DUF4476 domain-containing protein

Overview
NameDUF4476 domain-containing protein
Smed IDSMED30005870
Length (bp)1006
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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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Anatomical Expression

PAGE et. al., 2020



SMED30005870

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
testisSMED30005870SMESG000045760.1 PL06017B1C11_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
early male germ cellSMED30005870SMESG000045760.1 PL06017B1C11_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism asexual adult cDNA to DNA expression microarray evidence
testis primordiumSMED30005870SMESG000045760.1 PL06017B1C11_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism juvenile cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of DUF4476 domain-containing protein vs. TrEMBL
Match: A0A3R7DG61 (DUF4476 domain-containing protein OS=Clonorchis sinensis OX=79923 GN=CSKR_6925s PE=4 SV=1)

HSP 1 Score: 228.409 bits (581), Expect = 9.427e-70
Identity = 113/207 (54.59%), Postives = 146/207 (70.53%), Query Frame = 1 
Query:  139 MAKKPADESYFMDLVRNLKEETDSIDKKFNIVYYGKGFFSGTQAAILLKSFKTAPEKLKVIKSLDKRLCRMTCAEGKEILIAMQPINNDRLEALNIIKRTLIDHQCTEGMEHILSAFPFQSDKLKALGILTTVSSYVADQLPSGGHQQYAPVGGLYSQNFPLRENLFGSLEDQLLRMPGSGLPAIPLRARPGKVPSLYTSHPSYKYD 759
            MAK P  +S F  L+  L  ET   +KKF  +YY +G FSG QAA LL  FKTAPE+++VI++L++RLCRM CAE +EIL  +Q  NNDRL ALN +KRTL+DH+ TEG+E+ILSAFPF++DK KAL IL TVS +   QL SGGHQ YAP GGLY+Q+FP +E L+G LEDQ+        P++P+ A     PS + + PSY Y+
Sbjct:    1 MAKVPLSDSDFNRLLSLLISETSDKEKKFEKLYYSRGCFSGIQAAALLACFKTAPERVRVIRALERRLCRMCCAEAREILNIIQLTNNDRLTALNCVKRTLVDHETTEGIEYILSAFPFETDKKKALEILATVSMHATQQLASGGHQHYAPFGGLYTQSFPGKEGLYGPLEDQVAAKEHKVKPSLPVTACTKPPPSAFVAAPSYIYN 207
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BLAST of DUF4476 domain-containing protein vs. TrEMBL
Match: A0A2H1CWM4 (DUF4476 domain-containing protein OS=Fasciola hepatica OX=6192 GN=D915_00471 PE=4 SV=1)

HSP 1 Score: 227.639 bits (579), Expect = 1.926e-69
Identity = 113/207 (54.59%), Postives = 155/207 (74.88%), Query Frame = 1 
Query:  139 MAKKPADESYFMDLVRNLKEETDSIDKKFNIVYYGKGFFSGTQAAILLKSFKTAPEKLKVIKSLDKRLCRMTCAEGKEILIAMQPINNDRLEALNIIKRTLIDHQCTEGMEHILSAFPFQSDKLKALGILTTVSSYVADQLPSGGHQQYAPVGGLYSQNFPLRENLFGSLEDQLLRMPGSGLPAIPLRARPGKVPSLYTSHPSYKYD 759
            MAK P  +  F  L++ L  ETDS+++KF   YY KG FSG QAA L+ +FKTAPE+++VIK+L++RLCRM CAE +EIL  +Q  N+DR+ AL+ IKRTL+DH+ TEG+E+ILSAFPF++DK +A+ IL+TVS YV  +L SGGHQ  AP+GGLY+Q+FPLRE LFG + +QL        P++P+ AR  K+PS++ + PSY Y+
Sbjct:    1 MAKHPLSDGDFSRLLKLLAAETDSMERKFEKFYYSKGCFSGAQAAALMAAFKTAPERVRVIKALERRLCRMCCAEAREILNVVQLTNHDRVFALDCIKRTLVDHETTEGIEYILSAFPFETDKKRAMQILSTVSMYVNKELASGGHQINAPLGGLYTQSFPLREALFGPINEQLAMKNHEVKPSLPVTARVKKIPSMFAAAPSYIYN 207
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BLAST of DUF4476 domain-containing protein vs. TrEMBL
Match: A0A4S2MIM0 (DUF4476 domain-containing protein OS=Opisthorchis felineus OX=147828 GN=CRM22_000628 PE=4 SV=1)

