C2H2-type domain-containing protein

Overview
NameC2H2-type domain-containing protein
Smed IDSMED30019653
Length (bp)385
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 C2H2-type domain-containing protein (SMED30019653) t-SNE clustered cells

Violin plots show distribution of expression levels for C2H2-type domain-containing protein (SMED30019653) 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.
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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



SMED30019653

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
enteric muscle cellSMED30019653 dd_Smed_v4_79185_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of C2H2-type domain-containing protein vs. Ensembl Celegans
Match: ZC53.4 (pep chromosome:WBcel235:X:1925750:1937689:1 gene:WBGene00022511.1 transcript:ZC53.4.1 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:ZC53.4)

HSP 1 Score: 55.0694 bits (131), Expect = 1.071e-9
Identity = 32/82 (39.02%), Postives = 43/82 (52.44%), Query Frame = 2 
Query:   59 SKRTMTLTESDIENFMQSRICYLC----NKELVIPT--HDHEHNTGRYLSAACNSCNLSRKIKYLLPVVFHNLKAYDLHHIL 286
            S R   LT+ +   F +++ C  C    N E +  T   DH+H TG Y    C SCN+ R+    +PV FHNLK YD H I+
Sbjct:  955 SVRMKKLTQDEWTEFNKNQECPHCQVQYNTEDMKTTKVRDHDHWTGEYRGPFCGSCNILRRKNNFIPVFFHNLKGYDSHLIV 1036
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BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: A0A1I8H705 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 84.3445 bits (207), Expect = 2.974e-16
Identity = 41/100 (41.00%), Postives = 59/100 (59.00%), Query Frame = 2 
Query:   80 TESDIENFMQSRICYLCNKELVIPTH---DHEHNTGRYLSAACNSCN-LSRKIKYLLPVVFHNLKAYDLHHILKYELSSFKNWKLNVIP-TTEKFLSLMV 364
            ++ +  +F  +  CYLCN   +  +    DH+H +G Y  AAC SCN L+R  +  LP+VFHNL+ YDLH I    L     W+++VIP T E +LS+ V
Sbjct:  783 SDDNRRSFQDATQCYLCNAVFISSSDKHWDHDHLSGEYKGAACASCNKLARLKRRFLPIVFHNLRGYDLHLIFSTALGDMTGWRVSVIPQTAESYLSMRV 882
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BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: A0A267E704 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig004794g3 PE=4 SV=1)

HSP 1 Score: 80.4925 bits (197), Expect = 4.629e-15
Identity = 43/121 (35.54%), Postives = 71/121 (58.68%), Query Frame = 2 
Query:   26 ERIVLPYYYNYSKRTMTLTESDI---ENFMQSRICYLCNKELVIPT---HDHEHNTGRYLSAACNSCN-LSRKIKYLLPVVFHNLKAYDLHHILKYELSSFKNWKLNVIP-TTEKFLSLMV 364
            ER+    Y    + +    E+D    + F +S  C+ C+++        +DH+H TG++  AAC+ CN L++  +  LP+ FHNL+ YD+H +    L + KNWKL+VIP T+E+++SL V
Sbjct:  369 ERVAREVYEWNRRHSYQTAEADTIASQIFSESSNCHYCDRQFTDTNDKHYDHDHLTGKFKGAACSRCNKLAQLRRRFLPIFFHNLRNYDMHLLFSTALGNMKNWKLSVIPQTSERYMSLRV 489
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BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: A0A267H0H8 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig004794g8 PE=4 SV=1)

