Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0003587

Physical Location & Seq

Genomic Coordinates Reverse (-)

16739652 .. 16744442

Gene Structure 4791 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG178600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 897 bp

ATGTTGAATAAGGGGCACGGTGCTGATTTTTTGGTTTTCAATAACTTGATCAAAGGGTTCTTGAATTTGGAGAATTTGGACAAGGCCAATGAGCTTTTTGACGAGCAGGTGTTTGGTGTAGATGGGGTTGTCAATGCCACCTTTATGGATTGGTTCTTCAATAAGGGGAAAGAGAAGGAGGCAATGGATTCATACAGGTCATTGCTTGATAGGCAGTTTAGGATGATCCCAGCTACCTGCAATGTTCTCTTGGAAGTGTTGCTTAAGCATGACAAGAAGGAGGCGTGGGCTTTGTTCGAACAAATACTGGATAATCACACCCCACCCAATACCCAGGCAGTTAACTCCGAGACTTTTAATATGATGGTCAATGAGTGTTTTAAGCTTGGGAAGTTTGGTGAGGCGTTTGACACCTTCAAGAAGGTGGGAACAAATGTGAAGTCAAAGCCTTTTTCCATGGACGTTGCGGGGTATAATAATATCATTGCTAGGTATTGTGAGAATGGGATGTTATCGGAGGCTGATGAACTATTTAGAGAATTGTCGTCAAAGTCACTGACCCCAGACGTAACAACACATAGGACTCTGATTGATGCATATTTGAATTTAGAGAGGATAGATGATGCTCTTAAGATATTTAACAGAATGGTGGATGTTGGGTTGCGGGTGGTTGCTAGTTTTGGTGACAAGGTGTTTACTGAGTTGATTGAGAATGGGAAGGCAGTGGACTGTGCAAAAATTTTGAAGAAAATGGGAGATAAAGATCCTAAACCAGATGCCAGTTGCTATGATGTAGTGATCAGAGGGCTTTGCAATGAAGGTGAACTTGACCCAAGCCTTGATATACTGGCAGAAATGCATGCAGAGGAAGTAGTAGTGGATCGAGTTGAAGCATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0003006 GO:0003674 GO:0003676 GO:0003723 GO:0003824 GO:0004518 GO:0004519 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005737 GO:0005739 GO:0006139 GO:0006725 GO:0006807 GO:0007275 GO:0008150 GO:0008152 GO:0009451 GO:0009790 GO:0009791 GO:0009793 GO:0009987 GO:0010154 GO:0016070 GO:0016787 GO:0016788 GO:0022414 GO:0032501 GO:0032502 GO:0034641 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043412 GO:0044237 GO:0044238 GO:0044424 GO:0044444 GO:0044464 GO:0046483 GO:0048316 GO:0048608 GO:0048731 GO:0048856 GO:0051301 GO:0061458 GO:0071704 GO:0090304 GO:0090305 GO:0097159 GO:1901360 GO:1901363

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PPR PPR_1 PPR_2

Protein Analysis

298

Amino Acids

33.65

Weight (kDa)

4.85

Isoelectric Point (pI)

17.31

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	154 - 201	4.9e-12	PPR repeat family
TPR_24	PF23276	168 - 282	2.5e-06	Fungal tetratrico peptide repeats

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: OG0003587)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G10270 AT3G60980
fragaria_vesca	FvH4_5g27880
malus_domestica	MD08G1246600.v1.1 MD15G1441500.v1.1
prunus_persica	Prupe.1G583600_v2.0.a1 Prupe.1G583600_v2.0.a1 Prupe.1G583600_v2.0.a1
pyrus_communis	pycom08g21380 pycom11g13110 pycom11g13120 pycom15g38950 pycom17g02590
rosa_chinensis	RchiOBHm_Chr3g0472581 RchiOBHm_Chr7g0220071
rosa_laevigata	RLG00000002259 RLG00000024069
rosa_multiflora	Rmu_co8321059.1_g000001 Rmu_sc0003510.1_g000024 Rmu_sc0003510.1_g000025 Rmu_sc0005838.1_g000004 Rmu_sc0007553.1_g000004 Rmu_sc0011581.1_g000008
rosa_roxburghii	Rroxscaffold_3G00239800 Rroxscaffold_6G00408800
rosa_rugosa	Rorug07G0188700
rosa_samantha	Rh3AG178600 Rh3BG204500 Rh3CG194900 Rh3CG201900 Rh7AG332400 Rh7BG322300 Rh7CG349900 Rh7DG328000
rosa_wichuraiana	Rw7G027990

