SMED30008674

Overview


Name	SMED30008674
Smed ID	SMED30008674
Length (bp)	247

Neoblast Clusters

▻ 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 SMED30008674 (SMED30008674) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30008674 (SMED30008674) in cells (dots) of each of the 12 neoblast clusters.

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 SMED30008674 (SMED30008674) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30008674 (SMED30008674) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

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

Anatomical Expression

PAGE et. al., 2020

SMED30008674

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

PAGE Curations: 5

Expressed In	Reference Transcript	Published Transcript	Transcriptome	Publication
X1 cell	SMED30008674	SmedASXL_002418	SmedAsxl_ww_GCZZ01	PMID:26114597 Zhu et al., 2015
epidermis	SMED30008674	dd_Smed_v4_2720_0_1	dd_Smed_v4	PMID:29674431 Fincher et al., 2018
neoblast	SMED30008674	dd_Smed_v4_2720_0_1	dd_Smed_v4	PMID:29674431 Fincher et al., 2018
parenchymal cell	SMED30008674	dd_Smed_v4_2720_0_1	dd_Smed_v4	PMID:29674431 Fincher et al., 2018
muscle cell	SMED30008674	dd_Smed_v4_2720_0_1	dd_Smed_v4	PMID:29674431 Fincher et al., 2018

Note: Hover over icons to view figure legend

Alignments

SMED30008674 aligns in the following genomic locations:


Alignment Location	Alignment Score
v31.004777:33760..34131 -	1088

Homology

[Close]

BLAST of SMED30008674 vs. Ensembl Human
Match: POLR2K (RNA polymerase II subunit K [Source:HGNC Symbol;Acc:HGNC:9198])

HSP 1 Score: 66.2402 bits (160), Expect = 7.565e-16
Identity = 29/58 (50.00%), Postives = 41/58 (70.69%), Query Frame = -1

Query:   26 MNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 199
            M+   + +   Q+P+IY+CGEC  + E+K +D IRC ECG RI++KKRT RL VF+ R
Sbjct:    1 MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 58

[Close]

BLAST of SMED30008674 vs. Ensembl Human
Match: POLR2K (RNA polymerase II subunit K [Source:HGNC Symbol;Acc:HGNC:9198])

HSP 1 Score: 57.3806 bits (137), Expect = 2.668e-12
Identity = 25/51 (49.02%), Postives = 36/51 (70.59%), Query Frame = -1

Query:   47 MNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLR 199
            M+   + +   Q+P+IY+CGEC  + E+K +D IRC ECG RI++KKRT R
Sbjct:    1 MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKR 51

[Close]

BLAST of SMED30008674 vs. Ensembl Celegans
Match: rpb-12 (RNA Polymerase II (B) subunit [Source:UniProtKB/TrEMBL;Acc:X5M5N4])

HSP 1 Score: 59.6918 bits (143), Expect = 1.120e-13
Identity = 26/44 (59.09%), Postives = 34/44 (77.27%), Query Frame = -1

Query:   26 IIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 157
            +IY+CGEC  + E+KPKD IRC ECG RIL+KKR  +L V++ R
Sbjct:   19 MIYICGECHAENEIKPKDAIRCRECGYRILYKKRCRKLMVYDAR 62

[Close]

BLAST of SMED30008674 vs. Ensembl Fly
Match: Rpb12 (gene:FBgn0262954 transcript:FBtr0112379)

HSP 1 Score: 65.4698 bits (158), Expect = 7.615e-16
Identity = 28/56 (50.00%), Postives = 40/56 (71.43%), Query Frame = -1

Query:   26 NSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 193
            + + +K  V+  + Y+CGEC  + EM+P+D IRC ECG RI++KKRT RL VF+ R
Sbjct:    2 SETSSKDNVKTAMTYICGECHHENEMRPRDPIRCRECGYRIMYKKRTKRLVVFDAR 57

[Close]

