SMED30011587

Overview
NameSMED30011587
Smed IDSMED30011587
Length (bp)707
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 SMED30011587 (SMED30011587) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30011587 (SMED30011587) 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 SMED30011587 (SMED30011587) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30011587 (SMED30011587) 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



SMED30011587

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
protonephridiaSMED30011587h1SMcG0008612 dd_Smed_v4_8691_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30011587h1SMcG0008612 dd_Smed_v4_8691_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30011587h1SMcG0008612 dd_Smed_v4_8691_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30011587h1SMcG0008612 Contig51646newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
tail regionSMED30011587h1SMcG0008612 dd_Smed_v6_8691_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30011587h1SMcG0008612 dd_Smed_v4_8691_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30011587h1SMcG0008612 dd_Smed_v4_8691_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30011587h1SMcG0008612 dd_Smed_v4_8691_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
Alignments
SMED30011587 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000158:141695..142583 -3438
Homology
[Close]
BLAST of SMED30011587 vs. Ensembl Fly
Match: CG2926 (gene:FBgn0037344 transcript:FBtr0078752)

HSP 1 Score: 49.6766 bits (117), Expect = 1.269e-6
Identity = 23/58 (39.66%), Postives = 29/58 (50.00%), Query Frame = 3 
Query:  147 CCICLNEISGDK-GEIADCTHCFCLGCIEQWCRSNTTCPLDRKQISMITIYDDNNFRR 317
            C ICL      + G  A C H FC  CI+ W R+  TCP+DR +   I + D    RR
Sbjct:  155 CPICLLTFRQQEIGTPATCEHIFCAACIDAWSRNVQTCPIDRIEFDRIIVRDSYASRR 212
[Close]
BLAST of SMED30011587 vs. Ensembl Fly
Match: CG2926 (gene:FBgn0037344 transcript:FBtr0336762)

HSP 1 Score: 48.9062 bits (115), Expect = 1.889e-6
Identity = 23/58 (39.66%), Postives = 29/58 (50.00%), Query Frame = 3 
Query:  147 CCICLNEISGDK-GEIADCTHCFCLGCIEQWCRSNTTCPLDRKQISMITIYDDNNFRR 317
            C ICL      + G  A C H FC  CI+ W R+  TCP+DR +   I + D    RR
Sbjct:  155 CPICLLTFRQQEIGTPATCEHIFCAACIDAWSRNVQTCPIDRIEFDRIIVRDSYASRR 212
[Close]
BLAST of SMED30011587 vs. Ensembl Xenopus
Match: bcl7a (BCL7A, BAF complex component [Source:Xenbase;Acc:XB-GENE-5754603])

HSP 1 Score: 48.1358 bits (113), Expect = 6.973e-6
Identity = 20/51 (39.22%), Postives = 28/51 (54.90%), Query Frame = 3 
Query:  147 CCICLNEISGDKGEIADCTHCFCLGCIEQWCRSNTTCPLDRKQISMITIYD 299
            C ICLN +  D     +C H FC  CI +W  ++T+CP+DRK    +   D
Sbjct:   39 CPICLNFLRKDVAYPENCYHAFCFTCILKWSETSTSCPVDRKPFHAVIKID 89
[Close]
BLAST of SMED30011587 vs. Ensembl Xenopus
Match: bcl7a (BCL7A, BAF complex component [Source:Xenbase;Acc:XB-GENE-5754603])

HSP 1 Score: 48.1358 bits (113), Expect = 7.853e-6
Identity = 20/51 (39.22%), Postives = 28/51 (54.90%), Query Frame = 3 
Query:  147 CCICLNEISGDKGEIADCTHCFCLGCIEQWCRSNTTCPLDRKQISMITIYD 299
            C ICLN +  D     +C H FC  CI +W  ++T+CP+DRK    +   D
Sbjct:   39 CPICLNFLRKDVAYPENCYHAFCFTCILKWSETSTSCPVDRKPFHAVIKID 89
[Close]
BLAST of SMED30011587 vs. Ensembl Xenopus
Match: bcl7a (BCL7A, BAF complex component [Source:Xenbase;Acc:XB-GENE-5754603])

