Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4C

Orthogroup ID

OG0006654

Physical Location & Seq

Genomic Coordinates Forward (+)

48933238 .. 48934593

Gene Structure 1356 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4CG242600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1167 bp

ATGAAGCACTCAAAACCTCTGAACCGCAATTACACACCACTAGTGAACCAAGTCCTGACAGCCATGCTCAAAAACCAACCTTTTGACCCAAACCCCTCAGTTTCAGCCACCACAACTCAACCATGGACCTCCGACTCAGTCTCCCAAGTCCTAACCTCCATCCCCAGATTCTTCTTCCAGTCCCCTCGCTCCATAGGTCGCCAAACCGGCTTCCGGCACCGCGCTCCGTTAAAGCAACGCCATCTCAGGCAAGAAACGTATAAATTCCACAACGACATGCTCATTCTTGGCCCAGCAGCTGCCCACAGAGACCTCAGCAAGGTCAATCTGGGAGTGGACAAAGCCCTCGATTTTTACTACTGGGTCGAAACCCATTTCGGGTTCAACCACAATGAGCGAACTTGCAGAGACATGGCTGTCGTTTTGGCTAAAGGGAATCGGTTGAAGGCCCTCTGGGATTTTCTGAAAGACATGTCGAAGAGAGGGAGTAGTGAAAGCCCTCTTGTAACGACACAGTCCATCACCTGTTTGATGAAATGCCTAGGAGAAGAGGGATTGGTTAATGAAGCATTGGCGGCTTTCTATAGGATGAAGCAGTTTCATTGCAAACCGGATGTGTATGCTTACAACACTATTATTTACGCGCTTTGCAGAGTTGGGGATTTCAAGAAGGCTCGGTTTTTGCTGGAGCAGATGGAGCTGCCGGGTTTTAGATGCCCGCCGGATACATTCACTTACACGATTTTGATAAGCTCTTATTGTAGATATGGGTTGGAGACTGGGTGCAGGAAGGCCACTAGGAGGAGATACTATGCTGCTGTTAATGAGATTGACAAGGCTGTGGATATGTTAAGAAGGATGCAGAATATGAATCATGGATTGGCCACTTCAAGTTCGTATACTCCAATCATTCATGCCATGTGTGAAGCAGGAAGGGTTACAGAGGCTTGGGGTTTTCTTGTTGAGTTGGTTGATGGAGGGTCAATACCTAGAGAATATACTTACAAATTAGTTTGCAATGCAATGAGTTCAGCTGGAGAGGTCAATTTACTTGATGATGGCTTGCGAAAAAGAATAGAAGATGGTATGCAGAGGAGATATAAGCACGTAATGAAGGTGAAGCCAATAATGACTCGCAAAGGGTATGATAGCATGGTGGAAACATGA

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_2 PPR_3

Protein Analysis

388

Amino Acids

44.5

Weight (kDa)

9.46

Isoelectric Point (pI)

39.31

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	173 - 218	2.4e-09	PPR repeat family
PPR_1	PF12854	201 - 233	1.7e-09	PPR repeat
PPR_2	PF13041	204 - 255	3.2e-13	PPR repeat family
PPR_1	PF12854	239 - 257	6.2e-06	PPR repeat

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0006654)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G77405
fragaria_vesca	FvH4_2g27550
malus_domestica	MD00G1030400.v1.1
prunus_persica	Prupe.1G492400_v2.0.a1
pyrus_communis	pycom15g30800
rosa_chinensis	RchiOBHm_Chr4g0420811 RchiOBHm_Chr4g0420821
rosa_laevigata	RLG00000007736 RLG00000011697
rosa_multiflora	Rmu_co8321563.1_g000001 Rmu_sc0005104.1_g000002 Rmu_sc0006997.1_g000002 Rmu_sc0006997.1_g000003
rosa_roxburghii	Rroxscaffold_5G00363250
rosa_rugosa	Rorug04G0166200 Rorug04G0166300 Rorug06G0261900
rosa_samantha	Rh4AG227600 Rh4BG230600 Rh4BG230700 Rh4BG230800 Rh4CG242600 Rh4CG242700 Rh6BG381400
rosa_wichuraiana	Rw4G019690 Rw6G032550

