Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000002

Orthogroup ID

OG0003670

Physical Location & Seq

Genomic Coordinates Reverse (-)

7366417 .. 7377305

Gene Structure 10889 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_2G00084950.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 546 bp

ATGTACTCCTATAAATACCTCTTTAACAAAAGAATGCAAACCTTGAAGCACGGAGATGATCCTGTTGCTCAAAATGATTTGAATGCAATCAAAAATGGTATGACCAACAGGGAGGATCTTGAAGAAGCTTCCGAATGCCATAATGATCGCAATACCCCACCATTTAATGCTTCTGCCACCACTCCCCAGGAGGCTTATCCACTGGAAAAGATCATCTCCACAGCAGACTGGAAATTCCTCCAAGATATCCGTAGGGGGATCAGAACTTCCCCGGATGAAGAGAAGAAGAACAAGCTTGCTTGTATTTTCTCATATATTATGCACCTTATAAAGTTCAAAGATCTGCATTCCATGGAGCTCAAGGGGCATTTCTTTCCAAAGGCCCACAGATTCCCAAGCATTATAAGGGACAAATTTTCAAGAATGTTTGATGCAGTGTCGAGAAAGCTATCAACCGAAAAAAGTAATCTTCTCATTAGTTATGTCCTGGTGCTCACTCTATTTGTGGATGAATTCCAAACAAGTTTGACAGACATAGCAAATTAA

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

181

Amino Acids

21.09

Weight (kDa)

8.45

Isoelectric Point (pI)

42.3

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_I_A49	PF06870	15 - 81	3e-10	A49-like RNA polymerase I associated factor
RNA_pol_I_A49	PF06870	90 - 181	1.8e-11	A49-like RNA polymerase I associated factor

