DUF862 domain-containing protein

Overview
NameDUF862 domain-containing protein
Smed IDSMED30014469
Length (bp)701
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 DUF862 domain-containing protein (SMED30014469) t-SNE clustered cells

Violin plots show distribution of expression levels for DUF862 domain-containing protein (SMED30014469) 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 DUF862 domain-containing protein (SMED30014469) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for DUF862 domain-containing protein (SMED30014469) 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



SMED30014469

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30014469SMESG000007684.1 Contig680GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
pharynxSMED30014469SMESG000007684.1 dd_Smed_v4_1938_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30014469SMESG000007684.1 dd_Smed_v4_1938_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30014469SMESG000007684.1 dd_Smed_v4_1938_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30014469SMESG000007684.1 dd_Smed_v4_1938_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30014469SMESG000007684.1 dd_Smed_v4_1938_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30014469SMESG000007684.1 dd_Smed_v4_1938_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30014469SMESG000007684.1 dd_Smed_v4_1938_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30014469SMESG000007684.1 dd_Smed_v4_1938_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30014469SMESG000007684.1 dd_Smed_v4_1938_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30014469SMESG000007684.1 dd_Smed_v4_1938_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
Homology
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BLAST of DUF862 domain-containing protein vs. TrEMBL
Match: G0NDH0 (Uncharacterized protein OS=Caenorhabditis brenneri OX=135651 GN=CAEBREN_19348 PE=4 SV=1)

HSP 1 Score: 65.0846 bits (157), Expect = 2.296e-9
Identity = 54/173 (31.21%), Postives = 80/173 (46.24%), Query Frame = 3 
Query:  108 MAKGLSWEGKIFYVDD-----ITKPKEIYNQ--HEILPKIGSKETIKEIELYNTPLQGLDFINNAKIEKVV--HHAFVVVKTTNFYFSFDKNGQGIFIQKSKKKEDVLLSIFGDQRS--RVSLLKSNYNVNVDFAKIIQWIIN-DELKRGYYIFNFKINCQGFASCLYSEVTR 590
            M+ G  W G + + DD     I    +  +Q    +L   G      EI  Y+     LD I   +I       H + +V+TTN+Y+S +K  +G+F+Q+SK K  +      D RS  R     SN +   +  KI QWIIN  EL   Y++ +   NC  FAS L+  + R
Sbjct:    1 MSFGGDWTGCLHFWDDDKKKWIQVSADKVHQFFRNVLKAEGEIIIFSEIRKYD-----LDMIPEWRIPGWFGNWHEYTLVETTNWYWSVEKMAEGLFVQRSKSKNIIRCKFGADDRSKDRSEGRSSNVSFGENLMKIAQWIINRRELGNTYHVLDR--NCHHFASLLHEAIVR 166
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BLAST of DUF862 domain-containing protein vs. TrEMBL
Match: G0MPJ3 (Uncharacterized protein OS=Caenorhabditis brenneri OX=135651 GN=CAEBREN_06627 PE=4 SV=1)

HSP 1 Score: 64.3142 bits (155), Expect = 3.577e-8
Identity = 35/100 (35.00%), Postives = 62/100 (62.00%), Query Frame = 3 
Query:  297 VHHAFVVVKTTNFYFSFDKNGQGIFIQKSKKKEDVLLSIFGDQRSR--VSLLKSNYNVNVDFAKIIQWIIN-----DELKRGYYIFNFKINCQGFASCLY 575
            ++HAF  V+TTN+++SFDK  +GI +Q+SKKK++V     G  R++   S   + ++   +  ++ +WII+     +EL + Y++  +K NCQ FA  +Y
Sbjct:   71 LYHAFTTVETTNWHWSFDKMAEGIHVQRSKKKDEVCSYFEGKMRTKKPSSWRSAKFSNGKNILEVAKWIIDSGTPENELNKIYHV--WKQNCQLFAHTIY 168
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BLAST of DUF862 domain-containing protein vs. TrEMBL
Match: A0A3M6TM43 (Uncharacterized protein OS=Pocillopora damicornis OX=46731 GN=pdam_00021733 PE=4 SV=1)

