Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000006

Orthogroup ID

OG0004365

Physical Location & Seq

Genomic Coordinates Reverse (-)

18405676 .. 18407777

Gene Structure 2102 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_6G00396840.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1332 bp

ATGGATATAGATACGGGTATGTTTACGGTTCCTCAAACTGTTGGCAGCGTACTGTGTTGCAAATGTGGTATTCCCATGGCACCAAATGCCGCCAATATGTGCGTCAAGTGTTTGCGCTCTGAAGTTGACATTACTGAAGGTTTGCAGAAGCATGTGACTATTGTGCATTGCCCTGAATGTGATACCTACTTGCAGCCTCCGAGAACTTGGATTAAAGCCCAACTAGAATCGAAGGAGCTGCTAACTTTCTGTGTGAAGAGACTGAAGAACTTGAATAAAATTAGGTTGGTTCATGCTGAATTCATTTGGACTGAACCTCACTCCAAGAGGATTAAGGTTAAGTTGGTAGTTCAGAAGGAAGTTCTTAATGGAGCAATACTTGAGCAATCGTATACTGTTGAGTATGTTCAGCAAGAACATATGTGTGAGTCTTGTGCAAGAGTCCAAGCCAACCCTGACCAGTGGGTTGCAGCTGTACAGCTTCGCCAGCATGTTTCTCACAGACGCACTTTTTTCTATCTGGAACAGCTGATTCTGAAGCATGGTGCTGCTGCCAGTGCCATAAAGATTACGCAGATGGACCAGGGTATCGATTTCTTTTTCTCAAACCGCAGTCATGGTGTGAAATTTGTGGAGTTTGTGGGTAAAGTTGCTCCAGTAAGGAGTCGTAATGACAAACAGCTGGTTTCCCAGGATTCTAAGAGTAATACTTATCATTACAAGTATACATTCTCAGTTGAAATCTCCCCCATTTGCCGTGAGGATTTGATCTGTCTGCCTCCCAAGGTTAGATCTAGTTTTGGGAATCTTGGTCCTCTAGTGATTTGCACTAAAGTGACTAACAGTATTGCTTTGCTTGATCCTTTGACCTTGAGGCATTGTTTCTTGGATGCTGATCAATATTGGAGGTCAAGCTTTAAGTCGCTACATACGAGCCGGGAGTTAGTGGAGTATATAGTGCTCGATGTAGAGATGGTTTCATCTGAAGTTAATGTTGGTGGCACAAGGTATGCTTTAGCTGATGCACAAGTTGCCCGTGTGTCTGATTTTGGGAAGAATGACACTATTTTCAACATAAAAACGCATATAGGCCATCTTTTAAACCCTGGGGATTATGCTCTTGGTTATGACTTATATGGGGCAAACAGTAATGACGAGGAACTAGACAAGTATAAGGGTCTAGTCATTCCAGATGTAATTTTGATAAAGAAGAGCTATGAAGAAAAGCGCCTGAAGAAGCGTGCAAAGCCTCGTGCATGGAAGCTTAAATCCCTTGCCATGGAAGTGGATGCTAAAGGTAGAGGCACTAGAAAAGGAGGCCTCAGAGTATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

ko03008 ko03013 map03008 map03013

Pfam Domains

Protein Families

NMD3

Protein Analysis

443

Amino Acids

50.21

Weight (kDa)

9.02

Isoelectric Point (pI)

37.36

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
NMD3	PF04981	19 - 248	1.4e-76	NMD3 family
NMD_SH3	PF21193	251 - 295	9.5e-18	NMD3 SH3 domain
OB_NMD3	PF21192	315 - 404	3.4e-31	NMD3 OB-fold domain

