Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000001

Orthogroup ID

OG0010170

Physical Location & Seq

Genomic Coordinates Reverse (-)

21416419 .. 21423289

Gene Structure 6871 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_1G00017270.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 600 bp

ATGTTCTACCTTAGCCGAATTGAGCACTCATTGCGCCTGCCTCCTTCTCTGCTTAGCTTTCGTCTACAAGATGCAGTTAAGGGAGAGCTTGAGAAGCTATTCTTAGATAAGGTTATCTCGAATTTGGGACTTTGCATTTCTGTCTATGATATCCAATCCATTAAAGATCACTTCATCTTACCAAATGATGGTCATCCAACTCTAACGGTGGTGTTCACACTGATTATGTTTCGTCCATTTGTGGGAGAGATAATTACTGCAAAAGTCATAGAGTCTACCGCTGATGGTTTACGTTTGTCACTTGGATTTTTTGATGATATTTATATACCTACTCATCGTTTTCCTACACCATGCCACAAGAAGGATGGCTCAAAAAAGAATGTTGTCTTATGGTATTGGAAGCCTTCTGATGATGAATTTTCAATTGATTTGAAGGACCAGATACGATTCCAGGTTGAAAGTGTAAACTATCCGAAAATTCCTATTGAGCAGCCAGAAAACTCAAAACCATTTGCCCCTATGGAGGTTAAAGGGTCAATTGATTTTGATGGTTTAGGGCCTGTTCATTGGTGGCAAGATGTAGATGAAGAAACTTCTTAA

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

199

Amino Acids

22.88

Weight (kDa)

5.21

Isoelectric Point (pI)

41.78

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
SHS2_Rpb7-N	PF03876	8 - 64	1.2e-11	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
RNA_pol_Rbc25	PF08292	83 - 191	8.7e-20	RNA polymerase III subunit Rpc25

