Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr2A

Orthogroup ID

OG0003037

Physical Location & Seq

Genomic Coordinates Reverse (-)

7776471 .. 7778410

Gene Structure 1940 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh2AG092600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 828 bp

ATGCAGAGGAGGTTCATACCAAAAGGATCTCGCCCGAAGGCTGAAGTTAAACCCGACCCGGAGGAGGAAGAGCAAGCTAGTCATGCTGAAAAGGAGAGGGAGCTGCTCAGACGTTTCCATGAACAATCTTTGAGGGTAAAGCCGAAAAACGAAAAGAAAGAGAAGCCTGTGGAAGTTGCATTTGGTTCTGGGGGTCAATCATCATCCACCATAAGATCATATGGGGCTCCCAGGGGTGCTAATGGTGGTGGTTTTAACCCGGTCATTCAAGAGGAGAAAGAATACAAGTCACCATTTGATATCTACGGTCATTACCCTATATCTCTTCCTCTGAGGCAGCCATCTTATGAAGATCCTGCAATTCTTAACCAGCAAGAATTTGGGGATGGTTCAGAGGAATCAATTTATGATGAAAATGCAACACCAGCGGCAGATGATCTTGATCTAAAGGAGGAAAATAGAGCAACAAGTATGTTCTTTCTTCATCTACCACCGACCTTGCCTATTTTAAAGCAACCAGCAGGCCAACAGGTAACCAGTAGCTCAGGGGCACCGGGAGGAGCACATAATACAGAGAAGCCTTGTTCTTTGGGTGAGTTACCAGCTGGCTTCATGGGTAAGATGCTGGTGTACAGAAGTGGTGCTATCAAGCTGAAGCTAGGAGACACCCTCTATGATGTCTCTACAGGAATGAACTGTGATTTTGCCCAGGATGTTGTGGCTATTAATACCACAGAGAAGAAGTGTTGCACTATTGGGGAGCTCAACAAGCGAGCTGTTGTGACCCCAGATATTGACTCTGTTTTGAACAGTTTAGAGGATTTATGA

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

275

Amino Acids

30.21

Weight (kDa)

5.23

Isoelectric Point (pI)

59.11

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpc4	PF05132	157 - 265	2.2e-25	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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Align Labels (Cladogram)

