Integrase catalytic domain-containing protein

Overview
NameIntegrase catalytic domain-containing protein
Smed IDSMED30014067
Length (bp)920
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 Integrase catalytic domain-containing protein (SMED30014067) t-SNE clustered cells

Violin plots show distribution of expression levels for Integrase catalytic domain-containing protein (SMED30014067) 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 Integrase catalytic domain-containing protein (SMED30014067) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Integrase catalytic domain-containing protein (SMED30014067) 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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Anatomical Expression

PAGE et. al., 2020




SMED30014067

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Category 3 cellSMED30014067 dd_Smed_v4_16497_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Integrase catalytic domain-containing protein vs. TrEMBL
Match: A0A1L8HJG0 (Uncharacterized protein OS=Xenopus laevis OX=8355 GN=XELAEV_18013881mg PE=4 SV=1)

HSP 1 Score: 107.842 bits (268), Expect = 3.109e-22
Identity = 47/86 (54.65%), Postives = 58/86 (67.44%), Query Frame = 1
Query:  415 VIFGQFLTDRANYSVNACDNSIKRFAVEHPPCQPKGPFPMDPNQNNRNF*EKYYERTTKAVLKLPVNWLCYSQKLDYVYCEPCWLF 672
            VI   F+TDR +Y +   D +IK+F + H PC+PKGPFP D  Q +R F E YYE  TK   K+P+ WLCYS KL+  YCEPCWLF
Sbjct:  184 VIGQAFVTDRGHYPITITDPNIKKFILAHGPCRPKGPFPRD--QAHRRFSENYYETITKTGHKIPITWLCYSPKLNAAYCEPCWLF 267          
BLAST of Integrase catalytic domain-containing protein vs. TrEMBL
Match: H3A5Y3 (DUF4371 domain-containing protein OS=Latimeria chalumnae OX=7897 PE=4 SV=1)

HSP 1 Score: 97.0561 bits (240), Expect = 1.244e-18
Identity = 44/79 (55.70%), Postives = 52/79 (65.82%), Query Frame = 1
Query:  436 TDRANYSVNACDNSIKRFAVEHPPCQPKGPFPMDPNQNNRNF*EKYYERTTKAVLKLPVNWLCYSQKLDYVYCEPCWLF 672
            TDR N+ + A  +S KR+ +   PC+P GPFP D NQ  R F   YY+ TTKA +KL   WLCYS KLD  YCEPCWLF
Sbjct:  112 TDRGNFPL-AIKDSQKRYIISQGPCKPNGPFPQDKNQEGRCFSTTYYDITTKAEVKLTRTWLCYSPKLDSAYCEPCWLF 189          
BLAST of Integrase catalytic domain-containing protein vs. TrEMBL
Match: A0A3B3YLV2 (DUF4371 domain-containing protein OS=Poecilia mexicana OX=48701 PE=4 SV=1)

HSP 1 Score: 93.5893 bits (231), Expect = 1.885e-17
Identity = 46/95 (48.42%), Postives = 62/95 (65.26%), Query Frame = 1
Query:  388 VETEDISNIVIFGQFLTDRANYSVNACDNSIKRFAVEHPPCQPKGPFPMDPNQNNRNF*EKYYERTTKAVLKLPVNWLCYSQKLDYVYCEPCWLF 672
             +T D+ N+ +   F TD+A++  N  D +IKR+ ++  PC+PK PFP D N  NR+F E YY  T K  +K P +W+CYS KLD  YCEPCWLF
Sbjct:   73 TQTADVENLSL-ECFPTDQASFVENIQDANIKRYILKMGPCRPKFPFPTDIN--NRSFSESYYTSTNKVGMKFPRSWMCYSPKLDCCYCEPCWLF 164          
BLAST of Integrase catalytic domain-containing protein vs. TrEMBL
Match: A0A2S2QZ08 (Zinc finger MYM-type protein 1 OS=Sipha flava OX=143950 GN=ZMYM1_98 PE=4 SV=1)

HSP 1 Score: 83.1889 bits (204), Expect = 4.620e-14
Identity = 56/163 (34.36%), Postives = 86/163 (52.76%), Query Frame = 1
Query:  229 ITSHFNEGNVETQ------PSIL--EVCSTSSIVANSIEAFDPNTIGAKNIETEKKLDVIPVETEDISNIVIFGQFLTDRANYSVNACDNSIKRFAVEHPPCQPKGPFPMDPNQNNRNF*EKYYERTTKAVLKLPVNWLCYSQKLDYVYCEPCWLF--HSQMS 687
            I ++F + + ET+      P IL  ++ + S+ V+        +TI  KN+E             +I N +I  +F TD+ ++         KRF +   PCQPKGPFP D + N+R+F EK+Y  T +A + L   WLCYS  L+ +YC+ CWLF  H ++S
Sbjct:   28 IDTYFKQNHEETEEQDIDNPGILLNKIKTASNSVSEPTATSSIDTINTKNVE------------PNIFNSLICERFPTDKVHFK-EPLSYQEKRFIISQGPCQPKGPFPADSD-NSRSFSEKFYYFTNQANITLKRAWLCYSLTLNKIYCQCCWLFSTHDRIS 176          
BLAST of Integrase catalytic domain-containing protein vs. TrEMBL
Match: A0A3S2LTU0 (DUF4371 domain-containing protein OS=Chilo suppressalis OX=168631 GN=evm_011541 PE=4 SV=1)

