Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5C

Orthogroup ID

OG0003142

Physical Location & Seq

Genomic Coordinates Reverse (-)

50370719 .. 50377402

Gene Structure 6684 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5CG383500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 474 bp

ATGAAGGAGACCCTAACCCTAAACACTTTTCCTGTTTACGGTTTGGGGCCGACTACATTTTCCCTCTCTCTCACATCGATTTCATCCTTCACTCACTCACCCGGAGTCTTGAATCCACGTGACAAGGCCTTCATTTCTGGTCAAAAGATGGTTGATCGTCTTTTTGAGGATATCTTTCAAATACTACAGTTAAACCCAGATGGAAAAAAGTTTGATAAGGTTACTCGAATTGAAGCAAAAAGTGAGACATGCGAGATGTTCATGCACCTAGATGTGAATACAGAGGTGTATCCCATGAAGGAAGGTGAGAAGTTCTCAATGGCTCTAACTTCTACACTCAACTTGGATGGAACACCTGACACTGGCTATTTCACTCCGGGAAATCGCAAGACGTTGGCCGATGAATATGAGTACGTCATGCAAGGGAAGCTTTTTAAAATCTCAGAAGGTTCTAAACGGGATCCTAAAGCGTAA

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

157

Amino Acids

17.68

Weight (kDa)

5.73

Isoelectric Point (pI)

22.46

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb8	PF03870	56 - 153	6e-34	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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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