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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)
AccB1I	GGYRCC	1 cut(s)	550
AciI	CCGC	1 cut(s)	428
AclWI	GGATC	2 cut(s)	34, 347
AcsI	RAATTY	1 cut(s)	377
AcuI	CTGAAG	2 cut(s)	63, 674
AfaI	GTAC	1 cut(s)	632
AfiI	CCNNNNNNNGG	1 cut(s)	64
AgsI	TTSAA	2 cut(s)	269, 808
AjnI	CCWGG	2 cut(s)	230, 708
AjuI	GAANNNNNNNTTGG	2 cut(s)	165, 197
AluBI	AGCT	8 cut(s)	77, 103, 543, 605, 652, 658, 763, 776
AluI	AGCT	8 cut(s)	77, 103, 543, 605, 652, 658, 763, 776
Alw21I	GWGCWC	2 cut(s)	565, 765
Alw26I	GTCTC	2 cut(s)	657, 685
AlwI	GGATC	2 cut(s)	34, 347
AoxI	GGCC	1 cut(s)	523
ApeKI	GCWGC	2 cut(s)	103, 337
ApoI	RAATTY	1 cut(s)	377
AseI	ATTAAT	1 cut(s)	726
AsuC2I	CCSGG	3 cut(s)	59, 260, 555
AsuHPI	GGTGA	2 cut(s)	282, 605
BaeGI	GKGCMC	1 cut(s)	553
BanI	GGYRCC	1 cut(s)	550
BanII	GRGCYC	2 cut(s)	229, 765
Bbv12I	GWGCWC	2 cut(s)	565, 765
BbvI	GCAGC	2 cut(s)	90, 349
BccI	CCATC	2 cut(s)	349, 380
BciT130I	CCWGG	2 cut(s)	232, 710
BcnI	CCSGG	3 cut(s)	59, 260, 555
BcoDI	GTCTC	2 cut(s)	657, 685
BfaI	CTAG	2 cut(s)	78, 659
BfmI	CTRYAG	1 cut(s)	684
BisI	GCNGC	3 cut(s)	104, 338, 429
BlsI	GCNGC	3 cut(s)	105, 339, 430
Bme1390I	CCNGG	5 cut(s)	59, 232, 260, 555, 710
BmiI	GGNNCC	2 cut(s)	228, 552
BmrFI	CCNGG	5 cut(s)	59, 232, 260, 555, 710
BmsI	GCATC	1 cut(s)	612
BplI	GAGNNNNNCTC	2 cut(s)	654, 686
Bpu10I	CCTNAGC	1 cut(s)	544
BpuMI	CCSGG	3 cut(s)	59, 260, 555
BsaBI	GATNNNNATC	1 cut(s)	441
BsaJI	CCNNGG	3 cut(s)	230, 231, 708
Bsc4I	CCNNNNNNNGG	1 cut(s)	64
Bse1I	ACTGG	1 cut(s)	537
Bse8I	GATNNNNATC	1 cut(s)	441
BseBI	CCWGG	2 cut(s)	232, 710
BseDI	CCNNGG	3 cut(s)	230, 231, 708
BseGI	GGATG	3 cut(s)	203, 391, 718
BseJI	GATNNNNATC	1 cut(s)	441
BseLI	CCNNNNNNNGG	1 cut(s)	64
BseMII	CTCAG	3 cut(s)	121, 323, 558
BseNI	ACTGG	1 cut(s)	537
BseRI	GAGGAG	4 cut(s)	22, 77, 287, 573
BseSI	GKGCMC	1 cut(s)	553
BseXI	GCAGC	2 cut(s)	90, 349
BshFI	GGCC	1 cut(s)	525
BshNI	GGYRCC	1 cut(s)	550
BsiHKAI	GWGCWC	2 cut(s)	565, 765
BsiSI	CCGG	3 cut(s)	59, 260, 554
BslI	CCNNNNNNNGG	1 cut(s)	64
BsmAI	GTCTC	2 cut(s)	657, 685
BsnI	GGCC	1 cut(s)	525
Bsp1286I	GDGCHC	4 cut(s)	229, 553, 565, 765
Bsp1407I	TGTACA	1 cut(s)	630
Bsp143I	GATC	5 cut(s)	26, 215, 352, 436, 442
BspACI	CCGC	1 cut(s)	428
BspANI	GGCC	1 cut(s)	525
BspCNI	CTCAG	3 cut(s)	120, 324, 557
BspLI	GGNNCC	2 cut(s)	228, 552
BspPI	GGATC	2 cut(s)	34, 347
BspQI	GCTCTTC	1 cut(s)	63
BspT107I	GGYRCC	1 cut(s)	550
BsrGI	TGTACA	1 cut(s)	630
