Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3D

Orthogroup ID

OG0009695

Physical Location & Seq

Genomic Coordinates Reverse (-)

6251564 .. 6254656

Gene Structure 3093 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3DG080900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 582 bp

ATGCCAATTAGCCCTGAACAAGAAGCTCTTGAAGCGCAGAAGGATGCGCAGGAAGTGCACAGGTATGCGGTATGGGGCCTCCTACCAGAGAATGCGAACACAAGGATCAAGAAGGTGATGGAGGCGCTCCGGGACGAATTTGGTGGGCCGGAGATCGAGCCCCACATCACCATAGTCGGATCCTGCCTAATGACGGAAGATGAAGCGATCGGCTCATTTAGAGAAGGTTGTAACTCGGTCAAGCAAATCTATTGCAAAGTCGAAAACTTCGAGACTAGTAAATTCTATTTCCAGTGTCTTTCTCTCGTCATGGAAATTACCGAGGACCTAAAGGCTCAAACTCGTTGGTTTGCCGGTTGTATGAATCGCCCCTTCCCTGCTATGCCACATTTGAGCCTCCTATATGGGAGTTTGACAGATGAAGAGAAAAAAAGAGCTAAAGAGAAAGTTCTTGCTATGGATGAGAGCATTGCTGGACTAACATTCCTCTTAAGTAGGATGGCATTGTACAGAGTCAACTTTGCAGATAGAACTCAAAAATCCTGGGTGAGGATTCTTGAGGGCCACCTTCGAGTCAACTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000394 GO:0003674 GO:0003824 GO:0004112 GO:0004113 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0006139 GO:0006388 GO:0006396 GO:0006399 GO:0006725 GO:0006753 GO:0006793 GO:0006796 GO:0006807 GO:0008033 GO:0008081 GO:0008150 GO:0008152 GO:0008380 GO:0009117 GO:0009187 GO:0009987 GO:0010467 GO:0016070 GO:0016787 GO:0016788 GO:0019637 GO:0034470 GO:0034641 GO:0034660 GO:0042578 GO:0043170 GO:0044237 GO:0044238 GO:0044281 GO:0044424 GO:0044464 GO:0046483 GO:0055086 GO:0071704 GO:0090304 GO:1901360

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

2_5_RNA_ligase2 CPDase

Protein Analysis

193

Amino Acids

22.11

Weight (kDa)

5.67

Isoelectric Point (pI)

52.1

Instability Index

Protein Domains (Pfam)

No Pfam domains detected for this protein.

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)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0009695)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_6g07310 FvH4_6g07320
rosa_chinensis	RchiOBHm_Chr3g0456921 RchiOBHm_Chr3g0456931
rosa_laevigata	RLG00000025263 RLG00000025264
rosa_multiflora	Rmu_co8272005.1_g000001 Rmu_sc0000133.1_g000001 Rmu_sc0000133.1_g000002 Rmu_sc0016008.1_g000001
rosa_roxburghii	Rroxscaffold_6G00422360
rosa_rugosa	Rorug03G0017100 Rorug03G0017200 Rorug03G0017300 Rorug03G0017400
rosa_samantha	Rh3AG077200 Rh3AG077400 Rh3BG079200 Rh3BG079300 Rh3CG079100 Rh3CG079200 Rh3DG080900

