Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000006

Orthogroup ID

OG0005462

Physical Location & Seq

Genomic Coordinates Forward (+)

3430849 .. 3436108

Gene Structure 5260 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_6G00389580.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1116 bp

ATGCTGTGGGTAGACAAGTACAGACCCAAAACCCTAGACCAGGCAATGGTCCACCAAGACACGGCGCAAAACCTCAAGAAACTTGTCGCAGAGCAGGACTGCCCCCATTTGCTCTTTTACGGGCCTTCCGGCTCCGGCAAGAAAACCCTAATCATCGCCCTTATTCGTCAGATTTTCGGACCCAGCGCCGACAAGGTGAAGGTGGAAAACAGGACATGGAAAGTTGATGCTGGGAGTAGAACCATTGACATAGAGCTGACTACATTATCAAGCACCAATCACATTGAACTCAACCCCAGTGATGCAGGCTTTCAGGACAGATACATTGTTCAAGAGATAATTAAGGAAATGGCTAAAAATAGACCCATTGACACAAAAGGGAAAAAAGGATATAAAATCTTGGTGTTGAATGAAGTTGACAAACTTTCAAGAGAAGCACAGCATTCTCTTCGAAGAACTATGGAGAAATATAGTGCTTATTGCCGCCTAATACTATGCTGTAACAGTTCTTCAAAGGTGACTGAAGCAATCCGATCACGGTGTCTAAATGTGCGAATAAATGCACCAACAGATGGACAGGTTGGAGTTGCTGGCTTCTATCTTATTGTTAAGGCATTGGAGTTCATTGGAAAGAAAGAAGGGCTTCAATTTCCTTCTGGATTTGCTGCTCATATAGCTGAAAAATCAAACAGGAGCTTAAGGAGAGCTATATTGTCTCTAGAAACTTGTCATGTTCAACAGTATCCCTTTACAAGTAACCAAATAATTCCCTCAATGGATTGGGAGGAATATGTTTCAGAAATTGTATCTGATATAATGAAGGAGCAGAGTCCGAAAAGGCTTTATCTGGTGCGGCAAAAGTTGTATGAGCTACTTGTTAATTGTATCCCTCCAGAGATCATTCTTAAGACATTGTCGAGAAGGCTGCTTTATGAGTTATTGAAGAAATTGGATGCAGAATTGAAGCATGAGGTCTGCCATTGGGCAGCATATTATAGTGATATGATCTCACAATCTCCTTGTAGTGGGATTTTCTCACCCTCCTACTGGGTTGGTATGCTTGCCAGCAAGCGCCTGGCCCCAACTGCTGTCCCCTACTTGCCACTGATTCTTTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005657 GO:0005663 GO:0005694 GO:0006139 GO:0006259 GO:0006260 GO:0006261 GO:0006275 GO:0006281 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009889 GO:0009891 GO:0009893 GO:0009987 GO:0010556 GO:0010557 GO:0010604 GO:0019219 GO:0019222 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0031390 GO:0032991 GO:0033554 GO:0034641 GO:0034645 GO:0043085 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0044093 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044422 GO:0044424 GO:0044427 GO:0044446 GO:0044464 GO:0045935 GO:0046483 GO:0048518 GO:0048522 GO:0050789 GO:0050790 GO:0050794 GO:0050896 GO:0051052 GO:0051054 GO:0051171 GO:0051173 GO:0051338 GO:0051347 GO:0051716 GO:0060255 GO:0065007 GO:0065009 GO:0071704 GO:0080090 GO:0090304 GO:0090329 GO:1900262 GO:1900264 GO:1901360 GO:1901576 GO:2000112 GO:2000278 GO:2000573

KEGG Pathways

Metabolic & Signaling

ko03030 ko03420 ko03430 map03030 map03420 map03430

Pfam Domains

Protein Families

DNA_pol3_delta2

Protein Analysis

371

Amino Acids

42.21

Weight (kDa)

9.15

Isoelectric Point (pI)

