DNA-directed RNA polymerase subunit

Overview
NameDNA-directed RNA polymerase subunit
Smed IDSMED30016023
Length (bp)1016
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 DNA-directed RNA polymerase subunit (SMED30016023) t-SNE clustered cells

Violin plots show distribution of expression levels for DNA-directed RNA polymerase subunit (SMED30016023) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

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 DNA-directed RNA polymerase subunit (SMED30016023) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for DNA-directed RNA polymerase subunit (SMED30016023) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30016023

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



PAGE Curations: 14

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30016023h1SMcG0012336 Contig2915GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
testisSMED30016023h1SMcG0012336 PL06005B2F10smed_ncbi_20240424PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
copulatory apparatusSMED30016023h1SMcG0012336 PL06005B2F10smed_ncbi_20240424PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
reproductive organSMED30016023h1SMcG0012336 Contig52894uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30016023h1SMcG0012336 Contig52894newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30016023h1SMcG0012336 Contig47584uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30016023h1SMcG0012336 Contig47584newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30016023h1SMcG0012336 Contig38335uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30016023h1SMcG0012336 Contig38335newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30016023h1SMcG0012336 Contig33315newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30016023h1SMcG0012336 Contig33315uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
testisSMED30016023h1SMcG0012336 Contig6058_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
early male germ cellSMED30016023h1SMcG0012336 Contig6058_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism asexual adult cDNA to DNA expression microarray evidence
testis primordiumSMED30016023h1SMcG0012336 Contig6058_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism juvenile stagecDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Human
Match: POLR3K (RNA polymerase III subunit K [Source:HGNC Symbol;Acc:HGNC:14121])

HSP 1 Score: 59.6918 bits (143), Expect = 8.965e-11
Identity = 29/55 (52.73%), Postives = 35/55 (63.64%), Query Frame = 3 
Query:  282 VLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSC--QKCRHIW 440
            VL     +     T E+CPKC H RA++MQ+QTRSADEPMTT Y C   +C H W
Sbjct:   52 VLGGAAAWENVDSTAESCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGHRW 106
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Celegans
Match: rpc-11 (DNA-directed RNA polymerase subunit [Source:UniProtKB/TrEMBL;Acc:U4PMG8])

HSP 1 Score: 58.9214 bits (141), Expect = 6.872e-11
Identity = 37/115 (32.17%), Postives = 50/115 (43.48%), Query Frame = 3 
Query:  102 ILFCPVDKFLLNFEKEVTKCSSYLRCSNPNCFYQLEIVDQIIQTFHRSESETNGKEVTGFVLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSC--QKCRHIW 440
            + FCP    +L  E         +R S P C Y   +   +    +    + +       VL     +     T+ETCP C H RA++MQ+QTRSADEP T  Y C    C H W
Sbjct:    2 LTFCPECGCVLQIESG----EQCMRFSCPACPYVCPVTQTVTSRIYPKLKDIDD------VLGGPGAWANAQVTDETCPVCSHGRAYFMQLQTRSADEPSTIFYRCADNACAHRW 106
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Celegans
Match: rpoa-12 (DNA-directed RNA polymerase subunit [Source:UniProtKB/TrEMBL;Acc:O17587])

HSP 1 Score: 55.8398 bits (133), Expect = 1.144e-9
Identity = 30/79 (37.97%), Postives = 45/79 (56.96%), Query Frame = 3 
Query:  207 EIVDQII----QTFHRSESETNGKEVTGFVLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSCQKCR 431
            E VDQ++    + + R+ ++T+G         IE++    A  +  C KCGH++A Y  MQTRSADE  T  Y+C KC+
Sbjct:   43 ERVDQVVSRVEKIYERTVADTDG---------IENDESADAVVDHICTKCGHSKASYSTMQTRSADEGQTVFYTCLKCK 112
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Celegans
Match: rpoa-12 (DNA-directed RNA polymerase subunit [Source:UniProtKB/TrEMBL;Acc:O17587])

