Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4D

Orthogroup ID

OG0002735

Physical Location & Seq

Genomic Coordinates Forward (+)

61257522 .. 61261342

Gene Structure 3821 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4DG396000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1092 bp

ATGTTGTTTGGAAAGCGTGGGAAGAGTGGTTTGGTTGCCTTGAACCTGGATTTCGCCCAAGTCGTCACCTTTGTGAAGGAGCGACTAGGCAAAGAGGTTGAGATGGGTGGCTGCAAAGGACCCATCACAACATTCATTGTCGAGCCCTTCATTCCCCACAATGAAGAGTTTTACATTAACATCGTCTCAGATAGACTTGGGAATAGCATAAGCTTCTCAGAGTGTGGAGGAATTGACATTGAGGAGAACTGGGATAAGGTCAAGACCATATTTGTCCCAACGGGAGCTTCCCTTACACCAGATGTATCTGCTCCACTTGTTGCAACCCTTCCCTTGGAGATTAAAAGCGAAATTGAGGAGTTTATCAAGTCCGTATTTGCTCTATTTCAAGATCTCGACTTCACTTTTCTGGAGATGAATCCTTTTGCATTGGTTGATGGAAAGCCATATCCTTTGGATATGAGAGGCGAGCTGGATGACACTGCTGCTTTCAAGAACTTCAAAAAGTGGGGCAATATTGAATTTCCAATGCCATTTGGAAGAGTTATGAGTCCTACAGAAAAGTTTATTCACGGGCTAGATGAAAAGACAAGTGCATCTTTGAAATTTACAGTTCTGAACCCTAAGGGACGAATTTGGACTATGGTTGCTGGAGGAGGTGCAAGTGTTATTTATGCAGACACGGTTGGTGATCTTGGCTTTGCTAATGAGCTCGGAAACTATGCTGAATATAGTGGAGCACCAAATGAAGAGGAGGTATTGCAGTATGCCAGAGTTGTGATTGATTGTGCAACTTCTGATCCTGATGGCCGTAAGAGAGCCCTTGTAATTGGAGGGGGAATTGCTAACTTCACTGATGTAGCTGCAACATTCAATGGCATTATTAGAGCCTTGAAGGAGAAGGAATCAAAGCTTAAAGCTGCTAGGATGCATCTTTATGTCAGGAGAGGAGGTCCCAACTACCAGAGGGGACTTGCAAAAATGAGGGCACTTGCAGAGGAAATTGGCCTCCCTATTGAGGTCTATGGTCCTGAAGCAACAATGACTGGTATTTGCAAGCAGGCAATTCAGTGCATCAGTGCTGCTGCATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003824 GO:0003878 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005829 GO:0006082 GO:0006084 GO:0006085 GO:0006139 GO:0006163 GO:0006164 GO:0006629 GO:0006631 GO:0006633 GO:0006637 GO:0006725 GO:0006732 GO:0006753 GO:0006790 GO:0006793 GO:0006796 GO:0006807 GO:0008150 GO:0008152 GO:0008610 GO:0009058 GO:0009108 GO:0009117 GO:0009150 GO:0009152 GO:0009165 GO:0009259 GO:0009260 GO:0009346 GO:0009987 GO:0016053 GO:0016740 GO:0016746 GO:0018130 GO:0019438 GO:0019637 GO:0019693 GO:0019752 GO:0032787 GO:0032991 GO:0033865 GO:0033866 GO:0033875 GO:0034030 GO:0034032 GO:0034033 GO:0034641 GO:0034654 GO:0035383 GO:0035384 GO:0043436 GO:0043603 GO:0043604 GO:0044237 GO:0044238 GO:0044249 GO:0044255 GO:0044271 GO:0044272 GO:0044281 GO:0044283 GO:0044424 GO:0044444 GO:0044464 GO:0046390 GO:0046394 GO:0046483 GO:0046912 GO:0051186 GO:0051188 GO:0055086 GO:0071616 GO:0071704 GO:0072330 GO:0072521 GO:0072522 GO:0090407 GO:1901135 GO:1901137 GO:1901293 GO:1901360 GO:1901362 GO:1901564 GO:1901566 GO:1901576

