BEN domain-containing protein

Overview
NameBEN domain-containing protein
Smed IDSMED30028469
Length (bp)1102
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 BEN domain-containing protein (SMED30028469) t-SNE clustered cells

Violin plots show distribution of expression levels for BEN domain-containing protein (SMED30028469) 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 BEN domain-containing protein (SMED30028469) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for BEN domain-containing protein (SMED30028469) 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



SMED30028469

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30028469SMESG000000832.1 dd_Smed_v4_10870_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30028469SMESG000000832.1 dd_Smed_v4_10870_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30028469SMESG000000832.1 dd_Smed_v4_10870_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
oocyteSMED30028469SMESG000000832.1 Contig2348GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30028469SMESG000000832.1 Contig2348GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
epidermisSMED30028469SMESG000000832.1 dd_Smed_v4_10870_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 BEN domain-containing protein vs. TrEMBL
Match: A0A4Z2CZR1 (BEN domain isoform 2 OS=Schistosoma japonicum OX=6182 GN=EWB00_006211 PE=4 SV=1)

HSP 1 Score: 179.489 bits (454), Expect = 1.749e-46
Identity = 79/129 (61.24%), Postives = 105/129 (81.40%), Query Frame = 1 
Query:  562 NLTVKRKTFRGTSDEENEIDTTFKPIEINNEVILSKNYSDIRVGKDLFYMMLLKASNSATRLIRLLMKNFFCQKELEVSSLSGEGYYKQKLNPQIITAIKEFIKTRHPKLKNGSINLCMTDVCVQARRV 948
            N + K+  FRGTS+EEN++   FKP+E+NN+++LS+ + ++++ KD+FY +++K+S SATRLIRLLMK+FF Q EL  SSLSGEG YKQ+L P +  AIK FI+ RHP+LK GSINLCMTDVCVQARRV
Sbjct:  527 NSSPKKSNFRGTSEEENKVAPNFKPVEVNNQILLSEAHPNVKLSKDIFYSLIVKSSGSATRLIRLLMKSFFTQDELAASSLSGEGIYKQRLEPSVTEAIKIFIRQRHPQLKTGSINLCMTDVCVQARRV 655
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BLAST of BEN domain-containing protein vs. TrEMBL
Match: A0A068WX88 (BEN domain OS=Echinococcus granulosus OX=6210 GN=EgrG_000333200 PE=4 SV=1)

HSP 1 Score: 173.326 bits (438), Expect = 1.918e-46
Identity = 83/146 (56.85%), Postives = 107/146 (73.29%), Query Frame = 1 
Query:  556 SSNLTVKRKTFRGTSDEENEIDTTFKPIEINNEVILSKNYSDIRVGKDLFYMMLLKASNSATRLIRLLMKNFFCQKELEVSSLSGEGYYKQKLNPQIITAIKEFIKTRHPKLKNGSINLCMTDVCVQARRVY-----RTKDPKTKL 978
            S  L  K+ +FRGTS+EENE+   FKP+E N  +ILS+ +  + + K+++  +++K+S SATRLIRLLMK+FF Q+EL  SSLSGEG YKQ+L P+I  AIK FI+ RHP+LK GSINLCMTDVCVQARRV      R + PK  L
Sbjct:  212 SGPLLSKKPSFRGTSEEENEVCPHFKPVEQNGHIILSELHPSVMLPKEVYQSLIIKSSGSATRLIRLLMKSFFSQEELAASSLSGEGIYKQRLQPEITEAIKAFIRKRHPQLKTGSINLCMTDVCVQARRVANNQRSRVRGPKKPL 357
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BLAST of BEN domain-containing protein vs. TrEMBL
Match: A0A068XZR7 (BEN domain OS=Echinococcus multilocularis OX=6211 GN=EmuJ_000333200 PE=4 SV=1)