HSP 1 Score: 55.8398 bits (133), Expect = 1.144e-9
Identity = 30/79 (37.97%), Postives = 45/79 (56.96%), Query Frame = 3 
Query:  207 EIVDQII----QTFHRSESETNGKEVTGFVLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSCQKCR 431
            E VDQ++    + + R+ ++T+G         IE++    A  +  C KCGH++A Y  MQTRSADE  T  Y+C KC+
Sbjct:   43 ERVDQVVSRVEKIYERTVADTDG---------IENDESADAVVDHICTKCGHSKASYSTMQTRSADEGQTVFYTCLKCK 112
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Fly
Match: CG33785 (gene:FBgn0061362 transcript:FBtr0091786)

HSP 1 Score: 62.3882 bits (150), Expect = 5.747e-12
Identity = 45/116 (38.79%), Postives = 61/116 (52.59%), Query Frame = 3 
Query:  102 ILFCPVDKFLLNFEKEVTKCSSYLRCSNPNCFYQLEIVDQI-IQTFHRSESETNGKEVTGFVLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSC--QKCRHIW 440
            + FCP    +L  E++ T C  +   +   C Y  +I  +I  +TF R       KEV   VL  +  +     T+  CP CGH RA++MQ+QTRSADEPMTT Y C   +C H W
Sbjct:    2 LFFCPSCGNILIIEED-TNCHRF---TCNTCPYISKIRRKISTKTFPRL------KEV-DHVLGGKAAWENVDSTDAECPTCGHKRAYFMQIQTRSADEPMTTFYKCCNHECNHTW 106
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Zebrafish
Match: polr3k (polymerase (RNA) III (DNA directed) polypeptide K [Source:ZFIN;Acc:ZDB-GENE-040718-291])

HSP 1 Score: 58.5362 bits (140), Expect = 1.682e-10
Identity = 42/115 (36.52%), Postives = 55/115 (47.83%), Query Frame = 3 
Query:  102 ILFCPVDKFLLNFEKEVTKCSSYLRCSNPNCFYQLEIVDQIIQTFHRSESETNGKEVTGFVLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSC--QKCRHIW 440
            +LFCP    +L  E E  +C    R +   C Y   I  ++    +    E +       VL     +     T E CPKC H RA++MQ+QTRSADEPMTT Y C   +C H W
Sbjct:    2 LLFCPTCGNVLIVE-EGQRC---FRFACNTCPYVHNITRKVNNRKYPKLKEVDD------VLGGSAAWENVDSTAEPCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIQCGHRW 106
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Xenopus
Match: csgalnact1 (chondroitin sulfate N-acetylgalactosaminyltransferase 1 [Source:Xenbase;Acc:XB-GENE-976931])

HSP 1 Score: 60.077 bits (144), Expect = 5.815e-11
Identity = 30/55 (54.55%), Postives = 35/55 (63.64%), Query Frame = 3 
Query:  282 VLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSC--QKCRHIW 440
            VL     +     T ETCPKC H RA++MQ+QTRSADEPMTT Y C   +C H W
Sbjct:   52 VLGGSAAWENVDSTAETCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNIQCGHRW 106
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Mouse
Match: Polr3k (polymerase (RNA) III (DNA directed) polypeptide K [Source:MGI Symbol;Acc:MGI:1914255])

HSP 1 Score: 59.3066 bits (142), Expect = 1.078e-10
Identity = 29/55 (52.73%), Postives = 34/55 (61.82%), Query Frame = 3 
Query:  282 VLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSC--QKCRHIW 440
            VL     +     T E CPKC H RA++MQ+QTRSADEPMTT Y C   +C H W
Sbjct:   52 VLGGAAAWENVDSTAEPCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGHRW 106
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. UniProt/SwissProt
Match: sp|O13896|RPC10_SCHPO (DNA-directed RNA polymerase III subunit RPC10 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=rpc11 PE=3 SV=1)

