SMED30026593

Overview
NameSMED30026593
Smed IDSMED30026593
Length (bp)1237
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 SMED30026593 (SMED30026593) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30026593 (SMED30026593) 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 SMED30026593 (SMED30026593) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30026593 (SMED30026593) 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




SMED30026593

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymal cellSMED30026593SMESG000067829.1 dd_Smed_v4_11715_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30026593 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001714:82200..83429 -6078
Homology
BLAST of SMED30026593 vs. TrEMBL
Match: I1ZIH9 (IAP domain containing-1 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 115.931 bits (289), Expect = 1.699e-28
Identity = 55/56 (98.21%), Postives = 55/56 (98.21%), Query Frame = -3
Query:  225 TERLLCLTCNFCKKNQVSILYEPCYHVVICRTCFVSSMKICQVCNAPIHQYHLIYI 392
            TERLLCLTCNFCKKNQVSILYEPCYHVVICRTCFVSSMKICQVCN PIHQYHLIYI
Sbjct:    1 TERLLCLTCNFCKKNQVSILYEPCYHVVICRTCFVSSMKICQVCNVPIHQYHLIYI 56          
BLAST of SMED30026593 vs. Planmine SMEST
Match: SMESG000067829.1 (SMESG000067829.1)

HSP 1 Score: 617.461 bits (1591), Expect = 0.000e+0
Identity = 307/310 (99.03%), Postives = 309/310 (99.68%), Query Frame = -3
Query:  225 MFRKKTKLLCYIFDEIKIFLGTDYISVDYYQLYEISESLTHFLIEYFHEKLAFSQPLLKLCCFVMHKNQIDISKENVFDCFWELMELRLKENYRIIINSWILNIDLIQRKILEIRKDKSVDYLKCQICGSCQVEISSLTRNNVVLCFGCYRFDRISSLIKFYQSFKPRELLSLLKSFEHEYVGSLHREFSYDVSLLKLCSWLEQSNGNLSKKGLSDCYRKLLIYKTIKKEFEKTFANIEKYVDEIEKQIPILLKTERLLCLTCNFCKKNQVSILYEPCYHVVICRTCFVSSMKICQVCNAPIHQYHLIYI 1154
            MFRKKTKLLCYIFDEIKIFLGTDYISVDYYQLYEISESLTHFLIEYFHEKLAFSQPLLKLCCFVMHKNQIDISKENVFDCFWELMELRLKENYRIIINSWILNIDLIQ+KILEIRKDKSVDYLKCQICGSCQVEISSLTRNNVVLCFGCYRFDRISSLIKFYQSFKPRELLSLLKSFEHEYVGSLHREFSYD+SLLKLCSWLEQSNGNLSKKGLSDCYRKLLIYKTIKKEFEKTFANIEKYVDEIEKQIPILLKTERLLCLTCNFCKKNQVSILYEPCYHVVICRTCFVSSMKICQVCN PIHQYHLIYI
Sbjct:    1 MFRKKTKLLCYIFDEIKIFLGTDYISVDYYQLYEISESLTHFLIEYFHEKLAFSQPLLKLCCFVMHKNQIDISKENVFDCFWELMELRLKENYRIIINSWILNIDLIQQKILEIRKDKSVDYLKCQICGSCQVEISSLTRNNVVLCFGCYRFDRISSLIKFYQSFKPRELLSLLKSFEHEYVGSLHREFSYDISLLKLCSWLEQSNGNLSKKGLSDCYRKLLIYKTIKKEFEKTFANIEKYVDEIEKQIPILLKTERLLCLTCNFCKKNQVSILYEPCYHVVICRTCFVSSMKICQVCNVPIHQYHLIYI 310          
BLAST of SMED30026593 vs. Planmine SMEST
Match: SMESG000067794.1 (SMESG000067794.1)

HSP 1 Score: 92.0485 bits (227), Expect = 1.426e-21
Identity = 61/162 (37.65%), Postives = 92/162 (56.79%), Query Frame = -3
Query:  225 SLIKFYQSFKPRELLSLLKSFEHEYVGSLHREFSYDVSLLKLCSWLEQSN-GNLSKKGLSDCYRKLLIYK-------TIKKEFEKTFANIEKYVDEIEKQIPILLKTERLLCLTCNFCKKNQVSILYEPCYHVVICRTCFVSSMKICQVCNAPIHQYHLIYI 686
             L+   Q+ +P +L  + +S  H  +  L + F ++ S+LK+C+ L Q N   +  + L+D + K    +       TI + + + F  IEK+++E  K+     K++    LTC  CK+NQVSILY PC H+V C TCFVSS K CQVC  PI  +HLIY+
Sbjct:   48 DLVSNPQNIEPFQLAQISESLRHPSIRFLRQTFDFNESILKMCTCLLQLNLMEIDNEILNDYFWKFSTLRLTDPDSRTIIQYWLENFEKIEKFIEERLKEFS---KSK----LTCFECKENQVSILYLPCGHLVTCGTCFVSSRKHCQVCETPIDNFHLIYL 202          

