Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3B

Orthogroup ID

OG0001472

Physical Location & Seq

Genomic Coordinates Reverse (-)

15792621 .. 15793136

Gene Structure 516 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3BG179700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 516 bp

ATGGCAGAAAGAGGTGTGGCTCCAAACTCAGTGTGCTTCACTACTCTGATAGACATATATTGCAAGGAAGGAGACTTGGTCGAAGCAAAGCGGGTATTTCAGGAGATGGAAAGTAAAGGAGAGAGGCCTAATAACGTAACATACAATGCTCTAATTGATGGGCATACCAAGAAAGGTAAACTGAAGGAAGCGCATAAGATAAAAGAGGAGATGGAAGACAAGGGTTTGATGGCAGATTCGTATACATATTCATCGCTTATACATGGTGAATGTATTGCTGGCAACGTGGATGCGGCACTGACATTGTTTCATGAAATGTCCCAGAGGGGTTTAACTCGAAACGTTGTCACATACACAGTAATTATTTCGGGTTTGTCTAAGGTGGGGAGAAAAGAAGAAGCTTTCAAATTGTACGATGACATGAAAAAAGCAAGCATCATACCTGATGACAGGGTATATAATTCACTTGTACAAGGCCTTTATACAGACAAGTCTAGCTCTATGACAGATGAGTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PPR PPR_1 PPR_2 PPR_3

Protein Analysis

171

Amino Acids

19.13

Weight (kDa)

5.65

Isoelectric Point (pI)

20.95

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_long	PF17177	1 - 94	1.1e-06	Pentacotripeptide-repeat region of PRORP
PPR_3	PF13812	1 - 53	7.2e-11	Pentatricopeptide repeat domain
PPR_1	PF12854	4 - 37	5e-12	PPR repeat
PPR_2	PF13041	8 - 54	6.8e-17	PPR repeat family
PPR	PF01535	11 - 40	3.3e-09	PPR repeat
PPR_1	PF12854	40 - 72	1.2e-09	PPR repeat
PPR_2	PF13041	43 - 91	5.4e-17	PPR repeat family
TPR_24	PF23276	45 - 140	7.4e-07	Fungal tetratrico peptide repeats
PPR	PF01535	46 - 76	3.1e-08	PPR repeat
PPR_3	PF13812	66 - 123	2.6e-11	Pentatricopeptide repeat domain
PPR_1	PF12854	74 - 107	7.8e-10	PPR repeat
PPR	PF01535	81 - 111	3.4e-07	PPR repeat
PPR_2	PF13041	85 - 127	1.4e-11	PPR repeat family
PPR_3	PF13812	102 - 157	4.1e-09	Pentatricopeptide repeat domain
PPR_1	PF12854	109 - 142	6.4e-09	PPR repeat
PPR_2	PF13041	113 - 160	1.7e-15	PPR repeat family
PPR	PF01535	116 - 144	9.4e-08	PPR repeat

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Orthologous Genes (Group: OG0001472)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G12615
fragaria_vesca	FvH4_3g40110
malus_domestica	MD04G1014300.v1.1 MD04G1014400.v1.1 MD04G1015100.v1.1 MD04G1015700.v1.1 MD04G1015800.v1.1 MD04G1015900.v1.1 MD04G1016200.v1.1 MD04G1021600.v1.1 MD05G1145400.v1.1 MD07G1093000.v1.1 MD10G1069200.v1.1 MD11G1128800.v1.1
prunus_persica	Prupe.1G160300_v2.0.a1 Prupe.1G162600_v2.0.a1 Prupe.1G166700_v2.0.a1 Prupe.1G167000_v2.0.a1 Prupe.6G346200_v2.0.a1
pyrus_communis	pycom04g01130 pycom04g01150 pycom04g01200 pycom04g01740 pycom04g01770 pycom04g10990
rosa_chinensis	RchiOBHm_Chr4g0414121 RchiOBHm_Chr7g0237341
rosa_laevigata	RLG00000008171 RLG00000008172 RLG00000036265
rosa_multiflora	Rmu_co8044332.1_g000001 Rmu_co8232951.1_g000001 Rmu_sc0003264.1_g000004 Rmu_sc0012180.1_g000010 Rmu_sc0012322.1_g000001 Rmu_sc0029476.1_g000001
rosa_roxburghii	Rroxscaffold_1G00018610 Rroxscaffold_5G00358060 Rroxscaffold_5G00358070 Rroxscaffold_5G00358080
rosa_rugosa	Rorug04G0125800 Rorug04G0125900 Rorug04G0126000
rosa_samantha	Rh1DG083800 Rh3BG179700 Rh3DG195400 Rh4AG184400 Rh4BG183800 Rh4DG179700 Rh7BG314900
rosa_wichuraiana	Rw4G015690