46.29

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DNA_pol3_delta2	PF13177	19 - 188	2e-12	DNA polymerase III, delta subunit
AAA	PF00004	37 - 182	1.6e-06	ATPase family associated with various cellular activities (AAA)
RCF1-5-like_lid	PF21960	205 - 243	6.6e-10	RCF1/5-like, AAA+ ATPase lid domain
RFC_C	PF22534	261 - 337	2.2e-15	Replication factor C subunit 3, C-terminal domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0005462)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G27740
fragaria_vesca	FvH4_1g23560 FvH4_2g04970 FvH4_2g04970 FvH4_2g04970
malus_domestica	MD04G1041000.v1.1 MD04G1041300.v1.1 MD12G1011300.v1.1
prunus_persica	Prupe.1G194700_v2.0.a1 Prupe.1G194700_v2.0.a1 Prupe.4G268900_v2.0.a1 Prupe.4G268900_v2.0.a1 Prupe.7G013300_v2.0.a1 Prupe.7G013300_v2.0.a1 Prupe.7G013300_v2.0.a1
pyrus_communis	pycom12g00880
rosa_chinensis	RchiOBHm_Chr3g0496081
rosa_laevigata	RLG00000022564
rosa_multiflora	Rmu_sc0002392.1_g000001
rosa_roxburghii	Rroxscaffold_6G00389580
rosa_rugosa	Rorug03G0279300 Rorug03G0279400 Rorug03G0279400 Rorug03G0279400 Rorug03G0279500
rosa_samantha	Rh3AG326500 Rh3BG362800 Rh3DG362200
rosa_wichuraiana	Rw3G028590