HSP 2 Score: 67.0106 bits (162), Expect = 1.228e-12
Identity = 44/136 (32.35%), Postives = 73/136 (53.68%), Query Frame = -3
Query:  693 LGTDYISVDYYQLYEISESLTHFLIEYFHEKLAFSQPLLKLCCFVMHKNQIDISKENVFDCFWELMELRLKE-NYRIIINSWILNIDLIQRKILEIRKDKSVDYLKCQICGSCQVEISSLTRNNVVLCFGCYRFDR 1097
            L ++  +++ +QL +ISESL H  I +  +   F++ +LK+C  ++  N ++I  E + D FW+   LRL + + R II  W+ N + I++ I E  K+ S   L C  C   QV I  L   ++V C  C+   R
Sbjct:   49 LVSNPQNIEPFQLAQISESLRHPSIRFLRQTFDFNESILKMCTCLLQLNLMEIDNEILNDYFWKFSTLRLTDPDSRTIIQYWLENFEKIEKFIEERLKEFSKSKLTCFECKENQVSILYLPCGHLVTCGTCFVSSR 184          
BLAST of SMED30026593 vs. Planmine SMEST
Match: SMESG000067794.1 (SMESG000067794.1)

HSP 1 Score: 92.0485 bits (227), Expect = 1.503e-21
Identity = 61/162 (37.65%), Postives = 92/162 (56.79%), Query Frame = -3
Query:  225 SLIKFYQSFKPRELLSLLKSFEHEYVGSLHREFSYDVSLLKLCSWLEQSN-GNLSKKGLSDCYRKLLIYK-------TIKKEFEKTFANIEKYVDEIEKQIPILLKTERLLCLTCNFCKKNQVSILYEPCYHVVICRTCFVSSMKICQVCNAPIHQYHLIYI 686
             L+   Q+ +P +L  + +S  H  +  L + F ++ S+LK+C+ L Q N   +  + L+D + K    +       TI + + + F  IEK+++E  K+     K++    LTC  CK+NQVSILY PC H+V C TCFVSS K CQVC  PI  +HLIY+
Sbjct:   49 DLVSNPQNIEPFQLAQISESLRHPSIRFLRQTFDFNESILKMCTCLLQLNLMEIDNEILNDYFWKFSTLRLTDPDSRTIIQYWLENFEKIEKFIEERLKEFS---KSK----LTCFECKENQVSILYLPCGHLVTCGTCFVSSRKHCQVCETPIDNFHLIYL 203          

HSP 2 Score: 66.6254 bits (161), Expect = 1.298e-12
Identity = 44/136 (32.35%), Postives = 73/136 (53.68%), Query Frame = -3
Query:  693 LGTDYISVDYYQLYEISESLTHFLIEYFHEKLAFSQPLLKLCCFVMHKNQIDISKENVFDCFWELMELRLKE-NYRIIINSWILNIDLIQRKILEIRKDKSVDYLKCQICGSCQVEISSLTRNNVVLCFGCYRFDR 1097
            L ++  +++ +QL +ISESL H  I +  +   F++ +LK+C  ++  N ++I  E + D FW+   LRL + + R II  W+ N + I++ I E  K+ S   L C  C   QV I  L   ++V C  C+   R
Sbjct:   50 LVSNPQNIEPFQLAQISESLRHPSIRFLRQTFDFNESILKMCTCLLQLNLMEIDNEILNDYFWKFSTLRLTDPDSRTIIQYWLENFEKIEKFIEERLKEFSKSKLTCFECKENQVSILYLPCGHLVTCGTCFVSSR 185          
BLAST of SMED30026593 vs. Planmine SMEST
Match: SMESG000067788.1 (SMESG000067788.1)

