DNA-directed RNA polymerases I, II, and III subunit RPABC2

Overview
NameDNA-directed RNA polymerases I, II, and III subunit RPABC2
Smed IDSMED30027916
Length (bp)510
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 polymerases I, II, and III subunit RPABC2 (SMED30027916) t-SNE clustered cells

Violin plots show distribution of expression levels for DNA-directed RNA polymerases I, II, and III subunit RPABC2 (SMED30027916) 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 DNA-directed RNA polymerases I, II, and III subunit RPABC2 (SMED30027916) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for DNA-directed RNA polymerases I, II, and III subunit RPABC2 (SMED30027916) 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



SMED30027916

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
X1 cellSMED30027916SMESG000043366.1 SMESG000043360.1 SmedASXL_008544SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
neoblastSMED30027916SMESG000043360.1 dd_Smed_v4_3539_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 DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Human
Match: POLR2F (RNA polymerase II subunit F [Source:HGNC Symbol;Acc:HGNC:9193])

HSP 1 Score: 128.257 bits (321), Expect = 3.577e-38
Identity = 65/115 (56.52%), Postives = 80/115 (69.57%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            L D E  +   Q+N  ++ SG          +     KR TTPY+TKYERARVLGTRALQI++CAP+MVEL+ E DPL IA KEL+A KIP IIRR+LP G+YEDW V+ELI+ D
Sbjct:   17 LDDLENAEEEGQENVEILPSGE---------RPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD 122
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Human
Match: POLR2F (RNA polymerase II subunit F [Source:HGNC Symbol;Acc:HGNC:9193])

HSP 1 Score: 128.257 bits (321), Expect = 4.533e-38
Identity = 65/115 (56.52%), Postives = 80/115 (69.57%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            L D E  +   Q+N  ++ SG          +     KR TTPY+TKYERARVLGTRALQI++CAP+MVEL+ E DPL IA KEL+A KIP IIRR+LP G+YEDW V+ELI+ D
Sbjct:   22 LDDLENAEEEGQENVEILPSGE---------RPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD 127
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Human
Match: POLR2F (RNA polymerase II subunit F [Source:HGNC Symbol;Acc:HGNC:9193])

HSP 1 Score: 118.627 bits (296), Expect = 1.906e-34
Identity = 58/98 (59.18%), Postives = 71/98 (72.45%), Query Frame = 2 
Query:  170 QDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVE 463
            Q+N  ++ SG          +     KR TTPY+TKYERARVLGTRALQI++CAP+MVEL+ E DPL IA KEL+A KIP IIRR+LP G+YEDW V+
Sbjct:   24 QENVEILPSGE---------RPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVD 112
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Human
Match: POLR2F (RNA polymerase II subunit F [Source:HGNC Symbol;Acc:HGNC:9193])

HSP 1 Score: 85.1149 bits (209), Expect = 1.262e-21
Identity = 45/86 (52.33%), Postives = 56/86 (65.12%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELR 394
            L D E  +   Q+N  ++ SG          +     KR TTPY+TKYERARVLGTRALQI++CAP+MVEL+ E DPL IA KEL+
Sbjct:   22 LDDLENAEEEGQENVEILPSGE---------RPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELK 98
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Human
Match: POLR2F (RNA polymerase II subunit F [Source:HGNC Symbol;Acc:HGNC:9193])

HSP 1 Score: 85.5001 bits (210), Expect = 1.959e-21
Identity = 45/86 (52.33%), Postives = 56/86 (65.12%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELR 394
            L D E  +   Q+N  ++ SG          +     KR TTPY+TKYERARVLGTRALQI++CAP+MVEL+ E DPL IA KEL+
Sbjct:   22 LDDLENAEEEGQENVEILPSGE---------RPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELK 98
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Celegans
Match: rpb-6 (Probable DNA-directed RNA polymerases I, II, and III subunit RPABC2 [Source:UniProtKB/Swiss-Prot;Acc:Q17684])

