Bridging integrator 3
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., 2020SMED30010586 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Homology
BLAST of Bridging integrator 3 vs. Ensembl Xenopus
Match: bin3 (bridging integrator 3 [Source:NCBI gene;Acc:595053]) HSP 1 Score: 66.2402 bits (160), Expect = 8.320e-12 Identity = 61/226 (26.99%), Postives = 113/226 (50.00%), Query Frame = 3 Query: 324 QMEKDSKKLNDTFAKSIEAE----RHIVNELADYVNNQTTK-----VKLVKWLDSISEKQKSMNQS-IKIINDFLITPGKRFSEFFPALVTLNKKRDQLLQENTALESKIQKFESKERTGQNILKAHEFKQEYQKGVXXXXXXXXXXXEDGDLILNLAHPFFSITLKSLMQSNLALFESLNKESLLVSELFNNDPDLLKLGSTPEEHLN-SQLHNLKSELSIVRSD 968 Q+E KKL KSIEA+ + V +D + N + +++V LD+ ++ + NQ + + ++ P KR+S FP+L K+R+Q LQE L++K++K+E K++TG I K H+ ++E + + N ++++ N FF + +SL+++ + + +++ V D ++L E N ++L L+S LSIV D Sbjct: 47 QLEDQIKKLQKDMKKSIEADLAMSKSAVRISSDLLGNPLCEPDADFLQMVTALDTAMKRMDAFNQEKVNQVQKTVMDPLKRYSSVFPSLNMAVKRREQALQEYKRLQTKVEKYEEKDKTGAMIAKLHQAREELRPVREDFEAKNRQLLDEMPKFYNSRTDFFKPSFQSLIRAQVVYYTEMSR----VFGDLAQQVDEVQLSDAEREQENEARLAELRS-LSIVADD 267
BLAST of Bridging integrator 3 vs. Ensembl Xenopus
Match: bin3 (bridging integrator 3 [Source:NCBI gene;Acc:595053]) HSP 1 Score: 65.0846 bits (157), Expect = 1.916e-11 Identity = 61/226 (26.99%), Postives = 113/226 (50.00%), Query Frame = 3 Query: 324 QMEKDSKKLNDTFAKSIEAE----RHIVNELADYVNNQTTK-----VKLVKWLDSISEKQKSMNQS-IKIINDFLITPGKRFSEFFPALVTLNKKRDQLLQENTALESKIQKFESKERTGQNILKAHEFKQEYQKGVXXXXXXXXXXXEDGDLILNLAHPFFSITLKSLMQSNLALFESLNKESLLVSELFNNDPDLLKLGSTPEEHLN-SQLHNLKSELSIVRSD 968 Q+E KKL KSIEA+ + V +D + N + +++V LD+ ++ + NQ + + ++ P KR+S FP+L K+R+Q LQE L++K++K+E K++TG I K H+ ++E + + N ++++ N FF + +SL+++ + + +++ V D ++L E N ++L L+S LSIV D Sbjct: 32 QLEDQIKKLQKDMKKSIEADLAMSKSAVRISSDLLGNPLCEPDADFLQMVTALDTAMKRMDAFNQEKVNQVQKTVMDPLKRYSSVFPSLNMAVKRREQALQEYKRLQTKVEKYEEKDKTGAMIAKLHQAREELRPVREDFEAKNRQLLDEMPKFYNSRTDFFKPSFQSLIRAQVVYYTEMSR----VFGDLAQQVDEVQLSDAEREQENEARLAELRS-LSIVADD 252
BLAST of Bridging integrator 3 vs. UniProt/SwissProt
Match: sp|Q5PPZ5|BIN3_XENLA (Bridging integrator 3 homolog OS=Xenopus laevis OX=8355 GN=bin3 PE=2 SV=1) HSP 1 Score: 63.929 bits (154), Expect = 2.596e-10 Identity = 61/226 (26.99%), Postives = 115/226 (50.88%), Query Frame = 3 Query: 324 QMEKDSKKLNDTFAKSIEAE----RHIVNELADYVNNQTTK-----VKLVKWLDSISEKQKSMNQS-IKIINDFLITPGKRFSEFFPALVTLNKKRDQLLQENTALESKIQKFESKERTGQNILKAHEFKQEYQKGVXXXXXXXXXXXEDGDLILNLAHPFFSITLKSLMQSNLALFESLNKESLLVSELFNNDPDLLKLGSTPEEHLN-SQLHNLKSELSIVRSD 968 Q+E KKL KSIEA+ + V +D + N + +++V LD+ ++ + NQ + I ++ P KR+S FP+L K+R+Q LQ+ L++K++K+E K++TG I K H+ ++E + ++ N+ ++++ N FF + +SL+++ + + +++ V D ++L E N ++L L+S LSIV D Sbjct: 32 QLEDQIKKLQKDMKKSIEADLAMSKSAVRISSDLLGNPLCEPDVDFLQMVTALDTAMKRMDAFNQEKVNQIQKTVMDPLKRYSSVFPSLNMAVKRREQALQDYKRLQTKVEKYEEKDKTGAMIAKLHQAREELRPVRDDFEAKNHQLLDEMPKFYNSRTDFFKPSFQSLIRAQVVYYTEMSR----VFGDLAQQVDEVQLSDAEREQENEARLAELRS-LSIVADD 252
