Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6A

Orthogroup ID

OG0004335

Physical Location & Seq

Genomic Coordinates Forward (+)

11487037 .. 11491263

Gene Structure 4227 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6AG078900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 717 bp

ATGGAGGGGAAATCGTACCAGAGGTTCCCGCGGGTGAAAATCCGTGAAATGAGGCACGACTACCTCAAGTTCGAGCTCCGCGACACCGACGCGAGCGTGGCCAACGCGCTCCGGCGCGTGATGATCGCCGAGGTCCCCACCGTCGCCATCGACCTCGTCGAGATCGAAATCAACTCCTCCGTCCTCAACGACGAGTTCATCGCCCACCGCCTCGGCCTCATCCCCTTGACCAGCGACCGCGCCATGAGCATGCGCTTCTCACGTGACTGCGACGCCTGCGACGGCGACGGCCAGTGCGAGTACTGCTCCGTCGAGTTTCACCTCCGCGCCCGCTGCCACTCCGACCAAACCCTAGATGTCACCAGCAAGGAACTCCTCAGCTCCGACCACACCGTCGTCCCCGTCGATTTCTCCGACGCCTCCGGTTACGAAGCTTCCGAACAGAGAGGAATTATCATTGTGAAGTTGCGAAGGGGGCAAGAGCTGAGGCTGAGGGCTATTGCTAGGAAGGGGATTGGGAAAGATCATGCGAAGTGGTCACCTGCGGCTACTGTCACTTTCATGTATGAACCCGACATTCGCATCAATGAGGAGATGATGGATACTTTGTCACTCGAGGAGAAGACAGCTTGGGTTGATAGCAGTCCTACCAAAGTCTTTGAGCTTGATCCTAGTACTGGCAAGGTTGGTACTTGTTTGCGTCTGTGTTTATTTTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000418 GO:0000419 GO:0000428 GO:0003002 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0005730 GO:0005737 GO:0007275 GO:0007389 GO:0008150 GO:0009791 GO:0009888 GO:0010374 GO:0010375 GO:0016591 GO:0030880 GO:0031974 GO:0031981 GO:0032501 GO:0032502 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:0044464 GO:0048856 GO:0055029 GO:0061695 GO:0070013 GO:0090558 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

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

Pfam Domains

Protein Families

RNA_pol_A_bac RNA_pol_L

Protein Analysis

238

Amino Acids

26.98

Weight (kDa)

5.46

Isoelectric Point (pI)

39.07

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_L	PF01193	23 - 100	2.8e-10	RNA polymerase Rpb3/Rpb11 dimerisation domain
RNA_pol_A_bac	PF01000	55 - 178	4.1e-19	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: OG0004335)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G15400 AT2G15400 AT2G15430 AT2G15430 AT2G15430
fragaria_vesca	FvH4_2g05450
malus_domestica	MD05G1087400.v1.1 MD10G1096200.v1.1
prunus_persica	Prupe.8G132000_v2.0.a1 Prupe.8G132000_v2.0.a1 Prupe.8G132400_v2.0.a1
pyrus_communis	pycom05g08690
rosa_chinensis	RchiOBHm_Chr5g0063881 RchiOBHm_Chr6g0255731
rosa_laevigata	RLG00000014818 RLG00000027736
rosa_multiflora	Rmu_sc0009240.1_g000038 Rmu_ssc0000136.1_g000018
rosa_roxburghii	Rroxscaffold_7G00209720
rosa_rugosa	Rorug05G0560800 Rorug06G0006400
rosa_samantha	Rh1DG021100 Rh2DG345600 Rh2DG346900 Rh5CG269200 Rh6AG078900 Rh6BG072000 Rh6CG070100 Rh6DG067300 Rh7AG302700 Rh7CG321200
rosa_wichuraiana	Rw6G006800