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

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0004365)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G03820
fragaria_vesca	FvH4_1g26190 FvH4_1g26190 FvH4_4g00390 FvH4_4g00390
prunus_persica	Prupe.4G217800_v2.0.a1 Prupe.4G217800_v2.0.a1 Prupe.4G273200_v2.0.a1
pyrus_communis	pycom04g00430
rosa_chinensis	RchiOBHm_Chr3g0485681 RchiOBHm_Chr3g0485701 RchiOBHm_Chr4g0385341
rosa_laevigata	RLG00000010236 RLG00000023132
rosa_multiflora	Rmu_sc0001259.1_g000008 Rmu_sc0003005.1_g000028
rosa_roxburghii	Rroxscaffold_5G00333270 Rroxscaffold_6G00396510 Rroxscaffold_6G00396820 Rroxscaffold_6G00396840
rosa_rugosa	Rorug03G0220700 Rorug03G0300500
rosa_samantha	Rh3AG269900 Rh3BG305700 Rh3CG303800 Rh3DG300100 Rh4AG004200 Rh4BG003600 Rh4CG005300 Rh4DG003800
rosa_wichuraiana	Rw3G024040 Rw4G000480

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	79
AccI	GTMKAC	2 cut(s)	392, 725
AciI	CCGC	2 cut(s)	90, 610
AclWI	GGATC	1 cut(s)	854
AcsI	RAATTY	2 cut(s)	299, 626
AcuI	CTGAAG	6 cut(s)	141, 156, 284, 557, 1005, 1253
AfaI	GTAC	2 cut(s)	51, 477
AfiI	CCNNNNNNNGG	1 cut(s)	1279
AgsI	TTSAA	3 cut(s)	274, 740, 1072
AjnI	CCWGG	3 cut(s)	582, 690, 1105
AjuI	GAANNNNNNNTTGG	2 cut(s)	978, 1010
AleI	CACNNNNGTG	1 cut(s)	833
AluBI	AGCT	9 cut(s)	238, 473, 481, 529, 682, 915, 1019, 1215, 1264
AluI	AGCT	9 cut(s)	238, 473, 481, 529, 682, 915, 1019, 1215, 1264
Alw21I	GWGCWC	1 cut(s)	963
Alw26I	GTCTC	1 cut(s)	253
AlwI	GGATC	1 cut(s)	854
AoxI	GGCC	2 cut(s)	1090, 1318
ApeKI	GCWGC	6 cut(s)	45, 193, 238, 470, 548, 551
ApoI	RAATTY	2 cut(s)	299, 626
AspLEI	GCGC	2 cut(s)	117, 1230
AspS9I	GGNCC	2 cut(s)	580, 812
AsuC2I	CCSGG	1 cut(s)	938
AvaII	GGWCC	2 cut(s)	580, 812
BaeI	ACNNNNGTAYC	2 cut(s)	571, 604
BanI	GGYRCC	1 cut(s)	79
BauI	CACGAG	1 cut(s)	1251
Bbv12I	GWGCWC	1 cut(s)	963
BbvI	GCAGC	6 cut(s)	57, 205, 225, 482, 535, 538
BccI	CCATC	3 cut(s)	571, 967, 1101
BceAI	ACGGC	1 cut(s)	741
BcgI	CGANNNNNNTGC	2 cut(s)	220, 254
BciT130I	CCWGG	3 cut(s)	584, 692, 1107
BclI	TGATCA	1 cut(s)	895
BcnI	CCSGG	1 cut(s)	938
BcoDI	GTCTC	1 cut(s)	253