KEGG Pathways

Metabolic & Signaling

ko00020 ko00720 ko01100 ko01110 ko01120 ko01130 map00020 map00720 map01100 map01110 map01120 map01130

Pfam Domains

Protein Families

ATP-grasp_2 Citrate_bind

Protein Analysis

363

Amino Acids

39.68

Weight (kDa)

5.21

Isoelectric Point (pI)

36.43

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Citrate_synth_N	PF24948	1 - 170	6.2e-54	ATP-citrate synthase ATP-grasp domain
ATP-grasp_2	PF08442	2 - 143	1.2e-11	ATP-grasp domain
Citrate_bind	PF16114	181 - 357	2.5e-84	ATP citrate lyase citrate-binding

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: OG0002735)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G10670 AT1G10670 AT1G10670 AT1G10670 AT1G60810 AT1G60810
fragaria_vesca	FvH4_4g32950 FvH4_4g32950 FvH4_4g32950
malus_domestica	MD13G1095200.v1.1 MD16G1096300.v1.1
prunus_persica	Prupe.1G250100_v2.0.a1 Prupe.1G250100_v2.0.a1
pyrus_communis	pycom05g10590 pycom13g08300 pycom16g08220
rosa_chinensis	RchiOBHm_Chr4g0441981 RchiOBHm_Chr7g0181761
rosa_laevigata	RLG00000006053 RLG00000018726
rosa_multiflora	Rmu_co8081680.1_g000001 Rmu_sc0000905.1_g000020
rosa_roxburghii	Rroxscaffold_1G00051200 Rroxscaffold_5G00359300 Rroxscaffold_5G00382850
rosa_rugosa	Rorug04G0337500 Rorug04G0337500 Rorug04G0337500
rosa_samantha	Rh2BG270200 Rh4AG389500 Rh4BG402900 Rh4CG418100 Rh4DG118600 Rh4DG396000 Rh7AG279300 Rh7CG298400 Rh7DG045400
rosa_wichuraiana	Rw4G033630 Rw6G021030

