SMED30030250

Overview
NameSMED30030250
Smed IDSMED30030250
Length (bp)512
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 SMED30030250 (SMED30030250) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30030250 (SMED30030250) in cells (dots) of each of the 12 neoblast clusters.

 

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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




SMED30030250

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymaSMED30030250SMESG000005782.1 dd_Smed_v4_8069_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
Alignments
SMED30030250 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000646:78937..85545 -2445
Homology
BLAST of SMED30030250 vs. TrEMBL
Match: A0A0H3YJB4 (Slc31a-1 OS=Schmidtea mediterranea OX=79327 GN=slc31a-1 PE=2 SV=1)

HSP 1 Score: 63.5438 bits (153), Expect = 1.684e-9
Identity = 41/123 (33.33%), Postives = 70/123 (56.91%), Query Frame = -1
Query:  117 MFFHSKINIHLLLFDWKIDTSSKLIIACIGIFIFSLVFEFFKALKS-NLMISRNMGQNANSELYENLNQTRKRRXXXXXXXXXXXXXXXFVDVICNIILMFFIITFNLYLFISVNFGRMIGYF 482
            M+F+  +N +LL   W+I + SKL  ACIG FI +L++E FK L+  ++    N+  N++  L   L ++  R++   +  + L   ++ +    +  LM  I++FN Y+FISV  G  +GYF
Sbjct:   20 MYFNEDLNFYLLFGAWQITSQSKLAAACIGSFICALLYELFKRLREYHVNYEINLVANSSESL---LRKSVTRKVPVFSRANFLQSLMHLIQTTVSYFLMLIIMSFNTYVFISVIAGLTVGYF 139          
BLAST of SMED30030250 vs. TrEMBL
Match: W6UH38 (High affinity copper uptake protein OS=Echinococcus granulosus OX=6210 GN=EGR_04151 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 1.492e-7
Identity = 37/148 (25.00%), Postives = 70/148 (47.30%), Query Frame = -1
Query:  117 MFFHSKINIHLLLFDWKIDTSSKLIIACIGIFIFSLVFEFFKALKSNLMISR----NMGQNANSELYEN----------------------LNQTRKRRXXXXXXXXXXXXXXXFVDVICNIILMFFIITFNLYLFISVNFGRMIGYF 482
            M+F++ +  HLL   W IDT  KLI AC G+F+ +L++E  K  + +L++ +    + G +ANS +Y+                       +  T            +L   ++ + +  + +LM  ++T+N YL +++  G  +GYF
Sbjct:  452 MYFNTDLPFHLLFETWHIDTVGKLIGACAGVFLLALLYEGIKGFRDHLLVQKLTPLSPGGHANSTIYDEAIHSSVLAVDGGMRQGDHVVPLVQGTGSGWRSYCNPDHILQSLMHLIQLFFSYMLMLVVMTYNAYLLVALLLGSCLGYF 599          
BLAST of SMED30030250 vs. TrEMBL
Match: A0A087VYS6 (CTR1 high affinity copper uptake protein 1 OS=Echinococcus multilocularis OX=6211 GN=EmuJ_000124300 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 2.255e-7
Identity = 36/148 (24.32%), Postives = 70/148 (47.30%), Query Frame = -1
Query:  117 MFFHSKINIHLLLFDWKIDTSSKLIIACIGIFIFSLVFEFFKALKSNLMISR----NMGQNANSELYEN----------------------LNQTRKRRXXXXXXXXXXXXXXXFVDVICNIILMFFIITFNLYLFISVNFGRMIGYF 482
            M+F++ +  HLL   W IDT  KLI AC G+F+ +L++E  K  + +L++ +    + G +ANS +++                       +  T            +L   ++ + +  + +LM  ++T+N YL +++  G  +GYF
Sbjct:   21 MYFNTDLPFHLLFETWHIDTVGKLIGACAGVFLLALLYEGIKGFRDHLLVQKLTPLSPGGHANSTIHDEAIHSSVFAVDGGMRQGDHVVPLVQGTGSGWRSYCNPDHILQSLMHLIQLFFSYMLMLVVMTYNAYLLVALLLGSCLGYF 168          
BLAST of SMED30030250 vs. TrEMBL
Match: A0A0R3WTY9 (Uncharacterized protein OS=Hydatigena taeniaeformis OX=6205 GN=TTAC_LOCUS4214 PE=4 SV=1)