HSP 1 Score: 47.7506 bits (112), Expect = 8.507e-6
Identity = 20/51 (39.22%), Postives = 28/51 (54.90%), Query Frame = 3 
Query:  147 CCICLNEISGDKGEIADCTHCFCLGCIEQWCRSNTTCPLDRKQISMITIYD 299
            C ICLN +  D     +C H FC  CI +W  ++T+CP+DRK    +   D
Sbjct:   39 CPICLNFLRKDVAYPENCYHAFCFTCILKWSETSTSCPVDRKPFHAVIKID 89
[Close]
BLAST of SMED30011587 vs. UniProt/SwissProt
Match: sp|Q84TF5|RHA4A_ARATH (Probable E3 ubiquitin-protein ligase RHA4A OS=Arabidopsis thaliana OX=3702 GN=RHA4A PE=2 SV=1)

HSP 1 Score: 52.7582 bits (125), Expect = 2.435e-7
Identity = 29/81 (35.80%), Postives = 42/81 (51.85%), Query Frame = 3 
Query:   96 KREIIFIKSEMNTYQSICCICLNE--ISGDKGEIADCTHCFCLGCIEQWCRSNTTCPLDRKQISMI---TIYDDNNFRRNS 323
            K  ++    E+ T  S+CC+CL E  +  +  E+  C H F L CI  W  S+ TCPL R  +S+    T  DD+N   +S
Sbjct:   88 KLHVVLFNEELGTRDSLCCVCLGEFELKEELVEMPLCKHIFHLDCIHLWLYSHNTCPLCRSSVSISSTKTSVDDDNDHPDS 168
[Close]
BLAST of SMED30011587 vs. TrEMBL
Match: A0A5N5TCM2 (Protein SCAF11 OS=Armadillidium nasatum OX=96803 GN=Anas_13680 PE=4 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 8.472e-8
Identity = 28/71 (39.44%), Postives = 39/71 (54.93%), Query Frame = 3 
Query:  147 CCICLNEISGDKGEIADCTHCFCLGCIEQWCRSNTTCPLDRKQISMITIYDDNNFRRNSIDIQSINQPQES 359
            C IC  +++G  G    C H FCL CI QW +   TCPLDRK  S I +++    + +  D  SI+ P+ S
Sbjct:    9 CPICCEKLTGKIGSPGQCNHFFCLDCISQWAKRRRTCPLDRKGFSSIQLFEKREGKMHKSDEDSIDLPENS 79
[Close]
BLAST of SMED30011587 vs. TrEMBL
Match: M4DB91 (RING-type domain-containing protein OS=Brassica rapa subsp. pekinensis OX=51351 PE=4 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 2.472e-7
Identity = 31/81 (38.27%), Postives = 44/81 (54.32%), Query Frame = 3 
Query:   96 KREIIFIKSEMNTYQSICCICLNE--ISGDKGEIADCTHCFCLGCIEQWCRSNTTCPLDRKQI---SMITIYDDNNFRRNS 323
            K  ++F   E+ T  S+CC+CL E  +  +  E+  C H F L CI  W  S+TTCPL R  +   S  T+ DDN+   +S
Sbjct:   87 KLHVVFFNEELETRDSLCCVCLGEFELKEELVEMPSCKHIFHLDCIHLWLYSHTTCPLCRSSVFIPSTKTLVDDNDHPDSS 167
[Close]
BLAST of SMED30011587 vs. TrEMBL
Match: M4DRV9 (RING-type domain-containing protein OS=Brassica rapa subsp. pekinensis OX=51351 PE=4 SV=1)

