Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000004

Orthogroup ID

OG0002242

Physical Location & Seq

Genomic Coordinates Reverse (-)

62574628 .. 62578828

Gene Structure 4201 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_4G00329320.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 423 bp

ATGGTGAGAATCTATTCAAATTGTTGTGGGTTTGAGTGTTTGAGTCACCTCTCAATTGAAGATGAAGAAACCTCCGCCCTAAAGCACTCCAAGTTCCAGAAATTCCTTGACAACTTCTGCAAAGCAAGTGATTACTTCAGCGCAATCCAGCTGATTCTTCCGAACCTCGATCGGGAGCGCGGAAGCTGTGGCCTTAAGGAGTCGGTGCTTGCCACCTGCCTCACCGACGCTCTCGGCATGTCCCGGGACTCCGACAACGCTCTTCGCCTCATCAATTGGTGCAAGGGCGGCGCCAAGACCTGTGCCAATGCCTGCAATTTAGCCCTCGTCGCCATAGAGGTGCTGCAATGCAGACAGGGACTTAGTTCAGGTGGACTAACGATTAAGGAGTTGAATGACTTGCTTGATCGTTTGGTCGGGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000726 GO:0003674 GO:0003824 GO:0003909 GO:0003910 GO:0005575 GO:0005576 GO:0005622 GO:0005623 GO:0005634 GO:0005737 GO:0005911 GO:0006139 GO:0006259 GO:0006266 GO:0006281 GO:0006289 GO:0006297 GO:0006302 GO:0006303 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0008150 GO:0008152 GO:0009314 GO:0009506 GO:0009628 GO:0009987 GO:0010165 GO:0010212 GO:0016874 GO:0016886 GO:0030054 GO:0032807 GO:0032991 GO:0033554 GO:0034641 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044237 GO:0044238 GO:0044260 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0046483 GO:0048046 GO:0050896 GO:0051103 GO:0051716 GO:0055044 GO:0071704 GO:0090304 GO:0140097 GO:1901360

KEGG Pathways

Metabolic & Signaling

ko03450 map03450

Pfam Domains

Protein Families

BRCT_2 DNA_ligase_A_C DNA_ligase_A_M DNA_ligase_A_N DNA_ligase_IV

Protein Analysis

140

Amino Acids

15.31

Weight (kDa)

5.66

Isoelectric Point (pI)

41.62

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DNA_ligase_A_N	PF04675	19 - 138	4.4e-13	DNA ligase N terminus

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: OG0002242)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G57160 AT5G57160
fragaria_vesca	FvH4_4g07160
malus_domestica	MD16G1247900.v1.1
prunus_persica	Prupe.1G074600_v2.0.a1 Prupe.1G074600_v2.0.a1
pyrus_communis	pycom12g16110 pycom12g16210 pycom16g20800
rosa_chinensis	RchiOBHm_Chr0c22g0500591 RchiOBHm_Chr4g0399311 RchiOBHm_Chr5g0052491 RchiOBHm_Chr7g0206661
rosa_laevigata	RLG00000009274 RLG00000012027 RLG00000013478 RLG00000013735 RLG00000034678
rosa_multiflora	Rmu_co8101330.1_g000001 Rmu_co8329359.1_g000001 Rmu_sc0000924.1_g000031 Rmu_sc0003135.1_g000008
rosa_roxburghii	Rroxscaffold_4G00283390 Rroxscaffold_4G00329320 Rroxscaffold_5G00344240
rosa_rugosa	Rorug04G0016500
rosa_samantha	Rh2AG218900 Rh2BG192100 Rh2BG230700 Rh2CG361900 Rh2DG225100 Rh3BG254200 Rh3DG357600 Rh4AG094200 Rh4AG102100 Rh4BG091600 Rh4CG102400 Rh4CG110300 Rh4DG086300 Rh7DG237100 Rh7DG335000 Rh7DG335200
rosa_wichuraiana	Rw4G007730