HSP 1 Score: 226.098 bits (575), Expect = 9.250e-69
Identity = 112/207 (54.11%), Postives = 144/207 (69.57%), Query Frame = 1 
Query:  139 MAKKPADESYFMDLVRNLKEETDSIDKKFNIVYYGKGFFSGTQAAILLKSFKTAPEKLKVIKSLDKRLCRMTCAEGKEILIAMQPINNDRLEALNIIKRTLIDHQCTEGMEHILSAFPFQSDKLKALGILTTVSSYVADQLPSGGHQQYAPVGGLYSQNFPLRENLFGSLEDQLLRMPGSGLPAIPLRARPGKVPSLYTSHPSYKYD 759
            MAK P  +  F  L+  L  ET   +KKF  +YY +G FSG Q A LL  FKTAPE+++VI++L++RLCRM CAE +EIL  +Q  NNDRL ALN +KRTL+DH+ TEG+E+ILSAFPF++DK KAL IL TVS +   QL SGGHQ YAP GGLY+Q+FP RE L+G LEDQ+        P++P+ A     PS + + PSY Y+
Sbjct:    1 MAKVPLSDGDFNRLLSLLISETSDKEKKFEKLYYSRGCFSGIQVAALLACFKTAPERVRVIRALERRLCRMCCAEAREILNIIQLTNNDRLTALNCVKRTLVDHETTEGIEYILSAFPFETDKKKALEILATVSMHATQQLASGGHQNYAPFGGLYTQSFPGREALYGPLEDQVAVKEHKVKPSLPVTACTKPPPSAFVAAPSYIYN 207
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BLAST of DUF4476 domain-containing protein vs. TrEMBL
Match: A0A183VRR7 (DUF4476 domain-containing protein OS=Trichobilharzia regenti OX=157069 GN=TRE_LOCUS3173 PE=4 SV=1)

HSP 1 Score: 224.557 bits (571), Expect = 1.511e-68
Identity = 110/206 (53.40%), Postives = 147/206 (71.36%), Query Frame = 1 
Query:  139 MAKKPADESYFMDLVRNLKEETDSIDKKFNIVYYGKGFFSGTQAAILLKSFKTAPEKLKVIKSLDKRLCRMTCAEGKEILIAMQPINNDRLEALNIIKRTLIDHQCTEGMEHILSAFPFQSDKLKALGILTTVSSYVADQLPSGGHQQYAPVGGLYSQNFPLRENLFGSLEDQLLRMPGSGLPAIPLRARPGKVPSLYTSHPSYKY 756
            MAK P  +S F  L R L  ET S+  KF+ +YY KG+F+G QAA +L  +KTAPE+++VIK+L KRLCRMTCAE  EIL  MQ  N+DR+ AL+ +K TLIDH+ TEG+E+IL AF ++SDK+KAL IL+TVS +V+ +L SGGHQ YAP GGLY+Q+FP RE L+G + +QL        P++P+ AR     S++ + PSY Y
Sbjct:   39 MAKTPLSDSEFERLRRALISETTSVADKFDKLYYSKGYFTGVQAAAILACYKTAPERVQVIKALKKRLCRMTCAEAAEILKVMQLTNHDRIFALDCVKHTLIDHETTEGIEYILKAFIYESDKMKALHILSTVSMHVSRELASGGHQVYAPFGGLYTQSFPGRETLYGPISEQLAVKNHEVKPSLPVTARMNLPESIFRAAPSYAY 244
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BLAST of DUF4476 domain-containing protein vs. TrEMBL
Match: A0A074ZLG6 (DUF4476 domain-containing protein OS=Opisthorchis viverrini OX=6198 GN=T265_06132 PE=4 SV=1)

HSP 1 Score: 224.942 bits (572), Expect = 2.099e-68
Identity = 113/207 (54.59%), Postives = 145/207 (70.05%), Query Frame = 1 
Query:  139 MAKKPADESYFMDLVRNLKEETDSIDKKFNIVYYGKGFFSGTQAAILLKSFKTAPEKLKVIKSLDKRLCRMTCAEGKEILIAMQPINNDRLEALNIIKRTLIDHQCTEGMEHILSAFPFQSDKLKALGILTTVSSYVADQLPSGGHQQYAPVGGLYSQNFPLRENLFGSLEDQLLRMPGSGLPAIPLRARPGKVPSLYTSHPSYKYD 759
            MAK P  +  F  L+  L  ET   +KKF  +YY +G FSG QAA LL  FKTAPE+++VI++L++RLCRM CAE +EIL  +Q  NNDRL ALN +KRTL+DH+ TEG+E+ILSAFPF++DK KAL IL TVS +   QL SGGHQ YAP GGLY+Q+FP RE+L+G LEDQ         P++P+ A     PS + + PSY Y+
Sbjct:    1 MAKVPLSDGDFNRLLSLLVSETSDKEKKFEKLYYSRGCFSGIQAAALLACFKTAPERVRVIRALERRLCRMCCAEAREILNVIQLTNNDRLTALNCVKRTLVDHETTEGIEYILSAFPFETDKKKALEILATVSMHATQQLASGGHQHYAPFGGLYTQSFPGRESLYGPLEDQ-----HKVKPSLPVTACTKPPPSAFVAAPSYIYN 202
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BLAST of DUF4476 domain-containing protein vs. Planmine SMEST
Match: SMESG000045760.1 (SMESG000045760.1)

