Retrovirus Pol polyprotein from transposon opus

Overview
NameRetrovirus Pol polyprotein from transposon opus
Smed IDSMED30019573
Length (bp)531
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 Retrovirus Pol polyprotein from transposon opus (SMED30019573) t-SNE clustered cells

Violin plots show distribution of expression levels for Retrovirus Pol polyprotein from transposon opus (SMED30019573) 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 Retrovirus Pol polyprotein from transposon opus (SMED30019573) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Retrovirus Pol polyprotein from transposon opus (SMED30019573) 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




SMED30019573

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
body wall musculatureSMED30019573h1SMcG0021163 dd_Smed_v4_8812_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 2 cellSMED30019573h1SMcG0021163 dd_Smed_v4_8812_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 Retrovirus Pol polyprotein from transposon opus vs. TrEMBL
Match: A0A4Z2CKZ9 (Uncharacterized protein OS=Schistosoma japonicum OX=6182 GN=EWB00_010164 PE=4 SV=1)

HSP 1 Score: 90.1225 bits (222), Expect = 6.283e-20
Identity = 50/131 (38.17%), Postives = 75/131 (57.25%), Query Frame = 1
Query:   97 NEKYQKLLQKFNEYVDFKNLSVKRVIVAGVIHELSGLCLLTGLWYMCYKIRPVGKVIKSLPFYNNASHQKDISLAKQKINQIAIISWFSK--THKRMLISGTESFVLRKLLLPVTIPAKIYFAYHLSGYFC 483
            N   +KL    N  +D K  S  R+ VA + HE  G+ LL G W +CYK +P+  ++ S P      + K +S + +K++++ +  W S      R+L+SG ES+VLRK+L P+TIP KIY A  +SG  C
Sbjct:    4 NSATEKLFHHLN--IDTKQWSYSRITVAVLSHESLGIGLLVGFWIICYKKQPIKHLMLSSPVNIQNVYSKGLSWSAKKLDRLPL--WISSRVDPNRILVSGAESYVLRKILSPITIPGKIYLAVLISGLIC 130          
BLAST of Retrovirus Pol polyprotein from transposon opus vs. TrEMBL
Match: A0A094ZNN2 (Uncharacterized protein (Fragment) OS=Schistosoma haematobium OX=6185 GN=MS3_02839 PE=4 SV=1)

HSP 1 Score: 87.0409 bits (214), Expect = 1.251e-18
Identity = 49/125 (39.20%), Postives = 70/125 (56.00%), Query Frame = 1
Query:  109 QKLLQKFNEYVDFKNLSVKRVIVAGVIHELSGLCLLTGLWYMCYKIRPVGKVIKSLPFYNNASHQKDISLAKQKINQIAIISWFSKTHKRMLISGTESFVLRKLLLPVTIPAKIYFAYHLSGYFC 483
            +KL Q FN  +D K  S  R+ VA + HE  G+ L  G W +CYK +PV  +    P      + K ++ + +K+ Q+ +         R+LISG ES+VLRK+L P+TIP KIY A  +SG  C
Sbjct:    8 EKLFQHFN--IDTKQWSYSRITVALLAHESFGIGLALGFWIICYKKQPVRCLTSFAPVAIQNIYSKGLNWSARKLRQLPLFVSSQADPNRILISGAESYVLRKILSPLTIPGKIYIAVLVSGIVC 130          
BLAST of Retrovirus Pol polyprotein from transposon opus vs. TrEMBL
Match: A0A5K4F6U6 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 PE=4 SV=1)

