Basic Information

Type: gene

Biological Identity

Species

rosa_wichuraiana

Chromosome

Chr6

Orthogroup ID

OG0003037

Physical Location & Seq

Genomic Coordinates Reverse (-)

23867453 .. 23873380

Gene Structure 5928 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rw6G012910.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 885 bp

ATGGAGGATTTCGCATCTCCGAATGGGAAAAGGAAAAGGAAATTGAAGAAGAAGCAACCGCTTTCACCACAGCCACTCTATCAGGTTTGCCGATCTTATCTTGAAAGCAGAGAAGCAAATGCTTGGCTTCAATGTGCCATAATACACGTCATTGAGGTTTTAATTGATTTCTCAAGGGATTTTTCGAGTACGATTGGGAATCTTGCTCGTGTATTTTTCTTCCTTGATTTTGCGAGAATTTTGGGAAAGTATTTTTATATTGGTTTTCGAATTTGTTTTTCTTCACCATACTTGGATTGTTATATTTTATCTTTAGCTAGCTCATTGCTCCTCTTCACAACACCTTTCTATTTGGATCTCTCTCACCATCCTCTCTCTCTATCTCTGTGCGAAACCCCTATCTCTCCTTGGGGTAATGAGAAGGAATTTGTTGAGGATGCTGCAAAGGAGTATGATGAGAGTACTATTACTTGTGCTTCAGAACTCGGGCTGCTGGAGCAAAATGCCAAAGAGAAGTTGCTCTTTGTTCAGTTGCCTCCTACTCTACCATTGGTCAAGCGACCAACTAGTGCAAAGGGGAAAGAGAAAGTCGGAAGCTCAGCACCATCAGAGAAGGTAGGTGCTGCAAGGAAGGGCGGTAGTTTGGAAGAGTTATCTGAGGGGTATGTGGGGAAGAAGCTGGTTTACAAGAGTGGAGCAGTCAAGTTCAAAATAGGAGATGCACTGTATGATGTTTCACCCGGTTCAGATTGTATATTTGCTCAAGATGTTGCTGCAATCAACACTGCAGCGAGAAAGTGTTGTGTTCTTGGAGAGCTTGGCCAGCAAGTTGTTATAACTCCTGATGTGGATTCCCTACTAGACGCAACGATTGAGTTGGACTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0001817 GO:0001819 GO:0002682 GO:0002684 GO:0003674 GO:0003682 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005737 GO:0005829 GO:0008150 GO:0016604 GO:0016607 GO:0030880 GO:0031347 GO:0031349 GO:0031974 GO:0031981 GO:0032479 GO:0032481 GO:0032648 GO:0032728 GO:0032991 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0045088 GO:0045089 GO:0048518 GO:0048583 GO:0048584 GO:0050776 GO:0050778 GO:0050789 GO:0051239 GO:0051240 GO:0055029 GO:0061695 GO:0065007 GO:0070013 GO:0080134 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_Rpc4

Protein Analysis

294

Amino Acids

32.49

Weight (kDa)

6.03

Isoelectric Point (pI)

40.9

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpc4	PF05132	171 - 283	1.9e-23	RNA polymerase III RPC4

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Publication-ready

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Orthologous Genes (Group: OG0003037)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G09380 AT5G09380 AT5G09380
fragaria_vesca	FvH4_1g08400 FvH4_1g08400 FvH4_7g27240 FvH4_7g27240
malus_domestica	MD01G1181300.v1.1 MD02G1088300.v1.1 MD07G1251400.v1.1
prunus_persica	Prupe.2G275200_v2.0.a1 Prupe.7G201300_v2.0.a1
pyrus_communis	pycom02g07090 pycom07g22410
rosa_chinensis	RchiOBHm_Chr1g0374021 RchiOBHm_Chr2g0094511 RchiOBHm_Chr3g0487921
rosa_laevigata	RLG00000016497 RLG00000026785
rosa_multiflora	Rmu_sc0004359.1_g000044 Rmu_sc0006924.1_g000006 Rmu_sc0009793.1_g000002
rosa_roxburghii	Rroxscaffold_2G00147110 Rroxscaffold_4G00283820
rosa_rugosa	Rorug01G0380300 Rorug02G0044300.1
rosa_samantha	Rh1AG390800 Rh1BG354900 Rh1CG368000 Rh1DG385600 Rh2AG092600 Rh2BG092800 Rh2CG095300 Rh2DG091700 Rh3AG285100 Rh6AG149200
rosa_wichuraiana	Rw1G034440 Rw6G012910