BLAST of Bridging integrator 3 vs. TrEMBL
Match: A0A0L8HRB7 (BAR domain-containing protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22008269mg PE=4 SV=1) HSP 1 Score: 69.3218 bits (168), Expect = 1.022e-9 Identity = 48/170 (28.24%), Postives = 92/170 (54.12%), Query Frame = 3 Query: 318 CCQMEKDSKKLNDTFAKSIEAERHIVNEL-ADYVNNQTTKV--KLVKWLDSISEKQKSMNQSIKIINDFLITPGKRFSEFFPALVTLNKKRDQLLQENTALESKIQKFESKERTGQNILKAHEFKQEYQKGVXXXXXXXXXXXEDGDLILNLAHPFFSITLKSLMQSNLA 818 C ++ KDSKK ++T + + ER I +L A + +K+ +W +SI + M + I L+ P K+FS FP+L KKR+Q L+E E+K++K++ +ERTG NI+K ++ ++ ++ ++ED + +L ++ +++L++S +A Sbjct: 38 CRKLYKDSKKCSETASSLSKCERRITQDLMASTLCKSESKLMHHCEEWDNSIVKLNLHMQEMNSNIQKTLVEPVKKFSSIFPSLHAAKKKREQALEEYKRCEAKVKKYQDRERTGNNIVKLNQSQKSLTPAKEEFYELHTILMEDMPKLYDLRISYYQPCIEALIKSQVA 207
BLAST of Bridging integrator 3 vs. TrEMBL
Match: A0A0L8HR21 (BAR domain-containing protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22008269mg PE=4 SV=1) HSP 1 Score: 69.3218 bits (168), Expect = 1.345e-9 Identity = 48/170 (28.24%), Postives = 92/170 (54.12%), Query Frame = 3 Query: 318 CCQMEKDSKKLNDTFAKSIEAERHIVNEL-ADYVNNQTTKV--KLVKWLDSISEKQKSMNQSIKIINDFLITPGKRFSEFFPALVTLNKKRDQLLQENTALESKIQKFESKERTGQNILKAHEFKQEYQKGVXXXXXXXXXXXEDGDLILNLAHPFFSITLKSLMQSNLA 818 C ++ KDSKK ++T + + ER I +L A + +K+ +W +SI + M + I L+ P K+FS FP+L KKR+Q L+E E+K++K++ +ERTG NI+K ++ ++ ++ ++ED + +L ++ +++L++S +A Sbjct: 47 CRKLYKDSKKCSETASSLSKCERRITQDLMASTLCKSESKLMHHCEEWDNSIVKLNLHMQEMNSNIQKTLVEPVKKFSSIFPSLHAAKKKREQALEEYKRCEAKVKKYQDRERTGNNIVKLNQSQKSLTPAKEEFYELHTILMEDMPKLYDLRISYYQPCIEALIKSQVA 216
BLAST of Bridging integrator 3 vs. TrEMBL
Match: A0A210PPC7 (Bridging integrator 3 OS=Mizuhopecten yessoensis OX=6573 GN=KP79_PYT17253 PE=4 SV=1) HSP 1 Score: 67.0106 bits (162), Expect = 6.714e-9 Identity = 44/189 (23.28%), Postives = 103/189 (54.50%), Query Frame = 3 Query: 270 RKIETSISQIEKIKNGCCQMEKDSKKLNDTFAKSIEAERHIVNELADYVNNQTTKV------KLVKWLDSISEKQKSMNQSIKIINDFLITPGKRFSEFFPALVTLNKKRDQLLQENTALESKIQKFESKERTGQNILKAHEFKQEYQKGVXXXXXXXXXXXEDGDLILNLAHPFFSITLKSLMQSNLA 818 R++E + ++E+++ ++ KD+K+ ++ I +E I L +++Q ++ ++ W S+ +++ M + + ++ P K+F+ FP++ T KKR+Q LQE +SK++K++ ++RTGQN++K ++ Q + N+ + ED +++ +F +L++L++S + Sbjct: 24 RELEKEVKKVERLEETSRKLYKDTKRWVESNQGVIASEHKITQNL---LSSQLCQMEPQLGAQITDWDRSLDKQELYMKELNTTVQRAVLEPMKKFNSIFPSIQTAVKKREQSLQEYNKCQSKVEKYQGRDRTGQNVIKMESSRKSLQSAKDEFETQNSALTEDLPKMIDGRVDYFQPSLEALIKSQVT 209
BLAST of Bridging integrator 3 vs. TrEMBL
