Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000006

Orthogroup ID

OG0003176

Physical Location & Seq

Genomic Coordinates Forward (+)

34589123 .. 34589806

Gene Structure 684 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_6G00412000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 684 bp

ATGACTCCAAGACAGGCATGCATAGTCATCAAGCTTGATATGGTCATGATTCGAGATGCACAGTTTTCTATAGATGTTGATGTTGTGAAAGAATCAATTTTAAAAGTTCCGAGAATCAAACTGAAGCAAGAGAATATTCAAGTTCCAGATAACGAAACTTTGGAAGTGTATTCTCAGGACAAGGATAGACGCAGACTTTATTTTGAGCTCTACAGATTAATGAGTATCCTCCCCAATGTTACAGTAAGGGGCATAACGACAGTTCAGCGTGTTGTCATTGATGAAAGTGATGTGAAAAAGGATAAAGAAGATGTTCAAGTTAAAGGTGCAGATGTTGTTGGTAAGAAGTACAGGTTGTTTGCTGAAGGCAAGGGACTTCTGGCAGTAATGAGCACTGAAGGAGTAGATGGTTGTAAAACCACAAGTAATGACATTATTGAAGTGCAGCAGACACTTGGGATTGAAGCTGCGAGAATTTCTATCATAGAGGAGATAAAGTATACTATGAAGCAACATGGAATGAACATAGATGATCGCCATATGATGCTTTTAGCGGATGCAATGACTTCCAGGGGTCAAGTTCTTGGAATGACGAGATTTGGCCTTCAAAAGATGGACAAAAGTGTTTTAATGGGTGCTTCATTTGAGCGAACAGATGATCATCTGTTTAATGCTTGTGTGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0001817 GO:0001819 GO:0002376 GO:0003674 GO:0003824 GO:0003899 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005737 GO:0005829 GO:0006139 GO:0006351 GO:0006725 GO:0006807 GO:0006950 GO:0006952 GO:0006955 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0010467 GO:0016070 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019438 GO:0030880 GO:0031974 GO:0031981 GO:0032479 GO:0032481 GO:0032648 GO:0032728 GO:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0045087 GO:0046483 GO:0048518 GO:0050789 GO:0050896 GO:0051239 GO:0051240 GO:0055029 GO:0061695 GO:0065007 GO:0070013 GO:0071704 GO:0090304 GO:0097659 GO:0097747 GO:0140098 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

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

Pfam Domains

Protein Families

RNA_pol_Rpb1_1 RNA_pol_Rpb1_2 RNA_pol_Rpb1_3 RNA_pol_Rpb1_4 RNA_pol_Rpb1_5

Protein Analysis

227

Amino Acids

25.76

Weight (kDa)

6.34

Isoelectric Point (pI)

35.33

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb1_5	PF04998	48 - 209	1.8e-23	RNA polymerase Rpb1, domain 5

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

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Orthologous Genes (Group: OG0003176)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G60040 AT5G60040
fragaria_vesca	FvH4_3g34290 FvH4_3g34290 FvH4_3g34290 FvH4_6g15631
malus_domestica	MD03G1106800.v1.1 MD09G1157000.v1.1
prunus_persica	Prupe.6G089600_v2.0.a1 Prupe.6G089600_v2.0.a1
pyrus_communis	pycom03g08620 pycom09g07570
rosa_chinensis	RchiOBHm_Chr3g0469301 RchiOBHm_Chr3g0469321 RchiOBHm_Chr5g0061861
rosa_laevigata	RLG00000024360 RLG00000035511
rosa_multiflora	Rmu_sc0004134.1_g000001 Rmu_sc0011641.1_g000013 Rmu_sc0011641.1_g000015 Rmu_sc0019271.1_g000001 Rmu_sc0022191.1_g000001
rosa_roxburghii	Rroxscaffold_1G00018870 Rroxscaffold_6G00411990 Rroxscaffold_6G00412000
rosa_rugosa	Rorug03G0100400 Rorug05G0344900 Rorug05G0345000
rosa_samantha	Rh3AG149800 Rh3BG173400 Rh3CG164500 Rh3DG202000 Rh5AG405500 Rh5BG418300 Rh5CG442800 Rh5DG432400
rosa_wichuraiana	Rw5G038070

