GCR156
Overview
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 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 App
Neoblast Population
Sub-lethal Irradiated Surviving X1 and X2 Cell Population
Embryonic 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., 2020SMED30032279 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Homology
BLAST of GCR156 vs. TrEMBL
Match: A0A193KUR6 (GCR156 OS=Schmidtea mediterranea OX=79327 GN=gcr156 PE=2 SV=1) HSP 1 Score: 352.443 bits (903), Expect = 1.446e-156 Identity = 209/210 (99.52%), Postives = 209/210 (99.52%), Query Frame = 2 Query: 227 MLNITNCGKNASDYQKPVQWYFYPSYFAXXXXXXXXXXXXXXXXXKYRRRLTFKFNIFNYLTFNLIIIDFTQSIVXXXXXXXXXXXENRSENILLEGFLSLRNCLISCHAITLLFMATNRYRAIKHPQMVNDPRSVLIKLYRIIYVTISIPFLVRFALVFCLRDCLLLQEIDNALKMSIGIATALVVMVIICIYSVLFGLLCCRNFPSTS 856 MLNITNCGKNAS YQKPVQWYFYPSYFALFFLSLLLNFVFINSFIKYRRRLTFKFNIFNYLTFNLIIIDFTQSIVLLIDILLIMIMENRSENILLEGFLSLRNCLISCHAITLLFMATNRYRAIKHPQMVNDPRSVLIKLYRIIYVTISIPFLVRFALVFCLRDCLLLQEIDNALKMSIGIATALVVMVIICIYSVLFGLLCCRNFPSTS Sbjct: 1 MLNITNCGKNASYYQKPVQWYFYPSYFALFFLSLLLNFVFINSFIKYRRRLTFKFNIFNYLTFNLIIIDFTQSIVLLIDILLIMIMENRSENILLEGFLSLRNCLISCHAITLLFMATNRYRAIKHPQMVNDPRSVLIKLYRIIYVTISIPFLVRFALVFCLRDCLLLQEIDNALKMSIGIATALVVMVIICIYSVLFGLLCCRNFPSTS 210 HSP 2 Score: 231.876 bits (590), Expect = 1.446e-156 Identity = 112/112 (100.00%), Postives = 112/112 (100.00%), Query Frame = 1 Query: 856 KPTGNFSKIHPYPNERKSTTVGKVFKRHFGKSVKFAQVLFSITILMMISYAPVFLTNVNLIKYPGQAIYYLFYLPVLGDPLILILSREDIRQEMIRPFSLTTSQSVTNIYFT 1191 KPTGNFSKIHPYPNERKSTTVGKVFKRHFGKSVKFAQVLFSITILMMISYAPVFLTNVNLIKYPGQAIYYLFYLPVLGDPLILILSREDIRQEMIRPFSLTTSQSVTNIYFT Sbjct: 211 KPTGNFSKIHPYPNERKSTTVGKVFKRHFGKSVKFAQVLFSITILMMISYAPVFLTNVNLIKYPGQAIYYLFYLPVLGDPLILILSREDIRQEMIRPFSLTTSQSVTNIYFT 322
BLAST of GCR156 vs. Planmine SMEST
Match: SMESG000062328.1 (SMESG000062328.1) HSP 1 Score: 65.0846 bits (157), Expect = 3.705e-21 Identity = 26/65 (40.00%), Postives = 45/65 (69.23%), Query Frame = 1 Query: 949 SVKFAQVLFSITILMMISYAPVFLTNVNLIKYPGQAIYYLFYLPVLGDPLILILSREDIRQEMIR 1143 S+KF +VLF + +LM+ISY P L N I++P ++YYLF+L LGDP++ ++R ++ +++ Sbjct: 272 SIKFVKVLFGVNLLMIISYLPAILYNAECIQFPSFSVYYLFFLHALGDPILFFMTRRELLNSLLK 336 HSP 2 Score: 55.8398 bits (133), Expect = 3.705e-21 Identity = 45/155 (29.03%), Postives = 85/155 (54.84%), Query Frame = 2 Query: 485 ENRSENILLEGFLSLRNCLISCHAITLLFMATNRYRAIKHPQMVNDPR-SVLIKLYRIIYVTISIPFLVRFALVFCLRDCLLLQEIDNALKMSIGIATALVVMVIICIYSVLFGLLCCR------------NFPSTSNRREISVKST-RIRMKEN 907 ++ I+L+G+L++R+ IS I L+ +A +R A P + N R ++K+++I ++ + + +RF L+ +C + + ID+ +K+ IGI +++++ + IY +LF LLC R NF S N +E+ KS +I K+N Sbjct: 93 KDHDTFIVLDGYLAIRDFAISSQMIILVLIAIDRLLAFLLP-LSNFWRIGRVLKVFKIFFILTLLFYSIRFTLLTVNINCDIKKSIDSDVKLFIGIFGGILMVINLIIYCILFALLCRRQIFNHKDSLLSANFKSL-NVKELESKSIPKIENKKN 245
BLAST of GCR156 vs. Planmine SMEST
Match: SMESG000077660.1 (SMESG000077660.1) HSP 1 Score: 62.3882 bits (150), Expect = 1.374e-19 Identity = 30/90 (33.33%), Postives = 53/90 (58.89%), Query Frame = 1 Query: 895 NERKSTTVGKVFKRHFGKSVKFAQVLFSITILMMISYAPVFLTNVNLIKYPGQAIYYLFYLPVLGDPLILILSREDIRQEMIRPFSLTTS 1164 N ++S+ K S++FA+ LF+I +LM+ISY P L NV + + ++YYLF+L LGDP++ +R +++ ++R + S Sbjct: 242 NNKRSSLKNKFKSNKKSASIRFAKPLFAINLLMIISYLPAILYNVRFVGFHSYSVYYLFFLHALGDPILFFSTRPELKLALLRCLCIKKS 331 HSP 2 Score: 53.1434 bits (126), Expect = 1.374e-19 Identity = 33/113 (29.20%), Postives = 59/113 (52.21%), Query Frame = 2 Query: 503 ILLEGFLSLRNCLISCHAITLLFMATNRYRAIKHPQMVNDPRSVLIKLYRIIYVTISIPFLVRFALVFCLRDCLLLQEIDNALKMSIGIATALVVMVIICIYSVLFGLLCCRN 841 I ++G+L++R+ IS + +A +R + HPQ+ + +IK+ + I + +L+RF + C +D +K+ IGI +++ + IY VLFGLLC R Sbjct: 91 IAVDGYLAVRDFSISSQMTIFVAIAIDRLLTLTHPQITKRRTNTIIKVLQTAVFFIGLFYLLRFIFLTIDIKCNSKVLLDKYMKLFIGIVGGVLMTTNLIIYLVLFGLLCHRQ 203
