Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6D

Orthogroup ID

OG0000643

Physical Location & Seq

Genomic Coordinates Reverse (-)

14082924 .. 14093251

Gene Structure 10328 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6DG108300.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 465 bp

ATGATCCACATACCAGAGAGACCGCCAGTGAAGCGACCAGATTATGATCAGGTCCTTACCATGGAGCAACTGGAAGGTTCTGTGATCACGAGAGATCAAAAGTCTAACCTTCAATGTTATCGGAGTAATTTGATTGTTGGAACAACATCACTGCAAGAAGACCTAATGTTTCTGAGCTGGAGCAGAAGCTTTCAGAACAATACTCTCTTACATCTTCAACAAAAGGTTGATGATTTGGCATCAAAGCATGCTTACAAACCACATGAGGAGTATGCAGATGTGGAATCCACATTGCGTTCGCATTTGGAATCTTTTCTAGAAACTGCAAGATCATTCAATATGATTTACACCAAGGAAATACGTCCCTGGCAACACATGATGGAGGTACCCCAGCTCCATGGGTTCGGGCCTGCAGCCAATCGCTTATTAGAGGCATATAAGATGCTTTTGAAGGTATCTCATTGA

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

154

Amino Acids

18.04

Weight (kDa)

6.44

Isoelectric Point (pI)

52.75

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Plant_NMP1	PF06694	62 - 152	5e-45	Plant nuclear matrix protein 1 (NMP1)

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Align Labels (Cladogram)