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AclWI	GGATC	1 cut(s)	794
AcoI	YGGCCR	1 cut(s)	808
AcsI	RAATTY	3 cut(s)	521, 605, 633
AcuI	CTGAAG	1 cut(s)	1053
AfiI	CCNNNNNNNGG	2 cut(s)	334, 1018
AgsI	TTSAA	8 cut(s)	43, 389, 493, 502, 521, 604, 874, 895
AjnI	CCWGG	1 cut(s)	45
AjuI	GAANNNNNNNTTGG	4 cut(s)	14, 46, 271, 303
AleI	CACNNNNGTG	1 cut(s)	71
AluBI	AGCT	7 cut(s)	213, 287, 472, 712, 863, 913, 920
AluI	AGCT	7 cut(s)	213, 287, 472, 712, 863, 913, 920
Alw21I	GWGCWC	2 cut(s)	714, 742
Alw26I	GTCTC	1 cut(s)	190
AlwI	GGATC	1 cut(s)	794
AoxI	GGCC	2 cut(s)	808, 1006
ApeKI	GCWGC	6 cut(s)	111, 485, 863, 920, 1082, 1085
ApoI	RAATTY	3 cut(s)	521, 605, 633
AspS9I	GGNCC	3 cut(s)	119, 953, 1028
AsuHPI	GGTGA	2 cut(s)	58, 701
AvaII	GGWCC	3 cut(s)	119, 953, 1028
AxyI	CCTNAGG	1 cut(s)	624
BaeGI	GKGCMC	1 cut(s)	991
BanII	GRGCYC	3 cut(s)	147, 714, 823
Bbv12I	GWGCWC	2 cut(s)	714, 742
BbvI	GCAGC	6 cut(s)	98, 472, 850, 907, 1069, 1072
BccI	CCATC	4 cut(s)	97, 131, 431, 800
BceAI	ACGGC	1 cut(s)	795
BciT130I	CCWGG	1 cut(s)	47
BcoDI	GTCTC	1 cut(s)	190
BfaI	CTAG	3 cut(s)	86, 578, 924
BfmI	CTRYAG	1 cut(s)	555
BglII	AGATCT	1 cut(s)	391
BisI	GCNGC	6 cut(s)	112, 486, 864, 921, 1083, 1086
BlsI	GCNGC	6 cut(s)	113, 487, 865, 922, 1084, 1087
Bme1390I	CCNGG	1 cut(s)	47
Bme18I	GGWCC	3 cut(s)	119, 953, 1028
BmgT120I	GGNCC	3 cut(s)	119, 953, 1028
BmiI	GGNNCC	2 cut(s)	121, 955
BmrFI	CCNGG	1 cut(s)	47
BmrI	ACTGGG	1 cut(s)	259
BmsI	GCATC	4 cut(s)	605, 918, 940, 1083
BmuI	ACTGGG	1 cut(s)	259
BpmI	CTGGAG	2 cut(s)	431, 672
BsaJI	CCNNGG	1 cut(s)	333
BsaXI	ACNNNNNCTCC	2 cut(s)	937, 967
Bsc4I	CCNNNNNNNGG	2 cut(s)	334, 1018
Bse1I	ACTGG	2 cut(s)	254, 1051
Bse21I	CCTNAGG	1 cut(s)	624
BseBI	CCWGG	1 cut(s)	47
BseDI	CCNNGG	1 cut(s)	333
BseGI	GGATG	2 cut(s)	481, 933
BseLI	CCNNNNNNNGG	2 cut(s)	334, 1018
BseMII	CTCAG	2 cut(s)	201, 231
BseNI	ACTGG	2 cut(s)	254, 1051
BseRI	GAGGAG	5 cut(s)	257, 371, 669, 767, 963
BseSI	GKGCMC	1 cut(s)	991
BseXI	GCAGC	6 cut(s)	98, 472, 850, 907, 1069, 1072
BshFI	GGCC	2 cut(s)	810, 1008
BsiHKAI	GWGCWC	2 cut(s)	714, 742
BslFI	GGGAC	4 cut(s)	260, 642, 939, 984
BslI	CCNNNNNNNGG	2 cut(s)	334, 1018
BsmAI	GTCTC	1 cut(s)	190
BsmBI	CGTCTC	1 cut(s)	190
BsmFI	GGGAC	4 cut(s)	260, 642, 939, 984
BsnI	GGCC	2 cut(s)	810, 1008
Bsp1286I	GDGCHC	5 cut(s)	147, 714, 742, 823, 991
Bsp143I	GATC	3 cut(s)	391, 691, 799
BspANI	GGCC	2 cut(s)	810, 1008
BspCNI	CTCAG	2 cut(s)	200, 230
BspLI	GGNNCC	2 cut(s)	121, 955
BspPI	GGATC	1 cut(s)	794
