SWIM-type domain-containing protein

Overview
NameSWIM-type domain-containing protein
Smed IDSMED30004979
Length (bp)381
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30004979

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
neuronSMED30004979 Contig40435newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
neuronSMED30004979 Contig40435uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
lateral branchSMED30004979 Contig40435newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
lateral branchSMED30004979 Contig40435uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SWIM-type domain-containing protein vs. Ensembl Human
Match: CDC45 (cell division cycle 45 [Source:HGNC Symbol;Acc:HGNC:1739])

HSP 1 Score: 45.4394 bits (106), Expect = 6.213e-6
Identity = 26/107 (24.30%), Postives = 60/107 (56.07%), Query Frame = 3 
Query:   42 EDLFLPSFVGNCGFNEELSATDMTFILAALLDTKKPEDKEEFSEKFMKAVNILSINNPNRIDEGLQLAKEYIQTLNKFTKSILQSGKITVCGTFILVAVSKIEPQVL 362
            +D+ + +F  + GF  +  A+D+ F   +L+++  PE     ++ F++A++ LS +N +++  GL+LAK+ ++   +   S L +  +   G F+  ++ +  P V+
Sbjct:  103 KDMRVQTFSIHFGFKHKFLASDVVFATMSLMES--PEKDGSGTDHFIQALDSLSRSNLDKLYHGLELAKKQLRATQQTIASCLCTNLVISQGPFLYCSLMEGTPDVM 207
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BLAST of SWIM-type domain-containing protein vs. Ensembl Human
Match: CDC45 (cell division cycle 45 [Source:HGNC Symbol;Acc:HGNC:1739])

HSP 1 Score: 45.0542 bits (105), Expect = 8.044e-6
Identity = 26/107 (24.30%), Postives = 60/107 (56.07%), Query Frame = 3 
Query:   42 EDLFLPSFVGNCGFNEELSATDMTFILAALLDTKKPEDKEEFSEKFMKAVNILSINNPNRIDEGLQLAKEYIQTLNKFTKSILQSGKITVCGTFILVAVSKIEPQVL 362
            +D+ + +F  + GF  +  A+D+ F   +L+++  PE     ++ F++A++ LS +N +++  GL+LAK+ ++   +   S L +  +   G F+  ++ +  P V+
Sbjct:  186 KDMRVQTFSIHFGFKHKFLASDVVFATMSLMES--PEKDGSGTDHFIQALDSLSRSNLDKLYHGLELAKKQLRATQQTIASCLCTNLVISQGPFLYCSLMEGTPDVM 290
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BLAST of SWIM-type domain-containing protein vs. Ensembl Mouse
Match: Cdc45 (cell division cycle 45 [Source:MGI Symbol;Acc:MGI:1338073])

HSP 1 Score: 47.3654 bits (111), Expect = 8.627e-7
Identity = 28/106 (26.42%), Postives = 60/106 (56.60%), Query Frame = 3 
Query:   42 EDLFLPSFVGNCGFNEELSATDMTFILAALLDTKKPEDKEEFSEKFMKAVNILSINNPNRIDEGLQLAKEYIQTLNKFTKSILQSGKITVCGTFILVAVSKIEPQV 359
            +D+ + +F    GF  +  A+D+ F   +L+++  PE     ++ F++A++ LS +N +++  GL+LAK+++Q   +   S L +  +T  G F+  ++ +  P V
Sbjct:  308 KDMRVQTFSIQFGFKHKFLASDVVFATMSLMES--PEKDGSGTDHFIQALDSLSRSNLDKLYLGLELAKKHLQATQQTIASCLCTNLVTSQGPFLYCSLMEGTPDV 411
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BLAST of SWIM-type domain-containing protein vs. Ensembl Mouse
Match: Cdc45 (cell division cycle 45 [Source:MGI Symbol;Acc:MGI:1338073])

HSP 1 Score: 47.3654 bits (111), Expect = 8.900e-7
Identity = 28/106 (26.42%), Postives = 60/106 (56.60%), Query Frame = 3 
Query:   42 EDLFLPSFVGNCGFNEELSATDMTFILAALLDTKKPEDKEEFSEKFMKAVNILSINNPNRIDEGLQLAKEYIQTLNKFTKSILQSGKITVCGTFILVAVSKIEPQV 359
            +D+ + +F    GF  +  A+D+ F   +L+++  PE     ++ F++A++ LS +N +++  GL+LAK+++Q   +   S L +  +T  G F+  ++ +  P V
Sbjct:  354 KDMRVQTFSIQFGFKHKFLASDVVFATMSLMES--PEKDGSGTDHFIQALDSLSRSNLDKLYLGLELAKKHLQATQQTIASCLCTNLVTSQGPFLYCSLMEGTPDV 457
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BLAST of SWIM-type domain-containing protein vs. UniProt/SwissProt
Match: sp|Q9Z1X9|CDC45_MOUSE (Cell division control protein 45 homolog OS=Mus musculus OX=10090 GN=Cdc45 PE=1 SV=2)

