Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1C

Orthogroup ID

OG0000643

Physical Location & Seq

Genomic Coordinates Reverse (-)

33947994 .. 33958794

Gene Structure 10801 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1CG153300.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 717 bp

ATGATGAAAACAAAGTTATGGTTGATATCCCAGCATCTCAAATGCGACTTGAGTCCCTCTCAACTGCCGGATGATGATAAGGAAGATGGGAGCCGGTTTGAGAAGAAGTGCGTGTCATTGGTGGGGAAGCCACGTGGCATTGGGAGGGAGGGGTCAAGGAGCGTTGGATCGGAGAGTAGGATGAAGAAGAGGTGGGAGATTCCTAGTGAGGTGGTGGTGTTCCAGGGTTTGGAGGAGGACGGTGTTGCTGAAATGGGCATGATGTTTCAGAGCTGGAACAAAGGCTTACAGAACAATCAAAGATACTCTCAAGTCTTCAACAACAGGTTGATGATTTGGCATCAAAGGCATGATGTTTCTGAGCTGGAGCAAAAGCTTACAGAACAATCAAAGATACTCTCAAGTCTTCAACAAAAGGTTGATGATTTGGCATCAAAGGATATACGTCCCTGGACACACATGATGGAGGTACCCCAGCTCCATGGGTTCGGGCCAGCTGCCAATCGCTTGTTGGAGGCATATAATGATGCTTTTGAAGGGAACTTGAGGAATCTTAGAGACTCACATGCTGCTCTTGCTGTTGGATCATCTGACTCGGTTGCTGGTGAGCCCTCTTCTGTCACAAGAATAATCTCAGAATGTGAATCTGCGTTGACATTCTTAAATCGTGACCTTGGAATTCTCTCGGCTTCCATTGCTCGAGAGCAAGGTGAATAG

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

238

Amino Acids

26.8

Weight (kDa)

5.93

Isoelectric Point (pI)

53.64

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Plant_NMP1	PF06694	145 - 235	6.3e-43	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

