Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5B

Orthogroup ID

OG0003142

Physical Location & Seq

Genomic Coordinates Reverse (-)

55797665 .. 55804647

Gene Structure 6983 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5BG358000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 765 bp

ATGGAGGCTGGACGGAGCGGGGCCGATCCGGTGGTCGAGTCGGTGCTGCTGGCCGGTTTGGATCGGTGCAGTGATGGGATTTGGTTGAGGCCTGCTGGAATGGTTGGTCAGCCGATGTTGCAGGCTCAGGAGGCGTTCTGGGCGAGCAGGAGGTGGCTACGCAGGTGGTGGCTAGGAAGGGCTTGCGGTCCCCGATCTGGTCGAAGGCGTGGGTGTGGGCTGCAGGTGGTGCTGATGCGCGGGGGGGCACTGAGCGAGGCCCGGGTGGAGGCTGGAGGTTGGGATCTGCTGCAGGCGGCAGGTCTCCTCTTCTTCGATTCGCTTGGACCTTGGAGCTTGGAGATTGAATTTCTAGCCGCTTCAGTCTCTATATCTCATCCAGATGGGAAAAAGTTTGATAAGGTTACTCGAATTGAAGCAAAAAGTGAGACATGCGAGATGTTCATGCACCTAGATGTGAATACAGAGGTGTATCCCATGAAGGAAGGTGAGAAGTTCTCAATGGCTCTAACTTCTACACTCAACTTGGATGGAACACCTGACACTGGCTATTTCACTCCGGGAAATCGCAAGACGTTGGCTGATGAATATGAGTACGTCATGCAAGGGAAGCTTTTTAAAATCTCAGAAGGTTCTAAACGGGATCCTAAAGCGGAGGTGAATGCTTCATTTGCTGGGCTGTTGATGATGCTCAAGGGGGAATCCTCTCAATTCAAGAACTTTGAACTGGATCAAAGGCTGTTTCTCCTCATCAGGAAGCTATAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0003674 GO:0003676 GO:0003677 GO:0003697 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0005666 GO:0005730 GO:0005736 GO:0006139 GO:0006351 GO:0006366 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0010467 GO:0016070 GO:0016591 GO:0018130 GO:0019438 GO:0030880 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0032993 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044452 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0090304 GO:0097159 GO:0097659 GO:1901360 GO:1901362 GO:1901363 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05016 ko05169 map00230 map00240 map01100 map03020 map04623 map05016 map05169

Pfam Domains

Protein Families

RNA_pol_Rpb8

Protein Analysis

254

Amino Acids

28.31

Weight (kDa)

7.64

Isoelectric Point (pI)

42.89

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb8	PF03870	123 - 253	7.2e-45	RNA polymerase Rpb8

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: OG0003142)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G54250 AT3G59600
fragaria_vesca	FvH4_7g05580 FvH4_7g05580 FvH4_7g05580 FvH4_7g05580 FvH4_7g05580 FvH4_7g05580 FvH4_7g05580
malus_domestica	MD03G1174900.v1.1 MD04G1053300.v1.1 MD05G1057600.v1.1 MD11G1193000.v1.1
prunus_persica	Prupe.4G249600_v2.0.a1 Prupe.4G249600_v2.0.a1
pyrus_communis	pycom03g13240 pycom11g16850
rosa_chinensis	RchiOBHm_Chr1g0332731 RchiOBHm_Chr5g0052071 RchiOBHm_Chr6g0273601
rosa_laevigata	RLG00000034845
rosa_multiflora	Rmu_sc0001587.1_g000001 Rmu_sc0032204.1_g000001 Rmu_ssc0000098.1_g000004
rosa_roxburghii	Rroxscaffold_1G00027860 Rroxscaffold_4G00318050
rosa_rugosa	Rorug01G0104600 Rorug05G0275000 Rorug05G0275100
rosa_samantha	Rh1AG127600 Rh1BG097000 Rh1CG121400 Rh5BG358000 Rh5CG383500 Rh5DG373400 Rh6CG194200
rosa_wichuraiana	Rw5G032800