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	2 cut(s)	46, 572
AccI	GTMKAC	1 cut(s)	12
AciI	CCGC	2 cut(s)	484, 853
AcuI	CTGAAG	1 cut(s)	543
AfaI	GTAC	1 cut(s)	20
AfiI	CCNNNNNNNGG	6 cut(s)	40, 46, 61, 572, 1025, 1047
AflII	CTTAAG	2 cut(s)	697, 905
AgsI	TTSAA	9 cut(s)	287, 332, 409, 429, 513, 647, 737, 943, 964
AjnI	CCWGG	2 cut(s)	39, 1074
AluBI	AGCT	5 cut(s)	256, 677, 696, 707, 871
AluI	AGCT	5 cut(s)	256, 677, 696, 707, 871
Alw26I	GTCTC	1 cut(s)	720
AoxI	GGCC	2 cut(s)	122, 1077
ApeKI	GCWGC	3 cut(s)	665, 925, 986
Asp700I	GAANNNNTTC	1 cut(s)	642
AspLEI	GCGC	3 cut(s)	67, 188, 1074
AspS9I	GGNCC	4 cut(s)	49, 122, 179, 1078
AsuHPI	GGTGA	3 cut(s)	208, 529, 1029
AsuII	TTCGAA	1 cut(s)	451
AvaII	GGWCC	2 cut(s)	49, 179
BarI	GAAGNNNNNNTAC	2 cut(s)	493, 525
BbvI	GCAGC	3 cut(s)	652, 912, 998
BccI	CCATC	1 cut(s)	566
BceAI	ACGGC	1 cut(s)	78
BcgI	CGANNNNNNTGC	4 cut(s)	431, 465, 907, 941
BciT130I	CCWGG	2 cut(s)	41, 1076
BciVI	GTATCC	2 cut(s)	753, 896
BcoDI	GTCTC	1 cut(s)	720
BfaI	CTAG	2 cut(s)	35, 719
BfoI	RGCGCY	2 cut(s)	189, 1075
BfrI	CTTAAG	2 cut(s)	697, 905
BfuI	GTATCC	2 cut(s)	753, 896
BisI	GCNGC	5 cut(s)	484, 666, 854, 926, 987
BlsI	GCNGC	5 cut(s)	485, 667, 855, 927, 988
Bme1390I	CCNGG	2 cut(s)	41, 1076
Bme18I	GGWCC	2 cut(s)	49, 179
BmgT120I	GGNCC	4 cut(s)	49, 122, 179, 1078
BmiI	GGNNCC	3 cut(s)	133, 181, 1080
BmrFI	CCNGG	2 cut(s)	41, 1076
BmrI	ACTGGG	2 cut(s)	291, 1057
BmsI	GCATC	3 cut(s)	217, 292, 943
BmuI	ACTGGG	2 cut(s)	291, 1057
BpmI	CTGGAG	1 cut(s)	876
Bpu14I	TTCGAA	1 cut(s)	451
BpuEI	CTTGAG	1 cut(s)	59
Bsc4I	CCNNNNNNNGG	6 cut(s)	40, 46, 61, 572, 1025, 1047
Bse1I	ACTGG	2 cut(s)	297, 1052
Bse3DI	GCAATG	1 cut(s)	51
BseBI	CCWGG	2 cut(s)	41, 1076
BseGI	GGATG	1 cut(s)	958
BseLI	CCNNNNNNNGG	6 cut(s)	40, 46, 61, 572, 1025, 1047
BseMI	GCAATG	1 cut(s)	51
BseNI	ACTGG	2 cut(s)	297, 1052
BseXI	GCAGC	3 cut(s)	652, 912, 998
BseYI	CCCAGC	2 cut(s)	182, 230
BshFI	GGCC	2 cut(s)	124, 1079
BsiSI	CCGG	2 cut(s)	129, 135
BslFI	GGGAC	1 cut(s)	1076
BslI	CCNNNNNNNGG	6 cut(s)	40, 46, 61, 572, 1025, 1047
BsmAI	GTCTC	1 cut(s)	720
BsmFI	GGGAC	1 cut(s)	1076
BsmI	GAATGC	1 cut(s)	442
BsnI	GGCC	2 cut(s)	124, 1079
Bsp119I	TTCGAA	1 cut(s)	451
Bsp143I	GATC	3 cut(s)	533, 897, 1005
BspACI	CCGC	2 cut(s)	484, 853
BspANI	GGCC	2 cut(s)	124, 1079
BspLI	GGNNCC	3 cut(s)	133, 181, 1080
BspT104I	TTCGAA	1 cut(s)	451
BspTI	CTTAAG	2 cut(s)	697, 905
BsrDI	GCAATG	1 cut(s)	51
BsrI	ACTGG	2 cut(s)	297, 1052
BssMI	GATC	3 cut(s)	533, 897, 1005
Bst2UI	CCWGG	2 cut(s)	41, 1076
Bst4CI	ACNGT	3 cut(s)	506, 540, 741
