Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0007965

Physical Location & Seq

Genomic Coordinates Forward (+)

82745296 .. 82749285

Gene Structure 3990 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG536200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1146 bp

ATGTCGTCCAGTAACGAAAATACGACCTCAAGCTCTGGGTCTGAGCAATCAGATTCCGGAAACGACACACTGGATTTCATAGAGAAGCTCTCAGATGTGCCAATGGGGAAGCTACCTCCACACATCGATTTCCAGAGGACACGTGTCGATTGCAAGGCTGATGCTCCCATTCACACTGATACTTTTCAATACTCTGGTGCTTATGCATCGATGGGAGTGGATAATAGCTTGTTGGATAGCTTCTCGAGCAACTTTAGAGTTGAGGTGATTCGTCTCGAAAAGGATGAAATGGAGTTTGATATGATTGGTATTGATCCGGCTATTGCCAATGCGTTCAGGAGGATCCTCATAGCTGAGGTTCCCACGATGGCTATTGAAAGAGTTCTTATTGCAAATAATACATCAGTAATCCAAGATGAAGTCCTTTCCCACAGATTGGGTCTTATTCCAATCAAGGCTGACCCAAGATTGTTTGAATTTACAGAAAATAATGCGGCAAATGAAAAGAACACCATTGTTTTTGGGCTCAAAGTGAGGTGTGAAAAACAAGGTAAACGAAAGGGACCAAAACGGGAGGGGCAAGAACAAGATGGACAAACACGTATCACAGTCAAGTCAAAAGATTTGGTTTGGTTGCCAAATGGGAGTAACTTTGCCTTGGAATCAGAAGGTTCAAGTTCAAATTCATCCTCAAAACCAAAAACCTACACATCATTTACTTGCAGCCAGGATTCCCTGCCAGAATTTTCCACCAATCCAGTTGGTCCGACAGATGGAGATATTACAATTGCTAGACTAGGCCCTGGCCAGGAAATTGAACTGGAAGCACTAGCTGTTAAGGGCATTGGCAAAACACATGCAAAATGGTCCCCAGTTGCCCCTGCTTGGTATAGGATGCTTCCGGAGGTTATCATTCTGAAAGATATTGAAGATGAGCTGGCTGAGAAACTTGTGGCAACATGCCCAGTCAAGGTGTTTGATATTGAAGACATTGGCAATGGTAAAAAAAGGGCTGCTGTAGCTAGACCACGAAAATGCACACTGTGTAGGGAGTGCATCAGAGAAGGGAAGGGATGGGAGGATTCTTTGTCATTACGACGTGTCAAGGATCATTTCATTTGTAAGTACTATGTTTTTTTTTACTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005730 GO:0005736 GO:0030880 GO:0031974 GO:0031981 GO:0032991 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044452 GO:0044464 GO:0055029 GO:0061695 GO:0070013 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05169 map00230 map00240 map01100 map03020 map04623 map05169

Pfam Domains

Protein Families

RNA_pol_A_bac RNA_pol_L

Protein Analysis

381

Amino Acids

42.38

Weight (kDa)

5.51

Isoelectric Point (pI)

45.04

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_L	PF01193	98 - 200	9.6e-11	RNA polymerase Rpb3/Rpb11 dimerisation domain
RNA_pol_A_bac	PF01000	139 - 288	6.3e-11	RNA polymerase Rpb3/RpoA insert 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: OG0007965)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G60620 AT1G60620
fragaria_vesca	FvH4_3g42690 FvH4_3g42690
malus_domestica	MD03G1029700.v1.1 MD11G1033100.v1.1 MD11G1033500.v1.1
prunus_persica	Prupe.6G025800_v2.0.a1 Prupe.6G025800_v2.0.a1 Prupe.6G025800_v2.0.a1 Prupe.6G025800_v2.0.a1 Prupe.6G025800_v2.0.a1
pyrus_communis	pycom03g02470 pycom11g02880
rosa_chinensis	RchiOBHm_Chr5g0076331
rosa_laevigata	RLG00000036618
rosa_multiflora	Rmu_sc0002400.1_g000006
rosa_roxburghii	Rroxscaffold_1G00005480
rosa_rugosa	Rorug05G0447400
rosa_samantha	Rh5AG502300 Rh5BG524100 Rh5CG547700 Rh5DG536200
rosa_wichuraiana	Rw5G046610

