SMED30023250

Overview
NameSMED30023250
Smed IDSMED30023250
Length (bp)5057
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 SMED30023250 (SMED30023250) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023250 (SMED30023250) 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 SMED30023250 (SMED30023250) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023250 (SMED30023250) 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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Alignments
SMED30023250 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005302:9080..13556 -16794
Homology
BLAST of SMED30023250 vs. TrEMBL
Match: A0A3Q0KCA4 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 3.658e-6
Identity = 58/218 (26.61%), Postives = 100/218 (45.87%), Query Frame = 1
Query:  208 FTDKFTSIIDLDAINKEFNDVIDRLKSLYENHYTVYLNPEVVLDTQIA-INTGDQREMKPLRQFANLILQNDSSILNLELDMTSYAA---------YVDSAIKGLHNVGISATKS----------GNGLSIIVSISSP----------TPQSRADLGKQCKEKLHKTNKELDKVYEKHCKKLRNKEIIAMVSKEELVNCAEHLKMQVKKYHEESEKLF 771
             T +  S +  D +NKEF +V+ R ++      ++ + P+   D  +  +N         L Q AN+ILQN     N+  +MTS  +         Y+   + G   + +SA K+          G+G S + ++S            T +SR     Q  E LH+T  E+DK+Y  H K L +KE    +S+++L    E+L+  VK+ H+ +E ++
Sbjct:   62 ITAEVLSFLKEDKMNKEFQNVLSRFQNFIVQRLSLRMTPQTFFDIMLPELNV-------KLGQVANIILQN-----NMNQNMTSKDSHNKANLGNQYLLVDLTGRPELFVSARKAVIAFLDPCKDGSGESRVQTVSQCAFTIQLNTVITKESRQRALAQGHELLHQTIHEMDKIYHAHNKLLNSKEAKEKLSEDDLFMAREYLRTVVKEQHKLAESMW 267          
BLAST of SMED30023250 vs. Planmine SMEST
Match: SMESG000024775.1 (SMESG000024775.1)

HSP 1 Score: 282.722 bits (722), Expect = 5.469e-88
Identity = 137/137 (100.00%), Postives = 137/137 (100.00%), Query Frame = 1
Query:  376 MKPLRQFANLILQNDSSILNLELDMTSYAAYVDSAIKGLHNVGISATKSGNGLSIIVSISSPTPQSRADLGKQCKEKLHKTNKELDKVYEKHCKKLRNKEIIAMVSKEELVNCAEHLKMQVKKYHEESEKLFQWKTE 786
            MKPLRQFANLILQNDSSILNLELDMTSYAAYVDSAIKGLHNVGISATKSGNGLSIIVSISSPTPQSRADLGKQCKEKLHKTNKELDKVYEKHCKKLRNKEIIAMVSKEELVNCAEHLKMQVKKYHEESEKLFQWKTE
Sbjct:    1 MKPLRQFANLILQNDSSILNLELDMTSYAAYVDSAIKGLHNVGISATKSGNGLSIIVSISSPTPQSRADLGKQCKEKLHKTNKELDKVYEKHCKKLRNKEIIAMVSKEELVNCAEHLKMQVKKYHEESEKLFQWKTE 137          
BLAST of SMED30023250 vs. Planmine SMEST
Match: SMESG000066109.1 (SMESG000066109.1)

HSP 1 Score: 42.743 bits (99), Expect = 7.202e-10
Identity = 23/59 (38.98%), Postives = 37/59 (62.71%), Query Frame = 2
Query: 4013 ERRITHRELSSRLNVTKKTV*NILEAIGIRNLWIRFVPRFLTEEIRKKQM*KFQENLTI 4189
            ER IT +EL  RLN++   V  IL+ +G R L  R+ PRFL+ E+ + ++   Q+ L++
Sbjct:  748 ERWITLKELQRRLNISDGKVREILKDLGTRKLASRYFPRFLSGEMCQVRLECCQQCLSL 806          