HSP 1 Score: 63.929 bits (154), Expect = 1.569e-11
Identity = 37/77 (48.05%), Postives = 45/77 (58.44%), Query Frame = 3 
Query:  225 IQTFHRSESETNGKEVTGFVLSIEDEFRGTAETEETC--PKCGHNRAHYMQMQTRSADEPMTTKYSCQKCRHIWVEK 449
            I TF  S  E   KEV   VL  E+ F    +TE TC   KC +NRA++ Q+Q RSADEPM+T Y C KC+  W E 
Sbjct:   34 ISTFLYSRHEFAQKEVDD-VLGGEEAFESNQQTEVTCENTKCDNNRAYFFQLQIRSADEPMSTFYRCTKCKFQWREN 109
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. UniProt/SwissProt
Match: sp|Q9Y2Y1|RPC10_HUMAN (DNA-directed RNA polymerase III subunit RPC10 OS=Homo sapiens OX=9606 GN=POLR3K PE=1 SV=2)

HSP 1 Score: 59.6918 bits (143), Expect = 4.305e-10
Identity = 29/55 (52.73%), Postives = 35/55 (63.64%), Query Frame = 3 
Query:  282 VLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSC--QKCRHIW 440
            VL     +     T E+CPKC H RA++MQ+QTRSADEPMTT Y C   +C H W
Sbjct:   52 VLGGAAAWENVDSTAESCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGHRW 106
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. UniProt/SwissProt
Match: sp|Q56254|TFS_THECE (Transcription factor S OS=Thermococcus celer OX=2264 GN=tfs PE=1 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 7.101e-10
Identity = 24/53 (45.28%), Postives = 35/53 (66.04%), Query Frame = 3 
Query:  282 VLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSCQKCRHIW 440
            ++ IE + +    T+ TCPKCG++ A++ +MQTR+ DEP T  Y C KC H W
Sbjct:   54 IVVIEQDLKTLPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGHTW 106
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. UniProt/SwissProt
Match: sp|Q9CQZ7|RPC10_MOUSE (DNA-directed RNA polymerase III subunit RPC10 OS=Mus musculus OX=10090 GN=Polr3k PE=3 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 7.543e-10
Identity = 29/55 (52.73%), Postives = 34/55 (61.82%), Query Frame = 3 
Query:  282 VLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSC--QKCRHIW 440
            VL     +     T E CPKC H RA++MQ+QTRSADEPMTT Y C   +C H W
Sbjct:   52 VLGGAAAWENVDSTAEPCPKCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGHRW 106
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. UniProt/SwissProt
Match: sp|Q2M2S7|RPC10_BOVIN (DNA-directed RNA polymerase III subunit RPC10 OS=Bos taurus OX=9913 GN=POLR3K PE=3 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 9.933e-10
Identity = 30/58 (51.72%), Postives = 36/58 (62.07%), Query Frame = 3 
Query:  291 IEDEFRGTA------ETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSC--QKCRHIW 440
            ++DE  G A       T E CPKC H RA++MQ+QTR ADEPMTT Y C   +C H W
Sbjct:   49 VDDELGGAAAWENVDSTAEPCPKCEHPRAYFMQLQTRYADEPMTTFYKCCNAQCGHRW 106
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. TrEMBL
Match: A0A4S2LL89 (DNA-directed RNA polymerase subunit OS=Opisthorchis felineus OX=147828 GN=CRM22_006399 PE=3 SV=1)

HSP 1 Score: 115.161 bits (287), Expect = 5.604e-28
Identity = 59/117 (50.43%), Postives = 75/117 (64.10%), Query Frame = 3 
Query:   96 MSILFCPVDKFLLNFEKEVTKCSSYLRCSNPNCFYQLEIVDQIIQTFHRSESETNGKEVTGFVLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSCQKCRHIWVE 446
            M +LFCP+   LL  E E   C S L CS P C YQ  +   ++Q  H+   +   +     V SI+D++  +A+ EE CPKCGHNRA+++QMQTRSADEP TTKYSC KCRHIW E
Sbjct:    1 MPVLFCPLCHSLLMVE-ESANCYS-LNCSTPCCSYQWFVTQPLVQE-HKPRQDVRLRLEEDAVFSIDDQYSSSAQIEEKCPKCGHNRAYFVQMQTRSADEPSTTKYSCMKCRHIWTE 114
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. TrEMBL
Match: A0A5J4NIK0 (DNA-directed RNA polymerase subunit OS=Paragonimus westermani OX=34504 GN=DEA37_0005218 PE=3 SV=1)