HSP 1 Score: 86.2705 bits (212), Expect = 2.211e-18
Identity = 47/125 (37.60%), Postives = 69/125 (55.20%), Query Frame = 1
Query:  109 QKLLQKFNEYVDFKNLSVKRVIVAGVIHELSGLCLLTGLWYMCYKIRPVGKVIKSLPFYNNASHQKDISLAKQKINQIAIISWFSKTHKRMLISGTESFVLRKLLLPVTIPAKIYFAYHLSGYFC 483
            + L Q FN  +D K  S  R+ VA + HE  G+ L  G W +CYK +P+  +    P      + K ++ + +K+ Q+ +         R+LISG ES+VLRK+L P+TIP KIY A  +SG  C
Sbjct:    8 ENLFQHFN--IDTKQWSYSRITVALLAHESFGIGLAVGFWIICYKKQPIRYLTSYAPVVIQNIYSKGLNWSARKLRQLPLFVSSQADPNRILISGAESYVLRKILSPLTIPGKIYLAVLVSGIVC 130          
BLAST of Retrovirus Pol polyprotein from transposon opus vs. TrEMBL
Match: A0A430Q033 (Uncharacterized protein OS=Schistosoma bovis OX=6184 GN=DC041_0008071 PE=4 SV=1)

HSP 1 Score: 85.1149 bits (209), Expect = 5.166e-18
Identity = 48/125 (38.40%), Postives = 70/125 (56.00%), Query Frame = 1
Query:  109 QKLLQKFNEYVDFKNLSVKRVIVAGVIHELSGLCLLTGLWYMCYKIRPVGKVIKSLPFYNNASHQKDISLAKQKINQIAIISWFSKTHKRMLISGTESFVLRKLLLPVTIPAKIYFAYHLSGYFC 483
            +KL Q FN  +D K  S  R+ VA + HE  G+ L  G W +CYK +PV  +    P      + K ++ + +K+ ++ +         R+LISG ES+VLRK+L P+TIP KIY A  +SG  C
Sbjct:    8 EKLFQHFN--IDTKQWSYSRITVALLAHESFGIGLALGFWIICYKKQPVRCLTSFAPVAIQNIYSKGLNWSARKLRRLPLFVSSQADPNRILISGAESYVLRKILSPLTIPGKIYIAVLVSGIVC 130          
BLAST of Retrovirus Pol polyprotein from transposon opus vs. TrEMBL
Match: A0A4S2L8V1 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_009139 PE=4 SV=1)

HSP 1 Score: 84.7297 bits (208), Expect = 8.518e-18
Identity = 41/118 (34.75%), Postives = 65/118 (55.08%), Query Frame = 1
Query:  127 FNEYVDFKNLSVKRVIVAGVIHELSGLCLLTGLWYMCYKIRPVGKVIKSLPFYNNASHQKDISLAKQKINQIAIISWFSKTHKRMLISGTESFVLRKLLLPVTIPAKIYFAYHLSGYF 480
            F    D       R+++A   HE  GL +L G W  CYK +P+ ++I   P    AS+ + ++ + +++ ++          +R+LISG ESFVLRK+L P+T+P KIY A   S +F
Sbjct:   11 FGRRFDTSKWPYLRIMIAVAAHEALGLGILVGFWVGCYKFQPLRQIIYRAPDPIRASYDRGMAWSSRRLQRVPAYIKHRTDPQRLLISGAESFVLRKVLTPITVPGKIYLAVLFSAFF 128          
BLAST of Retrovirus Pol polyprotein from transposon opus vs. Planmine SMEST
Match: SMESG000024333.1 (SMESG000024333.1)

HSP 1 Score: 280.026 bits (715), Expect = 3.018e-98
Identity = 134/137 (97.81%), Postives = 137/137 (100.00%), Query Frame = 1
Query:   76 MNEDSNTNEKYQKLLQKFNEYVDFKNLSVKRVIVAGVIHELSGLCLLTGLWYMCYKIRPVGKVIKSLPFYNNASHQKDISLAKQKINQIAIISWFSKTHKRMLISGTESFVLRKLLLPVTIPAKIYFAYHLSGYFCK 486
            MN+DSNTNEKYQKLLQKFNEYVDFKNLS+KRVIVAGVIHELSGLCLLTGLWYMCYKIRPVGKVIKSLPFYNNASHQKDISLAKQKINQ+AIISWFSKTHKRMLISGTESFVLRKLLLPVTIPAKIYFAYHLSGYFCK
Sbjct:    1 MNKDSNTNEKYQKLLQKFNEYVDFKNLSIKRVIVAGVIHELSGLCLLTGLWYMCYKIRPVGKVIKSLPFYNNASHQKDISLAKQKINQMAIISWFSKTHKRMLISGTESFVLRKLLLPVTIPAKIYFAYHLSGYFCK 137          
BLAST of Retrovirus Pol polyprotein from transposon opus vs. Planmine SMEST
Match: SMESG000024306.1 (SMESG000024306.1)