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	224
Acc36I	ACCTGC	1 cut(s)	224
AccB1I	GGYRCC	1 cut(s)	290
AccII	CGCG	1 cut(s)	180
AciI	CCGC	3 cut(s)	75, 180, 288
AcsI	RAATTY	1 cut(s)	101
AcuI	CTGAAG	1 cut(s)	121
AcyI	GRCGYC	1 cut(s)	291
AfiI	CCNNNNNNNGG	1 cut(s)	172
AflII	CTTAAG	1 cut(s)	194
AgsI	TTSAA	3 cut(s)	18, 59, 394
AluBI	AGCT	2 cut(s)	151, 186
AluI	AGCT	2 cut(s)	151, 186
Ama87I	CYCGRG	1 cut(s)	243
AoxI	GGCC	1 cut(s)	190
ApeKI	GCWGC	1 cut(s)	343
ApoI	RAATTY	1 cut(s)	101
Asp700I	GAANNNNTTC	1 cut(s)	13
AspLEI	GCGC	3 cut(s)	143, 180, 293
AsuC2I	CCSGG	2 cut(s)	244, 245
AsuHPI	GGTGA	3 cut(s)	16, 38, 214
AvaI	CYCGRG	1 cut(s)	243
BanI	GGYRCC	1 cut(s)	290
BbvI	GCAGC	1 cut(s)	330
BcnI	CCSGG	2 cut(s)	244, 245
BfoI	RGCGCY	1 cut(s)	294
BfrI	CTTAAG	1 cut(s)	194
BfuAI	ACCTGC	1 cut(s)	224
BisI	GCNGC	2 cut(s)	289, 344
BlsI	GCNGC	2 cut(s)	290, 345
Bme1390I	CCNGG	2 cut(s)	244, 245
BmeT110I	CYCGRG	1 cut(s)	243
BmiI	GGNNCC	1 cut(s)	292
BmrFI	CCNGG	2 cut(s)	244, 245
BpuMI	CCSGG	2 cut(s)	244, 245
BsaHI	GRCGYC	1 cut(s)	291
BsaJI	CCNNGG	1 cut(s)	243
Bsc4I	CCNNNNNNNGG	1 cut(s)	172
Bse3DI	GCAATG	1 cut(s)	353
BseDI	CCNNGG	1 cut(s)	243
BseLI	CCNNNNNNNGG	1 cut(s)	172
BseMI	GCAATG	1 cut(s)	353
BseXI	GCAGC	1 cut(s)	330
Bsh1236I	CGCG	1 cut(s)	180
Bsh1285I	CGRYCG	1 cut(s)	172
BshFI	GGCC	1 cut(s)	192
BshNI	GGYRCC	1 cut(s)	290
BsiEI	CGRYCG	1 cut(s)	172
BsiHKCI	CYCGRG	1 cut(s)	243
BsiSI	CCGG	1 cut(s)	244
BslFI	GGGAC	3 cut(s)	226, 260, 372
BslI	CCNNNNNNNGG	1 cut(s)	172
BsmFI	GGGAC	3 cut(s)	226, 260, 372
BsnI	GGCC	1 cut(s)	192
BsoBI	CYCGRG	1 cut(s)	243
Bsp143I	GATC	2 cut(s)	169, 406
BspACI	CCGC	3 cut(s)	75, 180, 288
BspANI	GGCC	1 cut(s)	192
BspFNI	CGCG	1 cut(s)	180
BspLI	GGNNCC	1 cut(s)	292
BspMI	ACCTGC	1 cut(s)	224
BspQI	GCTCTTC	1 cut(s)	267
BspT107I	GGYRCC	1 cut(s)	290
BspTI	CTTAAG	1 cut(s)	194
BsrDI	GCAATG	1 cut(s)	353
BssECI	CCNNGG	1 cut(s)	243
BssMI	GATC	2 cut(s)	169, 406
BssNI	GRCGYC	1 cut(s)	291
Bst6I	CTCTTC	1 cut(s)	267
BstACI	GRCGYC	1 cut(s)	291
BstAFI	CTTAAG	1 cut(s)	194
BstC8I	GCNNGC	2 cut(s)	210, 313
BstDEI	CTNAG	1 cut(s)	362
BstFNI	CGCG	1 cut(s)	180