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

Tree File

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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)	188
AccI	GTMKAC	2 cut(s)	64, 275
AciI	CCGC	1 cut(s)	279
AcsI	RAATTY	3 cut(s)	121, 416, 477
AfiI	CCNNNNNNNGG	4 cut(s)	188, 242, 361, 523
AgsI	TTSAA	3 cut(s)	423, 433, 458
AjnI	CCWGG	1 cut(s)	450
AluBI	AGCT	3 cut(s)	57, 88, 97
AluI	AGCT	3 cut(s)	57, 88, 97
Alw21I	GWGCWC	1 cut(s)	27
AoxI	GGCC	1 cut(s)	557
ApeKI	GCWGC	1 cut(s)	490
ApoI	RAATTY	3 cut(s)	121, 416, 477
Asp700I	GAANNNNTTC	1 cut(s)	98
AspLEI	GCGC	1 cut(s)	36
AspS9I	GGNCC	2 cut(s)	436, 557
AvaII	GGWCC	1 cut(s)	436
Bbv12I	GWGCWC	1 cut(s)	27
BbvI	GCAGC	1 cut(s)	502
BccI	CCATC	4 cut(s)	182, 278, 359, 542
BciT130I	CCWGG	1 cut(s)	452
BisI	GCNGC	1 cut(s)	491
BlpI	GCTNAGC	1 cut(s)	53
BlsI	GCNGC	1 cut(s)	492
Bme1390I	CCNGG	1 cut(s)	452
Bme18I	GGWCC	1 cut(s)	436
BmgT120I	GGNCC	2 cut(s)	436, 557
BmrFI	CCNGG	1 cut(s)	452
BmsI	GCATC	1 cut(s)	61
Bpu10I	CCTNAGC	1 cut(s)	11
Bpu1102I	GCTNAGC	1 cut(s)	53
BpuEI	CTTGAG	1 cut(s)	110
BsaBI	GATNNNNATC	1 cut(s)	192
Bsc4I	CCNNNNNNNGG	4 cut(s)	188, 242, 361, 523
Bse3DI	GCAATG	1 cut(s)	29
Bse8I	GATNNNNATC	1 cut(s)	192
BseBI	CCWGG	1 cut(s)	452
BseGI	GGATG	2 cut(s)	193, 370
BseJI	GATNNNNATC	1 cut(s)	192
BseLI	CCNNNNNNNGG	4 cut(s)	188, 242, 361, 523
BseMI	GCAATG	1 cut(s)	29
BseXI	GCAGC	1 cut(s)	502
BshFI	GGCC	1 cut(s)	559
BsiHKAI	GWGCWC	1 cut(s)	27
BslFI	GGGAC	1 cut(s)	141
BslI	CCNNNNNNNGG	4 cut(s)	188, 242, 361, 523
BsmFI	GGGAC	1 cut(s)	141
BsnI	GGCC	1 cut(s)	559
Bsp1286I	GDGCHC	1 cut(s)	27
Bsp143I	GATC	1 cut(s)	166
Bsp1720I	GCTNAGC	1 cut(s)	53
BspACI	CCGC	1 cut(s)	279
BspANI	GGCC	1 cut(s)	559
BsrDI	GCAATG	1 cut(s)	29
BssMI	GATC	1 cut(s)	166
Bst2UI	CCWGG	1 cut(s)	452
Bst4CI	ACNGT	1 cut(s)	208
BstAPI	GCANNNNNTGC	1 cut(s)	31
BstC8I	GCNNGC	1 cut(s)	38
BstDEI	CTNAG	3 cut(s)	11, 53, 103
BstF5I	GGATG	2 cut(s)	193, 370
BstHHI	GCGC	1 cut(s)	36
BstKTI	GATC	1 cut(s)	169
BstMBI	GATC	1 cut(s)	166
BstMWI	GCNNNNNNNGC	2 cut(s)	31, 94
BstNI	CCWGG	1 cut(s)	452
BstSCI	CCNGG	1 cut(s)	450
BstV1I	GCAGC	1 cut(s)	502
BsuRI	GGCC	1 cut(s)	559
BtsCI	GGATG	2 cut(s)	193, 370
BtsIMutI	CAGTG	1 cut(s)	218
Cac8I	GCNNGC	1 cut(s)	38
CfoI	GCGC	1 cut(s)	36
Cfr13I	GGNCC	2 cut(s)	436, 557
CviAII	CATG	1 cut(s)	351
CviJI	RGCY	8 cut(s)	15, 57, 88, 97, 369, 403, 493, 559
CviKI_1	RGCY	8 cut(s)	15, 57, 88, 97, 369, 403, 493, 559
DdeI	CTNAG	3 cut(s)	11, 53, 103
DpnI	GATC	1 cut(s)	168
DpnII	GATC	1 cut(s)	166
Eco32I	GATATC	1 cut(s)	151
Eco47I	GGWCC	1 cut(s)	436
EcoO109I	RGGNCCY	1 cut(s)	557
EcoRII	CCWGG	1 cut(s)	450
EcoRV	GATATC	1 cut(s)	151
FaeI	CATG	1 cut(s)	354
FaiI	YATR	8 cut(s)	147, 227, 269, 324, 326, 352, 391, 521
FalI	AAGNNNNNCTT	2 cut(s)	86, 118
FaqI	GGGAC	1 cut(s)	141
FatI	CATG	1 cut(s)	350