HSP 1 Score: 55.8398 bits (133), Expect = 4.133e-7
Identity = 21/52 (40.38%), Postives = 36/52 (69.23%), Query Frame = -1
Query:  327 MFFHSKINIHLLLFDWKIDTSSKLIIACIGIFIFSLVFEFFKALKSNLMISR 482
            M+F++ +  HLL   W +DT  KL+ AC+GIF+ +LV+E  K ++  L++S+
Sbjct:    1 MYFNTDLPFHLLFEAWNVDTVGKLVGACVGIFLLALVYEGTKGIRDRLLVSK 52          
BLAST of SMED30030250 vs. TrEMBL
Match: A0A068WVL3 (CTR1 high affinity copper uptake protein 1 OS=Echinococcus granulosus OX=6210 GN=EgrG_000124300 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 6.391e-7
Identity = 37/148 (25.00%), Postives = 69/148 (46.62%), Query Frame = -1
Query:  117 MFFHSKINIHLLLFDWKIDTSSKLIIACIGIFIFSLVFEFFKALKSNLMISR----NMGQNANSELYEN----------------------LNQTRKRRXXXXXXXXXXXXXXXFVDVICNIILMFFIITFNLYLFISVNFGRMIGYF 482
            M+F++ +  HLL   W IDT  KLI AC G+F+ +L++E  K  + +L++ +    + G +ANS +Y                        +  T            +L   ++ + +  + +LM  ++T+N YL +++  G  +GYF
Sbjct:   91 MYFNTDLPFHLLFETWHIDTVGKLIGACAGVFLLALLYEGIKGFRDHLLVQKLTPLSPGGHANSTIYVEAIHSSVLAVDGGMRQGDHVVPLVQGTGSGWRSYCNPDHILQSLMHLIQLFFSYMLMLVVMTYNAYLLVALLLGSCLGYF 238          
BLAST of SMED30030250 vs. Ensembl Nematostella
Match: EDO27532 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7T904])

HSP 1 Score: 44.2838 bits (103), Expect = 3.165e-6
Identity = 35/132 (26.52%), Postives = 57/132 (43.18%), Query Frame = -1
Query:  117 FFHSKINIHLLLFDWKIDTSSKLIIACIGIFIFSLVFEFFKALKSNL-----------MISRNMGQNANSELYENLNQTRKRRXXXXXXXXXXXXXXXFVDVICNIILMFFIITFNLYLFISVNFGRMIGYF 479
            FF SK  + +L   W +DT   +I +CI +FI ++++E  K  +  L           M ++  G N N  +     +    R         +   L+ V V  +  LM   +T+N +L I+V  G   GYF
Sbjct:    3 FFFSKKTV-ILFEGWSVDTVGGMIGSCIAVFILAVLYEGLKVSREMLKRKYGYVMSVDMDTKVYGSNQNQTVTVTETRGHIPRSKICNLHHFIQSLLHIVQVTLSYFLMLIFMTYNGWLCIAVALGAGFGYF 133          
BLAST of SMED30030250 vs. Ensembl Nematostella
Match: EDO34361 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SPJ3])

HSP 1 Score: 44.2838 bits (103), Expect = 4.458e-6
Identity = 35/132 (26.52%), Postives = 57/132 (43.18%), Query Frame = -1
Query:  117 FFHSKINIHLLLFDWKIDTSSKLIIACIGIFIFSLVFEFFKALKSNL-----------MISRNMGQNANSELYENLNQTRKRRXXXXXXXXXXXXXXXFVDVICNIILMFFIITFNLYLFISVNFGRMIGYF 479
            FF SK  + +L   W +DT   +I +CI +FI ++++E  K  +  L           M ++  G N N  +     +    R         +   L+ V V  +  LM   +T+N +L I+V  G   GYF
Sbjct:   33 FFFSKKTV-ILFEGWSVDTVGGMIGSCIAVFILAVLYEGLKVSREMLKRRYGYVMNVDMDTKVYGSNQNQTVTVTETRGHIPRSKICNLHHFIQSLLHIVQVTLSYFLMLIFMTYNGWLCIAVALGAGFGYF 163          
BLAST of SMED30030250 vs. Planmine SMEST
Match: SMESG000005782.1 (SMESG000005782.1)