Match: A0A1L8GRN6 (BAR domain-containing protein OS=Xenopus laevis OX=8355 GN=bin3 PE=4 SV=1) HSP 1 Score: 66.6254 bits (161), Expect = 9.278e-9 Identity = 65/231 (28.14%), Postives = 116/231 (50.22%), Query Frame = 3 Query: 312 NG-CCQMEKDSKKLNDTFAKSIEAE----RHIVNELADYVNNQTTK-----VKLVKWLDSISEKQKSMNQS-IKIINDFLITPGKRFSEFFPALVTLNKKRDQLLQENTALESKIQKFESKERTGQNILKAHEFKQEYQKGVXXXXXXXXXXXEDGDLILNLAHPFFSITLKSLMQSNLALFESLNKESLLVSELFNNDPDLLKLGSTPEEHLN-SQLHNLKSELSIVRSD 968 NG Q+E KKL KSIEA+ + V +D + N + +++V LD+ ++ + NQ + I ++ P KR+S FP+L K+R+Q LQE L++K++K+E K++TG I K H+ ++E + + N ++++ N FF+ + +SL+++ + + +++ V D ++L E N S+L L+S LSIV D Sbjct: 27 NGKLQQLEDQIKKLQKDMKKSIEADLAMSKSAVRISSDLLGNPLCEPDVDFLQMVTALDTAMKRMDAFNQEKVNQIQKTVMDPLKRYSSVFPSLNMAVKRREQALQEYKRLQTKVEKYEEKDKTGTMIAKLHQAREELRPVREDFEAKNRQLLDEMPKFYNSRTDFFNPSFQSLIRAQVVYYTEMSR----VFGDLAQQVDEVQLSDAEREQENESRLAELRS-LSIVADD 252
BLAST of Bridging integrator 3 vs. TrEMBL
Match: A0A5G3KDK9 (BAR domain-containing protein OS=Xenopus tropicalis OX=8364 GN=bin3 PE=4 SV=1) HSP 1 Score: 66.2402 bits (160), Expect = 1.306e-8 Identity = 61/226 (26.99%), Postives = 113/226 (50.00%), Query Frame = 3 Query: 324 QMEKDSKKLNDTFAKSIEAE----RHIVNELADYVNNQTTK-----VKLVKWLDSISEKQKSMNQS-IKIINDFLITPGKRFSEFFPALVTLNKKRDQLLQENTALESKIQKFESKERTGQNILKAHEFKQEYQKGVXXXXXXXXXXXEDGDLILNLAHPFFSITLKSLMQSNLALFESLNKESLLVSELFNNDPDLLKLGSTPEEHLN-SQLHNLKSELSIVRSD 968 Q+E KKL KSIEA+ + V +D + N + +++V LD+ ++ + NQ + + ++ P KR+S FP+L K+R+Q LQE L++K++K+E K++TG I K H+ ++E + + N ++++ N FF + +SL+++ + + +++ V D ++L E N ++L L+S LSIV D Sbjct: 47 QLEDQIKKLQKDMKKSIEADLAMSKSAVRISSDLLGNPLCEPDADFLQMVTALDTAMKRMDAFNQEKVNQVQKTVMDPLKRYSSVFPSLNMAVKRREQALQEYKRLQTKVEKYEEKDKTGAMIAKLHQAREELRPVREDFEAKNRQLLDEMPKFYNSRTDFFKPSFQSLIRAQVVYYTEMSR----VFGDLAQQVDEVQLSDAEREQENEARLAELRS-LSIVADD 267
BLAST of Bridging integrator 3 vs. Ensembl Sea Lamprey
Match: bin3 (bridging integrator 3 [Source:ZFIN;Acc:ZDB-GENE-030131-2696]) HSP 1 Score: 54.299 bits (129), Expect = 2.464e-9 Identity = 30/102 (29.41%), Postives = 58/102 (56.86%), Query Frame = 3 Query: 534 RFSEFFPALVTLNKKRDQLLQENTALESKIQKFESKERTGQNILKAHEFKQEYQKGVXXXXXXXXXXXEDGDLILNLAHPFFSITLKSLMQSNLALFESLNK 839 RFS FP+L K+R+Q LQE L++K++K+E +E+TG NI K H+ ++E + N ++E+ + +F + ++L++S + + ++K Sbjct: 5 RFSSVFPSLNVAVKRREQALQECKKLQAKLEKYEEREKTGPNIAKTHQSREEMKPVREEFEQRNKALLEEMPQLYTSRADYFQPSFEALVRSQVNYYAEVSK 106
BLAST of Bridging integrator 3 vs. Ensembl Medaka
Match: bin3 (bridging integrator 3 [Source:NCBI gene;Acc:101168469]) HSP 1 Score: 60.077 bits (144), Expect = 6.376e-10 Identity = 43/145 (29.66%), Postives = 82/145 (56.55%), Query Frame = 3 Query: 264 ISRKIETSISQIEKIKNGCCQMEKDSKKLNDT-FAKSIEAERHIVNELADYVNNQTTK-VKLVKWLDSISEKQKSMNQS-IKIINDFLITPGKRFSEFFPALVTLNKKRDQLLQENTALESKIQKFESKERTGQNILKAHEFKQE 689 + R E +++K+++ ++ KD KK + A S A + V+ L++ + Q ++ + LD+ ++ S NQ + I +I P K++S FP+L K+R+Q LQ+ L+SK++K+E K++TG ++K H+ K+E Sbjct: 18 VERDFEREYDKLQKLEDQTKKLHKDMKKSTEADLAMSKAAVKISVDLLSNPLCEQDQAFLEAMSALDTAMKRMDSFNQEKVTQIQKTVIEPLKKYSGVFPSLNMAVKRREQALQDYKRLQSKVEKYEEKDKTGPVMVKLHQAKEE 162