HSP 1 Score: 56.9954 bits (136), Expect = 6.037e-7
Identity = 30/87 (34.48%), Postives = 46/87 (52.87%), Query Frame = 3 
Query:   96 KREIIFIKSEMNTYQSICCICLNE--ISGDKGEIADCTHCFCLGCIEQWCRSNTTCPLDRKQI---SMITIYDDNNFRRNSIDIQSI 341
            K  ++    E+ T  S+CC+CL E  +  +  E+  C H F L CI  W  S+TTCPL R  +   S  T  DD+N + +S++   +
Sbjct:   30 KLHVVLFNEELGTRDSLCCVCLGEFELKEELVEMPSCKHIFHLDCIHLWLYSHTTCPLCRSSVLISSTKTSVDDDNNQPDSLETSPV 116
[Close]
BLAST of SMED30011587 vs. TrEMBL
Match: A0A182T6M7 (Uncharacterized protein OS=Anopheles maculatus OX=74869 PE=4 SV=1)

HSP 1 Score: 60.4622 bits (145), Expect = 8.465e-7
Identity = 27/74 (36.49%), Postives = 41/74 (55.41%), Query Frame = 3 
Query:  147 CCICLNEISGDKGEIAD-CTHCFCLGCIEQWCRSNTTCPLDRKQISMITIYDDNNFRRNSIDIQSINQPQESGA 365
            C ICL  +   +  + + C H FC  CIE+W R+ +TCP+DRK   +I IY D   R+   ++Q + + Q   A
Sbjct:  123 CPICLLSLHNQEVGVPEVCEHVFCAPCIEEWSRNVSTCPIDRKGFELINIYTDLERRQQQKEVQRVYRVQPKPA 196
[Close]
BLAST of SMED30011587 vs. TrEMBL
Match: A0A078JVU2 (BnaAnng35440D protein (Fragment) OS=Brassica napus OX=3708 GN=BnaAnng35440D PE=4 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 1.112e-6
Identity = 31/81 (38.27%), Postives = 43/81 (53.09%), Query Frame = 3 
Query:   96 KREIIFIKSEMNTYQSICCICLNE--ISGDKGEIADCTHCFCLGCIEQWCRSNTTCPLDRKQI---SMITIYDDNNFRRNS 323
            K  ++F   E+ T  S+CC+CL E  +  +  E+  C H F L CI  W  S+TTCPL R  +   S  T  DDN+   +S
Sbjct:   18 KLHVVFFNEELETRDSLCCVCLGEFELKEELVEMPSCKHIFHLDCIHLWLYSHTTCPLCRSSVFIPSTKTSVDDNDHPDSS 98
[Close]
BLAST of SMED30011587 vs. Ensembl Sea Lamprey
Match: ENSPMAT00000008781.1 (pep scaffold:Pmarinus_7.0:GL478673:190102:212513:-1 gene:ENSPMAG00000007949.1 transcript:ENSPMAT00000008781.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 45.0542 bits (105), Expect = 7.518e-6
Identity = 19/50 (38.00%), Postives = 31/50 (62.00%), Query Frame = 3 
Query:  147 CCICLNEISGDK-GEIADCTHCFCLGCIEQWCRSNTTCPLDRKQISMITI 293
            C ICLN +   + G   +C H FCL CI +W ++  +CP+DRK  + +++
Sbjct:   96 CPICLNGLRDQELGTPENCAHLFCLDCILEWAKNMNSCPVDRKVFTSVSV 145
[Close]
BLAST of SMED30011587 vs. Ensembl Yeast
Match: IRC20 (E3 ubiquitin ligase and putative helicase; involved in synthesis-dependent strand annealing-mediated homologous recombination; ensures precise end-joining along with Srs2p in the Yku70p/Yku80p/Lig4p-dependent nonhomologous end joining (NHEJ) pathway; localizes to both the mitochondrion and the nucleus; contains a Snf2/Swi2 family ATPase/helicase and a RING finger domain; interacts with Cdc48p and Smt3p; null mutant displays increased levels of spontaneous Rad52p foci [Source:SGD;Acc:S000004237])

