SMED30022928

Overview
NameSMED30022928
Smed IDSMED30022928
Length (bp)1457
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 SMED30022928 (SMED30022928) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30022928 (SMED30022928) 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




SMED30022928

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30022928SMESG000000986.1 SMESG000000983.1 SmedASXL_015862SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30022928SMESG000000986.1 SMESG000000983.1 dd_Smed_v4_26967_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30022928SMESG000000986.1 SMESG000000983.1 dd_Smed_v4_26967_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30022928SMESG000000986.1 SMESG000000983.1 dd_Smed_v4_26967_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30022928SMESG000000986.1 SMESG000000983.1 dd_Smed_v4_26967_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30022928 dd_Smed_v6_64626_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30022928SMESG000000986.1 SMESG000000983.1 OX_Smed_1.0.10180ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30022928 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.011766:17842..19252 -6186
Homology
BLAST of SMED30022928 vs. Ensembl Xenopus
Match: acsl1 (acyl-CoA synthetase long chain family member 1 protein [Source:Xenbase;Acc:XB-GENE-5739727])

HSP 1 Score: 53.1434 bits (126), Expect = 1.197e-6
Identity = 22/39 (56.41%), Postives = 24/39 (61.54%), Query Frame = -1
Query:  735 LPYPDYPEKVFFFLNQTHHPRDWCLKFISWPYPFIKLLI 851
            LPYP     VFFFL Q   PR WCLK +  PYPF  L+I
Sbjct:   23 LPYPTLAPVVFFFLTQESRPRSWCLKMVCNPYPFYMLVI 61          
BLAST of SMED30022928 vs. Ensembl Xenopus
Match: acsl1 (acyl-CoA synthetase long chain family member 1 protein [Source:Xenbase;Acc:XB-GENE-5739727])

HSP 1 Score: 52.373 bits (124), Expect = 1.664e-6
Identity = 22/39 (56.41%), Postives = 24/39 (61.54%), Query Frame = -1
Query:  735 LPYPDYPEKVFFFLNQTHHPRDWCLKFISWPYPFIKLLI 851
            LPYP     VFFFL Q   PR WCLK +  PYPF  L+I
Sbjct:   21 LPYPTLAPVVFFFLTQESRPRSWCLKMVCNPYPFYMLVI 59          
BLAST of SMED30022928 vs. Ensembl Xenopus
Match: acsl1 (acyl-CoA synthetase long chain family member 1 protein [Source:Xenbase;Acc:XB-GENE-5739727])

HSP 1 Score: 52.373 bits (124), Expect = 1.874e-6
Identity = 22/39 (56.41%), Postives = 24/39 (61.54%), Query Frame = -1
Query:  735 LPYPDYPEKVFFFLNQTHHPRDWCLKFISWPYPFIKLLI 851
            LPYP     VFFFL Q   PR WCLK +  PYPF  L+I
Sbjct:   21 LPYPTLAPVVFFFLTQESRPRSWCLKMVCNPYPFYMLVI 59          
BLAST of SMED30022928 vs. Ensembl Xenopus
Match: acsl1 (acyl-CoA synthetase long chain family member 1 protein [Source:Xenbase;Acc:XB-GENE-5739727])

HSP 1 Score: 52.373 bits (124), Expect = 1.876e-6
Identity = 22/39 (56.41%), Postives = 24/39 (61.54%), Query Frame = -1
Query:  735 LPYPDYPEKVFFFLNQTHHPRDWCLKFISWPYPFIKLLI 851
            LPYP     VFFFL Q   PR WCLK +  PYPF  L+I
Sbjct:   56 LPYPTLAPVVFFFLTQESRPRSWCLKMVCNPYPFYMLVI 94          
BLAST of SMED30022928 vs. Ensembl Xenopus
Match: acsl1 (acyl-CoA synthetase long chain family member 1 protein [Source:Xenbase;Acc:XB-GENE-5739727])

HSP 1 Score: 52.373 bits (124), Expect = 2.046e-6
Identity = 22/39 (56.41%), Postives = 24/39 (61.54%), Query Frame = -1
Query:  735 LPYPDYPEKVFFFLNQTHHPRDWCLKFISWPYPFIKLLI 851
            LPYP     VFFFL Q   PR WCLK +  PYPF  L+I
Sbjct:   56 LPYPTLAPVVFFFLTQESRPRSWCLKMVCNPYPFYMLVI 94          
BLAST of SMED30022928 vs. TrEMBL
Match: A0A3Q1BFZ0 (Uncharacterized protein OS=Amphiprion ocellaris OX=80972 PE=4 SV=1)