BsrI	ACTGG	1 cut(s)	537
BssECI	CCNNGG	3 cut(s)	230, 231, 708
BssMI	GATC	5 cut(s)	26, 215, 352, 436, 442
Bst2UI	CCWGG	2 cut(s)	232, 710
Bst4CI	ACNGT	3 cut(s)	308, 698, 812
Bst6I	CTCTTC	2 cut(s)	63, 330
BstAUI	TGTACA	1 cut(s)	630
BstC8I	GCNNGC	4 cut(s)	75, 523, 607, 774
BstDEI	CTNAG	3 cut(s)	107, 332, 544
BstEII	GGTNACC	1 cut(s)	532
BstF5I	GGATG	3 cut(s)	203, 391, 718
BstKTI	GATC	5 cut(s)	29, 218, 355, 439, 445
BstMAI	GTCTC	2 cut(s)	657, 685
BstMBI	GATC	5 cut(s)	26, 215, 352, 436, 442
BstMWI	GCNNNNNNNGC	3 cut(s)	83, 425, 769
BstNI	CCWGG	2 cut(s)	232, 710
BstPI	GGTNACC	1 cut(s)	532
BstSCI	CCNGG	5 cut(s)	57, 230, 258, 553, 708
BstSFI	CTRYAG	1 cut(s)	684
BstSLI	GKGCMC	1 cut(s)	553
BstV1I	GCAGC	2 cut(s)	90, 349
BstX2I	RGATCY	2 cut(s)	26, 352
BstYI	RGATCY	2 cut(s)	26, 352
BsuRI	GGCC	1 cut(s)	525
BtsCI	GGATG	3 cut(s)	203, 391, 718
Cac8I	GCNNGC	4 cut(s)	75, 523, 607, 774
Csp6I	GTAC	1 cut(s)	631
CspCI	CAANNNNNGTGG	2 cut(s)	480, 515
CviAII	CATG	3 cut(s)	83, 119, 613
CviQI	GTAC	1 cut(s)	631
DdeI	CTNAG	3 cut(s)	107, 332, 544
DpnI	GATC	5 cut(s)	28, 217, 354, 438, 444
DpnII	GATC	5 cut(s)	26, 215, 352, 436, 442
DraI	TTTAAA	1 cut(s)	510
Eam1104I	CTCTTC	2 cut(s)	63, 330
EarI	CTCTTC	2 cut(s)	63, 330
Ecl136II	GAGCTC	1 cut(s)	763
Eco24I	GRGCYC	2 cut(s)	229, 765
Eco32I	GATATC	1 cut(s)	301
Eco53kI	GAGCTC	1 cut(s)	763
Eco57I	CTGAAG	2 cut(s)	63, 674
Eco91I	GGTNACC	1 cut(s)	532
EcoICRI	GAGCTC	1 cut(s)	763
EcoO65I	GGTNACC	1 cut(s)	532
EcoRII	CCWGG	2 cut(s)	230, 708
EcoRV	GATATC	1 cut(s)	301
EcoT38I	GRGCYC	2 cut(s)	229, 765
FaeI	CATG	3 cut(s)	86, 122, 616
FatI	CATG	3 cut(s)	82, 118, 612
FauNDI	CATATG	1 cut(s)	220
Fnu4HI	GCNGC	3 cut(s)	104, 338, 429
FokI	GGATG	3 cut(s)	190, 398, 725
FriOI	GRGCYC	2 cut(s)	229, 765
Fsp4HI	GCNGC	3 cut(s)	104, 338, 429
FspBI	CTAG	2 cut(s)	78, 659
GluI	GCNGC	3 cut(s)	104, 338, 429
HaeIII	GGCC	1 cut(s)	525
HapII	CCGG	3 cut(s)	59, 260, 554
Hin1II	CATG	3 cut(s)	86, 122, 616
HinfI	GANTC	2 cut(s)	398, 797
HpaII	CCGG	3 cut(s)	59, 260, 554
HphI	GGTGA	2 cut(s)	282, 605
Hpy166II	GTNNAC	1 cut(s)	631
Hpy188I	TCNGA	3 cut(s)	110, 333, 394
Hpy188III	TCNNGA	2 cut(s)	269, 440
Hpy8I	GTNNAC	1 cut(s)	631
HpyAV	CCTTC	1 cut(s)	31
HpyCH4III	ACNGT	3 cut(s)	308, 698, 812
HpyCH4IV	ACGT	1 cut(s)	112
HpyCH4V	TGCA	5 cut(s)	4, 179, 359, 419, 750
HpyF10VI	GCNNNNNNNGC	3 cut(s)	83, 425, 769
HpyF3I	CTNAG	3 cut(s)	107, 332, 544
HpySE526I	ACGT	1 cut(s)	112
Hsp92II	CATG	3 cut(s)	86, 122, 616