BLAST of SMED30008674 vs. Ensembl Zebrafish
Match: polr2k (polymerase (RNA) II (DNA directed) polypeptide K [Source:ZFIN;Acc:ZDB-GENE-070820-18])

HSP 1 Score: 65.855 bits (159), Expect = 6.259e-16
Identity = 29/58 (50.00%), Postives = 42/58 (72.41%), Query Frame = -1

Query:   26 MNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 199
            M++  + +   Q+P+IY+CGEC  + E+K +D IRC ECG RI++KKRT RL VF+ R
Sbjct:    1 MDSQKDIQPPKQQPMIYICGECHTENEIKARDPIRCRECGYRIMYKKRTKRLVVFDAR 58

[Close]

BLAST of SMED30008674 vs. Ensembl Xenopus
Match: polr2k (polymerase (RNA) II subunit K [Source:NCBI gene;Acc:549263])

HSP 1 Score: 66.6254 bits (161), Expect = 4.426e-16
Identity = 30/58 (51.72%), Postives = 40/58 (68.97%), Query Frame = -1

Query:   26 MNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 199
            M    +A    Q+P+IY+CGEC  + E+K +D IRC ECG RI++KKRT RL VF+ R
Sbjct:    1 MEGQKDAPPPKQQPMIYICGECHTENEIKARDPIRCRECGYRIMYKKRTKRLVVFDAR 58

[Close]

BLAST of SMED30008674 vs. Ensembl Xenopus
Match: polr2k (polymerase (RNA) II subunit K [Source:NCBI gene;Acc:549263])

HSP 1 Score: 60.077 bits (144), Expect = 2.418e-13
Identity = 27/55 (49.09%), Postives = 37/55 (67.27%), Query Frame = -1

Query:   35 MNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVF 199
            M    +A    Q+P+IY+CGEC  + E+K +D IRC ECG RI++KKRT R  +F
Sbjct:    1 MEGQKDAPPPKQQPMIYICGECHTENEIKARDPIRCRECGYRIMYKKRTKRCILF 55

[Close]

BLAST of SMED30008674 vs. Ensembl Mouse
Match: Polr2k (polymerase (RNA) II (DNA directed) polypeptide K [Source:MGI Symbol;Acc:MGI:102725])

HSP 1 Score: 68.5514 bits (166), Expect = 1.551e-16
Identity = 30/60 (50.00%), Postives = 42/60 (70.00%), Query Frame = -1

Query:   26 LNMNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 205
            L M+   + +   Q+P+IY+CGEC  + E+K +D IRC ECG RI++KKRT RL VF+ R
Sbjct:   40 LTMDAQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 99

[Close]

BLAST of SMED30008674 vs. Ensembl Mouse
Match: Polr2k (polymerase (RNA) II (DNA directed) polypeptide K [Source:MGI Symbol;Acc:MGI:102725])

HSP 1 Score: 65.855 bits (159), Expect = 8.047e-16
Identity = 29/58 (50.00%), Postives = 41/58 (70.69%), Query Frame = -1

Query:   26 MNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 199
            M+   + +   Q+P+IY+CGEC  + E+K +D IRC ECG RI++KKRT RL VF+ R
Sbjct:    1 MDAQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 58

[Close]

BLAST of SMED30008674 vs. UniProt/SwissProt
Match: sp|P53803|RPAB4_HUMAN (DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Homo sapiens OX=9606 GN=POLR2K PE=1 SV=1)

HSP 1 Score: 66.2402 bits (160), Expect = 3.633e-15
Identity = 29/58 (50.00%), Postives = 41/58 (70.69%), Query Frame = -1

Query:   26 MNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 199
            M+   + +   Q+P+IY+CGEC  + E+K +D IRC ECG RI++KKRT RL VF+ R
Sbjct:    1 MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 58

[Close]

BLAST of SMED30008674 vs. UniProt/SwissProt
Match: sp|Q3ZBC0|RPAB4_BOVIN (DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Bos taurus OX=9913 GN=POLR2K PE=1 SV=1)