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	2 cut(s)	153, 214
Acc36I	ACCTGC	3 cut(s)	153, 214, 290
AccBSI	CCGCTC	1 cut(s)	18
AccII	CGCG	1 cut(s)	240
AciI	CCGC	6 cut(s)	18, 186, 240, 296, 357, 653
AclWI	GGATC	6 cut(s)	20, 69, 291, 638, 651, 738
AcoI	YGGCCR	1 cut(s)	51
AcsI	RAATTY	1 cut(s)	347
AcuI	CTGAAG	1 cut(s)	345
AfaI	GTAC	1 cut(s)	596
AfiI	CCNNNNNNNGG	3 cut(s)	197, 268, 545
AgsI	TTSAA	4 cut(s)	347, 416, 715, 725
AluBI	AGCT	3 cut(s)	336, 613, 760
AluI	AGCT	3 cut(s)	336, 613, 760
Alw26I	GTCTC	3 cut(s)	308, 370, 422
AlwI	GGATC	6 cut(s)	20, 69, 291, 638, 651, 738
Ama87I	CYCGRG	1 cut(s)	261
AoxI	GGCC	4 cut(s)	21, 51, 89, 258
ApeKI	GCWGC	3 cut(s)	46, 220, 289
ApoI	RAATTY	1 cut(s)	347
AspLEI	GCGC	1 cut(s)	240
AspS9I	GGNCC	4 cut(s)	21, 188, 259, 326
AsuC2I	CCSGG	3 cut(s)	262, 263, 561
AsuHPI	GGTGA	2 cut(s)	500, 670
AvaI	CYCGRG	1 cut(s)	261
AvaII	GGWCC	2 cut(s)	188, 326
BaeGI	GKGCMC	1 cut(s)	250
BamHI	GGATCC	1 cut(s)	643
BbvI	GCAGC	3 cut(s)	33, 207, 276
BccI	CCATC	3 cut(s)	68, 377, 524
BciVI	GTATCC	1 cut(s)	483
BcnI	CCSGG	3 cut(s)	262, 263, 561
BcoDI	GTCTC	3 cut(s)	308, 370, 422
BfaI	CTAG	3 cut(s)	173, 353, 452
BfmI	CTRYAG	3 cut(s)	221, 290, 761
BfuAI	ACCTGC	3 cut(s)	153, 214, 290
BfuI	GTATCC	1 cut(s)	483
BisI	GCNGC	5 cut(s)	47, 221, 290, 297, 357
BlsI	GCNGC	5 cut(s)	48, 222, 291, 298, 358
Bme1390I	CCNGG	3 cut(s)	262, 263, 561
Bme18I	GGWCC	2 cut(s)	188, 326
BmeT110I	CYCGRG	1 cut(s)	261
BmgT120I	GGNCC	4 cut(s)	21, 188, 259, 326
BmiI	GGNNCC	3 cut(s)	22, 190, 645
BmrFI	CCNGG	3 cut(s)	262, 263, 561
BmsI	GCATC	2 cut(s)	225, 678
BplI	GAGNNNNNCTC	2 cut(s)	482, 514
BpmI	CTGGAG	1 cut(s)	294
Bpu10I	CCTNAGC	1 cut(s)	126
BpuEI	CTTGAG	1 cut(s)	677
BpuMI	CCSGG	3 cut(s)	262, 263, 561
BsaI	GGTCTC	1 cut(s)	308
BsaJI	CCNNGG	2 cut(s)	261, 329
BsaWI	WCCGGW	1 cut(s)	28
Bsc4I	CCNNNNNNNGG	3 cut(s)	197, 268, 545
Bse118I	RCCGGY	1 cut(s)	53
Bse1I	ACTGG	2 cut(s)	550, 732
BseDI	CCNNGG	2 cut(s)	261, 329
BseGI	GGATG	2 cut(s)	376, 535
BseLI	CCNNNNNNNGG	3 cut(s)	197, 268, 545
BseMII	CTCAG	3 cut(s)	140, 242, 639
BseNI	ACTGG	2 cut(s)	550, 732
BseRI	GAGGAG	2 cut(s)	296, 737
BseSI	GKGCMC	1 cut(s)	250
BseXI	GCAGC	3 cut(s)	33, 207, 276
