Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4D

Orthogroup ID

OG0010599

Physical Location & Seq

Genomic Coordinates Reverse (-)

14059578 .. 14063494

Gene Structure 3917 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4DG093100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 897 bp

ATGCTCATCAACTTCATACACAAACCCAACTTCCTCCTCCCCAAAATCATAGACCTCAAAGACTTCACCTACGCCTCCACCCTCTTCTCCCACATCCCCGAACCCAACGGCTACGCTTTCAACGTCATGCTCCGTGGCCTAACCACCACTTGGCAAAAGTACCCACTTACTCTTCAACTCTATTACCGAATGAAGTCTCTGGGTGTGATGCCGGATAATTTCACCTACCCATTTCTCTTCATTGCGTGTTGGAATCTCTCGGAGCTTAATCATGGCCGTGCAGCACATTCGTCTGTGTTGAAGACTGGGTTGGATGGTGATGGTCATGTGACTCACTCTCTGATCACAATGTACTCGATGTGTGGGGAACTGGGTTATGCACGGAAGGTGTTCGATGAAATTCCCCAGAGAGATTCGGTGTCGTGGAACTCGATGATTTCCGGGTATACGAAGATGGGGCGTGCAGGGGATGCGGTGGGGTTGTTTGGGGAGATGAGGGAGGCTGGATTTGAGCTGAATGAGATGACTCTGGTGAGTGTTCTCGGGGCGTGCGGGGACCTTGGGGATTTGAGCTTGGGGAGGTGGGTGGAGGATTTTGTTGTTGAGAAAAAGTTGCACCTGAATTCTTATTTGGGGTCTGCTTTGATTGGTATGTATGGAAAGTGTGGTGATTTGTGTTCGGCAAGGAGGGTGTTTGACAGTTTGAAGAAAAAGGATCGCGTCACTTGGAATGCCATGATTACAGGGTATGCTCAAAACGGAATGTCAGATGAAGCAATGGTGCTTTTTGATGGCATGAAAGAAGCAGGTGAGAAAGATGAGGTCATTTTTTTGGAGATTTTAATAATATATATATATATTTTTCTCCAAATGTGTATTTATAGTCAATATCATTAA

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

Protein Analysis

298

Amino Acids

33.72

Weight (kDa)

5.91

Isoelectric Point (pI)

31.47

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	138 - 184	5e-10	PPR repeat family
PPR_1	PF12854	138 - 166	9.4e-06	PPR repeat
PPR	PF01535	140 - 170	2.2e-09	PPR repeat
PPR_2	PF13041	239 - 270	1.2e-07	PPR repeat family
PPR_1	PF12854	239 - 267	6e-07	PPR repeat
PPR	PF01535	241 - 270	4.5e-10	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: OG0010599)

Species	Orthologous Gene IDs
malus_domestica	MD00G1010100.v1.1 MD00G1186800.v1.1 MD03G1030200.v1.1 MD07G1304900.v1.1
rosa_chinensis	RchiOBHm_Chr1g0383741 RchiOBHm_Chr4g0439821 RchiOBHm_Chr7g0203551
rosa_laevigata	RLG00000019369
rosa_multiflora	Rmu_co8232911.1_g000001 Rmu_sc0003151.1_g000002 Rmu_sc0010226.1_g000002 Rmu_sc0010675.1_g000007 Rmu_sc0010675.1_g000009 Rmu_ssc0000029.1_g000003
rosa_roxburghii	Rroxscaffold_3G00253700
rosa_rugosa	Rorug07G0205800
rosa_samantha	Rh1CG438200 Rh4CG108000 Rh4DG093100 Rh7AG206500 Rh7CG219000