HSP 1 Score: 172.94 bits (437), Expect = 2.573e-46
Identity = 83/146 (56.85%), Postives = 107/146 (73.29%), Query Frame = 1 
Query:  556 SSNLTVKRKTFRGTSDEENEIDTTFKPIEINNEVILSKNYSDIRVGKDLFYMMLLKASNSATRLIRLLMKNFFCQKELEVSSLSGEGYYKQKLNPQIITAIKEFIKTRHPKLKNGSINLCMTDVCVQARRVY-----RTKDPKTKL 978
            S  L  K+ +FRGTS+EENE+   FKP+E N  +ILS+ +  + + K+++  +++K+S SATRLIRLLMK+FF Q+EL  SSLSGEG YKQ+L P+I  AIK FI+ RHP+LK GSINLCMTDVCVQARRV      R + PK  L
Sbjct:  212 SGPLLSKKPSFRGTSEEENEVCPHFKPVEQNGHIILSELHPSVMLPKEVYQSLIIKSSGSATRLIRLLMKSFFSQEELAASSLSGEGIYKQRLQPEITEAIKAFIRKRHPQLKTGSINLCMTDVCVQARRVANNQRSRVRGPKKPL 357
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BLAST of BEN domain-containing protein vs. TrEMBL
Match: A0A5K4F236 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 PE=4 SV=1)

HSP 1 Score: 178.333 bits (451), Expect = 4.518e-46
Identity = 82/146 (56.16%), Postives = 111/146 (76.03%), Query Frame = 1 
Query:  562 NLTVKRKTFRGTSDEENEIDTTFKPIEINNEVILSKNYSDIRVGKDLFYMMLLKASNSATRLIRLLMKNFFCQKELEVSSLSGEGYYKQKLNPQIITAIKEFIKTRHPKLKNGSINLCMTDVCVQARRVYRTKDPKTKLLTNQ*TI 999
            N + K+  FRGTS+EEN++   FKPIE+N++++LS+ + ++++ KD+FY +++K+S SATRLIRLLMK+FF Q EL  SSLSGEG YKQ+L P +  AIK FI+ RHP+LK GSINLCMTDVCVQARRV   +  +   L N  T+
Sbjct:  526 NSSPKKSNFRGTSEEENKVAPNFKPIEVNSQILLSEAHPNVKLSKDIFYSLIVKSSGSATRLIRLLMKSFFTQDELAASSLSGEGIYKQRLEPSVTEAIKIFIRQRHPQLKTGSINLCMTDVCVQARRVANNQRSRQHPLRNSPTM 671
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BLAST of BEN domain-containing protein vs. TrEMBL
Match: A0A4S2LI88 (BEN domain-containing protein OS=Opisthorchis felineus OX=147828 GN=CRM22_007401 PE=4 SV=1)

HSP 1 Score: 177.563 bits (449), Expect = 8.179e-46
Identity = 80/125 (64.00%), Postives = 99/125 (79.20%), Query Frame = 1 
Query:  574 KRKTFRGTSDEENEIDTTFKPIEINNEVILSKNYSDIRVGKDLFYMMLLKASNSATRLIRLLMKNFFCQKELEVSSLSGEGYYKQKLNPQIITAIKEFIKTRHPKLKNGSINLCMTDVCVQARRV 948
            K+  FRGTS+EENE+   FKP E N ++ILS  + ++++ KD+FY +++K+S SATRLIRLLMK+FF Q EL  SSLSGEG YKQ+L P I  AIK FI+ RHP+LK GSINLCMTDVCVQARRV
Sbjct:  507 KKSNFRGTSEEENEVSPDFKPTEFNGQIILSDAHPNVKLSKDIFYSLIVKSSGSATRLIRLLMKSFFTQDELAASSLSGEGIYKQRLEPSITEAIKIFIRKRHPQLKTGSINLCMTDVCVQARRV 631
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BLAST of BEN domain-containing protein vs. Planmine SMEST
Match: SMESG000000832.1 (SMESG000000832.1)