BstH2I	RGCGCY	1 cut(s)	294
BstHHI	GCGC	3 cut(s)	143, 180, 293
BstKTI	GATC	2 cut(s)	172, 409
BstMBI	GATC	2 cut(s)	169, 406
BstMCI	CGRYCG	1 cut(s)	172
BstMWI	GCNNNNNNNGC	2 cut(s)	288, 329
BstNSI	RCATGY	1 cut(s)	241
BstSCI	CCNGG	2 cut(s)	242, 243
BstUI	CGCG	1 cut(s)	180
BstV1I	GCAGC	1 cut(s)	330
BsuRI	GGCC	1 cut(s)	192
BveI	ACCTGC	1 cut(s)	224
Cac8I	GCNNGC	2 cut(s)	210, 313
CfoI	GCGC	3 cut(s)	143, 180, 293
Cfr9I	CCCGGG	1 cut(s)	243
CseI	GACGC	1 cut(s)	236
CviAII	CATG	1 cut(s)	238
CviJI	RGCY	4 cut(s)	151, 186, 192, 323
CviKI_1	RGCY	4 cut(s)	151, 186, 192, 323
DdeI	CTNAG	1 cut(s)	362
DinI	GGCGCC	1 cut(s)	292
DpnI	GATC	2 cut(s)	171, 408
DpnII	GATC	2 cut(s)	169, 406
Eam1104I	CTCTTC	1 cut(s)	267
EarI	CTCTTC	1 cut(s)	267
EciI	GGCGGA	1 cut(s)	64
Eco57I	CTGAAG	1 cut(s)	121
Eco88I	CYCGRG	1 cut(s)	243
EgeI	GGCGCC	1 cut(s)	292
EheI	GGCGCC	1 cut(s)	292
FaeI	CATG	1 cut(s)	241
FaiI	YATR	2 cut(s)	239, 335
FaqI	GGGAC	3 cut(s)	226, 260, 372
FatI	CATG	1 cut(s)	237
Fnu4HI	GCNGC	2 cut(s)	289, 344
Fsp4HI	GCNGC	2 cut(s)	289, 344
GlaI	GCGC	3 cut(s)	142, 179, 292
GluI	GCNGC	2 cut(s)	289, 344
HaeII	RGCGCY	1 cut(s)	294
HaeIII	GGCC	1 cut(s)	192
HapII	CCGG	1 cut(s)	244
HgaI	GACGC	1 cut(s)	236
HhaI	GCGC	3 cut(s)	143, 180, 293
Hin1I	GRCGYC	1 cut(s)	291
Hin1II	CATG	1 cut(s)	241
Hin6I	GCGC	3 cut(s)	141, 178, 291
HinP1I	GCGC	3 cut(s)	141, 178, 291
HinfI	GANTC	5 cut(s)	9, 43, 154, 200, 248
HpaII	CCGG	1 cut(s)	244
HphI	GGTGA	3 cut(s)	16, 38, 214
Hpy166II	GTNNAC	1 cut(s)	374
Hpy188I	TCNGA	2 cut(s)	162, 253
Hpy188III	TCNNGA	2 cut(s)	97, 173
Hpy8I	GTNNAC	1 cut(s)	374
Hpy99I	CGWCG	2 cut(s)	230, 332
HpyCH4V	TGCA	5 cut(s)	120, 282, 315, 346, 351
HpyF10VI	GCNNNNNNNGC	2 cut(s)	288, 329
HpyF3I	CTNAG	1 cut(s)	362
Hsp92I	GRCGYC	1 cut(s)	291
Hsp92II	CATG	1 cut(s)	241
HspAI	GCGC	3 cut(s)	141, 178, 291
KasI	GGCGCC	1 cut(s)	290
Kzo9I	GATC	2 cut(s)	169, 406
LguI	GCTCTTC	1 cut(s)	267
LmnI	GCTCC	1 cut(s)	175
LpnPI	CCDG	8 cut(s)	110, 161, 229, 257, 313, 325, 341, 354
Lsp1109I	GCAGC	1 cut(s)	330
MaeIII	GTNAC	1 cut(s)	44
MalI	GATC	2 cut(s)	171, 408
MboI	GATC	2 cut(s)	169, 406
