SMED30002272

Overview
NameSMED30002272
Smed IDSMED30002272
Length (bp)1726
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 SMED30002272 (SMED30002272) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30002272 (SMED30002272) 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 SMED30002272 (SMED30002272) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30002272 (SMED30002272) 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



SMED30002272

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
head regionSMED30002272SMESG000071928.1 SmedASXL_012553SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30002272SMESG000071605.1 SMESG000055916.1 SMESG000055387.1 SmedASXL_021452SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30002272 SmedASXL_079418SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30002272SMESG000071928.1 dd_Smed_v4_36288_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30002272SMESG000071928.1 dd_Smed_v4_36288_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30002272SMESG000071928.1 dd_Smed_v4_36288_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30002272SMESG000071928.1 dd_Smed_v4_36288_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30002272SMESG000071605.1 SMESG000055916.1 SMESG000055387.1 dd_Smed_v6_41377_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30002272SMESG000071928.1 dd_Smed_v6_36288_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
photoreceptor neuronSMED30002272SMESG000071928.1 SMED30028255smed_20140614PMID:22884275
Lapan et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
head regionSMED30002272SMESG000071928.1 OX_Smed_1.0.11766ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30002272 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.027023:1..8577 -7488
Homology
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BLAST of SMED30002272 vs. Ensembl Sea Lamprey
Match: rbpms2a (RNA binding protein, mRNA processing factor 2a [Source:ZFIN;Acc:ZDB-GENE-040718-106])

HSP 1 Score: 46.595 bits (109), Expect = 1.768e-6
Identity = 19/31 (61.29%), Postives = 24/31 (77.42%), Query Frame = 3 
Query:  645 GIKFDPDSDQLMRLEFARTNTKMLKNKMCNS 737
            GI+FDPD  Q +RLEFA+ NTKM KNK+  +
Sbjct:   23 GIRFDPDIPQTLRLEFAKANTKMAKNKLLGT 53
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BLAST of SMED30002272 vs. Planmine SMEST
Match: SMESG000071928.1 (SMESG000071928.1)

HSP 1 Score: 359.377 bits (921), Expect = 3.629e-121
Identity = 175/175 (100.00%), Postives = 175/175 (100.00%), Query Frame = 3 
Query:  645 GIKFDPDSDQLMRLEFARTNTKMLKNKMCNSHIYNSGLNQQLSAGSIDANLLNSDMNLFLGYDGRLAFFAQSAFSPFGPALLPFNGTTFRPPNCSFAPIAVAAPNGLLNVTGTHSLSPFIGPQSGLLGETISQVLMHPSQNGLLYVQPFSIDLNEISAQPLETQFRMNSWNSNGE 1169
            GIKFDPDSDQLMRLEFARTNTKMLKNKMCNSHIYNSGLNQQLSAGSIDANLLNSDMNLFLGYDGRLAFFAQSAFSPFGPALLPFNGTTFRPPNCSFAPIAVAAPNGLLNVTGTHSLSPFIGPQSGLLGETISQVLMHPSQNGLLYVQPFSIDLNEISAQPLETQFRMNSWNSNGE
Sbjct:  110 GIKFDPDSDQLMRLEFARTNTKMLKNKMCNSHIYNSGLNQQLSAGSIDANLLNSDMNLFLGYDGRLAFFAQSAFSPFGPALLPFNGTTFRPPNCSFAPIAVAAPNGLLNVTGTHSLSPFIGPQSGLLGETISQVLMHPSQNGLLYVQPFSIDLNEISAQPLETQFRMNSWNSNGE 284
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BLAST of SMED30002272 vs. Planmine SMEST
Match: SMESG000055387.1 (SMESG000055387.1)

HSP 1 Score: 239.965 bits (611), Expect = 2.292e-92
Identity = 116/116 (100.00%), Postives = 116/116 (100.00%), Query Frame = 3 
Query:  138 MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH 485
            MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH
Sbjct:    1 MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH 116

HSP 2 Score: 119.398 bits (298), Expect = 2.292e-92
Identity = 54/54 (100.00%), Postives = 54/54 (100.00%), Query Frame = 1 
Query:  484 MSKYGPIEDIIVFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHPDFW 645
            MSKYGPIEDIIVFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHPDFW
Sbjct:  117 MSKYGPIEDIIVFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHPDFW 170
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BLAST of SMED30002272 vs. Planmine SMEST
Match: SMESG000071605.1 (SMESG000071605.1)