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	550
AasI	GACNNNNNNGTC	1 cut(s)	392
Acc36I	ACCTGC	1 cut(s)	550
AccII	CGCG	7 cut(s)	31, 81, 92, 107, 117, 240, 327
AciI	CCGC	8 cut(s)	29, 31, 79, 208, 238, 325, 331, 545
AclWI	GGATC	1 cut(s)	662
AcoI	YGGCCR	2 cut(s)	99, 289
AcvI	CACGTG	1 cut(s)	263
AcyI	GRCGYC	2 cut(s)	273, 417
AfaI	GTAC	4 cut(s)	17, 302, 676, 691
AfiI	CCNNNNNNNGG	1 cut(s)	677
AluBI	AGCT	6 cut(s)	76, 381, 434, 484, 629, 664
AluI	AGCT	6 cut(s)	76, 381, 434, 484, 629, 664
Alw21I	GWGCWC	1 cut(s)	78
AlwI	GGATC	1 cut(s)	662
Ama87I	CYCGRG	1 cut(s)	614
AoxI	GGCC	3 cut(s)	99, 214, 289
ApeKI	GCWGC	1 cut(s)	333
AspLEI	GCGC	5 cut(s)	109, 117, 242, 255, 329
AspS9I	GGNCC	1 cut(s)	133
AsuHPI	GGTGA	4 cut(s)	46, 311, 352, 531
AvaI	CYCGRG	1 cut(s)	614
AvaII	GGWCC	1 cut(s)	133
BalI	TGGCCA	1 cut(s)	101
BanII	GRGCYC	1 cut(s)	78
BbrPI	CACGTG	1 cut(s)	263
BbsI	GAAGAC	1 cut(s)	629
Bbv12I	GWGCWC	1 cut(s)	78
BbvCI	CCTCAGC	3 cut(s)	377, 485, 491
BbvI	GCAGC	1 cut(s)	320
BccI	CCATC	2 cut(s)	155, 592
BceAI	ACGGC	2 cut(s)	298, 304
BciVI	GTATCC	1 cut(s)	595
BfaI	CTAG	3 cut(s)	353, 504, 672
BfuAI	ACCTGC	1 cut(s)	550
BfuI	GTATCC	1 cut(s)	595
BisI	GCNGC	2 cut(s)	334, 546
BlsI	GCNGC	2 cut(s)	335, 547
BmcAI	AGTACT	2 cut(s)	302, 676
Bme18I	GGWCC	1 cut(s)	133
BmeT110I	CYCGRG	1 cut(s)	614
BmgT120I	GGNCC	1 cut(s)	133
BmiI	GGNNCC	2 cut(s)	26, 135
BmsI	GCATC	1 cut(s)	591
BpiI	GAAGAC	1 cut(s)	629
BplI	GAGNNNNNCTC	2 cut(s)	290, 322
Bpu10I	CCTNAGC	3 cut(s)	377, 485, 491
BpuEI	CTTGAG	1 cut(s)	50
BsaAI	YACGTR	1 cut(s)	263
BsaBI	GATNNNNATC	1 cut(s)	167
BsaHI	GRCGYC	2 cut(s)	273, 417
BsaJI	CCNNGG	3 cut(s)	29, 129, 211
BsaWI	WCCGGW	1 cut(s)	422
Bsc4I	CCNNNNNNNGG	1 cut(s)	677
Bse1I	ACTGG	2 cut(s)	292, 682
Bse8I	GATNNNNATC	1 cut(s)	167
BseDI	CCNNGG	3 cut(s)	29, 129, 211
BseGI	GGATG	1 cut(s)	219
BseJI	GATNNNNATC	1 cut(s)	167
BseLI	CCNNNNNNNGG	1 cut(s)	677
BseMII	CTCAG	3 cut(s)	391, 476, 482
BseNI	ACTGG	2 cut(s)	292, 682
BseRI	GAGGAG	4 cut(s)	166, 365, 605, 632
BseXI	GCAGC	1 cut(s)	320
Bsh1236I	CGCG	7 cut(s)	31, 81, 92, 107, 117, 240, 327
Bsh1285I	CGRYCG	1 cut(s)	238
BshFI	GGCC	3 cut(s)	101, 216, 291
BsiEI	CGRYCG	1 cut(s)	238
BsiHKAI	GWGCWC	1 cut(s)	78
BsiHKCI	CYCGRG	1 cut(s)	614
