Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr6

Orthogroup ID

OG0003805

Physical Location & Seq

Genomic Coordinates Forward (+)

58062006 .. 58062820

Gene Structure 815 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000030229

Sequence Viewer

CDS Protein Promoter (2k)

Length: 780 bp

ATGATGTCATTTTGTCGCCTCCTCCGCCGTGCATTTTCCACCGCCACCGCCACCACCACCCAACCCAAACCCACAACTGCCAAGAGCATCAAAGCCATCTCCGCCGACCTCGCCAATGCTAAGCGCTTCCATGCGATTGAAGAAATCCTAGAGGACCAGAAGAAGTACGGTCGTACCCAGATTTCTCCGACTAGGGCCGACATGTTTGATAATGCCCAAAAGGTGTTCGATGAAATGCCTCAAAGAAACTGTGGGCGTACTGTGTTGTCCTTCAATGCTCTCTTTGGGGCCTGTGTGAACTCCAAGAAGTTTGATATGGTTGAGAAGATTTTCGGGGACGTACCGAAAAAGTTGTCGATTGAGCCTGATTTGGTGTCGTACAATACTGTGATCAAGGCATTTTGCAAGATGGATTCGTTTAACTCTACGGTTTTGGTGATTGAGATAATGGACAAGAAGGGTGTGAAGCCGAATGTAATCACGTTTAATACGATTTTGGATTGCTTGTATGGGAGTAAGCGGTTTTCGGATGCTGAGAAGATATGGGGTCAAATGGCAGAGAAGAATGTTGTTCCTGATATTAGGAGCTATAAAGCCAAGTTGCTGGGGTTGGCTCTGGAGAAGAGGAGTGAAAAAGGGGCTCAATTAGTTGAAGAGTTGAGGAGTATAGGAGTGAAACCTAATGTGTTCACCATCAATACCTTGATCAACGGATTTGTGAATGAGGGGAACTTGGATGAAGCTAAGCGGTGGTATGGTCAAATAGAGAAGAGTAGTTGA

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:0005737 GO:0005739 GO:0006139 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009451 GO:0009987 GO:0016020 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:0044444 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_2 PPR_3

Protein Analysis

260

Amino Acids

29.12

Weight (kDa)

9.33

Isoelectric Point (pI)

45.98

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_3	PF13812	74 - 136	3.9e-08	Pentatricopeptide repeat domain
PPR_2	PF13041	87 - 136	3.5e-08	PPR repeat family
PPR_2	PF13041	122 - 169	1.1e-12	PPR repeat family
PPR_3	PF13812	147 - 199	7.5e-07	Pentatricopeptide repeat domain
PPR_2	PF13041	157 - 199	5.5e-09	PPR repeat family
PPR_1	PF12854	224 - 249	1e-06	PPR repeat

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Publication-ready

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Orthologous Genes (Group: OG0003805)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G55890 AT3G13160
fragaria_vesca	FvH4_3g03043 FvH4_3g03070 FvH4_3g03080 FvH4_3g03160
malus_domestica	MD05G1334700.v1.1
prunus_persica	Prupe.4G030500_v2.0.a1
pyrus_communis	pycom05g30630 pycom10g26130
rosa_chinensis	RchiOBHm_Chr5g0004741 RchiOBHm_Chr5g0004781
rosa_laevigata	RLG00000030227 RLG00000030229 RLG00000031256 RLG00000031258 RLG00000031259 RLG00000031261
rosa_multiflora	Rmu_co8370515.1_g000001 Rmu_sc0002210.1_g000010 Rmu_sc0002210.1_g000016 Rmu_sc0008308.1_g000003 Rmu_sc0008308.1_g000014 Rmu_sc0010871.1_g000008 Rmu_sc0010871.1_g000027
rosa_roxburghii	Rroxscaffold_1G00070810 Rroxscaffold_1G00070830
rosa_samantha	Rh5BG041400 Rh5CG044900 Rh5CG045300 Rh5DG041300 Rh5DG041500 Rh5DG041800
rosa_wichuraiana	Rw5G004020