HSP 1 Score: 47.3654 bits (111), Expect = 6.225e-6
Identity = 28/106 (26.42%), Postives = 60/106 (56.60%), Query Frame = 3 
Query:   42 EDLFLPSFVGNCGFNEELSATDMTFILAALLDTKKPEDKEEFSEKFMKAVNILSINNPNRIDEGLQLAKEYIQTLNKFTKSILQSGKITVCGTFILVAVSKIEPQV 359
            +D+ + +F    GF  +  A+D+ F   +L+++  PE     ++ F++A++ LS +N +++  GL+LAK+++Q   +   S L +  +T  G F+  ++ +  P V
Sbjct:  354 KDMRVQTFSIQFGFKHKFLASDVVFATMSLMES--PEKDGSGTDHFIQALDSLSRSNLDKLYLGLELAKKHLQATQQTIASCLCTNLVTSQGPFLYCSLMEGTPDV 457
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BLAST of SWIM-type domain-containing protein vs. TrEMBL
Match: A0A2T7PI79 (Uncharacterized protein OS=Pomacea canaliculata OX=400727 GN=C0Q70_08572 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 3.290e-8
Identity = 36/126 (28.57%), Postives = 66/126 (52.38%), Query Frame = 3 
Query:    3 LFKSHYQRFNILKEDLFLPSFVGNCGFNEELSATDMTFILAALLDTKKPEDKEEF-SEKFMKAVNILSINNPNRIDEGLQLAKEYIQTLNKFTKSILQSGKITVCGTFILVAVSK--IEPQVLSAP 371
            + + H  ++ +  +D+ +PSF   CG+   LSATD+     A+L+     D+ +  S+ F+ A +ILS  +   ID+ +QLAK  +  L    ++ L   +I   G F+ V V++  ++ +  S P
Sbjct:  338 MMQEHIAKYGLTMQDIVVPSFTAQCGYKTRLSATDVVLACVAVLEAV---DRNKLPSDNFLSAQDILSSYHTEAIDKAIQLAKRQLTALVTQVQTFLDMHQIISAGPFLYVFVNEGTVDMKYFSQP 460
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BLAST of SWIM-type domain-containing protein vs. TrEMBL
Match: A0A1E1X524 (Putative cdc45 cell division cycle 45-like protein (Fragment) OS=Amblyomma aureolatum OX=187763 PE=2 SV=1)

HSP 1 Score: 54.6842 bits (130), Expect = 5.032e-6
Identity = 32/101 (31.68%), Postives = 52/101 (51.49%), Query Frame = 3 
Query:   42 EDLFLPSFVGNCGFNEELSATDMTFILAALLDTKKPEDKEEFSEKFMKAVNILSINNPNRIDEGLQLAKEYIQTLNKFTKSILQSGKITVCGTFILVAVSK 344
            E+L    F+G CG+ +   A+D T+ L ALL++  P D  + +  F  A++ LS +N   +  G+QLAKE +    +   S +  G I   G F+   V +
Sbjct:  200 ENLLFACFIGKCGYRDHFFASDTTYGLMALLES--PAD--DVTTSFFSALDALSWSNTELLRHGIQLAKECLVVTMQQVHSFMDLGSIICAGPFLYGTVQE 296
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BLAST of SWIM-type domain-containing protein vs. TrEMBL
Match: T1EMC6 (SWIM-type domain-containing protein OS=Helobdella robusta OX=6412 GN=20197726 PE=4 SV=1)