HSP 1 Score: 57.7658 bits (138), Expect = 2.842e-6
Identity = 26/44 (59.09%), Postives = 31/44 (70.45%), Query Frame = -1
Query:  726 LPYPDYPEKVFFFLNQTHHPRDWCLKFISWPYPFI--KLLIRIF 851
            LPYP++   VFF+L QT  PR WCLK +S PYPFI   LL+R F
Sbjct:   73 LPYPEWAPVVFFYLKQTTRPRSWCLKMVSNPYPFIPRSLLMRTF 116          
BLAST of SMED30022928 vs. Ensembl Cavefish
Match: cacna1ib (calcium voltage-gated channel subunit alpha1 Ib [Source:ZFIN;Acc:ZDB-GENE-120215-18])

HSP 1 Score: 49.6766 bits (117), Expect = 8.021e-6
Identity = 27/61 (44.26%), Postives = 38/61 (62.30%), Query Frame = -1
Query:  672 VLPYPDYPEKVFFFLNQTHHPRDWCLKFISWPYPFIKLLIRIFN*PRL*SLVVFIISGITL 854
            V+PYP+    VFF L QT  PR WC++ +S PYP   LL   F   R+ S++V I++ +TL
Sbjct:   53 VVPYPELAPVVFFCLKQTTFPRSWCIRLVSSPYP---LLFTWFE--RV-SMMVIILNCVTL 107          
BLAST of SMED30022928 vs. Planmine SMEST
Match: SMESG000068737.1 (SMESG000068737.1)

HSP 1 Score: 57.3806 bits (137), Expect = 3.768e-19
Identity = 40/111 (36.04%), Postives = 57/111 (51.35%), Query Frame = 2
Query:  263 KELITEYEIEAEILYMPIIENKSDAFNR------------RTQYDFNE-----------FSLFREDRLRFIVIEARITISEQELREVIKKYGKYKS-----VQTDKGQVNV 511
            KELIT+YEI+ EI Y+P  +NKSD   R                DF E            S F  DRL+F++ E+ I +S+ EL+E+++K  K +S     V+  KGQ+ V
Sbjct:  254 KELITKYEIKVEIEYVPTNKNKSDVLTRIPSNWITKHSCNMALIDFGEDSIKNATEIHKLSHFGGDRLKFLIEESVINLSQNELKEIVEKCDKCQSIDPHPVKISKGQLEV 364          

HSP 2 Score: 56.9954 bits (136), Expect = 3.768e-19
Identity = 38/101 (37.62%), Postives = 52/101 (51.49%), Query Frame = 3
Query:    9 IIWYGASSFELGVALKIDRKMIEDVFYLSEEKVVSHINICELEGFVG---------------LSDN*FLVSRVYSA*IA**KISIKASPEISVKRKLIIIK 266
            I+W  ASS  +G AL+ID  ++ED  +L +EK + HIN+CELE  V                +SDN  +             I+ KAS E+ VKR+L IIK
Sbjct:  167 ILWCDASSIAIGAALEIDENIMEDACWLRKEKDIRHINLCELEAIVKGINLCIKWNLKFVKIMSDNKSV-------------ITTKASSEMLVKRRLSIIK 254          
BLAST of SMED30022928 vs. Planmine SMEST
Match: SMESG000020160.1 (SMESG000020160.1)

HSP 1 Score: 61.2326 bits (147), Expect = 4.237e-18
Identity = 39/109 (35.78%), Postives = 58/109 (53.21%), Query Frame = 2
Query:  263 KELITEYEIEAEILYMPIIENKSDAFNR-----------------------RTQYDFNEFSLFREDRLRFIVIEARITISEQELREVIKKYGKYKS-----VQTDKGQV 505
            KELITEYEI+AEI Y+P  +NKSD   R                       +   + ++ S F  DRL F++ E+ I++S+ EL+E++KK  K +S     V+  KGQ+
Sbjct:  410 KELITEYEIKAEIEYVPTNKNKSDVLTRIPSNWITKHSCNIALLDFCEDPIKNPTEIHKLSHFGGDRLNFLIEESGISLSQNELKEIVKKCDKCQSIDPHPVKISKGQL 518          