HSP 1 Score: 56.9954 bits (136), Expect = 3.351e-6
Identity = 41/132 (31.06%), Postives = 70/132 (53.03%), Query Frame = 3 
Query:  189 EILPKIGSKETIKEIELYNTPLQGLDFINNAKIEKVVHHAFVVVKTTNFYFSFDKNGQGIFIQKSKKKEDVLLSIFGDQR-SRVSLLKSNYNVNVDFAKIIQWIINDELKRGYYIFNFKINCQGFASCLYSE 581
            E L +I + E I+ I  Y  PL     + N K   + +H F+V++TTN+Y+S  K+ + I +Q+SK K  V     G  R + V+++  N         +I++I  +EL + Y +   + NCQ FA  L+++
Sbjct:   59 EDLHRITNSEEIQYIGSYQCPL-----VENMKGHLIAYHQFLVIETTNWYWSIGKDSEKILLQRSKVKNRVEERKEGQARYTPVTMIVENEGRG-SMRDLIKFICENELDKTYDL--LRDNCQQFAERLFNQ 182
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BLAST of DUF862 domain-containing protein vs. Planmine SMEST
Match: SMESG000007684.1 (SMESG000007684.1)

HSP 1 Score: 366.696 bits (940), Expect = 7.871e-131
Identity = 179/181 (98.90%), Postives = 181/181 (100.00%), Query Frame = 3 
Query:   75 MSFNKSFHNQSMAKGLSWEGKIFYVDDITKPKEIYNQHEILPKIGSKETIKEIELYNTPLQGLDFINNAKIEKVVHHAFVVVKTTNFYFSFDKNGQGIFIQKSKKKEDVLLSIFGDQRSRVSLLKSNYNVNVDFAKIIQWIINDELKRGYYIFNFKINCQGFASCLYSEVTREFIEESLFT 617
            MSFNKSFHNQSMAKGLSWEGKIFYVDDITKPKEIYN+HEILPKIGSKETIKEIELYNTPLQGLDFINNAKIEKVVHHA+VVVKTTNFYFSFDKNGQGIFIQKSKKKEDVLLSIFGDQRSRVSLLKSNYNVNVDFAKIIQWIINDELKRGYYIFNFKINCQGFASCLYSEVTREFIEESLFT
Sbjct:    1 MSFNKSFHNQSMAKGLSWEGKIFYVDDITKPKEIYNEHEILPKIGSKETIKEIELYNTPLQGLDFINNAKIEKVVHHAYVVVKTTNFYFSFDKNGQGIFIQKSKKKEDVLLSIFGDQRSRVSLLKSNYNVNVDFAKIIQWIINDELKRGYYIFNFKINCQGFASCLYSEVTREFIEESLFT 181
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BLAST of DUF862 domain-containing protein vs. Planmine SMEST
Match: SMESG000070711.1 (SMESG000070711.1)

HSP 1 Score: 248.44 bits (633), Expect = 3.373e-84
Identity = 116/169 (68.64%), Postives = 143/169 (84.62%), Query Frame = 3 
Query:  108 MAKGLSWEGKIFYVDDITKPKEIYNQHEILPKIGSKETIKEIELYNTPLQGLDFINNAKIEKVVHHAFVVVKTTNFYFSFDKNGQGIFIQKSKKKEDVLLSIFGDQRSRVSLLKSNYNVNVDFAKIIQWIINDELKRGYYIFNFKINCQGFASCLYSEVTREFIEESLF 614
            MAKG +WEGKIFY+DD+ +P+EIYNQHEIL KIGSKETI EI++Y TPLQGLDF+     EK+VHHAFVVVKTTNFYFSFDKNG+GI+IQKS+ K+DVL S+FGDQRSR   LKSN NV VDF  II+WII DELKRGY+I NF+ NCQGF++ LY++V+++ + + +F
Sbjct:    1 MAKGQNWEGKIFYIDDLERPEEIYNQHEILQKIGSKETIVEIDVYKTPLQGLDFVEEKVYEKIVHHAFVVVKTTNFYFSFDKNGRGIYIQKSENKDDVLKSVFGDQRSRPVKLKSNTNVRVDFDTIIKWIIRDELKRGYHILNFETNCQGFSASLYTKVSKQTMMQFIF 169
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BLAST of DUF862 domain-containing protein vs. Planmine SMEST
Match: SMESG000024663.1 (SMESG000024663.1)

