Coagulation factor 5/8 type domain protein

Overview
NameCoagulation factor 5/8 type domain protein
Smed IDSMED30017166
Length (bp)965
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 Coagulation factor 5/8 type domain protein (SMED30017166) t-SNE clustered cells

Violin plots show distribution of expression levels for Coagulation factor 5/8 type domain protein (SMED30017166) 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 Coagulation factor 5/8 type domain protein (SMED30017166) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Coagulation factor 5/8 type domain protein (SMED30017166) 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.
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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



SMED30017166

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30017166SMESG000024895.1 SMESG000024884.1 SmedASXL_015416SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30017166SMESG000024895.1 SmedASXL_074011SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30017166SMESG000024895.1 dd_Smed_v4_28554_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30017166SMESG000024895.1 dd_Smed_v4_28554_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30017166SMESG000024895.1 dd_Smed_v4_28554_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of Coagulation factor 5/8 type domain protein vs. Planmine SMEST
Match: SMESG000046841.1 (SMESG000046841.1)

HSP 1 Score: 167.548 bits (423), Expect = 3.048e-50
Identity = 100/219 (45.66%), Postives = 149/219 (68.04%), Query Frame = 1 
Query:  259 KEILISRSRPTFSS--LGNNYYYGPEKAVDGNYDGNMKNGFCYHSVLTSAVKWWLIVLDXXXXXXXXXXXXXXXXXXXXXXXLYFYVGFQNFSQFLNDNLNFHNIYYYPGPPASGQSVSEFSLTRVFARSLAISKSFEDDAINICELEIYGYSIVKSNS-TYMFSQSLNLYKNMA-YEQRKVRSKLECGKICSETDSCLSFTFMITYQCFIYSHPGGEY 903
            +  L+SR RPTF++  + N  Y+  +KAVDGNYDGNM +G CYHS   ++ KWWLI+LDS+SVV+R+VIYSRT+CCT RTS L FYV + N +    ++ +F N+ YYPG P  G+ ++  + TR++AR+LAISK F +   N+CELE+YGY  +K+   T+ + ++L++Y ++       V S L+   IC +   C+SF+   + +CFIY+H GGE+
Sbjct:   22 QNALLSRGRPTFAANVIDNQPYWSSDKAVDGNYDGNMVDGHCYHSKELNSTKWWLIILDSLSVVTRVVIYSRTECCTQRTSLLSFYVSYTNSTSLSTNSNDFTNVSYYPGSPPPGEFITTLNFTRLYARTLAISKPFAEQPFNLCELEVYGYPFIKTMPMTFKYLRALSIYDSLGNIGTFPVLSNLDSAMICLQEAKCISFSVQFSVKCFIYAHIGGEF 240
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BLAST of Coagulation factor 5/8 type domain protein vs. Planmine SMEST
Match: SMESG000046835.1 (SMESG000046835.1)

HSP 1 Score: 164.081 bits (414), Expect = 3.422e-47
Identity = 104/220 (47.27%), Postives = 148/220 (67.27%), Query Frame = 1 
Query:  268 LISRSRPTFSS--LGNNYYYGPEKAVDGNYDGNMKNGFCYHSVLTSAVKWWLIVLDXXXXXXXXXXXXXXXXXXXXXXXLYFYVGFQNFSQFLNDNLNFHNIYYYPGPPASGQSVSEFSLTRVFARSLAISKSFEDDAINICELEIYGYSIVKSNST---YMFSQSLNLYKNMA-YEQRKVRSKLECGKICSETDSCLSFTFMITYQCFIYSHPGGEYHL 909
            L+SRSRPTF++  + N   +  +KAVDGNYD NM +G+CYHS   ++ KWWL++LDS+SVV+R+VIYSRT+CCT RTS L FYV + N +    ++ +F NI YY GPP  G+ ++  + TR++ R+LAISK F + A+NICELE+YGY+ +K  S    Y   QS  LY ++  +    V+S ++C  IC +   CLSF+      CFIY+H GGE+ +
Sbjct:  191 LLSRSRPTFAANVIANYPLWTSDKAVDGNYDCNMHHGYCYHSEELNSTKWWLVILDSLSVVTRVVIYSRTECCTQRTSLLSFYVSYTNSTSLSTNSNDFVNISYYVGPPPPGEFITTLNFTRLYMRTLAISKPFGEQALNICELEVYGYTFIKKMSMIFKYFGRQS--LYDSLGNFGTFPVQSNIDCAIICLQEAKCLSFSVQFGVSCFIYAHIGGEFSI 408
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BLAST of Coagulation factor 5/8 type domain protein vs. Planmine SMEST
Match: SMESG000024886.1 (SMESG000024886.1)