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	242
AciI	CCGC	2 cut(s)	91, 293
AclI	AACGTT	1 cut(s)	342
AcuI	CTGAAG	1 cut(s)	203
AfaI	GTAC	2 cut(s)	413, 471
AgsI	TTSAA	1 cut(s)	406
AluBI	AGCT	2 cut(s)	401, 498
AluI	AGCT	2 cut(s)	401, 498
Alw26I	GTCTC	1 cut(s)	66
AoxI	GGCC	2 cut(s)	125, 475
AspLEI	GCGC	1 cut(s)	193
AsuHPI	GGTGA	1 cut(s)	278
BbsI	GAAGAC	1 cut(s)	222
BccI	CCATC	4 cut(s)	100, 152, 205, 223
BcoDI	GTCTC	1 cut(s)	66
BfaI	CTAG	1 cut(s)	495
BisI	GCNGC	1 cut(s)	294
BlsI	GCNGC	1 cut(s)	295
BmiI	GGNNCC	1 cut(s)	21
BmsI	GCATC	2 cut(s)	280, 444
BpiI	GAAGAC	1 cut(s)	222
BsaXI	ACNNNNNCTCC	2 cut(s)	63, 93
BseGI	GGATG	1 cut(s)	295
BseMII	CTCAG	1 cut(s)	42
BseRI	GAGGAG	1 cut(s)	221
BshFI	GGCC	2 cut(s)	127, 477
BslFI	GGGAC	1 cut(s)	304
BsmAI	GTCTC	1 cut(s)	66
BsmFI	GGGAC	1 cut(s)	304
BsnI	GGCC	2 cut(s)	127, 477
Bsp1407I	TGTACA	1 cut(s)	469
BspACI	CCGC	2 cut(s)	91, 293
BspANI	GGCC	2 cut(s)	127, 477
BspCNI	CTCAG	1 cut(s)	41
BspHI	TCATGA	1 cut(s)	310
BspLI	GGNNCC	1 cut(s)	21
BsrGI	TGTACA	1 cut(s)	469
BssNAI	GTATAC	1 cut(s)	243
Bst1107I	GTATAC	1 cut(s)	243
Bst4CI	ACNGT	1 cut(s)	358
BstAUI	TGTACA	1 cut(s)	469
BstC8I	GCNNGC	2 cut(s)	280, 433
BstDEI	CTNAG	2 cut(s)	28, 378
BstF5I	GGATG	1 cut(s)	295
BstHHI	GCGC	1 cut(s)	193
BstMAI	GTCTC	1 cut(s)	66
BstV2I	GAAGAC	1 cut(s)	222
BstZ17I	GTATAC	1 cut(s)	243
BsuRI	GGCC	2 cut(s)	127, 477
BtgZI	GCGATG	1 cut(s)	237
BtsCI	GGATG	1 cut(s)	295
BtsIMutI	CAGTG	2 cut(s)	36, 296
Cac8I	GCNNGC	2 cut(s)	280, 433
CciI	TCATGA	1 cut(s)	310
CfoI	GCGC	1 cut(s)	193
Csp6I	GTAC	2 cut(s)	412, 470
CviAII	CATG	3 cut(s)	263, 311, 421
CviJI	RGCY	5 cut(s)	20, 127, 401, 477, 498
CviKI_1	RGCY	5 cut(s)	20, 127, 401, 477, 498
CviQI	GTAC	2 cut(s)	412, 470
DdeI	CTNAG	2 cut(s)	28, 378
Eco147I	AGGCCT	2 cut(s)	127, 477
Eco57I	CTGAAG	1 cut(s)	203
FaeI	CATG	3 cut(s)	266, 314, 424
FaqI	GGGAC	1 cut(s)	304
FatI	CATG	3 cut(s)	262, 310, 420
FauI	CCCGC	1 cut(s)	84
FblI	GTMKAC	1 cut(s)	242
Fnu4HI	GCNGC	1 cut(s)	294
FokI	GGATG	1 cut(s)	302
Fsp4HI	GCNGC	1 cut(s)	294
FspBI	CTAG	1 cut(s)	495
GlaI	GCGC	1 cut(s)	192
GluI	GCNGC	1 cut(s)	294