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: 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)
AanI	TTATAA	2 cut(s)	329, 404
AclWI	GGATC	3 cut(s)	53, 123, 266
AcsI	RAATTY	3 cut(s)	233, 413, 512
AfaI	GTAC	1 cut(s)	5
AgsI	TTSAA	5 cut(s)	46, 82, 122, 337, 420
AjnI	CCWGG	2 cut(s)	186, 486
AluBI	AGCT	4 cut(s)	128, 295, 358, 448
AluI	AGCT	4 cut(s)	128, 295, 358, 448
Alw21I	GWGCWC	2 cut(s)	360, 495
AlwI	GGATC	3 cut(s)	53, 123, 266
AoxI	GGCC	1 cut(s)	381
ApoI	RAATTY	3 cut(s)	233, 413, 512
AspS9I	GGNCC	1 cut(s)	382
AsuC2I	CCSGG	1 cut(s)	272
BanII	GRGCYC	1 cut(s)	360
Bbv12I	GWGCWC	2 cut(s)	360, 495
BciT130I	CCWGG	2 cut(s)	188, 488
BcnI	CCSGG	1 cut(s)	272
BglII	AGATCT	1 cut(s)	340
Bme1390I	CCNGG	3 cut(s)	188, 272, 488
BmgT120I	GGNCC	1 cut(s)	382
BmrFI	CCNGG	3 cut(s)	188, 272, 488
BmsI	GCATC	1 cut(s)	421
BpuEI	CTTGAG	1 cut(s)	344
BpuMI	CCSGG	1 cut(s)	272
BsaJI	CCNNGG	3 cut(s)	186, 270, 351
Bse1I	ACTGG	2 cut(s)	207, 233
BseBI	CCWGG	2 cut(s)	188, 488
BseDI	CCNNGG	3 cut(s)	186, 270, 351
BseGI	GGATG	2 cut(s)	280, 514
BseNI	ACTGG	2 cut(s)	207, 233
BshFI	GGCC	1 cut(s)	383
BsiHKAI	GWGCWC	2 cut(s)	360, 495
BsiSI	CCGG	1 cut(s)	272
BslFI	GGGAC	1 cut(s)	422
BsmFI	GGGAC	1 cut(s)	422
BsmI	GAATGC	4 cut(s)	39, 88, 140, 346
BsnI	GGCC	1 cut(s)	383
Bsp1286I	GDGCHC	2 cut(s)	360, 495
Bsp143I	GATC	6 cut(s)	58, 115, 145, 210, 258, 340
Bsp19I	CCATGG	1 cut(s)	351
BspANI	GGCC	1 cut(s)	383
BspPI	GGATC	3 cut(s)	53, 123, 266
BsrI	ACTGG	2 cut(s)	207, 233
BssECI	CCNNGG	3 cut(s)	186, 270, 351
BssMI	GATC	6 cut(s)	58, 115, 145, 210, 258, 340
BssT1I	CCWWGG	1 cut(s)	351
Bst2UI	CCWGG	2 cut(s)	188, 488
Bst6I	CTCTTC	1 cut(s)	273
BstC8I	GCNNGC	1 cut(s)	297
BstDSI	CCRYGG	1 cut(s)	351
BstF5I	GGATG	2 cut(s)	280, 514
BstKTI	GATC	6 cut(s)	61, 118, 148, 213, 261, 343
BstMBI	GATC	6 cut(s)	58, 115, 145, 210, 258, 340
BstMWI	GCNNNNNNNGC	1 cut(s)	364
BstNI	CCWGG	2 cut(s)	188, 488
BstSCI	CCNGG	3 cut(s)	186, 270, 486
BstX2I	RGATCY	2 cut(s)	115, 340
BstYI	RGATCY	2 cut(s)	115, 340
BsuRI	GGCC	1 cut(s)	383
BtgI	CCRYGG	1 cut(s)	351
BtsCI	GGATG	2 cut(s)	280, 514
BtsI	GCAGTG	1 cut(s)	441
BtsIMutI	CAGTG	2 cut(s)	200, 441
Cac8I	GCNNGC	1 cut(s)	297
Cfr13I	GGNCC	1 cut(s)	382
Csp6I	GTAC	1 cut(s)	4
CviAII	CATG	1 cut(s)	352
CviJI	RGCY	6 cut(s)	128, 194, 295, 358, 383, 448
CviKI_1	RGCY	6 cut(s)	128, 194, 295, 358, 383, 448
CviQI	GTAC	1 cut(s)	4
DpnI	GATC	6 cut(s)	60, 117, 147, 212, 260, 342
DpnII	GATC	6 cut(s)	58, 115, 145, 210, 258, 340
Eam1104I	CTCTTC	1 cut(s)	273
EarI	CTCTTC	1 cut(s)	273
Ecl136II	GAGCTC	1 cut(s)	358
Eco130I	CCWWGG	1 cut(s)	351
Eco24I	GRGCYC	1 cut(s)	360
Eco32I	GATATC	1 cut(s)	247
Eco53kI	GAGCTC	1 cut(s)	358
