RRM domain-containing protein

Overview
NameRRM domain-containing protein
Smed IDSMED30005808
Length (bp)1484
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 RRM domain-containing protein (SMED30005808) t-SNE clustered cells

Violin plots show distribution of expression levels for RRM domain-containing protein (SMED30005808) 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 RRM domain-containing protein (SMED30005808) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for RRM domain-containing protein (SMED30005808) 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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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




SMED30005808

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
headSMED30005808SMESG000017955.1 SmedASXL_069213SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
non-ciliated epidermisSMED30005808 dd_Smed_v4_39989_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 RRM domain-containing protein vs. TrEMBL
Match: T1G7R5 (Uncharacterized protein OS=Helobdella robusta OX=6412 GN=20217112 PE=4 SV=1)

HSP 1 Score: 70.4774 bits (171), Expect = 1.626e-11
Identity = 38/74 (51.35%), Postives = 47/74 (63.51%), Query Frame = 3
Query: 1149 MANLCPGLLWSVLWFLALIFVFYPFAGFCAGWYILFLPCTVCCDCTTAITDLLFKGVQWPLTCAKNIMEMRGCC 1370
            MANLCPGLLWS+LWF+ +IFV +P A F A  YI  +P   C      + D L   VQ PLT A+N+M M+ CC
Sbjct:    1 MANLCPGLLWSLLWFIGIIFVAWPIAFFLAWVYIFLIPFAACITPLKGLCDGLLGLVQLPLTFAQNMMAMKPCC 74          
BLAST of RRM domain-containing protein vs. TrEMBL
Match: A0A1L8DAA4 (Putative salivary secreted peptide OS=Nyssomyia neivai OX=330878 PE=4 SV=1)

HSP 1 Score: 68.9366 bits (167), Expect = 4.671e-11
Identity = 34/64 (53.12%), Postives = 43/64 (67.19%), Query Frame = 3
Query: 1173 LWSVLWFLALIFVFYPFAGFCAGWYILFLPCTVCCDCTTAITDLLFKGVQWPLTCAKNIMEMRG 1364
            LW V+W L LIF+ +  AGFCAGWYIL  P TVC    ++I+DLL +G Q+   CAK +ME R 
Sbjct:    5 LWFVVWLLILIFIAFFVAGFCAGWYILIYPLTVCIPALSSISDLLLQGAQFTHYCAKGMMECRS 68          
BLAST of RRM domain-containing protein vs. TrEMBL
Match: A0A0L8GA89 (Uncharacterized protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22037269mg PE=4 SV=1)

HSP 1 Score: 68.5514 bits (166), Expect = 7.382e-11
Identity = 35/74 (47.30%), Postives = 47/74 (63.51%), Query Frame = 3
Query: 1149 MANLCPGLLWSVLWFLALIFVFYPFAGFCAGWYILFLPCTVCCDCTTAITDLLFKGVQWPLTCAKNIMEMRGCC 1370
            MA +CPGLLW+++WFL LIFV +P     A  YI  LP  VC +    + D L K VQ+PLT A+N++ M+  C
Sbjct:    1 MAEICPGLLWAIVWFLLLIFVGWPLGFMIAFLYIFLLPFGVCLEPIKGVCDALLKVVQFPLTFAENMVAMKSPC 74          
BLAST of RRM domain-containing protein vs. TrEMBL
Match: A0A087UU40 (Uncharacterized protein (Fragment) OS=Stegodyphus mimosarum OX=407821 GN=X975_13380 PE=4 SV=1)

HSP 1 Score: 68.1662 bits (165), Expect = 1.030e-10
Identity = 33/66 (50.00%), Postives = 42/66 (63.64%), Query Frame = 3
Query: 1173 LWSVLWFLALIFVFYPFAGFCAGWYILFLPCTVCCDCTTAITDLLFKGVQWPLTCAKNIMEMRGCC 1370
            L S++W L LIF+ YP   F AGWY+LF P   CCD  + IT  L K  Q+PL C KN++E +G C
Sbjct:    5 LCSIVWLLILIFIGYPVGFFFAGWYVLFCPLEACCDGCSGITGFLLKATQFPLYCTKNMLEGKGLC 70          
BLAST of RRM domain-containing protein vs. TrEMBL
Match: A0A267FKX2 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig014448g1 PE=4 SV=1)