BsiSI	CCGG	2 cut(s)	112, 423
BslFI	GGGAC	2 cut(s)	119, 383
BslI	CCNNNNNNNGG	1 cut(s)	677
BsmFI	GGGAC	2 cut(s)	119, 383
BsnI	GGCC	3 cut(s)	101, 216, 291
BsoBI	CYCGRG	1 cut(s)	614
Bsp1286I	GDGCHC	1 cut(s)	78
Bsp143I	GATC	4 cut(s)	123, 162, 523, 667
BspACI	CCGC	8 cut(s)	29, 31, 79, 208, 238, 325, 331, 545
BspANI	GGCC	3 cut(s)	101, 216, 291
BspCNI	CTCAG	3 cut(s)	390, 477, 483
BspFNI	CGCG	7 cut(s)	31, 81, 92, 107, 117, 240, 327
BspLI	GGNNCC	2 cut(s)	26, 135
BspMI	ACCTGC	1 cut(s)	550
BspPI	GGATC	1 cut(s)	662
BsrI	ACTGG	2 cut(s)	292, 682
BssECI	CCNNGG	3 cut(s)	29, 129, 211
BssMI	GATC	4 cut(s)	123, 162, 523, 667
BssNI	GRCGYC	2 cut(s)	273, 417
Bst4CI	ACNGT	3 cut(s)	142, 394, 553
BstACI	GRCGYC	2 cut(s)	273, 417
BstBAI	YACGTR	1 cut(s)	263
BstC8I	GCNNGC	4 cut(s)	94, 251, 277, 331
BstDEI	CTNAG	3 cut(s)	377, 485, 491
BstDSI	CCRYGG	1 cut(s)	29
BstEII	GGTNACC	1 cut(s)	537
BstF5I	GGATG	1 cut(s)	219
BstFNI	CGCG	7 cut(s)	31, 81, 92, 107, 117, 240, 327
BstHHI	GCGC	5 cut(s)	109, 117, 242, 255, 329
BstKTI	GATC	4 cut(s)	126, 165, 526, 670
BstMBI	GATC	4 cut(s)	123, 162, 523, 667
BstMCI	CGRYCG	1 cut(s)	238
BstMWI	GCNNNNNNNGC	6 cut(s)	98, 246, 276, 303, 333, 475
BstNSI	RCATGY	1 cut(s)	253
BstPI	GGTNACC	1 cut(s)	537
BstUI	CGCG	7 cut(s)	31, 81, 92, 107, 117, 240, 327
BstV1I	GCAGC	1 cut(s)	320
BstV2I	GAAGAC	1 cut(s)	629
BsuI	GTATCC	1 cut(s)	595
BsuRI	GGCC	3 cut(s)	101, 216, 291
BtgI	CCRYGG	1 cut(s)	29
BtgZI	GCGATG	1 cut(s)	184
BtsCI	GGATG	1 cut(s)	219
BtsIMutI	CAGTG	1 cut(s)	299
BveI	ACCTGC	1 cut(s)	550
Cac8I	GCNNGC	4 cut(s)	94, 251, 277, 331
CfoI	GCGC	5 cut(s)	109, 117, 242, 255, 329
Cfr13I	GGNCC	1 cut(s)	133
Cfr42I	CCGCGG	1 cut(s)	32
CseI	GACGC	4 cut(s)	98, 281, 425, 689
Csp6I	GTAC	4 cut(s)	16, 301, 675, 690
CviAII	CATG	4 cut(s)	244, 250, 527, 562
CviQI	GTAC	4 cut(s)	16, 301, 675, 690
DdeI	CTNAG	3 cut(s)	377, 485, 491
DpnI	GATC	4 cut(s)	125, 164, 525, 669
DpnII	GATC	4 cut(s)	123, 162, 523, 667
DrdI	GACNNNNNNGTC	1 cut(s)	392
DseDI	GACNNNNNNGTC	1 cut(s)	392
EaeI	YGGCCR	2 cut(s)	99, 289
Ecl136II	GAGCTC	1 cut(s)	76
Eco24I	GRGCYC	1 cut(s)	78
Eco47I	GGWCC	1 cut(s)	133
Eco53kI	GAGCTC	1 cut(s)	76
Eco72I	CACGTG	1 cut(s)	263
Eco88I	CYCGRG	1 cut(s)	614