BfaI	CTAG	6 cut(s)	224, 795, 818, 1163, 1181, 1308
BfoI	RGCGCY	1 cut(s)	1231
BglII	AGATCT	1 cut(s)	791
BisI	GCNGC	7 cut(s)	46, 90, 194, 239, 471, 549, 552
BlsI	GCNGC	7 cut(s)	47, 91, 195, 240, 472, 550, 553
Bme1390I	CCNGG	4 cut(s)	584, 692, 938, 1107
Bme18I	GGWCC	2 cut(s)	580, 812
BmgT120I	GGNCC	2 cut(s)	580, 812
BmiI	GGNNCC	2 cut(s)	30, 81
BmrFI	CCNGG	4 cut(s)	584, 692, 938, 1107
BmsI	GCATC	3 cut(s)	880, 1012, 1279
BpmI	CTGGAG	1 cut(s)	639
BpuEI	CTTGAG	2 cut(s)	401, 892
BpuMI	CCSGG	1 cut(s)	938
Bsa29I	ATCGAT	1 cut(s)	591
BsaBI	GATNNNNATC	1 cut(s)	894
BsaJI	CCNNGG	7 cut(s)	75, 583, 690, 783, 1105, 1106, 1278
Bsc4I	CCNNNNNNNGG	1 cut(s)	1279
Bse1I	ACTGG	3 cut(s)	460, 555, 656
Bse3DI	GCAATG	1 cut(s)	166
Bse8I	GATNNNNATC	1 cut(s)	894
BseBI	CCWGG	3 cut(s)	584, 692, 1107
BseCI	ATCGAT	1 cut(s)	591
BseDI	CCNNGG	7 cut(s)	75, 583, 690, 783, 1105, 1106, 1278
BseGI	GGATG	2 cut(s)	895, 1294
BseJI	GATNNNNATC	1 cut(s)	894
BseLI	CCNNNNNNNGG	1 cut(s)	1279
BseMI	GCAATG	1 cut(s)	166
BseMII	CTCAG	1 cut(s)	747
BseNI	ACTGG	3 cut(s)	460, 555, 656
BseXI	GCAGC	6 cut(s)	57, 205, 225, 482, 535, 538
BshFI	GGCC	2 cut(s)	1092, 1320
BshNI	GGYRCC	1 cut(s)	79
BshVI	ATCGAT	1 cut(s)	591
BsiHKAI	GWGCWC	1 cut(s)	963
BsiSI	CCGG	1 cut(s)	937
BslI	CCNNNNNNNGG	1 cut(s)	1279
BsmAI	GTCTC	1 cut(s)	253
BsnI	GGCC	2 cut(s)	1092, 1320
Bsp1286I	GDGCHC	1 cut(s)	963
Bsp1407I	TGTACA	1 cut(s)	475
Bsp143I	GATC	4 cut(s)	768, 791, 859, 895
Bsp19I	CCATGG	2 cut(s)	75, 1278
BspACI	CCGC	2 cut(s)	90, 610
BspANI	GGCC	2 cut(s)	1092, 1320
BspCNI	CTCAG	1 cut(s)	746
BspDI	ATCGAT	1 cut(s)	591
BspLI	GGNNCC	2 cut(s)	30, 81
BspPI	GGATC	1 cut(s)	854
BspQI	GCTCTTC	1 cut(s)	1205
BspT107I	GGYRCC	1 cut(s)	79
BsrDI	GCAATG	1 cut(s)	166
BsrGI	TGTACA	1 cut(s)	475
BsrI	ACTGG	3 cut(s)	460, 555, 656
BssECI	CCNNGG	7 cut(s)	75, 583, 690, 783, 1105, 1106, 1278
BssMI	GATC	4 cut(s)	768, 791, 859, 895
BssNAI	GTATAC	2 cut(s)	393, 726
BssSI	CACGAG	1 cut(s)	1251
BssT1I	CCWWGG	3 cut(s)	75, 783, 1278
Bst1107I	GTATAC	2 cut(s)	393, 726
Bst2BI	CACGAG	1 cut(s)	1251
Bst2UI	CCWGG	3 cut(s)	584, 692, 1107
Bst4CI	ACNGT	6 cut(s)	28, 40, 54, 397, 845, 1148