MboII	GAAGA	4 cut(s)	71, 77, 149, 254
MfeI	CAATTG	2 cut(s)	54, 274
MluCI	AATT	5 cut(s)	19, 54, 101, 274, 316
Mly113I	GGCGCC	1 cut(s)	291
MlyI	GAGTC	3 cut(s)	52, 209, 242
MmeI	TCCRAC	1 cut(s)	276
MnlI	CCTC	7 cut(s)	59, 82, 176, 230, 278, 331, 335
MroXI	GAANNNNTTC	1 cut(s)	13
MseI	TTAA	2 cut(s)	195, 384
MslI	CAYNNNNRTG	1 cut(s)	338
MspA1I	CMGCKG	1 cut(s)	151
MspCI	CTTAAG	1 cut(s)	194
MspI	CCGG	1 cut(s)	244
MspR9I	CCNGG	2 cut(s)	244, 245
MunI	CAATTG	2 cut(s)	54, 274
MvnI	CGCG	1 cut(s)	180
MwoI	GCNNNNNNNGC	2 cut(s)	288, 329
NarI	GGCGCC	1 cut(s)	291
NciI	CCSGG	2 cut(s)	244, 245
NdeII	GATC	2 cut(s)	169, 406
NlaIII	CATG	1 cut(s)	241
NlaIV	GGNNCC	1 cut(s)	292
NmeAIII	GCCGAG	1 cut(s)	213
NmuCI	GTSAC	1 cut(s)	44
NspI	RCATGY	1 cut(s)	241
PaqCI	CACCTGC	1 cut(s)	224
PciSI	GCTCTTC	1 cut(s)	267
PdmI	GAANNNNTTC	1 cut(s)	13
PfeI	GAWTC	2 cut(s)	9, 154
PkrI	GCNGC	2 cut(s)	290, 345
Ple19I	CGATCG	1 cut(s)	172
PleI	GAGTC	3 cut(s)	51, 208, 242
PluTI	GGCGCC	1 cut(s)	294
PpsI	GAGTC	3 cut(s)	51, 208, 242
PspN4I	GGNNCC	1 cut(s)	292
PvuI	CGATCG	1 cut(s)	172
PvuII	CAGCTG	1 cut(s)	151
RseI	CAYNNNNRTG	1 cut(s)	338
SapI	GCTCTTC	1 cut(s)	267
SaqAI	TTAA	2 cut(s)	195, 384
SatI	GCNGC	2 cut(s)	289, 344
Sau3AI	GATC	2 cut(s)	169, 406
SchI	GAGTC	3 cut(s)	52, 209, 242
ScrFI	CCNGG	2 cut(s)	244, 245
SetI	ASST	9 cut(s)	51, 74, 153, 168, 188, 218, 302, 342, 373
SfoI	GGCGCC	1 cut(s)	292
SmaI	CCCGGG	1 cut(s)	245
SmiMI	CAYNNNNRTG	1 cut(s)	338
SmlI	CTYRAG	1 cut(s)	194
SmoI	CTYRAG	1 cut(s)	194
Sse9I	AATT	5 cut(s)	19, 54, 101, 274, 316
SsiI	CCGC	3 cut(s)	75, 180, 288
SspDI	GGCGCC	1 cut(s)	290
StyD4I	CCNGG	2 cut(s)	242, 243
TaqI	TCGA	1 cut(s)	168
TasI	AATT	5 cut(s)	19, 54, 101, 274, 316
TauI	GCSGC	1 cut(s)	291
TfiI	GAWTC	2 cut(s)	9, 154
Tru1I	TTAA	2 cut(s)	195, 384
Tru9I	TTAA	2 cut(s)	195, 384
TseFI	GTSAC	1 cut(s)	44
TseI	GCWGC	1 cut(s)	343
Tsp45I	GTSAC	1 cut(s)	44
TspDTI	ATGAA	1 cut(s)	78
TspMI	CCCGGG	1 cut(s)	243
Vha464I	CTTAAG	1 cut(s)	194
XapI	RAATTY	1 cut(s)	101
XceI	RCATGY	1 cut(s)	241
XmaI	CCCGGG	1 cut(s)	243
XmnI	GAANNNNTTC	1 cut(s)	13

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