HSP 1 Score: 66.2402 bits (160), Expect = 3.633e-15
Identity = 29/58 (50.00%), Postives = 41/58 (70.69%), Query Frame = -1

Query:   26 MNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 199
            M+   + +   Q+P+IY+CGEC  + E+K +D IRC ECG RI++KKRT RL VF+ R
Sbjct:    1 MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 58

[Close]

BLAST of SMED30008674 vs. UniProt/SwissProt
Match: sp|Q63871|RPAB4_MOUSE (DNA-directed RNA polymerases I, II, and III subunit RPABC4 OS=Mus musculus OX=10090 GN=Polr2k PE=3 SV=2)

HSP 1 Score: 65.855 bits (159), Expect = 5.629e-15
Identity = 29/58 (50.00%), Postives = 41/58 (70.69%), Query Frame = -1

Query:   26 MNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 199
            M+   + +   Q+P+IY+CGEC  + E+K +D IRC ECG RI++KKRT RL VF+ R
Sbjct:    1 MDAQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 58

[Close]

BLAST of SMED30008674 vs. UniProt/SwissProt
Match: sp|Q9FLM8|NRPBC_ARATH (DNA-directed RNA polymerases II, IV and V subunit 12 OS=Arabidopsis thaliana OX=3702 GN=NRPB12 PE=1 SV=1)

HSP 1 Score: 54.299 bits (129), Expect = 1.432e-10
Identity = 23/46 (50.00%), Postives = 34/46 (73.91%), Query Frame = -1

Query:   26 KPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 163
            +P+ YVCG+C ++  +K  D+I+C ECG RIL+KKRT R+  +E R
Sbjct:    6 EPVTYVCGDCGQENTLKSGDVIQCRECGYRILYKKRTRRVVQYEAR 51

[Close]

BLAST of SMED30008674 vs. UniProt/SwissProt
Match: sp|Q54R66|RPAB4_DICDI (DNA-directed RNA polymerases I, II, and III subunit rpabc4 OS=Dictyostelium discoideum OX=44689 GN=polr2k PE=3 SV=1)

HSP 1 Score: 51.6026 bits (122), Expect = 1.811e-9
Identity = 21/45 (46.67%), Postives = 33/45 (73.33%), Query Frame = -1

Query:   26 PIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 160
            P +Y+CGEC  + E+KPK+ ++C +C  RI++KKRT ++  FE R
Sbjct:    2 PCLYICGECGAEHEIKPKEPVKCKDCTHRIMYKKRTDKMIQFEAR 46

[Close]

BLAST of SMED30008674 vs. TrEMBL
Match: A0A182ILE8 (Uncharacterized protein OS=Anopheles atroparvus OX=41427 PE=4 SV=1)

HSP 1 Score: 73.559 bits (179), Expect = 1.490e-15
Identity = 33/58 (56.90%), Postives = 42/58 (72.41%), Query Frame = -1

Query:   26 MNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 199
            M+  S    V++ P+IYVCGEC  + EM+PKD IRC ECG RI++KKRT RL VF+ R
Sbjct:    1 MSEPSSKDTVLKTPMIYVCGECHHENEMRPKDAIRCRECGYRIMYKKRTKRLIVFDAR 58

[Close]

BLAST of SMED30008674 vs. TrEMBL
Match: B7QL52 (RNA polymerases I, II and III shared polypeptide, putative OS=Ixodes scapularis OX=6945 GN=8042911 PE=4 SV=1)

HSP 1 Score: 71.2478 bits (173), Expect = 1.039e-14
Identity = 31/57 (54.39%), Postives = 42/57 (73.68%), Query Frame = -1

Query:   26 NNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 196
              S E  Q V+ P+IY+CGEC ++ E++P+D IRC ECG RI++KKRT RL VF+ R
Sbjct:    3 GTSKEQTQTVKAPMIYICGECHQENEIRPRDPIRCRECGYRIMYKKRTKRLIVFDAR 59

[Close]

