Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1D

Orthogroup ID

OG0003945

Physical Location & Seq

Genomic Coordinates Forward (+)

59702282 .. 59704139

Gene Structure 1858 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1DG373200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 576 bp

ATGGAGTTTGATTTCACCAACTGTTTGTTACTGAAGATCAGTAGCAATAGTGAATCTACCTTATTTGCTATTGAGGATTGGTTACCTGCGATACTAGGTCAGCTGGCGGACCAAGTGACCAAGGCAGTAGACGACCTAGAACCAAGACTAGACGACCCGACCTACTGCGAGTTCGCCGCCGACTTGGAGAAAATATACAGAATATTATGCAAATTCCACTCCCGGGTCCCCAAACTAGAGCTCGCTCTACATCAATCCGGCGTCGTTTTGCACTCCGACTTAATCGAGCGAGTGTTGTCTCGGTGCTCGCTTTATATTGTGGGGTATAACAATTTGCTTGGTAGGTATGCTCAGGTTGAGAAGATGGTTGATGCGTATGAGCTGTTGAAAGAGATGAGGAGGAAGGGTTGTGAACCCAATGCGAGTTCGTATACGACTATGATTCAGGCACTTTGCGGGCAGGAGAAGATGGAGGAGGCGATGAGGGTGTTTGTGGAGATGGAGAGGAGTGGTTGTGAGGTTGATGTGACTTATACTACTTTGATTAATGGATTTGTAAGTGAGGGAAGATTGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003676 GO:0003723 GO:0003824 GO:0004518 GO:0004519 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0006139 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009451 GO:0009987 GO:0016070 GO:0016787 GO:0016788 GO:0034641 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043412 GO:0044237 GO:0044238 GO:0044424 GO:0044464 GO:0046483 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 PPR_3

Protein Analysis

191

Amino Acids

21.76

Weight (kDa)

4.83

Isoelectric Point (pI)

32.15

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	106 - 152	1.6e-15	PPR repeat family
PPR_3	PF13812	106 - 151	9.4e-08	Pentatricopeptide repeat domain
PPR_1	PF12854	135 - 168	3.3e-10	PPR repeat
PPR_2	PF13041	140 - 186	3.4e-14	PPR repeat family
PPR	PF01535	142 - 172	2.4e-08	PPR repeat

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

Font Size (px)

Line Width

Align Labels (Cladogram)

Image

Tree File

Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0003945)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_4g05081
malus_domestica	MD10G1101700.v1.1
pyrus_communis	pycom09g04910 pycom15g38900
rosa_chinensis	RchiOBHm_Chr2g0123831 RchiOBHm_Chr4g0385181 RchiOBHm_Chr5g0064611
rosa_laevigata	RLG00000008165 RLG00000018415 RLG00000019614
rosa_multiflora	Rmu_sc0000571.1_g000023 Rmu_sc0001609.1_g000009 Rmu_sc0002893.1_g000021 Rmu_sc0003314.1_g000036 Rmu_sc0004010.1_g000014 Rmu_sc0008955.1_g000004 Rmu_sc0026245.1_g000002 Rmu_sc0027612.1_g000001
rosa_roxburghii	Rroxscaffold_5G00379810 Rroxscaffold_7G00189080
rosa_rugosa	Rorug03G0223000 Rorug06G0045100
rosa_samantha	Rh1CG355700 Rh1DG373200 Rh2BG315600 Rh3BG307100 Rh3CG368600 Rh3DG369600 Rh6BG404300 Rh6DG233700 Rh6DG396800 Rh6DG396900 Rh7AG211300 Rh7CG234500

