Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6D

Orthogroup ID

OG0003945

Physical Location & Seq

Genomic Coordinates Reverse (-)

58778474 .. 58778812

Gene Structure 339 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6DG396800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 339 bp

ATGAGGAGGAAGGGTTGTGAGCCCAATGCGGGTTCGTATACGACTATGATTCAGGCACTTTGCTGGCAGGAGAAGATGGAGGAGGCGATGAGGGTGTTTGTGGAGATGGAGAGGAGTGGTTGTGAGGTTGATGTTGTGACTTATACTACTTTGATTAGTGGATTTTGTAAGTGGGGGAAGATTGTGAGGAGTTATGAGATTTTGGAGAGTATAATAAGGAAAGGGTTTACGCCGAGTCAGATGACTTACTTGCAGATTATGTTGGCTCATGAGAAGAAGGAAGACTTGGAGGCGTGTATAATTGATGGGGCAGATGAGGAAGATTGGTTGCATGCCTGA

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

112

Amino Acids

12.95

Weight (kDa)

4.92

Isoelectric Point (pI)

44.25

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_1	PF12854	4 - 37	4.6e-10	PPR repeat
PPR_2	PF13041	8 - 57	6.1e-20	PPR repeat family
PPR	PF01535	12 - 41	5e-09	PPR repeat
PPR_3	PF13812	31 - 87	4.1e-09	Pentatricopeptide repeat domain
PPR_1	PF12854	40 - 69	5.8e-10	PPR repeat
PPR_2	PF13041	44 - 85	3.5e-08	PPR repeat family
PPR	PF01535	46 - 76	6.3e-07	PPR repeat

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: 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)
AccI	GTMKAC	1 cut(s)	38
AciI	CCGC	1 cut(s)	29
AfiI	CCNNNNNNNGG	1 cut(s)	29
AjuI	GAANNNNNNNTTGG	2 cut(s)	269, 301
BanII	GRGCYC	1 cut(s)	24
BbsI	GAAGAC	1 cut(s)	288
BccI	CCATC	3 cut(s)	70, 100, 299
BpiI	GAAGAC	1 cut(s)	288
BsaXI	ACNNNNNCTCC	3 cut(s)	28, 106, 136
Bsc4I	CCNNNNNNNGG	1 cut(s)	29
BseLI	CCNNNNNNNGG	1 cut(s)	29
BseRI	GAGGAG	4 cut(s)	19, 95, 127, 202
BslI	CCNNNNNNNGG	1 cut(s)	29
Bsp1286I	GDGCHC	1 cut(s)	24
BspACI	CCGC	1 cut(s)	29
BspHI	TCATGA	1 cut(s)	268
BssNAI	GTATAC	1 cut(s)	39
Bst1107I	GTATAC	1 cut(s)	39
BstC8I	GCNNGC	2 cut(s)	65, 333
BstNSI	RCATGY	1 cut(s)	335
BstV2I	GAAGAC	1 cut(s)	288
BstZ17I	GTATAC	1 cut(s)	39
BtgZI	GCGATG	1 cut(s)	101
Cac8I	GCNNGC	2 cut(s)	65, 333
CciI	TCATGA	1 cut(s)	268
CviAII	CATG	2 cut(s)	269, 332
CviJI	RGCY	2 cut(s)	22, 266
CviKI_1	RGCY	2 cut(s)	22, 266
Eco24I	GRGCYC	1 cut(s)	24
EcoT38I	GRGCYC	1 cut(s)	24
FaeI	CATG	2 cut(s)	272, 335
FaiI	YATR	9 cut(s)	39, 47, 144, 195, 212, 260, 270, 299, 333
FalI	AAGNNNNNCTT	2 cut(s)	269, 301
FatI	CATG	2 cut(s)	268, 331
FauI	CCCGC	1 cut(s)	22
FblI	GTMKAC	1 cut(s)	38
FriOI	GRGCYC	1 cut(s)	24
Hin1II	CATG	2 cut(s)	272, 335
HinfI	GANTC	2 cut(s)	49, 235
Hpy166II	GTNNAC	2 cut(s)	39, 228
Hpy188I	TCNGA	1 cut(s)	240
Hpy188III	TCNNGA	1 cut(s)	269
Hpy8I	GTNNAC	2 cut(s)	39, 228
HpyAV	CCTTC	2 cut(s)	4, 271
HpyCH4V	TGCA	2 cut(s)	253, 331
Hsp92II	CATG	2 cut(s)	272, 335
LpnPI	CCDG	3 cut(s)	38, 49, 53
MaeIII	GTNAC	1 cut(s)	136
MboII	GAAGA	5 cut(s)	85, 190, 286, 293, 332
MhlI	GDGCHC	1 cut(s)	24
MluCI	AATT	1 cut(s)	300
MlyI	GAGTC	1 cut(s)	244
MnlI	CCTC	8 cut(s)	73, 76, 84, 105, 118, 180, 283, 310
NlaIII	CATG	2 cut(s)	272, 335
NmeAIII	GCCGAG	1 cut(s)	258
NmuCI	GTSAC	1 cut(s)	136
NspI	RCATGY	1 cut(s)	335
PaeI	GCATGC	1 cut(s)	335
PagI	TCATGA	1 cut(s)	268
PfeI	GAWTC	1 cut(s)	49
PleI	GAGTC	1 cut(s)	243
PpsI	GAGTC	1 cut(s)	243
SchI	GAGTC	1 cut(s)	244
SduI	GDGCHC	1 cut(s)	24
SetI	ASST	1 cut(s)	129
SgeI	CNNG	9 cut(s)	42, 65, 76, 80, 246, 262, 281, 298, 306
SphI	GCATGC	1 cut(s)	335
Sse9I	AATT	1 cut(s)	300
SsiI	CCGC	1 cut(s)	29
TasI	AATT	1 cut(s)	300
TfiI	GAWTC	1 cut(s)	49
TseFI	GTSAC	1 cut(s)	136
Tsp45I	GTSAC	1 cut(s)	136
XceI	RCATGY	1 cut(s)	335
XmiI	GTMKAC	1 cut(s)	38

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