Basic Information

Type: gene

Biological Identity

Species

rosa_wichuraiana

Chromosome

Chr5

Orthogroup ID

OG0010170

Physical Location & Seq

Genomic Coordinates Forward (+)

69113237 .. 69118621

Gene Structure 5385 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rw5G039120.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 765 bp

ATGGAGCTGGTGATGGGAGCGATGATGGACTTTAAAATTCCAGAGGGGAGGATCCATGGAGGACCTCTCATCCTTAAATCTTACTCTTGGGGTTGGGGAGAGCAGAAGCCGGAACTCAGGAAGACGAGCAGTCGAAGCAGACCGGAGGACGGAGAAAAGCCAATGTTCTACCGTAGCCGAATTGAGCACTCATTGCGTCTGCCTCCTTCTCTGCTTAGCCTTCGTCTACAAGATGCAGTTAAGGGAGAGCTTGAGAAGCTATTCTTAGATAAGGTTATCTCGAATTTGGGACTTTGCATTTCTGTCTATGATATCCAATCCATTAAAGATCACTTCATCTTGCCAAATGATGGTCATCCAACTCTAACGGTGGTGTTCACACTGATTATGTTTCGTCCATTTGTGGGAGAGATAATTACTGCAAAAGTCATAGAGTCTACTGCCATGGTTTACGTTGTAATGTCACTGGGATTTTTTGATGATATTTATATACCTACTCATCGTTTTCCTACACCATGCCACAAGAAGGATGACTCAAAAAAGAATGTTGTCTTATGGTATTGGAAGCCTTCTGATGATGAATTTTCAATTGATTTGAAGGACCAGATACGATTCCAGGTTGAAAGTGTAAACTATCCTAAAATTCCAATTGAGCAGCCAGAAAACTCAAAACCATTTGCCCCTATGGAGGTTAAAGGGTCAATTGATTTTGATGGTTTAGGGCCTGTTCATTGGTGGCAAGATGTAGATGAAGAAGCTTCTTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000228 GO:0000428 GO:0000785 GO:0000790 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005694 GO:0006139 GO:0006351 GO:0006352 GO:0006383 GO:0006384 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0010467 GO:0016070 GO:0018130 GO:0019438 GO:0030880 GO:0031974 GO:0031981 GO:0032774 GO:0032991 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:0044427 GO:0044428 GO:0044446 GO:0044451 GO:0044454 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0090304 GO:0097659 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_Rbc25 SHS2_Rpb7-N

Protein Analysis

254

Amino Acids

29.22

Weight (kDa)

5.55

Isoelectric Point (pI)

44.97

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
SHS2_Rpb7-N	PF03876	62 - 118	8.3e-12	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
RNA_pol_Rbc25	PF08292	137 - 246	6.9e-17	RNA polymerase III subunit Rpc25

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

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Publication-ready

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Orthologous Genes (Group: OG0010170)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G06790 AT1G06790
fragaria_vesca	FvH4_1g22880
malus_domestica	MD08G1227600.v1.1
prunus_persica	Prupe.2G103200_v2.0.a1 Prupe.2G103200_v2.0.a1 Prupe.2G103200_v2.0.a1 Prupe.2G103200_v2.0.a1 Prupe.2G103200_v2.0.a1 Prupe.7G016800_v2.0.a1
rosa_chinensis	RchiOBHm_Chr5g0063451
rosa_laevigata	RLG00000022776 RLG00000035635
rosa_multiflora	Rmu_sc0016394.1_g000005
rosa_roxburghii	Rroxscaffold_1G00017270
rosa_rugosa	Rorug05G0357400
rosa_samantha	Rh5AG416500 Rh5BG431600 Rh5CG454900 Rh5DG445100
rosa_wichuraiana	Rw5G039120

