Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3D

Orthogroup ID

OG0000643

Physical Location & Seq

Genomic Coordinates Forward (+)

5810699 .. 5815465

Gene Structure 4767 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3DG076100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 402 bp

ATGGTTCTCACGACTAAACTTTGCCGCTTCAGTGGTGCCAAGATCTACCCTGGTAGGGGCATCAGATTCATCCACTCCGATTCTCAGGTTTCCCTGTTCATAAATTCCAAGTGCAAGAGGTACTTTAACAACCGCCTCAAGCCATCCAAGATCACATGGACTGCCATGTTCAGAAAGCAGCACAAGAAGCATGCTTACAACCCAAATGAGGAGTATGCAGATGTGGAATCCACATTGCGTTCGCATTTGGAATCTTTTCTAGAAACTACAAGATCATTCAATATGATTTACACCAAGGAAATACGTCCCTGGACACACATGATGGAGGTACCCCAGCTCCATGGGTTCGGGCCTGCAGCCAATCGCTTATTGGAGGCATATAAGATGCTTTTGAAGATATAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005819 GO:0005856 GO:0005874 GO:0005876 GO:0008017 GO:0008092 GO:0009524 GO:0015630 GO:0015631 GO:0043226 GO:0043228 GO:0043229 GO:0043232 GO:0044422 GO:0044424 GO:0044430 GO:0044444 GO:0044446 GO:0044464 GO:0051011 GO:0099080 GO:0099081 GO:0099512 GO:0099513

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Plant_NMP1

Protein Analysis

133

Amino Acids

15.72

Weight (kDa)

10.01

Isoelectric Point (pI)

33.47

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Ribosomal_L24e	PF01246	5 - 64	7.7e-25	Ribosomal protein L24e
Plant_NMP1	PF06694	59 - 133	7.1e-40	Plant nuclear matrix protein 1 (NMP1)

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

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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: OG0000643)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G28230
fragaria_vesca	FvH4_3g16300 FvH4_6g12751 FvH4_6g44570 FvH4_6g44594 FvH4_7g07660
malus_domestica	MD09G1096400.v1.1 MD17G1084500.v1.1
prunus_persica	Prupe.3G231100_v2.0.a1
pyrus_communis	pycom09g02090 pycom17g08160
rosa_chinensis	RchiOBHm_Chr1g0342751 RchiOBHm_Chr2g0157591 RchiOBHm_Chr2g0161781 RchiOBHm_Chr3g0469881
rosa_laevigata	RLG00000007135 RLG00000010298 RLG00000021299 RLG00000021302 RLG00000029173 RLG00000029192
rosa_multiflora	Rmu_sc0000173.1_g000045 Rmu_sc0001403.1_g000033 Rmu_sc0001403.1_g000034 Rmu_sc0001993.1_g000002 Rmu_sc0001993.1_g000020 Rmu_sc0003662.1_g000014 Rmu_sc0011563.1_g000010 Rmu_sc0012276.1_g000010 Rmu_sc0026352.1_g000003
rosa_roxburghii	Rroxscaffold_1G00038970 Rroxscaffold_2G00088610 Rroxscaffold_3G00231870 Rroxscaffold_4G00288710 Rroxscaffold_4G00313230 Rroxscaffold_6G00396080 Rroxscaffold_7G00184860
rosa_rugosa	Rorug01G0146100.1 Rorug02G0491800 Rorug02G0492600 Rorug03G0291200 Rorug05G0303900 Rorug05G0335100 Rorug05G0335200
rosa_samantha	Rh1AG028300 Rh1AG137400 Rh1AG162800 Rh1AG163600 Rh1AG163700 Rh1AG164400 Rh1AG164500 Rh1BG129500 Rh1BG129600 Rh1CG025800 Rh1CG129600 Rh1CG151800 Rh1CG152300 Rh1CG152800 Rh1CG153300 Rh1DG044700 Rh1DG133100 Rh2AG558000 Rh2BG571600 Rh2CG541700 Rh2DG549600 Rh2DG580500 Rh3BG178200 Rh3CG168900 Rh3DG076100 Rh3DG260000 Rh5AG515900 Rh6BG166400 Rh6DG108300 Rh7AG194200 Rh7DG200800 Rh7DG369800
rosa_wichuraiana	Rw2G046170