HSP 1 Score: 109.768 bits (273), Expect = 6.306e-30
Identity = 58/167 (34.73%), Postives = 97/167 (58.08%), Query Frame = 3 
Query:   90 SFHNQSMAKGLSWEGKIFYVDDITKPKEIYNQHEILPKIGSKETIKEIELYNTPLQGLDFINNAKIEKVVHHAFVVVKTTNFYFSFDKNGQGIFIQKSKKKEDVLLSIFGDQRSRVSLLKSNYNVNVDFAKIIQWIINDELKRGYYIFNFKINCQGFASCLYSEVTR 590
            S + ++  KG +WE +I ++++ + P E++N  E+   I + ETI ++  Y   L      +       ++HAFV+ +T ++Y+S +KNG GI+IQKSK K++++  I G++R+  +LL S     V    II+WI  +ELK  Y+  N   NCQGFA   Y+ + R
Sbjct:    2 SVNPKAQKKGGNWESRIHFINNTSAPNEVFNGSEMRKLIDTSETIVKVWKYKEKLVWWQITS-----FYLYHAFVIFETNDWYWSMEKNGSGIWIQKSKSKDNLVAKIGGNERNSTTLLDSCQGRFVTIKNIIEWIEKEELKSAYWYMNSDDNCQGFADRGYNHIVR 163
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BLAST of DUF862 domain-containing protein vs. Planmine SMEST
Match: SMESG000024661.1 (SMESG000024661.1)

HSP 1 Score: 94.3597 bits (233), Expect = 5.859e-24
Identity = 49/157 (31.21%), Postives = 88/157 (56.05%), Query Frame = 3 
Query:  114 KGLSWEGKIFYVDDITKPKEIYNQHEILPKIGSKETIKEIELYNTPLQGLDFINNAKIEKVVHHAFVVVKTTNFYFSFDKNGQGIFIQKSKKKEDVLLSIFGDQRSRVSLLKSNYNVNVDFAKIIQWIINDELKRGYYIFNFKINCQGFASCLYSEV 584
            KG +W  +IF++++ + P +++   E+   I + ETI +   Y   L      +       ++HAFV+ +T ++Y+S +KNG GI+IQKSK K +++    G++R+  +LL S +   +   ++I+W+ N+EL   Y+      NCQGFA   Y  +
Sbjct:   10 KGGNWLSRIFFINNTSAPNDVFKGSEMRKLIDTSETIIQAWKYKQKLVWFQITS-----FFLYHAFVIFETKDWYWSIEKNGSGIWIQKSKSKNELVTKNGGNERNSTTLLDSEFGNFITIGELIEWVENNELINRYFYIETYFNCQGFADRAYQHI 161
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BLAST of DUF862 domain-containing protein vs. Planmine SMEST
Match: SMESG000024669.1 (SMESG000024669.1)

