HMG box domain-containing protein

Overview
NameHMG box domain-containing protein
Smed IDSMED30015977
Length (bp)575
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



SMED30015977

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
testisSMED30015977SMESG000021063.1 DN307831.1ncbi_smed_estsPMID:22074376
Chong et al., 2011		whole organism adult hermaphrodite fluorescence in situ hybridization evidence
spermatogoniumSMED30015977SMESG000021063.1 DN307831.1ncbi_smed_estsPMID:22074376
Chong et al., 2011		whole organism adult hermaphrodite fluorescence in situ hybridization evidence
spermatocyteSMED30015977SMESG000021063.1 DN307831.1ncbi_smed_estsPMID:22074376
Chong et al., 2011		whole organism adult hermaphrodite fluorescence in situ hybridization evidence
spermatidSMED30015977SMESG000021063.1 DN307831.1ncbi_smed_estsPMID:22074376
Chong et al., 2011		whole organism adult hermaphrodite fluorescence in situ hybridization evidence
testis primordiumSMED30015977SMESG000021063.1 Contig7215_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 HMG box domain-containing protein vs. TrEMBL
Match: A0A068WMW9 (High mobility group HMG1 HMG2 OS=Echinococcus granulosus OX=6210 GN=EgrG_000430600 PE=4 SV=1)

HSP 1 Score: 79.7221 bits (195), Expect = 1.104e-15
Identity = 42/101 (41.58%), Postives = 60/101 (59.41%), Query Frame = 1 
Query:  157 IKRFANPYSLFLKSMRTHYNGDFVQFSRQCAETWKVMNWXXXXXXXXXXXXXXXIYEKAKGFTIVSPYLKFVSEKYWEIKKSHPDWNSKQIKDETMQQYRN 459
             KR   PY+LFL+SM++ Y GD V FSR  A  W+ ++  ++  Y  ++  LK  Y      +  S YLKFV+  Y  +++ HPDW+SKQI+D  MQ YR 
Sbjct:   27 TKRPPGPYALFLQSMKSCYCGDLVAFSRLVAGKWRQLDAKQKAIYEKRAQSLKAKYNSPCKNSACSKYLKFVNAAYRCLRQQHPDWSSKQIRDAVMQSYRG 127
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BLAST of HMG box domain-containing protein vs. TrEMBL
Match: A0A068Y465 (High mobility group HMG1 HMG2 OS=Echinococcus multilocularis OX=6211 GN=EmuJ_000430600 PE=4 SV=1)

HSP 1 Score: 76.6406 bits (187), Expect = 1.777e-14
Identity = 41/101 (40.59%), Postives = 59/101 (58.42%), Query Frame = 1 
Query:  157 IKRFANPYSLFLKSMRTHYNGDFVQFSRQCAETWKVMNWXXXXXXXXXXXXXXXIYEKAKGFTIVSPYLKFVSEKYWEIKKSHPDWNSKQIKDETMQQYRN 459
             KR    Y+LFL+SM++ Y GD V FSR  A  W+ ++  ++  Y  ++  LK  Y      +  S YLKFV+  Y  +++ HPDW+SKQI+D  MQ YR 
Sbjct:   27 TKRPPGAYALFLQSMKSCYCGDLVAFSRLVAGKWRQLDAKQKAIYEKRAQSLKAKYSSPCKNSACSKYLKFVNAAYRCLRQQHPDWSSKQIRDAVMQSYRG 127
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BLAST of HMG box domain-containing protein vs. TrEMBL
Match: W6V8J2 (HMG box domain-containing protein OS=Echinococcus granulosus OX=6210 GN=EGR_02295 PE=4 SV=1)

HSP 1 Score: 67.3958 bits (163), Expect = 1.284e-10
Identity = 37/92 (40.22%), Postives = 55/92 (59.78%), Query Frame = 1 
Query:  160 KRFANPYSLFLKSMRTHYNGDFVQFSRQCAETWKVMNWXXXXXXXXXXXXXXXIYEKAKGFTIVSPYLKFVSEKYWEIKKSHPDWNSKQIKD 435
            KR    Y+LFL+SM++ Y GD V FSR  A  W+ ++  ++  Y  ++  LK  Y      +  S YLKFV+  Y  +++ HPDW+SKQI+D
Sbjct:   28 KRPPGAYALFLQSMKSCYCGDLVAFSRLVAGKWRQLDAKQKAIYEKRAQSLKAKYNSPCKNSACSKYLKFVNAAYRCLRQQHPDWSSKQIRD 119
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BLAST of HMG box domain-containing protein vs. TrEMBL
Match: A0A075AJU6 (HMG box domain-containing protein OS=Opisthorchis viverrini OX=6198 GN=T265_00197 PE=4 SV=1)