HSP 1 Score: 155.221 bits (391), Expect = 2.923e-45
Identity = 98/217 (45.16%), Postives = 143/217 (65.90%), Query Frame = 1 
Query:  262 EILISRSRPTFSSLGNNY-YYGPEKAVDGNYDGNMKNGFCYHSVLTSAVKWWLIVLDXXXXXXXXXXXXXXXXXXXXXXXLYFYVGFQNFSQFLNDNLNFHNIYYYPGPPASGQSVSEFSLTRVFARSLAISKSFEDDAINICELEIYGYSIVKSNST-YMFSQSLNLYKNMA-YEQRKVRSKLECGKICSETDSCLSFTFMITYQCFIYSHPGGEY 903
            ++++SR RPTF ++   Y  + P+KAVDGNYDGN  NG C+HS   +  KWWL++LDS+SVV+++VIYSRTDCCT RTS + FYV ++N +   N+  +F NI YY GPP  G+ ++  +  R++AR+LAISK    D IN+CELE+YGY ++KS  T + +  +L+LY ++       V S L+C   C   + C SF+  +   CF Y H GG++
Sbjct:   40 DLILSRGRPTFGTIIAGYSVWEPQKAVDGNYDGNQFNGSCFHSEGPNVNKWWLVILDSLSVVTKVVIYSRTDCCTNRTSFISFYVSYKNSTSLTNNMNDFFNISYYAGPPPPGEIITTLNFKRLYARTLAISKPLAADHINLCELEVYGYPLIKSMFTLFKYFGTLSLYDSLGNVGIFTVVSNLDCALKCLLNEKCYSFSVQLKVYCFNYGHTGGDF 256
[Close]
BLAST of Coagulation factor 5/8 type domain protein vs. Planmine SMEST
Match: SMESG000024705.1 (SMESG000024705.1)

HSP 1 Score: 152.525 bits (384), Expect = 1.745e-44
Identity = 100/217 (46.08%), Postives = 148/217 (68.20%), Query Frame = 1 
Query:  259 KEILISRSRPTFSSLGNNYYYGPEKAVDGNYDGNMKNGFCYHSVLTSAVKWWLIVLDXXXXXXXXXXXXXXXXXXXXXXXLYFYVGFQNFSQFLNDNLNFHNIYYYPGPPASGQSVSEFSLTRVFARSLAISKSFEDDAINICELEIYGYSIVKSNS-TYMFSQSLNLYKNMA-YEQRKVRSKLECGKICSETDSCLSFTFMITYQCFIYSHPGGEY 903
            ++ L+S  RPTF++    + +  +KAVDGNY+GNM  G CYHS   +  KWWL++LDS+SVV+++VIYSRTDCCT RTS L FYV +++ +   N+N +F N+ YY GPP  G+ ++  + TR++AR+LAISK   +DAIN+CELE+YGY   K+ S T+ +  +L++Y ++  +    V+S L+C  IC     CLSF+     +CFIY H GG++
Sbjct:   22 EDSLLSIGRPTFAN-NAMFPWTSDKAVDGNYNGNMSKGSCYHSETFNYDKWWLVILDSLSVVTKVVIYSRTDCCTQRTSLLSFYVSYKSSTSLSNNNNDFVNVSYYAGPPPPGEFITTLNFTRLYARTLAISKPSLEDAINLCELEVYGYPFTKTMSMTFKYFGALSIYDSLGNFGTFPVQSNLDCAMICLLEAKCLSFSVQFGVKCFIYFHTGGDF 237
[Close]
BLAST of Coagulation factor 5/8 type domain protein vs. Planmine SMEST
Match: SMESG000024705.1 (SMESG000024705.1)