BseYI	CCCAGC	1 cut(s)	674
BsgI	GTGCAG	1 cut(s)	88
Bsh1236I	CGCG	1 cut(s)	240
BshFI	GGCC	4 cut(s)	23, 53, 91, 260
BsiHKCI	CYCGRG	1 cut(s)	261
BsiSI	CCGG	4 cut(s)	29, 54, 262, 560
BslFI	GGGAC	1 cut(s)	174
BslI	CCNNNNNNNGG	3 cut(s)	197, 268, 545
BsmAI	GTCTC	3 cut(s)	308, 370, 422
BsmFI	GGGAC	1 cut(s)	174
BsmI	GAATGC	1 cut(s)	667
BsnI	GGCC	4 cut(s)	23, 53, 91, 260
Bso31I	GGTCTC	1 cut(s)	308
BsoBI	CYCGRG	1 cut(s)	261
Bsp1286I	GDGCHC	1 cut(s)	250
Bsp143I	GATC	6 cut(s)	25, 61, 194, 283, 643, 730
BspACI	CCGC	6 cut(s)	18, 186, 240, 296, 357, 653
BspANI	GGCC	4 cut(s)	23, 53, 91, 260
BspCNI	CTCAG	3 cut(s)	139, 243, 638
BspFNI	CGCG	1 cut(s)	240
BspLI	GGNNCC	3 cut(s)	22, 190, 645
BspMAI	CTGCAG	2 cut(s)	225, 294
BspMI	ACCTGC	3 cut(s)	153, 214, 290
BspPI	GGATC	6 cut(s)	20, 69, 291, 638, 651, 738
BspTNI	GGTCTC	1 cut(s)	308
BsrBI	CCGCTC	1 cut(s)	18
BsrFI	RCCGGY	1 cut(s)	53
BsrI	ACTGG	2 cut(s)	550, 732
BssAI	RCCGGY	1 cut(s)	53
BssECI	CCNNGG	2 cut(s)	261, 329
BssMI	GATC	6 cut(s)	25, 61, 194, 283, 643, 730
BssT1I	CCWWGG	1 cut(s)	329
Bst6I	CTCTTC	1 cut(s)	314
BstAPI	GCANNNNNTGC	1 cut(s)	229
BstC8I	GCNNGC	6 cut(s)	51, 93, 123, 145, 184, 294
BstDEI	CTNAG	3 cut(s)	126, 251, 625
BstF5I	GGATG	2 cut(s)	376, 535
BstFNI	CGCG	1 cut(s)	240
BstHHI	GCGC	1 cut(s)	240
BstKTI	GATC	6 cut(s)	28, 64, 197, 286, 646, 733
BstMAI	GTCTC	3 cut(s)	308, 370, 422
BstMBI	GATC	6 cut(s)	25, 61, 194, 283, 643, 730
BstMWI	GCNNNNNNNGC	6 cut(s)	118, 131, 140, 229, 610, 671
BstNSI	RCATGY	1 cut(s)	435
BstSCI	CCNGG	3 cut(s)	260, 261, 559
BstSFI	CTRYAG	3 cut(s)	221, 290, 761
BstSLI	GKGCMC	1 cut(s)	250
BstUI	CGCG	1 cut(s)	240
BstV1I	GCAGC	3 cut(s)	33, 207, 276
BstX2I	RGATCY	2 cut(s)	283, 643
BstYI	RGATCY	2 cut(s)	283, 643
BsuI	GTATCC	1 cut(s)	483
BsuRI	GGCC	4 cut(s)	23, 53, 91, 260
BtsCI	GGATG	2 cut(s)	376, 535
BtsI	GCAGTG	1 cut(s)	76
BtsIMutI	CAGTG	3 cut(s)	76, 248, 543
BveI	ACCTGC	3 cut(s)	153, 214, 290
Cac8I	GCNNGC	6 cut(s)	51, 93, 123, 145, 184, 294
CfoI	GCGC	1 cut(s)	240
Cfr10I	RCCGGY	1 cut(s)	53
Cfr13I	GGNCC	4 cut(s)	21, 188, 259, 326
Cfr9I	CCCGGG	1 cut(s)	261
Csp6I	GTAC	1 cut(s)	595
CviAII	CATG	4 cut(s)	432, 445, 478, 601
CviQI	GTAC	1 cut(s)	595