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc65I	GGTACC	1 cut(s)	328
AccB1I	GGYRCC	2 cut(s)	35, 328
AciI	CCGC	2 cut(s)	25, 133
AcsI	RAATTY	1 cut(s)	103
AcuI	CTGAAG	1 cut(s)	13
AfaI	GTAC	2 cut(s)	122, 330
AfiI	CCNNNNNNNGG	3 cut(s)	55, 56, 208
AgsI	TTSAA	2 cut(s)	280, 394
AjnI	CCWGG	2 cut(s)	49, 308
AluBI	AGCT	1 cut(s)	337
AluI	AGCT	1 cut(s)	337
AoxI	GGCC	1 cut(s)	350
ApeKI	GCWGC	2 cut(s)	178, 356
ApoI	RAATTY	1 cut(s)	103
Asp700I	GAANNNNTTC	1 cut(s)	255
Asp718I	GGTACC	1 cut(s)	328
AspS9I	GGNCC	1 cut(s)	350
BanI	GGYRCC	2 cut(s)	35, 328
BarI	GAAGNNNNNNTAC	2 cut(s)	179, 211
BbvI	GCAGC	2 cut(s)	190, 368
BccI	CCATC	2 cut(s)	151, 316
BciT130I	CCWGG	2 cut(s)	51, 310
BfaI	CTAG	1 cut(s)	260
BfmI	CTRYAG	1 cut(s)	354
BglII	AGATCT	1 cut(s)	42
BisI	GCNGC	3 cut(s)	25, 179, 357
BlsI	GCNGC	3 cut(s)	26, 180, 358
Bme1390I	CCNGG	2 cut(s)	51, 310
BmgT120I	GGNCC	1 cut(s)	350
BmiI	GGNNCC	2 cut(s)	37, 330
BmrFI	CCNGG	2 cut(s)	51, 310
BmsI	GCATC	2 cut(s)	69, 375
BpuEI	CTTGAG	1 cut(s)	122
BsaJI	CCNNGG	4 cut(s)	49, 294, 308, 340
BsaXI	ACNNNNNCTCC	2 cut(s)	321, 351
Bsc4I	CCNNNNNNNGG	3 cut(s)	55, 56, 208
Bse3DI	GCAATG	1 cut(s)	233
BseBI	CCWGG	2 cut(s)	51, 310
BseDI	CCNNGG	4 cut(s)	49, 294, 308, 340
BseGI	GGATG	2 cut(s)	69, 143
BseLI	CCNNNNNNNGG	3 cut(s)	55, 56, 208
BseMI	GCAATG	1 cut(s)	233
BseMII	CTCAG	1 cut(s)	98
BseRI	GAGGAG	1 cut(s)	224
BseXI	GCAGC	2 cut(s)	190, 368
BseYI	CCCAGC	1 cut(s)	333
BshFI	GGCC	1 cut(s)	352
BshNI	GGYRCC	2 cut(s)	35, 328
BslFI	GGGAC	1 cut(s)	291
BslI	CCNNNNNNNGG	3 cut(s)	55, 56, 208
BsmFI	GGGAC	1 cut(s)	291
BsnI	GGCC	1 cut(s)	352
Bsp143I	GATC	3 cut(s)	42, 150, 272
Bsp19I	CCATGG	1 cut(s)	340
BspACI	CCGC	2 cut(s)	25, 133
BspANI	GGCC	1 cut(s)	352
BspCNI	CTCAG	1 cut(s)	97
BspLI	GGNNCC	2 cut(s)	37, 330
BspMAI	CTGCAG	1 cut(s)	358
BspT107I	GGYRCC	2 cut(s)	35, 328
BsrDI	GCAATG	1 cut(s)	233
BssECI	CCNNGG	4 cut(s)	49, 294, 308, 340
BssMI	GATC	3 cut(s)	42, 150, 272