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AciI	CCGC	6 cut(s)	25, 42, 48, 102, 520, 748
AfaI	GTAC	5 cut(s)	167, 175, 259, 342, 380
AfeI	AGCGCT	1 cut(s)	125
AflIII	ACRYGT	1 cut(s)	201
AgsI	TTSAA	3 cut(s)	140, 274, 653
AluBI	AGCT	2 cut(s)	588, 743
AluI	AGCT	2 cut(s)	588, 743
Aor51HI	AGCGCT	1 cut(s)	125
AoxI	GGCC	2 cut(s)	195, 288
ArsI	GACNNNNNNTTYG	2 cut(s)	338, 370
Asp700I	GAANNNNTTC	1 cut(s)	329
AspLEI	GCGC	1 cut(s)	126
AspS9I	GGNCC	3 cut(s)	154, 195, 288
AsuHPI	GGTGA	2 cut(s)	448, 682
AvaII	GGWCC	1 cut(s)	154
BaeI	ACNNNNGTAYC	2 cut(s)	157, 190
BanII	GRGCYC	1 cut(s)	643
BccI	CCATC	3 cut(s)	104, 403, 701
BceAI	ACGGC	1 cut(s)	12
BclI	TGATCA	2 cut(s)	390, 705
BfaI	CTAG	2 cut(s)	149, 192
BfoI	RGCGCY	1 cut(s)	127
BlpI	GCTNAGC	2 cut(s)	120, 744
Bme18I	GGWCC	1 cut(s)	154
BmgT120I	GGNCC	3 cut(s)	154, 195, 288
BmiI	GGNNCC	1 cut(s)	289
BmsI	GCATC	2 cut(s)	96, 520
BpmI	CTGGAG	1 cut(s)	638
Bpu1102I	GCTNAGC	2 cut(s)	120, 744
BseGI	GGATG	2 cut(s)	535, 742
BseMII	CTCAG	1 cut(s)	525
BseRI	GAGGAG	3 cut(s)	11, 640, 676
BseYI	CCCAGC	1 cut(s)	604
Bsh1285I	CGRYCG	1 cut(s)	172
BshFI	GGCC	2 cut(s)	197, 290
BsiEI	CGRYCG	1 cut(s)	172
BslFI	GGGAC	1 cut(s)	350
BsmFI	GGGAC	1 cut(s)	350
BsnI	GGCC	2 cut(s)	197, 290
Bsp1286I	GDGCHC	1 cut(s)	643
Bsp143I	GATC	2 cut(s)	390, 705
Bsp1720I	GCTNAGC	2 cut(s)	120, 744
BspACI	CCGC	6 cut(s)	25, 42, 48, 102, 520, 748
BspANI	GGCC	2 cut(s)	197, 290
BspCNI	CTCAG	1 cut(s)	526
BspLI	GGNNCC	1 cut(s)	289
BssMI	GATC	2 cut(s)	390, 705
Bst4CI	ACNGT	5 cut(s)	170, 251, 262, 388, 430
Bst6I	CTCTTC	3 cut(s)	617, 648, 764
BstDEI	CTNAG	3 cut(s)	120, 534, 744
BstF5I	GGATG	2 cut(s)	535, 742
BstH2I	RGCGCY	1 cut(s)	127
BstHHI	GCGC	1 cut(s)	126
BstKTI	GATC	2 cut(s)	393, 708
BstMBI	GATC	2 cut(s)	390, 705
BstMCI	CGRYCG	1 cut(s)	172
BstMWI	GCNNNNNNNGC	3 cut(s)	24, 101, 110
BstNSI	RCATGY	1 cut(s)	205
BstXI	CCANNNNNNTGG	1 cut(s)	604
BsuRI	GGCC	2 cut(s)	197, 290
BtsCI	GGATG	2 cut(s)	535, 742
CfoI	GCGC	1 cut(s)	126
Cfr13I	GGNCC	3 cut(s)	154, 195, 288
Csp6I	GTAC	5 cut(s)	166, 174, 258, 341, 379
CviAII	CATG	2 cut(s)	131, 202
CviQI	GTAC	5 cut(s)	166, 174, 258, 341, 379
DdeI	CTNAG	3 cut(s)	120, 534, 744
DpnI	GATC	2 cut(s)	392, 707
DpnII	GATC	2 cut(s)	390, 705
Eam1104I	CTCTTC	3 cut(s)	617, 648, 764
EarI	CTCTTC	3 cut(s)	617, 648, 764
EciI	GGCGGA	2 cut(s)	14, 91
Eco24I	GRGCYC	1 cut(s)	643
Eco47I	GGWCC	1 cut(s)	154
Eco47III	AGCGCT	1 cut(s)	125
EcoO109I	RGGNCCY	1 cut(s)	288
EcoT38I	GRGCYC	1 cut(s)	643
FaeI	CATG	2 cut(s)	134, 205
FaiI	YATR	8 cut(s)	132, 203, 317, 510, 544, 591, 668, 756
FaqI	GGGAC	1 cut(s)	350
FatI	CATG	2 cut(s)	130, 201