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	797
Acc36I	ACCTGC	1 cut(s)	797
AccB7I	CCANNNNNTGG	1 cut(s)	150
AccI	GTMKAC	1 cut(s)	446
AccII	CGCG	1 cut(s)	720
AciI	CCGC	2 cut(s)	473, 552
AclWI	GGATC	1 cut(s)	723
AcoI	YGGCCR	1 cut(s)	274
AcsI	RAATTY	2 cut(s)	399, 622
AfaI	GTAC	2 cut(s)	161, 353
AfiI	CCNNNNNNNGG	1 cut(s)	150
AgsI	TTSAA	4 cut(s)	121, 176, 301, 706
AjuI	GAANNNNNNNTTGG	4 cut(s)	293, 325, 614, 646
AluBI	AGCT	3 cut(s)	265, 514, 573
AluI	AGCT	3 cut(s)	265, 514, 573
Alw26I	GTCTC	1 cut(s)	201
AlwI	GGATC	1 cut(s)	723
Ama87I	CYCGRG	1 cut(s)	542
AoxI	GGCC	2 cut(s)	136, 274
ApeKI	GCWGC	1 cut(s)	281
ApoI	RAATTY	2 cut(s)	399, 622
Asp700I	GAANNNNTTC	1 cut(s)	389
AspS9I	GGNCC	1 cut(s)	556
AsuC2I	CCSGG	1 cut(s)	442
AsuHPI	GGTGA	6 cut(s)	58, 214, 329, 544, 680, 821
AvaI	CYCGRG	1 cut(s)	542
AvaII	GGWCC	1 cut(s)	556
BbsI	GAAGAC	1 cut(s)	308
BbvI	GCAGC	1 cut(s)	293
BccI	CCATC	4 cut(s)	308, 314, 448, 785
BceAI	ACGGC	2 cut(s)	124, 261
BcgI	CGANNNNNNTGC	2 cut(s)	270, 304
BclI	TGATCA	1 cut(s)	342
BcnI	CCSGG	1 cut(s)	442
BcoDI	GTCTC	1 cut(s)	201
BfuAI	ACCTGC	1 cut(s)	797
BisI	GCNGC	1 cut(s)	282
BlsI	GCNGC	1 cut(s)	283
Bme1390I	CCNGG	1 cut(s)	442
Bme18I	GGWCC	1 cut(s)	556
BmeT110I	CYCGRG	1 cut(s)	542
BmgT120I	GGNCC	1 cut(s)	556
BmiI	GGNNCC	1 cut(s)	557
BmrFI	CCNGG	1 cut(s)	442
BmrI	ACTGGG	2 cut(s)	315, 380
BmsI	GCATC	2 cut(s)	198, 460
BmuI	ACTGGG	2 cut(s)	315, 380
BpiI	GAAGAC	1 cut(s)	308
BpuMI	CCSGG	1 cut(s)	442
BsaJI	CCNNGG	2 cut(s)	133, 559
Bsc4I	CCNNNNNNNGG	1 cut(s)	150
Bse1I	ACTGG	2 cut(s)	310, 375
Bse3DI	GCAATG	2 cut(s)	240, 783
BseDI	CCNNGG	2 cut(s)	133, 559
BseGI	GGATG	3 cut(s)	93, 319, 475
BseLI	CCNNNNNNNGG	1 cut(s)	150
BseMI	GCAATG	2 cut(s)	240, 783
BseNI	ACTGG	2 cut(s)	310, 375
BseRI	GAGGAG	1 cut(s)	26
BseXI	GCAGC	1 cut(s)	293
BsgI	GTGCAG	2 cut(s)	300, 483
Bsh1236I	CGCG	1 cut(s)	720
BshFI	GGCC	2 cut(s)	138, 276
BsiHKCI	CYCGRG	1 cut(s)	542
BsiSI	CCGG	2 cut(s)	212, 441
BslFI	GGGAC	1 cut(s)	569
BslI	CCNNNNNNNGG	1 cut(s)	150
BsmAI	GTCTC	1 cut(s)	201
BsmFI	GGGAC	1 cut(s)	569
BsmI	GAATGC	1 cut(s)	736
BsnI	GGCC	2 cut(s)	138, 276
BsoBI	CYCGRG	1 cut(s)	542
Bsp143I	GATC	2 cut(s)	342, 715
BspACI	CCGC	2 cut(s)	473, 552
BspANI	GGCC	2 cut(s)	138, 276
BspFNI	CGCG	1 cut(s)	720
BspLI	GGNNCC	1 cut(s)	557
BspMI	ACCTGC	1 cut(s)	797