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc36I	ACCTGC	1 cut(s)	94
AccI	GTMKAC	2 cut(s)	129, 431
AciI	CCGC	3 cut(s)	107, 177, 456
AcsI	RAATTY	1 cut(s)	212
AcuI	CTGAAG	1 cut(s)	53
AcyI	GRCGYC	1 cut(s)	261
AfiI	CCNNNNNNNGG	1 cut(s)	223
AgsI	TTSAA	1 cut(s)	388
AluBI	AGCT	3 cut(s)	103, 241, 382
AluI	AGCT	3 cut(s)	103, 241, 382
Alw21I	GWGCWC	2 cut(s)	243, 308
Alw26I	GTCTC	1 cut(s)	303
Ama87I	CYCGRG	1 cut(s)	222
ApoI	RAATTY	1 cut(s)	212
AseI	ATTAAT	1 cut(s)	546
AspS9I	GGNCC	2 cut(s)	109, 226
AsuC2I	CCSGG	2 cut(s)	223, 224
AsuHPI	GGTGA	1 cut(s)	7
AvaI	CYCGRG	1 cut(s)	222
AvaII	GGWCC	2 cut(s)	109, 226
BanII	GRGCYC	1 cut(s)	243
Bbv12I	GWGCWC	2 cut(s)	243, 308
BccI	CCATC	3 cut(s)	358, 463, 493
BcnI	CCSGG	2 cut(s)	223, 224
BcoDI	GTCTC	1 cut(s)	303
BfaI	CTAG	4 cut(s)	95, 137, 149, 236
BfuAI	ACCTGC	1 cut(s)	94
BisI	GCNGC	1 cut(s)	177
BlsI	GCNGC	1 cut(s)	178
Bme1390I	CCNGG	2 cut(s)	223, 224
Bme18I	GGWCC	2 cut(s)	109, 226
BmeT110I	CYCGRG	1 cut(s)	222
BmgT120I	GGNCC	2 cut(s)	109, 226
BmiI	GGNNCC	2 cut(s)	227, 228
BmrFI	CCNGG	2 cut(s)	223, 224
BmsI	GCATC	1 cut(s)	361
Bpu10I	CCTNAGC	1 cut(s)	351
BpuMI	CCSGG	2 cut(s)	223, 224
BsaHI	GRCGYC	1 cut(s)	261
BsaJI	CCNNGG	2 cut(s)	120, 222
BsaXI	ACNNNNNCTCC	4 cut(s)	391, 421, 499, 529
Bsc4I	CCNNNNNNNGG	1 cut(s)	223
BseDI	CCNNGG	2 cut(s)	120, 222
BseLI	CCNNNNNNNGG	1 cut(s)	223
BseMII	CTCAG	1 cut(s)	365
BseRI	GAGGAG	3 cut(s)	412, 488, 520
BsiHKAI	GWGCWC	2 cut(s)	243, 308
BsiHKCI	CYCGRG	1 cut(s)	222
BsiSI	CCGG	2 cut(s)	223, 258
BslFI	GGGAC	1 cut(s)	212
BslI	CCNNNNNNNGG	1 cut(s)	223
BsmAI	GTCTC	1 cut(s)	303
BsmFI	GGGAC	1 cut(s)	212
BsoBI	CYCGRG	1 cut(s)	222
Bsp1286I	GDGCHC	2 cut(s)	243, 308
Bsp143I	GATC	1 cut(s)	36
BspACI	CCGC	3 cut(s)	107, 177, 456
BspCNI	CTCAG	1 cut(s)	364
BspLI	GGNNCC	2 cut(s)	227, 228
BspMI	ACCTGC	1 cut(s)	94
BssECI	CCNNGG	2 cut(s)	120, 222
BssMI	GATC	1 cut(s)	36
BssNAI	GTATAC	1 cut(s)	432
BssNI	GRCGYC	1 cut(s)	261
BssT1I	CCWWGG	1 cut(s)	120
Bst1107I	GTATAC	1 cut(s)	432
Bst4CI	ACNGT	1 cut(s)	23
BstACI	GRCGYC	1 cut(s)	261
BstC8I	GCNNGC	4 cut(s)	105, 243, 308, 458
BstDEI	CTNAG	1 cut(s)	351
BstEII	GGTNACC	1 cut(s)	81
BstKTI	GATC	1 cut(s)	39
BstMAI	GTCTC	1 cut(s)	303
BstMBI	GATC	1 cut(s)	36
BstPI	GGTNACC	1 cut(s)	81
BstSCI	CCNGG	2 cut(s)	221, 222
BstZ17I	GTATAC	1 cut(s)	432
BtgZI	GCGATG	1 cut(s)	494
BveI	ACCTGC	1 cut(s)	94
Cac8I	GCNNGC	4 cut(s)	105, 243, 308, 458
Cfr13I	GGNCC	2 cut(s)	109, 226
Cfr9I	CCCGGG	1 cut(s)	222
CseI	GACGC	1 cut(s)	250
CviJI	RGCY	3 cut(s)	103, 241, 382
CviKI_1	RGCY	3 cut(s)	103, 241, 382
DdeI	CTNAG	1 cut(s)	351
DpnI	GATC	1 cut(s)	38
DpnII	GATC	1 cut(s)	36
EciI	GGCGGA	1 cut(s)	122
Ecl136II	GAGCTC	1 cut(s)	241
Eco130I	CCWWGG	1 cut(s)	120
Eco24I	GRGCYC	1 cut(s)	243
Eco47I	GGWCC	2 cut(s)	109, 226
Eco53kI	GAGCTC	1 cut(s)	241
Eco57I	CTGAAG	1 cut(s)	53
Eco88I	CYCGRG	1 cut(s)	222
Eco91I	GGTNACC	1 cut(s)	81
