Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr2A

Orthogroup ID

OG0003670

Physical Location & Seq

Genomic Coordinates Forward (+)

81992827 .. 81997154

Gene Structure 4328 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh2AG588500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 972 bp

ATGGATTCAGAAGACACCATATCCCAACAAGAGCCATCAACACCAGCTCGCAAGCACAAGAAGAAGAGAATGAAAGTCGCACCAGAAGACACGCGAAGCAACCCACAGAAGCCCCAAACAGTCATCAAAGTCATCCCAGGAAACCCAGAGAGAATGGCACCTTTGGTGGGCTATTTCCCATCTGGGTTTGATCCCACCAAAAGCTCAGATCTAAACTCAACCAAAGTTGGGGTCTTCAGGCACAAAGAGAGAAGTGGTACTCGGCTTCAGCTTGTGGTAACCCCAGAAAAGGATGCTGAAGTTGATTTCGTTGGAACTAGCTATGCTGGTGAGGCTCAGGCTGGGGAGCACTGCGCTTATGGACTTGGTATTCTTGATAAGGCCACCCACACATTGAAGATTGTGCCTATTGCTAATAACAAGGTATTTAGATTAGAACCAAAAGTTCAAGGTGCTGACTCCTCTAATAAGGAGCTTGCAAGTTCAGTGATTGGAAAACTTTCTGCACATGAGAAGACAGAAAAACTTACAGAACTTCATAATCGTTATGGAACAAAGAAGTCAATACGGCAGAACAAAAGAATGCAAACCTTGAAGCACGGAGATGATCCTGTAGCTCAAAATGATTTGAATGCAATTAAAAATGGTATGACGAACAGGGAGGATCTTGAAGAAGCTTCCGAATGCTATAATGATCGCAATACCCCACCATTTAATGCTTCTGCCACCACTCCCCAGGAGGCTTATCCACTGGACAAGATCATCTCCACAGCAGAGTGGAAATTCCTCCAAGATATCCATAAGCTTGTGGAAGGGGGATCAGAACTTCCCCGGTTTGTTAGCAACCGAATCCATAAACTGCAGCAGATTGTGTGGGTTGAAGTTGTTACTGGAAGAAAGCAACTCTGTCCTCCTCCACATGGTTCTAAACAACCTTTTAAAATTCAAGCTAGAACAAACTTGGTGGATTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0003674 GO:0003824 GO:0003899 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005730 GO:0005736 GO:0006139 GO:0006351 GO:0006360 GO:0006725 GO:0006807 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:0032774 GO:0032991 GO:0034062 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:0044428 GO:0044446 GO:0044452 GO:0044464 GO:0046483 GO:0055029 GO:0061695 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 map00230 map00240 map01100 map03020

Pfam Domains

Protein Families

RNA_pol_I_A49

Protein Analysis

323

Amino Acids

36.02

Weight (kDa)

9.21

Isoelectric Point (pI)

40.06

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_I_A49	PF06870	73 - 268	5.1e-25	A49-like RNA polymerase I associated factor

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready

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Orthologous Genes (Group: OG0003670)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G13940
fragaria_vesca	FvH4_2g14600 FvH4_2g14600 FvH4_2g14600 FvH4_6g34180 FvH4_6g47280
malus_domestica	MD09G1187900.v1.1 MD17G1172300.v1.1
prunus_persica	Prupe.3G044800_v2.0.a1
pyrus_communis	pycom09g10420 pycom09g10430 pycom17g16990 pycom17g17000
rosa_chinensis	RchiOBHm_Chr2g0144531 RchiOBHm_Chr2g0166351
rosa_laevigata	RLG00000020086 RLG00000021613
rosa_multiflora	Rmu_sc0005789.1_g000005 Rmu_sc0007974.1_g000004 Rmu_sc0029020.1_g000001 Rmu_sc0029020.1_g000002
rosa_roxburghii	Rroxscaffold_2G00084950 Rroxscaffold_2G00101230
rosa_rugosa	Rorug02G0387600 Rorug02G0522400
rosa_samantha	Rh2AG439600 Rh2AG588500 Rh2BG449700 Rh2BG600500 Rh2CG426600 Rh2CG571300 Rh2DG459600 Rh2DG610700
rosa_wichuraiana	Rw2G035960 Rw2G049040

