SMED30005650

Overview
NameSMED30005650
Smed IDSMED30005650
Length (bp)2198
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 SMED30005650 (SMED30005650) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30005650 (SMED30005650) 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 SMED30005650 (SMED30005650) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30005650 (SMED30005650) 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




SMED30005650

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X2 cellSMED30005650 SmedASXL_070989SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30005650 SmedASXL_059487SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30005650 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000712:36918..39211 -10689
v31.001950:61252..63404 +8530
v31.002640:27493..29812 -8475
v31.003270:52890..61619 -7101
v31.001100:24271..26376 -6521
Homology
BLAST of SMED30005650 vs. Planmine SMEST
Match: SMESG000010307.1 (SMESG000010307.1)

HSP 1 Score: 110.923 bits (276), Expect = 2.339e-26
Identity = 97/254 (38.19%), Postives = 128/254 (50.39%), Query Frame = -1
Query:   90 HSRYHLFNILNATSNRTSKNGDMDHHGRNQMEENR----DFN-QRDHAQESDSTRINWIKGSHTTLKIPHRFVGRYRQAL*DR*YSLYTYGSREWPYQNSSQ-DEDVEMPSLTMKRTEXXXXXXXXXXGYVAKIIASRKEIPVEG----------KPSTQTTG*NKLQHRKRLH-----------PSSDGYVPEYGMAFXXXXXXXXXXXDPVYLAIQMQIVQPDILEIPSDRTSEEHACSRRPLIRKSTKQKF 770
             SR   ++I    SN   + GD   + R  M  NR    D N Q      S ++   W     TTL IP +F GRYRQAL D  YSL TYG+ EWP ++  + DEDVE+PSL +KR    +          A+ I    E+ ++           K S Q         RKRL             SSDGY+P+Y +AF+ +D ALL L  PV++A+   I+Q DILE   DRTSEEHA S+RPL R+  ++KF
Sbjct:    4 QSRTKNYDINVHESNLRKEEGDYSANIRPSM--NRMIKCDINFQESEGYPSGNSGTQWKDDERTTLIIPSKFAGRYRQALWDGVYSLSTYGTSEWPNRSRIRHDEDVELPSLAIKREPGRN---------TARKIRHEAEVALQQFDHLERKYRWKASLQ---------RKRLMRINKDIASGRISSSDGYLPDYNIAFDPEDPALLELSAPVHMALPKHIMQRDILEALDDRTSEEHAYSQRPLKREMPRRKF 237          

HSP 2 Score: 75.0998 bits (183), Expect = 2.857e-14
Identity = 35/58 (60.34%), Postives = 44/58 (75.86%), Query Frame = -2
Query:  269 GRNPAREIRHETEVMLRKLLHLERKFRWKANLQRRRLARINSNIASGCIPAPMATFPN 442
            GRN AR+IRHE EV L++  HLERK+RWKA+LQR+RL RIN +IASG I +     P+
Sbjct:  120 GRNTARKIRHEAEVALQQFDHLERKYRWKASLQRKRLMRINKDIASGRISSSDGYLPD 177          
BLAST of SMED30005650 vs. Planmine SMEST
Match: SMESG000059844.1 (SMESG000059844.1)

HSP 1 Score: 112.079 bits (279), Expect = 4.140e-26
Identity = 81/212 (38.21%), Postives = 122/212 (57.55%), Query Frame = -1
Query:   75 ENRDFNQRDHAQESDST-RINWIKGSHTTLKIPHRFVGRYRQAL*DR*YSLYTYGSREWPYQNSSQ-DEDVEMPSLTMKRTEXXXXXXXXXXGYVAKIIASRKEIPVEGKPSTQTTG*NKLQHRKRLH----------PSSDGYVPEYGMAFXXXXXXXXXXXDPVYLAIQMQIVQPDILEIPSDRTSEEHACSRRPLIRKSTKQKF*NEFT 674
            E RD  +  + Q+ D     +W++    TL IP +F GRYRQAL D  YSL T+G+ EWPY+N ++ DED+E+ SL +KR    +             +A ++ + +E K   + +    LQ R+ +           PSSDGY+ EY + FN +D A L L+ PV+LA+  +++QPDILE  +DRT EEHA SRRPL R++  + + ++ T
Sbjct:   28 EKRDSYRLANGQQDDGNPSTHWMENDQNTLTIPSKFAGRYRQALWDPRYSLSTHGTSEWPYRNKNRHDEDMELLSLAIKREPGRNPAREIRHEAE---VALQQFVHLERKYHWKAS----LQLRRLVKINKDIAGGRIPSSDGYLLEYNVTFNPEDPAFLELNTPVHLALPKRLLQPDILEALTDRTYEEHAYSRRPLNREAPPRNYGHKIT 232          