HSP 1 Score: 79.7221 bits (195), Expect = 8.587e-15
Identity = 42/121 (34.71%), Postives = 71/121 (58.68%), Query Frame = 2 
Query:   26 ERIVLPYYYNYSKRTMTLTESDI---ENFMQSRICYLCNKELVIPT---HDHEHNTGRYLSAACNSCN-LSRKIKYLLPVVFHNLKAYDLHHILKYELSSFKNWKLNVIP-TTEKFLSLMV 364
            ER+    Y    + +    E+D    + F +S  C+ C+++        +DH+H TG++  AAC+ CN L++  +  LP+ FHNL+ YD+H +    L + KNWKL+VIP T+E+++SL +
Sbjct:  368 ERVAREVYDWNRRHSYQTAEADTTASQIFSESSNCHYCDRQFTDTNDKHYDHDHLTGKFKGAACSRCNKLAQLRRRFLPIFFHNLRNYDMHLLFSTALGNMKNWKLSVIPQTSERYMSLRI 488
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BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: A0A1I8GQP5 (WW domain-containing protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 78.9518 bits (193), Expect = 1.802e-14
Identity = 41/117 (35.04%), Postives = 63/117 (53.85%), Query Frame = 2 
Query:   29 RIVLPYYYNYSKRTMTLTESDIENFMQSRICYLCNKELVIPTH---DHEHNTGRYLSAACNSCNLSRKIKY-LLPVVFHNLKAYDLHHILKYELSSFKNWKLNVIP-TTEKFLSLMV 364
            R V  +   +S++    TE     F ++  C  C  E    ++   DH+H +G +  AAC  CN+  ++K   LPVVFHN K YDLH ++   L   + WK++VIP   E+FLS+ +
Sbjct:  676 REVYGWNTEFSRQAAIRTEMAGRQFREATACCYCRSEFTEGSNKHWDHDHLSGEFRGAACADCNMKARLKRSFLPVVFHNFKGYDLHLMMSSALGLMEGWKISVIPLNPEQFLSMKI 792
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BLAST of C2H2-type domain-containing protein vs. TrEMBL
Match: A0A267FMM4 (DNA_pol_B_2 domain-containing protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig020163g11 PE=4 SV=1)

HSP 1 Score: 78.5666 bits (192), Expect = 2.326e-14
Identity = 41/117 (35.04%), Postives = 63/117 (53.85%), Query Frame = 2 
Query:   29 RIVLPYYYNYSKRTMTLTESDIENFMQSRICYLCNKELVIPTH---DHEHNTGRYLSAACNSCNLSRKIK-YLLPVVFHNLKAYDLHHILKYELSSFKNWKLNVIP-TTEKFLSLMV 364
            R V  +   +S++    TE     F ++  C  C  E    ++   DH+H +G +  AAC  CN+  ++K   LPVVFHN K YDLH ++   L   + WK++VIP   E+FLS+ +
Sbjct:   37 REVYGWNTEFSRQAAIRTEMAGRQFREATACCYCRSEFTEGSNKHWDHDHLSGEFRGAACADCNMKARLKRSFLPVVFHNFKGYDLHLMMSSALGLMEGWKISVIPLNPEQFLSMKI 153
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BLAST of C2H2-type domain-containing protein vs. Ensembl Nematostella
Match: EDO46109 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7RR56])

HSP 1 Score: 59.6918 bits (143), Expect = 1.492e-11
Identity = 37/100 (37.00%), Postives = 53/100 (53.00%), Query Frame = 2 
Query:   65 RTMTLTESDIENFMQSRICYLCNKELV-IPTHDHEHNTGRYLSAACNSCNLSRKIKYLLPVVFHNLKAYDLHHILKYELSSFKNWKLNVIPTT-EKFLSL 358
            + + +T  D  N+  +  C++C  EL      DH H TG+Y  AA N+CNL  +     PV+FHNL  YD H  +K   +S    K+N IP   EK++S 
Sbjct:  900 KEVEMTREDEMNYDNATHCHICGGELGEDKVLDHCHLTGKYRGAAHNACNLRFRAPKFFPVLFHNLSGYDSHLFVKNLGTS--EGKINCIPNNEEKYISF 997
[Close]
BLAST of C2H2-type domain-containing protein vs. Planmine SMEST
Match: SMESG000008378.1 (SMESG000008378.1)

HSP 1 Score: 144.821 bits (364), Expect = 5.445e-41
Identity = 69/129 (53.49%), Postives = 94/129 (72.87%), Query Frame = 2 
Query:    2 LLKMEHIGERIVLPYYYNYSKRTMTLTESDIENFMQSRICYLCNKELVIPTHDHEHNTGRYLSAACNSCNLSRKIKYLLPVVFHNLKAYDLHHILKYELSSFKNWKLNVIP-TTEKFLSLMV*INNLTV 385
            L ++ +I    VLP+Y N  K+ + LT+SDI +F  +  CYLCNK L +P  DH++ TG+YL AAC+ CN+SR+I++  PVVFHNL+ YDLHHILKY +S FK W+++ IP T+EKFLSL   I+ LTV
Sbjct: 1559 LQEINNISINTVLPFYQNNYKKKIILTDSDILSFSSATCCYLCNKILSVPVKDHDNFTGKYLGAACSKCNISRQIRFEFPVVFHNLRGYDLHHILKYGMSDFKMWEISCIPVTSEKFLSLSARISGLTV 1687
[Close]
BLAST of C2H2-type domain-containing protein vs. Planmine SMEST
Match: SMESG000031049.1 (SMESG000031049.1)

