Expressed conserved protein

Overview
NameExpressed conserved protein
Smed IDSMED30013233
Length (bp)861
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 Expressed conserved protein (SMED30013233) t-SNE clustered cells

Violin plots show distribution of expression levels for Expressed conserved protein (SMED30013233) 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 Expressed conserved protein (SMED30013233) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Expressed conserved protein (SMED30013233) 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



SMED30013233

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



PAGE Curations: 17

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30013233h1SMcG0016957 SmedASXL_012461SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30013233h1SMcG0016957 SmedASXL_012461SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30013233h1SMcG0016957 Contig10973newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013233h1SMcG0016957 Contig10973uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
neoblastSMED30013233h1SMcG0016957 dd_Smed_v4_565_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynxSMED30013233h1SMcG0016957 dd_Smed_v4_565_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30013233h1SMcG0016957 dd_Smed_v4_565_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30013233h1SMcG0016957 dd_Smed_v4_565_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30013233h1SMcG0016957 dd_Smed_v4_565_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30013233h1SMcG0016957 dd_Smed_v4_565_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30013233h1SMcG0016957 dd_Smed_v4_565_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30013233h1SMcG0016957 dd_Smed_v4_565_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30013233h1SMcG0016957 dd_Smed_v4_565_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30013233h1SMcG0016957 dd_Smed_v4_565_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30013233h1SMcG0016957 dd_Smed_v4_565_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30013233h1SMcG0016957 dd_Smed_v6_565_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30013233h1SMcG0016957 dd_Smed_v4_565_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 Expressed conserved protein vs. TrEMBL
Match: A0A4E0RXV9 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_008103 PE=4 SV=1)

HSP 1 Score: 68.1662 bits (165), Expect = 5.467e-10
Identity = 54/164 (32.93%), Postives = 81/164 (49.39%), Query Frame = 1 
Query:   73 RRRSARLAGLDKEKPEESP---RLRXXXXXXXXXXXXXXXXXXXGDVELDSSVENIN---------------------HNDKKENEEHDVSKDKVNDIEK--EEAND-----EGGDFVVVKKSEIPSPSSNEVKEAIKAQGEDGELLVNYVQVTHDDVPDTKTV 471
            RR+SAR+A +    P +SP     RK++  ++        +  +  ++ +SSVE +N                        K + E  D SKD+V   +K  +  ND     EG DF VV+K ++P P S EV+ AI  QGEDG+LL  +VQV  DD+P T ++
Sbjct:   17 RRQSARIAAVQAASPAKSPVKSPRRKRQSTEQGKTHSEDTESQQSQIKRESSVEELNGLETSSSKDLESVADPQELPSKKAKVDKENGDASKDEVTGPQKVVDAVNDKPLSKEGVDFEVVEKRDVPPPDSAEVRAAISVQGEDGQLLAGFVQVDKDDLPSTTSL 180
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BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A0R3UN24 (Uncharacterized protein OS=Mesocestoides corti OX=53468 GN=MCOS_LOCUS9171 PE=4 SV=1)

HSP 1 Score: 67.3958 bits (163), Expect = 1.930e-9
Identity = 33/54 (61.11%), Postives = 43/54 (79.63%), Query Frame = 1 
Query:  295 EKEEANDEGGDFVVVKKSEIPSPSSNEVKEAIKAQGEDGELLVNYVQVTHDDVP 456
            E + A DEG  F VV+KS++P P S++VK AI AQGEDG+LLVN+VQV+ DD+P
Sbjct:  130 EHQTATDEG--FEVVEKSDVPQPDSDDVKSAIAAQGEDGQLLVNFVQVSKDDLP 181
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BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A2H1BTT9 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_010140 PE=4 SV=1)

HSP 1 Score: 67.3958 bits (163), Expect = 2.858e-9
Identity = 52/163 (31.90%), Postives = 81/163 (49.69%), Query Frame = 1 
Query:   73 RRRSARLAGLDKEKPEESP---RLRXXXXXXXXXXXXXXXXXXXGDVELDSSVENIN---------------------HNDKKENEEHDVSKDKVNDIEK------EEANDEGGDFVVVKKSEIPSPSSNEVKEAIKAQGEDGELLVNYVQVTHDDVPDTKTV 471
            RR+SAR+A +    P +SP     RK++  +         +  +  ++ +SSVE +N                        K + E  DVSKD+V   ++      E+ + +  DF VV+KS++P P S EV+ AI  QGEDG+LL  +VQV  DD+P T ++
Sbjct:   17 RRQSARIAAVQAASPAKSPVKSPRRKRQSTEPSKTHSEDTESQQSQIKSESSVEELNGLETSSSKDLESVADPQELPSKKAKVDEENGDVSKDEVTGPQEVVETVHEKPSSKDVDFEVVEKSDVPPPDSAEVRAAISVQGEDGQLLAGFVQVDKDDLPSTTSL 179
[Close]
BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A068WG38 (Uncharacterized protein (Fragment) OS=Echinococcus granulosus OX=6210 GN=EgrG_000652300 PE=4 SV=1)