HSP 1 Score: 114.775 bits (286), Expect = 8.370e-28
Identity = 58/117 (49.57%), Postives = 75/117 (64.10%), Query Frame = 3 
Query:   96 MSILFCPVDKFLLNFEKEVTKCSSYLRCSNPNCFYQLEIVDQIIQTFHRSESETNGKEVTGFVLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSCQKCRHIWVE 446
            M +LFCP+   LL  + E   C S L CS P C YQ  +   ++Q  H+   +   +     V SI+D++  +A+ EE CPKCGHNRA+++QMQTRSADEP TTKYSC KCRHIW E
Sbjct:    1 MPVLFCPLCHSLLMIQ-ESANCYS-LNCSTPCCAYQWFVTQPLVQE-HKPRQDVRLRLEEDAVFSIDDQYSSSAQIEEKCPKCGHNRAYFVQMQTRSADEPSTTKYSCMKCRHIWTE 114
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. TrEMBL
Match: A0A183B9F3 (DNA-directed RNA polymerase subunit OS=Echinostoma caproni OX=27848 GN=ECPE_LOCUS15838 PE=3 SV=1)

HSP 1 Score: 113.235 bits (282), Expect = 3.065e-27
Identity = 57/117 (48.72%), Postives = 75/117 (64.10%), Query Frame = 3 
Query:   96 MSILFCPVDKFLLNFEKEVTKCSSYLRCSNPNCFYQLEIVDQIIQTFHRSESETNGKEVTGFVLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSCQKCRHIWVE 446
            M +LFCP+   LL+ E E   C S L CS P C Y+  +   ++Q  H+   +   +     V SI+D++  +A+ EE CPKC HNRA+++QMQTRSADEP TTKYSC KCRHIW E
Sbjct:    1 MPVLFCPLCHSLLSIE-ESANCYS-LNCSTPCCPYRWYVTQPLVQV-HKPRQDVRLRLEEDAVFSIDDQYSSSAQIEERCPKCDHNRAYFVQMQTRSADEPSTTKYSCMKCRHIWTE 114
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. TrEMBL
Match: A0A075ADJ7 (TFIIS-type domain-containing protein OS=Opisthorchis viverrini OX=6198 GN=T265_00110 PE=4 SV=1)

HSP 1 Score: 115.161 bits (287), Expect = 5.604e-27
Identity = 59/117 (50.43%), Postives = 75/117 (64.10%), Query Frame = 3 
Query:   96 MSILFCPVDKFLLNFEKEVTKCSSYLRCSNPNCFYQLEIVDQIIQTFHRSESETNGKEVTGFVLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSCQKCRHIWVE 446
            M +LFCP+   LL  E E   C S L CS P C YQ  +   ++Q  H+   +   +     V SI+D++  +A+ EE CPKCGHNRA+++QMQTRSADEP TTKYSC KCRHIW E
Sbjct:   83 MPVLFCPLCHSLLMVE-ESANCYS-LNCSTPCCSYQWFVTQPLVQE-HKPRQDIRLRLEEDAVFSIDDQYSSSAQIEEKCPKCGHNRAYFVQMQTRSADEPSTTKYSCMKCRHIWTE 196
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. TrEMBL
Match: A0A094ZCS3 (DNA-directed RNA polymerase III subunit RPC10 (Fragment) OS=Schistosoma haematobium OX=6185 GN=MS3_11552 PE=4 SV=1)