HSP 1 Score: 116.701 bits (291), Expect = 6.156e-34
Identity = 54/88 (61.36%), Postives = 69/88 (78.41%), Query Frame = 2 
Query:  218 ISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
              Q KAV  S+  TTP++TKYERARVLGTRALQI++ AP+MVEL+ E DPL+IA KEL+  +IP I+RR+LP G+YEDW  ++L L D
Sbjct:   49 FDQGKAVPTSEHVTTPFMTKYERARVLGTRALQIAMGAPVMVELEGETDPLEIARKELKQRRIPIIVRRYLPDGSYEDWPTDQLQLAD 136
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Fly
Match: RpII18 (gene:FBgn0003275 transcript:FBtr0078787)

HSP 1 Score: 126.716 bits (317), Expect = 9.445e-38
Identity = 58/82 (70.73%), Postives = 69/82 (84.15%), Query Frame = 2 
Query:  236 VEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            V  SKR TT Y+TKYERARVLGTRALQI++CAPIMVELD E DPL+IA KEL+  KIP IIRR+LP  +YEDW ++ELI++D
Sbjct:   49 VPKSKRITTKYMTKYERARVLGTRALQIAMCAPIMVELDGETDPLQIAMKELKQKKIPIIIRRYLPDHSYEDWSIDELIMVD 130
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Zebrafish
Match: polr2f (polymerase (RNA) II (DNA directed) polypeptide F [Source:ZFIN;Acc:ZDB-GENE-040718-279])

HSP 1 Score: 126.331 bits (316), Expect = 1.597e-37
Identity = 62/115 (53.91%), Postives = 82/115 (71.30%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            L D E ++  +Q+N  ++ +G  Q  +          KR TT Y+TKYERARVLGTRALQI++CAP+MVEL+ E DPL+IA KEL++ KIP IIRR+LP G+YEDW  +ELI+ D
Sbjct:   29 LDDLENVEDEDQENVQILPAGEGQQAN---------QKRITTQYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKSRKIPIIIRRYLPDGSYEDWGCDELIITD 134
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Zebrafish
Match: polr2f (polymerase (RNA) II (DNA directed) polypeptide F [Source:ZFIN;Acc:ZDB-GENE-040718-279])

HSP 1 Score: 126.331 bits (316), Expect = 1.612e-37
Identity = 62/115 (53.91%), Postives = 82/115 (71.30%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            L D E ++  +Q+N  ++ +G  Q  +          KR TT Y+TKYERARVLGTRALQI++CAP+MVEL+ E DPL+IA KEL++ KIP IIRR+LP G+YEDW  +ELI+ D
Sbjct:   22 LDDLENVEDEDQENVQILPAGEGQQAN---------QKRITTQYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKSRKIPIIIRRYLPDGSYEDWGCDELIITD 127
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Xenopus
Match: polr2f (polymerase (RNA) II subunit F [Source:NCBI gene;Acc:448728])

HSP 1 Score: 125.946 bits (315), Expect = 3.513e-37
Identity = 65/112 (58.04%), Postives = 82/112 (73.21%), Query Frame = 2 
Query:  149 EKMDTAEQ-DNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            + +D AE+ D  NV +  A + +  +Q       KR TT Y+TKYERARVLGTRALQI++CAP+MVEL+ E DPL IA KEL+A KIP IIRR+LP G+YEDW V+ELI+ D
Sbjct:   23 DDLDNAEEEDQENVAILPAGEGQQANQ-------KRITTNYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD 127
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Mouse
Match: Polr2f (polymerase (RNA) II (DNA directed) polypeptide F [Source:MGI Symbol;Acc:MGI:1349393])

HSP 1 Score: 127.487 bits (319), Expect = 5.983e-38
Identity = 65/115 (56.52%), Postives = 80/115 (69.57%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            L D E  +   Q+N  ++ SG          +     KR TTPY+TKYERARVLGTRALQI++CAP+MVEL+ E DPL IA KEL+A KIP IIRR+LP G+YEDW V+ELI+ D
Sbjct:   22 LDDLENAEEEGQENVEILPSGE---------RPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIISD 127
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Mouse
Match: Polr2f (polymerase (RNA) II (DNA directed) polypeptide F [Source:MGI Symbol;Acc:MGI:1349393])