Eco91I	GGTNACC	1 cut(s)	537
EcoICRI	GAGCTC	1 cut(s)	76
EcoO109I	RGGNCCY	1 cut(s)	133
EcoO65I	GGTNACC	1 cut(s)	537
EcoT38I	GRGCYC	1 cut(s)	78
FaeI	CATG	4 cut(s)	247, 253, 530, 565
FaiI	YATR	5 cut(s)	245, 251, 528, 563, 567
FaqI	GGGAC	2 cut(s)	119, 383
FatI	CATG	4 cut(s)	243, 249, 526, 561
FauI	CCCGC	3 cut(s)	24, 36, 338
Fnu4HI	GCNGC	2 cut(s)	334, 546
FokI	GGATG	1 cut(s)	206
FriOI	GRGCYC	1 cut(s)	78
Fsp4HI	GCNGC	2 cut(s)	334, 546
FspBI	CTAG	3 cut(s)	353, 504, 672
GlaI	GCGC	5 cut(s)	108, 116, 241, 254, 328
GluI	GCNGC	2 cut(s)	334, 546
HaeIII	GGCC	3 cut(s)	101, 216, 291
HapII	CCGG	2 cut(s)	112, 423
HgaI	GACGC	4 cut(s)	98, 281, 425, 689
HhaI	GCGC	5 cut(s)	109, 117, 242, 255, 329
Hin1I	GRCGYC	2 cut(s)	273, 417
Hin1II	CATG	4 cut(s)	247, 253, 530, 565
Hin6I	GCGC	5 cut(s)	107, 115, 240, 253, 327
HinP1I	GCGC	5 cut(s)	107, 115, 240, 253, 327
HindIII	AAGCTT	1 cut(s)	432
HpaII	CCGG	2 cut(s)	112, 423
HphI	GGTGA	4 cut(s)	46, 311, 352, 531
Hpy188I	TCNGA	4 cut(s)	343, 385, 415, 439
Hpy188III	TCNNGA	1 cut(s)	160
HpyAV	CCTTC	2 cut(s)	465, 502
HpyCH4III	ACNGT	3 cut(s)	142, 394, 553
HpyCH4IV	ACGT	1 cut(s)	262
HpyF10VI	GCNNNNNNNGC	6 cut(s)	98, 246, 276, 303, 333, 475
HpyF3I	CTNAG	3 cut(s)	377, 485, 491
HpySE526I	ACGT	1 cut(s)	262
Hsp92I	GRCGYC	2 cut(s)	273, 417
Hsp92II	CATG	4 cut(s)	247, 253, 530, 565
HspAI	GCGC	5 cut(s)	107, 115, 240, 253, 327
KspI	CCGCGG	1 cut(s)	32
Kzo9I	GATC	4 cut(s)	123, 162, 523, 667
LmnI	GCTCC	4 cut(s)	81, 114, 311, 386
LpnPI	CCDG	9 cut(s)	32, 125, 244, 289, 305, 376, 436, 555, 663
Lsp1109I	GCAGC	1 cut(s)	320
LweI	GCATC	1 cut(s)	591
MaeI	CTAG	3 cut(s)	353, 504, 672
MaeII	ACGT	1 cut(s)	262
MaeIII	GTNAC	6 cut(s)	263, 358, 425, 537, 553, 609
MalI	GATC	4 cut(s)	125, 164, 525, 669
MboI	GATC	4 cut(s)	123, 162, 523, 667
MboII	GAAGA	1 cut(s)	634
MhlI	GDGCHC	1 cut(s)	78
MlsI	TGGCCA	1 cut(s)	101
MluCI	AATT	1 cut(s)	450
MluNI	TGGCCA	1 cut(s)	101
MmeI	TCCRAC	3 cut(s)	366, 408, 438
Mox20I	TGGCCA	1 cut(s)	101
MscI	TGGCCA	1 cut(s)	101
MslI	CAYNNNNRTG	2 cut(s)	248, 560
Msp20I	TGGCCA	1 cut(s)	101
MspA1I	CMGCKG	2 cut(s)	31, 333
MspI	CCGG	2 cut(s)	112, 423
MvnI	CGCG	7 cut(s)	31, 81, 92, 107, 117, 240, 327
MwoI	GCNNNNNNNGC	6 cut(s)	98, 246, 276, 303, 333, 475
