Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1C

Orthogroup ID

OG0000643

Physical Location & Seq

Genomic Coordinates Forward (+)

28480844 .. 28487787

Gene Structure 6944 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1CG129600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 402 bp

ATGTTTCTGAGCTGGAGCAGAAGCTTTCATAACAATACTCTCTTACATCTTCAACAAAAGGTTGATGATTTGGCATCAAAGCATGCTTACAACCCACATGAGGAGTATGCAGATGTGGAATCCACATTGCGTTCGCATTTGGAATCTTTTCTAGAAACTGCAAGATCATTCAATATGATTTACACCAAGGAAATACGTCCCTGGACACACATGATGGAGGTACCCCAGCTCCATGGGTTCGAGCCTGCAGCCAATCGCTTATTGGAGGCATATAAGATGCTTTTGAAGTGTTGTAGGGGTAAAACTTATATTTGGAGGTCCGTTTGTGATTGCACTTCTGATATACAAGTGGCGAAGAAGACATTGGTCAACCTACAACACTATCGAAGATTTTCTGCATAG

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

15.75

Weight (kDa)

8.71

Isoelectric Point (pI)

53.95

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Plant_NMP1	PF06694	10 - 100	3e-46	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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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)	220
AccB1I	GGYRCC	1 cut(s)	220
AfaI	GTAC	1 cut(s)	222
AfiI	CCNNNNNNNGG	1 cut(s)	100
AgsI	TTSAA	3 cut(s)	53, 172, 286
AjnI	CCWGG	1 cut(s)	200
AjuI	GAANNNNNNNTTGG	2 cut(s)	347, 379
AluBI	AGCT	3 cut(s)	12, 24, 229
AluI	AGCT	3 cut(s)	12, 24, 229
ApeKI	GCWGC	1 cut(s)	248
Asp700I	GAANNNNTTC	2 cut(s)	147, 391
Asp718I	GGTACC	1 cut(s)	220
AspS9I	GGNCC	1 cut(s)	318
AvaII	GGWCC	1 cut(s)	318
BanI	GGYRCC	1 cut(s)	220
BbsI	GAAGAC	1 cut(s)	365
BbvI	GCAGC	1 cut(s)	260
BccI	CCATC	1 cut(s)	208
BciT130I	CCWGG	1 cut(s)	202
BfaI	CTAG	1 cut(s)	152
BfmI	CTRYAG	1 cut(s)	246
BisI	GCNGC	1 cut(s)	249
BlsI	GCNGC	1 cut(s)	250
Bme1390I	CCNGG	1 cut(s)	202
Bme18I	GGWCC	1 cut(s)	318
BmgT120I	GGNCC	1 cut(s)	318
BmiI	GGNNCC	1 cut(s)	222
BmrFI	CCNGG	1 cut(s)	202
BmsI	GCATC	2 cut(s)	83, 267
BoxI	GACNNNNGTC	1 cut(s)	365
BpiI	GAAGAC	1 cut(s)	365
BpmI	CTGGAG	1 cut(s)	34
BsaJI	CCNNGG	3 cut(s)	186, 200, 232
BsaXI	ACNNNNNCTCC	2 cut(s)	213, 243
Bsc4I	CCNNNNNNNGG	1 cut(s)	100
Bse3DI	GCAATG	1 cut(s)	125
BseBI	CCWGG	1 cut(s)	202
BseDI	CCNNGG	3 cut(s)	186, 200, 232
BseLI	CCNNNNNNNGG	1 cut(s)	100
BseMI	GCAATG	1 cut(s)	125
BseRI	GAGGAG	1 cut(s)	116
BseXI	GCAGC	1 cut(s)	260
BseYI	CCCAGC	1 cut(s)	225
BshNI	GGYRCC	1 cut(s)	220
BslFI	GGGAC	1 cut(s)	183
BslI	CCNNNNNNNGG	1 cut(s)	100
BsmFI	GGGAC	1 cut(s)	183
Bsp143I	GATC	1 cut(s)	164
Bsp19I	CCATGG	1 cut(s)	232
BspLI	GGNNCC	1 cut(s)	222
BspMAI	CTGCAG	1 cut(s)	250
BspT107I	GGYRCC	1 cut(s)	220
BsrDI	GCAATG	1 cut(s)	125
BssECI	CCNNGG	3 cut(s)	186, 200, 232
BssMI	GATC	1 cut(s)	164
BssT1I	CCWWGG	2 cut(s)	186, 232
Bst2UI	CCWGG	1 cut(s)	202
BstC8I	GCNNGC	2 cut(s)	84, 246
BstDEI	CTNAG	1 cut(s)	8
BstDSI	CCRYGG	1 cut(s)	232
BstKTI	GATC	1 cut(s)	167
BstMBI	GATC	1 cut(s)	164
BstNI	CCWGG	1 cut(s)	202
BstNSI	RCATGY	1 cut(s)	86
BstPAI	GACNNNNGTC	1 cut(s)	365
BstSCI	CCNGG	1 cut(s)	200
