Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4D

Orthogroup ID

OG0001032

Physical Location & Seq

Genomic Coordinates Reverse (-)

61870091 .. 61870507

Gene Structure 417 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4DG403200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 417 bp

ATGTGTAAGGAAGCAAACTTTAGTGGAGTTGAGACGATCTTCAGTGAGATGTCGGAGACGGGGTTTATTCCAGACAAATATGTATACACTTCTTGGATTGCTGGGCTATGCAGACAGGGTAATCTGGTCGAGGCTTTTAGACTCAAGAATAAAATGGTTAAAGAGGGCATCAGCCCGGATTTGTTTACTTATAGCTCACTTATTTTTGGTTTAGCAAGTAAGGGACTCATGGTTGAAGCACAACAGGTTTTCGATGATATGTTGAAAAGAGGAATTACTCCTGACCGTCATGTCTTTGGTATTCTGATAAGAGGGTATTATGATGAGGGTAATGATGTTGCCATTTTAGGTTTGCATGATGAAATGAGAAAGAGAGGGCTTGTAATCACAGGAGGTAAAGGAGATGGAGAGCATTGA

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

138

Amino Acids

15.39

Weight (kDa)

5.6

Isoelectric Point (pI)

23.16

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_long	PF17177	10 - 111	2.5e-06	Pentacotripeptide-repeat region of PRORP
PPR_3	PF13812	13 - 68	8.4e-09	Pentatricopeptide repeat domain
PPR_1	PF12854	21 - 53	4.7e-08	PPR repeat
PPR_2	PF13041	24 - 72	1.1e-14	PPR repeat family
PPR	PF01535	28 - 57	1.2e-06	PPR repeat
PPR_1	PF12854	56 - 87	5.7e-10	PPR repeat
PPR	PF01535	62 - 92	2.2e-07	PPR repeat
PPR_2	PF13041	67 - 106	4.8e-09	PPR repeat family

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Orthologous Genes (Group: OG0001032)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G27830 AT5G27830 AT5G27830 AT5G27830 AT5G27830 AT5G27830
fragaria_vesca	FvH4_6g06800 FvH4_6g06800 FvH4_6g06800
malus_domestica	MD04G1198500.v1.1
prunus_persica	Prupe.6G319500_v2.0.a1
pyrus_communis	pycom04g17560 pycom12g19820
rosa_chinensis	RchiOBHm_Chr2g0123281 RchiOBHm_Chr3g0456161 RchiOBHm_Chr3g0458101 RchiOBHm_Chr4g0442861 RchiOBHm_Chr4g0442871 RchiOBHm_Chr4g0442951
rosa_laevigata	RLG00000005970 RLG00000010014
rosa_multiflora	Rmu_sc0000121.1_g000021 Rmu_sc0000124.1_g000039 Rmu_sc0000279.1_g000039 Rmu_sc0000384.1_g000020 Rmu_sc0001917.1_g000005 Rmu_sc0002607.1_g000043 Rmu_sc0007295.1_g000002 Rmu_sc0042689.1_g000001
rosa_roxburghii	Rroxscaffold_6G00423260 Rroxscaffold_6G00423720
rosa_rugosa	Rorug03G0012000 Rorug03G0012100 Rorug04G0109700 Rorug04G0343700
rosa_samantha	Rh1CG037400 Rh2BG184700 Rh2BG311600 Rh3AG072300 Rh3AG085600 Rh3BG074200 Rh3BG088300 Rh3CG073700 Rh3DG075500 Rh3DG089200 Rh4AG396600 Rh4AG396900 Rh4AG397000 Rh4AG397400 Rh4AG397800 Rh4BG409300 Rh4CG424800 Rh4DG403200 Rh4DG403500 Rh4DG403600 Rh4DG404100 Rh5BG556500 Rh6BG383200
rosa_wichuraiana	Rw2G024280 Rw3G005860 Rw3G006140