HSP 2 Score: 75.485 bits (184), Expect = 3.572e-14
Identity = 34/51 (66.67%), Postives = 42/51 (82.35%), Query Frame = -2
Query:  290 GRNPAREIRHETEVMLRKLLHLERKFRWKANLQRRRLARINSNIASGCIPA 442
            GRNPAREIRHE EV L++ +HLERK+ WKA+LQ RRL +IN +IA G IP+
Sbjct:  110 GRNPAREIRHEAEVALQQFVHLERKYHWKASLQLRRLVKINKDIAGGRIPS 160          
BLAST of SMED30005650 vs. Planmine SMEST
Match: SMESG000010307.1 (SMESG000010307.1)

HSP 1 Score: 109.768 bits (273), Expect = 6.409e-26
Identity = 82/197 (41.62%), Postives = 107/197 (54.31%), Query Frame = -1
Query:   90 WIKGSHTTLKIPHRFVGRYRQAL*DR*YSLYTYGSREWPYQNSSQ-DEDVEMPSLTMKRTEXXXXXXXXXXGYVAKIIASRKEIPVEG----------KPSTQTTG*NKLQHRKRLH-----------PSSDGYVPEYGMAFXXXXXXXXXXXDPVYLAIQMQIVQPDILEIPSDRTSEEHACSRRPLIRKSTKQKF 614
            W     TTL IP +F GRYRQAL D  YSL TYG+ EWP ++  + DEDVE+PSL +KR    +          A+ I    E+ ++           K S Q         RKRL             SSDGY+P+Y +AF+ +D ALL L  PV++A+   I+Q DILE   DRTSEEHA S+RPL R+  ++KF
Sbjct:   61 WKDDERTTLIIPSKFAGRYRQALWDGVYSLSTYGTSEWPNRSRIRHDEDVELPSLAIKREPGRN---------TARKIRHEAEVALQQFDHLERKYRWKASLQ---------RKRLMRINKDIASGRISSSDGYLPDYNIAFDPEDPALLELSAPVHMALPKHIMQRDILEALDDRTSEEHAYSQRPLKREMPRRKF 239          

HSP 2 Score: 74.7146 bits (182), Expect = 3.141e-14
Identity = 35/58 (60.34%), Postives = 44/58 (75.86%), Query Frame = -2
Query:  269 GRNPAREIRHETEVMLRKLLHLERKFRWKANLQRRRLARINSNIASGCIPAPMATFPN 442
            GRN AR+IRHE EV L++  HLERK+RWKA+LQR+RL RIN +IASG I +     P+
Sbjct:  122 GRNTARKIRHEAEVALQQFDHLERKYRWKASLQRKRLMRINKDIASGRISSSDGYLPD 179          
BLAST of SMED30005650 vs. Planmine SMEST
Match: SMESG000050791.1 (SMESG000050791.1)

HSP 1 Score: 99.7525 bits (247), Expect = 2.931e-24
Identity = 79/148 (53.38%), Postives = 102/148 (68.92%), Query Frame = -1
Query:   72 SQDEDVEMPSLTMKRTEXXXXXXXXXXGYVAKIIASRKEIPVEGKPSTQTTG*NKLQHRK--RLH--------PSSDGYVPEYGMAFXXXXXXXXXXXDPVYLAIQMQIVQPDILEIPSDRTSEEHACSRRPLIRKSTKQKF*NEFTK 485
            SQDE+VE+PSL++KR     R+ + +  + A+++  + E  +E K   +      LQ R+  R++        PSSDGYVP+YGM FN DD ALLNLD PV+LAI  QIVQPDIL+I SDRTSE+HA SR PLIRKSTKQK+ N+FTK
Sbjct:    5 SQDEEVEIPSLSIKRE--PGRNPAREIRHEAEVMLQQFE-HLEMKFRWKAN----LQRRRLARINSDIVNGRIPSSDGYVPKYGMVFNPDDPALLNLDAPVHLAIPKQIVQPDILKILSDRTSEKHAYSRCPLIRKSTKQKYGNKFTK 145          