HSP 1 Score: 88.9669 bits (219), Expect = 4.091e-23
Identity = 51/115 (44.35%), Postives = 65/115 (56.52%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            L D E  +   Q+N  ++ SG          +     KR TTPY+TK               +CAP+MVEL+ E DPL IA KEL+A KIP IIRR+LP G+YEDW V+ELI+ D
Sbjct:   22 LDDLENAEEEGQENVEILPSGE---------RPQANQKRITTPYMTK---------------MCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIISD 112
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Mouse
Match: Polr2f (polymerase (RNA) II (DNA directed) polypeptide F [Source:MGI Symbol;Acc:MGI:1349393])

HSP 1 Score: 85.1149 bits (209), Expect = 8.665e-22
Identity = 45/86 (52.33%), Postives = 56/86 (65.12%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELR 394
            L D E  +   Q+N  ++ SG          +     KR TTPY+TKYERARVLGTRALQI++CAP+MVEL+ E DPL IA KEL+
Sbjct:   22 LDDLENAEEEGQENVEILPSGE---------RPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELK 98
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. UniProt/SwissProt
Match: sp|Q5R592|RPAB2_PONAB (DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Pongo abelii OX=9601 GN=POLR2F PE=2 SV=1)

HSP 1 Score: 128.257 bits (321), Expect = 2.177e-37
Identity = 65/115 (56.52%), Postives = 80/115 (69.57%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            L D E  +   Q+N  ++ SG          +     KR TTPY+TKYERARVLGTRALQI++CAP+MVEL+ E DPL IA KEL+A KIP IIRR+LP G+YEDW V+ELI+ D
Sbjct:   22 LDDLENAEEEGQENVEILPSGE---------RPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD 127
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. UniProt/SwissProt
Match: sp|P61218|RPAB2_HUMAN (DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Homo sapiens OX=9606 GN=POLR2F PE=1 SV=1)

HSP 1 Score: 128.257 bits (321), Expect = 2.177e-37
Identity = 65/115 (56.52%), Postives = 80/115 (69.57%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            L D E  +   Q+N  ++ SG          +     KR TTPY+TKYERARVLGTRALQI++CAP+MVEL+ E DPL IA KEL+A KIP IIRR+LP G+YEDW V+ELI+ D
Sbjct:   22 LDDLENAEEEGQENVEILPSGE---------RPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD 127
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. UniProt/SwissProt
Match: sp|P61217|RPAB2_CRIGR (DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Cricetulus griseus OX=10029 GN=POLR2F PE=2 SV=1)

HSP 1 Score: 128.257 bits (321), Expect = 2.177e-37
Identity = 65/115 (56.52%), Postives = 80/115 (69.57%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            L D E  +   Q+N  ++ SG          +     KR TTPY+TKYERARVLGTRALQI++CAP+MVEL+ E DPL IA KEL+A KIP IIRR+LP G+YEDW V+ELI+ D
Sbjct:   22 LDDLENAEEEGQENVEILPSGE---------RPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD 127
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. UniProt/SwissProt
Match: sp|O88828|RPAB2_RAT (DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Rattus norvegicus OX=10116 GN=Polr2f PE=1 SV=1)

HSP 1 Score: 127.487 bits (319), Expect = 4.185e-37
Identity = 65/115 (56.52%), Postives = 80/115 (69.57%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            L D E  +   Q+N  ++ SG          +     KR TTPY+TKYERARVLGTRALQI++CAP+MVEL+ E DPL IA KEL+A KIP IIRR+LP G+YEDW V+ELI+ D
Sbjct:   22 LDDLENAEEEGQENVEILPSGE---------RPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIISD 127
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. UniProt/SwissProt
Match: sp|P61219|RPAB2_MOUSE (DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Mus musculus OX=10090 GN=Polr2f PE=2 SV=1)