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	836
AciI	CCGC	2 cut(s)	59, 636
AclWI	GGATC	1 cut(s)	363
AcoI	YGGCCR	1 cut(s)	820
AcsI	RAATTY	3 cut(s)	237, 270, 425
AcuI	CTGAAG	1 cut(s)	462
AfaI	GTAC	2 cut(s)	190, 463
AflIII	ACRYGT	1 cut(s)	145
AgsI	TTSAA	4 cut(s)	46, 104, 131, 709
AhlI	ACTAGT	1 cut(s)	566
AjiI	CACGTC	1 cut(s)	148
AluBI	AGCT	5 cut(s)	317, 321, 597, 679, 817
AluI	AGCT	5 cut(s)	317, 321, 597, 679, 817
AlwI	GGATC	1 cut(s)	363
Ama87I	CYCGRG	1 cut(s)	485
AoxI	GGCC	1 cut(s)	820
ApeKI	GCWGC	5 cut(s)	440, 490, 623, 773, 788
ApoI	RAATTY	3 cut(s)	237, 270, 425
AsuC2I	CCSGG	1 cut(s)	741
AsuHPI	GGTGA	4 cut(s)	57, 276, 356, 729
AsuII	TTCGAA	1 cut(s)	268
AsuNHI	GCTAGC	1 cut(s)	317
AvaI	CYCGRG	1 cut(s)	485
BalI	TGGCCA	1 cut(s)	822
BarI	GAAGNNNNNNTAC	2 cut(s)	668, 700
BauI	CACGAG	1 cut(s)	207
BbvI	GCAGC	5 cut(s)	427, 477, 610, 760, 800
BccI	CCATC	2 cut(s)	375, 613
BcnI	CCSGG	1 cut(s)	741
BcuI	ACTAGT	1 cut(s)	566
BfaI	CTAG	3 cut(s)	318, 567, 860
BfmI	CTRYAG	1 cut(s)	786
BisI	GCNGC	5 cut(s)	441, 491, 624, 774, 789
BlpI	GCTNAGC	1 cut(s)	598
BlsI	GCNGC	5 cut(s)	442, 492, 625, 775, 790
BmcAI	AGTACT	1 cut(s)	463
Bme1390I	CCNGG	1 cut(s)	741
BmeT110I	CYCGRG	1 cut(s)	485
BmgBI	CACGTC	1 cut(s)	148
BmrFI	CCNGG	1 cut(s)	741
BmsI	GCATC	3 cut(s)	23, 427, 709
BmtI	GCTAGC	1 cut(s)	321
BpmI	CTGGAG	1 cut(s)	515
Bpu1102I	GCTNAGC	1 cut(s)	598
Bpu14I	TTCGAA	1 cut(s)	268
BpuEI	CTTGAG	2 cut(s)	157, 747
BpuMI	CCSGG	1 cut(s)	741
BsaJI	CCNNGG	1 cut(s)	407
Bse3DI	GCAATG	1 cut(s)	323
BseDI	CCNNGG	1 cut(s)	407
BseGI	GGATG	2 cut(s)	367, 442
BseMI	GCAATG	1 cut(s)	323
BseMII	CTCAG	2 cut(s)	612, 648
BseRI	GAGGAG	1 cut(s)	320
BseXI	GCAGC	5 cut(s)	427, 477, 610, 760, 800
BshFI	GGCC	1 cut(s)	822
BsiHKCI	CYCGRG	1 cut(s)	485
BsiSI	CCGG	1 cut(s)	741
BsnI	GGCC	1 cut(s)	822
BsoBI	CYCGRG	1 cut(s)	485
Bsp119I	TTCGAA	1 cut(s)	268
Bsp143I	GATC	2 cut(s)	92, 355
Bsp1720I	GCTNAGC	1 cut(s)	598
BspACI	CCGC	2 cut(s)	59, 636
BspANI	GGCC	1 cut(s)	822
BspCNI	CTCAG	2 cut(s)	611, 649
BspMAI	CTGCAG	1 cut(s)	790
BspOI	GCTAGC	1 cut(s)	321
BspPI	GGATC	1 cut(s)	363
BspT104I	TTCGAA	1 cut(s)	268