HSP 1 Score: 110.153 bits (274), Expect = 4.593e-26
Identity = 58/118 (49.15%), Postives = 74/118 (62.71%), Query Frame = 3 
Query:   96 MSILFCPVDKFLLNFEKEVTKCSSYLRCSNPNCFYQLEIVDQIIQTFHRSESETNGKEVTGFVLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSCQKCRHIWVEK 449
            M +LFCP+   LL  E E   C S L CS P C Y+   V Q +   H+   +   +     V S+EDE+  +A+T+E CPKCGH RA+++QMQTRSADEP TTKYSC KC HIW E+
Sbjct:    1 MPVLFCPLCHSLLMIE-ESAHCYS-LNCSAPLCSYRW-FVTQPLVLEHKPRQDVRLRLEEDAVFSVEDEYSSSAQTDEKCPKCGHTRAYFVQMQTRSADEPSTTKYSCMKCHHIWTEQ 115
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Cavefish
Match: polr3k (RNA polymerase III subunit K [Source:NCBI gene;Acc:103032815])

HSP 1 Score: 61.6178 bits (148), Expect = 1.205e-11
Identity = 44/115 (38.26%), Postives = 57/115 (49.57%), Query Frame = 3 
Query:  102 ILFCPVDKFLLNFEKEVTKCSSYLRCSNPNCFYQLEIVDQIIQTFHRSESETNGKEVTGFVLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSC--QKCRHIW 440
            +LFCP    +L  E E  KC  +  C+   C Y   I  ++    +    E +       VL     +     T ETCPKC H RA++MQ+QTRSADEPMTT Y C   +C H W
Sbjct:    2 LLFCPACGNVLIVE-EGQKCYRFA-CNT--CPYIHNITRKVNNRKYPKLKEVDD------VLGGAAAWENVDSTAETCPKCEHPRAYFMQIQTRSADEPMTTFYKCCSPQCGHRW 106
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Cavefish
Match: tcea1 (transcription elongation factor A1 [Source:NCBI gene;Acc:103034860])

HSP 1 Score: 48.9062 bits (115), Expect = 3.380e-6
Identity = 24/44 (54.55%), Postives = 27/44 (61.36%), Query Frame = 3 
Query:  309 GTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSCQKCRHIW 440
            GT     TC KC  NR  Y Q+QTRSADEPMTT   C +C + W
Sbjct:  264 GTVTDLFTCGKCKKNRCTYTQVQTRSADEPMTTFVFCNECGNRW 307
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Cavefish
Match: tcea1 (transcription elongation factor A1 [Source:NCBI gene;Acc:103034860])

HSP 1 Score: 48.521 bits (114), Expect = 4.233e-6
Identity = 29/60 (48.33%), Postives = 32/60 (53.33%), Query Frame = 3 
Query:  309 GTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSCQKCRHIWVEK*NCFLYFQSLYFC 488
            GT     TC KC  NR  Y Q+QTRSADEPMTT   C +C + W  K        SL FC
Sbjct:  251 GTVTDLFTCGKCKKNRCTYTQVQTRSADEPMTTFVFCNECGNRWKLK-------ISLLFC 303
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Yeast
Match: RPC11 (RNA polymerase III subunit C11; mediates pol III RNA cleavage activity and is important for termination of transcription; homologous to TFIIS [Source:SGD;Acc:S000002452])

HSP 1 Score: 49.6766 bits (117), Expect = 2.292e-8
Identity = 23/46 (50.00%), Postives = 28/46 (60.87%), Query Frame = 3 
Query:  318 ETEETCPK---CGHNRAHYMQMQTRSADEPMTTKYSCQKCRHIWVE 446
            +T+  CP    CG   A++ Q+Q RSADEPMTT Y C  C H W E
Sbjct:   64 QTKTQCPNYDTCGGESAYFFQLQIRSADEPMTTFYKCVNCGHRWKE 109
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Yeast
Match: RPA12 (RNA polymerase I subunit A12.2; contains two zinc binding domains, and the N terminal domain is responsible for anchoring to the RNA pol I complex; physically interacts with transcriptional activator Msn4p, to regulate transcription of AYR1, a gene involved in lipid metabolism [Source:SGD;Acc:S000003824])