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	97
Acc36I	ACCTGC	2 cut(s)	97, 245
AciI	CCGC	2 cut(s)	467, 664
AclWI	GGATC	3 cut(s)	220, 758, 888
AcsI	RAATTY	4 cut(s)	64, 73, 604, 738
AflII	CTTAAG	2 cut(s)	263, 629
AgsI	TTSAA	8 cut(s)	7, 40, 64, 160, 418, 604, 745, 890
AjnI	CCWGG	1 cut(s)	333
AluBI	AGCT	3 cut(s)	94, 233, 385
AluI	AGCT	3 cut(s)	94, 233, 385
Alw26I	GTCTC	1 cut(s)	344
AlwI	GGATC	3 cut(s)	220, 758, 888
AoxI	GGCC	1 cut(s)	84
ApoI	RAATTY	4 cut(s)	64, 73, 604, 738
ArsI	GACNNNNNNTTYG	2 cut(s)	425, 457
AsuHPI	GGTGA	3 cut(s)	410, 695, 833
AsuII	TTCGAA	1 cut(s)	297
BaeGI	GKGCMC	1 cut(s)	18
BccI	CCATC	2 cut(s)	116, 358
BciT130I	CCWGG	1 cut(s)	335
BclI	TGATCA	2 cut(s)	48, 798
BcoDI	GTCTC	1 cut(s)	344
BfaI	CTAG	2 cut(s)	489, 675
BfrI	CTTAAG	2 cut(s)	263, 629
BfuAI	ACCTGC	2 cut(s)	97, 245
Bme1390I	CCNGG	1 cut(s)	335
BmrFI	CCNGG	1 cut(s)	335
BmsI	GCATC	3 cut(s)	583, 613, 766
Bpu14I	TTCGAA	1 cut(s)	297
BsaBI	GATNNNNATC	1 cut(s)	762
BsaJI	CCNNGG	2 cut(s)	333, 456
Bse1I	ACTGG	3 cut(s)	312, 780, 852
Bse3DI	GCAATG	5 cut(s)	189, 200, 247, 483, 820
Bse8I	GATNNNNATC	1 cut(s)	762
BseBI	CCWGG	1 cut(s)	335
BseDI	CCNNGG	2 cut(s)	333, 456
BseGI	GGATG	3 cut(s)	228, 513, 658
BseJI	GATNNNNATC	1 cut(s)	762
BseMI	GCAATG	5 cut(s)	189, 200, 247, 483, 820
BseMII	CTCAG	1 cut(s)	690
BseNI	ACTGG	3 cut(s)	312, 780, 852
BseSI	GKGCMC	1 cut(s)	18
BseYI	CCCAGC	1 cut(s)	229
BshFI	GGCC	1 cut(s)	86
BsmAI	GTCTC	1 cut(s)	344
BsnI	GGCC	1 cut(s)	86
Bsp119I	TTCGAA	1 cut(s)	297
Bsp1286I	GDGCHC	1 cut(s)	18
Bsp143I	GATC	5 cut(s)	48, 225, 763, 798, 880
Bsp19I	CCATGG	1 cut(s)	456
BspACI	CCGC	2 cut(s)	467, 664
BspANI	GGCC	1 cut(s)	86
BspCNI	CTCAG	1 cut(s)	691
BspMI	ACCTGC	2 cut(s)	97, 245
BspPI	GGATC	3 cut(s)	220, 758, 888
BspT104I	TTCGAA	1 cut(s)	297
BspTI	CTTAAG	2 cut(s)	263, 629
BsrDI	GCAATG	5 cut(s)	189, 200, 247, 483, 820
BsrI	ACTGG	3 cut(s)	312, 780, 852
BssECI	CCNNGG	2 cut(s)	333, 456
BssMI	GATC	5 cut(s)	48, 225, 763, 798, 880
BssT1I	CCWWGG	1 cut(s)	456
Bst2UI	CCWGG	1 cut(s)	335
Bst4CI	ACNGT	2 cut(s)	20, 731
BstAFI	CTTAAG	2 cut(s)	263, 629
BstBI	TTCGAA	1 cut(s)	297
BstC8I	GCNNGC	1 cut(s)	861
BstDEI	CTNAG	1 cut(s)	699