Kzo9I	GATC	5 cut(s)	26, 215, 352, 436, 442
LguI	GCTCTTC	1 cut(s)	63
LmnI	GCTCC	4 cut(s)	100, 232, 560, 760
Lsp1109I	GCAGC	2 cut(s)	90, 349
LweI	GCATC	1 cut(s)	612
MaeI	CTAG	2 cut(s)	78, 659
MaeII	ACGT	1 cut(s)	112
MaeIII	GTNAC	4 cut(s)	288, 532, 597, 781
MalI	GATC	5 cut(s)	28, 217, 354, 438, 444
MboI	GATC	5 cut(s)	26, 215, 352, 436, 442
MboII	GAAGA	5 cut(s)	80, 317, 362, 473, 751
MflI	RGATCY	2 cut(s)	26, 352
MhlI	GDGCHC	4 cut(s)	229, 553, 565, 765
MluCI	AATT	3 cut(s)	360, 377, 402
MlyI	GAGTC	1 cut(s)	791
MseI	TTAA	5 cut(s)	48, 255, 366, 509, 726
MspA1I	CMGCKG	2 cut(s)	428, 605
MspI	CCGG	3 cut(s)	59, 260, 554
MspR9I	CCNGG	5 cut(s)	59, 232, 260, 555, 710
MvaI	CCWGG	2 cut(s)	232, 710
MwoI	GCNNNNNNNGC	3 cut(s)	83, 425, 769
NciI	CCSGG	3 cut(s)	59, 260, 555
NdeI	CATATG	1 cut(s)	220
NdeII	GATC	5 cut(s)	26, 215, 352, 436, 442
NlaIII	CATG	3 cut(s)	86, 122, 616
NlaIV	GGNNCC	2 cut(s)	228, 552
NmuCI	GTSAC	2 cut(s)	288, 781
PasI	CCCWGGG	1 cut(s)	231
PciSI	GCTCTTC	1 cut(s)	63
PfeI	GAWTC	1 cut(s)	398
PkrI	GCNGC	3 cut(s)	105, 339, 430
PleI	GAGTC	1 cut(s)	791
PpsI	GAGTC	1 cut(s)	791
PshBI	ATTAAT	1 cut(s)	726
Psp124BI	GAGCTC	1 cut(s)	765
Psp6I	CCWGG	2 cut(s)	230, 708
PspEI	GGTNACC	1 cut(s)	532
PspGI	CCWGG	2 cut(s)	230, 708
PspN4I	GGNNCC	2 cut(s)	228, 552
PsuI	RGATCY	2 cut(s)	26, 352
PvuII	CAGCTG	1 cut(s)	605
RsaI	GTAC	1 cut(s)	632
RsaNI	GTAC	1 cut(s)	631
SacI	GAGCTC	1 cut(s)	765
SapI	GCTCTTC	1 cut(s)	63
SaqAI	TTAA	5 cut(s)	48, 255, 366, 509, 726
SatI	GCNGC	3 cut(s)	104, 338, 429
Sau3AI	GATC	5 cut(s)	26, 215, 352, 436, 442
SchI	GAGTC	1 cut(s)	791
ScrFI	CCNGG	5 cut(s)	59, 232, 260, 555, 710
SduI	GDGCHC	4 cut(s)	229, 553, 565, 765
SfaNI	GCATC	1 cut(s)	612
SfcI	CTRYAG	1 cut(s)	684
Sse9I	AATT	3 cut(s)	360, 377, 402
SsiI	CCGC	1 cut(s)	428
SspMI	CTAG	2 cut(s)	78, 659
SstI	GAGCTC	1 cut(s)	765
StyD4I	CCNGG	5 cut(s)	57, 230, 258, 553, 708
TaaI	ACNGT	3 cut(s)	308, 698, 812
TaiI	ACGT	1 cut(s)	115
TasI	AATT	3 cut(s)	360, 377, 402
TatI	WGTACW	1 cut(s)	630
TauI	GCSGC	1 cut(s)	431
TfiI	GAWTC	1 cut(s)	398
Tru1I	TTAA	5 cut(s)	48, 255, 366, 509, 726
Tru9I	TTAA	5 cut(s)	48, 255, 366, 509, 726
TseFI	GTSAC	2 cut(s)	288, 781
TseI	GCWGC	2 cut(s)	103, 337
Tsp45I	GTSAC	2 cut(s)	288, 781
TspDTI	ATGAA	7 cut(s)	4, 135, 363, 426, 473, 601, 707
VspI	ATTAAT	1 cut(s)	726
XapI	RAATTY	1 cut(s)	377
XcmI	CCANNNNNNNNNTGG	1 cut(s)	377
XspI	CTAG	2 cut(s)	78, 659

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