BLAST of Bridging integrator 3 vs. Planmine SMEST
Match: SMESG000029355.1 (SMESG000029355.1) HSP 1 Score: 464.537 bits (1194), Expect = 5.804e-166 Identity = 250/264 (94.70%), Postives = 250/264 (94.70%), Query Frame = 3 Query: 195 MNNEKDFKVMYCINKFIKIRIQEISRKIETSISQIEKIKNGCCQMEKDSKKLNDTFAKSIEAERHIVNELADYVNNQTTKVKLVKWLDSISEKQKSMNQSIKIINDFLITPGKRFSEFFPALVTLNKKRDQLLQENTALESKIQKFESKERTGQNILKAHEFKQEYQKGVXXXXXXXXXXXEDGDLILNLAHPFFSITLKSLMQSNLALFESLNKESLLVSELFNNDPDLLKLGSTPEEHLNSQLHNLKSELSIVRSDNAVGDD 986 MNNEKDFK EISRKIETSISQIEKIKNGCCQMEKDSKKLNDTFAKSIEAERHIVNELADYVNNQTTKVKLVKWLDSISEKQKSMNQSIKIINDFLITPGKRFSEFFPALVTLNKKRDQLLQENTALESKIQKFESKERTGQNILKAHEFKQEYQKGVNNLLLINNTIIEDGDLILNLAHPFFSITLKSLMQSNLALFESLNKESLLVSELFNNDPDLLKLGSTPEEHLNSQLHNLKSELSIVRSDNAVGDD Sbjct: 1 MNNEKDFK--------------EISRKIETSISQIEKIKNGCCQMEKDSKKLNDTFAKSIEAERHIVNELADYVNNQTTKVKLVKWLDSISEKQKSMNQSIKIINDFLITPGKRFSEFFPALVTLNKKRDQLLQENTALESKIQKFESKERTGQNILKAHEFKQEYQKGVNNLLLINNTIIEDGDLILNLAHPFFSITLKSLMQSNLALFESLNKESLLVSELFNNDPDLLKLGSTPEEHLNSQLHNLKSELSIVRSDNAVGDD 250 The following BLAST results are available for this feature:
BLAST of Bridging integrator 3 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of Bridging integrator 3 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of Bridging integrator 3 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of Bridging integrator 3 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of Bridging integrator 3 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 2
BLAST of Bridging integrator 3 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of Bridging integrator 3 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 1
BLAST of Bridging integrator 3 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 5
BLAST of Bridging integrator 3 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of Bridging integrator 3 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 1
BLAST of Bridging integrator 3 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of Bridging integrator 3 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of Bridging integrator 3 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 1
BLAST of Bridging integrator 3 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 >SMED30010586 ID=SMED30010586|Name=Bridging integrator 3|organism=Schmidtea mediterranea sexual|type=transcript|length=1141bpback to top protein sequence of SMED30010586-orf-1 >SMED30010586-orf-1 ID=SMED30010586-orf-1|Name=SMED30010586-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=265bp MNNEKDFKVMYCINKFIKIRIQEISRKIETSISQIEKIKNGCCQMEKDSKback 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
|