HSP 1 Score: 45.0542 bits (105), Expect = 5.583e-6
Identity = 30/89 (33.71%), Postives = 49/89 (55.06%), Query Frame = 3 
Query:  114 IKSEMNTYQSICC-ICLNEISGDKGEIADCTHCFCLGCIEQWCRSNTTCPLDRKQISMITIYDDNNFR-RNSIDI--QSINQPQESGAN 368
            +K  +N  Q + C ICL E+  + G I  C H FC  CI  W R+++ CP+ +   S+  +Y   NF+ +NS +   + I +P+  GA+
Sbjct: 1227 LKDTLNDNQILSCSICLGEV--EIGAIIKCGHYFCKSCILTWLRAHSKCPICKGFCSISEVY---NFKFKNSTEKREKEIQEPRREGAD 1310
[Close]
BLAST of SMED30011587 vs. Ensembl Medaka
Match: ENSORLT00000033722.1 (pep primary_assembly:ASM223467v1:23:4024791:4037751:1 gene:ENSORLG00000028222.1 transcript:ENSORLT00000033722.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 54.6842 bits (130), Expect = 2.635e-8
Identity = 23/56 (41.07%), Postives = 34/56 (60.71%), Query Frame = 3 
Query:  147 CCICLNEISGDKGEIA---DCTHCFCLGCIEQWCRSNTTCPLDRKQISMITIYDDN 305
            C ICL  ++G  GE+A    C H FCLGC+  W  ++ +CP+DR+  S +  +D N
Sbjct:   61 CPICLGALAG--GELAMPDSCCHVFCLGCLLTWAEASPSCPVDRRPFSSVCRWDGN 114
[Close]
BLAST of SMED30011587 vs. Planmine SMEST
Match: SMESG000002176.1 (SMESG000002176.1)

HSP 1 Score: 236.498 bits (602), Expect = 6.145e-80
Identity = 127/127 (100.00%), Postives = 127/127 (100.00%), Query Frame = 3 
Query:  126 MNTYQSICCICLNEISGDKGEIADCTHCFCLGCIEQWCRSNTTCPLDRKQISMITIYDDNNFRRNSIDIQSINQPQESGANXXXXXXXXXXXXGEFYNFWRSRHFVHSGFYFNEIELVERRKQSPIT 506
            MNTYQSICCICLNEISGDKGEIADCTHCFCLGCIEQWCRSNTTCPLDRKQISMITIYDDNNFRRNSIDIQSINQPQESGANFDSISLDIDFDIGEFYNFWRSRHFVHSGFYFNEIELVERRKQSPIT
Sbjct:    1 MNTYQSICCICLNEISGDKGEIADCTHCFCLGCIEQWCRSNTTCPLDRKQISMITIYDDNNFRRNSIDIQSINQPQESGANFDSISLDIDFDIGEFYNFWRSRHFVHSGFYFNEIELVERRKQSPIT 127
[Close]
BLAST of SMED30011587 vs. Planmine SMEST
Match: SMESG000074546.1 (SMESG000074546.1)

HSP 1 Score: 51.6026 bits (122), Expect = 2.334e-8
Identity = 21/51 (41.18%), Postives = 32/51 (62.75%), Query Frame = 3 
Query:  147 CCICLNEISGDKGEIADCTHCFCLGCIEQWCRSNTTCPLDRKQISMITIYD 299
            C ICL E + + G++ +C H FC  CIE+W   +  CP+D + I+ + IYD
Sbjct:    6 CSICLRECNTEIGQLTECGHEFCRTCIEEWLSDSNKCPMDTQPITEMLIYD 56
[Close]
BLAST of SMED30011587 vs. Planmine SMEST
Match: SMESG000045165.1 (SMESG000045165.1)

