Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000004

Orthogroup ID

OG0013559

Physical Location & Seq

Genomic Coordinates Reverse (-)

80530 .. 94378

Gene Structure 13849 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_4G00276510.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1542 bp

ATGATGGCTGCTGCTGCTGCTGCTGCTGTTGGGCTTAGTAGTACGGGGAAGAGGCTCTTTAGCTCTTCCTTGTATTATTCAGATATCACAGATAAGCTCTTTTATCTCAATGATCACGGCTTTGTAAATTGTCAATTGTCTTCAACAAAGAATGTTGTCACTGCCAGAAAGTCGTCTTCCAATTACAGTAATTCCAGATTTCCATCTTCAAATAGACATCAAGATCAGTCCATCAGGGCTTTAAAAGAGCATGCAGATACTGCATCTGCTCCTTCATCAACCACACATCAATTGCTAGAAGATTACAACGACTTGGAGGAGGAAAGCTCCGATCTTGAATATTCAGTGGAGGCGCTTCTTCTGCTACAGAAGTCTATGCTGGAAAAGCAGTGGAATCTTTCCTTTGAGAAAAAACTGTCAAGAAGAAAAATAACTGATAAGAAGATACCTGTCACTTGTTCTGGGGTATCTGCTCGGCAGAGGAGGATGAGTACTAAGAGGAAAGCTTTCAGCAAAAATACTTTAGAAATGCAACCTAGCATCAACAAGCATCTCAGAGCAAGTATCAGTCCGAGGCTGCTGCAGAATCGTATAAAGGGTTATGTGAAGGGCGTTACGAGTGAGCATTTGCTGACTCACACTGAGGTCGTACGCCTGTCAAAGAAAATTAAGATCGGGCTTTTAGTGGAGGAGCATAAATCAAGACTGAAGGAGAAACTGGGTTGTGAGCCCTCTGACGAACAACTCGCAACTTCATTGAGGATTTCCCGCACTGAACTACAGTCAAAGTTAATCCAATGTTCTTTGGCAAGAGAGAAGCTGACAATGAGCAATGTTCGTCTGGTCATGTCCATTGCCCAAAGATATGATAACATGGGTGCTGAAATGGCTGACCTTGTCCAGGGTGGCTTAATTGGACTACTACGCGGGATTGAGAAATTTGATTCATCAAAGGGGTTCAAAATTTCTACTTATGTTTACTGGTGGATACGTCAGGGTGTTTCAAGAGCACTGGTTGAAAATTCAAGAACCTTAAGACTGCCTACACATTTGCATGAGAGGTTAGGGTTAATCAGAAATGCAAAAGTTAGATTGGAAGAGAAAGGAATAACTCCATCTATTGATAGGATTGCAGAAAGCCTGAATATGTCCAAAAAGAAAGTTAGGAATGCTACTGAGGCAATCAGTAAGGTTTTTTCGCTTGATAGAGATGCATTCCCCTCTTTGAATGGCCTTCCAGGAGAAACTCATCATAGTTACATTGCTGATAATCGCCATGAGAACATCCCATGGCATGGGGTGGATGAGTTGGCACTCAAGGATGAAGTAAACAAGCTCATAAATATGATGCTTGTGGAGCGTGAGCGAGAGATCATACGGCTTTACTATGGTCTGGATAATGAATGTCTTACATGGGAGGACATTAGTAAACGTATAGGATTGTCCAGAGAAAGAGTTAGGCAAGTCGGACTGGTTGCTCTAGAGAAACTGAAACATGGTGCGAGGAAAAAAGAGATGGAGGCCATGCTAGTCCAACATTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000988 GO:0000990 GO:0003674 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0006139 GO:0006351 GO:0006352 GO:0006355 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009314 GO:0009416 GO:0009507 GO:0009536 GO:0009628 GO:0009889 GO:0009987 GO:0010109 GO:0010467 GO:0010468 GO:0010556 GO:0016070 GO:0016987 GO:0018130 GO:0019219 GO:0019222 GO:0019438 GO:0031323 GO:0031326 GO:0032774 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043254 GO:0044087 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044424 GO:0044444 GO:0044464 GO:0046483 GO:0050789 GO:0050794 GO:0050896 GO:0051128 GO:0051171 GO:0051252 GO:0051716 GO:0051775 GO:0060255 GO:0065007 GO:0071214 GO:0071461 GO:0071478 GO:0071482 GO:0071704 GO:0080005 GO:0080090 GO:0090304 GO:0097659 GO:0104004 GO:0140110 GO:1901360 GO:1901362 GO:1901576 GO:1903506 GO:2000112 GO:2000142 GO:2001141