HSP 1 Score: 83.5741 bits (205), Expect = 9.453e-21
Identity = 56/145 (38.62%), Postives = 76/145 (52.41%), Query Frame = 1
Query:   76 MNEDSNTNEKYQKLLQKFNEYVDFKNLSVKRVIVAGVIHELSGLCLLTGLWYMCYKIRPVGKVIKSLPFYNNASHQKDISLAKQKINQIAIISWFSKTHKRMLISGTESFVLRKLLLPVTIPAKIYFAYHLSGYFCK*IFIDFLL 510
            MNE+S  NEKY+ L  K  E +D  N S KR+I+   I+ +S +CL T    +CYK   +GK+I+    YN+ S Q+ I     K  +  +      TH   + +  ES VLR  L+PV  PAKIY  Y LS Y C  I+    L
Sbjct:    1 MNENSFFNEKYKNLHYKSYENLDNNNFSSKRIILGVAIYSMSEICLRTVYSCICYKFPQMGKLIRRSWIYNHHSVQEYIIFLNHKRFKKTVD---MNTHMMKMNNLHESSVLRAYLMPVAYPAKIYLGYSLSEYVCNDIYWRLFL 142          
BLAST of Retrovirus Pol polyprotein from transposon opus vs. Planmine SMEST
Match: SMESG000024298.1 (SMESG000024298.1)

HSP 1 Score: 80.1073 bits (196), Expect = 1.593e-19
Identity = 52/137 (37.96%), Postives = 74/137 (54.01%), Query Frame = 1
Query:   76 MNEDSNTNEKYQKLLQKFNEYVDFKNLSVKRVIVAGVIHELSGLCLLTGLWYMCYKIRPVGKVIKSLPFYNNASHQKDISLAKQKINQIAIISWFSKTHKRMLISGTESF-VLRKLLLPVTIPAKIYFAYHLSGYFC 483
            MN++S  NEKY+ L  K  E +D  N S KR+I+  +I+ LSG+C+  GL +M +K   +G  I+    Y    H  +     + I+ I  I + + T +  L++    F VLR    PV  PAKIY AY LSGY C
Sbjct:    1 MNKNSINNEKYKNLHYKSYENLDNNNFSSKRIILGILIYPLSGICMSAGLMFMLFKKPIIGNYIRRSSLY----HWLEAPKLVKSIDGILSILYVNPTIRLNLVNFVMDFMVLRIYFTPVIFPAKIYSAYSLSGYLC 133          
BLAST of Retrovirus Pol polyprotein from transposon opus vs. Planmine SMEST
Match: SMESG000024299.1 (SMESG000024299.1)

