SMED30010277
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., 2020SMED30010277 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 10
Alignments
SMED30010277 aligns in the following genomic locations:
Homology
BLAST of SMED30010277 vs. Ensembl Human
Match: CCDC34 (coiled-coil domain containing 34 [Source:HGNC Symbol;Acc:HGNC:25079]) HSP 1 Score: 57.3806 bits (137), Expect = 3.861e-8 Identity = 24/53 (45.28%), Postives = 32/53 (60.38%), Query Frame = 3 Query: 1407 SQTAFKHWLEEHKDHHLPVPYSYGISDGKLTSYYDKTSNPPPAFFNPKPWIPV 1565 ++ F+ WLE K P SYG ++GKLT +Y S P PAF+NP PW P+ Sbjct: 272 AEKKFQEWLENAKHKPRPAAKSYGYANGKLTGFYSGNSYPEPAFYNPIPWKPI 324
BLAST of SMED30010277 vs. Ensembl Xenopus
Match: cdc73 (cell division cycle 73 [Source:Xenbase;Acc:XB-GENE-949345]) HSP 1 Score: 54.299 bits (129), Expect = 3.447e-7 Identity = 24/47 (51.06%), Postives = 29/47 (61.70%), Query Frame = 3 Query: 1404 KSQTAFKHWLEEHKDHHLPVPYSYGISDGKLTSYYDKTSNPPPAFFN 1544 K+ FK WLE+ KD P SYG +GKLT YYD +S P P F+N Sbjct: 234 KASKVFKEWLEQAKDKPRPTLNSYGYVNGKLTGYYDASSYPAPGFYN 280
BLAST of SMED30010277 vs. Ensembl Mouse
Match: Ccdc34 (coiled-coil domain containing 34 [Source:MGI Symbol;Acc:MGI:1915451]) HSP 1 Score: 57.7658 bits (138), Expect = 1.967e-8 Identity = 25/53 (47.17%), Postives = 31/53 (58.49%), Query Frame = 3 Query: 1407 SQTAFKHWLEEHKDHHLPVPYSYGISDGKLTSYYDKTSNPPPAFFNPKPWIPV 1565 ++ FK WLE K+ P SYG S GKLT +Y S P P F+NP PW P+ Sbjct: 266 AEKKFKEWLENAKNKPRPAAKSYGYSSGKLTGFYSGNSYPEPTFYNPIPWKPI 318
BLAST of SMED30010277 vs. UniProt/SwissProt
Match: sp|Q3UI66|CCD34_MOUSE (Coiled-coil domain-containing protein 34 OS=Mus musculus OX=10090 GN=Ccdc34 PE=2 SV=1) HSP 1 Score: 57.7658 bits (138), Expect = 1.376e-7 Identity = 25/53 (47.17%), Postives = 31/53 (58.49%), Query Frame = 3 Query: 1407 SQTAFKHWLEEHKDHHLPVPYSYGISDGKLTSYYDKTSNPPPAFFNPKPWIPV 1565 ++ FK WLE K+ P SYG S GKLT +Y S P P F+NP PW P+ Sbjct: 266 AEKKFKEWLENAKNKPRPAAKSYGYSSGKLTGFYSGNSYPEPTFYNPIPWKPI 318
BLAST of SMED30010277 vs. UniProt/SwissProt
Match: sp|Q96HJ3|CCD34_HUMAN (Coiled-coil domain-containing protein 34 OS=Homo sapiens OX=9606 GN=CCDC34 PE=1 SV=2) HSP 1 Score: 57.3806 bits (137), Expect = 1.854e-7 Identity = 24/53 (45.28%), Postives = 32/53 (60.38%), Query Frame = 3 Query: 1407 SQTAFKHWLEEHKDHHLPVPYSYGISDGKLTSYYDKTSNPPPAFFNPKPWIPV 1565 ++ F+ WLE K P SYG ++GKLT +Y S P PAF+NP PW P+ Sbjct: 272 AEKKFQEWLENAKHKPRPAAKSYGYANGKLTGFYSGNSYPEPAFYNPIPWKPI 324
BLAST of SMED30010277 vs. TrEMBL
