Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0003142

Physical Location & Seq

Genomic Coordinates Reverse (-)

56546076 .. 56552950

Gene Structure 6875 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG373400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 435 bp

ATGGTTGATCGTCTTTTTGAGGATATCTTTCAAATACTACAGTTAAACCCAGATGGGAAAAAGTTTGATAAGGTTACTCGAATTGAAGCAAAAAGTGAGACATGCGAGATGTTCATGCACCTAGATGTGAATACAGAGGTGTATCCCATGAAGGAAGGTGAGAAGTTCTCAATGGCTCTAACTTCTACACTCAACTTGGATGGAACACCTGACACTGGCTATTTCACTCCGGGAAATCGCAAGACGTTGGCTGATGAATATGAGTACGTCATGCAAGGGAAGCTTTTTAAAATCTCAGAAGGTTCTAAACGGGATCCTAAAGCGGAGGTGAATGCTTCATTTGCTGGGCTGTTGATGATGCTCAAGGGGGAATCCTCTCAATTCAAGAACTTTGAACTGGATCAAAGGCTGTTTCTCCTCATCAGGAAGCTATAG

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

144

Amino Acids

16.58

Weight (kDa)

5.29

Isoelectric Point (pI)

14.47

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb8	PF03870	7 - 143	3.5e-49	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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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)
AciI	CCGC	1 cut(s)	323
AclWI	GGATC	3 cut(s)	308, 321, 408
AfaI	GTAC	1 cut(s)	266
AfiI	CCNNNNNNNGG	1 cut(s)	215
AgsI	TTSAA	4 cut(s)	32, 86, 385, 395
AluBI	AGCT	2 cut(s)	283, 430
AluI	AGCT	2 cut(s)	283, 430
Alw26I	GTCTC	1 cut(s)	92
AlwI	GGATC	3 cut(s)	308, 321, 408
AsuC2I	CCSGG	1 cut(s)	231
AsuHPI	GGTGA	2 cut(s)	170, 340
BamHI	GGATCC	1 cut(s)	313
BccI	CCATC	2 cut(s)	47, 194
BciVI	GTATCC	1 cut(s)	153
BcnI	CCSGG	1 cut(s)	231
BcoDI	GTCTC	1 cut(s)	92
BfaI	CTAG	1 cut(s)	122
BfmI	CTRYAG	2 cut(s)	38, 431
BfuI	GTATCC	1 cut(s)	153
Bme1390I	CCNGG	1 cut(s)	231
BmiI	GGNNCC	1 cut(s)	315
BmrFI	CCNGG	1 cut(s)	231
BmsI	GCATC	1 cut(s)	348
BplI	GAGNNNNNCTC	2 cut(s)	152, 184
BpuEI	CTTGAG	1 cut(s)	347
BpuMI	CCSGG	1 cut(s)	231
Bsc4I	CCNNNNNNNGG	1 cut(s)	215
Bse1I	ACTGG	2 cut(s)	220, 402
BseGI	GGATG	1 cut(s)	205
BseLI	CCNNNNNNNGG	1 cut(s)	215
BseMII	CTCAG	1 cut(s)	309
BseNI	ACTGG	2 cut(s)	220, 402
BseRI	GAGGAG	1 cut(s)	407
BseYI	CCCAGC	1 cut(s)	344
BsiSI	CCGG	1 cut(s)	230
BslI	CCNNNNNNNGG	1 cut(s)	215
BsmAI	GTCTC	1 cut(s)	92
BsmI	GAATGC	1 cut(s)	337
Bsp143I	GATC	3 cut(s)	7, 313, 400
BspACI	CCGC	1 cut(s)	323
BspCNI	CTCAG	1 cut(s)	308
BspLI	GGNNCC	1 cut(s)	315
BspPI	GGATC	3 cut(s)	308, 321, 408
BsrI	ACTGG	2 cut(s)	220, 402
BssMI	GATC	3 cut(s)	7, 313, 400
Bst4CI	ACNGT	1 cut(s)	42
BstDEI	CTNAG	1 cut(s)	295
BstF5I	GGATG	1 cut(s)	205
BstKTI	GATC	3 cut(s)	10, 316, 403
BstMAI	GTCTC	1 cut(s)	92
BstMBI	GATC	3 cut(s)	7, 313, 400
BstMWI	GCNNNNNNNGC	2 cut(s)	280, 341
BstNSI	RCATGY	1 cut(s)	105
BstSCI	CCNGG	1 cut(s)	229
BstSFI	CTRYAG	2 cut(s)	38, 431
BstX2I	RGATCY	1 cut(s)	313
BstYI	RGATCY	1 cut(s)	313
BsuI	GTATCC	1 cut(s)	153
