SMED30005369

Overview
NameSMED30005369
Smed IDSMED30005369
Length (bp)920
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 SMED30005369 (SMED30005369) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30005369 (SMED30005369) 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 SMED30005369 (SMED30005369) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30005369 (SMED30005369) 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.
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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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Alignments
SMED30005369 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.017983:14439..15358 -3252
Homology
BLAST of SMED30005369 vs. Ensembl Zebrafish
Match: CR392001.3 (pep chromosome:GRCz11:8:38963323:38965260:-1 gene:ENSDARG00000117159.1 transcript:ENSDART00000181495.1 gene_biotype:protein_coding transcript_biotype:protein_coding gene_symbol:CR392001.3)

HSP 1 Score: 40.0466 bits (92), Expect = 8.376e-9
Identity = 19/59 (32.20%), Postives = 34/59 (57.63%), Query Frame = 3
Query:  576 LKETFRYRFKDFRELKLTLKFIIKSL*ADVNK*KVSLLPSIDLAQFDLQLMDLKSKDLW 752
            ++  F  RF +FR+ K+TL F +  L  +++   +S  P I  A  ++++ D+  KDLW
Sbjct:  461 MQTAFESRFCEFRKEKMTLSFPVTPL--EIDPSLLSTFPGIIQADLEMEMADISDKDLW 517          

HSP 2 Score: 38.5058 bits (88), Expect = 8.376e-9
Identity = 17/54 (31.48%), Postives = 32/54 (59.26%), Query Frame = 2
Query:  758 KFINLNSEL*DLERKKN*LSSQHNW*QLQIVKNFDEIVFDRWNCLLE*YNQLKN 919
            KF  L +EL D+ R+K  L+  H W +++ +   +++++D WN L + Y  +K 
Sbjct:  520 KFKRLTAELEDVTRQKAQLAQSHKWSEMEGLPVPEKLIYDTWNALPDCYKNMKT 573          
BLAST of SMED30005369 vs. TrEMBL
Match: A0A4Y2TCQ2 (Uncharacterized protein OS=Araneus ventricosus OX=182803 GN=AVEN_218326_1 PE=4 SV=1)

HSP 1 Score: 51.9878 bits (123), Expect = 1.437e-8
Identity = 26/64 (40.62%), Postives = 40/64 (62.50%), Query Frame = 3
Query:  567 FKKLKETFRYRFKDFRELKLTLKFIIKSL*ADVNK*KVSLLP-SIDLAQFDLQLMDLKSKDLWT 755
             K +K+ F  RFK F+  K TL F++  L  + N+  +++ P  ID   F +QL+DLK+KDLW+
Sbjct:   74 LKNIKDGFAERFKQFKTNKSTLAFVVNPLNTNANE--INIEPFGIDAGSFQMQLLDLKTKDLWS 135          

HSP 2 Score: 36.5798 bits (83), Expect = 1.437e-8
Identity = 20/53 (37.74%), Postives = 31/53 (58.49%), Query Frame = 2
Query:  758 KFINLNSEL*DLERKKN*LSSQHNW*QLQIVKNFDEIVFDRWNCLLE*YNQLK 916
            KF  L S+L +LE +K    +QH W  L+ +   + + F  WN LLE Y+++K
Sbjct:  137 KFTELKSKLEELEAQKCMNIAQHKWTALKEIPRVEALKFGAWNSLLECYSEVK 189          
BLAST of SMED30005369 vs. TrEMBL
Match: A0A3B3HT75 (Uncharacterized protein OS=Oryzias latipes OX=8090 PE=4 SV=1)

HSP 1 Score: 45.4394 bits (106), Expect = 2.719e-7
Identity = 23/63 (36.51%), Postives = 34/63 (53.97%), Query Frame = 3
Query:  564 FFKKLKETFRYRFKDFRELKLTLKFIIKSL*ADVNK*KVSLLPSIDLAQFDLQLMDLKSKDLW 752
            F   L ++F+ RF +FRE     KFI       V+   +S +P + +  F+LQ  DLK+ DLW
Sbjct:  461 FTSNLLQSFKARFGEFRERTPLFKFITHPHECAVDITDLSYIPGVSVRDFELQAADLKASDLW 523          