FbaI	TGATCA	2 cut(s)	390, 705
FokI	GGATG	2 cut(s)	542, 749
FriOI	GRGCYC	1 cut(s)	643
FspBI	CTAG	2 cut(s)	149, 192
GlaI	GCGC	1 cut(s)	125
GsaI	CCCAGC	1 cut(s)	608
GsuI	CTGGAG	1 cut(s)	638
HaeII	RGCGCY	1 cut(s)	127
HaeIII	GGCC	2 cut(s)	197, 290
HhaI	GCGC	1 cut(s)	126
Hin1II	CATG	2 cut(s)	134, 205
Hin6I	GCGC	1 cut(s)	124
HinP1I	GCGC	1 cut(s)	124
HinfI	GANTC	1 cut(s)	413
HphI	GGTGA	2 cut(s)	448, 682
Hpy166II	GTNNAC	2 cut(s)	298, 690
Hpy188I	TCNGA	2 cut(s)	189, 529
Hpy188III	TCNNGA	2 cut(s)	575, 617
Hpy8I	GTNNAC	2 cut(s)	298, 690
HpyAV	CCTTC	2 cut(s)	280, 451
HpyCH4III	ACNGT	5 cut(s)	170, 251, 262, 388, 430
HpyCH4IV	ACGT	2 cut(s)	339, 482
HpyCH4V	TGCA	2 cut(s)	32, 405
HpyF10VI	GCNNNNNNNGC	3 cut(s)	24, 101, 110
HpyF3I	CTNAG	3 cut(s)	120, 534, 744
HpySE526I	ACGT	2 cut(s)	339, 482
Hsp92II	CATG	2 cut(s)	134, 205
HspAI	GCGC	1 cut(s)	124
Ksp22I	TGATCA	2 cut(s)	390, 705
Kzo9I	GATC	2 cut(s)	390, 705
LmnI	GCTCC	1 cut(s)	585
LpnPI	CCDG	7 cut(s)	170, 191, 304, 378, 588, 590, 602
LweI	GCATC	2 cut(s)	96, 520
MaeI	CTAG	2 cut(s)	149, 192
MaeII	ACGT	2 cut(s)	339, 482
MalI	GATC	2 cut(s)	392, 707
MboI	GATC	2 cut(s)	390, 705
MboII	GAAGA	7 cut(s)	152, 172, 337, 550, 574, 634, 665
MhlI	GDGCHC	1 cut(s)	643
MluCI	AATT	1 cut(s)	644
MmeI	TCCRAC	1 cut(s)	212
MnlI	CCTC	8 cut(s)	29, 32, 119, 145, 249, 618, 654, 718
MroXI	GAANNNNTTC	1 cut(s)	329
MseI	TTAA	2 cut(s)	420, 486
MwoI	GCNNNNNNNGC	3 cut(s)	24, 101, 110
NdeII	GATC	2 cut(s)	390, 705
NlaIII	CATG	2 cut(s)	134, 205
NlaIV	GGNNCC	1 cut(s)	289
NspI	RCATGY	1 cut(s)	205
PciI	ACATGT	1 cut(s)	201
PcsI	WCGNNNNNNNCGW	1 cut(s)	488
PdmI	GAANNNNTTC	1 cut(s)	329
PfeI	GAWTC	1 cut(s)	413
PscI	ACATGT	1 cut(s)	201
PspFI	CCCAGC	1 cut(s)	604
PspN4I	GGNNCC	1 cut(s)	289
PspPI	GGNCC	3 cut(s)	154, 195, 288
RsaI	GTAC	5 cut(s)	167, 175, 259, 342, 380
RsaNI	GTAC	5 cut(s)	166, 174, 258, 341, 379
SaqAI	TTAA	2 cut(s)	420, 486
Sau3AI	GATC	2 cut(s)	390, 705
Sau96I	GGNCC	3 cut(s)	154, 195, 288
SduI	GDGCHC	1 cut(s)	643
SetI	ASST	8 cut(s)	111, 225, 342, 485, 590, 682, 704, 745
SfaNI	GCATC	2 cut(s)	96, 520
SinI	GGWCC	1 cut(s)	154
Sse9I	AATT	1 cut(s)	644
SsiI	CCGC	6 cut(s)	25, 42, 48, 102, 520, 748
SspMI	CTAG	2 cut(s)	149, 192
TaaI	ACNGT	5 cut(s)	170, 251, 262, 388, 430
TaiI	ACGT	2 cut(s)	342, 485
TaqI	TCGA	2 cut(s)	228, 356
TasI	AATT	1 cut(s)	644
TfiI	GAWTC	1 cut(s)	413
Tru1I	TTAA	2 cut(s)	420, 486
Tru9I	TTAA	2 cut(s)	420, 486
TspDTI	ATGAA	2 cut(s)	246, 753
TspGWI	ACGGA	1 cut(s)	726
VpaK11BI	GGWCC	1 cut(s)	154
XceI	RCATGY	1 cut(s)	205
XmnI	GAANNNNTTC	1 cut(s)	329
XspI	CTAG	2 cut(s)	149, 192

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