Tree File

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Publication-ready

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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)	469
AccB1I	GGYRCC	1 cut(s)	469
AccB7I	CCANNNNNTGG	1 cut(s)	229
AclWI	GGATC	2 cut(s)	175, 592
AcsI	RAATTY	1 cut(s)	678
AcvI	CACGTG	1 cut(s)	134
AfaI	GTAC	1 cut(s)	471
AfiI	CCNNNNNNNGG	1 cut(s)	229
AgsI	TTSAA	3 cut(s)	319, 410, 536
AjnI	CCWGG	2 cut(s)	222, 449
AluBI	AGCT	5 cut(s)	273, 364, 376, 478, 497
AluI	AGCT	5 cut(s)	273, 364, 376, 478, 497
Alw26I	GTCTC	1 cut(s)	552
AlwI	GGATC	2 cut(s)	175, 592
Ama87I	CYCGRG	1 cut(s)	699
AoxI	GGCC	1 cut(s)	491
ApeKI	GCWGC	2 cut(s)	497, 569
ApoI	RAATTY	1 cut(s)	678
Asp718I	GGTACC	1 cut(s)	469
AspS9I	GGNCC	1 cut(s)	491
AsuHPI	GGTGA	1 cut(s)	617
AvaI	CYCGRG	1 cut(s)	699
BanI	GGYRCC	1 cut(s)	469
BanII	GRGCYC	1 cut(s)	612
BbrPI	CACGTG	1 cut(s)	134
BbsI	GAAGAC	2 cut(s)	307, 398
BbvI	GCAGC	2 cut(s)	484, 556
BccI	CCATC	2 cut(s)	80, 457
BciT130I	CCWGG	2 cut(s)	224, 451
BcoDI	GTCTC	1 cut(s)	552
BfaI	CTAG	1 cut(s)	204
BisI	GCNGC	2 cut(s)	498, 570
BlsI	GCNGC	2 cut(s)	499, 571
Bme1390I	CCNGG	2 cut(s)	224, 451
BmeT110I	CYCGRG	1 cut(s)	699
BmgT120I	GGNCC	1 cut(s)	491
BmiI	GGNNCC	2 cut(s)	92, 471
BmrFI	CCNGG	2 cut(s)	224, 451
BmsI	GCATC	4 cut(s)	43, 349, 440, 517
BoxI	GACNNNNGTC	1 cut(s)	51
BpiI	GAAGAC	2 cut(s)	307, 398
BplI	GAGNNNNNCTC	2 cut(s)	43, 75
BpmI	CTGGAG	1 cut(s)	386
BpuEI	CTTGAG	4 cut(s)	70, 294, 385, 565
BsaAI	YACGTR	1 cut(s)	134
BsaJI	CCNNGG	4 cut(s)	223, 449, 481, 673
BsaXI	ACNNNNNCTCC	2 cut(s)	462, 492
Bsc4I	CCNNNNNNNGG	1 cut(s)	229
Bse118I	RCCGGY	1 cut(s)	93
Bse3DI	GCAATG	1 cut(s)	693
BseBI	CCWGG	2 cut(s)	224, 451
BseDI	CCNNGG	4 cut(s)	223, 449, 481, 673
BseGI	GGATG	2 cut(s)	76, 186
BseLI	CCNNNNNNNGG	1 cut(s)	229
BseMI	GCAATG	1 cut(s)	693
BseMII	CTCAG	2 cut(s)	351, 648
BseRI	GAGGAG	1 cut(s)	248
BseXI	GCAGC	2 cut(s)	484, 556
BseYI	CCCAGC	2 cut(s)	30, 474
BshFI	GGCC	1 cut(s)	493
BshNI	GGYRCC	1 cut(s)	469
BsiHKCI	CYCGRG	1 cut(s)	699
BsiSI	CCGG	2 cut(s)	68, 94
BslFI	GGGAC	2 cut(s)	39, 432
BslI	CCNNNNNNNGG	1 cut(s)	229
BsmAI	GTCTC	1 cut(s)	552
BsmFI	GGGAC	2 cut(s)	39, 432
BsnI	GGCC	1 cut(s)	493
BsoBI	CYCGRG	1 cut(s)	699
Bsp1286I	GDGCHC	1 cut(s)	612
Bsp143I	GATC	2 cut(s)	167, 584
Bsp19I	CCATGG	1 cut(s)	481
BspANI	GGCC	1 cut(s)	493
BspCNI	CTCAG	2 cut(s)	352, 647
BspLI	GGNNCC	2 cut(s)	92, 471
BspPI	GGATC	2 cut(s)	175, 592
BspT107I	GGYRCC	1 cut(s)	469
BsrDI	GCAATG	1 cut(s)	693
BsrFI	RCCGGY	1 cut(s)	93