DdeI	CTNAG	3 cut(s)	126, 251, 625
DpnI	GATC	6 cut(s)	27, 63, 196, 285, 645, 732
DpnII	GATC	6 cut(s)	25, 61, 194, 283, 643, 730
DraI	TTTAAA	1 cut(s)	619
EaeI	YGGCCR	1 cut(s)	51
Eam1104I	CTCTTC	1 cut(s)	314
EarI	CTCTTC	1 cut(s)	314
Eco130I	CCWWGG	1 cut(s)	329
Eco147I	AGGCCT	1 cut(s)	91
Eco31I	GGTCTC	1 cut(s)	308
Eco47I	GGWCC	2 cut(s)	188, 326
Eco57I	CTGAAG	1 cut(s)	345
Eco88I	CYCGRG	1 cut(s)	261
EcoT14I	CCWWGG	1 cut(s)	329
ErhI	CCWWGG	1 cut(s)	329
FaeI	CATG	4 cut(s)	435, 448, 481, 604
FaiI	YATR	7 cut(s)	371, 433, 446, 479, 591, 602, 763
FalI	AAGNNNNNCTT	2 cut(s)	597, 629
FaqI	GGGAC	1 cut(s)	174
FatI	CATG	4 cut(s)	431, 444, 477, 600
FauI	CCCGC	2 cut(s)	11, 233
Fnu4HI	GCNGC	5 cut(s)	47, 221, 290, 297, 357
FokI	GGATG	2 cut(s)	363, 542
Fsp4HI	GCNGC	5 cut(s)	47, 221, 290, 297, 357
FspBI	CTAG	3 cut(s)	173, 353, 452
GlaI	GCGC	1 cut(s)	239
GluI	GCNGC	5 cut(s)	47, 221, 290, 297, 357
GsaI	CCCAGC	1 cut(s)	678
GsuI	CTGGAG	1 cut(s)	294
HaeIII	GGCC	4 cut(s)	23, 53, 91, 260
HapII	CCGG	4 cut(s)	29, 54, 262, 560
HhaI	GCGC	1 cut(s)	240
Hin1II	CATG	4 cut(s)	435, 448, 481, 604
Hin6I	GCGC	1 cut(s)	238
HinP1I	GCGC	1 cut(s)	238
HindIII	AAGCTT	1 cut(s)	611
HinfI	GANTC	3 cut(s)	38, 317, 701
HpaII	CCGG	4 cut(s)	29, 54, 262, 560
HphI	GGTGA	2 cut(s)	500, 670
Hpy188I	TCNGA	1 cut(s)	628
Hpy188III	TCNNGA	4 cut(s)	128, 380, 715, 754
HpyAV	CCTTC	5 cut(s)	171, 198, 475, 479, 623
HpyCH4IV	ACGT	2 cut(s)	575, 597
HpyCH4V	TGCA	6 cut(s)	69, 121, 223, 292, 448, 604
HpyF10VI	GCNNNNNNNGC	6 cut(s)	118, 131, 140, 229, 610, 671
HpyF3I	CTNAG	3 cut(s)	126, 251, 625
HpySE526I	ACGT	2 cut(s)	575, 597
Hsp92II	CATG	4 cut(s)	435, 448, 481, 604
HspAI	GCGC	1 cut(s)	238
Kzo9I	GATC	6 cut(s)	25, 61, 194, 283, 643, 730
LmnI	GCTCC	2 cut(s)	15, 333
Lsp1109I	GCAGC	3 cut(s)	33, 207, 276
LweI	GCATC	2 cut(s)	225, 678
MaeI	CTAG	3 cut(s)	173, 353, 452
MaeII	ACGT	2 cut(s)	575, 597
MaeIII	GTNAC	1 cut(s)	403
MalI	GATC	6 cut(s)	27, 63, 196, 285, 645, 732
MbiI	CCGCTC	1 cut(s)	18
MboI	GATC	6 cut(s)	25, 61, 194, 283, 643, 730
MboII	GAAGA	2 cut(s)	301, 304
MflI	RGATCY	2 cut(s)	283, 643
MhlI	GDGCHC	1 cut(s)	250
MluCI	AATT	3 cut(s)	347, 411, 710
MlyI	GAGTC	1 cut(s)	47