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Sigma70_r2 Sigma70_r3 Sigma70_r4

Protein Analysis

513

Amino Acids

58.35

Weight (kDa)

9.64

Isoelectric Point (pI)

40.43

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Sigma70_r2	PF04542	276 - 343	2.8e-17	Sigma-70 region 2
Sigma70_r3	PF04539	353 - 424	4.6e-13	Sigma-70 region 3
Sigma70_r4	PF04545	451 - 499	3.9e-10	Sigma-70, region 4

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

Font Size (px)

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0013559)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G64860 AT1G64860
fragaria_vesca	FvH4_7g34280
malus_domestica	MD01G1240100.v1.1 MD07G1311500.v1.1
prunus_persica	Prupe.2G329700_v2.0.a1 Prupe.2G329700_v2.0.a1
pyrus_communis	pycom01g24680 pycom07g28370
rosa_chinensis	RchiOBHm_Chr1g0384631
rosa_laevigata	RLG00000026025
rosa_multiflora	Rmu_sc0012136.1_g000027
rosa_roxburghii	Rroxscaffold_4G00276510
rosa_samantha	Rh1AG474800 Rh1BG432900 Rh1CG446100 Rh1DG465500
rosa_wichuraiana	Rw1G039780

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	1295
AccII	CGCG	1 cut(s)	927
AciI	CCGC	2 cut(s)	769, 927
AcsI	RAATTY	3 cut(s)	938, 963, 1021
AcuI	CTGAAG	1 cut(s)	728
AfaI	GTAC	3 cut(s)	43, 493, 651
AfiI	CCNNNNNNNGG	2 cut(s)	901, 1295
AflII	CTTAAG	1 cut(s)	1033
AgsI	TTSAA	8 cut(s)	144, 210, 338, 961, 1005, 1019, 1026, 1228
AjnI	CCWGG	2 cut(s)	900, 1237
AluBI	AGCT	6 cut(s)	63, 97, 327, 506, 820, 1336
AluI	AGCT	6 cut(s)	63, 97, 327, 506, 820, 1336
Alw21I	GWGCWC	1 cut(s)	1012
AlwNI	CAGNNNCTG	1 cut(s)	260
AoxI	GGCC	2 cut(s)	1231, 1521
ApeKI	GCWGC	8 cut(s)	8, 11, 14, 17, 20, 23, 577, 580
ApoI	RAATTY	3 cut(s)	938, 963, 1021
Asp700I	GAANNNNTTC	1 cut(s)	506
AspLEI	GCGC	1 cut(s)	355
BanII	GRGCYC	1 cut(s)	732
BbsI	GAAGAC	2 cut(s)	132, 168
Bbv12I	GWGCWC	1 cut(s)	1012
BbvI	GCAGC	5 cut(s)	4, 7, 10, 564, 567
BccI	CCATC	4 cut(s)	211, 239, 1123, 1510
BceAI	ACGGC	2 cut(s)	133, 1394
BcgI	CGANNNNNNTGC	2 cut(s)	562, 596
