Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6B

Orthogroup ID

OG0005779

Physical Location & Seq

Genomic Coordinates Forward (+)

3668514 .. 3673273

Gene Structure 4760 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6BG025700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1239 bp

ATGTATTTGACTATCTCGATACTTGGCCTTAATGATGCTCATAATTCTTCATTGTTGCAGTCCTACTTTGACCGGAGAGAGTTTTCTTTCACACTGGATAATGATGTCTATCTGCGGTACAAAACTTTCAACTCCGTGTCTGAGCTTGAAAATTCTATCAAAGAGAAGTGCCCCGTCAAAATAGATATTGGGCCTGTGTACAATGTTGATCCTGCAAAGAGGCATTCCTATGCTCAAAGTGGTTGCTACCCCGAGGAGAGGGAACTGATTTTTGATATAGATATGTCAGATTACGATGATGTTAGATACTGCTGCTCAGGAGCTGATGTGTGCCTGGAGTGCTGGCCGCTTATGACAATTGCTATCAAAGTGATTGACACTGCCCTTCGAGATGACTTTGGTTTCAATCACATTCTCTGGGTATACAGTGGCCGACGTGGTGTTCATTGTTGGGTTTGTGATGGGAAAGCTAGAAGGCTCACAAATGAACTGAGAGCAGCTATTGCTGACTATTTTCGTGTCTACAAGGGCAATGAAAACAGTCATAAAAAGGTTTCTTTGATGGGCCCTGCTCTTCATCCATTCCTTGTGAGATCATATACCGAAGTTCTTAAGGATTTCTTTGAGAGGACATTGCTTTCCAGTCAAAAGATATTTTCTACTGCAGAGAGATATGAAAAGATCTTAGATATGATTCCTGATGAATGTGTCACTTCTGAGCTTCGGGGAAAGTGGCAAGATAATAGACGAACCTCCAATGCAAAAGAAGACATTAATGTTGCTCGTTGGGAGCAGCTGAAACATATGCTGCAATCTGGGAAACAGAAGATGCAAGGACTGCGTAGATGTGTGGAGGAGATTGTGTTCTCTTATACCTACCCTAGACTTGACATGGAGGTTTCAAAACATATGAACCATTTATTAAAGGCACCATTCTGTGTACATCCAAAGACAGGTCGTGTTTGTGTTCCGATTGATCCCAACCGTTGTGAGGAGTTTGATCCTACTGCAGTTCCAACCCTTTCCACTCTTATTGAAGAACTTAATAATGAGGGTTTGAGAGCAGAGGCTGATAACGAACGGGATAGAACGTCACTTGGAAAATCAATAAGATTCTTCCAATCATCATTTTTGGAGCCTTTGGTAAAATCTTGCAAGGAGGAGATGATAAGTTCCTACAATGCGAAAATGCAGCAGTCGAAGTTGCAGCAGTCAAAGAACGTGCTTGCTGCAGTCTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000228 GO:0000428 GO:0003674 GO:0003676 GO:0003677 GO:0003697 GO:0003824 GO:0003896 GO:0003899 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005657 GO:0005658 GO:0005694 GO:0006139 GO:0006259 GO:0006260 GO:0006261 GO:0006269 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0016070 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019438 GO:0030880 GO:0030894 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0032993 GO:0034062 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043596 GO:0043601 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044427 GO:0044428 GO:0044446 GO:0044454 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0090304 GO:0097159 GO:0097747 GO:0140098 GO:1901360 GO:1901362 GO:1901363 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03030 map00230 map00240 map01100 map03030

Pfam Domains

Protein Families

DNA_primase_S

Protein Analysis

412

Amino Acids

47.67

Weight (kDa)

6.57

Isoelectric Point (pI)

53.74

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DNA_primase_S	PF01896	91 - 326	2.9e-53	DNA primase small subunit

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0005779)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G41880
fragaria_vesca	FvH4_5g04460
malus_domestica	MD06G1105400.v1.1
prunus_persica	Prupe.5G117700_v2.0.a1
pyrus_communis	pycom06g09970
rosa_chinensis	RchiOBHm_Chr7g0195041
rosa_laevigata	RLG00000004150 RLG00000008501 RLG00000015305
rosa_multiflora	Rmu_sc0002246.1_g000003
rosa_roxburghii	Rroxscaffold_3G00260810
rosa_rugosa	Rorug07G0020100 Rorug07G0020200
rosa_samantha	Rh6BG025100 Rh6BG025600 Rh6BG025700 Rh6BG026500 Rh6BG026600 Rh6CG024600 Rh6DG024100 Rh6DG024400 Rh7AG147700 Rh7BG148300 Rh7CG152000
rosa_wichuraiana	Rw2G021680 Rw5G042100 Rw6G002490 Rw7G012610