HSP 1 Score: 127.487 bits (319), Expect = 4.185e-37
Identity = 65/115 (56.52%), Postives = 80/115 (69.57%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            L D E  +   Q+N  ++ SG          +     KR TTPY+TKYERARVLGTRALQI++CAP+MVEL+ E DPL IA KEL+A KIP IIRR+LP G+YEDW V+ELI+ D
Sbjct:   22 LDDLENAEEEGQENVEILPSGE---------RPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIISD 127
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. TrEMBL
Match: Q5D946 (SJCHGC05009 protein OS=Schistosoma japonicum OX=6182 PE=2 SV=1)

HSP 1 Score: 139.043 bits (349), Expect = 3.704e-39
Identity = 72/121 (59.50%), Postives = 88/121 (72.73%), Query Frame = 2 
Query:  140 SDDEKMDTAEQDNSNVIMSGATQV--KDISQLKA-------VEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELIL 475
            SD+E +D    D+ +    G T +   ++ +L +       VE SKR TTPYLTKYERARVLG RALQ+S+ AP+MVELD ERDPLKIAEKELRA KIP IIRRFLP G++EDW ++ELIL
Sbjct:   13 SDEEPLDEVPDDDLDTKPDGVTYITTDEVPRLSSGQSLAAPVEKSKRITTPYLTKYERARVLGARALQLSMSAPVMVELDGERDPLKIAEKELRANKIPIIIRRFLPDGSFEDWSLDELIL 133
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. TrEMBL
Match: A0A183S126 (Uncharacterized protein OS=Schistosoma rodhaini OX=6188 PE=3 SV=1)

HSP 1 Score: 139.043 bits (349), Expect = 4.372e-39
Identity = 68/112 (60.71%), Postives = 84/112 (75.00%), Query Frame = 2 
Query:  146 DEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            +E +DT  +  + +    A ++   +    VE SKR TTPYLTKYERARVLG RALQ+S+ AP+MVELD ERDPLKIAEKELRA KIP IIRRFLP G++EDW ++ELIL +
Sbjct:   23 EEDLDTKPEGVTYITADEAPRLSGQNMAAPVEKSKRVTTPYLTKYERARVLGARALQLSMSAPVMVELDGERDPLKIAEKELRANKIPIIIRRFLPDGSFEDWSLDELILTE 134
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. TrEMBL
Match: A0A183MM82 (Uncharacterized protein OS=Schistosoma margrebowiei OX=48269 GN=SMRZ_LOCUS17157 PE=3 SV=1)

HSP 1 Score: 138.658 bits (348), Expect = 6.988e-39
Identity = 68/112 (60.71%), Postives = 84/112 (75.00%), Query Frame = 2 
Query:  146 DEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            +E +DT  +  + +    A ++   +    VE SKR TTPYLTKYERARVLG RALQ+S+ AP+MVELD ERDPLKIAEKELRA KIP IIRRFLP G++EDW ++ELIL +
Sbjct:   23 EEDLDTKPEGVTYITADEAPRLSGQNMAAPVEKSKRITTPYLTKYERARVLGARALQLSMSAPVMVELDGERDPLKIAEKELRANKIPIIIRRFLPDGSFEDWSLDELILTE 134
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. TrEMBL
Match: A0A430QPC4 (DNA-directed RNA polymerases I, II, and III subunit RPABC2 OS=Schistosoma bovis OX=6184 GN=DC041_0005789 PE=3 SV=1)

HSP 1 Score: 135.576 bits (340), Expect = 1.954e-38
Identity = 64/82 (78.05%), Postives = 72/82 (87.80%), Query Frame = 2 
Query:  236 VEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            VE SKR TTPYLTKYERARVLG RALQ+S+ AP+MVELD ERDPLKIAEKELRA KIP IIRRFLP G++EDW ++ELIL +
Sbjct:    5 VEKSKRITTPYLTKYERARVLGARALQLSMSAPVMVELDGERDPLKIAEKELRANKIPIIIRRFLPDGSFEDWSLDELILTE 86
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. TrEMBL
Match: G4V787 (Putative DNA-directed rna polymerase subunit rpb6 OS=Schistosoma mansoni OX=6183 GN=Smp_073570 PE=3 SV=1)