HSP 1 Score: 51.9878 bits (123), Expect = 1.641e-7
Identity = 20/67 (29.85%), Postives = 36/67 (53.73%), Query Frame = 3 
Query:   99 REIIFIKSEMNTYQSICCICLNEISGDKGEIADCTHCFCLGCIEQWCRSNTTCPLDRKQISMITIYD 299
            ++I+F    ++  ++ CCIC ++          CTH FC  C+++WC     CP+DR  I ++ + D
Sbjct:   76 KDILFQNVILSNDETQCCICFSKYKSPVASTDSCTHSFCFECLKKWCTFKHECPMDRMPIKLLLLSD 142
[Close]
BLAST of SMED30011587 vs. Planmine SMEST
Match: SMESG000045165.1 (SMESG000045165.1)

HSP 1 Score: 51.9878 bits (123), Expect = 1.718e-7
Identity = 20/67 (29.85%), Postives = 36/67 (53.73%), Query Frame = 3 
Query:   99 REIIFIKSEMNTYQSICCICLNEISGDKGEIADCTHCFCLGCIEQWCRSNTTCPLDRKQISMITIYD 299
            ++I+F    ++  ++ CCIC ++          CTH FC  C+++WC     CP+DR  I ++ + D
Sbjct:   73 KDILFQNVILSNDETQCCICFSKYKSPVASTDSCTHSFCFECLKKWCTFKHECPMDRMPIKLLLLSD 139
[Close]
BLAST of SMED30011587 vs. Planmine SMEST
Match: SMESG000045165.1 (SMESG000045165.1)

HSP 1 Score: 51.6026 bits (122), Expect = 1.733e-7
Identity = 20/67 (29.85%), Postives = 36/67 (53.73%), Query Frame = 3 
Query:   99 REIIFIKSEMNTYQSICCICLNEISGDKGEIADCTHCFCLGCIEQWCRSNTTCPLDRKQISMITIYD 299
            ++I+F    ++  ++ CCIC ++          CTH FC  C+++WC     CP+DR  I ++ + D
Sbjct:   72 KDILFQNVILSNDETQCCICFSKYKSPVASTDSCTHSFCFECLKKWCTFKHECPMDRMPIKLLLLSD 138
The following BLAST results are available for this feature:
BLAST of SMED30011587 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 SMED30011587 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 SMED30011587 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 2
Match NameE-valueIdentityDescription
CG29261.269e-639.66gene:FBgn0037344 transcript:FBtr0078752[more]
CG29261.889e-639.66gene:FBgn0037344 transcript:FBtr0336762[more]
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BLAST of SMED30011587 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 SMED30011587 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 3
Match NameE-valueIdentityDescription
bcl7a6.973e-639.22BCL7A, BAF complex component [Source:Xenbase;Acc:X... [more]
bcl7a7.853e-639.22BCL7A, BAF complex component [Source:Xenbase;Acc:X... [more]
bcl7a8.507e-639.22BCL7A, BAF complex component [Source:Xenbase;Acc:X... [more]
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BLAST of SMED30011587 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 SMED30011587 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|Q84TF5|RHA4A_ARATH2.435e-735.80Probable E3 ubiquitin-protein ligase RHA4A OS=Arab... [more]
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BLAST of SMED30011587 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A5N5TCM28.472e-839.44Protein SCAF11 OS=Armadillidium nasatum OX=96803 G... [more]
M4DB912.472e-738.27RING-type domain-containing protein OS=Brassica ra... [more]
M4DRV96.037e-734.48RING-type domain-containing protein OS=Brassica ra... [more]
A0A182T6M78.465e-736.49Uncharacterized protein OS=Anopheles maculatus OX=... [more]
A0A078JVU21.112e-638.27BnaAnng35440D protein (Fragment) OS=Brassica napus... [more]
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BLAST of SMED30011587 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 SMED30011587 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ENSPMAT00000008781.17.518e-638.00pep scaffold:Pmarinus_7.0:GL478673:190102:212513:-... [more]
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BLAST of SMED30011587 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 1
Match NameE-valueIdentityDescription
IRC205.583e-633.71E3 ubiquitin ligase and putative helicase; involve... [more]
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BLAST of SMED30011587 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30011587 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ENSORLT00000033722.12.635e-841.07pep primary_assembly:ASM223467v1:23:4024791:403775... [more]
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BLAST of SMED30011587 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000002176.16.145e-80100.00SMESG000002176.1[more]
SMESG000074546.12.334e-841.18SMESG000074546.1[more]
SMESG000045165.11.641e-729.85SMESG000045165.1[more]
SMESG000045165.11.718e-729.85SMESG000045165.1[more]
SMESG000045165.11.733e-729.85SMESG000045165.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011587 ID=SMED30011587|Name=SMED30011587|organism=Schmidtea mediterranea sexual|type=transcript|length=707bp
GGCTTGATCCAATCATAAAACGGCACTGTGCATTACACATTCATGAACTT
AGAAATTTTCACCATTTCACTCATGCATAATAACCTTATTAATAAAAAAG
AGAAATTATATTTATTAAATCAGAAATGAATACCTACCAATCAATCTGCT
GCATATGCCTGAACGAGATCAGTGGAGATAAAGGGGAAATTGCCGACTGT
ACTCACTGCTTCTGTTTGGGATGCATTGAACAATGGTGCAGGAGCAACAC
GACTTGCCCCTTGGACAGAAAGCAGATCTCAATGATTACCATTTATGATG
ACAATAATTTTCGTCGGAATTCGATAGATATCCAATCAATAAATCAGCCG
CAGGAATCCGGTGCTAATTTCGATTCGATTTCTCTAGATATCGATTTCGA
TATTGGAGAATTCTACAACTTCTGGAGGTCGAGACACTTTGTTCATTCGG
GCTTTTATTTCAATGAAATTGAACTCGTTGAAAGGCGGAAGCAAAGTCCG
ATAACAAAATTGAAAAAATGGTGGAGGAAGCGCCGCCAGCGGAGTTCTTA
GACTTGGATTCATATTGATTGACTTTTTGATTATTCAAGCGTGACTTGGA
AGGACTGGATTGCAATAATGATGTTGTTATATTGAATTGAAAATGTCAGG
TTATCATTACAATGCTCATTGTCAAATAATTCATTGTTTTAAACGTGAGA
GATCGGA
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protein sequence of SMED30011587-orf-1