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	500
AciI	CCGC	1 cut(s)	554
AcsI	RAATTY	1 cut(s)	474
AcuI	CTGAAG	3 cut(s)	143, 384, 417
AfaI	GTAC	1 cut(s)	350
AgsI	TTSAA	5 cut(s)	140, 317, 440, 464, 608
AjnI	CCWGG	1 cut(s)	569
AluBI	AGCT	3 cut(s)	34, 208, 467
AluI	AGCT	3 cut(s)	34, 208, 467
Alw21I	GWGCWC	2 cut(s)	210, 395
AoxI	GGCC	1 cut(s)	601
ApeKI	GCWGC	2 cut(s)	445, 467
ApoI	RAATTY	1 cut(s)	474
AseI	ATTAAT	1 cut(s)	218
Asp700I	GAANNNNTTC	1 cut(s)	312
BanII	GRGCYC	1 cut(s)	210
Bbv12I	GWGCWC	2 cut(s)	210, 395
BbvI	GCAGC	2 cut(s)	454, 457
BccI	CCATC	2 cut(s)	401, 607
BciT130I	CCWGG	1 cut(s)	571
BciVI	GTATCC	1 cut(s)	236
BclI	TGATCA	1 cut(s)	658
BfmI	CTRYAG	2 cut(s)	69, 211
BfuI	GTATCC	1 cut(s)	236
BisI	GCNGC	2 cut(s)	446, 468
BlsI	GCNGC	2 cut(s)	447, 469
Bme1390I	CCNGG	1 cut(s)	571
BmrFI	CCNGG	1 cut(s)	571
BmsI	GCATC	3 cut(s)	46, 534, 547
BsaBI	GATNNNNATC	1 cut(s)	660
BsaJI	CCNNGG	1 cut(s)	570
BsaXI	ACNNNNNCTCC	2 cut(s)	482, 512
Bse3DI	GCAATG	1 cut(s)	567
Bse8I	GATNNNNATC	1 cut(s)	660
BseBI	CCWGG	1 cut(s)	571
BseDI	CCNNGG	1 cut(s)	570
BseGI	GGATG	1 cut(s)	562
BseJI	GATNNNNATC	1 cut(s)	660
BseMI	GCAATG	1 cut(s)	567
BseMII	CTCAG	1 cut(s)	188
BseRI	GAGGAG	1 cut(s)	503
BseXI	GCAGC	2 cut(s)	454, 457
BsgI	GTGCAG	2 cut(s)	348, 464
BshFI	GGCC	1 cut(s)	603
BsiHKAI	GWGCWC	2 cut(s)	210, 395
BslFI	GGGAC	1 cut(s)	387
BsmFI	GGGAC	1 cut(s)	387
BsnI	GGCC	1 cut(s)	603
Bsp1286I	GDGCHC	2 cut(s)	210, 395
Bsp143I	GATC	2 cut(s)	532, 658
BspACI	CCGC	1 cut(s)	554
BspANI	GGCC	1 cut(s)	603
BspCNI	CTCAG	1 cut(s)	187
BspHI	TCATGA	1 cut(s)	45
BsrDI	GCAATG	1 cut(s)	567
BssECI	CCNNGG	1 cut(s)	570
BssMI	GATC	2 cut(s)	532, 658
BssNAI	GTATAC	1 cut(s)	501
Bst1107I	GTATAC	1 cut(s)	501
Bst2UI	CCWGG	1 cut(s)	571
Bst4CI	ACNGT	3 cut(s)	63, 244, 262
BstC8I	GCNNGC	1 cut(s)	19
BstDEI	CTNAG	1 cut(s)	174
BstF5I	GGATG	1 cut(s)	562
BstKTI	GATC	2 cut(s)	535, 661
BstMBI	GATC	2 cut(s)	532, 658
BstNI	CCWGG	1 cut(s)	571
BstNSI	RCATGY	1 cut(s)	21
BstSCI	CCNGG	1 cut(s)	569
BstSFI	CTRYAG	2 cut(s)	69, 211
BstV1I	GCAGC	2 cut(s)	454, 457
BstZ17I	GTATAC	1 cut(s)	501
BsuI	GTATCC	1 cut(s)	236
BsuRI	GGCC	1 cut(s)	603
BtsCI	GGATG	1 cut(s)	562
BtsIMutI	CAGTG	1 cut(s)	393
Cac8I	GCNNGC	1 cut(s)	19
CciI	TCATGA	1 cut(s)	45
CseI	GACGC	1 cut(s)	198
Csp6I	GTAC	1 cut(s)	349
CviAII	CATG	3 cut(s)	18, 46, 515
CviJI	RGCY	4 cut(s)	34, 208, 467, 603
CviKI_1	RGCY	4 cut(s)	34, 208, 467, 603
CviQI	GTAC	1 cut(s)	349
DdeI	CTNAG	1 cut(s)	174
DpnI	GATC	2 cut(s)	534, 660
DpnII	GATC	2 cut(s)	532, 658
DraI	TTTAAA	1 cut(s)	102
Ecl136II	GAGCTC	1 cut(s)	208
Eco24I	GRGCYC	1 cut(s)	210
Eco53kI	GAGCTC	1 cut(s)	208
Eco57I	CTGAAG	3 cut(s)	143, 384, 417
EcoICRI	GAGCTC	1 cut(s)	208
EcoRII	CCWGG	1 cut(s)	569
EcoT22I	ATGCAT	1 cut(s)	23