HSP 2 Score: 49.2914 bits (116), Expect = 4.237e-18
Identity = 35/87 (40.23%), Postives = 50/87 (57.47%), Query Frame = 3
Query:    9 IIWYGASSFELGVALKIDRKMIEDVFYLSEEKVVSHINICELEGFVG-LSDN*FLVSRVYSA*IA**KISIKASPEISVKRKLIIIK 266
            I+W  ASS  +G AL+ID  ++ED  +L ++K            FV  +SDN  +VS V++      KI+ KAS E+ VKR+L IIK
Sbjct:  335 ILWCDASSIAIGAALEIDENIMEDACWLRKKK-----------NFVKIMSDNKSVVSWVHNVLTCERKITTKASSEMLVKRRLSIIK 410          
BLAST of SMED30022928 vs. Planmine SMEST
Match: SMESG000028308.1 (SMESG000028308.1)

HSP 1 Score: 68.1662 bits (165), Expect = 2.643e-17
Identity = 40/89 (44.94%), Postives = 60/89 (67.42%), Query Frame = 3
Query:    9 IIWYGASSFELGVALKIDRKMIEDVFYLSEEKVVSHINICELEGFVGLSDN---*FLVSRVYSA*IA**KISIKASPEISVKRKLIIIK 266
            I+W  ASS  +G AL+IDR ++ED  +L +EK V HIN+CELE  +   +N    + ++ V++A  +  KI++KAS E+ VKR+L IIK
Sbjct:   76 ILWCDASSIAIGAALEIDRNIMEDACWLRKEKDVRHINLCELEALIK-GNNLCIKWNLNWVHNALTSERKITMKASSEMLVKRRLSIIK 163          

HSP 2 Score: 39.6614 bits (91), Expect = 2.643e-17
Identity = 19/28 (67.86%), Postives = 22/28 (78.57%), Query Frame = 2
Query:  263 KELITEYEIEAEILYMPIIENKSDAFNR 346
            KELITEYEI+AEI Y+P  +NKSD   R
Sbjct:  163 KELITEYEIKAEIEYVPTNKNKSDVLTR 190          
BLAST of SMED30022928 vs. Planmine SMEST
Match: SMESG000012165.1 (SMESG000012165.1)

HSP 1 Score: 69.707 bits (169), Expect = 5.611e-13
Identity = 45/112 (40.18%), Postives = 65/112 (58.04%), Query Frame = 3
Query:    9 IIWYGASSFELGVALKIDRKMIEDVFYLSEEKVVSHINICELEGFVG---------------LSDN*FLVSRVYSA*IA**KISIKASPEISVKRKLIIIKN*LQNTK*KPK 299
            I+W  ASS  +G AL+ID  ++ED  +L +EK V HIN+CELE  V                +SDN  +VS V+++  +  KI++KAS E+ VKR+  IIK  +   + KPK
Sbjct:  190 ILWCDASSIAIGAALEIDGNIMEDACWLRKEKDVRHINLCELEAIVKGINLCIKWNLKFVKIMSDNKSVVSWVHNSLTSERKITMKASSEMLVKRRFSIIKELITEYEIKPK 301          
BLAST of SMED30022928 vs. Planmine SMEST
Match: SMESG000059416.1 (SMESG000059416.1)