HSP 2 Score: 38.5058 bits (88), Expect = 2.719e-7
Identity = 18/45 (40.00%), Postives = 30/45 (66.67%), Query Frame = 2
Query:  758 KFINLNSEL*DLERKKN*LSSQHNW*QLQIVKNFDEIVFDRWNCL 892
            KF +LN +L  LER+K  L+SQH W +++ ++  D+++   WN L
Sbjct:  526 KFKSLNEDLERLERQKAELASQHKWEEIKKLQPADQLILKTWNAL 570          
BLAST of SMED30005369 vs. TrEMBL
Match: A0A3B3HIM0 (Uncharacterized protein OS=Oryzias latipes OX=8090 PE=4 SV=1)

HSP 1 Score: 45.4394 bits (106), Expect = 2.805e-7
Identity = 23/63 (36.51%), Postives = 34/63 (53.97%), Query Frame = 3
Query:  564 FFKKLKETFRYRFKDFRELKLTLKFIIKSL*ADVNK*KVSLLPSIDLAQFDLQLMDLKSKDLW 752
            F   L ++F+ RF +FRE     KFI       V+   +S +P + +  F+LQ  DLK+ DLW
Sbjct:  488 FTSNLLQSFKARFGEFRERTPLFKFITHPHECAVDITDLSYIPGVSVRDFELQAADLKASDLW 550          

HSP 2 Score: 38.5058 bits (88), Expect = 2.805e-7
Identity = 18/45 (40.00%), Postives = 30/45 (66.67%), Query Frame = 2
Query:  758 KFINLNSEL*DLERKKN*LSSQHNW*QLQIVKNFDEIVFDRWNCL 892
            KF +LN +L  LER+K  L+SQH W +++ ++  D+++   WN L
Sbjct:  553 KFKSLNEDLERLERQKAELASQHKWEEIKKLQPADQLILKTWNAL 597          
BLAST of SMED30005369 vs. TrEMBL
Match: A0A4Y2RI40 (Uncharacterized protein OS=Araneus ventricosus OX=182803 GN=AVEN_138333_1 PE=4 SV=1)

HSP 1 Score: 46.595 bits (109), Expect = 3.218e-7
Identity = 25/63 (39.68%), Postives = 37/63 (58.73%), Query Frame = 3
Query:  567 FKKLKETFRYRFKDFRELKLTLKFIIKSL*ADVNK*KVSLLP-SIDLAQFDLQLMDLKSKDLW 752
             K +K+ F  RFK F+  K T  FI+  L  + N+  +++ P  ID     +QL+DLK+KDLW
Sbjct:   32 LKYMKDGFAERFKQFKTNKSTFAFIVNPLNTNTNE--INIEPFGIDAGSLQMQLLDLKTKDLW 92          

HSP 2 Score: 36.965 bits (84), Expect = 3.218e-7
Identity = 20/53 (37.74%), Postives = 31/53 (58.49%), Query Frame = 2
Query:  758 KFINLNSEL*DLERKKN*LSSQHNW*QLQIVKNFDEIVFDRWNCLLE*YNQLK 916
            KF  L S+L DLE +K    +QH W  L+ +   + ++F  WN L E Y+++K
Sbjct:   95 KFTELKSKLEDLEIQKCMHIAQHKWTALKEIPRVEALIFGAWNRLPECYSEVK 147          
BLAST of SMED30005369 vs. TrEMBL
Match: A0A4C1U683 (SCAN domain-containing protein 3 OS=Eumeta variegata OX=151549 GN=ZBED9 PE=4 SV=1)

HSP 1 Score: 50.447 bits (119), Expect = 3.276e-7
Identity = 25/63 (39.68%), Postives = 41/63 (65.08%), Query Frame = 3
Query:  570 KKLKETFRYRFKDFRELKLTLKFIIKSL*ADVNK*KVSLLP-SIDLAQFDLQLMDLKSKDLWT 755
            + +K+ F  RF+ F+ +K TL FI+  L  + N  ++ + P  +D A  ++QL+DLKSKDLW+
Sbjct:  247 QNIKDEFAGRFQQFKTIKTTLAFIVNPL--NTNSNEIHVEPFGVDTASLEMQLIDLKSKDLWS 307          