HSP 2 Score: 41.9726 bits (97), Expect = 7.202e-10
Identity = 35/94 (37.23%), Postives = 46/94 (48.94%), Query Frame = 3
Query: 3750 HSQRFVLKKMSASTISQRYLFLLFS*TGMKDIIYQLHGAY*NDPPSKATIYNWIREFSSGRNNVFVEERSERLHEIDEKFENLNFIGKRDELLT 4031
            H Q FV   M+         FL+   T   +I  QL   Y     SK T+Y+WI ++  GR +VF +ERS R  EID   EN   I KR E++ 
Sbjct:  657 HIQNFVKIAMNPVEYRSVIKFLVIRQTESSEISSQLSSTYGTTALSKTTVYHWIAQYRRGRQSVFDDERSGRPVEIDH--EN---IAKRCEIIV 745          
The following BLAST results are available for this feature:
BLAST of SMED30023250 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 SMED30023250 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 SMED30023250 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 SMED30023250 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 SMED30023250 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 SMED30023250 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 SMED30023250 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 SMED30023250 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A3Q0KCA43.658e-626.61Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
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BLAST of SMED30023250 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 SMED30023250 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 SMED30023250 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 SMED30023250 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 SMED30023250 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 SMED30023250 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000024775.15.469e-88100.00SMESG000024775.1[more]
SMESG000066109.17.202e-1038.98SMESG000066109.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023250 ID=SMED30023250|Name=SMED30023250|organism=Schmidtea mediterranea sexual|type=transcript|length=5057bp
TTTTTGTTTTGTTTATTTATTAATTAAAAAATGTTTAAATTTAAATCGTT
ATTTCTTTTAGTTTCAAGGATAGCTTTCAAAAATGTCAATCAAAAAATCA
GTTATTTTCCTCACTTTGGATTATTTTCTCAAAATAATTTAAATTTATTT
GCTATTCAAATTAACATAAAAAGATGTAAATCCAAATTAAAAGAAAAAAA
ATTTGTTTTTACTGACAAATTTACTTCTATAATAGATCTAGATGCAATAA
ATAAGGAATTCAATGATGTAATTGACCGTTTGAAATCGTTGTACGAGAAT
CATTACACCGTTTATTTGAATCCAGAAGTTGTTCTTGATACTCAAATCGC
GATAAACACTGGAGATCAAAGAGAAATGAAACCTCTAAGGCAGTTTGCCA
ATTTAATTTTGCAGAATGATTCATCAATCTTAAATTTAGAACTTGATATG
ACGTCTTATGCTGCTTATGTGGATAGTGCAATCAAGGGTTTGCATAATGT
AGGAATATCCGCCACTAAATCAGGCAATGGGTTATCTATTATAGTGTCGA
TTTCTTCACCAACTCCCCAATCGCGTGCTGATCTGGGAAAACAATGCAAA
GAAAAGTTACACAAAACTAACAAGGAACTCGACAAAGTCTATGAGAAACA
CTGTAAAAAGTTGCGCAATAAAGAAATCATTGCGATGGTCAGCAAAGAAG
AATTAGTGAATTGCGCTGAACATTTAAAAATGCAAGTGAAAAAATATCAC
GAAGAATCTGAAAAATTATTTCAATGGAAAACTGAATTACTAAAAAAATG