BssAI	RCCGGY	1 cut(s)	93
BssECI	CCNNGG	4 cut(s)	223, 449, 481, 673
BssMI	GATC	2 cut(s)	167, 584
BssT1I	CCWWGG	2 cut(s)	481, 673
Bst2UI	CCWGG	2 cut(s)	224, 451
Bst4CI	ACNGT	1 cut(s)	242
Bst6I	CTCTTC	2 cut(s)	182, 619
BstBAI	YACGTR	1 cut(s)	134
BstC8I	GCNNGC	1 cut(s)	495
BstDEI	CTNAG	3 cut(s)	360, 554, 634
BstDSI	CCRYGG	1 cut(s)	481
BstF5I	GGATG	2 cut(s)	76, 186
BstKTI	GATC	2 cut(s)	170, 587
BstMAI	GTCTC	1 cut(s)	552
BstMBI	GATC	2 cut(s)	167, 584
BstMWI	GCNNNNNNNGC	3 cut(s)	346, 575, 695
BstNI	CCWGG	2 cut(s)	224, 451
BstNSI	RCATGY	1 cut(s)	569
BstPAI	GACNNNNGTC	1 cut(s)	51
BstSCI	CCNGG	2 cut(s)	222, 449
BstV1I	GCAGC	2 cut(s)	484, 556
BstV2I	GAAGAC	2 cut(s)	307, 398
BstXI	CCANNNNNNTGG	1 cut(s)	482
BsuRI	GGCC	1 cut(s)	493
BtgI	CCRYGG	1 cut(s)	481
BtsCI	GGATG	2 cut(s)	76, 186
Cac8I	GCNNGC	1 cut(s)	495
Cfr10I	RCCGGY	1 cut(s)	93
Cfr13I	GGNCC	1 cut(s)	491
Csp6I	GTAC	1 cut(s)	470
CviAII	CATG	5 cut(s)	259, 350, 460, 482, 566
CviQI	GTAC	1 cut(s)	470
DdeI	CTNAG	3 cut(s)	360, 554, 634
DpnI	GATC	2 cut(s)	169, 586
DpnII	GATC	2 cut(s)	167, 584
Eam1104I	CTCTTC	2 cut(s)	182, 619
EarI	CTCTTC	2 cut(s)	182, 619
Eco130I	CCWWGG	2 cut(s)	481, 673
Eco24I	GRGCYC	1 cut(s)	612
Eco32I	GATATC	1 cut(s)	27
Eco72I	CACGTG	1 cut(s)	134
Eco88I	CYCGRG	1 cut(s)	699
EcoRI	GAATTC	1 cut(s)	678
EcoRII	CCWGG	2 cut(s)	222, 449
EcoRV	GATATC	1 cut(s)	27
EcoT14I	CCWWGG	2 cut(s)	481, 673
EcoT38I	GRGCYC	1 cut(s)	612
ErhI	CCWWGG	2 cut(s)	481, 673
FaeI	CATG	5 cut(s)	262, 353, 463, 485, 569
FaiI	YATR	9 cut(s)	19, 260, 351, 443, 461, 483, 520, 522, 567
FaqI	GGGAC	2 cut(s)	39, 432
FatI	CATG	5 cut(s)	258, 349, 459, 481, 565
Fnu4HI	GCNGC	2 cut(s)	498, 570
FokI	GGATG	2 cut(s)	83, 193
FriOI	GRGCYC	1 cut(s)	612
Fsp4HI	GCNGC	2 cut(s)	498, 570
FspBI	CTAG	1 cut(s)	204
GluI	GCNGC	2 cut(s)	498, 570
GsaI	CCCAGC	2 cut(s)	34, 478
GsuI	CTGGAG	1 cut(s)	386
HaeIII	GGCC	1 cut(s)	493
HapII	CCGG	2 cut(s)	68, 94
Hin1II	CATG	5 cut(s)	262, 353, 463, 485, 569
HincII	GTYRAC	1 cut(s)	654
HindII	GTYRAC	1 cut(s)	654
HindIII	AAGCTT	1 cut(s)	374
HinfI	GANTC	6 cut(s)	52, 199, 550, 560, 593, 644
HpaII	CCGG	2 cut(s)	68, 94
HphI	GGTGA	1 cut(s)	617
Hpy166II	GTNNAC	1 cut(s)	654
Hpy188I	TCNGA	5 cut(s)	172, 270, 361, 592, 637
Hpy188III	TCNNGA	2 cut(s)	668, 701
Hpy8I	GTNNAC	1 cut(s)	654
HpyAV	CCTTC	1 cut(s)	530
HpyCH4III	ACNGT	1 cut(s)	242
HpyCH4IV	ACGT	2 cut(s)	133, 445
HpyF10VI	GCNNNNNNNGC	3 cut(s)	346, 575, 695
HpyF3I	CTNAG	3 cut(s)	360, 554, 634
HpySE526I	ACGT	2 cut(s)	133, 445