HSP 1 Score: 137.117 bits (344), Expect = 2.079e-38
Identity = 67/112 (59.82%), Postives = 83/112 (74.11%), Query Frame = 2 
Query:  146 DEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            +E +DT  +  + +      ++   +    VE SKR TTPYLTKYERARVLG RALQ+S+ AP+MVELD ERDPLKIAEKELRA KIP IIRRFLP G++EDW ++ELIL +
Sbjct:   23 EEDLDTKPEGVTYITADETPRLSGQNMAAPVEKSKRVTTPYLTKYERARVLGARALQLSMSAPVMVELDGERDPLKIAEKELRANKIPIIIRRFLPDGSFEDWSLDELILTE 134
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Cavefish
Match: POLR2F (RNA polymerase II subunit F [Source:NCBI gene;Acc:103036223])

HSP 1 Score: 129.413 bits (324), Expect = 9.166e-39
Identity = 63/115 (54.78%), Postives = 83/115 (72.17%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            L D E ++  +Q+N  ++ +G  Q  +          KR TTPY+TKYERARVLGTRALQI++CAP+MVEL+ E DPL+IA KEL++ KIP IIRR+LP G+YEDW  +ELI+ D
Sbjct:   22 LDDLENVEDEDQENVQILPAGEGQQAN---------QKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKSRKIPIIIRRYLPDGSYEDWGCDELIISD 127
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Yeast
Match: RPO26 (RNA polymerase subunit ABC23; common to RNA polymerases I, II, and III; part of central core; similar to bacterial omega subunit [Source:SGD;Acc:S000006391])

HSP 1 Score: 122.094 bits (305), Expect = 1.700e-36
Identity = 58/110 (52.73%), Postives = 76/110 (69.09%), Query Frame = 2 
Query:  176 NSNVIMSGATQVKDISQL----------KAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELIL 475
            N   I++G    +D  Q           KA+   +R+TTPY+TKYERAR+LGTRALQIS+ AP+ V+L+ E DPL+IA KEL   KIP +IRR+LP G++EDW VEELI+
Sbjct:   44 NGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIV 153
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Nematostella
Match: EDO31295 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SYA5])

HSP 1 Score: 108.612 bits (270), Expect = 8.908e-32
Identity = 50/71 (70.42%), Postives = 62/71 (87.32%), Query Frame = 2 
Query:  269 LTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            +TKYERARVLGTRALQIS+ AP+MVEL+ E DPL+IA KEL+A KIP IIRR+LP G++EDW ++ELI+ D
Sbjct:    1 MTKYERARVLGTRALQISMGAPVMVELEGETDPLQIAMKELKARKIPIIIRRYLPDGSHEDWGIDELIVTD 71
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Medaka
Match: polr2f (RNA polymerase II subunit F [Source:NCBI gene;Acc:101154870])

HSP 1 Score: 127.872 bits (320), Expect = 3.634e-38
Identity = 62/115 (53.91%), Postives = 83/115 (72.17%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            L D E ++  +Q+N  ++ +G  Q  +          KR TTP++TKYERARVLGTRALQI++CAP+MVEL+ E DPL+IA KEL++ KIP IIRR+LP G+YEDW  +ELI+ D
Sbjct:   22 LDDLENVEDEDQENVQILPAGEGQQAN---------QKRITTPHMTKYERARVLGTRALQIAMCAPVMVELEGETDPLQIAMKELKSRKIPIIIRRYLPDGSYEDWGCDELIITD 127
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Planmine SMEST
Match: SMESG000043360.1 (SMESG000043360.1)

HSP 1 Score: 233.417 bits (594), Expect = 5.790e-80
Identity = 113/115 (98.26%), Postives = 115/115 (100.00%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            LSDDEKMDTA+QDNSNVIMSGATQVKD+SQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID
Sbjct:   16 LSDDEKMDTADQDNSNVIMSGATQVKDVSQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 130
[Close]
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Planmine SMEST
Match: SMESG000043366.1 (SMESG000043366.1)