BtsCI	GGATG	1 cut(s)	205
BtsIMutI	CAGTG	1 cut(s)	213
Csp6I	GTAC	1 cut(s)	265
CviAII	CATG	4 cut(s)	102, 115, 148, 271
CviJI	RGCY	7 cut(s)	176, 219, 251, 283, 349, 409, 430
CviKI_1	RGCY	7 cut(s)	176, 219, 251, 283, 349, 409, 430
CviQI	GTAC	1 cut(s)	265
DdeI	CTNAG	1 cut(s)	295
DpnI	GATC	3 cut(s)	9, 315, 402
DpnII	GATC	3 cut(s)	7, 313, 400
DraI	TTTAAA	1 cut(s)	289
Eco32I	GATATC	1 cut(s)	25
EcoRV	GATATC	1 cut(s)	25
FaeI	CATG	4 cut(s)	105, 118, 151, 274
FaiI	YATR	6 cut(s)	103, 116, 149, 261, 272, 433
FalI	AAGNNNNNCTT	2 cut(s)	267, 299
FatI	CATG	4 cut(s)	101, 114, 147, 270
FokI	GGATG	1 cut(s)	212
FspBI	CTAG	1 cut(s)	122
GsaI	CCCAGC	1 cut(s)	348
HapII	CCGG	1 cut(s)	230
Hin1II	CATG	4 cut(s)	105, 118, 151, 274
HindIII	AAGCTT	1 cut(s)	281
HinfI	GANTC	1 cut(s)	371
HpaII	CCGG	1 cut(s)	230
HphI	GGTGA	2 cut(s)	170, 340
Hpy188I	TCNGA	1 cut(s)	298
Hpy188III	TCNNGA	2 cut(s)	385, 424
HpyAV	CCTTC	3 cut(s)	145, 149, 293
HpyCH4III	ACNGT	1 cut(s)	42
HpyCH4IV	ACGT	2 cut(s)	245, 267
HpyCH4V	TGCA	2 cut(s)	118, 274
HpyF10VI	GCNNNNNNNGC	2 cut(s)	280, 341
HpyF3I	CTNAG	1 cut(s)	295
HpySE526I	ACGT	2 cut(s)	245, 267
Hsp92II	CATG	4 cut(s)	105, 118, 151, 274
Kzo9I	GATC	3 cut(s)	7, 313, 400
LpnPI	CCDG	7 cut(s)	63, 201, 222, 243, 330, 383, 409
LweI	GCATC	1 cut(s)	348
MaeI	CTAG	1 cut(s)	122
MaeII	ACGT	2 cut(s)	245, 267
MaeIII	GTNAC	1 cut(s)	73
MalI	GATC	3 cut(s)	9, 315, 402
MboI	GATC	3 cut(s)	7, 313, 400
MflI	RGATCY	1 cut(s)	313
MluCI	AATT	2 cut(s)	81, 380
MnlI	CCTC	5 cut(s)	13, 130, 319, 385, 428
MseI	TTAA	2 cut(s)	44, 288
MslI	CAYNNNNRTG	1 cut(s)	123
MspI	CCGG	1 cut(s)	230
MspR9I	CCNGG	1 cut(s)	231
Mva1269I	GAATGC	1 cut(s)	337
MwoI	GCNNNNNNNGC	2 cut(s)	280, 341
NciI	CCSGG	1 cut(s)	231
NdeII	GATC	3 cut(s)	7, 313, 400
NlaIII	CATG	4 cut(s)	105, 118, 151, 274
NlaIV	GGNNCC	1 cut(s)	315
NspI	RCATGY	1 cut(s)	105
PctI	GAATGC	1 cut(s)	337
PfeI	GAWTC	1 cut(s)	371
PfoI	TCCNGGA	1 cut(s)	229
PspFI	CCCAGC	1 cut(s)	344
PspN4I	GGNNCC	1 cut(s)	315
PsuI	RGATCY	1 cut(s)	313
RsaI	GTAC	1 cut(s)	266
RsaNI	GTAC	1 cut(s)	265
RseI	CAYNNNNRTG	1 cut(s)	123
SaqAI	TTAA	2 cut(s)	44, 288
Sau3AI	GATC	3 cut(s)	7, 313, 400
ScrFI	CCNGG	1 cut(s)	231
SfaNI	GCATC	1 cut(s)	348
SfcI	CTRYAG	2 cut(s)	38, 431
SmiMI	CAYNNNNRTG	1 cut(s)	123
SmlI	CTYRAG	1 cut(s)	362
SmoI	CTYRAG	1 cut(s)	362
Sse9I	AATT	2 cut(s)	81, 380
SsiI	CCGC	1 cut(s)	323
SspMI	CTAG	1 cut(s)	122
StyD4I	CCNGG	1 cut(s)	229
TaaI	ACNGT	1 cut(s)	42
TaiI	ACGT	2 cut(s)	248, 270
TaqI	TCGA	1 cut(s)	79
TasI	AATT	2 cut(s)	81, 380
TfiI	GAWTC	1 cut(s)	371
Tru1I	TTAA	2 cut(s)	44, 288
Tru9I	TTAA	2 cut(s)	44, 288
TscAI	CASTG	1 cut(s)	220
TspDTI	ATGAA	4 cut(s)	103, 164, 270, 327
TspRI	CASTG	1 cut(s)	220
XceI	RCATGY	1 cut(s)	105
XspI	CTAG	1 cut(s)	122

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