BsrI	ACTGG	2 cut(s)	254, 1051
BssECI	CCNNGG	1 cut(s)	333
BssMI	GATC	3 cut(s)	391, 691, 799
BssT1I	CCWWGG	1 cut(s)	333
Bst2UI	CCWGG	1 cut(s)	47
Bst4CI	ACNGT	2 cut(s)	613, 685
Bst6I	CTCTTC	4 cut(s)	17, 159, 535, 744
BstC8I	GCNNGC	3 cut(s)	470, 1058, 1062
BstDEI	CTNAG	3 cut(s)	187, 217, 624
BstF5I	GGATG	2 cut(s)	481, 933
BstKTI	GATC	3 cut(s)	394, 694, 802
BstMAI	GTCTC	1 cut(s)	190
BstMBI	GATC	3 cut(s)	391, 691, 799
BstNI	CCWGG	1 cut(s)	47
BstSCI	CCNGG	1 cut(s)	45
BstSFI	CTRYAG	1 cut(s)	555
BstSLI	GKGCMC	1 cut(s)	991
BstV1I	GCAGC	6 cut(s)	98, 472, 850, 907, 1069, 1072
BstX2I	RGATCY	1 cut(s)	391
BstYI	RGATCY	1 cut(s)	391
Bsu36I	CCTNAGG	1 cut(s)	624
BsuRI	GGCC	2 cut(s)	810, 1008
BtsCI	GGATG	2 cut(s)	481, 933
BtsI	GCAGTG	1 cut(s)	480
BtsIMutI	CAGTG	4 cut(s)	480, 852, 1076, 1084
Cac8I	GCNNGC	3 cut(s)	470, 1058, 1062
Cfr13I	GGNCC	3 cut(s)	119, 953, 1028
CviAII	CATG	1 cut(s)	1089
DdeI	CTNAG	3 cut(s)	187, 217, 624
DpnI	GATC	3 cut(s)	393, 693, 801
DpnII	GATC	3 cut(s)	391, 691, 799
EaeI	YGGCCR	1 cut(s)	808
Eam1104I	CTCTTC	4 cut(s)	17, 159, 535, 744
EarI	CTCTTC	4 cut(s)	17, 159, 535, 744
Ecl136II	GAGCTC	1 cut(s)	712
Eco130I	CCWWGG	1 cut(s)	333
Eco24I	GRGCYC	3 cut(s)	147, 714, 823
Eco47I	GGWCC	3 cut(s)	119, 953, 1028
Eco53kI	GAGCTC	1 cut(s)	712
Eco57I	CTGAAG	1 cut(s)	1053
Eco81I	CCTNAGG	1 cut(s)	624
EcoICRI	GAGCTC	1 cut(s)	712
EcoO109I	RGGNCCY	2 cut(s)	119, 953
EcoRII	CCWGG	1 cut(s)	45
EcoT14I	CCWWGG	1 cut(s)	333
EcoT22I	ATGCAT	1 cut(s)	933
EcoT38I	GRGCYC	3 cut(s)	147, 714, 823
ErhI	CCWWGG	1 cut(s)	333
Esp3I	CGTCTC	1 cut(s)	190
FaeI	CATG	1 cut(s)	1092
FalI	AAGNNNNNCTT	2 cut(s)	583, 615
FaqI	GGGAC	4 cut(s)	260, 642, 939, 984
FatI	CATG	1 cut(s)	1088
Fnu4HI	GCNGC	6 cut(s)	112, 486, 864, 921, 1083, 1086
FokI	GGATG	2 cut(s)	488, 940
FriOI	GRGCYC	3 cut(s)	147, 714, 823
Fsp4HI	GCNGC	6 cut(s)	112, 486, 864, 921, 1083, 1086
FspBI	CTAG	3 cut(s)	86, 578, 924
GluI	GCNGC	6 cut(s)	112, 486, 864, 921, 1083, 1086
GsuI	CTGGAG	2 cut(s)	431, 672
HaeIII	GGCC	2 cut(s)	810, 1008
Hin1II	CATG	1 cut(s)	1092
HindIII	AAGCTT	2 cut(s)	211, 911
HinfI	GANTC	3 cut(s)	418, 550, 905
HphI	GGTGA	2 cut(s)	58, 701
Hpy188I	TCNGA	5 cut(s)	190, 220, 618, 716, 799
Hpy188III	TCNNGA	8 cut(s)	262, 389, 395, 410, 493, 803, 943, 1031
HpyAV	CCTTC	5 cut(s)	70, 157, 338, 889, 895
HpyCH4III	ACNGT	2 cut(s)	613, 685
HpyF3I	CTNAG	3 cut(s)	187, 217, 624
Hsp92II	CATG	1 cut(s)	1092
Kzo9I	GATC	3 cut(s)	391, 691, 799
LmnI	GCTCC	4 cut(s)	79, 284, 316, 737