Bst6I	CTCTTC	1 cut(s)	453
BstAFI	CTTAAG	2 cut(s)	697, 905
BstBI	TTCGAA	1 cut(s)	451
BstC8I	GCNNGC	5 cut(s)	307, 592, 1062, 1066, 1070
BstENI	CCTNNNNNAGG	1 cut(s)	38
BstF5I	GGATG	1 cut(s)	958
BstH2I	RGCGCY	2 cut(s)	189, 1075
BstHHI	GCGC	3 cut(s)	67, 188, 1074
BstKTI	GATC	3 cut(s)	536, 900, 1008
BstMAI	GTCTC	1 cut(s)	720
BstMBI	GATC	3 cut(s)	533, 897, 1005
BstMWI	GCNNNNNNNGC	2 cut(s)	674, 1085
BstNI	CCWGG	2 cut(s)	41, 1076
BstSCI	CCNGG	2 cut(s)	39, 1074
BstV1I	GCAGC	3 cut(s)	652, 912, 998
BsuI	GTATCC	2 cut(s)	753, 896
BsuRI	GGCC	2 cut(s)	124, 1079
BtgZI	GCGATG	1 cut(s)	139
BtsCI	GGATG	1 cut(s)	958
BtsIMutI	CAGTG	2 cut(s)	304, 1103
Cac8I	GCNNGC	5 cut(s)	307, 592, 1062, 1066, 1070
CfoI	GCGC	3 cut(s)	67, 188, 1074
Cfr13I	GGNCC	4 cut(s)	49, 122, 179, 1078
Csp6I	GTAC	1 cut(s)	19
CviAII	CATG	3 cut(s)	216, 731, 968
CviQI	GTAC	1 cut(s)	19
DpnI	GATC	3 cut(s)	535, 899, 1007
DpnII	GATC	3 cut(s)	533, 897, 1005
Eam1104I	CTCTTC	1 cut(s)	453
EarI	CTCTTC	1 cut(s)	453
Eco47I	GGWCC	2 cut(s)	49, 179
Eco57I	CTGAAG	1 cut(s)	543
EcoNI	CCTNNNNNAGG	1 cut(s)	38
EcoRII	CCWGG	2 cut(s)	39, 1074
FaeI	CATG	3 cut(s)	219, 734, 971
FalI	AAGNNNNNCTT	2 cut(s)	627, 659
FaqI	GGGAC	1 cut(s)	1076
FatI	CATG	3 cut(s)	215, 730, 967
FblI	GTMKAC	1 cut(s)	12
Fnu4HI	GCNGC	5 cut(s)	484, 666, 854, 926, 987
FokI	GGATG	1 cut(s)	965
Fsp4HI	GCNGC	5 cut(s)	484, 666, 854, 926, 987
FspBI	CTAG	2 cut(s)	35, 719
GlaI	GCGC	3 cut(s)	66, 187, 1073
GluI	GCNGC	5 cut(s)	484, 666, 854, 926, 987
GsaI	CCCAGC	2 cut(s)	186, 234
GsuI	CTGGAG	1 cut(s)	876
HaeII	RGCGCY	2 cut(s)	189, 1075
HaeIII	GGCC	2 cut(s)	124, 1079
HapII	CCGG	2 cut(s)	129, 135
HhaI	GCGC	3 cut(s)	67, 188, 1074
Hin1II	CATG	3 cut(s)	219, 734, 971
Hin6I	GCGC	3 cut(s)	65, 186, 1072
HinP1I	GCGC	3 cut(s)	65, 186, 1072
HincII	GTYRAC	1 cut(s)	418
HindII	GTYRAC	1 cut(s)	418
HinfI	GANTC	2 cut(s)	829, 1108
HpaII	CCGG	2 cut(s)	129, 135
HphI	GGTGA	3 cut(s)	208, 529, 1029
Hpy166II	GTNNAC	3 cut(s)	13, 52, 418
Hpy188I	TCNGA	6 cut(s)	171, 179, 533, 799, 811, 834
Hpy188III	TCNNGA	8 cut(s)	76, 314, 332, 429, 657, 719, 893, 918
Hpy8I	GTNNAC	3 cut(s)	13, 52, 418
HpyAV	CCTTC	6 cut(s)	135, 193, 632, 663, 814, 915
HpyCH4III	ACNGT	3 cut(s)	506, 540, 741
HpyCH4V	TGCA	3 cut(s)	305, 563, 956
HpyF10VI	GCNNNNNNNGC	2 cut(s)	674, 1085
Hsp92II	CATG	3 cut(s)	219, 734, 971
HspAI	GCGC	3 cut(s)	65, 186, 1072
Kzo9I	GATC	3 cut(s)	533, 897, 1005
LmnI	GCTCC	3 cut(s)	137, 693, 823
Lsp1109I	GCAGC	3 cut(s)	652, 912, 998
LweI	GCATC	3 cut(s)	217, 292, 943
MaeI	CTAG	2 cut(s)	35, 719
MaeIII	GTNAC	3 cut(s)	500, 517, 755