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AasI	GACNNNNNNGTC	1 cut(s)	416
AccB1I	GGYRCC	1 cut(s)	216
AccI	GTMKAC	1 cut(s)	899
AccII	CGCG	2 cut(s)	222, 644
AciI	CCGC	4 cut(s)	25, 220, 575, 719
AcoI	YGGCCR	1 cut(s)	882
AcsI	RAATTY	1 cut(s)	263
AfiI	CCNNNNNNNGG	4 cut(s)	213, 319, 378, 801
AflIII	ACRYGT	1 cut(s)	471
AgsI	TTSAA	4 cut(s)	385, 445, 667, 891
AhlI	ACTAGT	1 cut(s)	40
AjuI	GAANNNNNNNTTGG	2 cut(s)	863, 895
AluBI	AGCT	4 cut(s)	299, 700, 753, 1034
AluI	AGCT	4 cut(s)	299, 700, 753, 1034
Alw26I	GTCTC	4 cut(s)	145, 303, 402, 770
AlwNI	CAGNNNCTG	1 cut(s)	299
AoxI	GGCC	4 cut(s)	289, 447, 792, 882
ApeKI	GCWGC	4 cut(s)	296, 299, 700, 815
ApoI	RAATTY	1 cut(s)	263
AspA2I	CCTAGG	1 cut(s)	541
AspLEI	GCGC	2 cut(s)	224, 646
AspS9I	GGNCC	3 cut(s)	126, 290, 448
AsuC2I	CCSGG	1 cut(s)	705
AsuHPI	GGTGA	2 cut(s)	514, 1129
AvaII	GGWCC	1 cut(s)	126
AvrII	CCTAGG	1 cut(s)	541
BalI	TGGCCA	1 cut(s)	884
BanI	GGYRCC	1 cut(s)	216
BbvCI	CCTCAGC	1 cut(s)	314
BbvI	GCAGC	4 cut(s)	286, 308, 687, 802
BccI	CCATC	7 cut(s)	167, 249, 527, 688, 968, 1052, 1076
BciVI	GTATCC	1 cut(s)	718
BcnI	CCSGG	1 cut(s)	705
BcoDI	GTCTC	4 cut(s)	145, 303, 402, 770
BcuI	ACTAGT	1 cut(s)	40
BfaI	CTAG	4 cut(s)	41, 542, 798, 990
BfmI	CTRYAG	1 cut(s)	583
BfuI	GTATCC	1 cut(s)	718
BglI	GCCNNNNNGGC	1 cut(s)	207
BisI	GCNGC	5 cut(s)	297, 300, 576, 701, 816
BlnI	CCTAGG	1 cut(s)	541
BlsI	GCNGC	5 cut(s)	298, 301, 577, 702, 817
Bme1390I	CCNGG	1 cut(s)	705
Bme18I	GGWCC	1 cut(s)	126
BmgT120I	GGNCC	3 cut(s)	126, 290, 448
BmiI	GGNNCC	1 cut(s)	218
BmrFI	CCNGG	1 cut(s)	705
BmrI	ACTGGG	2 cut(s)	370, 789
BmsI	GCATC	2 cut(s)	704, 849
BmuI	ACTGGG	2 cut(s)	370, 789
BpmI	CTGGAG	2 cut(s)	707, 1056
Bpu10I	CCTNAGC	1 cut(s)	314
BpuMI	CCSGG	1 cut(s)	705
BsaAI	YACGTR	1 cut(s)	1108
BsaI	GGTCTC	1 cut(s)	303
BsaJI	CCNNGG	2 cut(s)	122, 541
BsaWI	WCCGGW	1 cut(s)	610
BsaXI	ACNNNNNCTCC	4 cut(s)	125, 155, 767, 797
Bsc4I	CCNNNNNNNGG	4 cut(s)	213, 319, 378, 801
Bse118I	RCCGGY	1 cut(s)	206
Bse1I	ACTGG	3 cut(s)	178, 365, 784
Bse3DI	GCAATG	3 cut(s)	601, 1024, 1029