HSP 1 Score: 144.436 bits (363), Expect = 6.828e-41
Identity = 72/130 (55.38%), Postives = 92/130 (70.77%), Query Frame = 2 
Query:    2 LLKMEHIGERIVLPYYYNYSKRTMT-LTESDIENFMQSRICYLCNKELVIPTHDHEHNTGRYLSAACNSCNLSRKIKYLLPVVFHNLKAYDLHHILKYELSSFKNWKLNVIP-TTEKFLSLMV*INNLTV 385
            L K+E I   IVLPYY N+ K+ M  LT ++ + F+  R CYLC K +     DH+H TG+YL AAC +CN++RKI   LP+VFHNL+ YDLHHILKY L+ F +WKLN+IP TTEKF+SL+V I  L V
Sbjct:  854 LKKVEEIAVTIVLPYYENHGKKPMNNLTSNEEQQFIACRTCYLCKKLIRNKVKDHDHFTGQYLGAACRNCNINRKISKQLPIVFHNLRGYDLHHILKYGLNEFPSWKLNIIPTTTEKFISLIVNIKKLAV 983
[Close]
BLAST of C2H2-type domain-containing protein vs. Planmine SMEST
Match: SMESG000031049.1 (SMESG000031049.1)

HSP 1 Score: 144.05 bits (362), Expect = 8.594e-41
Identity = 72/130 (55.38%), Postives = 92/130 (70.77%), Query Frame = 2 
Query:    2 LLKMEHIGERIVLPYYYNYSKRTMT-LTESDIENFMQSRICYLCNKELVIPTHDHEHNTGRYLSAACNSCNLSRKIKYLLPVVFHNLKAYDLHHILKYELSSFKNWKLNVIP-TTEKFLSLMV*INNLTV 385
            L K+E I   IVLPYY N+ K+ M  LT ++ + F+  R CYLC K +     DH+H TG+YL AAC +CN++RKI   LP+VFHNL+ YDLHHILKY L+ F +WKLN+IP TTEKF+SL+V I  L V
Sbjct: 1111 LKKVEEIAVTIVLPYYENHGKKPMNNLTSNEEQQFIACRTCYLCKKLIRNKVKDHDHFTGQYLGAACRNCNINRKISKQLPIVFHNLRGYDLHHILKYGLNEFPSWKLNIIPTTTEKFISLIVNIKKLAV 1240
[Close]
BLAST of C2H2-type domain-containing protein vs. Planmine SMEST
Match: SMESG000066165.1 (SMESG000066165.1)

HSP 1 Score: 144.05 bits (362), Expect = 9.643e-41
Identity = 72/130 (55.38%), Postives = 92/130 (70.77%), Query Frame = 2 
Query:    2 LLKMEHIGERIVLPYYYNYSKRTMT-LTESDIENFMQSRICYLCNKELVIPTHDHEHNTGRYLSAACNSCNLSRKIKYLLPVVFHNLKAYDLHHILKYELSSFKNWKLNVIP-TTEKFLSLMV*INNLTV 385
            L K+E I   IVLPYY N+ K+ M  LT ++ + F+  R CYLC K +     DH+H TG+YL AAC +CN++RKI   LP+VFHNL+ YDLHHILKY L+ F +WKLN+IP TTEKF+SL+V I  L V
Sbjct:  387 LKKVEEIAVTIVLPYYENHGKKPMNNLTSNEEQQFIACRTCYLCKKLIRNKVKDHDHFTGQYLGAACRNCNINRKISKQLPIVFHNLRGYDLHHILKYGLNEFPSWKLNIIPTTTEKFISLIVNIKKLAV 516
[Close]
BLAST of C2H2-type domain-containing protein vs. Planmine SMEST
Match: SMESG000066165.1 (SMESG000066165.1)