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	157
AccII	CGCG	1 cut(s)	94
AclWI	GGATC	4 cut(s)	185, 602, 672, 826
AcsI	RAATTY	2 cut(s)	782, 942
AcuI	CTGAAG	3 cut(s)	220, 251, 318
AfaI	GTAC	1 cut(s)	259
AfiI	CCNNNNNNNGG	4 cut(s)	167, 228, 289, 920
AgsI	TTSAA	7 cut(s)	397, 449, 595, 631, 671, 881, 947
AjnI	CCWGG	2 cut(s)	136, 735
AluBI	AGCT	9 cut(s)	47, 204, 271, 321, 475, 617, 677, 805, 950
AluI	AGCT	9 cut(s)	47, 204, 271, 321, 475, 617, 677, 805, 950
Alw21I	GWGCWC	1 cut(s)	351
AlwI	GGATC	4 cut(s)	185, 602, 672, 826
AoxI	GGCC	1 cut(s)	381
ApeKI	GCWGC	1 cut(s)	862
ApoI	RAATTY	2 cut(s)	782, 942
ArsI	GACNNNNNNTTYG	2 cut(s)	216, 248
Asp700I	GAANNNNTTC	1 cut(s)	499
AspLEI	GCGC	1 cut(s)	356
AsuC2I	CCSGG	1 cut(s)	832
AsuHPI	GGTGA	1 cut(s)	341
BanI	GGYRCC	1 cut(s)	157
BbsI	GAAGAC	4 cut(s)	18, 93, 226, 521
Bbv12I	GWGCWC	1 cut(s)	351
BbvI	GCAGC	1 cut(s)	874
BccI	CCATC	2 cut(s)	43, 187
BceAI	ACGGC	1 cut(s)	584
BciT130I	CCWGG	2 cut(s)	138, 737
BcnI	CCSGG	1 cut(s)	832
BfaI	CTAG	2 cut(s)	318, 951
BfmI	CTRYAG	2 cut(s)	612, 860
BglII	AGATCT	1 cut(s)	208
BisI	GCNGC	1 cut(s)	863
BlsI	GCNGC	1 cut(s)	864
Bme1390I	CCNGG	3 cut(s)	138, 737, 832
BmiI	GGNNCC	1 cut(s)	159
BmrFI	CCNGG	3 cut(s)	138, 737, 832
BmsI	GCATC	1 cut(s)	283
BpiI	GAAGAC	4 cut(s)	18, 93, 226, 521
Bpu10I	CCTNAGC	1 cut(s)	336
BpuMI	CCSGG	1 cut(s)	832
BsaJI	CCNNGG	3 cut(s)	136, 735, 830
Bsc4I	CCNNNNNNNGG	4 cut(s)	167, 228, 289, 920
Bse1I	ACTGG	2 cut(s)	756, 895
BseBI	CCWGG	2 cut(s)	138, 737
BseDI	CCNNGG	3 cut(s)	136, 735, 830
BseGI	GGATG	2 cut(s)	132, 298
BseLI	CCNNNNNNNGG	4 cut(s)	167, 228, 289, 920
BseMII	CTCAG	2 cut(s)	219, 350
BseNI	ACTGG	2 cut(s)	756, 895
BseRI	GAGGAG	2 cut(s)	451, 903
BseXI	GCAGC	1 cut(s)	874
BseYI	CCCAGC	1 cut(s)	341
BsgI	GTGCAG	1 cut(s)	489
Bsh1236I	CGCG	1 cut(s)	94
BshFI	GGCC	1 cut(s)	383
BshNI	GGYRCC	1 cut(s)	157
BsiHKAI	GWGCWC	1 cut(s)	351
BsiSI	CCGG	1 cut(s)	832
BslI	CCNNNNNNNGG	4 cut(s)	167, 228, 289, 920
BsmI	GAATGC	3 cut(s)	588, 637, 689
BsnI	GGCC	1 cut(s)	383
Bsp1286I	GDGCHC	1 cut(s)	351
Bsp143I	GATC	7 cut(s)	190, 208, 607, 664, 694, 759, 818
BspANI	GGCC	1 cut(s)	383
BspCNI	CTCAG	2 cut(s)	218, 349
BspFNI	CGCG	1 cut(s)	94
BspLI	GGNNCC	1 cut(s)	159
BspMAI	CTGCAG	1 cut(s)	864
BspPI	GGATC	4 cut(s)	185, 602, 672, 826
BspT107I	GGYRCC	1 cut(s)	157