HSP 1 Score: 68.1662 bits (165), Expect = 1.134e-10
Identity = 37/79 (46.84%), Postives = 50/79 (63.29%), Query Frame = 3
Query: 1134 SSQN*MANLCPGLLWSVLWFLALIFVFYPFAGFCAGWYILFLPCTVCCDCTTAITDLLFKGVQWPLTCAKNIMEMRGCC 1370
            SS + MANLCPGLLW+++WFLALIF+ +P +   A  YIL LP + C      + D L   V   LTCA+N++ M+  C
Sbjct:    1 SSDSTMANLCPGLLWALIWFLALIFLAWPVSYIIAFVYILLLPFSACVGLLKPVCDTLLGVVNLCLTCAENMIAMKPLC 79          
BLAST of RRM domain-containing protein vs. Ensembl Nematostella
Match: EDO40799 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S654])

HSP 1 Score: 63.1586 bits (152), Expect = 6.980e-13
Identity = 29/64 (45.31%), Postives = 41/64 (64.06%), Query Frame = 3
Query: 1170 LLWSVLWFLALIFVFYPFAGFCAGWYILFLPCTVCCDCTTAITDLLFKGVQWPLTCAKNIMEMR 1361
            +LW+++WFL L FV +P   FCAGWY+   P   C D    +T+LL KGV  PL  AK+++E +
Sbjct:    3 ILWAIIWFLVLWFVGWPIGFFCAGWYVCLSPFEACIDALKGLTELLMKGVMLPLEVAKHMVEGK 66          
BLAST of RRM domain-containing protein vs. Ensembl Nematostella
Match: EDO30181 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S654])

HSP 1 Score: 63.1586 bits (152), Expect = 6.980e-13
Identity = 29/64 (45.31%), Postives = 41/64 (64.06%), Query Frame = 3
Query: 1170 LLWSVLWFLALIFVFYPFAGFCAGWYILFLPCTVCCDCTTAITDLLFKGVQWPLTCAKNIMEMR 1361
            +LW+++WFL L FV +P   FCAGWY+   P   C D    +T+LL KGV  PL  AK+++E +
Sbjct:    3 ILWAIIWFLVLWFVGWPIGFFCAGWYVCLSPFEACIDALKGLTELLMKGVMLPLEVAKHMVEGK 66          
BLAST of RRM domain-containing protein vs. Ensembl Nematostella
Match: EDO40535 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7S6X0])

HSP 1 Score: 60.077 bits (144), Expect = 7.793e-12
Identity = 26/65 (40.00%), Postives = 41/65 (63.08%), Query Frame = 3
Query: 1167 GLLWSVLWFLALIFVFYPFAGFCAGWYILFLPCTVCCDCTTAITDLLFKGVQWPLTCAKNIMEMR 1361
             +LW+++WFL L F+ +P   FCAGWY+   P   C D    +T+LL +GV+ PL  A +++E +
Sbjct:    2 NVLWAIIWFLVLWFIGWPIGFFCAGWYVCLSPFEACIDAIKQVTELLMRGVKLPLEVAVHMVEGK 66          
BLAST of RRM domain-containing protein vs. Planmine SMEST
Match: SMESG000017955.1 (SMESG000017955.1)

HSP 1 Score: 149.443 bits (376), Expect = 6.645e-44
Identity = 74/74 (100.00%), Postives = 74/74 (100.00%), Query Frame = 3
Query: 1149 MANLCPGLLWSVLWFLALIFVFYPFAGFCAGWYILFLPCTVCCDCTTAITDLLFKGVQWPLTCAKNIMEMRGCC 1370
            MANLCPGLLWSVLWFLALIFVFYPFAGFCAGWYILFLPCTVCCDCTTAITDLLFKGVQWPLTCAKNIMEMRGCC
Sbjct:    1 MANLCPGLLWSVLWFLALIFVFYPFAGFCAGWYILFLPCTVCCDCTTAITDLLFKGVQWPLTCAKNIMEMRGCC 74          
BLAST of RRM domain-containing protein vs. Planmine SMEST
Match: SMESG000017203.1 (SMESG000017203.1)