BciT130I	CCWGG	2 cut(s)	902, 1239
BciVI	GTATCC	1 cut(s)	981
BclI	TGATCA	1 cut(s)	112
BfaI	CTAG	4 cut(s)	296, 537, 1481, 1529
BfmI	CTRYAG	3 cut(s)	365, 581, 779
BfoI	RGCGCY	1 cut(s)	356
BfrI	CTTAAG	1 cut(s)	1033
BfuI	GTATCC	1 cut(s)	981
BisI	GCNGC	8 cut(s)	9, 12, 15, 18, 21, 24, 578, 581
BlsI	GCNGC	8 cut(s)	10, 13, 16, 19, 22, 25, 579, 582
BmcAI	AGTACT	1 cut(s)	493
Bme1390I	CCNGG	2 cut(s)	902, 1239
BmrFI	CCNGG	2 cut(s)	902, 1239
BmrI	ACTGGG	1 cut(s)	728
BmsI	GCATC	5 cut(s)	272, 549, 559, 1201, 1338
BmuI	ACTGGG	1 cut(s)	728
BpiI	GAAGAC	2 cut(s)	132, 168
BplI	GAGNNNNNCTC	2 cut(s)	311, 343
BpuEI	CTTGAG	1 cut(s)	1301
BsaBI	GATNNNNATC	1 cut(s)	202
BsaJI	CCNNGG	3 cut(s)	572, 901, 1289
BsaXI	ACNNNNNCTCC	2 cut(s)	475, 505
Bsc4I	CCNNNNNNNGG	2 cut(s)	901, 1295
Bse1I	ACTGG	4 cut(s)	723, 986, 1017, 1476
Bse3DI	GCAATG	3 cut(s)	838, 852, 1260
Bse8I	GATNNNNATC	1 cut(s)	202
BseBI	CCWGG	2 cut(s)	902, 1239
BseDI	CCNNGG	3 cut(s)	572, 901, 1289
BseGI	GGATG	4 cut(s)	492, 1284, 1309, 1327
BseJI	GATNNNNATC	1 cut(s)	202
BseLI	CCNNNNNNNGG	2 cut(s)	901, 1295
BseMI	GCAATG	3 cut(s)	838, 852, 1260
BseMII	CTCAG	3 cut(s)	568, 633, 1167
BseNI	ACTGG	4 cut(s)	723, 986, 1017, 1476
BseRI	GAGGAG	3 cut(s)	332, 496, 704
BseXI	GCAGC	5 cut(s)	4, 7, 10, 564, 567
Bsh1236I	CGCG	1 cut(s)	927
BshFI	GGCC	2 cut(s)	1233, 1523
BsiHKAI	GWGCWC	1 cut(s)	1012
BsiWI	CGTACG	1 cut(s)	649
BslI	CCNNNNNNNGG	2 cut(s)	901, 1295
BsmI	GAATGC	2 cut(s)	1174, 1214
BsnI	GGCC	2 cut(s)	1233, 1523
Bsp1286I	GDGCHC	2 cut(s)	732, 1012
Bsp143I	GATC	5 cut(s)	112, 223, 331, 672, 1371
Bsp19I	CCATGG	1 cut(s)	1289
BspACI	CCGC	2 cut(s)	769, 927
BspANI	GGCC	2 cut(s)	1233, 1523
BspCNI	CTCAG	3 cut(s)	567, 634, 1168
BspFNI	CGCG	1 cut(s)	927
BspMAI	CTGCAG	1 cut(s)	585
BspQI	GCTCTTC	1 cut(s)	70
BspTI	CTTAAG	1 cut(s)	1033
BsrDI	GCAATG	3 cut(s)	838, 852, 1260
BsrI	ACTGG	4 cut(s)	723, 986, 1017, 1476
BssECI	CCNNGG	3 cut(s)	572, 901, 1289
BssMI	GATC	5 cut(s)	112, 223, 331, 672, 1371
BssT1I	CCWWGG	1 cut(s)	1289