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	436
AccIII	TCCGGA	2 cut(s)	56, 901
AciI	CCGC	1 cut(s)	494
AclWI	GGATC	4 cut(s)	308, 337, 350, 1116
AcoI	YGGCCR	1 cut(s)	805
AcsI	RAATTY	3 cut(s)	476, 682, 743
AcvI	CACGTG	1 cut(s)	143
AdeI	CACNNNGTG	1 cut(s)	1044
AfaI	GTAC	1 cut(s)	1127
AfiI	CCNNNNNNNGG	5 cut(s)	436, 773, 808, 885, 970
AflIII	ACRYGT	4 cut(s)	140, 142, 599, 1099
AgsI	TTSAA	8 cut(s)	188, 377, 476, 675, 681, 818, 929, 986
AjiI	CACGTC	1 cut(s)	1100
AjnI	CCWGG	3 cut(s)	726, 802, 807
AluBI	AGCT	9 cut(s)	33, 88, 112, 228, 240, 353, 833, 937, 1022
AluI	AGCT	9 cut(s)	33, 88, 112, 228, 240, 353, 833, 937, 1022
Alw26I	GTCTC	1 cut(s)	278
AlwI	GGATC	4 cut(s)	308, 337, 350, 1116
Ama87I	CYCGRG	1 cut(s)	244
Aor13HI	TCCGGA	2 cut(s)	56, 901
AoxI	GGCC	2 cut(s)	799, 805
ApeKI	GCWGC	2 cut(s)	723, 1013
ApoI	RAATTY	3 cut(s)	476, 682, 743
Asp700I	GAANNNNTTC	1 cut(s)	381
AspS9I	GGNCC	4 cut(s)	563, 764, 800, 867
AsuHPI	GGTGA	1 cut(s)	277
AvaI	CYCGRG	1 cut(s)	244
AvaII	GGWCC	3 cut(s)	563, 764, 867
BalI	TGGCCA	1 cut(s)	807
BamHI	GGATCC	1 cut(s)	342
BanII	GRGCYC	1 cut(s)	528
BbrPI	CACGTG	1 cut(s)	143
BbsI	GAAGAC	1 cut(s)	993
BbvCI	CCTCAGC	1 cut(s)	354
BbvI	GCAGC	2 cut(s)	735, 1000
BccI	CCATC	5 cut(s)	205, 361, 584, 767, 1068
BciT130I	CCWGG	3 cut(s)	728, 804, 809
BcoDI	GTCTC	1 cut(s)	278
BfaI	CTAG	4 cut(s)	792, 797, 830, 1023
BfmI	CTRYAG	1 cut(s)	1017
BisI	GCNGC	3 cut(s)	495, 724, 1014
BlsI	GCNGC	3 cut(s)	496, 725, 1015
BmcAI	AGTACT	1 cut(s)	1127
Bme1390I	CCNGG	3 cut(s)	728, 804, 809
Bme18I	GGWCC	3 cut(s)	563, 764, 867
BmeT110I	CYCGRG	1 cut(s)	244
BmgBI	CACGTC	1 cut(s)	1100
BmgT120I	GGNCC	4 cut(s)	563, 764, 800, 867
BmiI	GGNNCC	4 cut(s)	344, 360, 564, 869
BmrFI	CCNGG	3 cut(s)	728, 804, 809
BmrI	ACTGGG	2 cut(s)	866, 959
BmsI	GCATC	4 cut(s)	151, 215, 885, 1065
BmuI	ACTGGG	2 cut(s)	866, 959
BoxI	GACNNNNGTC	1 cut(s)	143
BpiI	GAAGAC	1 cut(s)	993
BplI	GAGNNNNNCTC	2 cut(s)	74, 106
Bpu10I	CCTNAGC	1 cut(s)	354
BpuEI	CTTGAG	1 cut(s)	13
Bsa29I	ATCGAT	2 cut(s)	126, 209
BsaAI	YACGTR	2 cut(s)	143, 602
BsaJI	CCNNGG	2 cut(s)	657, 802
BsaWI	WCCGGW	2 cut(s)	56, 901
Bsc4I	CCNNNNNNNGG	5 cut(s)	436, 773, 808, 885, 970
Bse1I	ACTGG	6 cut(s)	9, 75, 758, 825, 872, 965
Bse3DI	GCAATG	1 cut(s)	1003
BseAI	TCCGGA	2 cut(s)	56, 901
BseBI	CCWGG	3 cut(s)	728, 804, 809