EcoICRI	GAGCTC	1 cut(s)	241
EcoO109I	RGGNCCY	1 cut(s)	226
EcoO65I	GGTNACC	1 cut(s)	81
EcoT14I	CCWWGG	1 cut(s)	120
EcoT38I	GRGCYC	1 cut(s)	243
ErhI	CCWWGG	1 cut(s)	120
FaiI	YATR	9 cut(s)	196, 208, 315, 327, 348, 378, 432, 440, 534
FaqI	GGGAC	1 cut(s)	212
FauI	CCCGC	1 cut(s)	449
FblI	GTMKAC	2 cut(s)	129, 431
Fnu4HI	GCNGC	1 cut(s)	177
FriOI	GRGCYC	1 cut(s)	243
Fsp4HI	GCNGC	1 cut(s)	177
FspBI	CTAG	4 cut(s)	95, 137, 149, 236
GluI	GCNGC	1 cut(s)	177
HapII	CCGG	2 cut(s)	223, 258
HgaI	GACGC	1 cut(s)	250
Hin1I	GRCGYC	1 cut(s)	261
HinfI	GANTC	2 cut(s)	53, 442
HpaII	CCGG	2 cut(s)	223, 258
HphI	GGTGA	1 cut(s)	7
Hpy166II	GTNNAC	3 cut(s)	130, 413, 432
Hpy188I	TCNGA	1 cut(s)	277
Hpy8I	GTNNAC	3 cut(s)	130, 413, 432
Hpy99I	CGWCG	1 cut(s)	266
HpyAV	CCTTC	1 cut(s)	397
HpyCH4III	ACNGT	1 cut(s)	23
HpyCH4V	TGCA	2 cut(s)	210, 271
HpyF3I	CTNAG	1 cut(s)	351
Hsp92I	GRCGYC	1 cut(s)	261
KflI	GGGWCCC	1 cut(s)	226
Kzo9I	GATC	1 cut(s)	36
LpnPI	CCDG	7 cut(s)	89, 99, 236, 271, 338, 431, 446
LweI	GCATC	1 cut(s)	361
MaeI	CTAG	4 cut(s)	95, 137, 149, 236
MaeIII	GTNAC	4 cut(s)	27, 81, 115, 526
MalI	GATC	1 cut(s)	38
MboI	GATC	1 cut(s)	36
MboII	GAAGA	3 cut(s)	46, 373, 478
MhlI	GDGCHC	2 cut(s)	243, 308
MluCI	AATT	2 cut(s)	212, 331
MmeI	TCCRAC	1 cut(s)	300
MnlI	CCTC	9 cut(s)	67, 390, 393, 466, 469, 477, 498, 511, 556
MseI	TTAA	2 cut(s)	281, 546
MspA1I	CMGCKG	1 cut(s)	103
MspI	CCGG	2 cut(s)	223, 258
MspR9I	CCNGG	2 cut(s)	223, 224
NciI	CCSGG	2 cut(s)	223, 224
NdeII	GATC	1 cut(s)	36
NlaIV	GGNNCC	2 cut(s)	227, 228
NmuCI	GTSAC	2 cut(s)	115, 526
PfeI	GAWTC	2 cut(s)	53, 442
PkrI	GCNGC	1 cut(s)	178
PpuMI	RGGWCCY	1 cut(s)	226
PshBI	ATTAAT	1 cut(s)	546
Psp124BI	GAGCTC	1 cut(s)	243
Psp5II	RGGWCCY	1 cut(s)	226
PspEI	GGTNACC	1 cut(s)	81
PspN4I	GGNNCC	2 cut(s)	227, 228
PspPI	GGNCC	2 cut(s)	109, 226
PspPPI	RGGWCCY	1 cut(s)	226
PvuII	CAGCTG	1 cut(s)	103
SacI	GAGCTC	1 cut(s)	243
SaqAI	TTAA	2 cut(s)	281, 546
SatI	GCNGC	1 cut(s)	177
Sau3AI	GATC	1 cut(s)	36
Sau96I	GGNCC	2 cut(s)	109, 226
ScrFI	CCNGG	2 cut(s)	223, 224
SduI	GDGCHC	2 cut(s)	243, 308
SfaNI	GCATC	1 cut(s)	361
SinI	GGWCC	2 cut(s)	109, 226
SmaI	CCCGGG	1 cut(s)	224
Sse9I	AATT	2 cut(s)	212, 331
SsiI	CCGC	3 cut(s)	107, 177, 456
SspI	AATATT	1 cut(s)	204
SspMI	CTAG	4 cut(s)	95, 137, 149, 236
SstI	GAGCTC	1 cut(s)	243
StyD4I	CCNGG	2 cut(s)	221, 222
StyI	CCWWGG	1 cut(s)	120
TaaI	ACNGT	1 cut(s)	23
TaqI	TCGA	1 cut(s)	285
TasI	AATT	2 cut(s)	212, 331
TauI	GCSGC	1 cut(s)	179
TfiI	GAWTC	2 cut(s)	53, 442
Tru1I	TTAA	2 cut(s)	281, 546
Tru9I	TTAA	2 cut(s)	281, 546
TseFI	GTSAC	2 cut(s)	115, 526
Tsp45I	GTSAC	2 cut(s)	115, 526
TspMI	CCCGGG	1 cut(s)	222
VpaK11BI	GGWCC	2 cut(s)	109, 226
VspI	ATTAAT	1 cut(s)	546
XapI	RAATTY	1 cut(s)	212
XmaI	CCCGGG	1 cut(s)	222
XmiI	GTMKAC	2 cut(s)	129, 431
XspI	CTAG	4 cut(s)	95, 137, 149, 236

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