Bst2UI	CCWGG	2 cut(s)	902, 1239
Bst4CI	ACNGT	3 cut(s)	188, 417, 783
Bst6I	CTCTTC	3 cut(s)	44, 70, 1092
BstAFI	CTTAAG	1 cut(s)	1033
BstAPI	GCANNNNNTGC	1 cut(s)	260
BstC8I	GCNNGC	1 cut(s)	252
BstDEI	CTNAG	5 cut(s)	35, 495, 554, 642, 1176
BstDSI	CCRYGG	1 cut(s)	1289
BstENI	CCTNNNNNAGG	1 cut(s)	899
BstF5I	GGATG	4 cut(s)	492, 1284, 1309, 1327
BstFNI	CGCG	1 cut(s)	927
BstH2I	RGCGCY	1 cut(s)	356
BstHHI	GCGC	1 cut(s)	355
BstKTI	GATC	5 cut(s)	115, 226, 334, 675, 1374
BstMBI	GATC	5 cut(s)	112, 223, 331, 672, 1371
BstNI	CCWGG	2 cut(s)	902, 1239
BstNSI	RCATGY	1 cut(s)	254
BstSCI	CCNGG	2 cut(s)	900, 1237
BstSFI	CTRYAG	3 cut(s)	365, 581, 779
BstUI	CGCG	1 cut(s)	927
BstV1I	GCAGC	5 cut(s)	4, 7, 10, 564, 567
BstV2I	GAAGAC	2 cut(s)	132, 168
BsuI	GTATCC	1 cut(s)	981
BsuRI	GGCC	2 cut(s)	1233, 1523
BtgI	CCRYGG	1 cut(s)	1289
BtsCI	GGATG	4 cut(s)	492, 1284, 1309, 1327
BtsI	GCAGTG	2 cut(s)	159, 395
BtsIMutI	CAGTG	6 cut(s)	159, 351, 395, 639, 771, 1010
Cac8I	GCNNGC	1 cut(s)	252
CaiI	CAGNNNCTG	1 cut(s)	260
CfoI	GCGC	1 cut(s)	355
Csp6I	GTAC	3 cut(s)	42, 492, 650
CviQI	GTAC	3 cut(s)	42, 492, 650
DdeI	CTNAG	5 cut(s)	35, 495, 554, 642, 1176
DpnI	GATC	5 cut(s)	114, 225, 333, 674, 1373
DpnII	GATC	5 cut(s)	112, 223, 331, 672, 1371
DraI	TTTAAA	1 cut(s)	243
Eam1104I	CTCTTC	3 cut(s)	44, 70, 1092
EarI	CTCTTC	3 cut(s)	44, 70, 1092
Eco130I	CCWWGG	1 cut(s)	1289
Eco24I	GRGCYC	1 cut(s)	732
Eco32I	GATATC	1 cut(s)	85
Eco57I	CTGAAG	1 cut(s)	728
EcoNI	CCTNNNNNAGG	1 cut(s)	899
EcoRII	CCWGG	2 cut(s)	900, 1237
EcoRV	GATATC	1 cut(s)	85
EcoT14I	CCWWGG	1 cut(s)	1289
EcoT22I	ATGCAT	1 cut(s)	1216
EcoT38I	GRGCYC	1 cut(s)	732
ErhI	CCWWGG	1 cut(s)	1289
FalI	AAGNNNNNCTT	2 cut(s)	41, 73
FauI	CCCGC	2 cut(s)	776, 920
FbaI	TGATCA	1 cut(s)	112
Fnu4HI	GCNGC	8 cut(s)	9, 12, 15, 18, 21, 24, 578, 581
FokI	GGATG	4 cut(s)	499, 1271, 1316, 1334
FriOI	GRGCYC	1 cut(s)	732
Fsp4HI	GCNGC	8 cut(s)	9, 12, 15, 18, 21, 24, 578, 581
FspBI	CTAG	4 cut(s)	296, 537, 1481, 1529
GlaI	GCGC	1 cut(s)	354