MalI	GATC	3 cut(s)	535, 899, 1007
MboI	GATC	3 cut(s)	533, 897, 1005
MboII	GAAGA	4 cut(s)	440, 465, 501, 955
MluCI	AATT	7 cut(s)	339, 647, 765, 801, 880, 947, 959
MlyI	GAGTC	1 cut(s)	838
MmeI	TCCRAC	1 cut(s)	562
MnlI	CCTC	6 cut(s)	83, 778, 781, 900, 964, 1051
MroXI	GAANNNNTTC	1 cut(s)	642
MseI	TTAA	5 cut(s)	342, 609, 698, 879, 906
MspCI	CTTAAG	2 cut(s)	697, 905
MspI	CCGG	2 cut(s)	129, 135
MspR9I	CCNGG	2 cut(s)	41, 1076
Mva1269I	GAATGC	1 cut(s)	442
MvaI	CCWGG	2 cut(s)	41, 1076
MwoI	GCNNNNNNNGC	2 cut(s)	674, 1085
NdeII	GATC	3 cut(s)	533, 897, 1005
NlaIII	CATG	3 cut(s)	219, 734, 971
NlaIV	GGNNCC	3 cut(s)	133, 181, 1080
NmuCI	GTSAC	1 cut(s)	517
NspV	TTCGAA	1 cut(s)	451
PctI	GAATGC	1 cut(s)	442
PdmI	GAANNNNTTC	1 cut(s)	642
PfeI	GAWTC	1 cut(s)	1108
PflFI	GACNNNGTC	1 cut(s)	913
PflMI	CCANNNNNTGG	2 cut(s)	46, 572
PkrI	GCNGC	5 cut(s)	485, 667, 855, 927, 988
PleI	GAGTC	1 cut(s)	837
PpsI	GAGTC	1 cut(s)	837
Psp6I	CCWGG	2 cut(s)	39, 1074
PspFI	CCCAGC	2 cut(s)	182, 230
PspGI	CCWGG	2 cut(s)	39, 1074
PspN4I	GGNNCC	3 cut(s)	133, 181, 1080
PspPI	GGNCC	4 cut(s)	49, 122, 179, 1078
PsyI	GACNNNGTC	1 cut(s)	913
RsaI	GTAC	1 cut(s)	20
RsaNI	GTAC	1 cut(s)	19
SaqAI	TTAA	5 cut(s)	342, 609, 698, 879, 906
SatI	GCNGC	5 cut(s)	484, 666, 854, 926, 987
Sau3AI	GATC	3 cut(s)	533, 897, 1005
Sau96I	GGNCC	4 cut(s)	49, 122, 179, 1078
SchI	GAGTC	1 cut(s)	838
ScrFI	CCNGG	2 cut(s)	41, 1076
SfaNI	GCATC	3 cut(s)	217, 292, 943
SfuI	TTCGAA	1 cut(s)	451
SinI	GGWCC	2 cut(s)	49, 179
SmlI	CTYRAG	3 cut(s)	74, 697, 905
SmoI	CTYRAG	3 cut(s)	74, 697, 905
Sse9I	AATT	7 cut(s)	339, 647, 765, 801, 880, 947, 959
SsiI	CCGC	2 cut(s)	484, 853
SspMI	CTAG	2 cut(s)	35, 719
StyD4I	CCNGG	2 cut(s)	39, 1074
TaaI	ACNGT	3 cut(s)	506, 540, 741
TaqI	TCGA	2 cut(s)	451, 917
TasI	AATT	7 cut(s)	339, 647, 765, 801, 880, 947, 959
TatI	WGTACW	1 cut(s)	18
TauI	GCSGC	2 cut(s)	486, 856
TfiI	GAWTC	1 cut(s)	1108
Tru1I	TTAA	5 cut(s)	342, 609, 698, 879, 906
Tru9I	TTAA	5 cut(s)	342, 609, 698, 879, 906
TscAI	CASTG	2 cut(s)	304, 1110
TseFI	GTSAC	1 cut(s)	517
TseI	GCWGC	3 cut(s)	665, 925, 986
Tsp45I	GTSAC	1 cut(s)	517
TspDTI	ATGAA	3 cut(s)	426, 613, 833
TspRI	CASTG	2 cut(s)	304, 1110
Tth111I	GACNNNGTC	1 cut(s)	913
Van91I	CCANNNNNTGG	2 cut(s)	46, 572
Vha464I	CTTAAG	2 cut(s)	697, 905
VpaK11BI	GGWCC	2 cut(s)	49, 179
XagI	CCTNNNNNAGG	1 cut(s)	38
XbaI	TCTAGA	1 cut(s)	718
XcmI	CCANNNNNNNNNTGG	1 cut(s)	1072
XmiI	GTMKAC	1 cut(s)	12
XmnI	GAANNNNTTC	1 cut(s)	642
XspI	CTAG	2 cut(s)	35, 719

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