HSP 2 Score: 33.113 bits (74), Expect = 3.276e-7
Identity = 17/51 (33.33%), Postives = 29/51 (56.86%), Query Frame = 2
Query:  758 KFINLNSEL*DLERKKN*LSSQHNW*QLQIVKNFDEIVFDRWNCLLE*YNQ 910
            KF  L S+L +LE +K    +Q  W  L+ +   + ++FD WN L + Y++
Sbjct:  309 KFTELKSKLEELEVQKCMYVTQQKWTALKKMPRVEALIFDAWNSLPDCYSE 359          
BLAST of SMED30005369 vs. Ensembl Medaka
Match: ENSORLT00000028910.1 (pep primary_assembly:ASM223467v1:18:2548265:2550717:1 gene:ENSORLG00000029755.1 transcript:ENSORLT00000028910.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 45.4394 bits (106), Expect = 2.074e-10
Identity = 23/63 (36.51%), Postives = 34/63 (53.97%), Query Frame = 3
Query:  564 FFKKLKETFRYRFKDFRELKLTLKFIIKSL*ADVNK*KVSLLPSIDLAQFDLQLMDLKSKDLW 752
            F   L ++F+ RF +FRE     KFI       V+   +S +P + +  F+LQ  DLK+ DLW
Sbjct:  461 FTSNLLQSFKARFGEFRERTPLFKFITHPHECAVDITDLSYIPGVSVRDFELQAADLKASDLW 523          

HSP 2 Score: 38.5058 bits (88), Expect = 2.074e-10
Identity = 18/45 (40.00%), Postives = 30/45 (66.67%), Query Frame = 2
Query:  758 KFINLNSEL*DLERKKN*LSSQHNW*QLQIVKNFDEIVFDRWNCL 892
            KF +LN +L  LER+K  L+SQH W +++ ++  D+++   WN L
Sbjct:  526 KFKSLNEDLERLERQKAELASQHKWEEIKKLQPADQLILKTWNAL 570          
BLAST of SMED30005369 vs. Ensembl Medaka
Match: ENSORLT00000035623.1 (pep primary_assembly:ASM223467v1:9:5067000:5069708:1 gene:ENSORLG00000026230.1 transcript:ENSORLT00000035623.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 45.4394 bits (106), Expect = 2.140e-10
Identity = 23/63 (36.51%), Postives = 34/63 (53.97%), Query Frame = 3
Query:  564 FFKKLKETFRYRFKDFRELKLTLKFIIKSL*ADVNK*KVSLLPSIDLAQFDLQLMDLKSKDLW 752
            F   L ++F+ RF +FRE     KFI       V+   +S +P + +  F+LQ  DLK+ DLW
Sbjct:  488 FTSNLLQSFKARFGEFRERTPLFKFITHPHECAVDITDLSYIPGVSVRDFELQAADLKASDLW 550          

HSP 2 Score: 38.5058 bits (88), Expect = 2.140e-10
Identity = 18/45 (40.00%), Postives = 30/45 (66.67%), Query Frame = 2
Query:  758 KFINLNSEL*DLERKKN*LSSQHNW*QLQIVKNFDEIVFDRWNCL 892
            KF +LN +L  LER+K  L+SQH W +++ ++  D+++   WN L
Sbjct:  553 KFKSLNEDLERLERQKAELASQHKWEEIKKLQPADQLILKTWNAL 597          
BLAST of SMED30005369 vs. Ensembl Medaka
Match: ENSORLT00000038486.1 (pep primary_assembly:ASM223467v1:11:14048492:14066451:1 gene:ENSORLG00000022236.1 transcript:ENSORLT00000038486.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 43.5134 bits (101), Expect = 8.614e-8
Identity = 21/52 (40.38%), Postives = 28/52 (53.85%), Query Frame = 3
Query:  597 RFKDFRELKLTLKFIIKSL*ADVNK*KVSLLPSIDLAQFDLQLMDLKSKDLW 752
            RF +FRE     KFI       VN   +S +P + +  F+LQ  DLK+ DLW
Sbjct:  362 RFGEFRERTRLFKFITHPHECAVNSTDLSYIPGVSVRDFELQAADLKASDLW 413          

HSP 2 Score: 31.187 bits (69), Expect = 8.614e-8
Identity = 18/45 (40.00%), Postives = 28/45 (62.22%), Query Frame = 2
Query:  758 KFINLNSEL*DLERKKN*LSSQHNW*QLQIVKNFDEIVFDRWNCL 892
            KF ++N +L  LER+K  L+SQH W   + +K  D+++   WN L
Sbjct:  416 KFKSMNEDLERLERQKAELASQHKWCYEEWLK--DQLILKTWNAL 458          
BLAST of SMED30005369 vs. Ensembl Medaka
Match: ENSORLT00000046478.1 (pep primary_assembly:ASM223467v1:19:14509913:14511832:1 gene:ENSORLG00000025829.1 transcript:ENSORLT00000046478.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 41.9726 bits (97), Expect = 9.290e-6
Identity = 19/63 (30.16%), Postives = 32/63 (50.79%), Query Frame = 3
Query:  564 FFKKLKETFRYRFKDFRELKLTLKFIIKSL*ADVNK*KVSLLPSIDLAQFDLQLMDLKSKDLW 752
            F   L ++F+ RF  F E     KFI  +     +   +  +P + +  F+L+ +DLK+ DLW
Sbjct:  267 FISNLPQSFKARFGQFCECTRLFKFITHTHECAADSTDLRYIPGVSVRDFELEAVDLKASDLW 329          