HSP 1 Score: 90.5077 bits (223), Expect = 6.984e-21
Identity = 56/158 (35.44%), Postives = 86/158 (54.43%), Query Frame = -3
Query:  225 RISSLIKFYQSFKPRELLSLLKSFEHEYVGSLHREFSYDVSLLKLCSWLEQSNG-NLSKKGLSDCYRKLLIYKTIKKEFEKTFANIEKYVDEIEKQIPILLKTERLLCLTCNFCKKNQVSILYEPCYHVVICRTCFVSSMKICQVCNAPIHQYHLIYI 695
             I  L + Y     + LL +LK F++  +   H  F Y+  +LKLCS+L + N  N++ + L+D +               +F N+ + +D IEK++  ++K      LTC  C+KN VSILY PC HVV+C  C+  S K CQ C + I ++H+IYI
Sbjct:   68 EIDELFRNYAKLNSKILLEILKLFKNSSIKFCHETFGYNKKILKLCSFLMERNKVNINHENLNDYFW--------------SFMNLSQ-LDGIEKEMCEIVKERNKQLLTCMGCQKNSVSILYLPCGHVVMCNKCYQISTKHCQACGSSIEEFHVIYI 210          

HSP 2 Score: 62.7734 bits (151), Expect = 3.654e-11
Identity = 38/129 (29.46%), Postives = 67/129 (51.94%), Query Frame = -3
Query:  702 DYISVDYYQLYEISESLTHFLIEYFHEKLAFSQPLLKLCCFVMHKNQIDISKENVFDCFWELMELRLKENYRIIINSWILNIDLIQRKILEIRKDKSVDYLKCQICGSCQVEISSLTRNNVVLCFGCYR 1088
            +Y  ++   L EI +   +  I++ HE   +++ +LKLC F+M +N+++I+ EN+ D FW  M L                +D I++++ EI K+++   L C  C    V I  L   +VV+C  CY+
Sbjct:   75 NYAKLNSKILLEILKLFKNSSIKFCHETFGYNKKILKLCSFLMERNKVNINHENLNDYFWSFMNLS--------------QLDGIEKEMCEIVKERNKQLLTCMGCQKNSVSILYLPCGHVVMCNKCYQ 189          
BLAST of SMED30026593 vs. Planmine SMEST
Match: SMESG000067789.1 (SMESG000067789.1)

HSP 1 Score: 87.4261 bits (215), Expect = 9.987e-20
Identity = 52/160 (32.50%), Postives = 86/160 (53.75%), Query Frame = -3
Query:  225 ISSLIKFYQSFKPRELLSLLKSFEHEYVGSLHREFSYDVSLLKLCSWLEQSNGNLSKKGLSDCYRKLLIYK----TIKKEFEKTFANIEKYVDEIEKQIPILLKTERLLCLTCNFCKKNQVSILYEPCYHVVICRTCFVSSMKICQVCNAPIHQYHLIYI 692
            +   I  Y +F  +E++++LK F++  +  L   F+YD  +LKL S+L      L K G+ +       +      +  E+ + F    +  D IE ++   L   +   LTC+ CK+NQVS+LY PC HV++C  C   + + CQ C+API++YH IY+
Sbjct:   56 VEDFINTYDTFTDKEIINILKIFKNPSIEYLIDIFNYDKCILKLSSYLMY----LDKTGMDNDSLNEYFWDCMELRLNPEYSRLFKEWIRKSDFIEDKLTEKLNDVKKRYLTCSICKENQVSVLYLPCGHVIVCSKCQDKNNRKCQACSAPINEYHAIYV 211          