HSP 2 Score: 86.2705 bits (212), Expect = 1.484e-19
Identity = 41/57 (71.93%), Postives = 46/57 (80.70%), Query Frame = -2
Query:  272 GRNPAREIRHETEVMLRKLLHLERKFRWKANLQRRRLARINSNIASGCIPAPMATFP 442
            GRNPAREIRHE EVML++  HLE KFRWKANLQRRRLARINS+I +G IP+     P
Sbjct:   22 GRNPAREIRHEAEVMLQQFEHLEMKFRWKANLQRRRLARINSDIVNGRIPSSDGYVP 78          
BLAST of SMED30005650 vs. Planmine SMEST
Match: SMESG000047667.1 (SMESG000047667.1)

HSP 1 Score: 100.523 bits (249), Expect = 2.237e-21
Identity = 74/205 (36.10%), Postives = 113/205 (55.12%), Query Frame = -1
Query:  108 HHGRNQMEENRDFNQRDHAQESDSTRINWIKGSHTTLKIPHRFVGRYRQAL*DR*YSLYTYGSREWPYQNSS-QDEDVEMPSLTMKR-----TEXXXXXXXXXXGYVAKIIAS--RKEIPVEGKPSTQTTG*NKLQHRKRLHPSSDGYVPEYGMAFXXXXXXXXXXXDPVYLAIQMQIVQPDILEIPSDRTSEEHACSRRPLIRK 698
            H  R   +++R+FN    + +             TTL +P +F GRYRQAL DR YS+ TYG+ EWP +N   +DED+++PSL +KR          R  S +  Y  + +    R+    +G+   + T    +       P SDGY+P+YG+A++  + ALL LD PVYL +  +++QPDI +  +D+ +EEHA S R L+RK
Sbjct: 1545 HGSRKTYDQHRNFNNGSSSSKCRDV-------ERTTLTVPSKFAGRYRQALWDRGYSISTYGTPEWPNRNPDRRDEDIKLPSLVIKREPGRNPAREIRQESEEALYKLEQLERRYRRLANQQGRRLVKIT----MDISSGRIPISDGYLPDYGVAYDPKNPALLALDAPVYLVVPKRLLQPDIRDALNDKGNEEHAYSCRHLMRK 1738          