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc16I	TGCGCA	1 cut(s)	48
AciI	CCGC	1 cut(s)	68
AclWI	GGATC	3 cut(s)	113, 174, 187
AcsI	RAATTY	2 cut(s)	137, 281
AfaI	GTAC	1 cut(s)	509
AfiI	CCNNNNNNNGG	2 cut(s)	193, 549
AflII	CTTAAG	1 cut(s)	490
AgsI	TTSAA	1 cut(s)	32
AhlI	ACTAGT	1 cut(s)	275
AjnI	CCWGG	1 cut(s)	542
AluBI	AGCT	2 cut(s)	26, 437
AluI	AGCT	2 cut(s)	26, 437
Alw21I	GWGCWC	1 cut(s)	60
Alw26I	GTCTC	1 cut(s)	266
Alw44I	GTGCAC	1 cut(s)	56
AlwI	GGATC	3 cut(s)	113, 174, 187
AoxI	GGCC	3 cut(s)	76, 146, 562
ApaLI	GTGCAC	1 cut(s)	56
ApoI	RAATTY	2 cut(s)	137, 281
AspLEI	GCGC	3 cut(s)	37, 49, 127
AspS9I	GGNCC	4 cut(s)	76, 146, 325, 562
AsuC2I	CCSGG	1 cut(s)	131
AsuHPI	GGTGA	3 cut(s)	127, 160, 559
AvaII	GGWCC	1 cut(s)	325
BaeGI	GKGCMC	1 cut(s)	60
BamHI	GGATCC	1 cut(s)	179
BanII	GRGCYC	1 cut(s)	162
Bbv12I	GWGCWC	1 cut(s)	60
BccI	CCATC	2 cut(s)	112, 493
BciT130I	CCWGG	1 cut(s)	544
BcnI	CCSGG	1 cut(s)	131
BcoDI	GTCTC	1 cut(s)	266
BcuI	ACTAGT	1 cut(s)	275
BfaI	CTAG	1 cut(s)	276
BfoI	RGCGCY	1 cut(s)	128
BfrI	CTTAAG	1 cut(s)	490
Bme1390I	CCNGG	2 cut(s)	131, 544
Bme18I	GGWCC	1 cut(s)	325
BmgT120I	GGNCC	4 cut(s)	76, 146, 325, 562
BmiI	GGNNCC	2 cut(s)	77, 181
BmrFI	CCNGG	2 cut(s)	131, 544
BmsI	GCATC	1 cut(s)	34
BpuEI	CTTGAG	1 cut(s)	578
BpuMI	CCSGG	1 cut(s)	131
BsaJI	CCNNGG	2 cut(s)	321, 543
Bsc4I	CCNNNNNNNGG	2 cut(s)	193, 549
Bse118I	RCCGGY	1 cut(s)	353
Bse1I	ACTGG	1 cut(s)	292
Bse3DI	GCAATG	1 cut(s)	468
BseBI	CCWGG	1 cut(s)	544
BseDI	CCNNGG	2 cut(s)	321, 543
BseGI	GGATG	3 cut(s)	49, 466, 504
BseLI	CCNNNNNNNGG	2 cut(s)	193, 549
BseMI	GCAATG	1 cut(s)	468
BseNI	ACTGG	1 cut(s)	292
BseSI	GKGCMC	1 cut(s)	60
Bsh1285I	CGRYCG	1 cut(s)	210
BshFI	GGCC	3 cut(s)	78, 148, 564
BsiEI	CGRYCG	1 cut(s)	210
BsiHKAI	GWGCWC	1 cut(s)	60
BsiSI	CCGG	3 cut(s)	130, 149, 354
BslFI	GGGAC	1 cut(s)	146
BslI	CCNNNNNNNGG	2 cut(s)	193, 549
BsmAI	GTCTC	1 cut(s)	266
BsmFI	GGGAC	1 cut(s)	146
BsmI	GAATGC	1 cut(s)	97
BsnI	GGCC	3 cut(s)	78, 148, 564
Bsp1286I	GDGCHC	2 cut(s)	60, 162
Bsp1407I	TGTACA	1 cut(s)	507
Bsp143I	GATC	4 cut(s)	105, 153, 179, 207
BspACI	CCGC	1 cut(s)	68
BspANI	GGCC	3 cut(s)	78, 148, 564
BspLI	GGNNCC	2 cut(s)	77, 181
BspPI	GGATC	3 cut(s)	113, 174, 187
BspTI	CTTAAG	1 cut(s)	490
BsrDI	GCAATG	1 cut(s)	468
BsrFI	RCCGGY	1 cut(s)	353
BsrGI	TGTACA	1 cut(s)	507
BsrI	ACTGG	1 cut(s)	292