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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)	385
AccB1I	GGYRCC	1 cut(s)	385
AciI	CCGC	1 cut(s)	23
AfaI	GTAC	1 cut(s)	387
AfiI	CCNNNNNNNGG	1 cut(s)	61
AgsI	TTSAA	4 cut(s)	113, 218, 337, 451
AjnI	CCWGG	1 cut(s)	365
AluBI	AGCT	3 cut(s)	177, 189, 394
AluI	AGCT	3 cut(s)	177, 189, 394
Alw26I	GTCTC	1 cut(s)	13
AoxI	GGCC	1 cut(s)	407
ApeKI	GCWGC	1 cut(s)	413
Asp700I	GAANNNNTTC	1 cut(s)	312
Asp718I	GGTACC	1 cut(s)	385
AspS9I	GGNCC	2 cut(s)	52, 407
AvaII	GGWCC	1 cut(s)	52
BanI	GGYRCC	1 cut(s)	385
BauI	CACGAG	1 cut(s)	88
BbsI	GAAGAC	1 cut(s)	165
BbvI	GCAGC	1 cut(s)	425
BccI	CCATC	1 cut(s)	373
BciT130I	CCWGG	1 cut(s)	367
BclI	TGATCA	2 cut(s)	46, 84
BcoDI	GTCTC	1 cut(s)	13
BfaI	CTAG	1 cut(s)	317
BfmI	CTRYAG	1 cut(s)	411
BisI	GCNGC	1 cut(s)	414
BlsI	GCNGC	1 cut(s)	415
Bme1390I	CCNGG	1 cut(s)	367
Bme18I	GGWCC	1 cut(s)	52
BmgT120I	GGNCC	2 cut(s)	52, 407
BmiI	GGNNCC	1 cut(s)	387
BmrFI	CCNGG	1 cut(s)	367
BmsI	GCATC	2 cut(s)	248, 432
BpiI	GAAGAC	1 cut(s)	165
BpmI	CTGGAG	1 cut(s)	199
BsaBI	GATNNNNATC	1 cut(s)	45
BsaI	GGTCTC	1 cut(s)	13
BsaJI	CCNNGG	4 cut(s)	60, 351, 365, 397
BsaXI	ACNNNNNCTCC	2 cut(s)	378, 408
Bsc4I	CCNNNNNNNGG	1 cut(s)	61
Bse1I	ACTGG	2 cut(s)	26, 75
Bse3DI	GCAATG	1 cut(s)	290
Bse8I	GATNNNNATC	1 cut(s)	45
BseBI	CCWGG	1 cut(s)	367
BseDI	CCNNGG	4 cut(s)	60, 351, 365, 397
BseJI	GATNNNNATC	1 cut(s)	45
BseLI	CCNNNNNNNGG	1 cut(s)	61
BseMI	GCAATG	1 cut(s)	290
BseMII	CTCAG	1 cut(s)	164
BseNI	ACTGG	2 cut(s)	26, 75
BseRI	GAGGAG	1 cut(s)	281
BseXI	GCAGC	1 cut(s)	425
BseYI	CCCAGC	1 cut(s)	390
BshFI	GGCC	1 cut(s)	409
BshNI	GGYRCC	1 cut(s)	385
BslFI	GGGAC	1 cut(s)	348
BslI	CCNNNNNNNGG	1 cut(s)	61
BsmAI	GTCTC	1 cut(s)	13
BsmFI	GGGAC	1 cut(s)	348
BsnI	GGCC	1 cut(s)	409
Bso31I	GGTCTC	1 cut(s)	13
Bsp143I	GATC	5 cut(s)	3, 46, 84, 94, 329
Bsp19I	CCATGG	2 cut(s)	60, 397
BspACI	CCGC	1 cut(s)	23
BspANI	GGCC	1 cut(s)	409
BspCNI	CTCAG	1 cut(s)	165
BspLI	GGNNCC	1 cut(s)	387
BspMAI	CTGCAG	1 cut(s)	415
BspT107I	GGYRCC	1 cut(s)	385
BspTNI	GGTCTC	1 cut(s)	13
BsrDI	GCAATG	1 cut(s)	290
BsrI	ACTGG	2 cut(s)	26, 75
BssECI	CCNNGG	4 cut(s)	60, 351, 365, 397
BssMI	GATC	5 cut(s)	3, 46, 84, 94, 329
BssSI	CACGAG	1 cut(s)	88
BssT1I	CCWWGG	3 cut(s)	60, 351, 397
Bst2BI	CACGAG	1 cut(s)	88
Bst2UI	CCWGG	1 cut(s)	367
BstC8I	GCNNGC	2 cut(s)	249, 411
BstDEI	CTNAG	1 cut(s)	173
BstDSI	CCRYGG	2 cut(s)	60, 397
BstKTI	GATC	5 cut(s)	6, 49, 87, 97, 332
BstMAI	GTCTC	1 cut(s)	13
BstMBI	GATC	5 cut(s)	3, 46, 84, 94, 329
BstMWI	GCNNNNNNNGC	1 cut(s)	31
BstNI	CCWGG	1 cut(s)	367
BstNSI	RCATGY	1 cut(s)	251
BstSCI	CCNGG	1 cut(s)	365
BstSFI	CTRYAG	1 cut(s)	411
BstV1I	GCAGC	1 cut(s)	425
BstV2I	GAAGAC	1 cut(s)	165
BstXI	CCANNNNNNTGG	1 cut(s)	398
BsuRI	GGCC	1 cut(s)	409
BtgI	CCRYGG	2 cut(s)	60, 397
BtsI	GCAGTG	1 cut(s)	149
BtsIMutI	CAGTG	2 cut(s)	33, 149
Cac8I	GCNNGC	2 cut(s)	249, 411
Cfr13I	GGNCC	2 cut(s)	52, 407
Csp6I	GTAC	1 cut(s)	386
CviAII	CATG	5 cut(s)	61, 248, 263, 376, 398