HSP 1 Score: 63.5438 bits (153), Expect = 4.673e-9
Identity = 34/55 (61.82%), Postives = 40/55 (72.73%), Query Frame = 1 
Query:  292 IEKEEANDEGGDFVVVKKSEIPSPSSNEVKEAIKAQGEDGELLVNYVQVTHDDVP 456
            +E E A + G  F VV+KS +P   S EVK AI AQGEDG+LLVNYVQV+ DDVP
Sbjct:   30 MEFEAAREAG--FEVVEKSNVPHSDSEEVKSAISAQGEDGQLLVNYVQVSKDDVP 82
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BLAST of Expressed conserved protein vs. TrEMBL
Match: A0A0R3SR42 (Uncharacterized protein OS=Hymenolepis diminuta OX=6216 GN=HDID_LOCUS7600 PE=4 SV=1)

HSP 1 Score: 65.4698 bits (158), Expect = 6.863e-9
Identity = 60/180 (33.33%), Postives = 84/180 (46.67%), Query Frame = 1 
Query:   22 MPNKTKKESNVSSEQLNRRRSARLAGLDKEK-PEESPRLRXXXXXXXXXXXXXXXXXXXGDVELDSSVENINHNDK----------KENEEHDVSKDKVNDI------------EKEEANDEG------------GDFVVVKKSEIPSPSSNEVKEAIKAQGEDGELLVNYVQVTHDDVP 456
            MP ++   +N SS  + RR+SAR+A     K P  SP  +K     K++    S          D+ VEN++HN            +E  E     ++ ND              KEE  ++G             DF VV K+  P+  S EVK+AI+AQGEDG+LLVNYVQV  D++P
Sbjct:    1 MPRRS---TNKSSSPVQRRQSARIAAASANKSPTPSPSPKKIRRSTKRDSASKS----------DAPVENVDHNGNESSSKQAPVLEEPPEKKARIEETNDTLEKEPETIQEQAPKEETTNDGEASKAEHDVAEEADFEVVDKASAPAADSEEVKKAIEAQGEDGQLLVNYVQVVKDELP 167
[Close]
BLAST of Expressed conserved protein vs. Planmine SMEST
Match: SMESG000062284.1 (SMESG000062284.1)

HSP 1 Score: 289.656 bits (740), Expect = 1.332e-99
Identity = 173/183 (94.54%), Postives = 174/183 (95.08%), Query Frame = 1 
Query:   22 MPNKTKKESNVSSEQLNRRRSARLAGLDKEKPEESPRLRXXXXXXXXXXXXXXXXXXXGDVELDSSVENINHNDKKENEEHDVSKDKVNDIEKEEANDEGGDFVVVKKSEIPSPSSNEVKEAIKAQGEDGELLVNYVQVTHDDVPDTKTVHSAFNGVCSNNNLETSKVEEPHQEVAEPKDGSV 570
            MPNKTKKESNVSSEQLNRRRSARLAGLDKEKPEESPRLRKKEPVKKK+KKGVSDKMSKGDVELDSSVEN NHNDKKENEEHDVSKDKVNDIEKEEANDE     VVKKSEIPSPSSNEVKEAIKAQGEDGELLVNYVQVT DDVPDTKTVHSA NGVCSNNNLETSKVEEPHQEVAEPKD SV
Sbjct:    1 MPNKTKKESNVSSEQLNRRRSARLAGLDKEKPEESPRLRKKEPVKKKSKKGVSDKMSKGDVELDSSVENRNHNDKKENEEHDVSKDKVNDIEKEEANDE-----VVKKSEIPSPSSNEVKEAIKAQGEDGELLVNYVQVTQDDVPDTKTVHSAVNGVCSNNNLETSKVEEPHQEVAEPKDSSV 178
[Close]
BLAST of Expressed conserved protein vs. Planmine SMEST
Match: SMESG000062284.1 (SMESG000062284.1)