EcoICRI	GAGCTC	1 cut(s)	358
EcoRI	GAATTC	1 cut(s)	512
EcoRII	CCWGG	2 cut(s)	186, 486
EcoRV	GATATC	1 cut(s)	247
EcoT14I	CCWWGG	1 cut(s)	351
EcoT38I	GRGCYC	1 cut(s)	360
ErhI	CCWWGG	1 cut(s)	351
FaeI	CATG	1 cut(s)	355
FaqI	GGGAC	1 cut(s)	422
FatI	CATG	1 cut(s)	351
FokI	GGATG	2 cut(s)	287, 521
FriOI	GRGCYC	1 cut(s)	360
HaeIII	GGCC	1 cut(s)	383
HapII	CCGG	1 cut(s)	272
Hin1II	CATG	1 cut(s)	355
HindIII	AAGCTT	2 cut(s)	126, 293
HinfI	GANTC	1 cut(s)	390
HpaII	CCGG	1 cut(s)	272
Hpy188I	TCNGA	2 cut(s)	133, 263
Hpy188III	TCNNGA	3 cut(s)	119, 420, 441
HpyCH4V	TGCA	5 cut(s)	37, 86, 322, 346, 434
HpyF10VI	GCNNNNNNNGC	1 cut(s)	364
Hsp92II	CATG	1 cut(s)	355
Kzo9I	GATC	6 cut(s)	58, 115, 145, 210, 258, 340
LmnI	GCTCC	1 cut(s)	355
LpnPI	CCDG	9 cut(s)	75, 94, 173, 188, 200, 214, 285, 473, 500
LweI	GCATC	1 cut(s)	421
MalI	GATC	6 cut(s)	60, 117, 147, 212, 260, 342
MboI	GATC	6 cut(s)	58, 115, 145, 210, 258, 340
MboII	GAAGA	5 cut(s)	134, 290, 295, 298, 461
MflI	RGATCY	2 cut(s)	115, 340
MhlI	GDGCHC	2 cut(s)	360, 495
MluCI	AATT	4 cut(s)	233, 413, 512, 541
MnlI	CCTC	4 cut(s)	29, 106, 184, 248
MseI	TTAA	3 cut(s)	24, 165, 544
MslI	CAYNNNNRTG	1 cut(s)	54
MspI	CCGG	1 cut(s)	272
MspR9I	CCNGG	3 cut(s)	188, 272, 488
Mva1269I	GAATGC	4 cut(s)	39, 88, 140, 346
MvaI	CCWGG	2 cut(s)	188, 488
MwoI	GCNNNNNNNGC	1 cut(s)	364
NciI	CCSGG	1 cut(s)	272
NcoI	CCATGG	1 cut(s)	351
NdeII	GATC	6 cut(s)	58, 115, 145, 210, 258, 340
NlaIII	CATG	1 cut(s)	355
PctI	GAATGC	4 cut(s)	39, 88, 140, 346
PfeI	GAWTC	1 cut(s)	390
PsiI	TTATAA	2 cut(s)	329, 404
Psp124BI	GAGCTC	1 cut(s)	360
Psp6I	CCWGG	2 cut(s)	186, 486
PspGI	CCWGG	2 cut(s)	186, 486
PspPI	GGNCC	1 cut(s)	382
PsuI	RGATCY	2 cut(s)	115, 340
RsaI	GTAC	1 cut(s)	5
RsaNI	GTAC	1 cut(s)	4
RseI	CAYNNNNRTG	1 cut(s)	54
SacI	GAGCTC	1 cut(s)	360
SaqAI	TTAA	3 cut(s)	24, 165, 544
Sau3AI	GATC	6 cut(s)	58, 115, 145, 210, 258, 340
Sau96I	GGNCC	1 cut(s)	382
ScrFI	CCNGG	3 cut(s)	188, 272, 488
SduI	GDGCHC	2 cut(s)	360, 495
SetI	ASST	7 cut(s)	21, 44, 130, 297, 327, 360, 450
SfaNI	GCATC	1 cut(s)	421
SmiMI	CAYNNNNRTG	1 cut(s)	54
SmlI	CTYRAG	1 cut(s)	359
SmoI	CTYRAG	1 cut(s)	359
Sse9I	AATT	4 cut(s)	233, 413, 512, 541
SstI	GAGCTC	1 cut(s)	360
StyD4I	CCNGG	3 cut(s)	186, 270, 486
StyI	CCWWGG	1 cut(s)	351
TaqI	TCGA	1 cut(s)	440
TasI	AATT	4 cut(s)	233, 413, 512, 541
TatI	WGTACW	1 cut(s)	3
TfiI	GAWTC	1 cut(s)	390
Tru1I	TTAA	3 cut(s)	24, 165, 544
Tru9I	TTAA	3 cut(s)	24, 165, 544
TscAI	CASTG	2 cut(s)	207, 441
TspDTI	ATGAA	2 cut(s)	291, 525
TspGWI	ACGGA	2 cut(s)	66, 239
TspRI	CASTG	2 cut(s)	207, 441
XapI	RAATTY	3 cut(s)	233, 413, 512

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