CviJI	RGCY	5 cut(s)	177, 189, 394, 409, 416
CviKI_1	RGCY	5 cut(s)	177, 189, 394, 409, 416
CviQI	GTAC	1 cut(s)	386
DdeI	CTNAG	1 cut(s)	173
DpnI	GATC	5 cut(s)	5, 48, 86, 96, 331
DpnII	GATC	5 cut(s)	3, 46, 84, 94, 329
Eco130I	CCWWGG	3 cut(s)	60, 351, 397
Eco31I	GGTCTC	1 cut(s)	13
Eco47I	GGWCC	1 cut(s)	52
EcoO109I	RGGNCCY	1 cut(s)	52
EcoRII	CCWGG	1 cut(s)	365
EcoT14I	CCWWGG	3 cut(s)	60, 351, 397
ErhI	CCWWGG	3 cut(s)	60, 351, 397
FaeI	CATG	5 cut(s)	64, 251, 266, 379, 401
FaqI	GGGAC	1 cut(s)	348
FatI	CATG	5 cut(s)	60, 247, 262, 375, 397
FbaI	TGATCA	2 cut(s)	46, 84
Fnu4HI	GCNGC	1 cut(s)	414
Fsp4HI	GCNGC	1 cut(s)	414
FspBI	CTAG	1 cut(s)	317
GluI	GCNGC	1 cut(s)	414
GsaI	CCCAGC	1 cut(s)	394
GsuI	CTGGAG	1 cut(s)	199
HaeIII	GGCC	1 cut(s)	409
Hin1II	CATG	5 cut(s)	64, 251, 266, 379, 401
HindIII	AAGCTT	1 cut(s)	187
HinfI	GANTC	2 cut(s)	284, 308
Hpy188I	TCNGA	3 cut(s)	123, 174, 195
Hpy188III	TCNNGA	2 cut(s)	88, 317
HpyAV	CCTTC	3 cut(s)	68, 119, 445
HpyCH4IV	ACGT	1 cut(s)	361
HpyCH4V	TGCA	4 cut(s)	154, 275, 326, 413
HpyF10VI	GCNNNNNNNGC	1 cut(s)	31
HpyF3I	CTNAG	1 cut(s)	173
HpySE526I	ACGT	1 cut(s)	361
Hsp92II	CATG	5 cut(s)	64, 251, 266, 379, 401
KpnI	GGTACC	1 cut(s)	389
Ksp22I	TGATCA	2 cut(s)	46, 84
Kzo9I	GATC	5 cut(s)	3, 46, 84, 94, 329
LmnI	GCTCC	3 cut(s)	64, 180, 399
Lsp1109I	GCAGC	1 cut(s)	425
LweI	GCATC	2 cut(s)	248, 432
MaeI	CTAG	1 cut(s)	317
MaeII	ACGT	1 cut(s)	361
MalI	GATC	5 cut(s)	5, 48, 86, 96, 331
MboI	GATC	5 cut(s)	3, 46, 84, 94, 329
MboII	GAAGA	2 cut(s)	170, 206
MluCI	AATT	1 cut(s)	127
MmeI	TCCRAC	1 cut(s)	118
MnlI	CCTC	3 cut(s)	259, 376, 424
MroXI	GAANNNNTTC	1 cut(s)	312
MspR9I	CCNGG	1 cut(s)	367
MvaI	CCWGG	1 cut(s)	367
MwoI	GCNNNNNNNGC	1 cut(s)	31
NcoI	CCATGG	2 cut(s)	60, 397
NdeII	GATC	5 cut(s)	3, 46, 84, 94, 329
NlaIII	CATG	5 cut(s)	64, 251, 266, 379, 401
NlaIV	GGNNCC	1 cut(s)	387
NspI	RCATGY	1 cut(s)	251
PaeI	GCATGC	1 cut(s)	251
PdmI	GAANNNNTTC	1 cut(s)	312
PfeI	GAWTC	2 cut(s)	284, 308
PkrI	GCNGC	1 cut(s)	415
PpuMI	RGGWCCY	1 cut(s)	52
Psp5II	RGGWCCY	1 cut(s)	52
Psp6I	CCWGG	1 cut(s)	365
PspFI	CCCAGC	1 cut(s)	390
PspGI	CCWGG	1 cut(s)	365
PspN4I	GGNNCC	1 cut(s)	387
PspPI	GGNCC	2 cut(s)	52, 407
PspPPI	RGGWCCY	1 cut(s)	52
PstI	CTGCAG	1 cut(s)	415
RsaI	GTAC	1 cut(s)	387
RsaNI	GTAC	1 cut(s)	386
SatI	GCNGC	1 cut(s)	414
Sau3AI	GATC	5 cut(s)	3, 46, 84, 94, 329
Sau96I	GGNCC	2 cut(s)	52, 407
ScrFI	CCNGG	1 cut(s)	367
SfaNI	GCATC	2 cut(s)	248, 432
SfcI	CTRYAG	1 cut(s)	411
SinI	GGWCC	1 cut(s)	52
SphI	GCATGC	1 cut(s)	251
Sse9I	AATT	1 cut(s)	127
SsiI	CCGC	1 cut(s)	23
SspMI	CTAG	1 cut(s)	317
StyD4I	CCNGG	1 cut(s)	365
StyI	CCWWGG	3 cut(s)	60, 351, 397
TaiI	ACGT	1 cut(s)	364
TasI	AATT	1 cut(s)	127
TfiI	GAWTC	2 cut(s)	284, 308
TscAI	CASTG	2 cut(s)	33, 156
TseI	GCWGC	1 cut(s)	413
TspRI	CASTG	2 cut(s)	33, 156
VpaK11BI	GGWCC	1 cut(s)	52
XbaI	TCTAGA	1 cut(s)	316
XceI	RCATGY	1 cut(s)	251
XcmI	CCANNNNNNNNNTGG	1 cut(s)	67
XmnI	GAANNNNTTC	1 cut(s)	312
XspI	CTAG	1 cut(s)	317

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