HSP 1 Score: 611.298 bits (1575), Expect = 0.000e+0
Identity = 297/298 (99.66%), Postives = 298/298 (100.00%), Query Frame = 1 
Query:   97 MTSNNCHRRKNKIPRKRDYTCLKYTTSNEDKETETSNSIDFNADYQKQNSIEDPSQSNNENFQTEINRSFKSNHSQYSAVHLIHSVLPVPRFQFHPNLQTLYEEIRSTCVNIDQMIDKYMKAYASTILQNISSTNSSPVSPDISPSLNGSMNKSSNLTVKRKTFRGTSDEENEIDTTFKPIEINNEVILSKNYSDIRVGKDLFYMMLLKASNSATRLIRLLMKNFFCQKELEVSSLSGEGYYKQKLNPQIITAIKEFIKTRHPKLKNGSINLCMTDVCVQARRVYRTKDPKTKLLTNQ 990
            MTSNNCHRRKNKIPRKRDYTCLKYTTSNEDKETETSNSIDFNADYQKQNSIEDPSQSNNENFQTEINRSFKSN+SQYSAVHLIHSVLPVPRFQFHPNLQTLYEEIRSTCVNIDQMIDKYMKAYASTILQNISSTNSSPVSPDISPSLNGSMNKSSNLTVKRKTFRGTSDEENEIDTTFKPIEINNEVILSKNYSDIRVGKDLFYMMLLKASNSATRLIRLLMKNFFCQKELEVSSLSGEGYYKQKLNPQIITAIKEFIKTRHPKLKNGSINLCMTDVCVQARRVYRTKDPKTKLLTNQ
Sbjct:    1 MTSNNCHRRKNKIPRKRDYTCLKYTTSNEDKETETSNSIDFNADYQKQNSIEDPSQSNNENFQTEINRSFKSNYSQYSAVHLIHSVLPVPRFQFHPNLQTLYEEIRSTCVNIDQMIDKYMKAYASTILQNISSTNSSPVSPDISPSLNGSMNKSSNLTVKRKTFRGTSDEENEIDTTFKPIEINNEVILSKNYSDIRVGKDLFYMMLLKASNSATRLIRLLMKNFFCQKELEVSSLSGEGYYKQKLNPQIITAIKEFIKTRHPKLKNGSINLCMTDVCVQARRVYRTKDPKTKLLTNQ 298
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BLAST of BEN domain-containing protein vs. Planmine SMEST
Match: SMESG000080064.1 (SMESG000080064.1)