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Enzyme	Recognition Site	Cut Count	Positions (bp)
AclWI	GGATC	2 cut(s)	455, 468
AcoI	YGGCCR	1 cut(s)	396
AcvI	CACGTG	1 cut(s)	119
AfaI	GTAC	1 cut(s)	413
AfiI	CCNNNNNNNGG	2 cut(s)	38, 362
AgsI	TTSAA	3 cut(s)	112, 179, 233
AluBI	AGCT	1 cut(s)	430
AluI	AGCT	1 cut(s)	430
Alw26I	GTCTC	2 cut(s)	2, 239
AlwI	GGATC	2 cut(s)	455, 468
AoxI	GGCC	3 cut(s)	47, 126, 396
AspS9I	GGNCC	1 cut(s)	47
AsuC2I	CCSGG	2 cut(s)	102, 378
AsuHPI	GGTGA	2 cut(s)	90, 317
BamHI	GGATCC	1 cut(s)	460
BbrPI	CACGTG	1 cut(s)	119
BccI	CCATC	3 cut(s)	142, 194, 341
BciVI	GTATCC	1 cut(s)	300
BcnI	CCSGG	2 cut(s)	102, 378
BcoDI	GTCTC	2 cut(s)	2, 239
BfaI	CTAG	1 cut(s)	269
BfmI	CTRYAG	1 cut(s)	185
BfuI	GTATCC	1 cut(s)	300
Bme1390I	CCNGG	2 cut(s)	102, 378
BmgT120I	GGNCC	1 cut(s)	47
BmiI	GGNNCC	2 cut(s)	48, 462
BmrFI	CCNGG	2 cut(s)	102, 378
BplI	GAGNNNNNCTC	2 cut(s)	299, 331
BpuMI	CCSGG	2 cut(s)	102, 378
Bsa29I	ATCGAT	1 cut(s)	77
BsaAI	YACGTR	1 cut(s)	119
BsaI	GGTCTC	1 cut(s)	2
Bsc4I	CCNNNNNNNGG	2 cut(s)	38, 362
Bse1I	ACTGG	1 cut(s)	367
BseCI	ATCGAT	1 cut(s)	77
BseGI	GGATG	2 cut(s)	83, 352
BseLI	CCNNNNNNNGG	2 cut(s)	38, 362
BseMII	CTCAG	1 cut(s)	456
BseNI	ACTGG	1 cut(s)	367
BshFI	GGCC	3 cut(s)	49, 128, 398
BshVI	ATCGAT	1 cut(s)	77
BsiSI	CCGG	2 cut(s)	102, 377
BslI	CCNNNNNNNGG	2 cut(s)	38, 362
BsmAI	GTCTC	2 cut(s)	2, 239
BsnI	GGCC	3 cut(s)	49, 128, 398
Bso31I	GGTCTC	1 cut(s)	2
Bsp143I	GATC	2 cut(s)	154, 460
BspANI	GGCC	3 cut(s)	49, 128, 398
BspCNI	CTCAG	1 cut(s)	455
BspDI	ATCGAT	1 cut(s)	77
BspLI	GGNNCC	2 cut(s)	48, 462
BspPI	GGATC	2 cut(s)	455, 468
BspTNI	GGTCTC	1 cut(s)	2
BsrI	ACTGG	1 cut(s)	367
BssMI	GATC	2 cut(s)	154, 460
Bst4CI	ACNGT	2 cut(s)	41, 189
BstBAI	YACGTR	1 cut(s)	119
BstDEI	CTNAG	1 cut(s)	442
BstF5I	GGATG	2 cut(s)	83, 352
BstKTI	GATC	2 cut(s)	157, 463
BstMAI	GTCTC	2 cut(s)	2, 239
BstMBI	GATC	2 cut(s)	154, 460
BstMWI	GCNNNNNNNGC	1 cut(s)	427
BstNSI	RCATGY	1 cut(s)	252
BstSCI	CCNGG	2 cut(s)	100, 376
BstSFI	CTRYAG	1 cut(s)	185
BstX2I	RGATCY	1 cut(s)	460
BstYI	RGATCY	1 cut(s)	460
Bsu15I	ATCGAT	1 cut(s)	77
BsuI	GTATCC	1 cut(s)	300
BsuRI	GGCC	3 cut(s)	49, 128, 398
BsuTUI	ATCGAT	1 cut(s)	77
BtsCI	GGATG	2 cut(s)	83, 352
BtsIMutI	CAGTG	1 cut(s)	360
Cfr13I	GGNCC	1 cut(s)	47
ClaI	ATCGAT	1 cut(s)	77
Csp6I	GTAC	1 cut(s)	412
CviAII	CATG	4 cut(s)	249, 262, 295, 418
CviJI	RGCY	6 cut(s)	49, 128, 323, 366, 398, 430
CviKI_1	RGCY	6 cut(s)	49, 128, 323, 366, 398, 430
CviQI	GTAC	1 cut(s)	412
DdeI	CTNAG	1 cut(s)	442
DpnI	GATC	2 cut(s)	156, 462
DpnII	GATC	2 cut(s)	154, 460
DraI	TTTAAA	1 cut(s)	436
EaeI	YGGCCR	1 cut(s)	396
Eco147I	AGGCCT	1 cut(s)	128
Eco31I	GGTCTC	1 cut(s)	2
Eco32I	GATATC	1 cut(s)	172
Eco72I	CACGTG	1 cut(s)	119