Hsp92II	CATG	5 cut(s)	262, 353, 463, 485, 569
KpnI	GGTACC	1 cut(s)	473
Kzo9I	GATC	2 cut(s)	167, 584
LmnI	GCTCC	4 cut(s)	90, 159, 367, 483
Lsp1109I	GCAGC	2 cut(s)	484, 556
LweI	GCATC	4 cut(s)	43, 349, 440, 517
MaeI	CTAG	1 cut(s)	204
MaeII	ACGT	2 cut(s)	133, 445
MaeIII	GTNAC	2 cut(s)	619, 668
MalI	GATC	2 cut(s)	169, 586
MboI	GATC	2 cut(s)	167, 584
MboII	GAAGA	7 cut(s)	95, 115, 196, 199, 307, 398, 606
MhlI	GDGCHC	1 cut(s)	612
MluCI	AATT	1 cut(s)	678
MlyI	GAGTC	3 cut(s)	61, 554, 587
MmeI	TCCRAC	3 cut(s)	145, 492, 562
MseI	TTAA	1 cut(s)	662
MspA1I	CMGCKG	1 cut(s)	497
MspI	CCGG	2 cut(s)	68, 94
MspR9I	CCNGG	2 cut(s)	224, 451
MvaI	CCWGG	2 cut(s)	224, 451
MwoI	GCNNNNNNNGC	3 cut(s)	346, 575, 695
NcoI	CCATGG	1 cut(s)	481
NdeII	GATC	2 cut(s)	167, 584
NlaIII	CATG	5 cut(s)	262, 353, 463, 485, 569
NlaIV	GGNNCC	2 cut(s)	92, 471
NmeAIII	GCCGAG	1 cut(s)	665
NmuCI	GTSAC	2 cut(s)	619, 668
NspI	RCATGY	1 cut(s)	569
PaeR7I	CTCGAG	1 cut(s)	699
PfeI	GAWTC	3 cut(s)	199, 550, 644
PflMI	CCANNNNNTGG	1 cut(s)	229
PkrI	GCNGC	2 cut(s)	499, 571
PleI	GAGTC	3 cut(s)	60, 554, 587
PmaCI	CACGTG	1 cut(s)	134
PmlI	CACGTG	1 cut(s)	134
PpsI	GAGTC	3 cut(s)	60, 554, 587
Ppu21I	YACGTR	1 cut(s)	134
PshAI	GACNNNNGTC	1 cut(s)	51
Psp6I	CCWGG	2 cut(s)	222, 449
PspCI	CACGTG	1 cut(s)	134
PspFI	CCCAGC	2 cut(s)	30, 474
PspGI	CCWGG	2 cut(s)	222, 449
PspN4I	GGNNCC	2 cut(s)	92, 471
PspPI	GGNCC	1 cut(s)	491
PvuII	CAGCTG	1 cut(s)	497
RsaI	GTAC	1 cut(s)	471
RsaNI	GTAC	1 cut(s)	470
SaqAI	TTAA	1 cut(s)	662
SatI	GCNGC	2 cut(s)	498, 570
Sau3AI	GATC	2 cut(s)	167, 584
Sau96I	GGNCC	1 cut(s)	491
SchI	GAGTC	3 cut(s)	61, 554, 587
ScrFI	CCNGG	2 cut(s)	224, 451
SduI	GDGCHC	1 cut(s)	612
SfaNI	GCATC	4 cut(s)	43, 349, 440, 517
Sfr274I	CTCGAG	1 cut(s)	699
SlaI	CTCGAG	1 cut(s)	699
SmlI	CTYRAG	5 cut(s)	49, 309, 400, 544, 699
SmoI	CTYRAG	5 cut(s)	49, 309, 400, 544, 699
Sse9I	AATT	1 cut(s)	678
SspMI	CTAG	1 cut(s)	204
StyD4I	CCNGG	2 cut(s)	222, 449
StyI	CCWWGG	2 cut(s)	481, 673
TaaI	ACNGT	1 cut(s)	242
TaiI	ACGT	2 cut(s)	136, 448
TaqI	TCGA	1 cut(s)	700
TasI	AATT	1 cut(s)	678
TfiI	GAWTC	3 cut(s)	199, 550, 644
Tru1I	TTAA	1 cut(s)	662
Tru9I	TTAA	1 cut(s)	662
TseFI	GTSAC	2 cut(s)	619, 668
TseI	GCWGC	2 cut(s)	497, 569
Tsp45I	GTSAC	2 cut(s)	619, 668
TspDTI	ATGAA	2 cut(s)	20, 197
Van91I	CCANNNNNTGG	1 cut(s)	229
XapI	RAATTY	1 cut(s)	678
XceI	RCATGY	1 cut(s)	569
XcmI	CCANNNNNNNNNTGG	1 cut(s)	508
XhoI	CTCGAG	1 cut(s)	699
XspI	CTAG	1 cut(s)	204

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