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	350
AccI	GTMKAC	2 cut(s)	226, 437
AclWI	GGATC	2 cut(s)	46, 59
AcsI	RAATTY	4 cut(s)	36, 283, 581, 642
AfiI	CCNNNNNNNGG	5 cut(s)	149, 350, 404, 526, 688
AgsI	TTSAA	3 cut(s)	588, 598, 623
AhdI	GACNNNNNGTC	1 cut(s)	129
AjnI	CCWGG	1 cut(s)	615
AluBI	AGCT	4 cut(s)	7, 250, 259, 758
AluI	AGCT	4 cut(s)	7, 250, 259, 758
Alw21I	GWGCWC	1 cut(s)	189
AlwI	GGATC	2 cut(s)	46, 59
AoxI	GGCC	1 cut(s)	722
ApeKI	GCWGC	1 cut(s)	655
ApoI	RAATTY	4 cut(s)	36, 283, 581, 642
Asp700I	GAANNNNTTC	1 cut(s)	260
AspS9I	GGNCC	3 cut(s)	62, 601, 722
AsuHPI	GGTGA	1 cut(s)	22
AvaII	GGWCC	2 cut(s)	62, 601
BamHI	GGATCC	1 cut(s)	51
BbsI	GAAGAC	1 cut(s)	128
Bbv12I	GWGCWC	1 cut(s)	189
BbvI	GCAGC	1 cut(s)	667
BccI	CCATC	4 cut(s)	7, 19, 344, 707
BciT130I	CCWGG	1 cut(s)	617
BisI	GCNGC	1 cut(s)	656
BlpI	GCTNAGC	1 cut(s)	215
BlsI	GCNGC	1 cut(s)	657
Bme1390I	CCNGG	1 cut(s)	617
Bme18I	GGWCC	2 cut(s)	62, 601
BmeRI	GACNNNNNGTC	1 cut(s)	129
BmgT120I	GGNCC	3 cut(s)	62, 601, 722
BmiI	GGNNCC	1 cut(s)	53
BmrFI	CCNGG	1 cut(s)	617
BmrI	ACTGGG	1 cut(s)	476
BmsI	GCATC	1 cut(s)	223
BmuI	ACTGGG	1 cut(s)	476
BpiI	GAAGAC	1 cut(s)	128
BplI	GAGNNNNNCTC	2 cut(s)	51, 83
Bpu1102I	GCTNAGC	1 cut(s)	215
BpuEI	CTTGAG	1 cut(s)	272
BsaBI	GATNNNNATC	1 cut(s)	354
BsaJI	CCNNGG	2 cut(s)	55, 444
BsaWI	WCCGGW	1 cut(s)	142
Bsc4I	CCNNNNNNNGG	5 cut(s)	149, 350, 404, 526, 688
Bse1I	ACTGG	1 cut(s)	471
Bse3DI	GCAATG	1 cut(s)	191
Bse8I	GATNNNNATC	1 cut(s)	354
BseBI	CCWGG	1 cut(s)	617
BseDI	CCNNGG	2 cut(s)	55, 444
BseGI	GGATG	3 cut(s)	69, 355, 535
BseJI	GATNNNNATC	1 cut(s)	354
BseLI	CCNNNNNNNGG	5 cut(s)	149, 350, 404, 526, 688
BseMI	GCAATG	1 cut(s)	191
BseMII	CTCAG	1 cut(s)	130
BseNI	ACTGG	1 cut(s)	471
BseXI	GCAGC	1 cut(s)	667
BshFI	GGCC	1 cut(s)	724
BsiHKAI	GWGCWC	1 cut(s)	189
BsiSI	CCGG	2 cut(s)	110, 143
BslFI	GGGAC	1 cut(s)	303
BslI	CCNNNNNNNGG	5 cut(s)	149, 350, 404, 526, 688
BsmFI	GGGAC	1 cut(s)	303
BsnI	GGCC	1 cut(s)	724
Bsp1286I	GDGCHC	1 cut(s)	189
Bsp143I	GATC	2 cut(s)	51, 328
Bsp1720I	GCTNAGC	1 cut(s)	215
Bsp19I	CCATGG	2 cut(s)	55, 444
BspANI	GGCC	1 cut(s)	724
BspCNI	CTCAG	1 cut(s)	129
BspLI	GGNNCC	1 cut(s)	53
BspPI	GGATC	2 cut(s)	46, 59
BsrDI	GCAATG	1 cut(s)	191
BsrI	ACTGG	1 cut(s)	471
BssECI	CCNNGG	2 cut(s)	55, 444