BssAI	RCCGGY	1 cut(s)	353
BssECI	CCNNGG	2 cut(s)	321, 543
BssMI	GATC	4 cut(s)	105, 153, 179, 207
Bst2UI	CCWGG	1 cut(s)	544
Bst6I	CTCTTC	1 cut(s)	417
BstAFI	CTTAAG	1 cut(s)	490
BstAPI	GCANNNNNTGC	1 cut(s)	55
BstAUI	TGTACA	1 cut(s)	507
BstENI	CCTNNNNNAGG	1 cut(s)	547
BstF5I	GGATG	3 cut(s)	49, 466, 504
BstH2I	RGCGCY	1 cut(s)	128
BstHHI	GCGC	3 cut(s)	37, 49, 127
BstKTI	GATC	4 cut(s)	108, 156, 182, 210
BstMAI	GTCTC	1 cut(s)	266
BstMBI	GATC	4 cut(s)	105, 153, 179, 207
BstMCI	CGRYCG	1 cut(s)	210
BstMWI	GCNNNNNNNGC	2 cut(s)	32, 55
BstNI	CCWGG	1 cut(s)	544
BstSCI	CCNGG	2 cut(s)	129, 542
BstSLI	GKGCMC	1 cut(s)	60
BstX2I	RGATCY	1 cut(s)	179
BstYI	RGATCY	1 cut(s)	179
BsuRI	GGCC	3 cut(s)	78, 148, 564
BtsCI	GGATG	3 cut(s)	49, 466, 504
BtsIMutI	CAGTG	1 cut(s)	299
CfoI	GCGC	3 cut(s)	37, 49, 127
Cfr10I	RCCGGY	1 cut(s)	353
Cfr13I	GGNCC	4 cut(s)	76, 146, 325, 562
Csp6I	GTAC	1 cut(s)	508
CviAII	CATG	1 cut(s)	310
CviQI	GTAC	1 cut(s)	508
DpnI	GATC	4 cut(s)	107, 155, 181, 209
DpnII	GATC	4 cut(s)	105, 153, 179, 207
Eam1104I	CTCTTC	1 cut(s)	417
EarI	CTCTTC	1 cut(s)	417
Eco24I	GRGCYC	1 cut(s)	162
Eco47I	GGWCC	1 cut(s)	325
EcoNI	CCTNNNNNAGG	1 cut(s)	547
EcoO109I	RGGNCCY	2 cut(s)	76, 325
EcoRII	CCWGG	1 cut(s)	542
EcoT38I	GRGCYC	1 cut(s)	162
FaeI	CATG	1 cut(s)	313
FaiI	YATR	9 cut(s)	66, 73, 173, 311, 362, 383, 403, 405, 458
FalI	AAGNNNNNCTT	2 cut(s)	12, 44
FaqI	GGGAC	1 cut(s)	146
FatI	CATG	1 cut(s)	309
FokI	GGATG	3 cut(s)	56, 473, 511
FriOI	GRGCYC	1 cut(s)	162
FspBI	CTAG	1 cut(s)	276
FspI	TGCGCA	1 cut(s)	48
GlaI	GCGC	3 cut(s)	36, 48, 126
HaeII	RGCGCY	1 cut(s)	128
HaeIII	GGCC	3 cut(s)	78, 148, 564
HapII	CCGG	3 cut(s)	130, 149, 354
HhaI	GCGC	3 cut(s)	37, 49, 127
Hin1II	CATG	1 cut(s)	313
Hin6I	GCGC	3 cut(s)	35, 47, 125
HinP1I	GCGC	3 cut(s)	35, 47, 125
HincII	GTYRAC	2 cut(s)	517, 577
HindII	GTYRAC	2 cut(s)	517, 577
HinfI	GANTC	4 cut(s)	364, 513, 553, 573
HpaII	CCGG	3 cut(s)	130, 149, 354
HphI	GGTGA	3 cut(s)	127, 160, 559
Hpy166II	GTNNAC	3 cut(s)	58, 517, 577
Hpy188I	TCNGA	1 cut(s)	179
Hpy188III	TCNNGA	4 cut(s)	29, 109, 271, 557
Hpy8I	GTNNAC	3 cut(s)	58, 517, 577
HpyAV	CCTTC	5 cut(s)	34, 106, 218, 382, 578
HpyCH4V	TGCA	3 cut(s)	58, 255, 524
HpyF10VI	GCNNNNNNNGC	2 cut(s)	32, 55
Hsp92II	CATG	1 cut(s)	313
HspAI	GCGC	3 cut(s)	35, 47, 125
Kzo9I	GATC	4 cut(s)	105, 153, 179, 207
LmnI	GCTCC	1 cut(s)	132
LweI	GCATC	1 cut(s)	34