HSP 1 Score: 85.8853 bits (211), Expect = 7.151e-21
Identity = 46/154 (29.87%), Postives = 82/154 (53.25%), Query Frame = 3 
Query:  123 SWEGKIFYVDDITKPKEIYNQHEILPKIGSKETIKEIELYNTPLQGLDFINNAKIEKVVHHAFVVVKTTNFYFSFDKNGQGIFIQKSKKKEDVLLSIFGDQRSRVSLLKSNYNVNVDFAKIIQWIINDELKRGYYIFNFKINCQGFASCLYSEV 584
             WEG+IF++ D   P E+YN  E+  +    + I  +  Y TP+  +   +        +H F+V++T  F++S +KN  GI+IQK + K DV+  + G++R+ V  L+        F  ++ WI  +EL++GY   ++  N +GF   +Y  +
Sbjct:    7 DWEGRIFFIRDTNCPNELYNGGEMKRQFDLSKPILHVWKYKTPMHWIQLTS-----FYFYHIFIVIETDEFFWSVEKNNLGIWIQKGRFKNDVISKMAGEERNLVICLEDLQGDFGQFRNLVDWIEINELQKGYSCNDYDFNSKGFGDKVYDNI 155
The following BLAST results are available for this feature:
BLAST of DUF862 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 DUF862 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 DUF862 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 DUF862 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 DUF862 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 DUF862 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 DUF862 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 DUF862 domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
G0NDH02.296e-931.21Uncharacterized protein OS=Caenorhabditis brenneri... [more]
G0MPJ33.577e-835.00Uncharacterized protein OS=Caenorhabditis brenneri... [more]
A0A3M6TM433.351e-631.06Uncharacterized protein OS=Pocillopora damicornis ... [more]
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BLAST of DUF862 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 DUF862 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 DUF862 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 DUF862 domain-containing protein 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 DUF862 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 DUF862 domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000007684.17.871e-13198.90SMESG000007684.1[more]
SMESG000070711.13.373e-8468.64SMESG000070711.1[more]
SMESG000024663.16.306e-3034.73SMESG000024663.1[more]
SMESG000024661.15.859e-2431.21SMESG000024661.1[more]
SMESG000024669.17.151e-2129.87SMESG000024669.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014469 ID=SMED30014469|Name=DUF862 domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=701bp
ATATAATATTTCAGAAATTTGAATTATTTTAAATTTTTTTTGTGATTTTT
TTGAACATTTGTTTATATTTCAAAATGAGCTTTAATAAATCGTTTCATAA
TCAGTCTATGGCCAAAGGTCTAAGTTGGGAAGGTAAGATTTTTTATGTTG
ATGATATTACAAAGCCTAAGGAAATTTATAATCAACATGAAATTTTACCA
AAGATTGGCAGTAAAGAAACGATAAAAGAAATAGAGTTGTATAATACGCC
ACTTCAAGGACTGGATTTTATTAATAATGCAAAAATTGAAAAAGTCGTTC
ACCATGCATTTGTTGTGGTTAAAACTACAAATTTCTATTTTTCTTTCGAT
AAAAATGGCCAAGGAATATTTATTCAAAAATCGAAGAAGAAAGAAGACGT
TTTATTATCAATATTTGGAGACCAAAGATCGAGAGTTTCGCTATTGAAGT
CCAATTATAACGTTAATGTGGATTTCGCTAAAATAATTCAGTGGATTATA
AATGATGAGTTGAAAAGAGGATATTACATATTTAATTTCAAAATAAATTG
CCAAGGATTTGCGTCTTGCCTTTACTCAGAGGTCACGAGGGAGTTCATTG
AGGAAAGCCTATTTACGTAATATTTGCGACAGTTTATCAAAACATTTTAA
TAGTTTCATTAGTTGTTATCTAAAATAATTTATATTTTAGTTAAAAAAAA
A
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protein sequence of SMED30014469-orf-1

>SMED30014469-orf-1 ID=SMED30014469-orf-1|Name=SMED30014469-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=182bp
MSFNKSFHNQSMAKGLSWEGKIFYVDDITKPKEIYNQHEILPKIGSKETI
KEIELYNTPLQGLDFINNAKIEKVVHHAFVVVKTTNFYFSFDKNGQGIFI
QKSKKKEDVLLSIFGDQRSRVSLLKSNYNVNVDFAKIIQWIINDELKRGY
YIFNFKINCQGFASCLYSEVTREFIEESLFT*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000026gut
PLANA:0000034epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000099neuron
PLANA:0000429neoblast
PLANA:0002032epidermal cell
PLANA:0003116parenchymal cell