>SMED30011587-orf-1 ID=SMED30011587-orf-1|Name=SMED30011587-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=142bp
MNTYQSICCICLNEISGDKGEIADCTHCFCLGCIEQWCRSNTTCPLDRKQ
ISMITIYDDNNFRRNSIDIQSINQPQESGANFDSISLDIDFDIGEFYNFW
RSRHFVHSGFYFNEIELVERRKQSPITKLKKWWRKRRQRSS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0000106ciliated epithelial cell
PLANA:0000421tail
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR001841Znf_RING
IPR013083Znf_RING/FYVE/PHD
IPR017907Znf_RING_CS
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
GO:0008270zinc ion binding
GO:0016740transferase activity
GO:0046872metal ion binding
GO:0061630ubiquitin protein ligase activity
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: biological process
TermDefinition
GO:0016567protein ubiquitination
GO:0043161proteasome-mediated ubiquitin-dependent protein catabolic process
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR013083Zinc finger, RING/FYVE/PHD-typeGENE3DG3DSA:3.30.40.10coord: 3..89
e-value: 7.4E-13
score: 50.3
IPR001841Zinc finger, RING-typePFAMPF13639zf-RING_2coord: 8..48
e-value: 1.4E-8
score: 34.9
IPR001841Zinc finger, RING-typePROSITEPS50089ZF_RING_2coord: 8..48
score: 11.87
IPR017907Zinc finger, RING-type, conserved sitePROSITEPS00518ZF_RING_1coord: 25..34
NoneNo IPR availableSUPERFAMILYSSF57850RING/U-boxcoord: 7..55