Bst6I	CTCTTC	2 cut(s)	251, 1205
BstAPI	GCANNNNNTGC	2 cut(s)	86, 1031
BstAUI	TGTACA	1 cut(s)	475
BstC8I	GCNNGC	2 cut(s)	488, 1242
BstDEI	CTNAG	3 cut(s)	699, 733, 1322
BstDSI	CCRYGG	2 cut(s)	75, 1278
BstF5I	GGATG	2 cut(s)	895, 1294
BstH2I	RGCGCY	1 cut(s)	1231
BstHHI	GCGC	2 cut(s)	117, 1230
BstKTI	GATC	4 cut(s)	771, 794, 862, 898
BstMAI	GTCTC	1 cut(s)	253
BstMBI	GATC	4 cut(s)	768, 791, 859, 895
BstMWI	GCNNNNNNNGC	5 cut(s)	86, 487, 557, 1031, 1246
BstNI	CCWGG	3 cut(s)	584, 692, 1107
BstNSI	RCATGY	2 cut(s)	155, 494
BstSCI	CCNGG	4 cut(s)	582, 690, 936, 1105
BstV1I	GCAGC	6 cut(s)	57, 205, 225, 482, 535, 538
BstX2I	RGATCY	1 cut(s)	791
BstXI	CCANNNNNNTGG	1 cut(s)	1285
BstYI	RGATCY	1 cut(s)	791
BstZ17I	GTATAC	2 cut(s)	393, 726
Bsu15I	ATCGAT	1 cut(s)	591
BsuRI	GGCC	2 cut(s)	1092, 1320
BsuTUI	ATCGAT	1 cut(s)	591
BtgI	CCRYGG	2 cut(s)	75, 1278
BtsCI	GGATG	2 cut(s)	895, 1294
BtsIMutI	CAGTG	2 cut(s)	467, 562
Cac8I	GCNNGC	2 cut(s)	488, 1242
CfoI	GCGC	2 cut(s)	117, 1230
Cfr13I	GGNCC	2 cut(s)	580, 812
ClaI	ATCGAT	1 cut(s)	591
CseI	GACGC	2 cut(s)	91, 513
Csp6I	GTAC	2 cut(s)	50, 476
CviAII	CATG	8 cut(s)	76, 152, 293, 491, 542, 617, 1257, 1279
CviQI	GTAC	2 cut(s)	50, 476
DdeI	CTNAG	3 cut(s)	699, 733, 1322
DpnI	GATC	4 cut(s)	770, 793, 861, 897
DpnII	GATC	4 cut(s)	768, 791, 859, 895
DraI	TTTAAA	1 cut(s)	1101
Eam1104I	CTCTTC	2 cut(s)	251, 1205
EarI	CTCTTC	2 cut(s)	251, 1205
Eco130I	CCWWGG	3 cut(s)	75, 783, 1278
Eco147I	AGGCCT	1 cut(s)	1320
Eco47I	GGWCC	2 cut(s)	580, 812
Eco57I	CTGAAG	6 cut(s)	141, 156, 284, 557, 1005, 1253
EcoRI	GAATTC	1 cut(s)	299
EcoRII	CCWGG	3 cut(s)	582, 690, 1105
EcoT14I	CCWWGG	3 cut(s)	75, 783, 1278
ErhI	CCWWGG	3 cut(s)	75, 783, 1278
FaeI	CATG	8 cut(s)	79, 155, 296, 494, 545, 620, 1260, 1282
FalI	AAGNNNNNCTT	2 cut(s)	997, 1029
FatI	CATG	8 cut(s)	75, 151, 292, 490, 541, 616, 1256, 1278
FauNDI	CATATG	1 cut(s)	420
FbaI	TGATCA	1 cut(s)	895
FblI	GTMKAC	2 cut(s)	392, 725
Fnu4HI	GCNGC	7 cut(s)	46, 90, 194, 239, 471, 549, 552
FokI	GGATG	2 cut(s)	902, 1301
Fsp4HI	GCNGC	7 cut(s)	46, 90, 194, 239, 471, 549, 552
FspBI	CTAG	6 cut(s)	224, 795, 818, 1163, 1181, 1308
GlaI	GCGC	2 cut(s)	116, 1229