BssMI	GATC	2 cut(s)	51, 328
BssT1I	CCWWGG	2 cut(s)	55, 444
Bst2UI	CCWGG	1 cut(s)	617
Bst4CI	ACNGT	2 cut(s)	173, 370
BstAPI	GCANNNNNTGC	1 cut(s)	193
BstDEI	CTNAG	3 cut(s)	116, 215, 265
BstDSI	CCRYGG	2 cut(s)	55, 444
BstF5I	GGATG	3 cut(s)	69, 355, 535
BstKTI	GATC	2 cut(s)	54, 331
BstMBI	GATC	2 cut(s)	51, 328
BstMWI	GCNNNNNNNGC	3 cut(s)	135, 193, 256
BstNI	CCWGG	1 cut(s)	617
BstSCI	CCNGG	1 cut(s)	615
BstV1I	GCAGC	1 cut(s)	667
BstV2I	GAAGAC	1 cut(s)	128
BstX2I	RGATCY	1 cut(s)	51
BstYI	RGATCY	1 cut(s)	51
BsuRI	GGCC	1 cut(s)	724
BtgI	CCRYGG	2 cut(s)	55, 444
BtgZI	GCGATG	1 cut(s)	35
BtsCI	GGATG	3 cut(s)	69, 355, 535
BtsIMutI	CAGTG	2 cut(s)	380, 464
Cfr13I	GGNCC	3 cut(s)	62, 601, 722
CseI	GACGC	1 cut(s)	185
CviAII	CATG	3 cut(s)	56, 445, 516
DdeI	CTNAG	3 cut(s)	116, 215, 265
DpnI	GATC	2 cut(s)	53, 330
DpnII	GATC	2 cut(s)	51, 328
DraI	TTTAAA	1 cut(s)	34
DriI	GACNNNNNGTC	1 cut(s)	129
Eam1105I	GACNNNNNGTC	1 cut(s)	129
Eco130I	CCWWGG	2 cut(s)	55, 444
Eco32I	GATATC	1 cut(s)	313
Eco47I	GGWCC	2 cut(s)	62, 601
EcoO109I	RGGNCCY	2 cut(s)	62, 722
EcoRII	CCWGG	1 cut(s)	615
EcoRV	GATATC	1 cut(s)	313
EcoT14I	CCWWGG	2 cut(s)	55, 444
ErhI	CCWWGG	2 cut(s)	55, 444
FaeI	CATG	3 cut(s)	59, 448, 519
FalI	AAGNNNNNCTT	2 cut(s)	248, 280
FaqI	GGGAC	1 cut(s)	303
FatI	CATG	3 cut(s)	55, 444, 515
FblI	GTMKAC	2 cut(s)	226, 437
Fnu4HI	GCNGC	1 cut(s)	656
FokI	GGATG	3 cut(s)	56, 342, 542
Fsp4HI	GCNGC	1 cut(s)	656
GluI	GCNGC	1 cut(s)	656
HaeIII	GGCC	1 cut(s)	724
HapII	CCGG	2 cut(s)	110, 143
HgaI	GACGC	1 cut(s)	185
Hin1II	CATG	3 cut(s)	59, 448, 519
HindIII	AAGCTT	1 cut(s)	756
HinfI	GANTC	3 cut(s)	434, 533, 612
HpaII	CCGG	2 cut(s)	110, 143
HphI	GGTGA	1 cut(s)	22
Hpy166II	GTNNAC	5 cut(s)	227, 378, 438, 451, 631
Hpy188I	TCNGA	1 cut(s)	574
Hpy188III	TCNNGA	3 cut(s)	41, 118, 280
Hpy8I	GTNNAC	5 cut(s)	227, 378, 438, 451, 631
HpyAV	CCTTC	5 cut(s)	216, 230, 520, 579, 592
HpyCH4III	ACNGT	2 cut(s)	173, 370
HpyCH4IV	ACGT	1 cut(s)	453
HpyCH4V	TGCA	3 cut(s)	236, 297, 422
HpyF10VI	GCNNNNNNNGC	3 cut(s)	135, 193, 256
HpyF3I	CTNAG	3 cut(s)	116, 215, 265
HpySE526I	ACGT	1 cut(s)	453
Hsp92II	CATG	3 cut(s)	59, 448, 519
Kzo9I	GATC	2 cut(s)	51, 328
LmnI	GCTCC	2 cut(s)	4, 17
Lsp1109I	GCAGC	1 cut(s)	667
LweI	GCATC	1 cut(s)	223
MaeII	ACGT	1 cut(s)	453