BseDI	CCNNGG	2 cut(s)	122, 541
BseGI	GGATG	4 cut(s)	159, 594, 619, 864
BseLI	CCNNNNNNNGG	4 cut(s)	213, 319, 378, 801
BseMI	GCAATG	3 cut(s)	601, 1024, 1029
BseMII	CTCAG	4 cut(s)	111, 150, 259, 328
BseNI	ACTGG	3 cut(s)	178, 365, 784
BseRI	GAGGAG	2 cut(s)	817, 1108
BseXI	GCAGC	4 cut(s)	286, 308, 687, 802
BseYI	CCCAGC	1 cut(s)	292
BsgI	GTGCAG	1 cut(s)	805
Bsh1236I	CGCG	2 cut(s)	222, 644
BshFI	GGCC	4 cut(s)	291, 449, 794, 884
BshNI	GGYRCC	1 cut(s)	216
BsiSI	CCGG	5 cut(s)	207, 214, 611, 704, 722
BslFI	GGGAC	1 cut(s)	166
BslI	CCNNNNNNNGG	4 cut(s)	213, 319, 378, 801
BsmAI	GTCTC	4 cut(s)	145, 303, 402, 770
BsmFI	GGGAC	1 cut(s)	166
BsnI	GGCC	4 cut(s)	291, 449, 794, 884
Bso31I	GGTCTC	1 cut(s)	303
Bsp19I	CCATGG	1 cut(s)	122
BspACI	CCGC	4 cut(s)	25, 220, 575, 719
BspANI	GGCC	4 cut(s)	291, 449, 794, 884
BspCNI	CTCAG	4 cut(s)	110, 149, 258, 327
BspFNI	CGCG	2 cut(s)	222, 644
BspLI	GGNNCC	1 cut(s)	218
BspT107I	GGYRCC	1 cut(s)	216
BspTNI	GGTCTC	1 cut(s)	303
BsrDI	GCAATG	3 cut(s)	601, 1024, 1029
BsrFI	RCCGGY	1 cut(s)	206
BsrI	ACTGG	3 cut(s)	178, 365, 784
BssAI	RCCGGY	1 cut(s)	206
BssECI	CCNNGG	2 cut(s)	122, 541
BssNAI	GTATAC	1 cut(s)	900
BssT1I	CCWWGG	2 cut(s)	122, 541
Bst1107I	GTATAC	1 cut(s)	900
Bst4CI	ACNGT	1 cut(s)	516
Bst6I	CTCTTC	2 cut(s)	473, 543
BstBAI	YACGTR	1 cut(s)	1108
BstC8I	GCNNGC	2 cut(s)	719, 1064
BstDEI	CTNAG	4 cut(s)	97, 136, 245, 314
BstDSI	CCRYGG	1 cut(s)	122
BstENI	CCTNNNNNAGG	1 cut(s)	317
BstF5I	GGATG	4 cut(s)	159, 594, 619, 864
BstFNI	CGCG	2 cut(s)	222, 644
BstHHI	GCGC	2 cut(s)	224, 646
BstMAI	GTCTC	4 cut(s)	145, 303, 402, 770
BstMWI	GCNNNNNNNGC	3 cut(s)	207, 575, 697
BstNSI	RCATGY	2 cut(s)	280, 475
BstSCI	CCNGG	1 cut(s)	703
BstSFI	CTRYAG	1 cut(s)	583
BstUI	CGCG	2 cut(s)	222, 644
BstV1I	GCAGC	4 cut(s)	286, 308, 687, 802
BstZ17I	GTATAC	1 cut(s)	900
BsuI	GTATCC	1 cut(s)	718
BsuRI	GGCC	4 cut(s)	291, 449, 794, 884
BtgI	CCRYGG	1 cut(s)	122
BtsCI	GGATG	4 cut(s)	159, 594, 619, 864
Cac8I	GCNNGC	2 cut(s)	719, 1064
CaiI	CAGNNNCTG	1 cut(s)	299