BsrDI	GCAATG	1 cut(s)	323
BssECI	CCNNGG	1 cut(s)	407
BssMI	GATC	2 cut(s)	92, 355
BssSI	CACGAG	1 cut(s)	207
BssT1I	CCWWGG	1 cut(s)	407
Bst2BI	CACGAG	1 cut(s)	207
Bst4CI	ACNGT	1 cut(s)	726
Bst6I	CTCTTC	2 cut(s)	338, 642
BstBI	TTCGAA	1 cut(s)	268
BstC8I	GCNNGC	2 cut(s)	319, 824
BstDEI	CTNAG	2 cut(s)	598, 657
BstF5I	GGATG	2 cut(s)	367, 442
BstKTI	GATC	2 cut(s)	95, 358
BstMBI	GATC	2 cut(s)	92, 355
BstMWI	GCNNNNNNNGC	2 cut(s)	496, 823
BstSCI	CCNGG	1 cut(s)	739
BstSFI	CTRYAG	1 cut(s)	786
BstV1I	GCAGC	5 cut(s)	427, 477, 610, 760, 800
BstX2I	RGATCY	1 cut(s)	355
BstYI	RGATCY	1 cut(s)	355
BsuRI	GGCC	1 cut(s)	822
BtrI	CACGTC	1 cut(s)	148
BtsCI	GGATG	2 cut(s)	367, 442
BtsI	GCAGTG	1 cut(s)	783
BtsIMutI	CAGTG	2 cut(s)	722, 783
Cac8I	GCNNGC	2 cut(s)	319, 824
CseI	GACGC	1 cut(s)	872
Csp6I	GTAC	2 cut(s)	189, 462
CviJI	RGCY	9 cut(s)	73, 127, 317, 321, 490, 597, 679, 817, 822
CviKI_1	RGCY	9 cut(s)	73, 127, 317, 321, 490, 597, 679, 817, 822
CviQI	GTAC	2 cut(s)	189, 462
DdeI	CTNAG	2 cut(s)	598, 657
DpnI	GATC	2 cut(s)	94, 357
DpnII	GATC	2 cut(s)	92, 355
EaeI	YGGCCR	1 cut(s)	820
Eam1104I	CTCTTC	2 cut(s)	338, 642
EarI	CTCTTC	2 cut(s)	338, 642
Eco130I	CCWWGG	1 cut(s)	407
Eco57I	CTGAAG	1 cut(s)	462
Eco88I	CYCGRG	1 cut(s)	485
EcoT14I	CCWWGG	1 cut(s)	407
ErhI	CCWWGG	1 cut(s)	407
FaiI	YATR	9 cut(s)	140, 258, 289, 303, 453, 666, 729, 755, 836
FalI	AAGNNNNNCTT	2 cut(s)	506, 538
Fnu4HI	GCNGC	5 cut(s)	441, 491, 624, 774, 789
FokI	GGATG	2 cut(s)	354, 449
Fsp4HI	GCNGC	5 cut(s)	441, 491, 624, 774, 789
FspBI	CTAG	3 cut(s)	318, 567, 860
GluI	GCNGC	5 cut(s)	441, 491, 624, 774, 789
GsuI	CTGGAG	1 cut(s)	515
HaeIII	GGCC	1 cut(s)	822
HapII	CCGG	1 cut(s)	741
HgaI	GACGC	1 cut(s)	872
HinfI	GANTC	2 cut(s)	199, 851
HpaII	CCGG	1 cut(s)	741
HphI	GGTGA	4 cut(s)	57, 276, 356, 729
Hpy166II	GTNNAC	1 cut(s)	685
Hpy188I	TCNGA	6 cut(s)	21, 481, 593, 610, 658, 748
Hpy188III	TCNNGA	3 cut(s)	101, 764, 842
Hpy8I	GTNNAC	1 cut(s)	685
HpyAV	CCTTC	3 cut(s)	415, 607, 625
HpyCH4III	ACNGT	1 cut(s)	726
HpyCH4IV	ACGT	1 cut(s)	147
HpyCH4V	TGCA	6 cut(s)	443, 572, 626, 722, 776, 788