BseCI	ATCGAT	2 cut(s)	126, 209
BseDI	CCNNGG	2 cut(s)	657, 802
BseGI	GGATG	4 cut(s)	289, 686, 900, 1079
BseLI	CCNNNNNNNGG	5 cut(s)	436, 773, 808, 885, 970
BseMI	GCAATG	1 cut(s)	1003
BseMII	CTCAG	4 cut(s)	33, 105, 345, 933
BseNI	ACTGG	6 cut(s)	9, 75, 758, 825, 872, 965
BseXI	GCAGC	2 cut(s)	735, 1000
BshFI	GGCC	2 cut(s)	801, 807
BshVI	ATCGAT	2 cut(s)	126, 209
BsiHKCI	CYCGRG	1 cut(s)	244
BsiSI	CCGG	3 cut(s)	57, 317, 902
BslFI	GGGAC	2 cut(s)	576, 853
BslI	CCNNNNNNNGG	5 cut(s)	436, 773, 808, 885, 970
BsmAI	GTCTC	1 cut(s)	278
BsmBI	CGTCTC	1 cut(s)	278
BsmFI	GGGAC	2 cut(s)	576, 853
BsnI	GGCC	2 cut(s)	801, 807
BsoBI	CYCGRG	1 cut(s)	244
Bsp1286I	GDGCHC	1 cut(s)	528
Bsp13I	TCCGGA	2 cut(s)	56, 901
Bsp143I	GATC	3 cut(s)	313, 342, 1108
BspACI	CCGC	1 cut(s)	494
BspANI	GGCC	2 cut(s)	801, 807
BspCNI	CTCAG	4 cut(s)	34, 104, 346, 934
BspDI	ATCGAT	2 cut(s)	126, 209
BspEI	TCCGGA	2 cut(s)	56, 901
BspLI	GGNNCC	4 cut(s)	344, 360, 564, 869
BspPI	GGATC	4 cut(s)	308, 337, 350, 1116
BsrDI	GCAATG	1 cut(s)	1003
BsrI	ACTGG	6 cut(s)	9, 75, 758, 825, 872, 965
BssECI	CCNNGG	2 cut(s)	657, 802
BssMI	GATC	3 cut(s)	313, 342, 1108
BssT1I	CCWWGG	1 cut(s)	657
Bst2UI	CCWGG	3 cut(s)	728, 804, 809
Bst4CI	ACNGT	2 cut(s)	610, 1044
BstBAI	YACGTR	2 cut(s)	143, 602
BstC8I	GCNNGC	1 cut(s)	939
BstDEI	CTNAG	4 cut(s)	42, 91, 354, 942
BstF5I	GGATG	4 cut(s)	289, 686, 900, 1079
BstKTI	GATC	3 cut(s)	316, 345, 1111
BstMAI	GTCTC	1 cut(s)	278
BstMBI	GATC	3 cut(s)	313, 342, 1108
BstMWI	GCNNNNNNNGC	2 cut(s)	246, 1019
BstNI	CCWGG	3 cut(s)	728, 804, 809
BstNSI	RCATGY	2 cut(s)	860, 963
BstPAI	GACNNNNGTC	1 cut(s)	143
BstSCI	CCNGG	3 cut(s)	726, 802, 807
BstSFI	CTRYAG	1 cut(s)	1017
BstV1I	GCAGC	2 cut(s)	735, 1000
BstV2I	GAAGAC	1 cut(s)	993
BstX2I	RGATCY	1 cut(s)	342
BstYI	RGATCY	1 cut(s)	342
Bsu15I	ATCGAT	2 cut(s)	126, 209
BsuRI	GGCC	2 cut(s)	801, 807
BsuTUI	ATCGAT	2 cut(s)	126, 209
BtrI	CACGTC	1 cut(s)	1100
BtsCI	GGATG	4 cut(s)	289, 686, 900, 1079
BtsIMutI	CAGTG	3 cut(s)	68, 174, 1040
Cac8I	GCNNGC	1 cut(s)	939
Cfr13I	GGNCC	4 cut(s)	563, 764, 800, 867
ClaI	ATCGAT	2 cut(s)	126, 209
Csp6I	GTAC	1 cut(s)	1126
CviAII	CATG	2 cut(s)	857, 960
CviQI	GTAC	1 cut(s)	1126
DdeI	CTNAG	4 cut(s)	42, 91, 354, 942
DpnI	GATC	3 cut(s)	315, 344, 1110
DpnII	GATC	3 cut(s)	313, 342, 1108
DraIII	CACNNNGTG	1 cut(s)	1044