NdeII	GATC	4 cut(s)	123, 162, 523, 667
NlaIII	CATG	4 cut(s)	247, 253, 530, 565
NlaIV	GGNNCC	2 cut(s)	26, 135
NmeAIII	GCCGAG	2 cut(s)	154, 192
NmuCI	GTSAC	5 cut(s)	263, 358, 537, 553, 609
NspI	RCATGY	1 cut(s)	253
PaeI	GCATGC	1 cut(s)	253
PaeR7I	CTCGAG	1 cut(s)	614
PaqCI	CACCTGC	1 cut(s)	550
PcsI	WCGNNNNNNNCGW	7 cut(s)	78, 156, 162, 294, 402, 411, 435
PflFI	GACNNNGTC	1 cut(s)	155
PkrI	GCNGC	2 cut(s)	335, 547
PmaCI	CACGTG	1 cut(s)	263
PmlI	CACGTG	1 cut(s)	263
Ppu21I	YACGTR	1 cut(s)	263
PpuMI	RGGWCCY	1 cut(s)	133
Psp124BI	GAGCTC	1 cut(s)	78
Psp5II	RGGWCCY	1 cut(s)	133
PspCI	CACGTG	1 cut(s)	263
PspEI	GGTNACC	1 cut(s)	537
PspN4I	GGNNCC	2 cut(s)	26, 135
PspPI	GGNCC	1 cut(s)	133
PspPPI	RGGWCCY	1 cut(s)	133
PspXI	VCTCGAGB	1 cut(s)	614
PsrI	GAACNNNNNNTAC	2 cut(s)	8, 40
PsyI	GACNNNGTC	1 cut(s)	155
RsaI	GTAC	4 cut(s)	17, 302, 676, 691
RsaNI	GTAC	4 cut(s)	16, 301, 675, 690
RseI	CAYNNNNRTG	2 cut(s)	248, 560
SacI	GAGCTC	1 cut(s)	78
SacII	CCGCGG	1 cut(s)	32
SatI	GCNGC	2 cut(s)	334, 546
Sau3AI	GATC	4 cut(s)	123, 162, 523, 667
Sau96I	GGNCC	1 cut(s)	133
ScaI	AGTACT	2 cut(s)	302, 676
SduI	GDGCHC	1 cut(s)	78
SfaNI	GCATC	1 cut(s)	591
Sfr274I	CTCGAG	1 cut(s)	614
Sfr303I	CCGCGG	1 cut(s)	32
SgrBI	CCGCGG	1 cut(s)	32
SinI	GGWCC	1 cut(s)	133
SlaI	CTCGAG	1 cut(s)	614
SmiMI	CAYNNNNRTG	2 cut(s)	248, 560
SmlI	CTYRAG	2 cut(s)	65, 614
SmoI	CTYRAG	2 cut(s)	65, 614
SphI	GCATGC	1 cut(s)	253
Sse9I	AATT	1 cut(s)	450
SsiI	CCGC	8 cut(s)	29, 31, 79, 208, 238, 325, 331, 545
SspMI	CTAG	3 cut(s)	353, 504, 672
SstI	GAGCTC	1 cut(s)	78
TaaI	ACNGT	3 cut(s)	142, 394, 553
TaiI	ACGT	1 cut(s)	265
TaqI	TCGA	7 cut(s)	72, 150, 159, 165, 312, 405, 615
TasI	AATT	1 cut(s)	450
TatI	WGTACW	2 cut(s)	300, 674
TauI	GCSGC	1 cut(s)	548
TscAI	CASTG	1 cut(s)	299
TseFI	GTSAC	5 cut(s)	263, 358, 537, 553, 609
TseI	GCWGC	1 cut(s)	333
Tsp45I	GTSAC	5 cut(s)	263, 358, 537, 553, 609
TspDTI	ATGAA	3 cut(s)	187, 550, 582
TspGWI	ACGGA	3 cut(s)	32, 169, 298
TspRI	CASTG	1 cut(s)	299
Tth111I	GACNNNGTC	1 cut(s)	155
VpaK11BI	GGWCC	1 cut(s)	133
XceI	RCATGY	1 cut(s)	253
XhoI	CTCGAG	1 cut(s)	614
XspI	CTAG	3 cut(s)	353, 504, 672
ZrmI	AGTACT	2 cut(s)	302, 676

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