HSP 1 Score: 54.6842 bits (130), Expect = 5.139e-6
Identity = 30/111 (27.03%), Postives = 60/111 (54.05%), Query Frame = 3 
Query:   15 HYQRFNILKEDLFLPSFVGNCGFNEELSATDMTFILAALL-DTKKPEDKEEFSEKFMKAVNILSINNPNRIDEGLQLAKEYIQTLNKFTKSILQSGKITVCGTFILVAVSK 344
            H +++ +L++DLFLP+F  + GF  + SA+D+ +   ALL D +  +D +  S  F++A++ L     + ++ G++  K   + L    +S L   ++   G F+   V +
Sbjct:  366 HAEKYGMLEQDLFLPTFQCHYGFKCKYSASDVVYACHALLVDVEDNQDDQLLSSNFLQALDALKRTQSDDLETGIEKFKGQTRILVAQVQSFLDMNQVISAGPFLYTFVQQ 476
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BLAST of SWIM-type domain-containing protein vs. TrEMBL
Match: H2XS25 (Uncharacterized protein OS=Ciona intestinalis OX=7719 GN=cdc45 PE=4 SV=1)

HSP 1 Score: 53.9138 bits (128), Expect = 6.879e-6
Identity = 32/101 (31.68%), Postives = 55/101 (54.46%), Query Frame = 3 
Query:   60 SFVGNCGFNEELSATDMTFILAALL---DTKKPEDKEEFSEKFMKAVNILSINNPNRIDEGLQLAKEYIQTLNKFTKSILQSGKITVCGTFILVAVSKIEP 353
            SF   CGFN +L A+D+ F + ++L   ++ KPE  E+ S  F+ A+  LS     +++EGLQLAK  ++ +     S +  G++   G F+   + +  P
Sbjct:   85 SFTAQCGFNHKLCASDVVFSVDSILTNTESSKPESYEDNS-NFVDALEGLSRITSPKLEEGLQLAKVQLRAIKNNVGSFIDIGQVLSYGPFLYTNIKEGSP 184
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BLAST of SWIM-type domain-containing protein vs. Ensembl Nematostella
Match: EDO50060 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7RF94])

HSP 1 Score: 43.5134 bits (101), Expect = 4.896e-6
Identity = 31/124 (25.00%), Postives = 66/124 (53.23%), Query Frame = 3 
Query:   21 QRFNILKEDLFLPSFVGNCGFNEELSATDMTFILAALLDTKK---PEDKEEFSEKFMKAVNILSINNPNRIDEGLQLAKEYIQTLNKFTKSILQSGKITVCGTFILVAVSKIEP--QVLSAPLM 377
            Q+F +  E++   SF    GF  +L ++D+   + ALL++      +  E  SEKF+ A++ LS +N   + +G+++AK+ +  L    +S++   ++   G F+   + +  P  ++ S P++
Sbjct:  350 QKFGM--EEMSYGSFNVQYGFRNKLCSSDVVHAVNALLESPSLLALQSDESKSEKFLDALDALSRSNSKLLLDGIEMAKKQLIALVTQVRSLIDMHQVVCAGPFLYAFLREGTPDLKMFSKPVV 471
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BLAST of SWIM-type domain-containing protein vs. Ensembl Medaka
Match: cdc45 (cell division cycle 45 [Source:NCBI gene;Acc:101173790])

HSP 1 Score: 46.595 bits (109), Expect = 1.490e-6
Identity = 33/113 (29.20%), Postives = 58/113 (51.33%), Query Frame = 3 
Query:   42 EDLFLPSFVGNCGFNEELSATDMTFILAALLDTKKPEDKEEFSEKFMKAVNILSINNPNRIDEGLQLAKEYIQTLNKFTKSILQSGKITVCGTFILVAVSKIEPQV--LSAPL 374
            +D+ + +F    GF     A+DM    AALL++   E  E  ++ F+KA++ LS +N NR+  G+ LAK+ +  + +   S + +  I   G F+   + +  P V   S P+
Sbjct:  357 KDIRIQTFGAQFGFKNRFLASDMVHAAAALLES--TEKDESDTDNFIKALDSLSRSNLNRLLSGIDLAKKKLIAIQQTVASCICTNLILSQGPFLYCYLMEGTPDVKLFSKPM 467
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BLAST of SWIM-type domain-containing protein vs. Planmine SMEST
Match: SMESG000045786.1 (SMESG000045786.1)