EaeI	YGGCCR	1 cut(s)	805
Eco130I	CCWWGG	1 cut(s)	657
Eco24I	GRGCYC	1 cut(s)	528
Eco47I	GGWCC	3 cut(s)	563, 764, 867
Eco72I	CACGTG	1 cut(s)	143
Eco88I	CYCGRG	1 cut(s)	244
EcoO109I	RGGNCCY	1 cut(s)	800
EcoRII	CCWGG	3 cut(s)	726, 802, 807
EcoT14I	CCWWGG	1 cut(s)	657
EcoT22I	ATGCAT	1 cut(s)	208
EcoT38I	GRGCYC	1 cut(s)	528
ErhI	CCWWGG	1 cut(s)	657
Esp3I	CGTCTC	1 cut(s)	278
FaeI	CATG	2 cut(s)	860, 963
FaiI	YATR	8 cut(s)	80, 204, 302, 350, 858, 891, 961, 1131
FaqI	GGGAC	2 cut(s)	576, 853
FatI	CATG	2 cut(s)	856, 959
Fnu4HI	GCNGC	3 cut(s)	495, 724, 1014
FokI	GGATG	4 cut(s)	296, 673, 907, 1086
FriOI	GRGCYC	1 cut(s)	528
Fsp4HI	GCNGC	3 cut(s)	495, 724, 1014
FspBI	CTAG	4 cut(s)	792, 797, 830, 1023
GluI	GCNGC	3 cut(s)	495, 724, 1014
HaeIII	GGCC	2 cut(s)	801, 807
HapII	CCGG	3 cut(s)	57, 317, 902
Hin1II	CATG	2 cut(s)	860, 963
HinfI	GANTC	5 cut(s)	53, 268, 662, 731, 1082
HpaII	CCGG	3 cut(s)	57, 317, 902
HphI	GGTGA	1 cut(s)	277
Hpy166II	GTNNAC	1 cut(s)	554
Hpy188I	TCNGA	7 cut(s)	43, 52, 94, 667, 768, 918, 1061
Hpy188III	TCNNGA	6 cut(s)	57, 133, 244, 275, 337, 902
Hpy8I	GTNNAC	1 cut(s)	554
Hpy99I	CGWCG	1 cut(s)	1101
HpyAV	CCTTC	3 cut(s)	662, 1058, 1063
HpyCH4III	ACNGT	2 cut(s)	610, 1044
HpyCH4IV	ACGT	3 cut(s)	142, 601, 1099
HpyCH4V	TGCA	7 cut(s)	153, 206, 392, 723, 860, 1038, 1056
HpyF10VI	GCNNNNNNNGC	2 cut(s)	246, 1019
HpyF3I	CTNAG	4 cut(s)	42, 91, 354, 942
HpySE526I	ACGT	3 cut(s)	142, 601, 1099
Hsp92II	CATG	2 cut(s)	860, 963
Kpn2I	TCCGGA	2 cut(s)	56, 901
Kzo9I	GATC	3 cut(s)	313, 342, 1108
LmnI	GCTCC	1 cut(s)	169
Lsp1109I	GCAGC	2 cut(s)	735, 1000
LweI	GCATC	4 cut(s)	151, 215, 885, 1065
MaeI	CTAG	4 cut(s)	792, 797, 830, 1023
MaeII	ACGT	3 cut(s)	142, 601, 1099
MaeIII	GTNAC	2 cut(s)	11, 647
MalI	GATC	3 cut(s)	315, 344, 1110
MboI	GATC	3 cut(s)	313, 342, 1108
MboII	GAAGA	2 cut(s)	941, 998
MfeI	CAATTG	1 cut(s)	786
MflI	RGATCY	1 cut(s)	342
MhlI	GDGCHC	1 cut(s)	528
MlsI	TGGCCA	1 cut(s)	807
MluCI	AATT	5 cut(s)	476, 682, 743, 786, 813
MluNI	TGGCCA	1 cut(s)	807
MmeI	TCCRAC	2 cut(s)	213, 791
Mox20I	TGGCCA	1 cut(s)	807
Mph1103I	ATGCAT	1 cut(s)	208
MroI	TCCGGA	2 cut(s)	56, 901
MroXI	GAANNNNTTC	1 cut(s)	381
MscI	TGGCCA	1 cut(s)	807
MseI	TTAA	1 cut(s)	837
MslI	CAYNNNNRTG	1 cut(s)	1033
Msp20I	TGGCCA	1 cut(s)	807
MspI	CCGG	3 cut(s)	57, 317, 902