HSP 1 Score: 80.1073 bits (196), Expect = 4.798e-13
Identity = 37/85 (43.53%), Postives = 54/85 (63.53%), Query Frame = 1
Query:  433 LTDRANYSVNACDNSIKRFAVEHPPCQPKGPFPMDPNQNNRNF*EKYYERTTKAVLKLPVNWLCYSQKLDYVYCEPCWLFHSQMS 687
            +TD+ N+     ++ +KRF +E+  C+PKGPF  D N  NR+F +KYY   +K+ +K+   WL YS  L   YCEPCWLF ++ S
Sbjct:   98 VTDKGNFK--ELNDQVKRFVIENGHCKPKGPFLRDSN--NRSFLDKYYYTVSKSGVKIERTWLSYSLLLQKAYCEPCWLFANRAS 178          
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
A0A1L8HJG03.109e-2254.65Uncharacterized protein OS=Xenopus laevis OX=8355 ... [more]
H3A5Y31.244e-1855.70DUF4371 domain-containing protein OS=Latimeria cha... [more]
A0A3B3YLV21.885e-1748.42DUF4371 domain-containing protein OS=Poecilia mexi... [more]
A0A2S2QZ084.620e-1434.36Zinc finger MYM-type protein 1 OS=Sipha flava OX=1... [more]
A0A3S2LTU04.798e-1343.53DUF4371 domain-containing protein OS=Chilo suppres... [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: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014067 ID=SMED30014067|Name=Integrase catalytic domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=920bp
TAGCAATTTTAAATTTCAAGATATTAACAAAATATAAAGCAGCCCAAAAT
GTCATATCAACACACAAGTGGAGCAAAACGTAAAAAAGAGTGAAGAAATG
CTAAGCTTAAGTAAAACACAAAAAATAAATCATTTTTGTAATCCAGCACC
TAAGAAAAGTCAATCTGCCTCTGCCGAGTTGAAAAGTCGACCAAGTCAAG
ATAGCTGTAATGATGCAGGTGAAACGCCATCACTAGCCACTTTAATGAAG
GAAATGTTGAAACTCAGCCATCAATTTTGGAAGTGTGTAGTACTAGTTCA
ATTGTTGCTAATTCAATCGAAGCATTTGATCCAAACACTATCGGAGCTAA
AAATATTGAAACTGAAAAAAAATTGGATGTTATTCCAGTCGAAACTGAAG
ACATCAGCAACATAGTGATTTTTGGACAATTCCTAACGGACAGAGCAAAC
TATTCTGTTAATGCATGTGACAATAGCATCAAACGTTTTGCAGTTGAACA
TCCACCATGCCAGCCCAAAGGTCCTTTTCCTATGGATCCGAATCAAAACA
ACAGGAACTTTTGAGAAAAGTATTATGAGAGAACAACTAAAGCTGTTTTG
AAATTACCAGTTAATTGGTTGTGTTATTCACAGAAACTTGATTATGTGTA
TTGTGAGCCATGTTGGCTTTTTCACTCCCAGATGTCGGCCTTTGCATATC
TTCTTTTCCTCACTTTACTAGTAACTTTAGCAACAGCAGAGAGGTCGTTC
TTCAAGCTTAAGCTCATCAAAAATTAATTGCGTAGTACTATGTGAAGTCC
ATGGTGAGATAGCCAAACCACTGAATGATATCATAAACAAATAATATAAA
AATGATATAAAAATGGTATAAAAAGTAATATGAATTCACGTAAGTCAGAT
TTCATGGCAACAGTTCCCAG
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protein sequence of SMED30014067-orf-1

>SMED30014067-orf-1 ID=SMED30014067-orf-1|Name=SMED30014067-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=106bp
MLSLSKTQKINHFCNPAPKKSQSASAELKSRPSQDSCNDAGETPSLATLM
KEMLKLSHQFWKCVVLVQLLLIQSKHLIQTLSELKILKLKKNWMLFQSKL
KTSAT*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
Vocabulary: biological process
TermDefinition
GO:0015074DNA integration
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell
PLANA:0000070intestinal phagocyte