BLAST of SMED30008674 vs. TrEMBL
Match: A0A3S3SI52 (RNA polymerases I: II and III shared polypeptide-like protein OS=Dinothrombium tinctorium OX=1965070 GN=B4U79_13312 PE=4 SV=1)

HSP 1 Score: 70.0922 bits (170), Expect = 3.140e-14
Identity = 31/59 (52.54%), Postives = 47/59 (79.66%), Query Frame = -1

Query:   26 MNNSSEAKQV-VQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 199
            M++SS+ +Q+ V++P++Y+C EC  + E+KP+D IRC ECG RI++KKRT RL VF+ R
Sbjct:    1 MDSSSKEQQIPVKQPMVYICAECHHENEIKPRDPIRCRECGYRIMYKKRTKRLIVFDAR 59

[Close]

BLAST of SMED30008674 vs. TrEMBL
Match: A0A3Q7WLP4 (DNA-directed RNA polymerases I, II, and III subunit RPABC4 isoform X1 OS=Ursus arctos horribilis OX=116960 GN=POLR2K PE=4 SV=1)

HSP 1 Score: 70.8626 bits (172), Expect = 3.236e-14
Identity = 31/62 (50.00%), Postives = 44/62 (70.97%), Query Frame = -1

Query:   26 YFLNMNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 211
            Y L+M+   + +   Q+P+IY+CGEC  + E+K +D IRC ECG RI++KKRT RL VF+ R
Sbjct:   28 YGLSMDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR 89

[Close]

BLAST of SMED30008674 vs. TrEMBL
Match: H9GQ41 (RNA polymerase II subunit K OS=Anolis carolinensis OX=28377 GN=POLR2K PE=4 SV=2)

HSP 1 Score: 70.0922 bits (170), Expect = 3.495e-14
Identity = 31/58 (53.45%), Postives = 43/58 (74.14%), Query Frame = -1

Query:   26 MNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 199
            M+  ++A    Q+P+IY+CGEC K+ E+K +D IRC ECG RI++KKRT RL VF+ R
Sbjct:    1 MDTQNDAPPPKQQPMIYICGECHKENEIKARDPIRCRECGYRIMYKKRTKRLVVFDAR 58

[Close]

BLAST of SMED30008674 vs. Ensembl Cavefish
Match: ENSAMXT00000035759.1 (RNA polymerase II subunit K [Source:NCBI gene;Acc:103021424])

HSP 1 Score: 65.4698 bits (158), Expect = 7.366e-16
Identity = 29/58 (50.00%), Postives = 41/58 (70.69%), Query Frame = -1

Query:   26 MNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 199
            M+   + +   Q+P+IY+CGEC  + E+K +D IRC ECG RI++KKRT RL VF+ R
Sbjct:    1 MDPQKDMQPPKQQPMIYICGECHTENEIKARDPIRCRECGYRIMYKKRTKRLVVFDAR 58

[Close]

BLAST of SMED30008674 vs. Ensembl Cavefish
Match: ENSAMXT00000039128.1 (RNA polymerase II subunit K [Source:NCBI gene;Acc:103021424])

HSP 1 Score: 55.0694 bits (131), Expect = 3.170e-11
Identity = 25/51 (49.02%), Postives = 36/51 (70.59%), Query Frame = -1

Query:   47 MNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLR 199
            M+   + +   Q+P+IY+CGEC  + E+K +D IRC ECG RI++KKRT R
Sbjct:    1 MDPQKDMQPPKQQPMIYICGECHTENEIKARDPIRCRECGYRIMYKKRTKR 51

[Close]

BLAST of SMED30008674 vs. Ensembl Cavefish
Match: ENSAMXT00000035248.1 (RNA polymerase II subunit K [Source:NCBI gene;Acc:103021424])

HSP 1 Score: 55.0694 bits (131), Expect = 3.170e-11
Identity = 25/51 (49.02%), Postives = 36/51 (70.59%), Query Frame = -1