MspR9I	CCNGG	3 cut(s)	728, 804, 809
MunI	CAATTG	1 cut(s)	786
MvaI	CCWGG	3 cut(s)	728, 804, 809
MwoI	GCNNNNNNNGC	2 cut(s)	246, 1019
NdeII	GATC	3 cut(s)	313, 342, 1108
NlaIII	CATG	2 cut(s)	860, 963
NlaIV	GGNNCC	4 cut(s)	344, 360, 564, 869
NsiI	ATGCAT	1 cut(s)	208
NspI	RCATGY	2 cut(s)	860, 963
PaeR7I	CTCGAG	1 cut(s)	244
PdmI	GAANNNNTTC	1 cut(s)	381
PfeI	GAWTC	5 cut(s)	53, 268, 662, 731, 1082
PflMI	CCANNNNNTGG	1 cut(s)	436
PkrI	GCNGC	3 cut(s)	496, 725, 1015
PmaCI	CACGTG	1 cut(s)	143
PmlI	CACGTG	1 cut(s)	143
Ppu21I	YACGTR	2 cut(s)	143, 602
PshAI	GACNNNNGTC	1 cut(s)	143
Psp6I	CCWGG	3 cut(s)	726, 802, 807
PspCI	CACGTG	1 cut(s)	143
PspGI	CCWGG	3 cut(s)	726, 802, 807
PspN4I	GGNNCC	4 cut(s)	344, 360, 564, 869
PspPI	GGNCC	4 cut(s)	563, 764, 800, 867
PsuI	RGATCY	1 cut(s)	342
RsaI	GTAC	1 cut(s)	1127
RsaNI	GTAC	1 cut(s)	1126
RseI	CAYNNNNRTG	1 cut(s)	1033
SaqAI	TTAA	1 cut(s)	837
SatI	GCNGC	3 cut(s)	495, 724, 1014
Sau3AI	GATC	3 cut(s)	313, 342, 1108
Sau96I	GGNCC	4 cut(s)	563, 764, 800, 867
ScaI	AGTACT	1 cut(s)	1127
ScrFI	CCNGG	3 cut(s)	728, 804, 809
SduI	GDGCHC	1 cut(s)	528
SfaNI	GCATC	4 cut(s)	151, 215, 885, 1065
SfcI	CTRYAG	1 cut(s)	1017
Sfr274I	CTCGAG	1 cut(s)	244
SinI	GGWCC	3 cut(s)	563, 764, 867
SlaI	CTCGAG	1 cut(s)	244
SmiMI	CAYNNNNRTG	1 cut(s)	1033
SmlI	CTYRAG	2 cut(s)	28, 244
SmoI	CTYRAG	2 cut(s)	28, 244
Sse9I	AATT	5 cut(s)	476, 682, 743, 786, 813
SsiI	CCGC	1 cut(s)	494
SspMI	CTAG	4 cut(s)	792, 797, 830, 1023
StyD4I	CCNGG	3 cut(s)	726, 802, 807
StyI	CCWWGG	1 cut(s)	657
TaaI	ACNGT	2 cut(s)	610, 1044
TaiI	ACGT	3 cut(s)	145, 604, 1102
TaqI	TCGA	5 cut(s)	126, 147, 209, 245, 276
TasI	AATT	5 cut(s)	476, 682, 743, 786, 813
TatI	WGTACW	1 cut(s)	1125
TauI	GCSGC	1 cut(s)	497
TfiI	GAWTC	5 cut(s)	53, 268, 662, 731, 1082
Tru1I	TTAA	1 cut(s)	837
Tru9I	TTAA	1 cut(s)	837
TscAI	CASTG	3 cut(s)	75, 181, 1047
TseI	GCWGC	2 cut(s)	723, 1013
TspDTI	ATGAA	6 cut(s)	67, 300, 432, 516, 675, 1105
TspRI	CASTG	3 cut(s)	75, 181, 1047
Van91I	CCANNNNNTGG	1 cut(s)	436
VpaK11BI	GGWCC	3 cut(s)	563, 764, 867
XapI	RAATTY	3 cut(s)	476, 682, 743
XceI	RCATGY	2 cut(s)	860, 963
XhoI	CTCGAG	1 cut(s)	244
XmnI	GAANNNNTTC	1 cut(s)	381
XspI	CTAG	4 cut(s)	792, 797, 830, 1023
ZrmI	AGTACT	1 cut(s)	1127
Zsp2I	ATGCAT	1 cut(s)	208

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