HaeIII	GGCC	2 cut(s)	127, 477
HhaI	GCGC	1 cut(s)	193
Hin1II	CATG	3 cut(s)	266, 314, 424
Hin6I	GCGC	1 cut(s)	191
HinP1I	GCGC	1 cut(s)	191
HindIII	AAGCTT	1 cut(s)	399
HinfI	GANTC	1 cut(s)	236
HphI	GGTGA	1 cut(s)	278
Hpy166II	GTNNAC	2 cut(s)	179, 243
Hpy188I	TCNGA	1 cut(s)	48
Hpy188III	TCNNGA	2 cut(s)	101, 311
Hpy8I	GTNNAC	2 cut(s)	179, 243
HpyAV	CCTTC	2 cut(s)	62, 178
HpyCH4III	ACNGT	1 cut(s)	358
HpyCH4IV	ACGT	3 cut(s)	135, 285, 342
HpyCH4V	TGCA	1 cut(s)	63
HpyF3I	CTNAG	2 cut(s)	28, 378
HpySE526I	ACGT	3 cut(s)	135, 285, 342
Hsp92II	CATG	3 cut(s)	266, 314, 424
HspAI	GCGC	1 cut(s)	191
LmnI	GCTCC	1 cut(s)	25
LpnPI	CCDG	5 cut(s)	86, 264, 335, 436, 456
LweI	GCATC	2 cut(s)	280, 444
MaeI	CTAG	1 cut(s)	495
MaeII	ACGT	3 cut(s)	135, 285, 342
MaeIII	GTNAC	2 cut(s)	136, 346
MboII	GAAGA	2 cut(s)	227, 407
MluCI	AATT	4 cut(s)	153, 360, 407, 460
MnlI	CCTC	4 cut(s)	5, 117, 199, 318
MseI	TTAA	1 cut(s)	332
NlaIII	CATG	3 cut(s)	266, 314, 424
NlaIV	GGNNCC	1 cut(s)	21
NmuCI	GTSAC	1 cut(s)	346
PagI	TCATGA	1 cut(s)	310
PceI	AGGCCT	2 cut(s)	127, 477
PfeI	GAWTC	1 cut(s)	236
PflFI	GACNNNGTC	1 cut(s)	77
PkrI	GCNGC	1 cut(s)	295
Psp1406I	AACGTT	1 cut(s)	342
PspN4I	GGNNCC	1 cut(s)	21
PsyI	GACNNNGTC	1 cut(s)	77
RsaI	GTAC	2 cut(s)	413, 471
RsaNI	GTAC	2 cut(s)	412, 470
SaqAI	TTAA	1 cut(s)	332
SatI	GCNGC	1 cut(s)	294
SetI	ASST	9 cut(s)	16, 138, 178, 288, 345, 384, 403, 445, 500
SfaNI	GCATC	2 cut(s)	280, 444
Sse9I	AATT	4 cut(s)	153, 360, 407, 460
SseBI	AGGCCT	2 cut(s)	127, 477
SsiI	CCGC	2 cut(s)	91, 293
SspMI	CTAG	1 cut(s)	495
StuI	AGGCCT	2 cut(s)	127, 477
TaaI	ACNGT	1 cut(s)	358
TaiI	ACGT	3 cut(s)	138, 288, 345
TaqI	TCGA	2 cut(s)	81, 337
TasI	AATT	4 cut(s)	153, 360, 407, 460
TatI	WGTACW	1 cut(s)	469
TauI	GCSGC	1 cut(s)	296
TfiI	GAWTC	1 cut(s)	236
Tru1I	TTAA	1 cut(s)	332
Tru9I	TTAA	1 cut(s)	332
TscAI	CASTG	2 cut(s)	36, 303
TseFI	GTSAC	1 cut(s)	346
Tsp45I	GTSAC	1 cut(s)	346
TspDTI	ATGAA	4 cut(s)	240, 299, 327, 437
TspRI	CASTG	2 cut(s)	36, 303
Tth111I	GACNNNGTC	1 cut(s)	77
XmiI	GTMKAC	1 cut(s)	242
XspI	CTAG	1 cut(s)	495

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