HSP 1 Score: 239.965 bits (611), Expect = 5.437e-92
Identity = 116/116 (100.00%), Postives = 116/116 (100.00%), Query Frame = 3 
Query:  138 MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH 485
            MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH
Sbjct:    1 MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH 116

HSP 2 Score: 118.627 bits (296), Expect = 5.437e-92
Identity = 53/54 (98.15%), Postives = 54/54 (100.00%), Query Frame = 1 
Query:  484 MSKYGPIEDIIVFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHPDFW 645
            MSKYGPIEDII+FPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHPDFW
Sbjct:  117 MSKYGPIEDIILFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHPDFW 170
[Close]
BLAST of SMED30002272 vs. Planmine SMEST
Match: SMESG000055916.1 (SMESG000055916.1)

HSP 1 Score: 240.736 bits (613), Expect = 1.005e-91
Identity = 116/116 (100.00%), Postives = 116/116 (100.00%), Query Frame = 3 
Query:  138 MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH 485
            MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH
Sbjct:    1 MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH 116

HSP 2 Score: 116.701 bits (291), Expect = 1.005e-91
Identity = 53/54 (98.15%), Postives = 53/54 (98.15%), Query Frame = 1 
Query:  484 MSKYGPIEDIIVFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHPDFW 645
            MSKYGPIEDIIVFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFH DFW
Sbjct:  117 MSKYGPIEDIIVFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHTDFW 170
[Close]
BLAST of SMED30002272 vs. Planmine SMEST
Match: SMESG000028861.1 (SMESG000028861.1)

HSP 1 Score: 132.494 bits (332), Expect = 1.245e-35
Identity = 62/131 (47.33%), Postives = 94/131 (71.76%), Query Frame = 3 
Query:   93 ECLLCLQTDNKLLLSMGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH 485
            ECL+CL+TDNKLL+S+G CNH CC++CGLES+R  M CPLD+  + +I I+ N    EK +      L I+S N +E L F+ V  A+LS+E +++R EI  ++ +D YL+++GPFV N++K++REM+ N+
Sbjct:    5 ECLICLETDNKLLMSIGGCNHKCCIICGLESMRNTMTCPLDREQITEITIYENTNGIEKEK------LKIKSLNSDENLTFEMVQRAILSIENIENRSEIEQIYTLDPYLIYIGPFVLNRNKVSREMIENY 129