HSP 1 Score: 226.868 bits (577), Expect = 2.063e-77
Identity = 108/115 (93.91%), Postives = 113/115 (98.26%), Query Frame = 2 
Query:  137 LSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVEGSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKELRAGKIPFIIRRFLPGGTYEDWKVEELILID 481
            LSDDEKMDTA+ DNSN+IMSGATQVKD+SQLKAVEGSKRSTTPY+TKYERARVLGTRALQISLCAPIMVELD ERDPLKIAEKELRAGKIPFIIRR+LPGGTYEDWKVEELILID
Sbjct:   16 LSDDEKMDTADHDNSNLIMSGATQVKDVSQLKAVEGSKRSTTPYMTKYERARVLGTRALQISLCAPIMVELDGERDPLKIAEKELRAGKIPFIIRRYLPGGTYEDWKVEELILID 130
The following BLAST results are available for this feature:
BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 5
Match NameE-valueIdentityDescription
POLR2F3.577e-3856.52RNA polymerase II subunit F [Source:HGNC Symbol;Ac... [more]
POLR2F4.533e-3856.52RNA polymerase II subunit F [Source:HGNC Symbol;Ac... [more]
POLR2F1.906e-3459.18RNA polymerase II subunit F [Source:HGNC Symbol;Ac... [more]
POLR2F1.262e-2152.33RNA polymerase II subunit F [Source:HGNC Symbol;Ac... [more]
POLR2F1.959e-2152.33RNA polymerase II subunit F [Source:HGNC Symbol;Ac... [more]
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BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 1
Match NameE-valueIdentityDescription
rpb-66.156e-3461.36Probable DNA-directed RNA polymerases I, II, and I... [more]
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BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
RpII189.445e-3870.73gene:FBgn0003275 transcript:FBtr0078787[more]
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BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 2
Match NameE-valueIdentityDescription
polr2f1.597e-3753.91polymerase (RNA) II (DNA directed) polypeptide F [... [more]
polr2f1.612e-3753.91polymerase (RNA) II (DNA directed) polypeptide F [... [more]
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BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
polr2f3.513e-3758.04polymerase (RNA) II subunit F [Source:NCBI gene;Ac... [more]
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BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 3
Match NameE-valueIdentityDescription
Polr2f5.983e-3856.52polymerase (RNA) II (DNA directed) polypeptide F [... [more]
Polr2f4.091e-2344.35polymerase (RNA) II (DNA directed) polypeptide F [... [more]
Polr2f8.665e-2252.33polymerase (RNA) II (DNA directed) polypeptide F [... [more]
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BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 5
Match NameE-valueIdentityDescription
sp|Q5R592|RPAB2_PONAB2.177e-3756.52DNA-directed RNA polymerases I, II, and III subuni... [more]
sp|P61218|RPAB2_HUMAN2.177e-3756.52DNA-directed RNA polymerases I, II, and III subuni... [more]
sp|P61217|RPAB2_CRIGR2.177e-3756.52DNA-directed RNA polymerases I, II, and III subuni... [more]
sp|O88828|RPAB2_RAT4.185e-3756.52DNA-directed RNA polymerases I, II, and III subuni... [more]
sp|P61219|RPAB2_MOUSE4.185e-3756.52DNA-directed RNA polymerases I, II, and III subuni... [more]
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BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
Q5D9463.704e-3959.50SJCHGC05009 protein OS=Schistosoma japonicum OX=61... [more]
A0A183S1264.372e-3960.71Uncharacterized protein OS=Schistosoma rodhaini OX... [more]
A0A183MM826.988e-3960.71Uncharacterized protein OS=Schistosoma margrebowie... [more]
A0A430QPC41.954e-3878.05DNA-directed RNA polymerases I, II, and III subuni... [more]
G4V7872.079e-3859.82Putative DNA-directed rna polymerase subunit rpb6 ... [more]
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BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
POLR2F9.166e-3954.78RNA polymerase II subunit F [Source:NCBI gene;Acc:... [more]
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BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 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 DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 1
Match NameE-valueIdentityDescription
RPO261.700e-3652.73RNA polymerase subunit ABC23; common to RNA polyme... [more]
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BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO312958.908e-3270.42Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
polr2f3.634e-3853.91RNA polymerase II subunit F [Source:NCBI gene;Acc:... [more]
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BLAST of DNA-directed RNA polymerases I, II, and III subunit RPABC2 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000043360.15.790e-8098.26SMESG000043360.1[more]
SMESG000043366.12.063e-7793.91SMESG000043366.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027916 ID=SMED30027916|Name=DNA-directed RNA polymerases I, II, and III subunit RPABC2|organism=Schmidtea mediterranea sexual|type=transcript|length=510bp
CATTTCTTTTATGAAATTATTTATTTAATTATTTAATTTTTAAATAATAA
ATTGTTTAAATATTAATTAAATTTTTTTTCTGGTTTCAATCATGGATTAT
GAAGTATATGACGAATATGAGGAAAATAACTGTGAATTATCAGACGATGA
GAAAATGGACACAGCTGAGCAAGATAATAGTAATGTAATAATGTCTGGTG
CTACTCAAGTTAAAGATATAAGTCAGTTGAAAGCTGTTGAGGGAAGTAAA
CGCAGTACTACTCCTTACTTGACCAAATACGAAAGAGCTCGAGTTCTTGG
AACTCGAGCACTACAAATTTCATTGTGTGCTCCAATTATGGTGGAATTGG
ATAGTGAAAGGGATCCATTAAAGATTGCTGAAAAAGAATTAAGAGCAGGG
AAAATACCTTTTATAATTCGAAGATTTCTACCCGGAGGCACTTATGAAGA
TTGGAAAGTTGAAGAATTAATTTTAATAGATTAAATATTTTGTCTTACTG
TAAAAAAAAA
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protein sequence of SMED30027916-orf-1