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	928
AccI	GTMKAC	2 cut(s)	423, 522
AciI	CCGC	2 cut(s)	115, 347
AclWI	GGATC	3 cut(s)	203, 971, 995
AcoI	YGGCCR	2 cut(s)	344, 430
AcsI	RAATTY	1 cut(s)	151
AfaI	GTAC	3 cut(s)	119, 200, 942
AfiI	CCNNNNNNNGG	3 cut(s)	258, 953, 991
AflII	CTTAAG	1 cut(s)	611
AgsI	TTSAA	5 cut(s)	130, 149, 406, 903, 1037
AjiI	CACGTC	1 cut(s)	437
AjnI	CCWGG	1 cut(s)	333
AloI	GAACNNNNNNTCC	2 cut(s)	848, 880
AluBI	AGCT	6 cut(s)	145, 323, 470, 500, 721, 796
AluI	AGCT	6 cut(s)	145, 323, 470, 500, 721, 796
AlwI	GGATC	3 cut(s)	203, 971, 995
AlwNI	CAGNNNCTG	2 cut(s)	323, 1070
Ama87I	CYCGRG	1 cut(s)	251
AoxI	GGCC	5 cut(s)	25, 191, 344, 430, 565
ApaI	GGGCCC	1 cut(s)	569
ApeKI	GCWGC	7 cut(s)	312, 497, 793, 808, 1192, 1207, 1229
ApoI	RAATTY	1 cut(s)	151
AseI	ATTAAT	1 cut(s)	774
AspS9I	GGNCC	3 cut(s)	191, 565, 566
AvaI	CYCGRG	1 cut(s)	251
BaeGI	GKGCMC	2 cut(s)	173, 569
BanI	GGYRCC	1 cut(s)	928
BanII	GRGCYC	1 cut(s)	569
BbsI	GAAGAC	1 cut(s)	774
BbvI	GCAGC	7 cut(s)	299, 509, 795, 805, 1204, 1216, 1219
BccI	CCATC	2 cut(s)	455, 556
BciT130I	CCWGG	1 cut(s)	335
BfaI	CTAG	3 cut(s)	471, 882, 1237
BfmI	CTRYAG	3 cut(s)	663, 1008, 1230
BfrI	CTTAAG	1 cut(s)	611
BglII	AGATCT	1 cut(s)	681
BisI	GCNGC	8 cut(s)	313, 347, 498, 794, 809, 1193, 1208, 1230
BlsI	GCNGC	8 cut(s)	314, 348, 499, 795, 810, 1194, 1209, 1231
Bme1390I	CCNGG	1 cut(s)	335
BmeT110I	CYCGRG	1 cut(s)	251
BmgBI	CACGTC	1 cut(s)	437
BmgT120I	GGNCC	3 cut(s)	191, 565, 566
BmiI	GGNNCC	3 cut(s)	567, 930, 1137
BmrFI	CCNGG	1 cut(s)	335
BmsI	GCATC	2 cut(s)	25, 819
BpiI	GAAGAC	1 cut(s)	774
BpmI	CTGGAG	1 cut(s)	356
Bpu10I	CCTNAGC	1 cut(s)	316
BsaBI	GATNNNNATC	1 cut(s)	108
BsaJI	CCNNGG	1 cut(s)	252
BsaWI	WCCGGW	1 cut(s)	72
BsaXI	ACNNNNNCTCC	4 cut(s)	312, 342, 848, 878
Bsc4I	CCNNNNNNNGG	3 cut(s)	258, 953, 991
Bse1I	ACTGG	2 cut(s)	99, 642
Bse3DI	GCAATG	2 cut(s)	538, 632
Bse8I	GATNNNNATC	1 cut(s)	108
BseBI	CCWGG	1 cut(s)	335
BseDI	CCNNGG	1 cut(s)	252
BseGI	GGATG	2 cut(s)	577, 943
BseJI	GATNNNNATC	1 cut(s)	108
BseLI	CCNNNNNNNGG	3 cut(s)	258, 953, 991
BseMI	GCAATG	2 cut(s)	538, 632
BseMII	CTCAG	4 cut(s)	132, 330, 482, 708
BseNI	ACTGG	2 cut(s)	99, 642