FblI	GTMKAC	2 cut(s)	64, 275
Fnu4HI	GCNGC	1 cut(s)	491
FokI	GGATG	2 cut(s)	180, 377
Fsp4HI	GCNGC	1 cut(s)	491
GlaI	GCGC	1 cut(s)	35
GluI	GCNGC	1 cut(s)	491
HaeIII	GGCC	1 cut(s)	559
HhaI	GCGC	1 cut(s)	36
Hin1II	CATG	1 cut(s)	354
Hin6I	GCGC	1 cut(s)	34
HinP1I	GCGC	1 cut(s)	34
HinfI	GANTC	2 cut(s)	272, 447
Hpy166II	GTNNAC	5 cut(s)	65, 216, 276, 290, 466
Hpy188I	TCNGA	2 cut(s)	409, 474
Hpy188III	TCNNGA	1 cut(s)	118
Hpy8I	GTNNAC	5 cut(s)	65, 216, 276, 290, 466
HpyAV	CCTTC	4 cut(s)	54, 355, 414, 427
HpyCH4III	ACNGT	1 cut(s)	208
HpyCH4IV	ACGT	1 cut(s)	292
HpyCH4V	TGCA	3 cut(s)	74, 135, 260
HpyF10VI	GCNNNNNNNGC	2 cut(s)	31, 94
HpyF3I	CTNAG	3 cut(s)	11, 53, 103
HpySE526I	ACGT	1 cut(s)	292
Hsp92II	CATG	1 cut(s)	354
HspAI	GCGC	1 cut(s)	34
Kzo9I	GATC	1 cut(s)	166
LpnPI	CCDG	6 cut(s)	50, 437, 452, 464, 507, 573
Lsp1109I	GCAGC	1 cut(s)	502
LweI	GCATC	1 cut(s)	61
MaeII	ACGT	1 cut(s)	292
MaeIII	GTNAC	1 cut(s)	297
MalI	GATC	1 cut(s)	168
MboI	GATC	1 cut(s)	166
MboII	GAAGA	1 cut(s)	599
MfeI	CAATTG	2 cut(s)	423, 537
MhlI	GDGCHC	1 cut(s)	27
MluCI	AATT	7 cut(s)	18, 121, 252, 416, 423, 477, 537
MlyI	GAGTC	1 cut(s)	281
MmeI	TCCRAC	1 cut(s)	221
MnlI	CCTC	2 cut(s)	51, 517
MroXI	GAANNNNTTC	1 cut(s)	98
MseI	TTAA	4 cut(s)	78, 162, 528, 598
MspA1I	CMGCKG	1 cut(s)	281
MspR9I	CCNGG	1 cut(s)	452
MunI	CAATTG	2 cut(s)	423, 537
MvaI	CCWGG	1 cut(s)	452
MwoI	GCNNNNNNNGC	2 cut(s)	31, 94
NdeII	GATC	1 cut(s)	166
NlaIII	CATG	1 cut(s)	354
NmuCI	GTSAC	1 cut(s)	297
PdmI	GAANNNNTTC	1 cut(s)	98
PfeI	GAWTC	1 cut(s)	447
PflMI	CCANNNNNTGG	1 cut(s)	188
PkrI	GCNGC	1 cut(s)	492
PleI	GAGTC	1 cut(s)	280
PpsI	GAGTC	1 cut(s)	280
Psp6I	CCWGG	1 cut(s)	450
PspGI	CCWGG	1 cut(s)	450
PspPI	GGNCC	2 cut(s)	436, 557
SaqAI	TTAA	4 cut(s)	78, 162, 528, 598
SatI	GCNGC	1 cut(s)	491
Sau3AI	GATC	1 cut(s)	166
Sau96I	GGNCC	2 cut(s)	436, 557
SchI	GAGTC	1 cut(s)	281
ScrFI	CCNGG	1 cut(s)	452
SduI	GDGCHC	1 cut(s)	27
SetI	ASST	9 cut(s)	12, 59, 90, 99, 114, 295, 331, 456, 528
SfaNI	GCATC	1 cut(s)	61
SinI	GGWCC	1 cut(s)	436
SmlI	CTYRAG	1 cut(s)	89
SmoI	CTYRAG	1 cut(s)	89
Sse9I	AATT	7 cut(s)	18, 121, 252, 416, 423, 477, 537
SsiI	CCGC	1 cut(s)	279
StyD4I	CCNGG	1 cut(s)	450
TaaI	ACNGT	1 cut(s)	208
TaiI	ACGT	1 cut(s)	295
TaqI	TCGA	1 cut(s)	119
TasI	AATT	7 cut(s)	18, 121, 252, 416, 423, 477, 537
TfiI	GAWTC	1 cut(s)	447
Tru1I	TTAA	4 cut(s)	78, 162, 528, 598
Tru9I	TTAA	4 cut(s)	78, 162, 528, 598
TscAI	CASTG	1 cut(s)	225
TseFI	GTSAC	1 cut(s)	297
TseI	GCWGC	1 cut(s)	490
Tsp45I	GTSAC	1 cut(s)	297
TspDTI	ATGAA	4 cut(s)	163, 429, 554, 600
TspRI	CASTG	1 cut(s)	225
Van91I	CCANNNNNTGG	1 cut(s)	188
VpaK11BI	GGWCC	1 cut(s)	436
XapI	RAATTY	3 cut(s)	121, 416, 477
XcmI	CCANNNNNNNNNTGG	1 cut(s)	362
XmiI	GTMKAC	2 cut(s)	64, 275
XmnI	GAANNNNTTC	1 cut(s)	98

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