GluI	GCNGC	7 cut(s)	46, 90, 194, 239, 471, 549, 552
GsuI	CTGGAG	1 cut(s)	639
HaeII	RGCGCY	1 cut(s)	1231
HaeIII	GGCC	2 cut(s)	1092, 1320
HapII	CCGG	1 cut(s)	937
HgaI	GACGC	2 cut(s)	91, 513
HhaI	GCGC	2 cut(s)	117, 1230
Hin1II	CATG	8 cut(s)	79, 155, 296, 494, 545, 620, 1260, 1282
Hin6I	GCGC	2 cut(s)	115, 1228
HinP1I	GCGC	2 cut(s)	115, 1228
HincII	GTYRAC	1 cut(s)	127
HindII	GTYRAC	1 cut(s)	127
HindIII	AAGCTT	2 cut(s)	913, 1262
HinfI	GANTC	7 cut(s)	227, 428, 441, 532, 664, 695, 805
HpaII	CCGG	1 cut(s)	937
Hpy166II	GTNNAC	4 cut(s)	24, 127, 393, 726
Hpy188I	TCNGA	7 cut(s)	121, 201, 354, 537, 985, 1045, 1325
Hpy188III	TCNNGA	2 cut(s)	521, 1190
Hpy8I	GTNNAC	4 cut(s)	24, 127, 393, 726
HpyAV	CCTTC	3 cut(s)	131, 226, 349
HpyCH4III	ACNGT	6 cut(s)	28, 40, 54, 397, 845, 1148
HpyF10VI	GCNNNNNNNGC	5 cut(s)	86, 487, 557, 1031, 1246
HpyF3I	CTNAG	3 cut(s)	699, 733, 1322
Hsp92II	CATG	8 cut(s)	79, 155, 296, 494, 545, 620, 1260, 1282
HspAI	GCGC	2 cut(s)	115, 1228
Ksp22I	TGATCA	1 cut(s)	895
Kzo9I	GATC	4 cut(s)	768, 791, 859, 895
LguI	GCTCTTC	1 cut(s)	1205
LmnI	GCTCC	3 cut(s)	235, 371, 658
Lsp1109I	GCAGC	6 cut(s)	57, 205, 225, 482, 535, 538
LweI	GCATC	3 cut(s)	880, 1012, 1279
MaeI	CTAG	6 cut(s)	224, 795, 818, 1163, 1181, 1308
MaeIII	GTNAC	2 cut(s)	154, 835
MalI	GATC	4 cut(s)	770, 793, 861, 897
MboI	GATC	4 cut(s)	768, 791, 859, 895
MboII	GAAGA	6 cut(s)	268, 277, 1066, 1222, 1232, 1246
MflI	RGATCY	1 cut(s)	791
MhlI	GDGCHC	1 cut(s)	963
MluCI	AATT	4 cut(s)	279, 299, 626, 1197
MlyI	GAGTC	3 cut(s)	437, 450, 673
MseI	TTAA	8 cut(s)	213, 333, 339, 366, 918, 990, 1100, 1266
MslI	CAYNNNNRTG	3 cut(s)	423, 833, 1283
MspA1I	CMGCKG	3 cut(s)	473, 529, 682
MspI	CCGG	1 cut(s)	937
MspR9I	CCNGG	4 cut(s)	584, 692, 938, 1107
MvaI	CCWGG	3 cut(s)	584, 692, 1107
MwoI	GCNNNNNNNGC	5 cut(s)	86, 487, 557, 1031, 1246
NciI	CCSGG	1 cut(s)	938
NcoI	CCATGG	2 cut(s)	75, 1278
NdeI	CATATG	1 cut(s)	420
NdeII	GATC	4 cut(s)	768, 791, 859, 895
NlaIII	CATG	8 cut(s)	79, 155, 296, 494, 545, 620, 1260, 1282
NlaIV	GGNNCC	2 cut(s)	30, 81
NmuCI	GTSAC	2 cut(s)	154, 835
NspI	RCATGY	2 cut(s)	155, 494
OliI	CACNNNNGTG	1 cut(s)	833