HSP 2 Score: 26.1794 bits (56), Expect = 9.290e-6
Identity = 13/29 (44.83%), Postives = 21/29 (72.41%), Query Frame = 2
Query:  758 KFINLNSEL*DLERKKN*LSSQHNW*QLQ 844
            +F +LN +L  LER++  L+SQH W +L+
Sbjct:  332 EFKSLNEDLERLERQQAELASQHKWEELK 360          
The following BLAST results are available for this feature:
BLAST of SMED30005369 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 SMED30005369 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 SMED30005369 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 SMED30005369 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
CR392001.38.376e-932.20pep chromosome:GRCz11:8:38963323:38965260:-1 gene:... [more]
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BLAST of SMED30005369 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 SMED30005369 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 SMED30005369 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 SMED30005369 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4Y2TCQ21.437e-840.63Uncharacterized protein OS=Araneus ventricosus OX=... [more]
A0A3B3HT752.719e-736.51Uncharacterized protein OS=Oryzias latipes OX=8090... [more]
A0A3B3HIM02.805e-736.51Uncharacterized protein OS=Oryzias latipes OX=8090... [more]
A0A4Y2RI403.218e-739.68Uncharacterized protein OS=Araneus ventricosus OX=... [more]
A0A4C1U6833.276e-739.68SCAN domain-containing protein 3 OS=Eumeta variega... [more]
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BLAST of SMED30005369 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 SMED30005369 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 SMED30005369 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 SMED30005369 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 SMED30005369 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 4
Match NameE-valueIdentityDescription
ENSORLT00000028910.12.074e-1036.51pep primary_assembly:ASM223467v1:18:2548265:255071... [more]
ENSORLT00000035623.12.140e-1036.51pep primary_assembly:ASM223467v1:9:5067000:5069708... [more]
ENSORLT00000038486.18.614e-840.38pep primary_assembly:ASM223467v1:11:14048492:14066... [more]
ENSORLT00000046478.19.290e-630.16pep primary_assembly:ASM223467v1:19:14509913:14511... [more]
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BLAST of SMED30005369 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005369 ID=SMED30005369|Name=SMED30005369|organism=Schmidtea mediterranea sexual|type=transcript|length=920bp
AAATTAATTTATTTTTATGATAATATTGAAAATTGAGGGATTTTTTTCCT
TTTCTGTTTTTATTGAGATCTTGTCATTAAAATAATTATCAAATATCACG
TGAGAATTTCGGATGAATTTTGTCAGAAATTTTCGAAAATTGCTGTATTT
TATATGATTATTATAAACGATAGTGATAATTAAATATTTTTACCGGATGC
TGGAAACTGGATATCAATGATTGATGGCAAAATGACAAGTTCAAATAGAG
AATCAAAATAAAAAAATAGAGGCTTTTAATTAAAAAATAGTGATTGAAAA
GATTTGAATTTAACGTTTAAAAAAATAATGATCTTATAAAATGTTTTAAA
AAGAAAATATAATAATGAGTTAAATTTATCAACTTATTTTATTATCGGAT
AATATAAACAAGTTAGGGGTTGGCAACCTGCGGCTCTGTACATTATTAAA
CTTATTTTAAAAATACATTTTTAACTCGAATCCCGAGATAATTTCCATTT
TTTACAGAAAATATTAAGAAGAATATAACAGTTCATCGATGTCGATTTTT
TTCCAAGAGGCATTTTTTTAAGAAACTTAAAGAAACATTCCGATATCGAT
TCAAAGACTTTAGAGAGCTCAAATTAACTTTAAAATTTATAATAAAATCT
CTTTAAGCTGATGTAAATAAGTAAAAAGTTTCATTATTACCATCAATCGA
TTTAGCTCAATTCGATTTACAGTTAATGGATTTAAAATCTAAGGATTTGT
GGACTATAAATTCATCAATCTTAATAGTGAATTATAAGATCTCGAAAGAA
AAAAAAACTAATTGTCTTCACAACATAATTGGTAACAATTACAAATTGTA
AAGAATTTTGACGAAATTGTGTTTGATAGATGGAATTGTCTCCTAGAGTA
GTATAACCAATTAAAAAATA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0002089reproductive organ