HSP 1 Score: 500.745 bits (1288), Expect = 0.000e+0
Identity = 258/258 (100.00%), Postives = 258/258 (100.00%), Query Frame = 1 
Query:  139 MAKKPADESYFMDLVRNLKEETDSIDKKFNIVYYGKGFFSGTQAAILLKSFKTAPEKLKVIKSLDKRLCRMTCAEGKEILIAMQPINNDRLEALNIIKRTLIDHQCTEGMEHILSAFPFQSDKLKALGILTTVSSYVADQLPSGGHQQYAPVGGLYSQNFPLRENLFGSLEDQLLRMPGSGLPAIPLRARPGKVPSLYTSHPSYKYDTTYTYLQDRGYPGARGFPEHDXXXXXXXXXXXXLGFHQGPPAPTGYQTLKE 912
            MAKKPADESYFMDLVRNLKEETDSIDKKFNIVYYGKGFFSGTQAAILLKSFKTAPEKLKVIKSLDKRLCRMTCAEGKEILIAMQPINNDRLEALNIIKRTLIDHQCTEGMEHILSAFPFQSDKLKALGILTTVSSYVADQLPSGGHQQYAPVGGLYSQNFPLRENLFGSLEDQLLRMPGSGLPAIPLRARPGKVPSLYTSHPSYKYDTTYTYLQDRGYPGARGFPEHDPRPPTYPSGSPPLGFHQGPPAPTGYQTLKE
Sbjct:    1 MAKKPADESYFMDLVRNLKEETDSIDKKFNIVYYGKGFFSGTQAAILLKSFKTAPEKLKVIKSLDKRLCRMTCAEGKEILIAMQPINNDRLEALNIIKRTLIDHQCTEGMEHILSAFPFQSDKLKALGILTTVSSYVADQLPSGGHQQYAPVGGLYSQNFPLRENLFGSLEDQLLRMPGSGLPAIPLRARPGKVPSLYTSHPSYKYDTTYTYLQDRGYPGARGFPEHDPRPPTYPSGSPPLGFHQGPPAPTGYQTLKE 258
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BLAST of DUF4476 domain-containing protein vs. Planmine SMEST
Match: SMESG000055714.1 (SMESG000055714.1)