HSP 1 Score: 65.855 bits (159), Expect = 2.093e-10
Identity = 37/105 (35.24%), Postives = 68/105 (64.76%), Query Frame = 1 
Query:  139 RLATIGIKRFANPYSLFLKSMRTHYNGDFVQFSRQCAETWKVMNWXXXXXXXXXXXXXXXIYEKAKGFTIVSPYLKFVSEKYWEIKKSHPDWNSKQIKDETMQQY 453
            R + +  +R   PY+LF+ SMR +Y+G F QFS+ CA TW+ ++ S+++K+  K+ K +K   +      ++ +L+FVS  Y  +++ HP+W SK+I+++ M+ Y
Sbjct:   11 RKSNLKSRRAPGPYALFVSSMRKNYSGSFTQFSKCCAATWRQLSESEKEKFRKKAKKQQKKPGRKHEPKSLA-FLRFVSRTYDCLRRKHPEWPSKKIREQLMKNY 114
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BLAST of HMG box domain-containing protein vs. TrEMBL
Match: A0A4E0R5I2 (High mobility group HMG1 HMG2 OS=Fasciola hepatica OX=6192 GN=D915_006496 PE=4 SV=1)

HSP 1 Score: 65.855 bits (159), Expect = 2.262e-10
Identity = 33/103 (32.04%), Postives = 56/103 (54.37%), Query Frame = 1 
Query:  157 IKRFANPYSLFLKSMRTHYNGDFVQFSRQCAETWKVMNWXXXXXXXXXXXXXXXIYEKAKGFTIVSPYLKFVSEKYWEIKKSHPDWNSKQIKDETMQQYRNIK 465
             KR   PY+LF++SM+  Y G+  +FSR CA  W+ ++     +      +   +    K     + YLKFV+  Y  +++ HP W +K+IK+E M+ Y+ +K
Sbjct:   20 TKRPPGPYALFVRSMKKFYTGNLAEFSRYCACEWRQLS---EAEREKFRKQAAALSRPKKRSPQSAAYLKFVASMYNCLRRKHPTWPAKRIKEELMKNYQKLK 119
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BLAST of HMG box domain-containing protein vs. Planmine SMEST
Match: SMESG000021063.1 (SMESG000021063.1)

HSP 1 Score: 227.639 bits (579), Expect = 3.122e-77
Identity = 137/137 (100.00%), Postives = 137/137 (100.00%), Query Frame = 1 
Query:   79 MANMKAYRVVXXXXXXXXXXRLATIGIKRFANPYSLFLKSMRTHYNGDFVQFSRQCAETWKVMNWXXXXXXXXXXXXXXXIYEKAKGFTIVSPYLKFVSEKYWEIKKSHPDWNSKQIKDETMQQYRNIKNSNKPLVN 489
            MANMKAYRVVKKHSKSHSHKRLATIGIKRFANPYSLFLKSMRTHYNGDFVQFSRQCAETWKVMNWSKRKKYVMKSLKLKKIYEKAKGFTIVSPYLKFVSEKYWEIKKSHPDWNSKQIKDETMQQYRNIKNSNKPLVN
Sbjct:    1 MANMKAYRVVKKHSKSHSHKRLATIGIKRFANPYSLFLKSMRTHYNGDFVQFSRQCAETWKVMNWSKRKKYVMKSLKLKKIYEKAKGFTIVSPYLKFVSEKYWEIKKSHPDWNSKQIKDETMQQYRNIKNSNKPLVN 137
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BLAST of HMG box domain-containing protein vs. Planmine SMEST
Match: SMESG000013665.1 (SMESG000013665.1)