Query:   47 MNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLR 199
            M+   + +   Q+P+IY+CGEC  + E+K +D IRC ECG RI++KKRT R
Sbjct:    1 MDPQKDMQPPKQQPMIYICGECHTENEIKARDPIRCRECGYRIMYKKRTKR 51

[Close]

BLAST of SMED30008674 vs. Ensembl Cavefish
Match: ENSAMXT00000039750.1 (pep primary_assembly:Astyanax_mexicanus-2.0:APWO02001230.1:25832:28142:-1 gene:ENSAMXG00000038868.1 transcript:ENSAMXT00000039750.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 42.743 bits (99), Expect = 7.616e-7
Identity = 24/60 (40.00%), Postives = 35/60 (58.33%), Query Frame = -1

Query:   26 MNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLS--VFEGR 199
            M+   + +   Q+P+IY+CG       +  +  IRC ECG RI++KKRT  LS  VF+ R
Sbjct:    1 MDPQKDMQPPKQQPMIYICGG-----NLTNQRPIRCRECGYRIMYKKRTRDLSVVVFDAR 55

[Close]

BLAST of SMED30008674 vs. Ensembl Yeast
Match: RPC10 (RNA polymerase subunit ABC10-alpha, found in RNA pol I, II, and III; relocalizes from nucleolus to cytoplasm upon DNA replication stress [Source:SGD;Acc:S000001185])

HSP 1 Score: 49.6766 bits (117), Expect = 2.426e-10
Identity = 23/66 (34.85%), Postives = 34/66 (51.52%), Query Frame = -1

Query:   26 NFKYFLNMNNSSEA-KQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLRLSVFEGR 220
             F+   N++ ++    Q     + Y+C EC   + +   D +RC +CG RIL K RT RL  FE R
Sbjct:    5 GFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR 70

[Close]

BLAST of SMED30008674 vs. Ensembl Nematostella
Match: EDO32620 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SUK1])

HSP 1 Score: 52.7582 bits (125), Expect = 3.510e-11
Identity = 23/40 (57.50%), Postives = 30/40 (75.00%), Query Frame = -1

Query:   47 QKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLR 166
            Q  +IY+CGEC  + E+K +D IRC ECG RI++KKRT R
Sbjct:   14 QHAMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTRR 53

[Close]

BLAST of SMED30008674 vs. Ensembl Medaka
Match: ENSORLT00000003472.2 (pep primary_assembly:ASM223467v1:11:7021459:7022964:1 gene:ENSORLG00000002783.2 transcript:ENSORLT00000003472.2 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 55.8398 bits (133), Expect = 5.118e-12
Identity = 25/51 (49.02%), Postives = 36/51 (70.59%), Query Frame = -1

Query:   47 MNNSSEAKQVVQKPIIYVCGECRKDIEMKPKDIIRCSECGCRILFKKRTLR 199
            M+   + +   Q+P+IY+CGEC  + E+K +D IRC ECG RI++KKRT R
Sbjct:    1 MDAQKDLQPPKQQPMIYICGECHTENEIKARDPIRCRECGYRIMYKKRTKR 51

The following BLAST results are available for this feature:

BLAST of SMED30008674 vs. Ensembl Human
BLAST of SMED30008674 vs. Ensembl Celegans
BLAST of SMED30008674 vs. Ensembl Fly
BLAST of SMED30008674 vs. Ensembl Zebrafish
BLAST of SMED30008674 vs. Ensembl Xenopus
BLAST of SMED30008674 vs. Ensembl Mouse
BLAST of SMED30008674 vs. UniProt/SwissProt
BLAST of SMED30008674 vs. TrEMBL
BLAST of SMED30008674 vs. Ensembl Cavefish
BLAST of SMED30008674 vs. Ensembl Sea Lamprey
BLAST of SMED30008674 vs. Ensembl Yeast
BLAST of SMED30008674 vs. Ensembl Nematostella
BLAST of SMED30008674 vs. Ensembl Medaka
BLAST of SMED30008674 vs. Planmine SMEST