MaeIII	GTNAC	1 cut(s)	462
MalI	GATC	2 cut(s)	53, 330
MboI	GATC	2 cut(s)	51, 328
MboII	GAAGA	2 cut(s)	133, 764
MfeI	CAATTG	3 cut(s)	588, 648, 702
MflI	RGATCY	1 cut(s)	51
MhlI	GDGCHC	1 cut(s)	189
MluCI	AATT	9 cut(s)	36, 180, 283, 414, 581, 588, 642, 648, 702
MlyI	GAGTC	2 cut(s)	443, 527
MmeI	TCCRAC	1 cut(s)	383
MnlI	CCTC	7 cut(s)	37, 42, 53, 75, 139, 213, 682
MroXI	GAANNNNTTC	1 cut(s)	260
MseI	TTAA	6 cut(s)	33, 75, 240, 324, 693, 763
MspI	CCGG	2 cut(s)	110, 143
MspR9I	CCNGG	1 cut(s)	617
MunI	CAATTG	3 cut(s)	588, 648, 702
MvaI	CCWGG	1 cut(s)	617
MwoI	GCNNNNNNNGC	3 cut(s)	135, 193, 256
NcoI	CCATGG	2 cut(s)	55, 444
NdeII	GATC	2 cut(s)	51, 328
NlaIII	CATG	3 cut(s)	59, 448, 519
NlaIV	GGNNCC	1 cut(s)	53
NmuCI	GTSAC	1 cut(s)	462
PdmI	GAANNNNTTC	1 cut(s)	260
PfeI	GAWTC	1 cut(s)	612
PflMI	CCANNNNNTGG	1 cut(s)	350
PkrI	GCNGC	1 cut(s)	657
PleI	GAGTC	2 cut(s)	442, 527
PpsI	GAGTC	2 cut(s)	442, 527
PpuMI	RGGWCCY	1 cut(s)	62
Psp5II	RGGWCCY	1 cut(s)	62
Psp6I	CCWGG	1 cut(s)	615
PspGI	CCWGG	1 cut(s)	615
PspN4I	GGNNCC	1 cut(s)	53
PspPI	GGNCC	3 cut(s)	62, 601, 722
PspPPI	RGGWCCY	1 cut(s)	62
PsuI	RGATCY	1 cut(s)	51
SaqAI	TTAA	6 cut(s)	33, 75, 240, 324, 693, 763
SatI	GCNGC	1 cut(s)	656
Sau3AI	GATC	2 cut(s)	51, 328
Sau96I	GGNCC	3 cut(s)	62, 601, 722
SchI	GAGTC	2 cut(s)	443, 527
ScrFI	CCNGG	1 cut(s)	617
SduI	GDGCHC	1 cut(s)	189
SfaNI	GCATC	1 cut(s)	223
SinI	GGWCC	2 cut(s)	62, 601
SmlI	CTYRAG	1 cut(s)	251
SmoI	CTYRAG	1 cut(s)	251
Sse9I	AATT	9 cut(s)	36, 180, 283, 414, 581, 588, 642, 648, 702
StyD4I	CCNGG	1 cut(s)	615
StyI	CCWWGG	2 cut(s)	55, 444
TaaI	ACNGT	2 cut(s)	173, 370
TaiI	ACGT	1 cut(s)	456
TaqI	TCGA	2 cut(s)	133, 281
TasI	AATT	9 cut(s)	36, 180, 283, 414, 581, 588, 642, 648, 702
TfiI	GAWTC	1 cut(s)	612
Tru1I	TTAA	6 cut(s)	33, 75, 240, 324, 693, 763
Tru9I	TTAA	6 cut(s)	33, 75, 240, 324, 693, 763
TscAI	CASTG	2 cut(s)	387, 471
TseFI	GTSAC	1 cut(s)	462
TseI	GCWGC	1 cut(s)	655
Tsp45I	GTSAC	1 cut(s)	462
TspDTI	ATGAA	4 cut(s)	325, 594, 719, 765
TspGWI	ACGGA	1 cut(s)	165
TspRI	CASTG	2 cut(s)	387, 471
Van91I	CCANNNNNTGG	1 cut(s)	350
VpaK11BI	GGWCC	2 cut(s)	62, 601
XapI	RAATTY	4 cut(s)	36, 283, 581, 642
XmiI	GTMKAC	2 cut(s)	226, 437
XmnI	GAANNNNTTC	1 cut(s)	260

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