Match: A0A267GVH9 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig005156g2 PE=4 SV=1) HSP 1 Score: 74.7146 bits (182), Expect = 1.977e-10 Identity = 32/57 (56.14%), Postives = 40/57 (70.18%), Query Frame = 3 Query: 1404 KSQTAFKHWLEEHKDHHLPVPYSYGISDGKLTSYYDKTSNPPPAFFNPKPWIPVIET 1574 KS+ AF W+E HK+ PYSYG +DG+L SYYDK SNPPP+F +PW+P ET Sbjct: 359 KSEAAFAKWVEAHKNVRPHAPYSYGYTDGRLMSYYDKNSNPPPSFVVAEPWLPPTET 415
BLAST of SMED30010277 vs. TrEMBL
Match: A0A267GXS2 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig005156g1 PE=4 SV=1) HSP 1 Score: 74.7146 bits (182), Expect = 2.097e-10 Identity = 32/57 (56.14%), Postives = 40/57 (70.18%), Query Frame = 3 Query: 1404 KSQTAFKHWLEEHKDHHLPVPYSYGISDGKLTSYYDKTSNPPPAFFNPKPWIPVIET 1574 KS+ AF W+E HK+ PYSYG +DG+L SYYDK SNPPP+F +PW+P ET Sbjct: 362 KSEAAFAKWVEAHKNVRPHAPYSYGYTDGRLMSYYDKNSNPPPSFVVAEPWLPPTET 418
BLAST of SMED30010277 vs. TrEMBL
Match: A0A267GBH3 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig021986g1 PE=4 SV=1) HSP 1 Score: 74.7146 bits (182), Expect = 2.154e-10 Identity = 32/57 (56.14%), Postives = 40/57 (70.18%), Query Frame = 3 Query: 1404 KSQTAFKHWLEEHKDHHLPVPYSYGISDGKLTSYYDKTSNPPPAFFNPKPWIPVIET 1574 KS+ AF W+E HK+ PYSYG +DG+L SYYDK SNPPP+F +PW+P ET Sbjct: 362 KSEAAFAKWVEAHKNVRPHAPYSYGYTDGRLMSYYDKNSNPPPSFVVAEPWLPPTET 418
BLAST of SMED30010277 vs. TrEMBL
Match: W5MHC9 (Coiled-coil domain containing 34 OS=Lepisosteus oculatus OX=7918 GN=CCDC34 PE=4 SV=1) HSP 1 Score: 63.1586 bits (152), Expect = 7.278e-7 Identity = 27/54 (50.00%), Postives = 36/54 (66.67%), Query Frame = 3 Query: 1404 KSQTAFKHWLEEHKDHHLPVPYSYGISDGKLTSYYDKTSNPPPAFFNPKPWIPV 1565 K++ F+ WL+ KD PV S+ S+GKLT YYD TS P P+F+NP PW P+ Sbjct: 229 KAEEKFQEWLKSAKDKPRPVSNSFAYSNGKLTGYYDGTSYPAPSFYNPIPWKPI 282
BLAST of SMED30010277 vs. TrEMBL
Match: W5MHB0 (Coiled-coil domain containing 34 OS=Lepisosteus oculatus OX=7918 GN=CCDC34 PE=4 SV=1) HSP 1 Score: 63.1586 bits (152), Expect = 7.307e-7 Identity = 27/54 (50.00%), Postives = 36/54 (66.67%), Query Frame = 3 Query: 1404 KSQTAFKHWLEEHKDHHLPVPYSYGISDGKLTSYYDKTSNPPPAFFNPKPWIPV 1565 K++ F+ WL+ KD PV S+ S+GKLT YYD TS P P+F+NP PW P+ Sbjct: 235 KAEEKFQEWLKSAKDKPRPVSNSFAYSNGKLTGYYDGTSYPAPSFYNPIPWKPI 288
BLAST of SMED30010277 vs. Planmine SMEST
Match: SMESG000000133.1 (SMESG000000133.1) HSP 1 Score: 669.463 bits (1726), Expect = 0.000e+0 Identity = 490/491 (99.80%), Postives = 491/491 (100.00%), Query Frame = 3 Query: 108 MSLRPEPVTSKFRKYYLNDILPIYHXXXXXXXXXXXXXXXXXXXXXXYRXXXXXXADLNYDSFDDLSIENNELKISDLPEQSLKRLNSQEFNSMTNKKFSKLKKQNGIFREIFNSSENRNFNVPKNRINKPSEKSCKRIIARKPDYPGSRITHVNYQQTMCEDRGLKPKKSSNPVHKNGIYKNKGNPMENEKASINEKSSSEKQIPRTIAKKSQNISENSIKDISTKAVSEQSDVPYSVCNFTSVSEEQKINQSNKSDKQSIDEXXXXXXXXXXXXXXXERSSVSNTDSVTDKQLPVPVPPQRMLNPWDDWFXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCQKKIADWLAKKEEERIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMIKIAKSQTAFKHWLEEHKDHHLPVPYSYGISDGKLTSYYDKTSNPPPAFFNPKPWIPVIETKN 