HSP 1 Score: 43.5134 bits (101), Expect = 4.499e-6
Identity = 18/47 (38.30%), Postives = 28/47 (59.57%), Query Frame = 3 
Query:  294 EDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSCQKCRH 434
            ++E +  A  +E CP+CG+   +Y  +Q RSADE  T  Y+C  C +
Sbjct:   73 KNELKDGATIKEKCPQCGNEEMNYHTLQLRSADEGATVFYTCTSCGY 119
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Nematostella
Match: EDO31766 (DNA-directed RNA polymerase subunit [Source:UniProtKB/TrEMBL;Acc:A7SWZ1])

HSP 1 Score: 70.8626 bits (172), Expect = 2.213e-15
Identity = 49/115 (42.61%), Postives = 62/115 (53.91%), Query Frame = 3 
Query:  102 ILFCPVDKFLLNFEKEVTKCSSYLRCSNPNCFYQLEIVDQIIQTFHRSESETNGKEVTGFVLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSCQKCRHIWVE 446
            +LFCP    +L  E E T  S+Y R +   C Y   I  ++      S+     KEV   VL  +  +     TEE CPKC HNRA++MQ+QTRSADEPMTT Y C  C + W E
Sbjct:    2 LLFCPSCANVLVVE-EGTGPSAY-RFACQTCPYVHNIAKKV-----SSKKYPKLKEVDD-VLGGKSAWENVDSTEERCPKCDHNRAYFMQIQTRSADEPMTTFYKCCSCGNRWKE 108
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Medaka
Match: polr3k (RNA polymerase III subunit K [Source:NCBI gene;Acc:101173392])

HSP 1 Score: 60.077 bits (144), Expect = 3.540e-11
Identity = 43/115 (37.39%), Postives = 57/115 (49.57%), Query Frame = 3 
Query:  102 ILFCPVDKFLLNFEKEVTKCSSYLRCSNPNCFYQLEIVDQIIQTFHRSESETNGKEVTGFVLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSC--QKCRHIW 440
            +LFCP    +L  E E  KC   LR +   C Y   +  ++    +    E +       VL     +     T ETCPKC H RA++MQ+QTRSADEPMTT Y C   +C + W
Sbjct:    2 LLFCPTCGNVLIVE-EGQKC---LRFACNTCPYVHNVTRKVNYRKYPKLKEVDD------VLGGAAAWENVDSTAETCPKCEHPRAYFMQIQTRSADEPMTTFYKCCNAQCGNRW 106
[Close]
BLAST of DNA-directed RNA polymerase subunit vs. Planmine SMEST
Match: SMESG000027575.1 (SMESG000027575.1)