>SMED30027916-orf-1 ID=SMED30027916-orf-1|Name=SMED30027916-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=131bp
MDYEVYDEYEENNCELSDDEKMDTAEQDNSNVIMSGATQVKDISQLKAVE
GSKRSTTPYLTKYERARVLGTRALQISLCAPIMVELDSERDPLKIAEKEL
RAGKIPFIIRRFLPGGTYEDWKVEELILID*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000429neoblast
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR036161RPB6/omega-like_sf
IPR006110Pol_omega/K/RPB6
IPR006111RpoK/Rpb6
IPR012293RNAP_RPB6_omega
IPR028363RPB6
IPR020708DNA-dir_RNA_polK_14-18kDa_CS
Vocabulary: molecular function
TermDefinition
GO:0003677DNA binding
GO:0003899DNA-directed 5'-3' RNA polymerase activity
Vocabulary: biological process
TermDefinition
GO:0006351transcription, DNA-templated
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
GO:0005665DNA-directed RNA polymerase II, core complex
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR006110RNA polymerase, subunit omega/K/RPB6SMARTSM01409RNA_pol_Rpb6_2coord: 54..107
e-value: 3.2E-5
score: 33.3
IPR006110RNA polymerase, subunit omega/K/RPB6PFAMPF01192RNA_pol_Rpb6coord: 56..107
e-value: 2.1E-16
score: 59.5
IPR028363DNA-directed RNA polymerase, subunit RPB6PIRSFPIRSF500154RPB6coord: 1..130
e-value: 6.7E-49
score: 163.3
IPR006111Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunitPIRSFPIRSF000778RpoK/RPB6coord: 1..130
e-value: 9.6E-45
score: 149.7
IPR012293RNA polymerase subunit, RPB6/omegaGENE3DG3DSA:3.90.940.10coord: 2..130
e-value: 7.4E-45
score: 154.0
NoneNo IPR availablePANTHERPTHR47227FAMILY NOT NAMEDcoord: 9..128
IPR020708DNA-directed RNA polymerase, 14-18kDa subunit, conserved sitePROSITEPS01111RNA_POL_K_14KDcoord: 61..75
IPR036161RPB6/omega subunit-like superfamilySUPERFAMILYSSF63562RPB6/omega subunit-likecoord: 11..129