1580 MSLRPEPVTSKFRKYYLNDILPIYHTSKLSLSNCSSTGSTSSLTSILYRNNNVNNADLNYDSFDDLSIENNELKISDLPEQSLKRLNSQEFNSMTNKKFSKLKKQNGIFREIFNSSENRNFNVPKNRINKPSEKSCKRIIARKPDYPGSRITHVNYQQTMCEDRGLKPKKSSNPVHKNGIYKNKGNPMENEKASINEKSSSEKQIPRTIAKKSQNISENSIKDISTKAVSEQSDVPYSVCNFTSVSEEQ+INQSNKSDKQSIDENNFSSIDDVNSISIDERSSVSNTDSVTDKQLPVPVPPQRMLNPWDDWFLRKEKEERKLSEELRKKMMREEAKKTEEAAAKEKRRELCQKKIADWLAKKEEERIKCLCKLKDEKKKKELKELEKDDLLKKSSKKYVSWKLKKIEQMKEKEKQEKEKQNKLEAEKMIKIAKSQTAFKHWLEEHKDHHLPVPYSYGISDGKLTSYYDKTSNPPPAFFNPKPWIPVIETKN Sbjct: 1 MSLRPEPVTSKFRKYYLNDILPIYHTSKLSLSNCSSTGSTSSLTSILYRNNNVNNADLNYDSFDDLSIENNELKISDLPEQSLKRLNSQEFNSMTNKKFSKLKKQNGIFREIFNSSENRNFNVPKNRINKPSEKSCKRIIARKPDYPGSRITHVNYQQTMCEDRGLKPKKSSNPVHKNGIYKNKGNPMENEKASINEKSSSEKQIPRTIAKKSQNISENSIKDISTKAVSEQSDVPYSVCNFTSVSEEQQINQSNKSDKQSIDENNFSSIDDVNSISIDERSSVSNTDSVTDKQLPVPVPPQRMLNPWDDWFLRKEKEERKLSEELRKKMMREEAKKTEEAAAKEKRRELCQKKIADWLAKKEEERIKCLCKLKDEKKKKELKELEKDDLLKKSSKKYVSWKLKKIEQMKEKEKQEKEKQNKLEAEKMIKIAKSQTAFKHWLEEHKDHHLPVPYSYGISDGKLTSYYDKTSNPPPAFFNPKPWIPVIETKN 491 The following BLAST results are available for this feature:
BLAST of SMED30010277 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 1
BLAST of SMED30010277 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30010277 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30010277 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30010277 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 1
BLAST of SMED30010277 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 1
BLAST of SMED30010277 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 2
BLAST of SMED30010277 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 5
BLAST of SMED30010277 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30010277 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30010277 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30010277 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30010277 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30010277 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 1
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30010277 ID=SMED30010277|Name=SMED30010277|organism=Schmidtea mediterranea sexual|type=transcript|length=1951bpback to top protein sequence of SMED30010277-orf-1 >SMED30010277-orf-1 ID=SMED30010277-orf-1|Name=SMED30010277-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=492bp MSLRPEPVTSKFRKYYLNDILPIYHTSKLSLSNCSSTGSTSSLTSILYRNback 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
|