MaeI	CTAG	1 cut(s)	276
MaeIII	GTNAC	1 cut(s)	230
MalI	GATC	4 cut(s)	107, 155, 181, 209
MboI	GATC	4 cut(s)	105, 153, 179, 207
MboII	GAAGA	2 cut(s)	209, 434
MflI	RGATCY	1 cut(s)	179
MhlI	GDGCHC	2 cut(s)	60, 162
MluCI	AATT	4 cut(s)	6, 137, 281, 315
MlyI	GAGTC	2 cut(s)	522, 582
MmeI	TCCRAC	1 cut(s)	157
MnlI	CCTC	7 cut(s)	89, 115, 316, 407, 497, 543, 553
MseI	TTAA	1 cut(s)	491
MslI	CAYNNNNRTG	1 cut(s)	63
MspCI	CTTAAG	1 cut(s)	490
MspI	CCGG	3 cut(s)	130, 149, 354
MspR9I	CCNGG	2 cut(s)	131, 544
Mva1269I	GAATGC	1 cut(s)	97
MvaI	CCWGG	1 cut(s)	544
MwoI	GCNNNNNNNGC	2 cut(s)	32, 55
NciI	CCSGG	1 cut(s)	131
NdeII	GATC	4 cut(s)	105, 153, 179, 207
NlaIII	CATG	1 cut(s)	313
NlaIV	GGNNCC	2 cut(s)	77, 181
NsbI	TGCGCA	1 cut(s)	48
PcsI	WCGNNNNNNNCGW	1 cut(s)	267
PctI	GAATGC	1 cut(s)	97
PfeI	GAWTC	2 cut(s)	364, 553
PfoI	TCCNGGA	1 cut(s)	129
Ple19I	CGATCG	1 cut(s)	210
PleI	GAGTC	2 cut(s)	521, 581
PpsI	GAGTC	2 cut(s)	521, 581
PpuMI	RGGWCCY	1 cut(s)	325
Psp5II	RGGWCCY	1 cut(s)	325
Psp6I	CCWGG	1 cut(s)	542
PspGI	CCWGG	1 cut(s)	542
PspN4I	GGNNCC	2 cut(s)	77, 181
PspPI	GGNCC	4 cut(s)	76, 146, 325, 562
PspPPI	RGGWCCY	1 cut(s)	325
PsuI	RGATCY	1 cut(s)	179
PvuI	CGATCG	1 cut(s)	210
RsaI	GTAC	1 cut(s)	509
RsaNI	GTAC	1 cut(s)	508
RseI	CAYNNNNRTG	1 cut(s)	63
SaqAI	TTAA	1 cut(s)	491
Sau3AI	GATC	4 cut(s)	105, 153, 179, 207
Sau96I	GGNCC	4 cut(s)	76, 146, 325, 562
SchI	GAGTC	2 cut(s)	522, 582
ScrFI	CCNGG	2 cut(s)	131, 544
SduI	GDGCHC	2 cut(s)	60, 162
SetI	ASST	7 cut(s)	28, 65, 117, 229, 330, 439, 570
SfaNI	GCATC	1 cut(s)	34
SinI	GGWCC	1 cut(s)	325
SmiMI	CAYNNNNRTG	1 cut(s)	63
SmlI	CTYRAG	2 cut(s)	490, 557
SmoI	CTYRAG	2 cut(s)	490, 557
SpeI	ACTAGT	1 cut(s)	275
Sse9I	AATT	4 cut(s)	6, 137, 281, 315
SsiI	CCGC	1 cut(s)	68
SspMI	CTAG	1 cut(s)	276
StyD4I	CCNGG	2 cut(s)	129, 542
TaqI	TCGA	4 cut(s)	156, 261, 270, 571
TaqII	GACCGA	1 cut(s)	226
TasI	AATT	4 cut(s)	6, 137, 281, 315
TatI	WGTACW	1 cut(s)	507
TfiI	GAWTC	2 cut(s)	364, 553
Tru1I	TTAA	1 cut(s)	491
Tru9I	TTAA	1 cut(s)	491
TscAI	CASTG	1 cut(s)	299
TspDTI	ATGAA	3 cut(s)	216, 377, 435
TspGWI	ACGGA	1 cut(s)	209
TspRI	CASTG	1 cut(s)	299
Vha464I	CTTAAG	1 cut(s)	490
VneI	GTGCAC	1 cut(s)	56
VpaK11BI	GGWCC	1 cut(s)	325
XagI	CCTNNNNNAGG	1 cut(s)	547
XapI	RAATTY	2 cut(s)	137, 281
XspI	CTAG	1 cut(s)	276

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