CfoI	GCGC	2 cut(s)	224, 646
Cfr10I	RCCGGY	1 cut(s)	206
Cfr13I	GGNCC	3 cut(s)	126, 290, 448
DdeI	CTNAG	4 cut(s)	97, 136, 245, 314
DrdI	GACNNNNNNGTC	1 cut(s)	416
DseDI	GACNNNNNNGTC	1 cut(s)	416
EaeI	YGGCCR	1 cut(s)	882
Eam1104I	CTCTTC	2 cut(s)	473, 543
EarI	CTCTTC	2 cut(s)	473, 543
Eco130I	CCWWGG	2 cut(s)	122, 541
Eco31I	GGTCTC	1 cut(s)	303
Eco47I	GGWCC	1 cut(s)	126
EcoNI	CCTNNNNNAGG	1 cut(s)	317
EcoO109I	RGGNCCY	1 cut(s)	448
EcoT14I	CCWWGG	2 cut(s)	122, 541
ErhI	CCWWGG	2 cut(s)	122, 541
FaqI	GGGAC	1 cut(s)	166
FauI	CCCGC	1 cut(s)	726
FblI	GTMKAC	1 cut(s)	899
Fnu4HI	GCNGC	5 cut(s)	297, 300, 576, 701, 816
FokI	GGATG	4 cut(s)	146, 601, 626, 871
Fsp4HI	GCNGC	5 cut(s)	297, 300, 576, 701, 816
FspBI	CTAG	4 cut(s)	41, 542, 798, 990
GlaI	GCGC	2 cut(s)	223, 645
GluI	GCNGC	5 cut(s)	297, 300, 576, 701, 816
GsaI	CCCAGC	1 cut(s)	296
GsuI	CTGGAG	2 cut(s)	707, 1056
HaeIII	GGCC	4 cut(s)	291, 449, 794, 884
HapII	CCGG	5 cut(s)	207, 214, 611, 704, 722
HhaI	GCGC	2 cut(s)	224, 646
Hin6I	GCGC	2 cut(s)	222, 644
HinP1I	GCGC	2 cut(s)	222, 644
HinfI	GANTC	5 cut(s)	134, 168, 436, 871, 1132
HpaII	CCGG	5 cut(s)	207, 214, 611, 704, 722
HphI	GGTGA	2 cut(s)	514, 1129
Hpy166II	GTNNAC	3 cut(s)	46, 337, 900
Hpy188I	TCNGA	3 cut(s)	21, 133, 465
Hpy188III	TCNNGA	2 cut(s)	55, 667
Hpy8I	GTNNAC	3 cut(s)	46, 337, 900
HpyAV	CCTTC	6 cut(s)	439, 664, 784, 849, 927, 1108
HpyCH4III	ACNGT	1 cut(s)	516
HpyCH4IV	ACGT	2 cut(s)	257, 1107
HpyCH4V	TGCA	8 cut(s)	405, 606, 651, 786, 862, 1017, 1022, 1090
HpyF10VI	GCNNNNNNNGC	3 cut(s)	207, 575, 697
HpyF3I	CTNAG	4 cut(s)	97, 136, 245, 314
HpySE526I	ACGT	2 cut(s)	257, 1107
HspAI	GCGC	2 cut(s)	222, 644
LmnI	GCTCC	4 cut(s)	194, 229, 688, 697
Lsp1109I	GCAGC	4 cut(s)	286, 308, 687, 802
LweI	GCATC	2 cut(s)	704, 849
MaeI	CTAG	4 cut(s)	41, 542, 798, 990
MaeII	ACGT	2 cut(s)	257, 1107
MaeIII	GTNAC	2 cut(s)	505, 937
MboII	GAAGA	5 cut(s)	163, 166, 490, 560, 1091
MlsI	TGGCCA	1 cut(s)	884
MluCI	AATT	4 cut(s)	28, 263, 1007, 1045
MluNI	TGGCCA	1 cut(s)	884
MlyI	GAGTC	2 cut(s)	128, 1126
MmeI	TCCRAC	2 cut(s)	156, 753