HSP 1 Score: 144.05 bits (362), Expect = 9.645e-41
Identity = 72/130 (55.38%), Postives = 92/130 (70.77%), Query Frame = 2 
Query:    2 LLKMEHIGERIVLPYYYNYSKRTMT-LTESDIENFMQSRICYLCNKELVIPTHDHEHNTGRYLSAACNSCNLSRKIKYLLPVVFHNLKAYDLHHILKYELSSFKNWKLNVIP-TTEKFLSLMV*INNLTV 385
            L K+E I   IVLPYY N+ K+ M  LT ++ + F+  R CYLC K +     DH+H TG+YL AAC +CN++RKI   LP+VFHNL+ YDLHHILKY L+ F +WKLN+IP TTEKF+SL+V I  L V
Sbjct:  425 LKKVEEIAVTIVLPYYENHGKKPMNNLTSNEEQQFIACRTCYLCKKLIRNKVKDHDHFTGQYLGAACRNCNINRKISKQLPIVFHNLRGYDLHHILKYGLNEFPSWKLNIIPTTTEKFISLIVNIKKLAV 554
The following BLAST results are available for this feature:
BLAST of C2H2-type domain-containing protein 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 C2H2-type domain-containing protein vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ZC53.41.071e-939.02pep chromosome:WBcel235:X:1925750:1937689:1 gene:W... [more]
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BLAST of C2H2-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 C2H2-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 C2H2-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 C2H2-type domain-containing protein 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 C2H2-type domain-containing protein 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 C2H2-type domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1I8H7052.974e-1641.00Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267E7044.629e-1535.54Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267H0H88.587e-1534.71Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8GQP51.802e-1435.04WW domain-containing protein OS=Macrostomum lignan... [more]
A0A267FMM42.326e-1435.04DNA_pol_B_2 domain-containing protein OS=Macrostom... [more]
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BLAST of C2H2-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 C2H2-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 C2H2-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 C2H2-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
EDO461091.492e-1137.00Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of C2H2-type domain-containing protein 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 C2H2-type domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000008378.15.445e-4153.49SMESG000008378.1[more]
SMESG000031049.16.828e-4155.38SMESG000031049.1[more]
SMESG000031049.18.594e-4155.38SMESG000031049.1[more]
SMESG000066165.19.643e-4155.38SMESG000066165.1[more]
SMESG000066165.19.645e-4155.38SMESG000066165.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30019653 ID=SMED30019653|Name=C2H2-type domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=385bp
TCTGTTAAAGATGGAGCATATTGGAGAACGCATTGTTTTGCCTTATTATT
ACAATTATAGTAAAAGAACTATGACACTAACAGAATCAGATATCGAAAAT
TTCATGCAGAGCAGAATCTGTTATTTATGTAATAAGGAATTGGTCATTCC
AACACATGACCATGAGCATAATACCGGACGTTATCTCAGCGCAGCTTGTA
ACAGTTGCAATTTATCACGGAAAATCAAATACTTGTTGCCTGTTGTATTT
CATAACTTGAAGGCTTATGATTTACATCATATCTTAAAATACGAACTTAG
CAGCTTCAAAAATTGGAAATTGAATGTAATTCCAACAACAGAGAAATTTT
TGTCGCTAATGGTATGAATCAATAATTTAACCGTG
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protein sequence of SMED30019653-orf-1

>SMED30019653-orf-1 ID=SMED30019653-orf-1|Name=SMED30019653-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=122bp
LLKMEHIGERIVLPYYYNYSKRTMTLTESDIENFMQSRICYLCNKELVIP
THDHEHNTGRYLSAACNSCNLSRKIKYLLPVVFHNLKAYDLHHILKYELS
SFKNWKLNVIPTTEKFLSLMV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003104enteric muscle cell
Vocabulary: molecular function
TermDefinition
GO:0000166nucleotide binding
GO:0003676nucleic acid binding
GO:0003677DNA binding
GO:0003887DNA-directed DNA polymerase activity
GO:00084083'-5' exonuclease activity
Vocabulary: biological process
TermDefinition
GO:0006260DNA replication
GO:0071897DNA biosynthetic process
GO:0090305nucleic acid phosphodiester bond hydrolysis