HSP 2 Score: 72.0182 bits (175), Expect = 2.100e-14
Identity = 34/77 (44.16%), Postives = 50/77 (64.94%), Query Frame = 1 
Query:  418 IYYGWARL*KTKARSQEKWFTIMSKYGPIEDIIVFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHPDFWE 648
            IY G   L + K  S+E     ++++GPI D+IV P  +Y +F SS+HG  A++   +E FYGE++T +SFHPD WE
Sbjct:  109 IYIGPFVLNRNKV-SREMIENYLNEFGPINDVIVKPNSAYAMFSSSQHGMRAKYERNKELFYGESVTIESFHPDTWE 184
The following BLAST results are available for this feature:
BLAST of SMED30002272 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 SMED30002272 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 SMED30002272 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 SMED30002272 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 SMED30002272 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 SMED30002272 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 SMED30002272 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 SMED30002272 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30002272 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 SMED30002272 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 1
Match NameE-valueIdentityDescription
rbpms2a1.768e-661.29RNA binding protein, mRNA processing factor 2a [So... [more]
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BLAST of SMED30002272 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 SMED30002272 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 SMED30002272 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 SMED30002272 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000071928.13.629e-121100.00SMESG000071928.1[more]
SMESG000055387.12.292e-92100.00SMESG000055387.1[more]
SMESG000071605.15.437e-92100.00SMESG000071605.1[more]
SMESG000055916.11.005e-91100.00SMESG000055916.1[more]
SMESG000028861.11.245e-3547.33SMESG000028861.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002272 ID=SMED30002272|Name=SMED30002272|organism=Schmidtea mediterranea sexual|type=transcript|length=1726bp
ATATTTATTTAATTTTTAAAATTTACAATTTGCAAATATAATATTATAAA
TATTAACAAACTTACAAAATGACATCAAATAATTATTATGATGAATGTTT
ATTATGTTTACAAACGGACAACAAATTGTTATTGTCTATGGGAAACTGCA
ATCACATCTGCTGTATGCTTTGCGGCCTTGAATCGCTGCGCCTCCAAATG
AAATGCCCGCTTGATAAAACCAATGTAAAGAAAATCAAAATATTTTCTAA
CAAATTCTGTTGTGAAAAAAACGAAAATATTCAAGAAAATATCCTGACAA
TCGAATCAGGAAATGAGGAGGAAACGTTAAAATTTCAAACTGTGCTCGAT
GCAGTTTTGAGCATGGAGGAGCTTGATGATCGAGAGGAGATTGGAAATAT
GTTTGAAATGGACAGATATTTATTATGGATGGGCCCGTTTGTAGAAAACA
AAAGCAAGATCACAAGAGAAATGGTTCACAATCATGAGTAAATACGGGCC
AATTGAAGATATAATTGTATTTCCCCAATGTAGCTATGTGTTATTTGGGA
GTAGCAAGCACGGATTTGCAGCAGAGCACAGTTGTAAACGGGAGGAATTT
TACGGAGAAGCAATTACAACTGACAGTTTTCATCCTGATTTCTGGGAATC
AAATTTGATCCAGATTCAGATCAGTTAATGAGATTAGAATTCGCCCGAAC
AAATACAAAAATGTTGAAAAACAAAATGTGTAACAGTCATATTTATAATT
CCGGTTTAAATCAGCAGTTATCTGCAGGTTCTATTGATGCAAACTTATTA
AATTCTGACATGAATCTATTTCTTGGTTATGACGGTCGACTAGCCTTTTT
TGCCCAATCTGCCTTTTCGCCTTTCGGGCCAGCTTTGTTGCCTTTTAATG
GAACTACATTTAGACCGCCTAATTGTTCCTTTGCTCCTATCGCTGTTGCT
GCACCTAATGGACTGTTAAATGTAACAGGAACGCATTCTCTTTCGCCATT
CATAGGTCCACAATCTGGATTGCTTGGAGAAACAATAAGTCAAGTTTTAA
TGCATCCAAGTCAGAATGGTTTATTATATGTACAACCATTTTCAATTGAC
CTCAATGAAATCAGTGCTCAACCCTTAGAGACCCAATTCAGAATGAATTC
ATGGAATTCAAACGGGGAGTGAAAACTGCCAATAATCAAGGCCTCATATT
ATTTCAATTTTATTACATTTGATGAATCATATCAAAATCCGATTATCAAA
ATAGTTTTTATTATCAAACCGAATTGCATATCATTTTGTTTAAATTGAAT
TGAATTTATTTTCTTTTTTTAATGAAATAAATAAACATTTTTATTCTTAA
CATGTAGAGAGAGAGAGAGAGATAGCTCAAAGAGATTTTAGTTCATTTTT
TATTCATTTTGCCTTCATGTTTTATTTGTCATGGAAAACAATTTCAGTGA
TTTTAACATTTTTTTTTGAAAAAGAATTTATTATTTATCAGGCGTGACAA
ATTTAATAAATAATTAGGAAACATTTAGTAATTGCTGTAGTCCCAATTGA
GCTCGACTTTTCATTTTGTCGGGTTTCATATTTTCTCGTCGTTTTTATTT
CGGTTGAGAAATCTTTAGACAGATTTCTATGATATCATTGGAATAGATGT
TAGATGAAGTAGTATTTCAGGAAGTGTTTTATTAATCTTGGAAAAGTATT
TTCTTGTTGAATGTTATGTCTATTTT
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protein sequence of SMED30002272-orf-1

>SMED30002272-orf-1 ID=SMED30002272-orf-1|Name=SMED30002272-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=141bp
MTSNNYYDECLLCLQTDNKLLLSMGNCNHICCMLCGLESLRLQMKCPLDK
TNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSME
ELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNHE*
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protein sequence of SMED30002272-orf-2

>SMED30002272-orf-2 ID=SMED30002272-orf-2|Name=SMED30002272-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=165bp
MRLEFARTNTKMLKNKMCNSHIYNSGLNQQLSAGSIDANLLNSDMNLFLG
YDGRLAFFAQSAFSPFGPALLPFNGTTFRPPNCSFAPIAVAAPNGLLNVT
GTHSLSPFIGPQSGLLGETISQVLMHPSQNGLLYVQPFSIDLNEISAQPL
ETQFRMNSWNSNGE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000017photoreceptor neuron
PLANA:0000099neuron
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR013083Znf_RING/FYVE/PHD
IPR001841Znf_RING
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
GO:0008270zinc ion binding