GluI	GCNGC	8 cut(s)	9, 12, 15, 18, 21, 24, 578, 581
HaeII	RGCGCY	1 cut(s)	356
HaeIII	GGCC	2 cut(s)	1233, 1523
HhaI	GCGC	1 cut(s)	355
Hin6I	GCGC	1 cut(s)	353
HinP1I	GCGC	1 cut(s)	353
HindIII	AAGCTT	1 cut(s)	504
HinfI	GANTC	4 cut(s)	394, 586, 634, 944
Hpy166II	GTNNAC	3 cut(s)	979, 1330, 1430
Hpy188I	TCNGA	7 cut(s)	82, 331, 557, 573, 736, 1076, 1469
Hpy8I	GTNNAC	3 cut(s)	979, 1330, 1430
HpyAV	CCTTC	4 cut(s)	282, 601, 703, 1244
HpyCH4III	ACNGT	3 cut(s)	188, 417, 783
HpyCH4IV	ACGT	2 cut(s)	991, 1432
HpyCH4V	TGCA	8 cut(s)	254, 263, 532, 583, 1054, 1082, 1133, 1214
HpyF3I	CTNAG	5 cut(s)	35, 495, 554, 642, 1176
HpySE526I	ACGT	2 cut(s)	991, 1432
HspAI	GCGC	1 cut(s)	353
Ksp22I	TGATCA	1 cut(s)	112
Kzo9I	GATC	5 cut(s)	112, 223, 331, 672, 1371
LguI	GCTCTTC	1 cut(s)	70
LmnI	GCTCC	4 cut(s)	274, 332, 691, 1357
Lsp1109I	GCAGC	5 cut(s)	4, 7, 10, 564, 567
LweI	GCATC	5 cut(s)	272, 549, 559, 1201, 1338
MaeI	CTAG	4 cut(s)	296, 537, 1481, 1529
MaeII	ACGT	2 cut(s)	991, 1432
MaeIII	GTNAC	4 cut(s)	157, 451, 613, 1256
MalI	GATC	5 cut(s)	114, 225, 333, 674, 1373
MboI	GATC	5 cut(s)	112, 223, 331, 672, 1371
MfeI	CAATTG	2 cut(s)	134, 290
MhlI	GDGCHC	2 cut(s)	732, 1012
MlyI	GAGTC	1 cut(s)	628
MmeI	TCCRAC	1 cut(s)	1447
Mph1103I	ATGCAT	1 cut(s)	1216
MroXI	GAANNNNTTC	1 cut(s)	506
MseI	TTAA	7 cut(s)	242, 669, 791, 911, 1034, 1070, 1540
MslI	CAYNNNNRTG	2 cut(s)	1053, 1343
MspCI	CTTAAG	1 cut(s)	1033
MspR9I	CCNGG	2 cut(s)	902, 1239
MunI	CAATTG	2 cut(s)	134, 290
Mva1269I	GAATGC	2 cut(s)	1174, 1214
MvaI	CCWGG	2 cut(s)	902, 1239
MvnI	CGCG	1 cut(s)	927
NcoI	CCATGG	1 cut(s)	1289
NdeII	GATC	5 cut(s)	112, 223, 331, 672, 1371
NmeAIII	GCCGAG	1 cut(s)	454
NmuCI	GTSAC	2 cut(s)	157, 451
NsiI	ATGCAT	1 cut(s)	1216
NspI	RCATGY	1 cut(s)	254
PaeI	GCATGC	1 cut(s)	254
PciSI	GCTCTTC	1 cut(s)	70
PctI	GAATGC	2 cut(s)	1174, 1214
PdmI	GAANNNNTTC	1 cut(s)	506
PfeI	GAWTC	3 cut(s)	394, 586, 944
Pfl23II	CGTACG	1 cut(s)	649
PflFI	GACNNNGTC	1 cut(s)	896
PflMI	CCANNNNNTGG	1 cut(s)	1295