HSP 1 Score: 67.781 bits (164), Expect = 4.410e-12
Identity = 45/101 (44.55%), Postives = 60/101 (59.41%), Query Frame = 3
Query:    9 IIWYGASSFELGVALKIDRKMIEDVFYLSEEKVVSHINICELEGFVG---------------LSDN*FLVSRVYSA*IA**KISIKASPEISVKRKLIIIK 266
            I W  ASS  +G AL+ID  ++ED  +L +EK V HIN+CELE  V                +SDN  +VS V++A I+  KI+ KAS E+ VKR+L IIK
Sbjct:  200 ISWCDASSIVIGAALEIDGNIMEDTSWLRKEKDVRHINLCELEAIVKGINLFIKWNLKFVKIMSDNKSVVSWVHNALISERKITTKASSEMLVKRRLSIIK 300          
The following BLAST results are available for this feature:
BLAST of SMED30022928 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 SMED30022928 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 SMED30022928 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 SMED30022928 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 SMED30022928 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 5
Match NameE-valueIdentityDescription
acsl11.197e-656.41acyl-CoA synthetase long chain family member 1 pro... [more]
acsl11.664e-656.41acyl-CoA synthetase long chain family member 1 pro... [more]
acsl11.874e-656.41acyl-CoA synthetase long chain family member 1 pro... [more]
acsl11.876e-656.41acyl-CoA synthetase long chain family member 1 pro... [more]
acsl12.046e-656.41acyl-CoA synthetase long chain family member 1 pro... [more]
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BLAST of SMED30022928 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 SMED30022928 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 SMED30022928 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A3Q1BFZ02.842e-659.09Uncharacterized protein OS=Amphiprion ocellaris OX... [more]
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BLAST of SMED30022928 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
cacna1ib8.021e-644.26calcium voltage-gated channel subunit alpha1 Ib [S... [more]
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BLAST of SMED30022928 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 SMED30022928 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 SMED30022928 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 SMED30022928 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 SMED30022928 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000068737.13.768e-1936.04SMESG000068737.1[more]
SMESG000020160.14.237e-1835.78SMESG000020160.1[more]
SMESG000028308.12.643e-1744.94SMESG000028308.1[more]
SMESG000012165.15.611e-1340.18SMESG000012165.1[more]
SMESG000059416.14.410e-1244.55SMESG000059416.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022928 ID=SMED30022928|Name=SMED30022928|organism=Schmidtea mediterranea sexual|type=transcript|length=1457bp
AATGCAAAATAATATGGTACGGTGCTAGCTCGTTTGAACTAGGAGTAGCA
TTAAAAATAGACAGGAAAATGATAGAGGATGTATTTTACTTAAGTGAAGA
AAAGGTTGTCAGTCATATAAATATATGTGAATTAGAAGGTTTCGTTGGTC
TTTCAGATAACTAATTTCTAGTCAGTCGGGTTTACAGTGCGTAAATAGCT
TAATGAAAGATCTCAATCAAAGCTTCACCAGAAATTTCGGTGAAAAGAAA
ATTGATCATCATAAAGAATTAATTACAGAATACGAAATAGAAGCCGAAAT
ATTGTATATGCCAATAATCGAAAACAAATCAGACGCGTTCAATAGACGAA
CTCAGTACGATTTTAACGAATTTAGTTTATTTAGGGAAGATCGACTGAGA
TTCATAGTTATAGAAGCAAGGATTACCATTTCTGAGCAGGAGTTACGAGA
AGTTATAAAGAAATATGGTAAATATAAATCAGTACAAACAGATAAGGGAC
AGGTAAATGTAAATATTAGGCTTTGGTTTGACAAAAAGTTAATTAAAAAG
AACATTGAAACCGCTGAATTCCGAGAGATTGTAAAGGATTATCTTATAAT
CGGAAATTGTCTCATTTAATTTTATATATTTTATTAAATTGTCATTTATT
AACTTGCCTGACTATTATTAATAAAGTAATTCCTGAAATTATAAATACGA
CCAAACTTTATAACCTGGGTTAATTAAATATCCGAATCAATAATTTGATA
AAAGGATATGGCCAAGAAATAAATTTTAAACACCAATCCCGTGGATGGTG
AGTTTGATTAAGGAAGAAGAATACTTTTTCTGGGTAGTCCGGATATGGAA
GCACTGGAATCTACCATGTACGACGACCTATCCAAATCATTGTTAAAATA
TAATCCACTGGGTTCGTTTGATGTACGCATTCGACTGCAAATTGATGATT
GATCATTGTAATCAGAAGTTCTCATAACAGTTTTCATTCAATGACCTATT
GAGACCTGTGTCTGATGATCGAGATTTGTTGAGGAAAGAGTCGTCGGGAG
TCAGTAAATATTCCATATTGACATAATATCTTTCAAATTCAGTTTGTTTT
ACACTATGTTCATGGTATTGTAAAGATATTTGACTTTTGAGAGGCACTGT
CCCGCAGTAGAATGCTATTTTTCATCATATTTTCATGTGTGATACATCAT
TTTAATACGCCAATCAAATTTAAGAAATCTCATAAAAAACCTTCCGTGTT
ACATTAATCCCTTGCTTGTATGTGTGTTTCTGAATACTAATAGAATTGTT
TAAAATATTGCAAGAGATTAAATTTATTTCTTTTGTATTTCGAATTTTAT
TAGAATCCATGGTAATAAAATTATTAATGAATTTAAAATTACATATTCAC
TAAATGTTTAGATGAAATTTTAAAATTTTAAGCGTTTTGAAACATTCATA
TGTTGGG
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protein sequence of SMED30022928-orf-1

>SMED30022928-orf-1 ID=SMED30022928-orf-1|Name=SMED30022928-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=139bp
MKDLNQSFTRNFGEKKIDHHKELITEYEIEAEILYMPIIENKSDAFNRRT
QYDFNEFSLFREDRLRFIVIEARITISEQELREVIKKYGKYKSVQTDKGQ
VNVNIRLWFDKKLIKKNIETAEFREIVKDYLIIGNCLI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
PLANA:0000420parapharyngeal region