MseI	TTAA	1 cut(s)	618
MslI	CAYNNNNRTG	2 cut(s)	381, 453
MspI	CCGG	4 cut(s)	29, 54, 262, 560
MspR9I	CCNGG	3 cut(s)	262, 263, 561
Mva1269I	GAATGC	1 cut(s)	667
MvnI	CGCG	1 cut(s)	240
MwoI	GCNNNNNNNGC	6 cut(s)	118, 131, 140, 229, 610, 671
NciI	CCSGG	3 cut(s)	262, 263, 561
NdeII	GATC	6 cut(s)	25, 61, 194, 283, 643, 730
NlaIII	CATG	4 cut(s)	435, 448, 481, 604
NlaIV	GGNNCC	3 cut(s)	22, 190, 645
NspI	RCATGY	1 cut(s)	435
PaqCI	CACCTGC	2 cut(s)	153, 214
PceI	AGGCCT	1 cut(s)	91
PctI	GAATGC	1 cut(s)	667
PfeI	GAWTC	2 cut(s)	317, 701
PfoI	TCCNGGA	1 cut(s)	559
PkrI	GCNGC	5 cut(s)	48, 222, 291, 298, 358
PleI	GAGTC	1 cut(s)	46
PpsI	GAGTC	1 cut(s)	46
PspFI	CCCAGC	1 cut(s)	674
PspN4I	GGNNCC	3 cut(s)	22, 190, 645
PspPI	GGNCC	4 cut(s)	21, 188, 259, 326
PstI	CTGCAG	2 cut(s)	225, 294
PsuI	RGATCY	2 cut(s)	283, 643
RsaI	GTAC	1 cut(s)	596
RsaNI	GTAC	1 cut(s)	595
RseI	CAYNNNNRTG	2 cut(s)	381, 453
SaqAI	TTAA	1 cut(s)	618
SatI	GCNGC	5 cut(s)	47, 221, 290, 297, 357
Sau3AI	GATC	6 cut(s)	25, 61, 194, 283, 643, 730
Sau96I	GGNCC	4 cut(s)	21, 188, 259, 326
SchI	GAGTC	1 cut(s)	47
ScrFI	CCNGG	3 cut(s)	262, 263, 561
SduI	GDGCHC	1 cut(s)	250
SfaNI	GCATC	2 cut(s)	225, 678
SfcI	CTRYAG	3 cut(s)	221, 290, 761
SinI	GGWCC	2 cut(s)	188, 326
SmaI	CCCGGG	1 cut(s)	263
SmiMI	CAYNNNNRTG	2 cut(s)	381, 453
SmlI	CTYRAG	1 cut(s)	692
SmoI	CTYRAG	1 cut(s)	692
Sse9I	AATT	3 cut(s)	347, 411, 710
SseBI	AGGCCT	1 cut(s)	91
SsiI	CCGC	6 cut(s)	18, 186, 240, 296, 357, 653
SspMI	CTAG	3 cut(s)	173, 353, 452
StuI	AGGCCT	1 cut(s)	91
StyD4I	CCNGG	3 cut(s)	260, 261, 559
StyI	CCWWGG	1 cut(s)	329
TaiI	ACGT	2 cut(s)	578, 600
TaqI	TCGA	4 cut(s)	36, 202, 315, 409
TasI	AATT	3 cut(s)	347, 411, 710
TauI	GCSGC	2 cut(s)	299, 359
TfiI	GAWTC	2 cut(s)	317, 701
Tru1I	TTAA	1 cut(s)	618
Tru9I	TTAA	1 cut(s)	618
TscAI	CASTG	3 cut(s)	76, 255, 550
TseI	GCWGC	3 cut(s)	46, 220, 289
TspDTI	ATGAA	4 cut(s)	433, 494, 600, 657
TspGWI	ACGGA	1 cut(s)	28
TspMI	CCCGGG	1 cut(s)	261
TspRI	CASTG	3 cut(s)	76, 255, 550
VpaK11BI	GGWCC	2 cut(s)	188, 326
XapI	RAATTY	1 cut(s)	347
XceI	RCATGY	1 cut(s)	435
XmaI	CCCGGG	1 cut(s)	261
XspI	CTAG	3 cut(s)	173, 353, 452

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