HMG box domain-containing protein
Overview
Neoblast Clusters
Zeng et. al., 2018
Overview
Single cell RNA-seq of pluripotent neoblasts and its early progeniesWe 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 AppEmbryonic Expression
Davies et. al., 2017
Hover the mouse over a column in the graph to view average RPKM values per sample. Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult. back to top Anatomical Expression
PAGE et. al., 2020SMED30015977 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 5
Homology
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Analyses
This transcript is derived from or has results from the following analyses 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=575bpback to top 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 MANMKAYRVVKKHSKSHSHKRLATIGIKRFANPYSLFLKSMRTHYNGDFVback to top Annotated Terms
The following terms have been associated with this transcript:
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
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