HSP 1 Score: 142.124 bits (357), Expect = 5.019e-44
Identity = 90/95 (94.74%), Postives = 92/95 (96.84%), Query Frame = -1
Query:   75 KALKSNLMISRNMGQNANSELYENLNQTRKRRXXXXXXXXXXXXXXXFVDVICNIILMFFIITFNLYLFISVNFGRMIGYFCARYFSIVPCVKNL 359
            +ALKSNLMISRNMGQNA+SELYENLNQTRKRRLFTGTSFSLLYLFLYFVDVICNIILMFFIITFNLYLFISVNFGRMIGYFCARYFSIVP  K L
Sbjct:   27 QALKSNLMISRNMGQNADSELYENLNQTRKRRLFTGTSFSLLYLFLYFVDVICNIILMFFIITFNLYLFISVNFGRMIGYFCARYFSIVPRGKKL 121          

HSP 2 Score: 49.2914 bits (116), Expect = 4.861e-8
Identity = 23/23 (100.00%), Postives = 23/23 (100.00%), Query Frame = -2
Query:  416 RCFFTVKLTSICCYLIGKLTQVQ 484
            RCFFTVKLTSICCYLIGKLTQVQ
Sbjct:    5 RCFFTVKLTSICCYLIGKLTQVQ 27          
BLAST of SMED30030250 vs. Planmine SMEST
Match: SMESG000005782.1 (SMESG000005782.1)

HSP 1 Score: 131.339 bits (329), Expect = 3.285e-40
Identity = 84/88 (95.45%), Postives = 85/88 (96.59%), Query Frame = -1
Query:   75 MISRNMGQNANSELYENLNQTRKRRXXXXXXXXXXXXXXXFVDVICNIILMFFIITFNLYLFISVNFGRMIGYFCARYFSIVPCVKNL 338
            MISRNMGQNA+SELYENLNQTRKRRLFTGTSFSLLYLFLYFVDVICNIILMFFIITFNLYLFISVNFGRMIGYFCARYFSIVP  K L
Sbjct:    1 MISRNMGQNADSELYENLNQTRKRRLFTGTSFSLLYLFLYFVDVICNIILMFFIITFNLYLFISVNFGRMIGYFCARYFSIVPRGKKL 88          
BLAST of SMED30030250 vs. Planmine SMEST
Match: SMESG000005782.1 (SMESG000005782.1)

HSP 1 Score: 122.094 bits (305), Expect = 1.295e-36
Identity = 79/83 (95.18%), Postives = 80/83 (96.39%), Query Frame = -1
Query:   75 MGQNANSELYENLNQTRKRRXXXXXXXXXXXXXXXFVDVICNIILMFFIITFNLYLFISVNFGRMIGYFCARYFSIVPCVKNL 323
            MGQNA+SELYENLNQTRKRRLFTGTSFSLLYLFLYFVDVICNIILMFFIITFNLYLFISVNFGRMIGYFCARYFSIVP  K L
Sbjct:    1 MGQNADSELYENLNQTRKRRLFTGTSFSLLYLFLYFVDVICNIILMFFIITFNLYLFISVNFGRMIGYFCARYFSIVPRGKKL 83          
BLAST of SMED30030250 vs. Planmine SMEST
Match: SMESG000005775.1 (SMESG000005775.1)

HSP 1 Score: 63.929 bits (154), Expect = 3.776e-13
Identity = 41/123 (33.33%), Postives = 70/123 (56.91%), Query Frame = -1
Query:  117 MFFHSKINIHLLLFDWKIDTSSKLIIACIGIFIFSLVFEFFKALKS-NLMISRNMGQNANSELYENLNQTRKRRXXXXXXXXXXXXXXXFVDVICNIILMFFIITFNLYLFISVNFGRMIGYF 482
            M+F+  +N +LL   W+I + SKL  ACIG FI +L++E FK L+  ++    N+  N++  L   L ++  R++   +  + L   ++ +    +  LM  I++FN Y+FISV  G  +GYF
Sbjct:   16 MYFNEDLNFYLLFGAWQITSQSKLAAACIGSFICALLYELFKRLREYHVNYEINLVANSSESL---LRKSVTRKVPVFSRANFLQSLMHLIQTTVSYFLMLIIMSFNTYVFISVIAGLTVGYF 135          
BLAST of SMED30030250 vs. Planmine SMEST
Match: SMESG000005775.1 (SMESG000005775.1)