BLAST of SMED30008674 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 2


Match Name	E-value	Identity	Description
POLR2K	7.565e-16	50.00	RNA polymerase II subunit K [Source:HGNC Symbol;Ac...	[more]
POLR2K	2.668e-12	49.02	RNA polymerase II subunit K [Source:HGNC Symbol;Ac...	[more]

BLAST of SMED30008674 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 1


Match Name	E-value	Identity	Description
rpb-12	1.120e-13	59.09	RNA Polymerase II (B) subunit [Source:UniProtKB/T...	[more]

BLAST of SMED30008674 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1


Match Name	E-value	Identity	Description
Rpb12	7.615e-16	50.00	gene:FBgn0262954 transcript:FBtr0112379	[more]

BLAST of SMED30008674 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 1


Match Name	E-value	Identity	Description
polr2k	6.259e-16	50.00	polymerase (RNA) II (DNA directed) polypeptide K [...	[more]

BLAST of SMED30008674 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 2


Match Name	E-value	Identity	Description
polr2k	4.426e-16	51.72	polymerase (RNA) II subunit K [Source:NCBI gene;Ac...	[more]
polr2k	2.418e-13	49.09	polymerase (RNA) II subunit K [Source:NCBI gene;Ac...	[more]

BLAST of SMED30008674 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 2


Match Name	E-value	Identity	Description
Polr2k	1.551e-16	50.00	polymerase (RNA) II (DNA directed) polypeptide K [...	[more]
Polr2k	8.047e-16	50.00	polymerase (RNA) II (DNA directed) polypeptide K [...	[more]

BLAST of SMED30008674 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 5


Match Name	E-value	Identity	Description
sp\|P53803\|RPAB4_HUMAN	3.633e-15	50.00	DNA-directed RNA polymerases I, II, and III subuni...	[more]
sp\|Q3ZBC0\|RPAB4_BOVIN	3.633e-15	50.00	DNA-directed RNA polymerases I, II, and III subuni...	[more]
sp\|Q63871\|RPAB4_MOUSE	5.629e-15	50.00	DNA-directed RNA polymerases I, II, and III subuni...	[more]
sp\|Q9FLM8\|NRPBC_ARATH	1.432e-10	50.00	DNA-directed RNA polymerases II, IV and V subunit ...	[more]
sp\|Q54R66\|RPAB4_DICDI	1.811e-9	46.67	DNA-directed RNA polymerases I, II, and III subuni...	[more]

BLAST of SMED30008674 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5


Match Name	E-value	Identity	Description
A0A182ILE8	1.490e-15	56.90	Uncharacterized protein OS=Anopheles atroparvus OX...	[more]
B7QL52	1.039e-14	54.39	RNA polymerases I, II and III shared polypeptide, ...	[more]
A0A3S3SI52	3.140e-14	52.54	RNA polymerases I: II and III shared polypeptide-l...	[more]
A0A3Q7WLP4	3.236e-14	50.00	DNA-directed RNA polymerases I, II, and III subuni...	[more]
H9GQ41	3.495e-14	53.45	RNA polymerase II subunit K OS=Anolis carolinensis...	[more]

BLAST of SMED30008674 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 4


Match Name	E-value	Identity	Description
ENSAMXT00000035759.1	7.366e-16	50.00	RNA polymerase II subunit K [Source:NCBI gene;Acc:...	[more]
ENSAMXT00000039128.1	3.170e-11	49.02	RNA polymerase II subunit K [Source:NCBI gene;Acc:...	[more]
ENSAMXT00000035248.1	3.170e-11	49.02	RNA polymerase II subunit K [Source:NCBI gene;Acc:...	[more]
ENSAMXT00000039750.1	7.616e-7	40.00	pep primary_assembly:Astyanax_mexicanus-2.0:APWO02...	[more]

BLAST of SMED30008674 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0


Match Name	E-value	Identity	Description

BLAST of SMED30008674 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 1


Match Name	E-value	Identity	Description
RPC10	2.426e-10	34.85	RNA polymerase subunit ABC10-alpha, found in RNA p...	[more]