BseRI	GAGGAG	4 cut(s)	269, 869, 1007, 1175
BseSI	GKGCMC	2 cut(s)	173, 569
BseXI	GCAGC	7 cut(s)	299, 509, 795, 805, 1204, 1216, 1219
BshFI	GGCC	5 cut(s)	27, 193, 346, 432, 567
BshNI	GGYRCC	1 cut(s)	928
BsiHKCI	CYCGRG	1 cut(s)	251
BsiSI	CCGG	1 cut(s)	73
BslI	CCNNNNNNNGG	3 cut(s)	258, 953, 991
BsmI	GAATGC	1 cut(s)	223
BsnI	GGCC	5 cut(s)	27, 193, 346, 432, 567
BsoBI	CYCGRG	1 cut(s)	251
Bsp120I	GGGCCC	1 cut(s)	565
Bsp1286I	GDGCHC	2 cut(s)	173, 569
Bsp1407I	TGTACA	2 cut(s)	198, 940
Bsp143I	GATC	5 cut(s)	208, 593, 681, 976, 1000
BspACI	CCGC	2 cut(s)	115, 347
BspANI	GGCC	5 cut(s)	27, 193, 346, 432, 567
BspCNI	CTCAG	4 cut(s)	133, 329, 483, 709
BspLI	GGNNCC	3 cut(s)	567, 930, 1137
BspMAI	CTGCAG	3 cut(s)	667, 1012, 1234
BspPI	GGATC	3 cut(s)	203, 971, 995
BspQI	GCTCTTC	1 cut(s)	579
BspT107I	GGYRCC	1 cut(s)	928
BspTI	CTTAAG	1 cut(s)	611
BsrDI	GCAATG	2 cut(s)	538, 632
BsrGI	TGTACA	2 cut(s)	198, 940
BsrI	ACTGG	2 cut(s)	99, 642
BssECI	CCNNGG	1 cut(s)	252
BssMI	GATC	5 cut(s)	208, 593, 681, 976, 1000
BssNAI	GTATAC	1 cut(s)	424
Bst1107I	GTATAC	1 cut(s)	424
Bst2UI	CCWGG	1 cut(s)	335
Bst4CI	ACNGT	3 cut(s)	428, 542, 986
Bst6I	CTCTTC	1 cut(s)	579
BstAFI	CTTAAG	1 cut(s)	611
BstAPI	GCANNNNNTGC	2 cut(s)	503, 838
BstAUI	TGTACA	2 cut(s)	198, 940
BstC8I	GCNNGC	2 cut(s)	344, 1227
BstDEI	CTNAG	5 cut(s)	141, 316, 491, 685, 717
BstF5I	GGATG	2 cut(s)	577, 943
BstKTI	GATC	5 cut(s)	211, 596, 684, 979, 1003
BstMBI	GATC	5 cut(s)	208, 593, 681, 976, 1000
BstMWI	GCNNNNNNNGC	3 cut(s)	339, 503, 838
BstNI	CCWGG	1 cut(s)	335
BstSCI	CCNGG	1 cut(s)	333
BstSFI	CTRYAG	3 cut(s)	663, 1008, 1230
BstSLI	GKGCMC	2 cut(s)	173, 569
BstV1I	GCAGC	7 cut(s)	299, 509, 795, 805, 1204, 1216, 1219
BstV2I	GAAGAC	1 cut(s)	774
BstX2I	RGATCY	1 cut(s)	681
BstYI	RGATCY	1 cut(s)	681
BstZ17I	GTATAC	1 cut(s)	424
BsuRI	GGCC	5 cut(s)	27, 193, 346, 432, 567
BtrI	CACGTC	1 cut(s)	437
BtsCI	GGATG	2 cut(s)	577, 943
BtsI	GCAGTG	1 cut(s)	378
BtsIMutI	CAGTG	3 cut(s)	92, 378, 433
Cac8I	GCNNGC	2 cut(s)	344, 1227
CaiI	CAGNNNCTG	2 cut(s)	323, 1070
Cfr13I	GGNCC	3 cut(s)	191, 565, 566
Csp6I	GTAC	3 cut(s)	118, 199, 941
CspCI	CAANNNNNGTGG	2 cut(s)	1015, 1050
CviAII	CATG	1 cut(s)	892
CviQI	GTAC	3 cut(s)	118, 199, 941