HSP 1 Score: 152.525 bits (384), Expect = 4.170e-44
Identity = 102/219 (46.58%), Postives = 149/219 (68.04%), Query Frame = 1 
Query:  259 KEILISRSRPTFSSLGNN--YYYGPEKAVDGNYDGNMKNGFCYHSVLTSAVKWWLIVLDXXXXXXXXXXXXXXXXXXXXXXXLYFYVGFQNFSQFLNDNLNFHNIYYYPGPPASGQSVSEFSLTRVFARSLAISKSFEDDAINICELEIYGYSIVKSNS-TYMFSQSLNLYKNMA-YEQRKVRSKLECGKICSETDSCLSFTFMITYQCFIYSHPGGEY 903
            ++ L+S  RPTF+   NN  + +  +KAVDGNY+GNM  G CYHS   +  KWWL++LDS+SVV+++VIYSRTDCCT RTS L FYV +++ +   N+N +F N+ YY GPP  G+ ++  + TR++AR+LAISK   +DAIN+CELE+YGY   K+ S T+ +  +L++Y ++  +    V+S L+C  IC     CLSF+     +CFIY H GG++
Sbjct:   61 EDSLLSIGRPTFA---NNAMFPWTSDKAVDGNYNGNMSKGSCYHSETFNYDKWWLVILDSLSVVTKVVIYSRTDCCTQRTSLLSFYVSYKSSTSLSNNNNDFVNVSYYAGPPPPGEFITTLNFTRLYARTLAISKPSLEDAINLCELEVYGYPFTKTMSMTFKYFGALSIYDSLGNFGTFPVQSNLDCAMICLLEAKCLSFSVQFGVKCFIYFHTGGDF 276
The following BLAST results are available for this feature:
BLAST of Coagulation factor 5/8 type domain 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 Coagulation factor 5/8 type domain 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 Coagulation factor 5/8 type domain 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 Coagulation factor 5/8 type domain 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 Coagulation factor 5/8 type domain 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 Coagulation factor 5/8 type domain 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 Coagulation factor 5/8 type domain 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 Coagulation factor 5/8 type domain protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Coagulation factor 5/8 type domain 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 Coagulation factor 5/8 type domain 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 Coagulation factor 5/8 type domain 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 Coagulation factor 5/8 type domain 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 Coagulation factor 5/8 type domain 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 Coagulation factor 5/8 type domain protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000046841.13.048e-5045.66SMESG000046841.1[more]
SMESG000046835.13.422e-4747.27SMESG000046835.1[more]
SMESG000024886.12.923e-4545.16SMESG000024886.1[more]
SMESG000024705.11.745e-4446.08SMESG000024705.1[more]
SMESG000024705.14.170e-4446.58SMESG000024705.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017166 ID=SMED30017166|Name=Coagulation factor 5/8 type domain protein|organism=Schmidtea mediterranea sexual|type=transcript|length=965bp
AGAGAGGACAATTAAAAATAATAAAAATTCCCTAGTGTTTTTGTCACCAC
TGTTCAAAGATAAACGAAACAAAAGTTCATATTCCACAAATAAGAGAAAA
CAATAAAACCGTTCAGTTACATTTCTAAATAGAATGTCGTTCGACATTAT
TGGCTCTGGAGTCGTATTTATTCCGTCTGAGGTTGTGAGGAAACATAAAA
AAATTTTCTAATGATAATTGTCAAGGCGGCTTTACTACTTTGGTTGGTAA
AGGCACAGAAAGAAATTTTGATTTCGAGAAGTCGACCAACCTTTAGTTCG
CTTGGAAACAACTATTATTACGGGCCAGAGAAAGCTGTGGACGGGAATTA
TGATGGCAATATGAAGAATGGATTTTGCTATCACAGTGTGCTAACTTCGG
CGGTAAAATGGTGGCTCATTGTGCTTGATTCTGTATCAGTTGTCAGCCGA
ATTGTCATTTATAGCCGAACTGATTGTTGCACAACAAGAACAAGTTCCTT
GTATTTCTATGTAGGTTTTCAAAACTTCAGTCAATTCCTGAATGATAATT
TAAATTTCCACAACATTTATTATTATCCTGGTCCACCAGCAAGTGGGCAG
TCGGTATCGGAATTTAGTTTGACACGAGTATTTGCCAGATCCCTCGCCAT
TTCCAAATCCTTTGAGGACGATGCAATAAACATTTGCGAGCTTGAAATTT
ACGGATATTCGATAGTCAAATCAAACTCAACTTACATGTTTTCGCAATCA
TTGAACCTCTATAAAAATATGGCATATGAACAGAGAAAAGTCCGATCTAA
ATTGGAGTGCGGAAAGATTTGTTCAGAAACAGATTCTTGCTTATCTTTCA
CGTTTATGATAACCTACCAATGTTTTATCTACAGTCATCCAGGAGGGGAA
TATCATTTGTGAAAATTAATTAATTTGATTTTTTACATATTTTTCTTGTT
TTATTTTATTTTGTT
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protein sequence of SMED30017166-orf-1

>SMED30017166-orf-1 ID=SMED30017166-orf-1|Name=SMED30017166-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=234bp
MIIVKAALLLWLVKAQKEILISRSRPTFSSLGNNYYYGPEKAVDGNYDGN
MKNGFCYHSVLTSAVKWWLIVLDSVSVVSRIVIYSRTDCCTTRTSSLYFY
VGFQNFSQFLNDNLNFHNIYYYPGPPASGQSVSEFSLTRVFARSLAISKS
FEDDAINICELEIYGYSIVKSNSTYMFSQSLNLYKNMAYEQRKVRSKLEC
GKICSETDSCLSFTFMITYQCFIYSHPGGEYHL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR008979Galactose-bd-like_sf
IPR003609Pan_app
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR008979Galactose-binding-like domain superfamilyGENE3DG3DSA:2.60.120.260coord: 22..167
e-value: 7.1E-22
score: 79.9
IPR008979Galactose-binding-like domain superfamilySUPERFAMILYSSF49785Galactose-binding domain-likecoord: 24..166
NoneNo IPR availableGENE3DG3DSA:3.50.4.10coord: 168..231
e-value: 3.9E-5
score: 25.6
NoneNo IPR availablePANTHERPTHR45713:SF6SI:CABZ01040626.2-RELATEDcoord: 27..168
NoneNo IPR availablePANTHERPTHR45713FAMILY NOT NAMEDcoord: 27..168
IPR003609PAN/Apple domainPROSITEPS50948PANcoord: 159..233
score: 7.59