BsrI	ACTGG	2 cut(s)	756, 895
BssECI	CCNNGG	3 cut(s)	136, 735, 830
BssMI	GATC	7 cut(s)	190, 208, 607, 664, 694, 759, 818
Bst2UI	CCWGG	2 cut(s)	138, 737
Bst4CI	ACNGT	1 cut(s)	121
Bst6I	CTCTTC	1 cut(s)	59
BstC8I	GCNNGC	3 cut(s)	49, 53, 477
BstDEI	CTNAG	2 cut(s)	205, 336
BstEII	GGTNACC	1 cut(s)	277
BstF5I	GGATG	2 cut(s)	132, 298
BstFNI	CGCG	1 cut(s)	94
BstHHI	GCGC	1 cut(s)	356
BstKTI	GATC	7 cut(s)	193, 211, 610, 667, 697, 762, 821
BstMBI	GATC	7 cut(s)	190, 208, 607, 664, 694, 759, 818
BstMWI	GCNNNNNNNGC	1 cut(s)	332
BstNI	CCWGG	2 cut(s)	138, 737
BstPI	GGTNACC	1 cut(s)	277
BstSCI	CCNGG	3 cut(s)	136, 735, 830
BstSFI	CTRYAG	2 cut(s)	612, 860
BstUI	CGCG	1 cut(s)	94
BstV1I	GCAGC	1 cut(s)	874
BstV2I	GAAGAC	4 cut(s)	18, 93, 226, 521
BstX2I	RGATCY	2 cut(s)	208, 664
BstYI	RGATCY	2 cut(s)	208, 664
BsuRI	GGCC	1 cut(s)	383
BtsCI	GGATG	2 cut(s)	132, 298
BtsI	GCAGTG	1 cut(s)	349
BtsIMutI	CAGTG	3 cut(s)	349, 492, 749
Cac8I	GCNNGC	3 cut(s)	49, 53, 477
CfoI	GCGC	1 cut(s)	356
Csp6I	GTAC	1 cut(s)	258
CspCI	CAANNNNNGTGG	1 cut(s)	945
CviAII	CATG	2 cut(s)	509, 920
CviQI	GTAC	1 cut(s)	258
DdeI	CTNAG	2 cut(s)	205, 336
DpnI	GATC	7 cut(s)	192, 210, 609, 666, 696, 761, 820
DpnII	GATC	7 cut(s)	190, 208, 607, 664, 694, 759, 818
DraI	TTTAAA	1 cut(s)	940
Eam1104I	CTCTTC	1 cut(s)	59
EarI	CTCTTC	1 cut(s)	59
Eco32I	GATATC	1 cut(s)	796
Eco57I	CTGAAG	3 cut(s)	220, 251, 318
Eco91I	GGTNACC	1 cut(s)	277
EcoO65I	GGTNACC	1 cut(s)	277
EcoRII	CCWGG	2 cut(s)	136, 735
EcoRV	GATATC	1 cut(s)	796
FaeI	CATG	2 cut(s)	512, 923
FatI	CATG	2 cut(s)	508, 919
Fnu4HI	GCNGC	1 cut(s)	863
FokI	GGATG	2 cut(s)	119, 305
Fsp4HI	GCNGC	1 cut(s)	863
FspBI	CTAG	2 cut(s)	318, 951
GlaI	GCGC	1 cut(s)	355
GluI	GCNGC	1 cut(s)	863
GsaI	CCCAGC	1 cut(s)	345
HaeIII	GGCC	1 cut(s)	383
HapII	CCGG	1 cut(s)	832
HhaI	GCGC	1 cut(s)	356
Hin1II	CATG	2 cut(s)	512, 923
Hin6I	GCGC	1 cut(s)	354
HinP1I	GCGC	1 cut(s)	354
HindIII	AAGCTT	2 cut(s)	675, 803
HinfI	GANTC	3 cut(s)	5, 458, 849
HpaII	CCGG	1 cut(s)	832
HphI	GGTGA	1 cut(s)	341
Hpy188I	TCNGA	4 cut(s)	10, 208, 682, 823
Hpy188III	TCNNGA	2 cut(s)	374, 668
HpyAV	CCTTC	1 cut(s)	806
HpyCH4III	ACNGT	1 cut(s)	121
HpyCH4V	TGCA	5 cut(s)	479, 506, 586, 635, 862
HpyF10VI	GCNNNNNNNGC	1 cut(s)	332
HpyF3I	CTNAG	2 cut(s)	205, 336
Hsp92II	CATG	2 cut(s)	512, 923