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AasI	GACNNNNNNGTC	1 cut(s)	290
AccI	GTMKAC	1 cut(s)	84
AcuI	CTGAAG	1 cut(s)	25
AgsI	TTSAA	2 cut(s)	236, 265
AluBI	AGCT	1 cut(s)	195
AluI	AGCT	1 cut(s)	195
Alw26I	GTCTC	2 cut(s)	26, 50
AsuC2I	CCSGG	1 cut(s)	176
BccI	CCATC	1 cut(s)	398
BcnI	CCSGG	1 cut(s)	176
BcoDI	GTCTC	2 cut(s)	26, 50
Bme1390I	CCNGG	1 cut(s)	176
BmrFI	CCNGG	1 cut(s)	176
BmsI	GCATC	1 cut(s)	177
BpuEI	CTTGAG	1 cut(s)	128
BpuMI	CCSGG	1 cut(s)	176
BsaXI	ACNNNNNCTCC	2 cut(s)	47, 77
BseYI	CCCAGC	1 cut(s)	101
BsiSI	CCGG	1 cut(s)	176
BslFI	GGGAC	1 cut(s)	237
BsmAI	GTCTC	2 cut(s)	26, 50
BsmBI	CGTCTC	2 cut(s)	26, 50
BsmFI	GGGAC	1 cut(s)	237
Bsp143I	GATC	1 cut(s)	36
BssMI	GATC	1 cut(s)	36
BssNAI	GTATAC	1 cut(s)	85
Bst1107I	GTATAC	1 cut(s)	85
Bst4CI	ACNGT	1 cut(s)	287
BstKTI	GATC	1 cut(s)	39
BstMAI	GTCTC	2 cut(s)	26, 50
BstMBI	GATC	1 cut(s)	36
BstSCI	CCNGG	1 cut(s)	174
BstZ17I	GTATAC	1 cut(s)	85
BtsIMutI	CAGTG	1 cut(s)	49
CviAII	CATG	3 cut(s)	229, 290, 356
CviJI	RGCY	5 cut(s)	106, 134, 174, 195, 379
CviKI_1	RGCY	5 cut(s)	106, 134, 174, 195, 379
DpnI	GATC	1 cut(s)	38
DpnII	GATC	1 cut(s)	36
DrdI	GACNNNNNNGTC	1 cut(s)	290
DseDI	GACNNNNNNGTC	1 cut(s)	290
Eco57I	CTGAAG	1 cut(s)	25
Esp3I	CGTCTC	2 cut(s)	26, 50
FaeI	CATG	3 cut(s)	232, 293, 359
FaiI	YATR	9 cut(s)	81, 85, 109, 192, 230, 260, 291, 321, 357
FaqI	GGGAC	1 cut(s)	237
FatI	CATG	3 cut(s)	228, 289, 355
FblI	GTMKAC	1 cut(s)	84
GsaI	CCCAGC	1 cut(s)	105
HapII	CCGG	1 cut(s)	176
Hin1II	CATG	3 cut(s)	232, 293, 359
HinfI	GANTC	2 cut(s)	141, 225
HpaII	CCGG	1 cut(s)	176
Hpy166II	GTNNAC	2 cut(s)	85, 186
Hpy188I	TCNGA	2 cut(s)	55, 306
Hpy188III	TCNNGA	3 cut(s)	71, 145, 281
Hpy8I	GTNNAC	2 cut(s)	85, 186
HpyCH4III	ACNGT	1 cut(s)	287
HpyCH4V	TGCA	2 cut(s)	111, 355
Hsp92II	CATG	3 cut(s)	232, 293, 359
Kzo9I	GATC	1 cut(s)	36
LpnPI	CCDG	8 cut(s)	84, 87, 101, 110, 189, 230, 294, 375
LweI	GCATC	1 cut(s)	177
MalI	GATC	1 cut(s)	38
MboI	GATC	1 cut(s)	36
MboII	GAAGA	1 cut(s)	31
MluCI	AATT	1 cut(s)	273
MlyI	GAGTC	2 cut(s)	135, 219
MmeI	TCCRAC	1 cut(s)	33
MnlI	CCTC	7 cut(s)	124, 157, 263, 305, 319, 368, 386
MseI	TTAA	1 cut(s)	159
MspI	CCGG	1 cut(s)	176
MspR9I	CCNGG	1 cut(s)	176
NciI	CCSGG	1 cut(s)	176
NdeII	GATC	1 cut(s)	36
NlaIII	CATG	3 cut(s)	232, 293, 359
PleI	GAGTC	2 cut(s)	135, 219
PpsI	GAGTC	2 cut(s)	135, 219
PspFI	CCCAGC	1 cut(s)	101
SaqAI	TTAA	1 cut(s)	159
Sau3AI	GATC	1 cut(s)	36
SchI	GAGTC	2 cut(s)	135, 219
ScrFI	CCNGG	1 cut(s)	176
SetI	ASST	4 cut(s)	197, 249, 352, 397
SfaNI	GCATC	1 cut(s)	177
SmlI	CTYRAG	1 cut(s)	143
SmoI	CTYRAG	1 cut(s)	143
Sse9I	AATT	1 cut(s)	273
StyD4I	CCNGG	1 cut(s)	174
TaaI	ACNGT	1 cut(s)	287
TaqI	TCGA	2 cut(s)	129, 252
TasI	AATT	1 cut(s)	273
Tru1I	TTAA	1 cut(s)	159
Tru9I	TTAA	1 cut(s)	159
TscAI	CASTG	1 cut(s)	49
TspDTI	ATGAA	1 cut(s)	375
TspRI	CASTG	1 cut(s)	49
XmiI	GTMKAC	1 cut(s)	84

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