HSP 1 Score: 77.411 bits (189), Expect = 2.182e-18
Identity = 51/136 (37.50%), Postives = 70/136 (51.47%), Query Frame = 1
Query:   76 MNEDSNTNEKYQKLLQKFNEYVDFKNLSVKRVIVAGVIHELSGLCLLTGLWYMCYKIRPVGKVIKSLPFYNNASHQKDISLAKQKINQIAIISWFSKTHKRMLISGTESFVLRKLLLPVTIPAKIYFAYHLSGYFC 483
            MN++S  NEKY+ L  K  E +D  N S KR+I+  +I+ LSG+C+  GL +M  K   +G  I+    Y      K   L K     ++ +    K    +LI+  +  VLR    PV  PAKIY AY LSGY C
Sbjct:    1 MNKNSINNEKYKNLHYKSYENLDNNNFSSKRIILGILIYPLSGICMSAGLIFMLSKKPIIGNYIRRSSLYRWLEAPK---LVKYGEGFLSTLISDPKERFYLLIAAADFIVLRIYFTPVIFPAKIYSAYSLSGYLC 133          
The following BLAST results are available for this feature:
BLAST of Retrovirus Pol polyprotein from transposon opus 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 Retrovirus Pol polyprotein from transposon opus 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 Retrovirus Pol polyprotein from transposon opus 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 Retrovirus Pol polyprotein from transposon opus 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 Retrovirus Pol polyprotein from transposon opus 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 Retrovirus Pol polyprotein from transposon opus 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 Retrovirus Pol polyprotein from transposon opus 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 Retrovirus Pol polyprotein from transposon opus vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4Z2CKZ96.283e-2038.17Uncharacterized protein OS=Schistosoma japonicum O... [more]
A0A094ZNN21.251e-1839.20Uncharacterized protein (Fragment) OS=Schistosoma ... [more]
A0A5K4F6U62.211e-1837.60Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
A0A430Q0335.166e-1838.40Uncharacterized protein OS=Schistosoma bovis OX=61... [more]
A0A4S2L8V18.518e-1834.75Uncharacterized protein OS=Opisthorchis felineus O... [more]
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BLAST of Retrovirus Pol polyprotein from transposon opus 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 Retrovirus Pol polyprotein from transposon opus 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 Retrovirus Pol polyprotein from transposon opus 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 Retrovirus Pol polyprotein from transposon opus 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 Retrovirus Pol polyprotein from transposon opus 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 Retrovirus Pol polyprotein from transposon opus vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000024333.13.018e-9897.81SMESG000024333.1[more]
SMESG000024306.19.453e-2138.62SMESG000024306.1[more]
SMESG000024298.11.593e-1937.96SMESG000024298.1[more]
SMESG000024299.12.182e-1837.50SMESG000024299.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30019573 ID=SMED30019573|Name=Retrovirus Pol polyprotein from transposon opus|organism=Schmidtea mediterranea sexual|type=transcript|length=531bp
AAAAAACGATAAAAATATATTTAAATTTATGCTAAAAATTATTTTTTGGA
AAATTTTAATTTTTAGCTAAAGCAAATGAATGAAGACAGCAATACTAATG
AAAAATATCAGAAATTGCTTCAAAAATTTAACGAATACGTAGATTTTAAA
AATTTATCAGTAAAGCGTGTGATTGTTGCTGGTGTAATTCATGAATTATC
TGGGCTTTGTTTGTTGACAGGACTTTGGTACATGTGTTATAAAATTCGAC
CAGTGGGTAAAGTAATTAAAAGCTTACCGTTTTATAATAATGCAAGTCAT
CAGAAAGATATTTCGTTGGCCAAACAGAAGATAAATCAGATAGCTATAAT
TTCTTGGTTTTCGAAAACTCATAAGAGGATGTTAATCAGTGGAACTGAAA
GTTTTGTGTTGCGTAAACTACTTTTACCTGTAACAATTCCCGCCAAGATT
TATTTTGCATATCATTTAAGTGGATATTTTTGTAAATAGATTTTTATTGA
CTTTTTATTATAAAATATTATGCTATTAGAT
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protein sequence of SMED30019573-orf-1

>SMED30019573-orf-1 ID=SMED30019573-orf-1|Name=SMED30019573-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=138bp
MNEDSNTNEKYQKLLQKFNEYVDFKNLSVKRVIVAGVIHELSGLCLLTGL
WYMCYKIRPVGKVIKSLPFYNNASHQKDISLAKQKINQIAIISWFSKTHK
RMLISGTESFVLRKLLLPVTIPAKIYFAYHLSGYFCK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000028Category 2 cell
PLANA:0000240body wall musculature
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 33..55