATGGAAAAGAAAAGTT
TAAATATGTTGCAAAAGTTAAAGATTCCAATTTTCGATGGAAAGGTGCTT
GAATTCGAAACATGGAAAGCATTCGGTTTTGACGTGAATCTACCGATAGA
AAAAATGTGGATGAAAAGGAAGGTATTAATTATGGTGGCTAGAATATTTG
GTCCTTTAGGAATTATTGGATCATTTATAATTCTTGGGGAAACGATAATA
CAGAGTATATGGTTAGAAGGATTACATTGGGATTTAGAACTTCTAAAAGA
GATAAGTAATAAAGTCGAAAAATGGATCCGAGAAGTTGAAGAACTACGGA
AAATAAGAATTGCACGATGTTTTATAATAGAGAAACATCCGACACAATTG
CATGCTTTCATGGATGCTTTAAGTATGTGGCAGTAATATATTTACGAGAA
AGTTTAATA
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protein sequence of SMED30035832-orf-1

>SMED30035832-orf-1 ID=SMED30035832-orf-1|Name=SMED30035832-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=134bp
MEKKSLNMLQKLKIPIFDGKVLEFETWKAFGFDVNLPIEKMWMKRKVLIM
VARIFGPLGIIGSFIILGETIIQSIWLEGLHWDLELLKEISNKVEKWIRE
VEELRKIRIARCFIIEKHPTQLHAFMDALSMWQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR008042Retrotrans_Pao
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0004386helicase activity
GO:0005524ATP binding
Vocabulary: cellular component
TermDefinition
GO:0005763mitochondrial small ribosomal subunit
Vocabulary: biological process
TermDefinition
GO:0015074DNA integration
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 87..107
NoneNo IPR availableTMHMMTMhelixcoord: 50..72
IPR008042Retrotransposon, PaoPFAMPF05380Peptidase_A17coord: 43..128
e-value: 1.2E-18
score: 67.6