HSP 1 Score: 173.326 bits (438), Expect = 6.827e-49
Identity = 85/135 (62.96%), Postives = 101/135 (74.81%), Query Frame = 1 
Query:  574 KRKTFRGTSDEENEIDTTFKPIEINNEVILSKNYSDIRVGKDLFYMMLLKASNSATRLIRLLMKNFFCQKELEVSSLSGEGYYKQKLNPQIITAIKEFIKTRHPKLKNGSINLCMTDVCVQARRVYRTKDPKTKL 978
            K+  FRGTS+ ENEIDT F P E+N E+IL   YS +R+ K+++  +  KA  SATRLIRLLMK+FF Q  L  SSLSGEG YK +L P +I AIK FIK RHPKLKNGSINLCMTDVCVQARRV   K+ +T+L
Sbjct:  333 KKSNFRGTSEAENEIDTAFIPREVNREIILCDEYSSVRLDKEVYNTLTSKAPRSATRLIRLLMKHFFSQDTLARSSLSGEGIYKDRLQPDVIEAIKLFIKRRHPKLKNGSINLCMTDVCVQARRV--NKNQRTRL 465
The following BLAST results are available for this feature:
BLAST of BEN domain-containing 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 BEN domain-containing 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 BEN domain-containing 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 BEN domain-containing 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 BEN domain-containing 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 BEN domain-containing 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 BEN domain-containing 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 BEN domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4Z2CZR11.749e-4661.24BEN domain isoform 2 OS=Schistosoma japonicum OX=6... [more]
A0A068WX881.918e-4656.85BEN domain OS=Echinococcus granulosus OX=6210 GN=E... [more]
A0A068XZR72.573e-4656.85BEN domain OS=Echinococcus multilocularis OX=6211 ... [more]
A0A5K4F2364.518e-4656.16Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
A0A4S2LI888.179e-4664.00BEN domain-containing protein OS=Opisthorchis feli... [more]
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BLAST of BEN domain-containing 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 BEN domain-containing 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 BEN domain-containing 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 BEN domain-containing 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 BEN domain-containing 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 BEN domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000000832.10.000e+099.66SMESG000000832.1[more]
SMESG000080064.16.827e-4962.96SMESG000080064.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028469 ID=SMED30028469|Name=BEN domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1102bp
ACTGAATCAAATATTATTTGAATTGTATTTTTTAAGAGTCTTTAAGAATT
AAATTTTTTCCATATTAATATTTTTGAAATCATTTTTTTGAATTAAATGA
CATCAAATAACTGTCATCGAAGAAAGAACAAAATTCCAAGAAAACGAGAT
TACACTTGTTTAAAATACACGACTTCAAATGAGGATAAAGAAACTGAAAC
TAGTAATTCAATAGATTTCAATGCAGATTATCAAAAACAAAATAGTATTG
AAGATCCATCACAAAGTAATAATGAAAATTTCCAAACAGAAATCAACAGA
TCATTTAAATCCAATCATTCTCAATACAGTGCAGTCCATTTGATTCATAG
TGTACTTCCGGTTCCACGGTTTCAGTTCCATCCAAATCTGCAAACACTTT
ATGAAGAAATCAGATCCACCTGTGTTAATATTGATCAAATGATCGACAAA
TATATGAAAGCTTATGCCTCAACAATTTTACAAAACATATCGTCAACAAA
TTCATCGCCCGTTTCGCCAGATATTTCGCCTTCATTAAACGGTTCAATGA
ATAAATCCTCAAATCTTACAGTCAAGCGGAAAACATTTAGGGGAACAAGT
GACGAAGAAAATGAAATTGATACTACCTTTAAACCGATAGAAATAAATAA
TGAAGTTATTTTATCAAAGAATTATTCTGATATCAGAGTCGGAAAAGATT
TATTTTATATGATGTTGCTCAAAGCTTCAAATAGTGCTACTAGATTGATA
AGGCTTTTAATGAAGAATTTTTTCTGTCAGAAAGAACTAGAGGTTAGTTC
ATTAAGTGGTGAAGGGTATTACAAACAAAAGTTAAATCCACAAATTATAA
CTGCTATCAAAGAATTCATCAAGACTAGGCATCCAAAATTAAAGAACGGC
TCAATTAATTTATGCATGACAGATGTTTGTGTCCAAGCTCGTAGAGTCTA
CCGCACAAAAGATCCCAAAACGAAGCTTTTGACCAATCAATAAACCATTT
ATTTTTACTATATAGTTTTAAATTTACATATTAATAAAATGGGGCTTTTC
CCTCTATTCATTTATTTAAATGAATATTTTATATTTTTTATCAATGATCA
TG
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protein sequence of SMED30028469-orf-1

>SMED30028469-orf-1 ID=SMED30028469-orf-1|Name=SMED30028469-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=299bp
MTSNNCHRRKNKIPRKRDYTCLKYTTSNEDKETETSNSIDFNADYQKQNS
IEDPSQSNNENFQTEINRSFKSNHSQYSAVHLIHSVLPVPRFQFHPNLQT
LYEEIRSTCVNIDQMIDKYMKAYASTILQNISSTNSSPVSPDISPSLNGS
MNKSSNLTVKRKTFRGTSDEENEIDTTFKPIEINNEVILSKNYSDIRVGK
DLFYMMLLKASNSATRLIRLLMKNFFCQKELEVSSLSGEGYYKQKLNPQI
ITAIKEFIKTRHPKLKNGSINLCMTDVCVQARRVYRTKDPKTKLLTNQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR018379BEN_domain
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR018379BEN domainPFAMPF10523BENcoord: 217..268
e-value: 5.3E-5
score: 23.4
IPR018379BEN domainPROSITEPS51457BENcoord: 193..285
score: 10.212