HSP 2 Score: 60.077 bits (144), Expect = 3.026e-10
Identity = 33/106 (31.13%), Postives = 55/106 (51.89%), Query Frame = -3
Query:  708 IEYFHEKLAFSQPLLKLCCFVMHKNQIDISKENVFDCFWELMELRLKENYRIIINSWILNIDLIQRKILEIRKDKSVDYLKCQICGSCQVEISSLTRNNVVLCFGC 1025
            IEY  +   + + +LKL  ++M+ ++  +  +++ + FW+ MELRL   Y  +   WI   D I+ K+ E   D    YL C IC   QV +  L   +V++C  C
Sbjct:   83 IEYLIDIFNYDKCILKLSSYLMYLDKTGMDNDSLNEYFWDCMELRLNPEYSRLFKEWIRKSDFIEDKLTEKLNDVKKRYLTCSICKENQVSVLYLPCGHVIVCSKC 188          
The following BLAST results are available for this feature:
BLAST of SMED30026593 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 SMED30026593 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 SMED30026593 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 SMED30026593 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 SMED30026593 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 SMED30026593 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 SMED30026593 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 SMED30026593 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZIH91.699e-2898.21IAP domain containing-1 (Fragment) OS=Schmidtea me... [more]
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BLAST of SMED30026593 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 SMED30026593 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 SMED30026593 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 SMED30026593 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 SMED30026593 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 SMED30026593 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000067829.10.000e+099.03SMESG000067829.1[more]
SMESG000067794.11.426e-2137.65SMESG000067794.1[more]
SMESG000067794.11.503e-2137.65SMESG000067794.1[more]
SMESG000067788.16.984e-2135.44SMESG000067788.1[more]
SMESG000067789.19.987e-2032.50SMESG000067789.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026593 ID=SMED30026593|Name=SMED30026593|organism=Schmidtea mediterranea sexual|type=transcript|length=1237bp
TGCCGCTGGAAATAGAAAATGAATTTTGGACTTTTCTTTTGGCAAAATAC
CTCATTAAAATCGAAACCGTCAAATATAAAAGCAGAACGTATTGGAATAA
AATATGTCACCACTGAACAATTAATCTTTGAAAGACATTTAATTAGTGAA
TTTCGGCTCGATTTTGAAAATAATATATTTATTATTCTAAAAAATTTTTT
GGGATTTCTGAAAATGCGCTGCTAGATGTAGATCAGATGATATTGATGAA
TGGGCGCATTGCAGACTTGGCAAATTTTCATACTACTCACAAAGCAAGTT
CTACAGATAACCACATGATAACATGGCTCATAAAGTATAGAAACTTGATT
TTTTTTACAAAAATTGCAAGTCAAGCACAATAAACGTTCTGTTTTCAATA
AAATCGGTATTTGTTTCTCTATTTCATCGACATATTTCTCTATGTTTGCA
AATGTTTTCTCAAATTCTTTCTTAATTGTTTTATATATTAGCAATTTCCT
GTAACAATCACTCAACCCTTTTTTACTCAAATTGCCATTCGATTGCTCTA
ACCAGCTGCACAGTTTCAATAAAGATACATCGTAACTGAATTCACGGTGC
AAACTACCAACGTATTCATGTTCGAAAGACTTTAAAAGGCTCAATAATTC
CCTTGGTTTGAAAGACTGATAAAACTTGATCAAGCTGGAAATCCGATCGA
ACCGATAGCAACCGAAACACAAAACAACATTGTTGCGAGTCAGAGAAGAA
ATCTCCACTTGACAACTGCCACAAATTTGACATTTTAAATAATCTACACT
TTTATCCTTCCGAATTTCCAAAATTTTCCGTTGAATTAAGTCGATATTTA
ATATCCAACTATTTATAATTATTCGGTAATTTTCTTTTAATCTCAATTCC
ATCAACTCCCAGAAACAGTCAAAAACGTTTTCTTTAGAAATATCAATTTG
GTTTTTATGCATTACGAAGCAGCATAATTTCAATAGTGGCTGTGAAAATG
CTAATTTTTCGTGAAAATATTCAATCAGAAAATGTGTCAGTGACTCTGAA
ATTTCATAAAGTTGATAGTAATCCACTGAAATATAATCTGTACCTAGGAA
AATTTTGATTTCATCGAAAATGTAGCATAATAATTTAGTTTTTTTTCGAA
ACATCTTCGTTTGAAAAGAAATTCTAAAAAATACAAAAAAAAGTAAAAAG
TGATTTTCTAAAACATTTCAACTACATTTTCGATGAA
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protein sequence of SMED30026593-orf-1

>SMED30026593-orf-1 ID=SMED30026593-orf-1|Name=SMED30026593-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=311bp
MFRKKTKLLCYIFDEIKIFLGTDYISVDYYQLYEISESLTHFLIEYFHEK
LAFSQPLLKLCCFVMHKNQIDISKENVFDCFWELMELRLKENYRIIINSW
ILNIDLIQRKILEIRKDKSVDYLKCQICGSCQVEISSLTRNNVVLCFGCY
RFDRISSLIKFYQSFKPRELLSLLKSFEHEYVGSLHREFSYDVSLLKLCS
WLEQSNGNLSKKGLSDCYRKLLIYKTIKKEFEKTFANIEKYVDEIEKQIP
ILLKTERLLCLTCNFCKKNQVSILYEPCYHVVICRTCFVSSMKICQVCNA
PIHQYHLIYI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR013083Znf_RING/FYVE/PHD
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 228..248
IPR013083Zinc finger, RING/FYVE/PHD-typeGENE3DG3DSA:3.30.40.10coord: 240..310
e-value: 9.3E-7
score: 30.2