HSP 1 Score: 58.5362 bits (140), Expect = 6.035e-11
Identity = 26/70 (37.14%), Postives = 44/70 (62.86%), Query Frame = 3
Query: 1161 CPGLLWSVLWFLALIFVFYPFAGFCAGWYILFLPCTVCCDCTTAITDLLFKGVQWPLTCAKNIMEMRGCC 1370
            CPG++ +++WFL +IF+ +P AGF AG Y+  LP   C     A+ + L + +Q P+  A+N++ M+  C
Sbjct:    3 CPGIVNAIVWFLLVIFIAWPLAGFLAGIYVFLLPFAGCFGALKAVLEPLLQLIQLPMQWAENMVAMKSLC 72          
The following BLAST results are available for this feature:
BLAST of RRM 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 RRM 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 RRM 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 RRM 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 RRM 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 RRM 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 RRM 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 RRM domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
T1G7R51.626e-1151.35Uncharacterized protein OS=Helobdella robusta OX=6... [more]
A0A1L8DAA44.671e-1153.13Putative salivary secreted peptide OS=Nyssomyia ne... [more]
A0A0L8GA897.382e-1147.30Uncharacterized protein OS=Octopus bimaculoides OX... [more]
A0A087UU401.030e-1050.00Uncharacterized protein (Fragment) OS=Stegodyphus ... [more]
A0A267FKX21.134e-1046.84Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
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BLAST of RRM 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 RRM 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 RRM 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 RRM domain-containing protein vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 3
Match NameE-valueIdentityDescription
EDO407996.980e-1345.31Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
EDO301816.980e-1345.31Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
EDO405357.793e-1240.00Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of RRM 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 RRM domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000017955.16.645e-44100.00SMESG000017955.1[more]
SMESG000017203.16.035e-1137.14SMESG000017203.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005808 ID=SMED30005808|Name=RRM domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1484bp
CTATCGCGTAAAAAGAGAATTAGGCGTATACTTATAAATATGATACAAAC
TTTAGATTAAAACAAAAATACAAAATTTAATATTCAAAAAACTAATTTTT
TTCAAGTACTTAAACCTTACTTGCGGATTATAGTGTATATGGAAACACGA
TTCCAAATCGTTAATACAGATTTACCGGATTTTACATTTTGGTAGTTTTA
ATTTTTAACCTTTTGTCTATGATGTGTTCAAATTGCAACAAAAAATTCAT
GTAAATGTCTTTATATATTTATTAGAAAACCACACTCGATTATAACTTAT
ACTATATATTTCGACATTCACTGTCATCATCAGGTAAAGGAGCATCAATT
AAGAACGTTCACTAAGAATGGGGAGGAAGGGGGTCTTCGTAAAATGAAGT
GCTTAAGACATCTAGAGNANNGGTTCTTAAACTTTTTTTGCGGACTACTA
AATAAAAATAGACGTTTTCATAATGAATAATAAAATTCAAATATTTATGC
ACTTCAATTTTAAATACGAAATTATTGATTCAAGATAAAATAAATTTAAA
AAAACAAATACAATAGCCATTGAGCCCTTTGATTTTAAGTATTTCTCACA
TGGAAGACCACTTGTGTGTAAATTTGCACCCAACCATATTTTCACTGTGT
TATTGCTAGTTTAAAGGTTTAAATGATCACACTTGGAATAACTAAAGGAT
GAATACGGTAGGTTCTAGATTTAACAGAAATTTTCAAAAAAATGTGATGC
TGGGGTGCACATATACCTATGGTTGCCAACTTTTATCCATTTCCGTCTTT
TAGAATGTTTTCCGAAAAATCACCGCAACTATTCTTTGTATTAAAATAAA
TAAATAATTAACGTTTCATTACATATTACATAAATGAACCAGAGAGTTAA
ACATGTGATGTTGGAAACTGTTAGAATCAACACAAAACAATATAAAAAAT
AATTGTGCAAAATGTGTTATTGAAAAAAAATCAAACAACTTCCATTGTCA
AACAAATGAAGCACGTGTCAATGAAAAAAAACATTTGTTATCAGCATAAA
AATAGGGATAAATTTATCGCCAGAGTTATTGGAAACGGTTGATAAGCAAC
AATCCAACGTAAATAATGCCAAGTTTCTATTTTAGTAGTCAAAATTGAAT
GGCAAATTTATGCCCAGGATTACTCTGGTCAGTTTTGTGGTTTCTAGCTC
TGATTTTTGTCTTTTATCCATTTGCCGGTTTTTGCGCTGGATGGTATATT
CTATTTCTCCCATGCACTGTTTGTTGTGATTGTACAACTGCTATTACGGA
TTTACTTTTTAAAGGTGTTCAATGGCCCCTGACATGTGCAAAAAACATAA
TGGAAATGCGTGGATGTTGTTAAGAACTGAATCATGCTCGAATGAATTTG
CAATTTTTTAACATTTAAGGGTAAAAGTACTTATTAATATTATTCTTATC
ATTTTTATTACTTTATGATTAATAAATAGCTGAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0003723RNA binding
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0002063non-ciliated epidermis
Vocabulary: INTERPRO
TermDefinition
IPR013809ENTH
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availablePANTHERPTHR39948FAMILY NOT NAMEDcoord: 1..73
NoneNo IPR availableTMHMMTMhelixcoord: 15..37