HSP 1 Score: 275.404 bits (703), Expect = 1.528e-92
Identity = 133/217 (61.29%), Postives = 166/217 (76.50%), Query Frame = 1 
Query:  139 MAKKPADESYFMDLVRNLKEETDSIDKKFNIVYYGKGFFSGTQAAILLKSFKTAPEKLKVIKSLDKRLCRMTCAEGKEILIAMQPINNDRLEALNIIKRTLIDHQCTEGMEHILSAFPFQSDKLKALGILTTVSSYVADQLPSGGHQQYAPVGGLYSQNFPLRENLFGSLEDQLLRMPGSGLPAIPLRARPGKVPSLYTSHPSYKYDTTYTYLQDRG 789
            MAK P D   F  L+ ++ +ET SI+KKFNIVYY K FF+G+QAA LL  +KTAPE+LKVI +L+KRLCRMTC E K IL A Q  NND++ AL+ IKRTLIDHQ TEG+E+ILSAFPF +DKLKA+ IL TVSSYV++++ +GGHQ Y+PVGGL+SQ+FPL+ NLFG +++QL    G G PAI   ARPGKV SLY SHPSY+YD   ++    G
Sbjct:    1 MAKTPVDSETFNILINDIVKETTSIEKKFNIVYYTKFFFAGSQAAHLLIQYKTAPERLKVISALEKRLCRMTCTEAKLILDAFQLTNNDKVFALDCIKRTLIDHQSTEGIEYILSAFPFTNDKLKAMSILATVSSYVSEKMSAGGHQLYSPVGGLFSQSFPLKANLFGPIDEQLENQQGKGQPAIAPHARPGKVDSLYRSHPSYRYDNGVSWKSSMG 217
The following BLAST results are available for this feature:
BLAST of DUF4476 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 DUF4476 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 DUF4476 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 DUF4476 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 DUF4476 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 DUF4476 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 DUF4476 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 DUF4476 domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A3R7DG619.427e-7054.59DUF4476 domain-containing protein OS=Clonorchis si... [more]
A0A2H1CWM41.926e-6954.59DUF4476 domain-containing protein OS=Fasciola hepa... [more]
A0A4S2MIM09.250e-6954.11DUF4476 domain-containing protein OS=Opisthorchis ... [more]
A0A183VRR71.511e-6853.40DUF4476 domain-containing protein OS=Trichobilharz... [more]
A0A074ZLG62.099e-6854.59DUF4476 domain-containing protein OS=Opisthorchis ... [more]
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BLAST of DUF4476 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 DUF4476 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 DUF4476 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 DUF4476 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 DUF4476 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 DUF4476 domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000045760.10.000e+0100.00SMESG000045760.1[more]
SMESG000055714.11.528e-9261.29SMESG000055714.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005870 ID=SMED30005870|Name=DUF4476 domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1006bp
CGAAACTTTGATATCTCATTATATAAATTTTAAAGATTAAATAAAAGTTC
TTTTTAATAAAAAATAAATGAACTCCTCCATTCCGGCATTAAGATAGTAA
CTATCACATATAAAAAGTTTCATATAAAAATATAAAAAATGGCTAAAAAA
CCGGCGGACGAGTCTTATTTTATGGACCTTGTGAGGAATCTAAAGGAAGA
AACAGATTCGATTGATAAAAAGTTTAACATTGTTTATTATGGAAAAGGCT
TCTTTAGTGGTACTCAGGCGGCAATTCTATTAAAATCCTTCAAAACTGCG
CCAGAAAAATTGAAGGTCATCAAAAGTTTGGATAAAAGACTTTGTCGAAT
GACTTGTGCAGAAGGCAAAGAAATTTTGATTGCTATGCAACCTATCAATA
ACGATCGGCTAGAAGCGTTAAACATTATCAAAAGAACTCTGATTGACCAC
CAATGCACCGAAGGCATGGAACACATTCTCAGCGCATTTCCTTTCCAATC
AGATAAATTGAAAGCTCTAGGAATACTAACGACGGTGAGCTCATATGTTG
CTGACCAATTGCCTTCAGGAGGTCATCAGCAATATGCTCCGGTTGGTGGA
CTTTATTCACAAAACTTTCCTTTAAGAGAAAATCTATTTGGGTCATTGGA
AGATCAATTATTACGAATGCCAGGGAGTGGCTTACCGGCAATACCTCTCA
GGGCAAGGCCAGGGAAAGTCCCATCACTCTATACTAGCCATCCTTCTTAT
AAGTACGACACAACATACACTTATCTTCAAGACAGAGGCTATCCTGGAGC
TCGAGGATTTCCTGAACATGATCCGCGACCTCCAACCTATCCAAGTGGAT
CTCCACCTTTGGGATTTCATCAAGGACCGCCTGCCCCCACTGGATATCAA
ACCTTAAAAGAAAATATAAATAATGGACACTTTTAATTTTAATTTAATTA
TTATTGCAATAACATACTACTTATAAATAAAGTACGCAATAGGTTTTAAA
AAAAAA
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protein sequence of SMED30005870-orf-1

>SMED30005870-orf-1 ID=SMED30005870-orf-1|Name=SMED30005870-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=266bp
MAKKPADESYFMDLVRNLKEETDSIDKKFNIVYYGKGFFSGTQAAILLKS
FKTAPEKLKVIKSLDKRLCRMTCAEGKEILIAMQPINNDRLEALNIIKRT
LIDHQCTEGMEHILSAFPFQSDKLKALGILTTVSSYVADQLPSGGHQQYA
PVGGLYSQNFPLRENLFGSLEDQLLRMPGSGLPAIPLRARPGKVPSLYTS
HPSYKYDTTYTYLQDRGYPGARGFPEHDPRPPTYPSGSPPLGFHQGPPAP
TGYQTLKENINNGHF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
PLANA:0002030early male germ cell
PLANA:0003304testis primordium
Vocabulary: INTERPRO
TermDefinition
IPR028011DUF4476
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR028011Domain of unknown function DUF4476PFAMPF14771DUF4476coord: 48..127
e-value: 1.7E-7
score: 31.5