EcoRV	GATATC	1 cut(s)	172
FaeI	CATG	4 cut(s)	252, 265, 298, 421
FaiI	YATR	5 cut(s)	250, 263, 296, 408, 419
FalI	AAGNNNNNCTT	2 cut(s)	414, 446
FatI	CATG	4 cut(s)	248, 261, 294, 417
FokI	GGATG	2 cut(s)	70, 359
FspBI	CTAG	1 cut(s)	269
HaeIII	GGCC	3 cut(s)	49, 128, 398
HapII	CCGG	2 cut(s)	102, 377
Hin1II	CATG	4 cut(s)	252, 265, 298, 421
HindIII	AAGCTT	1 cut(s)	428
HinfI	GANTC	2 cut(s)	105, 112
HpaII	CCGG	2 cut(s)	102, 377
HphI	GGTGA	2 cut(s)	90, 317
Hpy166II	GTNNAC	1 cut(s)	37
Hpy188I	TCNGA	1 cut(s)	445
Hpy188III	TCNNGA	1 cut(s)	109
Hpy8I	GTNNAC	1 cut(s)	37
HpyAV	CCTTC	5 cut(s)	97, 139, 292, 296, 440
HpyCH4III	ACNGT	2 cut(s)	41, 189
HpyCH4IV	ACGT	3 cut(s)	118, 392, 414
HpyCH4V	TGCA	2 cut(s)	265, 421
HpyF10VI	GCNNNNNNNGC	1 cut(s)	427
HpyF3I	CTNAG	1 cut(s)	442
HpySE526I	ACGT	3 cut(s)	118, 392, 414
Hsp92II	CATG	4 cut(s)	252, 265, 298, 421
Kzo9I	GATC	2 cut(s)	154, 460
LpnPI	CCDG	7 cut(s)	45, 115, 123, 210, 348, 369, 390
MaeI	CTAG	1 cut(s)	269
MaeII	ACGT	3 cut(s)	118, 392, 414
MaeIII	GTNAC	2 cut(s)	119, 220
MalI	GATC	2 cut(s)	156, 462
MboI	GATC	2 cut(s)	154, 460
MflI	RGATCY	1 cut(s)	460
MluCI	AATT	1 cut(s)	228
MlyI	GAGTC	1 cut(s)	114
MnlI	CCTC	3 cut(s)	74, 160, 277
MseI	TTAA	2 cut(s)	191, 435
MslI	CAYNNNNRTG	1 cut(s)	270
MspI	CCGG	2 cut(s)	102, 377
MspR9I	CCNGG	2 cut(s)	102, 378
MwoI	GCNNNNNNNGC	1 cut(s)	427
NciI	CCSGG	2 cut(s)	102, 378
NdeII	GATC	2 cut(s)	154, 460
NlaIII	CATG	4 cut(s)	252, 265, 298, 421
NlaIV	GGNNCC	2 cut(s)	48, 462
NmuCI	GTSAC	1 cut(s)	119
NspI	RCATGY	1 cut(s)	252
PceI	AGGCCT	1 cut(s)	128
PfeI	GAWTC	1 cut(s)	112
PfoI	TCCNGGA	1 cut(s)	376
PleI	GAGTC	1 cut(s)	113
PmaCI	CACGTG	1 cut(s)	119
PmlI	CACGTG	1 cut(s)	119
PpsI	GAGTC	1 cut(s)	113
Ppu21I	YACGTR	1 cut(s)	119
PspCI	CACGTG	1 cut(s)	119
PspN4I	GGNNCC	2 cut(s)	48, 462
PspPI	GGNCC	1 cut(s)	47
PsuI	RGATCY	1 cut(s)	460
RsaI	GTAC	1 cut(s)	413
RsaNI	GTAC	1 cut(s)	412
RseI	CAYNNNNRTG	1 cut(s)	270
SaqAI	TTAA	2 cut(s)	191, 435
Sau3AI	GATC	2 cut(s)	154, 460
Sau96I	GGNCC	1 cut(s)	47
SchI	GAGTC	1 cut(s)	114
ScrFI	CCNGG	2 cut(s)	102, 378
SfcI	CTRYAG	1 cut(s)	185
SmiMI	CAYNNNNRTG	1 cut(s)	270
Sse9I	AATT	1 cut(s)	228
SseBI	AGGCCT	1 cut(s)	128
SspMI	CTAG	1 cut(s)	269
StuI	AGGCCT	1 cut(s)	128
StyD4I	CCNGG	2 cut(s)	100, 376
TaaI	ACNGT	2 cut(s)	41, 189
TaiI	ACGT	3 cut(s)	121, 395, 417
TaqI	TCGA	2 cut(s)	77, 226
TasI	AATT	1 cut(s)	228
TfiI	GAWTC	1 cut(s)	112
Tru1I	TTAA	2 cut(s)	191, 435
Tru9I	TTAA	2 cut(s)	191, 435
TscAI	CASTG	1 cut(s)	367
TseFI	GTSAC	1 cut(s)	119
Tsp45I	GTSAC	1 cut(s)	119
TspDTI	ATGAA	6 cut(s)	17, 72, 121, 250, 311, 417
TspRI	CASTG	1 cut(s)	367
XceI	RCATGY	1 cut(s)	252
XspI	CTAG	1 cut(s)	269

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