BstDSI	CCRYGG	1 cut(s)	456
BstF5I	GGATG	3 cut(s)	228, 513, 658
BstKTI	GATC	5 cut(s)	51, 228, 766, 801, 883
BstMAI	GTCTC	1 cut(s)	344
BstMBI	GATC	5 cut(s)	48, 225, 763, 798, 880
BstMWI	GCNNNNNNNGC	1 cut(s)	211
BstNI	CCWGG	1 cut(s)	335
BstNSI	RCATGY	1 cut(s)	863
BstSCI	CCNGG	1 cut(s)	333
BstSLI	GKGCMC	1 cut(s)	18
BstX2I	RGATCY	1 cut(s)	763
BstXI	CCANNNNNNTGG	1 cut(s)	145
BstYI	RGATCY	1 cut(s)	763
BsuRI	GGCC	1 cut(s)	86
BtgI	CCRYGG	1 cut(s)	456
BtsCI	GGATG	3 cut(s)	228, 513, 658
BtsI	GCAGTG	1 cut(s)	729
BtsIMutI	CAGTG	2 cut(s)	554, 729
BveI	ACCTGC	2 cut(s)	97, 245
Cac8I	GCNNGC	1 cut(s)	861
CviAII	CATG	4 cut(s)	269, 457, 860, 894
CviJI	RGCY	9 cut(s)	86, 94, 233, 290, 385, 448, 521, 808, 837
CviKI_1	RGCY	9 cut(s)	86, 94, 233, 290, 385, 448, 521, 808, 837
DdeI	CTNAG	1 cut(s)	699
DpnI	GATC	5 cut(s)	50, 227, 765, 800, 882
DpnII	GATC	5 cut(s)	48, 225, 763, 798, 880
Eco130I	CCWWGG	1 cut(s)	456
EcoRII	CCWGG	1 cut(s)	333
EcoT14I	CCWWGG	1 cut(s)	456
EcoT22I	ATGCAT	2 cut(s)	598, 861
ErhI	CCWWGG	1 cut(s)	456
FaeI	CATG	4 cut(s)	272, 460, 863, 897
FalI	AAGNNNNNCTT	4 cut(s)	246, 278, 810, 842
FatI	CATG	4 cut(s)	268, 456, 859, 893
FauI	CCCGC	2 cut(s)	460, 657
FbaI	TGATCA	2 cut(s)	48, 798
FokI	GGATG	3 cut(s)	235, 520, 665
FspBI	CTAG	2 cut(s)	489, 675
GsaI	CCCAGC	1 cut(s)	233
HaeIII	GGCC	1 cut(s)	86
Hin1II	CATG	4 cut(s)	272, 460, 863, 897
HincII	GTYRAC	1 cut(s)	343
HindII	GTYRAC	1 cut(s)	343
HindIII	AAGCTT	1 cut(s)	383
HinfI	GANTC	2 cut(s)	188, 583
HpaI	GTTAAC	1 cut(s)	343
HphI	GGTGA	3 cut(s)	410, 695, 833
Hpy166II	GTNNAC	4 cut(s)	343, 696, 727, 824
Hpy188I	TCNGA	4 cut(s)	349, 517, 588, 803
Hpy188III	TCNNGA	2 cut(s)	61, 418
Hpy8I	GTNNAC	4 cut(s)	343, 696, 727, 824
HpyAV	CCTTC	6 cut(s)	169, 271, 415, 424, 712, 812
HpyCH4III	ACNGT	2 cut(s)	20, 731
HpyCH4IV	ACGT	2 cut(s)	462, 567
HpyCH4V	TGCA	6 cut(s)	240, 596, 734, 813, 859, 863
HpyF10VI	GCNNNNNNNGC	1 cut(s)	211
HpyF3I	CTNAG	1 cut(s)	699
HpySE526I	ACGT	2 cut(s)	462, 567
Hsp92II	CATG	4 cut(s)	272, 460, 863, 897
Ksp22I	TGATCA	2 cut(s)	48, 798
KspAI	GTTAAC	1 cut(s)	343
Kzo9I	GATC	5 cut(s)	48, 225, 763, 798, 880
LweI	GCATC	3 cut(s)	583, 613, 766
MaeI	CTAG	2 cut(s)	489, 675