EcoT38I	GRGCYC	1 cut(s)	210
FaeI	CATG	3 cut(s)	21, 49, 518
FaqI	GGGAC	1 cut(s)	387
FatI	CATG	3 cut(s)	17, 45, 514
FauNDI	CATATG	1 cut(s)	540
FbaI	TGATCA	1 cut(s)	658
FblI	GTMKAC	1 cut(s)	500
Fnu4HI	GCNGC	2 cut(s)	446, 468
FokI	GGATG	1 cut(s)	569
FriOI	GRGCYC	1 cut(s)	210
Fsp4HI	GCNGC	2 cut(s)	446, 468
GluI	GCNGC	2 cut(s)	446, 468
HaeIII	GGCC	1 cut(s)	603
HgaI	GACGC	1 cut(s)	198
Hin1II	CATG	3 cut(s)	21, 49, 518
HindIII	AAGCTT	1 cut(s)	32
HinfI	GANTC	4 cut(s)	4, 49, 92, 114
Hpy166II	GTNNAC	1 cut(s)	501
Hpy188I	TCNGA	1 cut(s)	111
Hpy188III	TCNNGA	4 cut(s)	46, 53, 146, 176
Hpy8I	GTNNAC	1 cut(s)	501
HpyAV	CCTTC	3 cut(s)	359, 392, 614
HpyCH4III	ACNGT	3 cut(s)	63, 244, 262
HpyCH4V	TGCA	5 cut(s)	21, 59, 329, 445, 560
HpyF3I	CTNAG	1 cut(s)	174
Hsp92II	CATG	3 cut(s)	21, 49, 518
Ksp22I	TGATCA	1 cut(s)	658
Kzo9I	GATC	2 cut(s)	532, 658
LpnPI	CCDG	6 cut(s)	159, 161, 337, 365, 556, 583
Lsp1109I	GCAGC	2 cut(s)	454, 457
LweI	GCATC	3 cut(s)	46, 534, 547
MaeIII	GTNAC	1 cut(s)	238
MalI	GATC	2 cut(s)	534, 660
MboI	GATC	2 cut(s)	532, 658
MboII	GAAGA	1 cut(s)	320
MhlI	GDGCHC	2 cut(s)	210, 395
MluCI	AATT	2 cut(s)	96, 474
MnlI	CCTC	2 cut(s)	239, 481
Mph1103I	ATGCAT	1 cut(s)	23
MroXI	GAANNNNTTC	1 cut(s)	312
MseI	TTAA	5 cut(s)	101, 218, 321, 629, 669
MspR9I	CCNGG	1 cut(s)	571
MvaI	CCWGG	1 cut(s)	571
NdeI	CATATG	1 cut(s)	540
NdeII	GATC	2 cut(s)	532, 658
NlaIII	CATG	3 cut(s)	21, 49, 518
NsiI	ATGCAT	1 cut(s)	23
NspI	RCATGY	1 cut(s)	21
PaeI	GCATGC	1 cut(s)	21
PagI	TCATGA	1 cut(s)	45
PdmI	GAANNNNTTC	1 cut(s)	312
PfeI	GAWTC	3 cut(s)	49, 92, 114
PkrI	GCNGC	2 cut(s)	447, 469
PshBI	ATTAAT	1 cut(s)	218
Psp124BI	GAGCTC	1 cut(s)	210
Psp6I	CCWGG	1 cut(s)	569
PspGI	CCWGG	1 cut(s)	569
RsaI	GTAC	1 cut(s)	350
RsaNI	GTAC	1 cut(s)	349
SacI	GAGCTC	1 cut(s)	210
SaqAI	TTAA	5 cut(s)	101, 218, 321, 629, 669
SatI	GCNGC	2 cut(s)	446, 468
Sau3AI	GATC	2 cut(s)	532, 658
ScrFI	CCNGG	1 cut(s)	571
SduI	GDGCHC	2 cut(s)	210, 395
SetI	ASST	5 cut(s)	36, 210, 328, 356, 469
SfaNI	GCATC	3 cut(s)	46, 534, 547
SfcI	CTRYAG	2 cut(s)	69, 211
SphI	GCATGC	1 cut(s)	21
Sse9I	AATT	2 cut(s)	96, 474
SsiI	CCGC	1 cut(s)	554
SspI	AATATT	1 cut(s)	136
SstI	GAGCTC	1 cut(s)	210
StyD4I	CCNGG	1 cut(s)	569
TaaI	ACNGT	3 cut(s)	63, 244, 262
TaqI	TCGA	1 cut(s)	52
TasI	AATT	2 cut(s)	96, 474
TatI	WGTACW	1 cut(s)	348
TfiI	GAWTC	3 cut(s)	49, 92, 114
Tru1I	TTAA	5 cut(s)	101, 218, 321, 629, 669
Tru9I	TTAA	5 cut(s)	101, 218, 321, 629, 669
TscAI	CASTG	1 cut(s)	400
TseI	GCWGC	2 cut(s)	445, 467
TspDTI	ATGAA	4 cut(s)	297, 521, 536, 630
TspRI	CASTG	1 cut(s)	400
VspI	ATTAAT	1 cut(s)	218
XapI	RAATTY	1 cut(s)	474
XceI	RCATGY	1 cut(s)	21
XmiI	GTMKAC	1 cut(s)	500
XmnI	GAANNNNTTC	1 cut(s)	312
Zsp2I	ATGCAT	1 cut(s)	23

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