HSP 1 Score: 58.9214 bits (141), Expect = 1.853e-11
Identity = 35/112 (31.25%), Postives = 67/112 (59.82%), Query Frame = 1 
Query:  154 GIKRFANPYSLFLKSMRTHYNGDFVQFSRQCAETWKVMNWXXXXXXXXXXXXXXXIYEKAKGFTI-VSPYLKFVSEKYWEIKKSHPDWNSKQIKDETMQQY----RNIKNSN 474
             +KR  + Y+LF+K  ++ + G+   FS+QCA  WK +++ KR +Y  K+ +   IY++ K   +  S +  F+ ++Y  ++  HP+W SK+I+ E ++++     N+K SN
Sbjct:    3 NLKRPLHAYNLFVKDQKSSFEGNIKNFSKQCANKWKNLSFIKRIQYENKARQYLNIYKQKKDKNVDTSLFCGFIKDEYRRLRGIHPNWTSKRIRREAVEKFYEMKSNLKESN 114
The following BLAST results are available for this feature:
BLAST of HMG box 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 HMG box 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 HMG box 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 HMG box 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 HMG box 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 HMG box 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 HMG box 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 HMG box domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A068WMW91.104e-1541.58High mobility group HMG1 HMG2 OS=Echinococcus gran... [more]
A0A068Y4651.777e-1440.59High mobility group HMG1 HMG2 OS=Echinococcus mult... [more]
W6V8J21.284e-1040.22HMG box domain-containing protein OS=Echinococcus ... [more]
A0A075AJU62.093e-1035.24HMG box domain-containing protein OS=Opisthorchis ... [more]
A0A4E0R5I22.262e-1032.04High mobility group HMG1 HMG2 OS=Fasciola hepatica... [more]
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BLAST of HMG box 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 HMG box 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 HMG box 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 HMG box 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 HMG box 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 HMG box domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000021063.13.122e-77100.00SMESG000021063.1[more]
SMESG000013665.11.853e-1131.25SMESG000013665.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015977 ID=SMED30015977|Name=HMG box domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=575bp
ATTAGAAATTAATTTAATTAAATTTTAATTCAAACTGACAATAAGGAGTT
ACCACTTTTATTCAAAATATCACAAATAATGGCAAATATGAAAGCTTATC
GAGTCGTGAAAAAGCATTCCAAGTCACACAGTCACAAGAGACTCGCAACA
ATCGGCATCAAAAGATTTGCAAATCCTTATTCGTTGTTCTTAAAGTCCAT
GCGTACTCATTACAATGGCGACTTTGTACAGTTTTCCCGTCAGTGCGCCG
AAACTTGGAAAGTAATGAATTGGAGTAAACGGAAAAAGTATGTCATGAAA
TCTCTGAAGCTGAAAAAGATCTATGAGAAGGCGAAAGGATTTACAATTGT
TAGTCCATATTTAAAATTCGTGTCGGAGAAATATTGGGAGATTAAGAAAA
GCCATCCCGACTGGAATTCAAAGCAAATCAAAGACGAAACAATGCAACAA
TATAGAAATATTAAAAATTCTAACAAACCACTCGTTAATTGAATATAAAT
AATTTCTTCAATTGAAATTAAGTTTATGGTAAAGATAAGTGGATTAAATA
AAATATTTGTATGGCCAAAAAAAAA
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protein sequence of SMED30015977-orf-1

>SMED30015977-orf-1 ID=SMED30015977-orf-1|Name=SMED30015977-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=138bp
MANMKAYRVVKKHSKSHSHKRLATIGIKRFANPYSLFLKSMRTHYNGDFV
QFSRQCAETWKVMNWSKRKKYVMKSLKLKKIYEKAKGFTIVSPYLKFVSE
KYWEIKKSHPDWNSKQIKDETMQQYRNIKNSNKPLVN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
PLANA:0000220spermatogonium
PLANA:0000221spermatocyte
PLANA:0000222spermatid
PLANA:0003304testis primordium
Vocabulary: INTERPRO
TermDefinition
IPR036910HMG_box_dom_sf
IPR009071HMG_box_dom
Vocabulary: molecular function
TermDefinition
GO:0003677DNA binding
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR036910High mobility group box domain superfamilyGENE3DG3DSA:1.10.30.10coord: 26..87
e-value: 7.0E-8
score: 34.8
IPR036910High mobility group box domain superfamilySUPERFAMILYSSF47095HMG-boxcoord: 27..85
IPR009071High mobility group box domainPROSITEPS50118HMG_BOX_2coord: 27..84
score: 8.555