HpyF10VI	GCNNNNNNNGC	2 cut(s)	496, 823
HpyF3I	CTNAG	2 cut(s)	598, 657
HpySE526I	ACGT	1 cut(s)	147
Kzo9I	GATC	2 cut(s)	92, 355
LmnI	GCTCC	3 cut(s)	333, 496, 695
LpnPI	CCDG	6 cut(s)	68, 479, 665, 754, 836, 855
Lsp1109I	GCAGC	5 cut(s)	427, 477, 610, 760, 800
LweI	GCATC	3 cut(s)	23, 427, 709
MaeI	CTAG	3 cut(s)	318, 567, 860
MaeII	ACGT	1 cut(s)	147
MalI	GATC	2 cut(s)	94, 357
MboI	GATC	2 cut(s)	92, 355
MboII	GAAGA	7 cut(s)	58, 61, 211, 273, 325, 659, 685
MflI	RGATCY	1 cut(s)	355
MlsI	TGGCCA	1 cut(s)	822
MluCI	AATT	5 cut(s)	41, 162, 237, 270, 425
MluNI	TGGCCA	1 cut(s)	822
MmeI	TCCRAC	2 cut(s)	571, 858
MnlI	CCTC	6 cut(s)	148, 341, 381, 427, 546, 652
Mox20I	TGGCCA	1 cut(s)	822
MscI	TGGCCA	1 cut(s)	822
MseI	TTAA	1 cut(s)	161
Msp20I	TGGCCA	1 cut(s)	822
MspI	CCGG	1 cut(s)	741
MspR9I	CCNGG	1 cut(s)	741
MwoI	GCNNNNNNNGC	2 cut(s)	496, 823
NciI	CCSGG	1 cut(s)	741
NdeII	GATC	2 cut(s)	92, 355
NheI	GCTAGC	1 cut(s)	317
NspV	TTCGAA	1 cut(s)	268
PfeI	GAWTC	2 cut(s)	199, 851
PkrI	GCNGC	5 cut(s)	442, 492, 625, 775, 790
PsiI	TTATAA	1 cut(s)	836
PstI	CTGCAG	1 cut(s)	790
PsuI	RGATCY	1 cut(s)	355
RsaI	GTAC	2 cut(s)	190, 463
RsaNI	GTAC	2 cut(s)	189, 462
SaqAI	TTAA	1 cut(s)	161
SatI	GCNGC	5 cut(s)	441, 491, 624, 774, 789
Sau3AI	GATC	2 cut(s)	92, 355
ScaI	AGTACT	1 cut(s)	463
ScrFI	CCNGG	1 cut(s)	741
SfaNI	GCATC	3 cut(s)	23, 427, 709
SfcI	CTRYAG	1 cut(s)	786
SfuI	TTCGAA	1 cut(s)	268
SmlI	CTYRAG	2 cut(s)	172, 762
SmoI	CTYRAG	2 cut(s)	172, 762
SpeI	ACTAGT	1 cut(s)	566
Sse9I	AATT	5 cut(s)	41, 162, 237, 270, 425
SsiI	CCGC	2 cut(s)	59, 636
SspMI	CTAG	3 cut(s)	318, 567, 860
StyD4I	CCNGG	1 cut(s)	739
StyI	CCWWGG	1 cut(s)	407
TaaI	ACNGT	1 cut(s)	726
TaiI	ACGT	1 cut(s)	150
TaqI	TCGA	2 cut(s)	185, 268
TasI	AATT	5 cut(s)	41, 162, 237, 270, 425
TatI	WGTACW	1 cut(s)	461
TfiI	GAWTC	2 cut(s)	199, 851
Tru1I	TTAA	1 cut(s)	161
Tru9I	TTAA	1 cut(s)	161
TscAI	CASTG	2 cut(s)	729, 790
TseI	GCWGC	5 cut(s)	440, 490, 623, 773, 788
TspRI	CASTG	2 cut(s)	729, 790
XapI	RAATTY	3 cut(s)	237, 270, 425
XspI	CTAG	3 cut(s)	318, 567, 860
ZrmI	AGTACT	1 cut(s)	463

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