HspAI	GCGC	1 cut(s)	354
Kzo9I	GATC	7 cut(s)	190, 208, 607, 664, 694, 759, 818
LmnI	GCTCC	2 cut(s)	346, 472
Lsp1109I	GCAGC	1 cut(s)	874
LweI	GCATC	1 cut(s)	283
MaeI	CTAG	2 cut(s)	318, 951
MaeIII	GTNAC	2 cut(s)	277, 886
MalI	GATC	7 cut(s)	192, 210, 609, 666, 696, 761, 820
MboI	GATC	7 cut(s)	190, 208, 607, 664, 694, 759, 818
MboII	GAAGA	9 cut(s)	23, 73, 76, 98, 226, 409, 526, 683, 906
MflI	RGATCY	2 cut(s)	208, 664
MhlI	GDGCHC	1 cut(s)	351
MluCI	AATT	3 cut(s)	636, 782, 942
MlyI	GAGTC	1 cut(s)	452
MmeI	TCCRAC	1 cut(s)	292
MnlI	CCTC	7 cut(s)	325, 472, 655, 733, 797, 921, 924
MroXI	GAANNNNTTC	1 cut(s)	499
MseI	TTAA	3 cut(s)	639, 714, 939
MslI	CAYNNNNRTG	1 cut(s)	603
MspI	CCGG	1 cut(s)	832
MspR9I	CCNGG	3 cut(s)	138, 737, 832
Mva1269I	GAATGC	3 cut(s)	588, 637, 689
MvaI	CCWGG	2 cut(s)	138, 737
MvnI	CGCG	1 cut(s)	94
MwoI	GCNNNNNNNGC	1 cut(s)	332
NciI	CCSGG	1 cut(s)	832
NdeII	GATC	7 cut(s)	190, 208, 607, 664, 694, 759, 818
NlaIII	CATG	2 cut(s)	512, 923
NlaIV	GGNNCC	1 cut(s)	159
NmeAIII	GCCGAG	1 cut(s)	241
PctI	GAATGC	3 cut(s)	588, 637, 689
PdmI	GAANNNNTTC	1 cut(s)	499
PfeI	GAWTC	2 cut(s)	5, 849
PkrI	GCNGC	1 cut(s)	864
PleI	GAGTC	1 cut(s)	452
PpsI	GAGTC	1 cut(s)	452
Psp6I	CCWGG	2 cut(s)	136, 735
PspEI	GGTNACC	1 cut(s)	277
PspFI	CCCAGC	1 cut(s)	341
PspGI	CCWGG	2 cut(s)	136, 735
PspN4I	GGNNCC	1 cut(s)	159
PstI	CTGCAG	1 cut(s)	864
PsuI	RGATCY	2 cut(s)	208, 664
RsaI	GTAC	1 cut(s)	259
RsaNI	GTAC	1 cut(s)	258
RseI	CAYNNNNRTG	1 cut(s)	603
SaqAI	TTAA	3 cut(s)	639, 714, 939
SatI	GCNGC	1 cut(s)	863
Sau3AI	GATC	7 cut(s)	190, 208, 607, 664, 694, 759, 818
SchI	GAGTC	1 cut(s)	452
ScrFI	CCNGG	3 cut(s)	138, 737, 832
SduI	GDGCHC	1 cut(s)	351
SfaNI	GCATC	1 cut(s)	283
SfcI	CTRYAG	2 cut(s)	612, 860
SmiMI	CAYNNNNRTG	1 cut(s)	603
Sse9I	AATT	3 cut(s)	636, 782, 942
SspMI	CTAG	2 cut(s)	318, 951
StyD4I	CCNGG	3 cut(s)	136, 735, 830
TaaI	ACNGT	1 cut(s)	121
TasI	AATT	3 cut(s)	636, 782, 942
TfiI	GAWTC	2 cut(s)	5, 849
Tru1I	TTAA	3 cut(s)	639, 714, 939
Tru9I	TTAA	3 cut(s)	639, 714, 939
TscAI	CASTG	3 cut(s)	356, 492, 756
TseI	GCWGC	1 cut(s)	862
TspDTI	ATGAA	2 cut(s)	86, 527
TspGWI	ACGGA	1 cut(s)	615
TspRI	CASTG	3 cut(s)	356, 492, 756
XapI	RAATTY	2 cut(s)	782, 942
XmnI	GAANNNNTTC	1 cut(s)	499
XspI	CTAG	2 cut(s)	318, 951

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