BLAST of SMED30008674 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1


Match Name	E-value	Identity	Description
EDO32620	3.510e-11	57.50	Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7...	[more]

BLAST of SMED30008674 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1


Match Name	E-value	Identity	Description
ENSORLT00000003472.2	5.118e-12	49.02	pep primary_assembly:ASM223467v1:11:7021459:702296...	[more]

BLAST of SMED30008674 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0


Match Name	E-value	Identity	Description

Analyses

This transcript is derived from or has results from the following analyses


Analysis Name	Date Performed
Embryonic Stages	2016-07-25
Schmidtea mediterranea smed_20140614 BLASTX Human e!99	2016-08-08
Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99	2020-05-01
Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99	2020-05-01
Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99	2016-08-08
Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99	2020-05-01
Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99	2020-05-01
Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt	2020-05-01
Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL	2020-05-01
Schmidtea mediterranea Sexual smed_20140614 transcriptome	2016-07-25
Schmidtea mediteranean smed_20140614 Interproscan	2020-05-01
Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99	2020-05-08
Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99	2020-05-08
Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46	2020-05-08
Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46	2020-05-08
Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99	2020-05-08
Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST	2020-05-08

Sequences

The following sequences are available for this feature:

transcript sequence

transcript sequence

>SMED30008674 ID=SMED30008674|Name=SMED30008674|organism=Schmidtea mediterranea sexual|type=transcript|length=247bp
CACAAATTTATTTAACAACACTTCAACGACCTTCAAAAACACTAAGTCTC
AATGTTCGTTTTTTAAATAAAATTCTACATCCACATTCACTACATCTTAT
AATGTCTTTAGGCTTCATTTCGATATCTTTTCTACATTCTCCACAAACAT
AAATTATAGGCTTTTGAACAACTTGTTTTGCTTCAGACGAATTATTCATA
TTTAAAAAATATTTGAAATTGTTCAAAATCCTCGTGCCGAATTCCTG

Annotated Terms

The following terms have been associated with this transcript:

Vocabulary: **Planarian Anatomy**
Term	Definition
PLANA:0000101	muscle cell
PLANA:0000429	neoblast
PLANA:0002109	X1 cell
PLANA:0003001	lateral region of the whole animal

Vocabulary: **INTERPRO**
Term	Definition
IPR039747	RPABC4
IPR006591	RNAP_P/RPABC4
IPR029040	RPABC4/Spt4

Vocabulary: **molecular function**
Term	Definition
GO:0008270	zinc ion binding
GO:0003677	DNA binding
GO:0003899	DNA-directed 5'-3' RNA polymerase activity

Vocabulary: **biological process**
Term	Definition
GO:0006351	transcription, DNA-templated

InterPro

Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR006591	RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4	SMART	SM00659	rpolcxc3	coord: 25..68 e-value: 9.6E-15 score: 65.0
IPR006591	RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4	PFAM	PF03604	DNA_RNApol_7kD	coord: 27..58 e-value: 2.1E-13 score: 49.7
None	No IPR available	GENE3D	G3DSA:2.20.28.30		coord: 11..68 e-value: 4.9E-21 score: 75.8
None	No IPR available	PRODOM	PD012151		coord: 31..68 e-value: 6.0E-7 score: 122.0
IPR039747	DNA-directed RNA polymerases I, II, and III subunit RPABC4	PANTHER	PTHR12056	DNA-DIRECTED RNA POLYMERASES I, II, AND III	coord: 11..67
IPR029040	RNA polymerase subunit RPABC4/transcription elongation factor Spt4	SUPERFAMILY	SSF63393	RNA polymerase subunits	coord: 24..67

Main menu

SMED30008674

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

Explore this single cell expression dataset with our NB Cluster Shiny App

Neoblast Population

Sub-lethal Irradiated Surviving X1 and X2 Cell Population

Davies et. al., 2017

PAGE et. al., 2020

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

PAGE Curations: 5

Owlery

blazegraph-runner