Mox20I	TGGCCA	1 cut(s)	884
MscI	TGGCCA	1 cut(s)	884
MseI	TTAA	4 cut(s)	230, 561, 822, 851
Msp20I	TGGCCA	1 cut(s)	884
MspA1I	CMGCKG	2 cut(s)	299, 1034
MspI	CCGG	5 cut(s)	207, 214, 611, 704, 722
MspR9I	CCNGG	1 cut(s)	705
MvnI	CGCG	2 cut(s)	222, 644
MwoI	GCNNNNNNNGC	3 cut(s)	207, 575, 697
NciI	CCSGG	1 cut(s)	705
NcoI	CCATGG	1 cut(s)	122
NlaIV	GGNNCC	1 cut(s)	218
NspI	RCATGY	2 cut(s)	280, 475
PciI	ACATGT	1 cut(s)	471
PfeI	GAWTC	3 cut(s)	168, 436, 871
PflFI	GACNNNGTC	2 cut(s)	137, 514
PkrI	GCNGC	5 cut(s)	298, 301, 577, 702, 817
PleI	GAGTC	2 cut(s)	128, 1126
PpsI	GAGTC	2 cut(s)	128, 1126
Ppu21I	YACGTR	1 cut(s)	1108
PscI	ACATGT	1 cut(s)	471
PspFI	CCCAGC	1 cut(s)	292
PspN4I	GGNNCC	1 cut(s)	218
PspPI	GGNCC	3 cut(s)	126, 290, 448
PsrI	GAACNNNNNNTAC	2 cut(s)	14, 46
PstNI	CAGNNNCTG	1 cut(s)	299
PsyI	GACNNNGTC	2 cut(s)	137, 514
PvuII	CAGCTG	2 cut(s)	299, 1034
SaqAI	TTAA	4 cut(s)	230, 561, 822, 851
SatI	GCNGC	5 cut(s)	297, 300, 576, 701, 816
Sau96I	GGNCC	3 cut(s)	126, 290, 448
SchI	GAGTC	2 cut(s)	128, 1126
ScrFI	CCNGG	1 cut(s)	705
SfaNI	GCATC	2 cut(s)	704, 849
SfcI	CTRYAG	1 cut(s)	583
SinI	GGWCC	1 cut(s)	126
SpeI	ACTAGT	1 cut(s)	40
Sse9I	AATT	4 cut(s)	28, 263, 1007, 1045
SsiI	CCGC	4 cut(s)	25, 220, 575, 719
SspMI	CTAG	4 cut(s)	41, 542, 798, 990
StyD4I	CCNGG	1 cut(s)	703
StyI	CCWWGG	2 cut(s)	122, 541
TaaI	ACNGT	1 cut(s)	516
TaiI	ACGT	2 cut(s)	260, 1110
TaqI	TCGA	3 cut(s)	348, 366, 476
TasI	AATT	4 cut(s)	28, 263, 1007, 1045
TauI	GCSGC	1 cut(s)	578
TfiI	GAWTC	3 cut(s)	168, 436, 871
Tru1I	TTAA	4 cut(s)	230, 561, 822, 851
Tru9I	TTAA	4 cut(s)	230, 561, 822, 851
TseI	GCWGC	4 cut(s)	296, 299, 700, 815
TspDTI	ATGAA	8 cut(s)	17, 548, 579, 590, 605, 884, 902, 1127
TspGWI	ACGGA	1 cut(s)	216
Tth111I	GACNNNGTC	2 cut(s)	137, 514
VpaK11BI	GGWCC	1 cut(s)	126
XagI	CCTNNNNNAGG	1 cut(s)	317
XapI	RAATTY	1 cut(s)	263
XceI	RCATGY	2 cut(s)	280, 475
XmaJI	CCTAGG	1 cut(s)	541
XmiI	GTMKAC	1 cut(s)	899
XspI	CTAG	4 cut(s)	41, 542, 798, 990

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