MaeII	ACGT	2 cut(s)	462, 567
MaeIII	GTNAC	3 cut(s)	552, 568, 683
MalI	GATC	5 cut(s)	50, 227, 765, 800, 882
MboI	GATC	5 cut(s)	48, 225, 763, 798, 880
MboII	GAAGA	2 cut(s)	148, 757
MflI	RGATCY	1 cut(s)	763
MhlI	GDGCHC	1 cut(s)	18
MluCI	AATT	5 cut(s)	64, 73, 539, 604, 738
MlyI	GAGTC	1 cut(s)	577
MnlI	CCTC	7 cut(s)	172, 274, 394, 511, 606, 797, 859
Mph1103I	ATGCAT	2 cut(s)	598, 861
MseI	TTAA	6 cut(s)	264, 342, 357, 381, 630, 639
MslI	CAYNNNNRTG	1 cut(s)	143
MspCI	CTTAAG	2 cut(s)	263, 629
MspR9I	CCNGG	1 cut(s)	335
MvaI	CCWGG	1 cut(s)	335
MwoI	GCNNNNNNNGC	1 cut(s)	211
NcoI	CCATGG	1 cut(s)	456
NdeII	GATC	5 cut(s)	48, 225, 763, 798, 880
NlaIII	CATG	4 cut(s)	272, 460, 863, 897
NmuCI	GTSAC	2 cut(s)	552, 683
NsiI	ATGCAT	2 cut(s)	598, 861
NspI	RCATGY	1 cut(s)	863
NspV	TTCGAA	1 cut(s)	297
PaeI	GCATGC	1 cut(s)	863
PaqCI	CACCTGC	1 cut(s)	97
PfeI	GAWTC	1 cut(s)	188
PleI	GAGTC	1 cut(s)	577
PpsI	GAGTC	1 cut(s)	577
Psp6I	CCWGG	1 cut(s)	333
PspFI	CCCAGC	1 cut(s)	229
PspGI	CCWGG	1 cut(s)	333
PsuI	RGATCY	1 cut(s)	763
RseI	CAYNNNNRTG	1 cut(s)	143
SaqAI	TTAA	6 cut(s)	264, 342, 357, 381, 630, 639
Sau3AI	GATC	5 cut(s)	48, 225, 763, 798, 880
SchI	GAGTC	1 cut(s)	577
ScrFI	CCNGG	1 cut(s)	335
SduI	GDGCHC	1 cut(s)	18
SfaNI	GCATC	3 cut(s)	583, 613, 766
SfuI	TTCGAA	1 cut(s)	297
SmiMI	CAYNNNNRTG	1 cut(s)	143
SmlI	CTYRAG	2 cut(s)	263, 629
SmoI	CTYRAG	2 cut(s)	263, 629
SphI	GCATGC	1 cut(s)	863
Sse9I	AATT	5 cut(s)	64, 73, 539, 604, 738
SsiI	CCGC	2 cut(s)	467, 664
SspMI	CTAG	2 cut(s)	489, 675
StyD4I	CCNGG	1 cut(s)	333
StyI	CCWWGG	1 cut(s)	456
TaaI	ACNGT	2 cut(s)	20, 731
TaiI	ACGT	2 cut(s)	465, 570
TaqI	TCGA	2 cut(s)	297, 883
TasI	AATT	5 cut(s)	64, 73, 539, 604, 738
TfiI	GAWTC	1 cut(s)	188
Tru1I	TTAA	6 cut(s)	264, 342, 357, 381, 630, 639
Tru9I	TTAA	6 cut(s)	264, 342, 357, 381, 630, 639
TscAI	CASTG	2 cut(s)	561, 729
TseFI	GTSAC	2 cut(s)	552, 683
Tsp45I	GTSAC	2 cut(s)	552, 683
TspDTI	ATGAA	3 cut(s)	180, 540, 831
TspRI	CASTG	2 cut(s)	561, 729
Vha464I	CTTAAG	2 cut(s)	263, 629
XapI	RAATTY	4 cut(s)	64, 73, 604, 738
XceI	RCATGY	1 cut(s)	863
XspI	CTAG	2 cut(s)	489, 675
Zsp2I	ATGCAT	2 cut(s)	598, 861

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