DdeI	CTNAG	5 cut(s)	141, 316, 491, 685, 717
DpnI	GATC	5 cut(s)	210, 595, 683, 978, 1002
DpnII	GATC	5 cut(s)	208, 593, 681, 976, 1000
EaeI	YGGCCR	2 cut(s)	344, 430
Eam1104I	CTCTTC	1 cut(s)	579
EarI	CTCTTC	1 cut(s)	579
Eco24I	GRGCYC	1 cut(s)	569
Eco88I	CYCGRG	1 cut(s)	251
EcoO109I	RGGNCCY	1 cut(s)	566
EcoRII	CCWGG	1 cut(s)	333
EcoT38I	GRGCYC	1 cut(s)	569
FaeI	CATG	1 cut(s)	895
FalI	AAGNNNNNCTT	2 cut(s)	605, 637
FatI	CATG	1 cut(s)	891
FauNDI	CATATG	2 cut(s)	804, 909
FblI	GTMKAC	2 cut(s)	423, 522
Fnu4HI	GCNGC	8 cut(s)	313, 347, 498, 794, 809, 1193, 1208, 1230
FokI	GGATG	2 cut(s)	564, 930
FriOI	GRGCYC	1 cut(s)	569
Fsp4HI	GCNGC	8 cut(s)	313, 347, 498, 794, 809, 1193, 1208, 1230
FspBI	CTAG	3 cut(s)	471, 882, 1237
GluI	GCNGC	8 cut(s)	313, 347, 498, 794, 809, 1193, 1208, 1230
GsuI	CTGGAG	1 cut(s)	356
HaeIII	GGCC	5 cut(s)	27, 193, 346, 432, 567
HapII	CCGG	1 cut(s)	73
Hin1II	CATG	1 cut(s)	895
HinfI	GANTC	2 cut(s)	694, 1113
HpaII	CCGG	1 cut(s)	73
Hpy166II	GTNNAC	4 cut(s)	199, 424, 523, 941
Hpy188I	TCNGA	4 cut(s)	142, 289, 718, 972
Hpy188III	TCNNGA	4 cut(s)	16, 318, 389, 698
Hpy8I	GTNNAC	4 cut(s)	199, 424, 523, 941
Hpy99I	CGWCG	1 cut(s)	438
HpyAV	CCTTC	2 cut(s)	395, 468
HpyCH4III	ACNGT	3 cut(s)	428, 542, 986
HpyCH4IV	ACGT	3 cut(s)	436, 1091, 1221
HpyF10VI	GCNNNNNNNGC	3 cut(s)	339, 503, 838
HpyF3I	CTNAG	5 cut(s)	141, 316, 491, 685, 717
HpySE526I	ACGT	3 cut(s)	436, 1091, 1221
Hsp92II	CATG	1 cut(s)	895
Kzo9I	GATC	5 cut(s)	208, 593, 681, 976, 1000
LguI	GCTCTTC	1 cut(s)	579
LmnI	GCTCC	3 cut(s)	320, 790, 1135
Lsp1109I	GCAGC	7 cut(s)	299, 509, 795, 805, 1204, 1216, 1219
LweI	GCATC	2 cut(s)	25, 819
MaeI	CTAG	3 cut(s)	471, 882, 1237
MaeII	ACGT	3 cut(s)	436, 1091, 1221
MaeIII	GTNAC	2 cut(s)	709, 1092
MalI	GATC	5 cut(s)	210, 595, 683, 978, 1002
MboI	GATC	5 cut(s)	208, 593, 681, 976, 1000
MboII	GAAGA	6 cut(s)	39, 566, 779, 838, 1049, 1108
MfeI	CAATTG	1 cut(s)	357
MflI	RGATCY	1 cut(s)	681
MhlI	GDGCHC	2 cut(s)	173, 569
MluCI	AATT	3 cut(s)	43, 151, 357
MmeI	TCCRAC	1 cut(s)	1040
MseI	TTAA	5 cut(s)	30, 612, 774, 923, 1044
MslI	CAYNNNNRTG	1 cut(s)	228
MspA1I	CMGCKG	1 cut(s)	796
MspCI	CTTAAG	1 cut(s)	611
MspI	CCGG	1 cut(s)	73
MspR9I	CCNGG	1 cut(s)	335