BssT1I	CCWWGG	2 cut(s)	294, 340
Bst2UI	CCWGG	2 cut(s)	51, 310
BstC8I	GCNNGC	2 cut(s)	192, 354
BstDEI	CTNAG	1 cut(s)	84
BstDSI	CCRYGG	1 cut(s)	340
BstF5I	GGATG	2 cut(s)	69, 143
BstKTI	GATC	3 cut(s)	45, 153, 275
BstMBI	GATC	3 cut(s)	42, 150, 272
BstMWI	GCNNNNNNNGC	1 cut(s)	187
BstNI	CCWGG	2 cut(s)	51, 310
BstNSI	RCATGY	1 cut(s)	194
BstSCI	CCNGG	2 cut(s)	49, 308
BstSFI	CTRYAG	1 cut(s)	354
BstV1I	GCAGC	2 cut(s)	190, 368
BstX2I	RGATCY	1 cut(s)	42
BstXI	CCANNNNNNTGG	1 cut(s)	341
BstYI	RGATCY	1 cut(s)	42
BsuRI	GGCC	1 cut(s)	352
BtgI	CCRYGG	1 cut(s)	340
BtsCI	GGATG	2 cut(s)	69, 143
BtsIMutI	CAGTG	1 cut(s)	37
Cac8I	GCNNGC	2 cut(s)	192, 354
Cfr13I	GGNCC	1 cut(s)	350
Csp6I	GTAC	2 cut(s)	121, 329
CviAII	CATG	5 cut(s)	156, 166, 191, 319, 341
CviJI	RGCY	4 cut(s)	142, 337, 352, 359
CviKI_1	RGCY	4 cut(s)	142, 337, 352, 359
CviQI	GTAC	2 cut(s)	121, 329
DdeI	CTNAG	1 cut(s)	84
DpnI	GATC	3 cut(s)	44, 152, 274
DpnII	GATC	3 cut(s)	42, 150, 272
Eco130I	CCWWGG	2 cut(s)	294, 340
Eco57I	CTGAAG	1 cut(s)	13
EcoRII	CCWGG	2 cut(s)	49, 308
EcoT14I	CCWWGG	2 cut(s)	294, 340
ErhI	CCWWGG	2 cut(s)	294, 340
FaeI	CATG	5 cut(s)	159, 169, 194, 322, 344
FalI	AAGNNNNNCTT	2 cut(s)	107, 139
FaqI	GGGAC	1 cut(s)	291
FatI	CATG	5 cut(s)	155, 165, 190, 318, 340
Fnu4HI	GCNGC	3 cut(s)	25, 179, 357
FokI	GGATG	2 cut(s)	56, 130
Fsp4HI	GCNGC	3 cut(s)	25, 179, 357
FspBI	CTAG	1 cut(s)	260
GluI	GCNGC	3 cut(s)	25, 179, 357
GsaI	CCCAGC	1 cut(s)	337
HaeIII	GGCC	1 cut(s)	352
Hin1II	CATG	5 cut(s)	159, 169, 194, 322, 344
HinfI	GANTC	4 cut(s)	66, 80, 227, 251
Hpy188I	TCNGA	3 cut(s)	65, 79, 173
Hpy188III	TCNNGA	2 cut(s)	10, 260
HpyCH4IV	ACGT	1 cut(s)	304
HpyCH4V	TGCA	3 cut(s)	114, 218, 356
HpyF10VI	GCNNNNNNNGC	1 cut(s)	187
HpyF3I	CTNAG	1 cut(s)	84
HpySE526I	ACGT	1 cut(s)	304
Hsp92II	CATG	5 cut(s)	159, 169, 194, 322, 344
KpnI	GGTACC	1 cut(s)	332
Kzo9I	GATC	3 cut(s)	42, 150, 272
LmnI	GCTCC	1 cut(s)	342