AAAAACATTTTTGTTCGCTTTTAAATTTGTGTAAATAATTAAGATTTAGT
TTTTTTAGAATTTGGCGGTTGTTTTAATATTCGTTATTTTTATTGCCAAT
TTAATTTATTGGGTAAATTTGAAATTGGATTTTAATTGAAGATTTTTAAC
TTTCAATAATTGTTTTATGGCTTTAAATCGGATGAGTTCATTTAAGTCAA
CAAAATTGTTTCAAATGTAGGGTTCCCAAAACATATCTTTTAAAGAGAAC
ATGTTGTCTTTTTTTTGGATTTTTTTTAACTCTTTAGTGAAGTTCTCCTT
TGTTCTCTATTTGGGTTTTAAATGAATTTAACCAAATGAAATTTAACCAG
TAACATTTTTTTCGTAATAAATTAATTTGAATACTATAAGCAACGATTTA
TCCGTGATTCGGTATTTACTAATTTGAATGTCCCTTTTTTCAGTTTGTTT
TTCTGTACCCAATAATATGTCATTCTAAAAATTTCAATTCAGACTAATAT
ATAAGGAAAATTAGATATTTAACAAAAAAGAAGAATAAACTATAATATTA
AGTAGTAAATTATATTTAAAAGTTTGATTGATTGATTTATGCTTAAAATT
ATACTAAGTTATTTATAACACTTAATTAAATTTTAAAAATTAATAAAGTA
AAAAAATTCCGTGTATAGCCCTCACCATGTAAATTTACTTTGAATTTATT
TTTTTATATAAGCCCCGAGTTATACGCCGAAATTTAAGGTATATTAGCAG
TATCTATATACAGATAATATAGGACAAAAACTACTTTGTTTATTCTAATT
TAATTTCAAACATCCATTAATAACATTTTATCTACTAATTATCAAAATAG
TGAAAATTTTGAAATTGAAATCATACATAATATAAATTTAAGTAATATTA
ATTACTCTGATTCGGATGATAAATTTTATGCTCCTGGTAAAATTATGGAA
TTAACACCAAATAAATGTGCAAAAAATATATTAAATTATGGAAAGAAATC
TAAATGAAATAAATACACAATTTTAGAACAATTTTGAACCTTGGAAATCG
CTAGTAAACAAGAATAGCCGCATGATATTAAAATAAAATAAGGCCAATGT
TCAATAAATCACATGAAAAGTAAATATGTAAATTTGTCGTAGTATTTAAA
AACTTTCCCATTTTATTCCCAAGAACTTCGAGAATAACAGCAAATGCTTC
TGTTTACCTAATTCCATCAAGTGTATTCGATTTATTAACAAAATTAAAAG
TAAACAATCGTAAAACCTATTTTTCAAAAATCTAACCTTGAATAATTTAT
GAATATTATAAAATGTACTTATACTTCAAGCATAGAAGTGACAATTATTA
AAAAAAAGCATATTTATATGATCGAATTGGAACTTACAATTAGAATTTGC
AATAACCTGTTTCATCATAATTCTAAAGTATAGTAAGAACGTAATTGTAA
GAGGATTTTTCAGTGTTGAGAAATATTAAAAATACATTTTTAAAAAACGG
TGAGATAAAATTCTTGGCCTATAGTGCACGGCCGTATAAATATTTTGCAG
CGTGTAAAGAGCTAAATATTAGTATACTTTCTTAGAATTATTTTTCAATT
TTGTCATTTTTTATTTTATAAAAAAAACGTTGATCTATAATCGGAATATA
ATGAAGACAAATGATATTAATATGCATTTGTAGATTAACGGTTTTCCTAC
ACATATGAGAAACACTGCAATAAATTATCCGATTATGTAATAATTTCAAA
CATTAATTAACCGTTTAATTACGAAATATTTTTTAGGTTTAAAGGCTCTG
AACAACGGAAACGCACACTCCTCGTAACAACCATGCATAAATAAGTTAAA
TATATACATTTATTGTTGTATAACACACTGTAAAAATTCATAGAAAATAT
ACGCTCTTCGTTCATTGGACACATACATAACGAAAGGGTTCATATATATG
GTATATTTTACATGTATGATCGTGTGTTAACATCCTAACGTATATATTAA
TAACATTTTCAGAAACTGCTTATACAAACTTGTGGATTTTATAAAGCTCT
GTGGTTAATCTAGAATTTATGATTGTAAATTTTATAAAGCCGTCATAAAT
ATAGAGTAGCAACAAATAGTTAATTAAATTTGGTCAAATAGATAGATAAT
TATTTTAAATACAATCAACATTGTCGATAACCTGTTCCATTTAAAACCCT
TTGAATATAACCATACTTTCTCGATAAGTCCTGTACACTAGAAAACATTT
GAATTTCTTGTAAACTAACACAGTATTGAACTAATGAAGCGAAGTCACAT
TCACAAATTGAACACACTTTTTGAATGAAATGGGTGCTAAAAGTGGATGA
CTTTACATTTAATACATGCATTTTCGCAGATTTTACTTGCATATTTGTCT
TTTTAATTTTCTCTTTATCAATGTCAAAACTCACAGTCTAGTATTGATAT
TTAATCTCATGGATTGAAATTGTTTTTCAGAAAAAATTAAAAAAATGTTC
GAATCTCATATTTATTTTTTGAACCACTCGATGTCACTTGTCATTTAATC
TCCCCCCTATCAGCTTTCTAATTTAAGCATATGGAAGTCTCATCCTCGAC