MunI	CAATTG	1 cut(s)	357
Mva1269I	GAATGC	1 cut(s)	223
MvaI	CCWGG	1 cut(s)	335
MwoI	GCNNNNNNNGC	3 cut(s)	339, 503, 838
NdeI	CATATG	2 cut(s)	804, 909
NdeII	GATC	5 cut(s)	208, 593, 681, 976, 1000
NlaIII	CATG	1 cut(s)	895
NlaIV	GGNNCC	3 cut(s)	567, 930, 1137
NmuCI	GTSAC	2 cut(s)	709, 1092
PciSI	GCTCTTC	1 cut(s)	579
PctI	GAATGC	1 cut(s)	223
PfeI	GAWTC	2 cut(s)	694, 1113
PkrI	GCNGC	8 cut(s)	314, 348, 499, 795, 810, 1194, 1209, 1231
PshBI	ATTAAT	1 cut(s)	774
Psp6I	CCWGG	1 cut(s)	333
PspGI	CCWGG	1 cut(s)	333
PspN4I	GGNNCC	3 cut(s)	567, 930, 1137
PspOMI	GGGCCC	1 cut(s)	565
PspPI	GGNCC	3 cut(s)	191, 565, 566
PstI	CTGCAG	3 cut(s)	667, 1012, 1234
PstNI	CAGNNNCTG	2 cut(s)	323, 1070
PsuI	RGATCY	1 cut(s)	681
PvuII	CAGCTG	1 cut(s)	796
RsaI	GTAC	3 cut(s)	119, 200, 942
RsaNI	GTAC	3 cut(s)	118, 199, 941
RseI	CAYNNNNRTG	1 cut(s)	228
SapI	GCTCTTC	1 cut(s)	579
SaqAI	TTAA	5 cut(s)	30, 612, 774, 923, 1044
SatI	GCNGC	8 cut(s)	313, 347, 498, 794, 809, 1193, 1208, 1230
Sau3AI	GATC	5 cut(s)	208, 593, 681, 976, 1000
Sau96I	GGNCC	3 cut(s)	191, 565, 566
ScrFI	CCNGG	1 cut(s)	335
SduI	GDGCHC	2 cut(s)	173, 569
SfaNI	GCATC	2 cut(s)	25, 819
SfcI	CTRYAG	3 cut(s)	663, 1008, 1230
SmiMI	CAYNNNNRTG	1 cut(s)	228
SmlI	CTYRAG	1 cut(s)	611
SmoI	CTYRAG	1 cut(s)	611
Sse9I	AATT	3 cut(s)	43, 151, 357
SsiI	CCGC	2 cut(s)	115, 347
SspMI	CTAG	3 cut(s)	471, 882, 1237
StyD4I	CCNGG	1 cut(s)	333
TaaI	ACNGT	3 cut(s)	428, 542, 986
TaiI	ACGT	3 cut(s)	439, 1094, 1224
TaqI	TCGA	3 cut(s)	17, 388, 1199
TasI	AATT	3 cut(s)	43, 151, 357
TatI	WGTACW	2 cut(s)	198, 940
TauI	GCSGC	1 cut(s)	349
TfiI	GAWTC	2 cut(s)	694, 1113
Tru1I	TTAA	5 cut(s)	30, 612, 774, 923, 1044
Tru9I	TTAA	5 cut(s)	30, 612, 774, 923, 1044
TscAI	CASTG	3 cut(s)	99, 385, 433
TseFI	GTSAC	2 cut(s)	709, 1092
TseI	GCWGC	7 cut(s)	312, 497, 793, 808, 1192, 1207, 1229
Tsp45I	GTSAC	2 cut(s)	709, 1092
TspDTI	ATGAA	8 cut(s)	39, 434, 501, 549, 566, 690, 717, 926
TspGWI	ACGGA	1 cut(s)	124
TspRI	CASTG	3 cut(s)	99, 385, 433
Vha464I	CTTAAG	1 cut(s)	611
VspI	ATTAAT	1 cut(s)	774
XapI	RAATTY	1 cut(s)	151
XmiI	GTMKAC	2 cut(s)	423, 522
XspI	CTAG	3 cut(s)	471, 882, 1237

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.