PfoI	TCCNGGA	1 cut(s)	1237
PkrI	GCNGC	8 cut(s)	10, 13, 16, 19, 22, 25, 579, 582
PleI	GAGTC	1 cut(s)	628
PpsI	GAGTC	1 cut(s)	628
Psp6I	CCWGG	2 cut(s)	900, 1237
PspGI	CCWGG	2 cut(s)	900, 1237
PspLI	CGTACG	1 cut(s)	649
PstI	CTGCAG	1 cut(s)	585
PstNI	CAGNNNCTG	1 cut(s)	260
PsyI	GACNNNGTC	1 cut(s)	896
RsaI	GTAC	3 cut(s)	43, 493, 651
RsaNI	GTAC	3 cut(s)	42, 492, 650
RseI	CAYNNNNRTG	2 cut(s)	1053, 1343
SapI	GCTCTTC	1 cut(s)	70
SaqAI	TTAA	7 cut(s)	242, 669, 791, 911, 1034, 1070, 1540
SatI	GCNGC	8 cut(s)	9, 12, 15, 18, 21, 24, 578, 581
Sau3AI	GATC	5 cut(s)	112, 223, 331, 672, 1371
ScaI	AGTACT	1 cut(s)	493
SchI	GAGTC	1 cut(s)	628
ScrFI	CCNGG	2 cut(s)	902, 1239
SduI	GDGCHC	2 cut(s)	732, 1012
SfaNI	GCATC	5 cut(s)	272, 549, 559, 1201, 1338
SfcI	CTRYAG	3 cut(s)	365, 581, 779
SmiMI	CAYNNNNRTG	2 cut(s)	1053, 1343
SmlI	CTYRAG	2 cut(s)	1033, 1316
SmoI	CTYRAG	2 cut(s)	1033, 1316
SphI	GCATGC	1 cut(s)	254
SsiI	CCGC	2 cut(s)	769, 927
SspI	AATATT	1 cut(s)	341
SspMI	CTAG	4 cut(s)	296, 537, 1481, 1529
StyD4I	CCNGG	2 cut(s)	900, 1237
StyI	CCWWGG	1 cut(s)	1289
TaaI	ACNGT	3 cut(s)	188, 417, 783
TaiI	ACGT	2 cut(s)	994, 1435
TatI	WGTACW	1 cut(s)	491
TfiI	GAWTC	3 cut(s)	394, 586, 944
Tru1I	TTAA	7 cut(s)	242, 669, 791, 911, 1034, 1070, 1540
Tru9I	TTAA	7 cut(s)	242, 669, 791, 911, 1034, 1070, 1540
TscAI	CASTG	6 cut(s)	166, 351, 395, 646, 778, 1017
TseFI	GTSAC	2 cut(s)	157, 451
TseI	GCWGC	8 cut(s)	8, 11, 14, 17, 20, 23, 577, 580
Tsp45I	GTSAC	2 cut(s)	157, 451
TspDTI	ATGAA	5 cut(s)	264, 744, 936, 1338, 1416
TspRI	CASTG	6 cut(s)	166, 351, 395, 646, 778, 1017
Tth111I	GACNNNGTC	1 cut(s)	896
Van91I	CCANNNNNTGG	1 cut(s)	1295
Vha464I	CTTAAG	1 cut(s)	1033
XagI	CCTNNNNNAGG	1 cut(s)	899
XapI	RAATTY	3 cut(s)	938, 963, 1021
XbaI	TCTAGA	1 cut(s)	1480
XceI	RCATGY	1 cut(s)	254
XmnI	GAANNNNTTC	1 cut(s)	506
XspI	CTAG	4 cut(s)	296, 537, 1481, 1529
ZrmI	AGTACT	1 cut(s)	493
Zsp2I	ATGCAT	1 cut(s)	1216

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