HSP 1 Score: 63.5438 bits (153), Expect = 3.863e-13
Identity = 41/123 (33.33%), Postives = 70/123 (56.91%), Query Frame = -1
Query:  117 MFFHSKINIHLLLFDWKIDTSSKLIIACIGIFIFSLVFEFFKALKS-NLMISRNMGQNANSELYENLNQTRKRRXXXXXXXXXXXXXXXFVDVICNIILMFFIITFNLYLFISVNFGRMIGYF 482
            M+F+  +N +LL   W+I + SKL  ACIG FI +L++E FK L+  ++    N+  N++  L   L ++  R++   +  + L   ++ +    +  LM  I++FN Y+FISV  G  +GYF
Sbjct:   14 MYFNEDLNFYLLFGAWQITSQSKLAAACIGSFICALLYELFKRLREYHVNYEINLVANSSESL---LRKSVTRKVPVFSRANFLQSLMHLIQTTVSYFLMLIIMSFNTYVFISVIAGLTVGYF 133          
The following BLAST results are available for this feature:
BLAST of SMED30030250 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 SMED30030250 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 SMED30030250 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030250 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 SMED30030250 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030250 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 SMED30030250 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030250 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A0H3YJB41.684e-933.33Slc31a-1 OS=Schmidtea mediterranea OX=79327 GN=slc... [more]
W6UH381.492e-725.00High affinity copper uptake protein OS=Echinococcu... [more]
A0A087VYS62.255e-724.32CTR1 high affinity copper uptake protein 1 OS=Echi... [more]
A0A0R3WTY94.133e-740.38Uncharacterized protein OS=Hydatigena taeniaeformi... [more]
A0A068WVL36.391e-725.00CTR1 high affinity copper uptake protein 1 OS=Echi... [more]
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BLAST of SMED30030250 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 SMED30030250 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 SMED30030250 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030250 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 2
Match NameE-valueIdentityDescription
EDO275323.165e-626.52Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
EDO343614.458e-626.52Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30030250 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30030250 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000005782.15.019e-4494.74SMESG000005782.1[more]
SMESG000005782.13.285e-4095.45SMESG000005782.1[more]
SMESG000005782.11.295e-3695.18SMESG000005782.1[more]
SMESG000005775.13.776e-1333.33SMESG000005775.1[more]
SMESG000005775.13.863e-1333.33SMESG000005775.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030250 ID=SMED30030250|Name=SMED30030250|organism=Schmidtea mediterranea sexual|type=transcript|length=512bp
TCATAAAAATCAAAAATATTTATTGAAATATCAAATCAAAATCATTGTGA
GTTATCTCAGGTTATTTTTGCTCAGAGGTTTTTGACGCAAGGTACTATCG
AAAAATATCTAGCACAAAAATACCCAATCATCCTACCAAAGTTTACCGAA
ATAAATAAGTAAAGGTTGAAAGTTATAATGAAGAACATCAAAATAATATT
GCATATAACATCCACAAAATATAAAAACAAATATAACAAGGAAAAACTAG
TGCCGGTAAAGAGCCTCCTTTTCCTAGTCTGATTTAAATTTTCATACAAT
TCCGAATTCGCATTCTGTCCCATGTTCCTGGAGATCATCAAATTACTTTT
TAAAGCCTTAAAAAATTCAAATACCAGAGAAAAAATAAATATGCCAATGC
ATGCAATAATTAATTTTGAACTTGTGTCAATTTTCCAATCAAATAACAAC
AGATGGATGTTAATTTTACTGTGAAAAAACATCTAGATTATTGTAAATTT
AAATGACATTTA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR007274Cop_transporter
Vocabulary: biological process
TermDefinition
GO:0035434copper ion transmembrane transport
Vocabulary: molecular function
TermDefinition
GO:0005375copper ion transmembrane transporter activity
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR007274Ctr copper transporterPFAMPF04145Ctrcoord: 1..123
e-value: 6.8E-15
score: 56.0
IPR007274Ctr copper transporterPANTHERPTHR12483SOLUTE CARRIER FAMILY 31 COPPER TRANSPORTERScoord: 1..128
NoneNo IPR availableTMHMMTMhelixcoord: 80..102
NoneNo IPR availableTMHMMTMhelixcoord: 22..44
NoneNo IPR availableTMHMMTMhelixcoord: 107..129