HSP 1 Score: 48.9062 bits (115), Expect = 2.217e-6
Identity = 23/44 (52.27%), Postives = 26/44 (59.09%), Query Frame = 3 
Query:  309 GTAETEETCPKCGHNRAHYMQMQTRSADEPMTTKYSCQKCRHIW 440
            GT      CPKC  ++  Y Q+QTRSADEPMTT   C  C H W
Sbjct:  273 GTESDLIKCPKCRESKCSYNQVQTRSADEPMTTFAYCNSCGHRW 316
The following BLAST results are available for this feature:
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 1
Match NameE-valueIdentityDescription
POLR3K8.965e-1152.73RNA polymerase III subunit K [Source:HGNC Symbol;A... [more]
back to top
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 3
Match NameE-valueIdentityDescription
rpc-116.872e-1132.17DNA-directed RNA polymerase subunit [Source:UniPr... [more]
rpoa-121.144e-937.97DNA-directed RNA polymerase subunit [Source:UniPr... [more]
rpoa-121.144e-937.97DNA-directed RNA polymerase subunit [Source:UniPr... [more]
back to top
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
CG337855.747e-1238.79gene:FBgn0061362 transcript:FBtr0091786[more]
back to top
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
polr3k1.682e-1036.52polymerase (RNA) III (DNA directed) polypeptide K ... [more]
back to top
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
csgalnact15.815e-1154.55chondroitin sulfate N-acetylgalactosaminyltransfer... [more]
back to top
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 1
Match NameE-valueIdentityDescription
Polr3k1.078e-1052.73polymerase (RNA) III (DNA directed) polypeptide K ... [more]
back to top
BLAST of DNA-directed RNA polymerase subunit vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 5
Match NameE-valueIdentityDescription
sp|O13896|RPC10_SCHPO1.569e-1148.05DNA-directed RNA polymerase III subunit RPC10 OS=S... [more]
sp|Q9Y2Y1|RPC10_HUMAN4.305e-1052.73DNA-directed RNA polymerase III subunit RPC10 OS=H... [more]
sp|Q56254|TFS_THECE7.101e-1045.28Transcription factor S OS=Thermococcus celer OX=22... [more]
sp|Q9CQZ7|RPC10_MOUSE7.543e-1052.73DNA-directed RNA polymerase III subunit RPC10 OS=M... [more]
sp|Q2M2S7|RPC10_BOVIN9.933e-1051.72DNA-directed RNA polymerase III subunit RPC10 OS=B... [more]
back to top
BLAST of DNA-directed RNA polymerase subunit vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4S2LL895.604e-2850.43DNA-directed RNA polymerase subunit OS=Opisthorchi... [more]
A0A5J4NIK08.370e-2849.57DNA-directed RNA polymerase subunit OS=Paragonimus... [more]
A0A183B9F33.065e-2748.72DNA-directed RNA polymerase subunit OS=Echinostoma... [more]
A0A075ADJ75.604e-2750.43TFIIS-type domain-containing protein OS=Opisthorch... [more]
A0A094ZCS34.593e-2649.15DNA-directed RNA polymerase III subunit RPC10 (Fra... [more]
back to top
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 3
Match NameE-valueIdentityDescription
polr3k1.205e-1138.26RNA polymerase III subunit K [Source:NCBI gene;Acc... [more]
tcea13.380e-654.55transcription elongation factor A1 [Source:NCBI ge... [more]
tcea14.233e-648.33transcription elongation factor A1 [Source:NCBI ge... [more]
back to top
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 2
Match NameE-valueIdentityDescription
RPC112.292e-850.00RNA polymerase III subunit C11; mediates pol III R... [more]
RPA124.499e-638.30RNA polymerase I subunit A12.2; contains two zinc ... [more]
back to top
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO317662.213e-1542.61DNA-directed RNA polymerase subunit [Source:UniPr... [more]
back to top
BLAST of DNA-directed RNA polymerase subunit vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
polr3k3.540e-1137.39RNA polymerase III subunit K [Source:NCBI gene;Acc... [more]
back to top
BLAST of DNA-directed RNA polymerase subunit vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000027575.12.217e-652.27SMESG000027575.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016023 ID=SMED30016023|Name=DNA-directed RNA polymerase subunit|organism=Schmidtea mediterranea sexual|type=transcript|length=1016bp
CAATATTAGGAATATTTTTTAAAAATAAAAGAATTTTGTATTTATAAATT
AATTAATTTATAGTTATTTTATATTAGTAAGTGAATATATTTAAGATGTC
AATTTTATTTTGCCCTGTCGATAAATTTCTTTTAAATTTCGAAAAAGAAG
TCACCAAATGTTCATCTTATTTAAGATGTTCTAATCCAAATTGCTTTTAT
CAGCTTGAAATTGTGGATCAAATAATTCAAACTTTTCATCGGTCTGAATC
AGAAACAAATGGTAAGGAGGTTACAGGATTCGTCCTTTCTATTGAAGACG
AATTCCGAGGTACTGCAGAAACAGAAGAAACATGTCCCAAATGTGGCCAC
AATCGGGCTCATTATATGCAAATGCAAACAAGGTCAGCGGATGAGCCTAT
GACAACTAAATATTCTTGTCAAAAATGTCGTCATATTTGGGTTGAAAAAT
AAAATTGTTTTCTTTATTTTCAATCTTTATATTTTTGTGATATAATTTTG
AGATTATGTTCTATATACATATTTTTCATATTTTAGTCAGATAAAATTGG
CGTTGTGTTTGTGGCTGGAGAAGCAGACGAAAGTGATGAAGACGTTGGCA
CTCTATCAATAACAAGGGTTCATAAAGTTGATGAATCGCAGTCTTTTAAT
GCTAAATATATCAGGTCCGATTCTAATGATTTAAAAGACATGTGCGTGAA
ATCATTACTTCACTCTAATCTTAACAACGATATGAAAATATTTATTCAAA
ATTTGCGAAAGTTTACATTTATTTTATACAATGAAACTAAAATTAGTATT
AATCTTATGCAAAACCAATTAATGTCTACCTATTCTTTGATTCAAAATGT
ATCCTACAATTTAAGAATATCGTCAAATGATTTGTTTTATCTTGAAGACA
ATATCGATTCGATATATTCTTTGGAAAACATACCAAATTTTAAAAATGTG
AATTAACTAATCAAAATATGTGATTTTTCATCAGTTTTTAGTTTTTCTTA
AATCTTTAACTTATTT
back to top