BspPI	GGATC	1 cut(s)	723
BsrDI	GCAATG	2 cut(s)	240, 783
BsrI	ACTGG	2 cut(s)	310, 375
BssECI	CCNNGG	2 cut(s)	133, 559
BssMI	GATC	2 cut(s)	342, 715
BssNAI	GTATAC	1 cut(s)	447
BssT1I	CCWWGG	1 cut(s)	559
Bst1107I	GTATAC	1 cut(s)	447
Bst4CI	ACNGT	1 cut(s)	701
Bst6I	CTCTTC	3 cut(s)	89, 177, 242
BstAPI	GCANNNNNTGC	1 cut(s)	470
BstC8I	GCNNGC	2 cut(s)	462, 550
BstDSI	CCRYGG	1 cut(s)	133
BstF5I	GGATG	3 cut(s)	93, 319, 475
BstFNI	CGCG	1 cut(s)	720
BstKTI	GATC	2 cut(s)	345, 718
BstMAI	GTCTC	1 cut(s)	201
BstMBI	GATC	2 cut(s)	342, 715
BstMWI	GCNNNNNNNGC	1 cut(s)	470
BstSCI	CCNGG	1 cut(s)	440
BstUI	CGCG	1 cut(s)	720
BstV1I	GCAGC	1 cut(s)	293
BstV2I	GAAGAC	1 cut(s)	308
BstZ17I	GTATAC	1 cut(s)	447
BsuRI	GGCC	2 cut(s)	138, 276
BtgI	CCRYGG	1 cut(s)	133
BtsCI	GGATG	3 cut(s)	93, 319, 475
BveI	ACCTGC	1 cut(s)	797
Cac8I	GCNNGC	2 cut(s)	462, 550
Cfr13I	GGNCC	1 cut(s)	556
CseI	GACGC	1 cut(s)	709
Csp6I	GTAC	2 cut(s)	160, 352
CviAII	CATG	5 cut(s)	127, 272, 326, 736, 796
CviJI	RGCY	7 cut(s)	111, 138, 265, 276, 503, 514, 573
CviKI_1	RGCY	7 cut(s)	111, 138, 265, 276, 503, 514, 573
CviQI	GTAC	2 cut(s)	160, 352
DpnI	GATC	2 cut(s)	344, 717
DpnII	GATC	2 cut(s)	342, 715
EaeI	YGGCCR	1 cut(s)	274
Eam1104I	CTCTTC	3 cut(s)	89, 177, 242
EarI	CTCTTC	3 cut(s)	89, 177, 242
Eco130I	CCWWGG	1 cut(s)	559
Eco47I	GGWCC	1 cut(s)	556
Eco88I	CYCGRG	1 cut(s)	542
EcoO109I	RGGNCCY	1 cut(s)	556
EcoRI	GAATTC	1 cut(s)	622
EcoT14I	CCWWGG	1 cut(s)	559
ErhI	CCWWGG	1 cut(s)	559
FaeI	CATG	5 cut(s)	130, 275, 329, 739, 799
FaqI	GGGAC	1 cut(s)	569
FatI	CATG	5 cut(s)	126, 271, 325, 735, 795
FauI	CCCGC	1 cut(s)	545
FbaI	TGATCA	1 cut(s)	342
FblI	GTMKAC	1 cut(s)	446
Fnu4HI	GCNGC	1 cut(s)	282
FokI	GGATG	3 cut(s)	80, 326, 482
Fsp4HI	GCNGC	1 cut(s)	282
GluI	GCNGC	1 cut(s)	282
HaeIII	GGCC	2 cut(s)	138, 276
HapII	CCGG	2 cut(s)	212, 441
HgaI	GACGC	1 cut(s)	709
Hin1II	CATG	5 cut(s)	130, 275, 329, 739, 799
HinfI	GANTC	4 cut(s)	253, 331, 413, 526
HpaII	CCGG	2 cut(s)	212, 441
HphI	GGTGA	6 cut(s)	58, 214, 329, 544, 680, 821
Hpy166II	GTNNAC	1 cut(s)	447
Hpy188I	TCNGA	3 cut(s)	262, 342, 769
Hpy8I	GTNNAC	1 cut(s)	447
HpyAV	CCTTC	1 cut(s)	379
HpyCH4III	ACNGT	1 cut(s)	701
HpyCH4IV	ACGT	1 cut(s)	123
HpyCH4V	TGCA	4 cut(s)	281, 380, 464, 616
HpyF10VI	GCNNNNNNNGC	1 cut(s)	470
HpySE526I	ACGT	1 cut(s)	123