TTAATGGAATATTTTATAGTTCAATGCCGAGTATATTATGTATAATATAG
TAATCTGTCTCCGAGCCGAGATGTCAAAAGATTTGTCTTTCTTGTCTGGT
TTTAAAATCAGTTTTGTGTTGAATGTTTTGTATTTTATCTAATTTGATAC
TATTCGTTAAAATGTTATTACGTAAATTGAAAGAAACAAGTTCAAATTTA
AAATAGATTTTTCCCCAAGAGATTAATTAATTATGTGGTGTGGATAAAAA
GTCTTTAGACTCGTATAGAAATGAAATTAATTAATCCGTAAAATTAAAAC
CGCAAAACAAAAATTATTGAGTTTTTTTTACCTATAGAACGTCTATTGGC
ATAGCCAACGCTTTGTTTTAAAAAAAATGTCAGCAAGTACAATTTCACAG
CGTTATCTTTTTTTACTTTTCAGTTAGACAGGAATGAAGGACATCATTTA
TCAGCTGCATGGAGCATATTAAAATGACCCACCAAGTAAGGCTACTATTT
ATAATTGGATTAGAGAGTTTTCCTCTGGCAGGAACAATGTGTTTGTTGAA
GAAAGAAGTGAACGACTCCATGAAATTGACGAGAAATTCGAAAATTTGAA
TTTTATTGGTAAGAGAGACGAATTACTCACAGAGAGCTGTCAAGTAGACT
TAATGTAACCAAGAAGACTGTGTAGAACATACTGGAAGCTATAGGAATCA
GAAACTTATGGATTCGATTCGTCCCACGTTTCTTGACAGAAGAGATCCGT
AAAAAGCAAATGTAAAAATTTCAAGAAAATCTGACAATCTTTCATGTTCT
TAAGCATAATATTTTAAAGAAAAATTTATAACGAATGATGAGAAGCATTT
GAATCTTTATGTTACAGTAAGCGCGAGTCTCGTGAATGGATTTTTCTGAG
GAAAGGTCACTAAAAATGTTTCGTCCACAAACATCTTACAAAAAGTGTCT
TATACTCAATGTGTTTTGAGATGAAAAGATGTAATCAAGACTGACTTTAC
TCCATAAATCATCAACTCTCACTACTATTGTGCACTGAGAAAGTTGCGAT
AGAAGCCCAGGATATTTTTTAAATTTTCTTTTCTGTATGATTTCACTCAA
ATCACACAATTTTTCAGATGGAATTTTCGAATTATTTTTGTAATTGGACA
TCTGAGAGATTTGATTTGAAAATTTGTTCCCCTTTTTACTTAAAATTTTG
TTAAGTATTTAGTGAATATGATTTAATTTTTAAAATTACCACTGATGATC
TCACACCTGACTTTGCTTTCTTGATAAATTATTGGCTCCTGAAACCTGTA
AGCCTTTACTAGTAGTGAGCATTGTGTATTTAGATTTTTTCATTAACCTT
AGGTTTCAGAACCATCATAACAAAAATATTTACATAAAAATTGTTTGATC
TTTCAAAATCTTGGCATGATGAAAATTTAATTAACAATAAATTGGAAAAT
CAAAAAAATATATCTAATTATTTACAATAAGTAGGAAGAAAGGCTAAAAA
ATTCGATTGAAATTTGAGACAGTTAATAATTTTATTATTAATCTTATTAC
CCATCAAATTTGATTCTCGTTTTACGAATTATTATTAAATTTTTGTGATT
AATTCGTCTCAATTAAAAATAATAGAAACTCACCCAGTATCATACATCAG
CGCCAAA
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protein sequence of SMED30023250-orf-1

>SMED30023250-orf-1 ID=SMED30023250-orf-1|Name=SMED30023250-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=257bp
MFKFKSLFLLVSRIAFKNVNQKISYFPHFGLFSQNNLNLFAIQINIKRCK
SKLKEKKFVFTDKFTSIIDLDAINKEFNDVIDRLKSLYENHYTVYLNPEV
VLDTQIAINTGDQREMKPLRQFANLILQNDSSILNLELDMTSYAAYVDSA
IKGLHNVGISATKSGNGLSIIVSISSPTPQSRADLGKQCKEKLHKTNKEL
DKVYEKHCKKLRNKEIIAMVSKEELVNCAEHLKMQVKKYHEESEKLFQWK
TELLKK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR036191RRF_sf
IPR023584Ribosome_recyc_fac_dom
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:1.10.132.20coord: 75..252
e-value: 1.3E-13
score: 52.8
NoneNo IPR availableGENE3DG3DSA:3.30.1360.40coord: 95..177
e-value: 1.3E-13
score: 52.8
IPR023584Ribosome recycling factor domainPFAMPF01765RRFcoord: 96..251
e-value: 5.4E-12
score: 46.0
IPR036191RRF superfamilySUPERFAMILYSSF55194Ribosome recycling factor, RRFcoord: 70..252