Lsp1109I	GCAGC	6 cut(s)	98, 472, 850, 907, 1069, 1072
LweI	GCATC	4 cut(s)	605, 918, 940, 1083
MaeI	CTAG	3 cut(s)	86, 578, 924
MaeIII	GTNAC	1 cut(s)	64
MalI	GATC	3 cut(s)	393, 693, 801
MboI	GATC	3 cut(s)	391, 691, 799
MboII	GAAGA	4 cut(s)	34, 176, 552, 761
MflI	RGATCY	1 cut(s)	391
MhlI	GDGCHC	5 cut(s)	147, 714, 742, 823, 991
MluCI	AATT	9 cut(s)	231, 351, 521, 605, 633, 828, 840, 1002, 1065
MlyI	GAGTC	1 cut(s)	559
Mph1103I	ATGCAT	1 cut(s)	933
MseI	TTAA	3 cut(s)	177, 342, 915
MslI	CAYNNNNRTG	2 cut(s)	71, 936
MspR9I	CCNGG	1 cut(s)	47
MvaI	CCWGG	1 cut(s)	47
NdeII	GATC	3 cut(s)	391, 691, 799
NlaIII	CATG	1 cut(s)	1092
NlaIV	GGNNCC	2 cut(s)	121, 955
NmuCI	GTSAC	1 cut(s)	64
NsiI	ATGCAT	1 cut(s)	933
OliI	CACNNNNGTG	1 cut(s)	71
PcsI	WCGNNNNNNNCGW	1 cut(s)	60
PfeI	GAWTC	2 cut(s)	418, 905
PkrI	GCNGC	6 cut(s)	113, 487, 865, 922, 1084, 1087
PleI	GAGTC	1 cut(s)	558
PpsI	GAGTC	1 cut(s)	558
PpuMI	RGGWCCY	2 cut(s)	119, 953
Psp124BI	GAGCTC	1 cut(s)	714
Psp5II	RGGWCCY	2 cut(s)	119, 953
Psp6I	CCWGG	1 cut(s)	45
PspGI	CCWGG	1 cut(s)	45
PspN4I	GGNNCC	2 cut(s)	121, 955
PspPI	GGNCC	3 cut(s)	119, 953, 1028
PspPPI	RGGWCCY	2 cut(s)	119, 953
PsuI	RGATCY	1 cut(s)	391
RseI	CAYNNNNRTG	2 cut(s)	71, 936
SacI	GAGCTC	1 cut(s)	714
SaqAI	TTAA	3 cut(s)	177, 342, 915
SatI	GCNGC	6 cut(s)	112, 486, 864, 921, 1083, 1086
Sau3AI	GATC	3 cut(s)	391, 691, 799
Sau96I	GGNCC	3 cut(s)	119, 953, 1028
SchI	GAGTC	1 cut(s)	559
ScrFI	CCNGG	1 cut(s)	47
SduI	GDGCHC	5 cut(s)	147, 714, 742, 823, 991
SfaNI	GCATC	4 cut(s)	605, 918, 940, 1083
SfcI	CTRYAG	1 cut(s)	555
SinI	GGWCC	3 cut(s)	119, 953, 1028
SmiMI	CAYNNNNRTG	2 cut(s)	71, 936
Sse9I	AATT	9 cut(s)	231, 351, 521, 605, 633, 828, 840, 1002, 1065
SspI	AATATT	1 cut(s)	517
SspMI	CTAG	3 cut(s)	86, 578, 924
SstI	GAGCTC	1 cut(s)	714
StyD4I	CCNGG	1 cut(s)	45
StyI	CCWWGG	1 cut(s)	333
TaaI	ACNGT	2 cut(s)	613, 685
TaqI	TCGA	2 cut(s)	141, 396
TasI	AATT	9 cut(s)	231, 351, 521, 605, 633, 828, 840, 1002, 1065
TfiI	GAWTC	2 cut(s)	418, 905
Tru1I	TTAA	3 cut(s)	177, 342, 915
Tru9I	TTAA	3 cut(s)	177, 342, 915
TscAI	CASTG	4 cut(s)	487, 859, 1076, 1084
TseFI	GTSAC	1 cut(s)	64
TseI	GCWGC	6 cut(s)	111, 485, 863, 920, 1082, 1085
Tsp45I	GTSAC	1 cut(s)	64
TspDTI	ATGAA	6 cut(s)	124, 139, 177, 431, 597, 762
TspGWI	ACGGA	1 cut(s)	361
TspRI	CASTG	4 cut(s)	487, 859, 1076, 1084
VpaK11BI	GGWCC	3 cut(s)	119, 953, 1028
XapI	RAATTY	3 cut(s)	521, 605, 633
XspI	CTAG	3 cut(s)	86, 578, 924
Zsp2I	ATGCAT	1 cut(s)	933

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