protein sequence of SMED30016023-orf-1

>SMED30016023-orf-1 ID=SMED30016023-orf-1|Name=SMED30016023-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=119bp
MSILFCPVDKFLLNFEKEVTKCSSYLRCSNPNCFYQLEIVDQIIQTFHRS
ESETNGKEVTGFVLSIEDEFRGTAETEETCPKCGHNRAHYMQMQTRSADE
PMTTKYSCQKCRHIWVEK*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: biological process
TermDefinition
GO:0042779tRNA 3'-trailer cleavage
GO:0006351transcription, DNA-templated
GO:0006379mRNA cleavage
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
Vocabulary: INTERPRO
TermDefinition
IPR034014Zn_ribbon_RPC11_C
IPR017245BLOC-1_complex_su-3
IPR001222Znf_TFIIS
IPR012164Rpa12/Rpb9/Rpc10/TFS
Vocabulary: molecular function
TermDefinition
GO:0008270zinc ion binding
GO:0003676nucleic acid binding
GO:0003899DNA-directed 5'-3' RNA polymerase activity
GO:0046872metal ion binding
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
GO:0005730nucleolus
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001222Zinc finger, TFIIS-typeSMARTSM00440Cys4_2coord: 78..117
e-value: 7.9E-19
score: 78.6
IPR001222Zinc finger, TFIIS-typePFAMPF01096TFIIS_Ccoord: 79..115
e-value: 8.9E-19
score: 67.1
IPR001222Zinc finger, TFIIS-typePROSITEPS00466ZF_TFIIS_1coord: 80..115
IPR001222Zinc finger, TFIIS-typePROSITEPS51133ZF_TFIIS_2coord: 76..116
score: 14.826
NoneNo IPR availableGENE3DG3DSA:2.20.25.10coord: 64..118
e-value: 7.8E-22
score: 78.3
NoneNo IPR availablePANTHERPTHR11239:SF12DNA-DIRECTED RNA POLYMERASE III SUBUNIT RPC10coord: 4..116
NoneNo IPR availablePANTHERPTHR11239DNA-DIRECTED RNA POLYMERASEcoord: 4..116
NoneNo IPR availableSUPERFAMILYSSF57783Zinc beta-ribboncoord: 67..117
IPR012164DNA-directed RNA polymerase subunit/transcription factor SPIRSFPIRSF005586RNApol_RpoMcoord: 3..118
e-value: 2.7E-21
score: 73.8
IPR034014Pol III subunit C11, C-terminal zinc ribbonCDDcd10509Zn-ribbon_RPC11coord: 72..117
e-value: 4.6419E-23
score: 82.2482