LpnPI	CCDG	8 cut(s)	36, 63, 71, 107, 295, 322, 347, 366
Lsp1109I	GCAGC	2 cut(s)	190, 368
LweI	GCATC	2 cut(s)	69, 375
MaeI	CTAG	1 cut(s)	260
MaeII	ACGT	1 cut(s)	304
MalI	GATC	3 cut(s)	44, 152, 274
MboI	GATC	3 cut(s)	42, 150, 272
MflI	RGATCY	1 cut(s)	42
MluCI	AATT	1 cut(s)	103
MnlI	CCTC	5 cut(s)	111, 146, 202, 319, 367
MroXI	GAANNNNTTC	1 cut(s)	255
MseI	TTAA	1 cut(s)	126
MspR9I	CCNGG	2 cut(s)	51, 310
MvaI	CCWGG	2 cut(s)	51, 310
MwoI	GCNNNNNNNGC	1 cut(s)	187
NcoI	CCATGG	1 cut(s)	340
NdeII	GATC	3 cut(s)	42, 150, 272
NlaIII	CATG	5 cut(s)	159, 169, 194, 322, 344
NlaIV	GGNNCC	2 cut(s)	37, 330
NspI	RCATGY	1 cut(s)	194
PaeI	GCATGC	1 cut(s)	194
PdmI	GAANNNNTTC	1 cut(s)	255
PfeI	GAWTC	4 cut(s)	66, 80, 227, 251
PkrI	GCNGC	3 cut(s)	26, 180, 358
Psp6I	CCWGG	2 cut(s)	49, 308
PspFI	CCCAGC	1 cut(s)	333
PspGI	CCWGG	2 cut(s)	49, 308
PspN4I	GGNNCC	2 cut(s)	37, 330
PspPI	GGNCC	1 cut(s)	350
PstI	CTGCAG	1 cut(s)	358
PsuI	RGATCY	1 cut(s)	42
RsaI	GTAC	2 cut(s)	122, 330
RsaNI	GTAC	2 cut(s)	121, 329
SaqAI	TTAA	1 cut(s)	126
SatI	GCNGC	3 cut(s)	25, 179, 357
Sau3AI	GATC	3 cut(s)	42, 150, 272
Sau96I	GGNCC	1 cut(s)	350
ScrFI	CCNGG	2 cut(s)	51, 310
SetI	ASST	5 cut(s)	90, 122, 307, 330, 339
SfaNI	GCATC	2 cut(s)	69, 375
SfcI	CTRYAG	1 cut(s)	354
SmlI	CTYRAG	1 cut(s)	137
SmoI	CTYRAG	1 cut(s)	137
SphI	GCATGC	1 cut(s)	194
Sse9I	AATT	1 cut(s)	103
SsiI	CCGC	2 cut(s)	25, 133
SspMI	CTAG	1 cut(s)	260
StyD4I	CCNGG	2 cut(s)	49, 308
StyI	CCWWGG	2 cut(s)	294, 340
TaiI	ACGT	1 cut(s)	307
TasI	AATT	1 cut(s)	103
TauI	GCSGC	1 cut(s)	27
TfiI	GAWTC	4 cut(s)	66, 80, 227, 251
Tru1I	TTAA	1 cut(s)	126
Tru9I	TTAA	1 cut(s)	126
TscAI	CASTG	1 cut(s)	37
TseI	GCWGC	2 cut(s)	178, 356
TspDTI	ATGAA	2 cut(s)	58, 88
TspRI	CASTG	1 cut(s)	37
XapI	RAATTY	1 cut(s)	103
XbaI	TCTAGA	1 cut(s)	259
XceI	RCATGY	1 cut(s)	194
XcmI	CCANNNNNNNNNTGG	1 cut(s)	367
XmnI	GAANNNNTTC	1 cut(s)	255
XspI	CTAG	1 cut(s)	260

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