PasI	CCCWGGG	1 cut(s)	1106
PceI	AGGCCT	1 cut(s)	1320
PciSI	GCTCTTC	1 cut(s)	1205
PcsI	WCGNNNNNNNCGW	1 cut(s)	929
PfeI	GAWTC	4 cut(s)	227, 532, 695, 805
PkrI	GCNGC	7 cut(s)	47, 91, 195, 240, 472, 550, 553
PleI	GAGTC	3 cut(s)	436, 449, 672
PpsI	GAGTC	3 cut(s)	436, 449, 672
Psp6I	CCWGG	3 cut(s)	582, 690, 1105
PspGI	CCWGG	3 cut(s)	582, 690, 1105
PspN4I	GGNNCC	2 cut(s)	30, 81
PspPI	GGNCC	2 cut(s)	580, 812
PsuI	RGATCY	1 cut(s)	791
PvuII	CAGCTG	3 cut(s)	473, 529, 682
RsaI	GTAC	2 cut(s)	51, 477
RsaNI	GTAC	2 cut(s)	50, 476
RseI	CAYNNNNRTG	3 cut(s)	423, 833, 1283
SapI	GCTCTTC	1 cut(s)	1205
SaqAI	TTAA	8 cut(s)	213, 333, 339, 366, 918, 990, 1100, 1266
SatI	GCNGC	7 cut(s)	46, 90, 194, 239, 471, 549, 552
Sau3AI	GATC	4 cut(s)	768, 791, 859, 895
Sau96I	GGNCC	2 cut(s)	580, 812
SchI	GAGTC	3 cut(s)	437, 450, 673
ScrFI	CCNGG	4 cut(s)	584, 692, 938, 1107
SduI	GDGCHC	1 cut(s)	963
SfaNI	GCATC	3 cut(s)	880, 1012, 1279
SinI	GGWCC	2 cut(s)	580, 812
SmiMI	CAYNNNNRTG	3 cut(s)	423, 833, 1283
SmlI	CTYRAG	2 cut(s)	380, 871
SmoI	CTYRAG	2 cut(s)	380, 871
Sse9I	AATT	4 cut(s)	279, 299, 626, 1197
SseBI	AGGCCT	1 cut(s)	1320
SsiI	CCGC	2 cut(s)	90, 610
SspI	AATATT	1 cut(s)	902
SspMI	CTAG	6 cut(s)	224, 795, 818, 1163, 1181, 1308
StuI	AGGCCT	1 cut(s)	1320
StyD4I	CCNGG	4 cut(s)	582, 690, 936, 1105
StyI	CCWWGG	3 cut(s)	75, 783, 1278
TaaI	ACNGT	6 cut(s)	28, 40, 54, 397, 845, 1148
TaqI	TCGA	3 cut(s)	230, 591, 963
TasI	AATT	4 cut(s)	279, 299, 626, 1197
TatI	WGTACW	1 cut(s)	475
TauI	GCSGC	1 cut(s)	92
TfiI	GAWTC	4 cut(s)	227, 532, 695, 805
Tru1I	TTAA	8 cut(s)	213, 333, 339, 366, 918, 990, 1100, 1266
Tru9I	TTAA	8 cut(s)	213, 333, 339, 366, 918, 990, 1100, 1266
TscAI	CASTG	2 cut(s)	467, 562
TseFI	GTSAC	2 cut(s)	154, 835
TseI	GCWGC	6 cut(s)	45, 193, 238, 470, 548, 551
Tsp45I	GTSAC	2 cut(s)	154, 835
TspDTI	ATGAA	4 cut(s)	281, 292, 969, 1233
TspRI	CASTG	2 cut(s)	467, 562
VpaK11BI	GGWCC	2 cut(s)	580, 812
XapI	RAATTY	2 cut(s)	299, 626
XceI	RCATGY	2 cut(s)	155, 494
XmiI	GTMKAC	2 cut(s)	392, 725
XspI	CTAG	6 cut(s)	224, 795, 818, 1163, 1181, 1308

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