BLAST of GCR156 vs. Planmine SMEST
Match: SMESG000062349.1 (SMESG000062349.1) HSP 1 Score: 68.1662 bits (165), Expect = 3.278e-19 Identity = 36/95 (37.89%), Postives = 56/95 (58.95%), Query Frame = 1 Query: 883 HPYPNERKSTTVGKV---------FKRHFGKSVKFAQVLFSITILMMISYAPVFLTNVNLIKYPGQAIYYLFYLPVLGDPLILILSREDIRQEMI 1140 +P NE T ++ F+R G S+KFA+VL I ILM++SY P L N I +P ++YYLF+L LGDP+I +L+R +++ ++ Sbjct: 228 NPEENETSITKSRRISSLNSRKLRFRRRIG-SIKFAKVLLGINILMIVSYLPGVLYNNKFIPFPSYSVYYLFFLHALGDPIIFLLTRRELKNGLL 321 HSP 2 Score: 46.2098 bits (108), Expect = 3.278e-19 Identity = 36/125 (28.80%), Postives = 67/125 (53.60%), Query Frame = 2 Query: 485 ENRSENILLEGFLSLRNCLISCHAITLLFMATNRYRAIKHPQMVNDPRSVLIKLYRIIYVTISIPFLVRFALVFCLRDCLLLQEIDNALKMSIGIATALVVMVIICIYSVLFGLLCCRNFPSTSN 859 E+ NI L+ FL++R+ IS ITL+ +A +R A +P + ++ + +++ + +S+ ++ R L+ CL ++ID K+ IGI+ + +++ + IY LF LLC R N Sbjct: 85 EDTDTNIFLDVFLAIRDLSISAQMITLVLIAIDRLFAFVNPLSNYWVLNTVMWILKVLMLFLSLSYITRLILLSIGISCLNKKKIDKYGKIIIGISGGVFMLINLVIYVSLFSLLCQRQLVRQRN 209
BLAST of GCR156 vs. Planmine SMEST
Match: SMESG000000172.1 (SMESG000000172.1) HSP 1 Score: 62.003 bits (149), Expect = 2.250e-10 Identity = 30/69 (43.48%), Postives = 44/69 (63.77%), Query Frame = 1 Query: 931 KRHFGKSVKFAQVLFSITILMMISYAPVFLTNVNLIKYPGQAIYYLFYLPVLGDPLILILSREDIRQEM 1137 K F S KFA V T ++++S+ PVFL+N ++K+PG +YY FYL L DP+ILI S+ +R + Sbjct: 214 KSKFNHSYKFAVVFSFATFILVVSFLPVFLSNTKMVKWPGYILYYGFYLHSLSDPIILIASKATLRNRI 282
BLAST of GCR156 vs. Planmine SMEST
Match: SMESG000012028.1 (SMESG000012028.1) HSP 1 Score: 50.8322 bits (120), Expect = 9.852e-7 Identity = 28/77 (36.36%), Postives = 47/77 (61.04%), Query Frame = 1 Query: 937 HFGKSV---KFAQVLFSITILMMISYAPVFLTNVNLIKYPGQAIY-YLFYLPVLGDPLILILSREDIRQEMIRPFSL 1155 +FGK + KF +VLF + +LM++S+ P L N L+K+ + YLFY+ LGD +I + R D+R+++ + L Sbjct: 243 NFGKRIIHMKFVKVLFWVNLLMIVSFLPGCLYNSGLLKFKAYNWFIYLFYVHSLGDAIIFLFIRLDLRKDLTKLLRL 319 The following BLAST results are available for this feature:
BLAST of GCR156 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of GCR156 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of GCR156 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of GCR156 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of GCR156 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of GCR156 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of GCR156 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of GCR156 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 1
BLAST of GCR156 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of GCR156 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of GCR156 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of GCR156 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of GCR156 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of GCR156 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 5
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30032279 ID=SMED30032279|Name=GCR156|organism=Schmidtea mediterranea sexual|type=transcript|length=1472bpback to top protein sequence of SMED30032279-orf-1 >SMED30032279-orf-1 ID=SMED30032279-orf-1|Name=SMED30032279-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=132bp MHLFGVVWFIVLSKLSVHFKPTGNFSKIHPYPNERKSTTVGKVFKRHFGKback to top protein sequence of SMED30032279-orf-2 >SMED30032279-orf-2 ID=SMED30032279-orf-2|Name=SMED30032279-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=243bp MLNITNCGKNASDYQKPVQWYFYPSYFALFFLSLLLNFVFINSFIKYRRRback 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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