HSP 2 Score: 58.9214 bits (141), Expect = 1.433e-8
Identity = 31/58 (53.45%), Postives = 38/58 (65.52%), Query Frame = -2
Query:  269 GRNPAREIRHETEVMLRKLLHLERKFRWKANLQRRRLARINSNIASGCIPAPMATFPN 442
            GRNPAREIR E+E  L KL  LER++R  AN Q RRL +I  +I+SG IP      P+
Sbjct: 1627 GRNPAREIRQESEEALYKLEQLERRYRRLANQQGRRLVKITMDISSGRIPISDGYLPD 1684          
The following BLAST results are available for this feature:
BLAST of SMED30005650 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 SMED30005650 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 SMED30005650 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 SMED30005650 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 SMED30005650 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 SMED30005650 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 SMED30005650 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 SMED30005650 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 SMED30005650 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 SMED30005650 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 SMED30005650 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 SMED30005650 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 SMED30005650 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 SMED30005650 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000010307.12.339e-2638.19SMESG000010307.1[more]
SMESG000059844.14.140e-2638.21SMESG000059844.1[more]
SMESG000010307.16.409e-2641.62SMESG000010307.1[more]
SMESG000050791.12.931e-2453.38SMESG000050791.1[more]
SMESG000047667.12.237e-2136.10SMESG000047667.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005650 ID=SMED30005650|Name=SMED30005650|organism=Schmidtea mediterranea sexual|type=transcript|length=2198bp
TTTTTTTTTTTTTTTTCCAATAGAGAAACATTATTTTAAATATTACAGGC
ATACATTTATACACACATCTATTTCGTGAATTCGTTTCAGAATTTCTGTT
TGGTAGATTTTCGTATCAGCGGACGCCGAGAACAAGCGTGTTCTTCACTT
GTCCGATCTGACGGAATTTCCAAGATATCAGGTTGTACTATCTGCATTTG
AATAGCCAAGTACACAGGATCATCAAGATTCAGGAGGGCCAGATCGTCTA
GATTGAATGCCATGCCATATTCGGGAACGTAGCCATCGGAGCTGGGATGC
AGCCGCTTGCGATGTTGGAGTTTATTCTAGCCAGTCGTCTGCGTTGAAGG
TTTGCCTTCCACCGGAATTTCCTTTCGAGATGCAATAATTTTCGCAACAT
AACCTCGGTCTCATGACGAATCTCTCGAGCCGGATTCCGTCCTTTTCATT
GTGAGGCTGGGCATTTCCACGTCTTCGTCTTGGCTCGAATTCTGGTAGGG
CCATTCCCGACTACCGTATGTATATAGAGAGTATCACCGATCCTATAGAG
CCTGTCTATATCGTCCTACGAATCGGTGGGGAATTTTCAAGGTCGTATGT
GATCCTTTTATCCAGTTGATTCGAGTAGAGTCGGATTCTTGCGCATGATC
TCTCTGGTTGAAATCTCGATTTTCCTCCATTTGGTTTCTTCCGTGGTGGT
CCATATCTCCATTCTTTGACGTTCGGTTACTGGTTGCATTTAGTATGTTG
AATAAGTGATACCGGCTATGTGGTACTGGTACGTATTTATATTGATCAGC
GGGTTGTGTTGACTACGAGCGCTCAGCTATCACTCGAGAATTATATTTGC
GATTTGTTTATATTGATTGTTGATTGTGGCTGCTGTTTCTGACAATTTTG
TTACCGTTATATATTTATCAGGTACGTGCAAAAATCCGTAAATCGTCACT
TGATTGGACCTCAGATTTGTTTATGTGACTAATTCATATATTGATTATTA
CTTCAGTAACTATTTTGTTTACGCCTGATTGGATGAATCACATAATCATT
AGTCAGGTTTATTTGACTTAAAGTGGTGTGTCTATGAGACACTGATTCGC
CGCCGTCCGTCATGTTATCTGCGATTATTGAATTTATAATATGCGGGCTA
TCGTTTACTCTCAAAATTTGGGATTTATTTAGTCAGGTTTTGTACATTTG
TAATTCTCGTATGATTTTTTCGTTCAACCGCTTAATTGTATTCGTAGATT
CTACTAATCATTTCGCCCGTCATCATTAGTGGAACTAACTATGGATTATC
TCTACCGTAAGCCTTGCGATTTCAAGTGATGGTTATCAATCAATTTGTCT
TTCTATTTCAGTATTTTCCTCAAATAGTGGTAAATTCAATCGTTCATCTT
TTGGTGTTCAGTGGCGGTAGTACAACTGAACTATATTTTTCTGGAATGGA
TCTTAATGGCTTGCATGATTTTAGTTTCCGTTGAATGTAATTATCTTTTA
TTAGGGTTTACTCTCAACCGATATCCTTTTCCAATGTCCTTTTCCTGGAT
ATGAATTTTCGCCTAAGCCCTATGTCATGTTTATTATTGATTGATTATGC
GTTTGTAGGACTTCGGAGCTCGATATATTTAACCTGATTAATATGCTGAA
TTGCATTTGCATTTGGCTTGAACATTGATCTTCATTTTGACGATTATTAC
CAGTAACTTTGGAATCAATTTAAGTCTTGATTTATTATTCAACTAATCGT
CTATTATTATGATTTGGACTAATTCCAACTTAATTCAATTAATATTCCAG
ATTTAATTCACGTTTAGCTCGGATATACAAATCTTCATTGCGGGATTACT
GCTACTAATATTGATTTTCGAACTGGAACCTTCGGTCGGCCTATCGGCAG
GTTCATTAATTTGATTGTCTTACATGAATTTGTTAATAAATTTGAGTCGG
TAGCTTTTCTTTTAATCGAGTGCCTGTTTTATCCTTTTTCGTTCATTTAA
GTTTGATTAATACTCCTATGCTTAGTTATAACTTGCAGTTATAAGGGTTC
CTAGTGGTGTCTTTTAGTCGAGAATTAATTATTTAATTTTTGATTGTTGG
GGTTTAATTTATCTAAATTTAATTGATATATTGTATCTGATTCGTATGTG
ATTCGTATGTGATTCAAATATATTATGCTTCCTTACTCGATTATTACC
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..21