Hsp92II	CATG	5 cut(s)	130, 275, 329, 739, 799
Ksp22I	TGATCA	1 cut(s)	342
Kzo9I	GATC	2 cut(s)	342, 715
LmnI	GCTCC	2 cut(s)	135, 262
Lsp1109I	GCAGC	1 cut(s)	293
LweI	GCATC	2 cut(s)	198, 460
MaeII	ACGT	1 cut(s)	123
MaeIII	GTNAC	2 cut(s)	328, 721
MalI	GATC	2 cut(s)	344, 717
MboI	GATC	2 cut(s)	342, 715
MboII	GAAGA	6 cut(s)	76, 164, 229, 313, 463, 718
MluCI	AATT	3 cut(s)	217, 399, 622
MlyI	GAGTC	2 cut(s)	325, 520
MmeI	TCCRAC	2 cut(s)	230, 291
MroXI	GAANNNNTTC	1 cut(s)	389
MseI	TTAA	3 cut(s)	267, 842, 895
MslI	CAYNNNNRTG	1 cut(s)	276
MspI	CCGG	2 cut(s)	212, 441
MspR9I	CCNGG	1 cut(s)	442
Mva1269I	GAATGC	1 cut(s)	736
MvnI	CGCG	1 cut(s)	720
MwoI	GCNNNNNNNGC	1 cut(s)	470
NciI	CCSGG	1 cut(s)	442
NdeII	GATC	2 cut(s)	342, 715
NlaIII	CATG	5 cut(s)	130, 275, 329, 739, 799
NlaIV	GGNNCC	1 cut(s)	557
NmuCI	GTSAC	2 cut(s)	328, 721
PaqCI	CACCTGC	1 cut(s)	797
PcsI	WCGNNNNNNNCGW	2 cut(s)	120, 428
PctI	GAATGC	1 cut(s)	736
PdmI	GAANNNNTTC	1 cut(s)	389
PfeI	GAWTC	2 cut(s)	253, 413
PflMI	CCANNNNNTGG	1 cut(s)	150
PkrI	GCNGC	1 cut(s)	283
PleI	GAGTC	2 cut(s)	325, 520
PpsI	GAGTC	2 cut(s)	325, 520
PpuMI	RGGWCCY	1 cut(s)	556
Psp5II	RGGWCCY	1 cut(s)	556
PspN4I	GGNNCC	1 cut(s)	557
PspPI	GGNCC	1 cut(s)	556
PspPPI	RGGWCCY	1 cut(s)	556
RsaI	GTAC	2 cut(s)	161, 353
RsaNI	GTAC	2 cut(s)	160, 352
RseI	CAYNNNNRTG	1 cut(s)	276
SaqAI	TTAA	3 cut(s)	267, 842, 895
SatI	GCNGC	1 cut(s)	282
Sau3AI	GATC	2 cut(s)	342, 715
Sau96I	GGNCC	1 cut(s)	556
SchI	GAGTC	2 cut(s)	325, 520
ScrFI	CCNGG	1 cut(s)	442
SfaNI	GCATC	2 cut(s)	198, 460
SinI	GGWCC	1 cut(s)	556
SmiMI	CAYNNNNRTG	1 cut(s)	276
Sse9I	AATT	3 cut(s)	217, 399, 622
SsiI	CCGC	2 cut(s)	473, 552
StyD4I	CCNGG	1 cut(s)	440
StyI	CCWWGG	1 cut(s)	559
TaaI	ACNGT	1 cut(s)	701
TaiI	ACGT	1 cut(s)	126
TaqI	TCGA	3 cut(s)	356, 393, 431
TasI	AATT	3 cut(s)	217, 399, 622
TatI	WGTACW	1 cut(s)	351
TfiI	GAWTC	2 cut(s)	253, 413
Tru1I	TTAA	3 cut(s)	267, 842, 895
Tru9I	TTAA	3 cut(s)	267, 842, 895
TseFI	GTSAC	2 cut(s)	328, 721
TseI	GCWGC	1 cut(s)	281
Tsp45I	GTSAC	2 cut(s)	328, 721
TspDTI	ATGAA	6 cut(s)	4, 206, 229, 411, 786, 812
TspGWI	ACGGA	3 cut(s)	122, 397, 774
Van91I	CCANNNNNTGG	1 cut(s)	150
VpaK11BI	GGWCC	1 cut(s)	556
XapI	RAATTY	2 cut(s)	399, 622
XmiI	GTMKAC	1 cut(s)	446
XmnI	GAANNNNTTC	1 cut(s)	389

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