BstSFI	CTRYAG	1 cut(s)	246
BstV1I	GCAGC	1 cut(s)	260
BstV2I	GAAGAC	1 cut(s)	365
BstXI	CCANNNNNNTGG	1 cut(s)	233
BtgI	CCRYGG	1 cut(s)	232
Cac8I	GCNNGC	2 cut(s)	84, 246
Cfr13I	GGNCC	1 cut(s)	318
Csp6I	GTAC	1 cut(s)	221
CviAII	CATG	4 cut(s)	83, 98, 211, 233
CviJI	RGCY	5 cut(s)	12, 24, 229, 244, 251
CviKI_1	RGCY	5 cut(s)	12, 24, 229, 244, 251
CviQI	GTAC	1 cut(s)	221
DdeI	CTNAG	1 cut(s)	8
DpnI	GATC	1 cut(s)	166
DpnII	GATC	1 cut(s)	164
Eco130I	CCWWGG	2 cut(s)	186, 232
Eco47I	GGWCC	1 cut(s)	318
EcoRII	CCWGG	1 cut(s)	200
EcoT14I	CCWWGG	2 cut(s)	186, 232
ErhI	CCWWGG	2 cut(s)	186, 232
FaeI	CATG	4 cut(s)	86, 101, 214, 236
FaqI	GGGAC	1 cut(s)	183
FatI	CATG	4 cut(s)	82, 97, 210, 232
Fnu4HI	GCNGC	1 cut(s)	249
Fsp4HI	GCNGC	1 cut(s)	249
FspBI	CTAG	1 cut(s)	152
GluI	GCNGC	1 cut(s)	249
GsaI	CCCAGC	1 cut(s)	229
GsuI	CTGGAG	1 cut(s)	34
Hin1II	CATG	4 cut(s)	86, 101, 214, 236
HincII	GTYRAC	1 cut(s)	370
HindII	GTYRAC	1 cut(s)	370
HindIII	AAGCTT	1 cut(s)	22
HinfI	GANTC	2 cut(s)	119, 143
Hpy166II	GTNNAC	1 cut(s)	370
Hpy188I	TCNGA	2 cut(s)	9, 340
Hpy188III	TCNNGA	1 cut(s)	152
Hpy8I	GTNNAC	1 cut(s)	370
HpyCH4IV	ACGT	1 cut(s)	196
HpyCH4V	TGCA	5 cut(s)	110, 161, 248, 333, 398
HpyF3I	CTNAG	1 cut(s)	8
HpySE526I	ACGT	1 cut(s)	196
Hsp92II	CATG	4 cut(s)	86, 101, 214, 236
KpnI	GGTACC	1 cut(s)	224
Kzo9I	GATC	1 cut(s)	164
LmnI	GCTCC	2 cut(s)	15, 234
LpnPI	CCDG	4 cut(s)	187, 214, 239, 258
Lsp1109I	GCAGC	1 cut(s)	260
LweI	GCATC	2 cut(s)	83, 267
MaeI	CTAG	1 cut(s)	152
MaeII	ACGT	1 cut(s)	196
MalI	GATC	1 cut(s)	166
MboI	GATC	1 cut(s)	164
MboII	GAAGA	4 cut(s)	41, 367, 370, 399
MnlI	CCTC	4 cut(s)	94, 211, 259, 309
MroXI	GAANNNNTTC	2 cut(s)	147, 391
MspR9I	CCNGG	1 cut(s)	202
MvaI	CCWGG	1 cut(s)	202
NcoI	CCATGG	1 cut(s)	232
NdeII	GATC	1 cut(s)	164
NlaIII	CATG	4 cut(s)	86, 101, 214, 236
NlaIV	GGNNCC	1 cut(s)	222
NspI	RCATGY	1 cut(s)	86
PaeI	GCATGC	1 cut(s)	86
PdmI	GAANNNNTTC	2 cut(s)	147, 391
PfeI	GAWTC	2 cut(s)	119, 143
PkrI	GCNGC	1 cut(s)	250
PshAI	GACNNNNGTC	1 cut(s)	365
Psp6I	CCWGG	1 cut(s)	200
PspFI	CCCAGC	1 cut(s)	225
PspGI	CCWGG	1 cut(s)	200
PspN4I	GGNNCC	1 cut(s)	222
PspPI	GGNCC	1 cut(s)	318
PstI	CTGCAG	1 cut(s)	250
RsaI	GTAC	1 cut(s)	222
RsaNI	GTAC	1 cut(s)	221
SatI	GCNGC	1 cut(s)	249
Sau3AI	GATC	1 cut(s)	164
Sau96I	GGNCC	1 cut(s)	318
ScrFI	CCNGG	1 cut(s)	202
SetI	ASST	8 cut(s)	14, 26, 63, 199, 222, 231, 320, 375
SfaNI	GCATC	2 cut(s)	83, 267
SfcI	CTRYAG	1 cut(s)	246
SinI	GGWCC	1 cut(s)	318
SphI	GCATGC	1 cut(s)	86
SspMI	CTAG	1 cut(s)	152
StyD4I	CCNGG	1 cut(s)	200
StyI	CCWWGG	2 cut(s)	186, 232
TaiI	ACGT	1 cut(s)	199
TaqI	TCGA	2 cut(s)	240, 385
TfiI	GAWTC	2 cut(s)	119, 143
TseI	GCWGC	1 cut(s)	248
TspDTI	ATGAA	1 cut(s)	17
TspGWI	ACGGA	1 cut(s)	310
VpaK11BI	GGWCC	1 cut(s)	318
XbaI	TCTAGA	1 cut(s)	151
XceI	RCATGY	1 cut(s)	86
XcmI	CCANNNNNNNNNTGG	1 cut(s)	259
XmnI	GAANNNNTTC	2 cut(s)	147, 391
XspI	CTAG	1 cut(s)	152

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