HSP 1 Score: 168.703 bits (426), Expect = 1.415e-50
Identity = 81/126 (64.29%), Postives = 98/126 (77.78%), Query Frame = 3 
Query:    3 LFKSHYQRFNILKEDLFLPSFVGNCGFNEELSATDMTFILAALLDTKKPEDKEEFSEKFMKAVNILSINNPNRIDEGLQLAKEYIQTLNKFTKSILQSGKITVCGTFILVAVSKIEPQVLSAPLMQ 380
            LFK +Y+RFNI KEDLFLPSFV  CGF EELSA D TFI+AA LD + PE KEEF +KF++AV  LSIN+   ID GL+LAK+YI+T+ KFT+SIL++  +TVCGTF+ V V K  P  LSAPLMQ
Sbjct:  338 LFKDNYERFNISKEDLFLPSFVAKCGFREELSAIDATFIIAAFLDHENPEIKEEFCDKFLRAVKFLSINDSRTIDYGLELAKDYIETIYKFTRSILETSDVTVCGTFLQVDVKKQNPLWLSAPLMQ 463
The following BLAST results are available for this feature:
BLAST of SWIM-type domain-containing protein vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 2
Match NameE-valueIdentityDescription
CDC456.213e-624.30cell division cycle 45 [Source:HGNC Symbol;Acc:HGN... [more]
CDC458.044e-624.30cell division cycle 45 [Source:HGNC Symbol;Acc:HGN... [more]
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BLAST of SWIM-type domain-containing protein 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 SWIM-type domain-containing protein 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 SWIM-type domain-containing protein 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 SWIM-type domain-containing protein 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 SWIM-type domain-containing protein vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 2
Match NameE-valueIdentityDescription
Cdc458.627e-726.42cell division cycle 45 [Source:MGI Symbol;Acc:MGI:... [more]
Cdc458.900e-726.42cell division cycle 45 [Source:MGI Symbol;Acc:MGI:... [more]
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BLAST of SWIM-type domain-containing protein vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|Q9Z1X9|CDC45_MOUSE6.225e-626.42Cell division control protein 45 homolog OS=Mus mu... [more]
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BLAST of SWIM-type domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
A0A2T7PI793.290e-828.57Uncharacterized protein OS=Pomacea canaliculata OX... [more]
A0A1E1X5245.032e-631.68Putative cdc45 cell division cycle 45-like protein... [more]
T1EMC65.139e-627.03SWIM-type domain-containing protein OS=Helobdella ... [more]
H2XS256.879e-631.68Uncharacterized protein OS=Ciona intestinalis OX=7... [more]
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BLAST of SWIM-type domain-containing protein 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 SWIM-type domain-containing protein 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 SWIM-type domain-containing protein 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 SWIM-type domain-containing protein vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO500604.896e-625.00Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SWIM-type domain-containing protein vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
cdc451.490e-629.20cell division cycle 45 [Source:NCBI gene;Acc:10117... [more]
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BLAST of SWIM-type domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000045786.11.415e-5064.29SMESG000045786.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004979 ID=SMED30004979|Name=SWIM-type domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=381bp
CATTATTCAAAAGTCACTATCAAAGATTTAACATTTTGAAGGAGGATTTG
TTTTTACCGTCATTTGTAGGAAATTGTGGCTTTAATGAAGAGCTGTCGGC
CACAGATATGACATTCATCCTTGCGGCATTACTCGATACTAAAAAACCGG
AAGATAAAGAAGAATTTAGTGAAAAGTTTATGAAAGCTGTAAATATTTTA
TCAATTAATAATCCAAATCGGATTGATGAAGGACTTCAACTGGCAAAAGA
ATACATTCAAACTTTAAATAAATTTACCAAATCCATTCTACAATCAGGCA
AAATTACAGTTTGTGGAACTTTCATTCTAGTGGCAGTATCGAAGATTGAA
CCTCAAGTGCTCTCCGCTCCGTTAATGCAAT
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protein sequence of SMED30004979-orf-1

>SMED30004979-orf-1 ID=SMED30004979-orf-1|Name=SMED30004979-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=126bp
LFKSHYQRFNILKEDLFLPSFVGNCGFNEELSATDMTFILAALLDTKKPE
DKEEFSEKFMKAVNILSINNPNRIDEGLQLAKEYIQTLNKFTKSILQSGK
ITVCGTFILVAVSKIEPQVLSAPLMQ
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0008270zinc ion binding
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000461lateral branch
Vocabulary: INTERPRO
TermDefinition
IPR003874CDC45
Vocabulary: biological process
TermDefinition
GO:0006270DNA replication initiation
GO:0051301cell division
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR003874CDC45 familyPFAMPF02724CDC45coord: 8..114
e-value: 4.6E-10
score: 38.5
IPR003874CDC45 familyPANTHERPTHR10507CDC45-RELATED PROTEINcoord: 9..122
NoneNo IPR availablePANTHERPTHR10507:SF0CELL DIVISION CONTROL PROTEIN 45 HOMOLOGcoord: 9..122