HSP 1 Score: 286.574 bits (732), Expect = 2.487e-98
Identity = 162/183 (88.52%), Postives = 162/183 (88.52%), Query Frame = 1 
Query:   22 MPNKTKKESNVSSEQLNRRRSARLAGLDKEKPEESPRLRXXXXXXXXXXXXXXXXXXXGDVELDSSVENINHNDKKENEEHDVSKDKVNDIEKEEANDEGGDFVVVKKSEIPSPSSNEVKEAIKAQGEDGELLVNYVQVTHDDVPDTKTVHSAFNGVCSNNNLETSKVEEPHQEVAEPKDGSV 570
            MPNKTKKESNVSSEQLNRRRSARLAGLDKEKPEESPRLRKKEPVK K           GDVELDSSVEN NHNDKKENEEHDVSKDKVNDIEKEEANDE     VVKKSEIPSPSSNEVKEAIKAQGEDGELLVNYVQVT DDVPDTKTVHSA NGVCSNNNLETSKVEEPHQEVAEPKD SV
Sbjct:    1 MPNKTKKESNVSSEQLNRRRSARLAGLDKEKPEESPRLRKKEPVKSKKGVSDKMSK--GDVELDSSVENRNHNDKKENEEHDVSKDKVNDIEKEEANDE-----VVKKSEIPSPSSNEVKEAIKAQGEDGELLVNYVQVTQDDVPDTKTVHSAVNGVCSNNNLETSKVEEPHQEVAEPKDSSV 176
The following BLAST results are available for this feature:
BLAST of Expressed conserved 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 Expressed conserved 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 Expressed conserved 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 Expressed conserved 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 Expressed conserved 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 Expressed conserved 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 Expressed conserved 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 Expressed conserved protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4E0RXV95.467e-1032.93Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
A0A0R3UN241.930e-961.11Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A2H1BTT92.858e-931.90Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
A0A068WG384.673e-961.82Uncharacterized protein (Fragment) OS=Echinococcus... [more]
A0A0R3SR426.863e-933.33Uncharacterized protein OS=Hymenolepis diminuta OX... [more]
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BLAST of Expressed conserved 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 Expressed conserved 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 Expressed conserved 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 Expressed conserved 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 Expressed conserved 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 Expressed conserved protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000062284.11.332e-9994.54SMESG000062284.1[more]
SMESG000062284.12.487e-9888.52SMESG000062284.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013233 ID=SMED30013233|Name=Expressed conserved protein|organism=Schmidtea mediterranea sexual|type=transcript|length=861bp
TCTATATAAATCTTATATGAAATGCCTAATAAAACGAAAAAAGAATCTAA
TGTATCAAGCGAGCAACTTAATCGTAGGAGAAGTGCAAGACTTGCTGGTT
TAGACAAGGAAAAACCTGAAGAATCGCCGAGGTTAAGGAAAAAAGAACCA
GTCAAGAAAAAGAATAAAAAAGGAGTCAGTGATAAAATGTCAAAGGGGGA
TGTTGAATTAGATTCAAGTGTTGAAAACATAAATCATAACGATAAAAAAG
AAAATGAAGAGCACGATGTATCAAAAGACAAAGTAAATGACATTGAAAAG
GAAGAAGCGAACGATGAAGGTGGTGATTTTGTAGTTGTTAAGAAGAGTGA
AATACCGTCCCCATCTAGTAATGAAGTTAAGGAAGCTATTAAAGCTCAAG
GAGAAGATGGTGAGCTTTTAGTAAATTATGTTCAAGTTACTCATGATGAT
GTGCCTGACACTAAAACTGTTCACTCTGCCTTTAACGGTGTTTGTTCGAA
TAATAATTTAGAAACAAGCAAAGTCGAAGAACCTCATCAGGAAGTTGCTG
AACCAAAGGATGGTTCTGTATAATGTTCTATCTTTATTGGAGCAGTTTTC
TCAATTTTATCCGCGCTTATTGATAATTGTGGTTATATCATTCTATTAAT
GTAGAGTGTTTATGTTGAATTAATGAACTAGTGTGATGTGTTTATTTGTT
TGATAAATTTTTGCATGATATTATTTATAGTTTGCCAACTTATGGAGTTC
GGTCTTCAATGTGACAGTTTAGGTCTTAGACCAGATGTAAGCAGCAAAAT
TATAAAATATTGTGTAATTTAAAGCAGCTTTGTAATGGTAAATAATATAT
AATTGTTGGAG
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protein sequence of SMED30013233-orf-1

>SMED30013233-orf-1 ID=SMED30013233-orf-1|Name=SMED30013233-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=184bp
MPNKTKKESNVSSEQLNRRRSARLAGLDKEKPEESPRLRKKEPVKKKNKK
GVSDKMSKGDVELDSSVENINHNDKKENEEHDVSKDKVNDIEKEEANDEG
GDFVVVKKSEIPSPSSNEVKEAIKAQGEDGELLVNYVQVTHDDVPDTKTV
HSAFNGVCSNNNLETSKVEEPHQEVAEPKDGSV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000429neoblast
PLANA:0002109X1 cell
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: 22..106
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 168..184
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..20
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..119
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 161..184