Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3C

Orthogroup ID

OG0000643

Physical Location & Seq

Genomic Coordinates Forward (+)

14700782 .. 14705562

Gene Structure 4781 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3CG168900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 210 bp

ATGAATGAGAGGAAGTTGTGGATATTGAAGGGAGAGAGGTTTGAAGTGGAAGAAAAGAAAAGAGGTTTGGTTCTTTGTGGTCAAATGGTTTGGAGTGGTGATCAAGAAATACATCCCTGGACACACATGATGGAGGTACCCCAGCTCCATGGGTTTGGGCCTGCAGCCAATCGCTTATTGGAGGCATATAAGATGCTTTTGAAGGTATAG

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

69

Amino Acids

8.13

Weight (kDa)

7.94

Isoelectric Point (pI)

32.59

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Plant_NMP1	PF06694	35 - 69	6.7e-19	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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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)	136
AccB1I	GGYRCC	1 cut(s)	136
AfaI	GTAC	1 cut(s)	138
AgsI	TTSAA	3 cut(s)	28, 44, 202
AjnI	CCWGG	1 cut(s)	116
AjuI	GAANNNNNNNTTGG	2 cut(s)	50, 82
AluBI	AGCT	1 cut(s)	145
AluI	AGCT	1 cut(s)	145
AoxI	GGCC	1 cut(s)	158
ApeKI	GCWGC	1 cut(s)	164
Asp718I	GGTACC	1 cut(s)	136
AspS9I	GGNCC	1 cut(s)	158
AsuHPI	GGTGA	1 cut(s)	110
BanI	GGYRCC	1 cut(s)	136
BbvI	GCAGC	1 cut(s)	176
BccI	CCATC	1 cut(s)	124
BciT130I	CCWGG	1 cut(s)	118
BclI	TGATCA	1 cut(s)	100
BfmI	CTRYAG	1 cut(s)	162
BisI	GCNGC	1 cut(s)	165
BlsI	GCNGC	1 cut(s)	166
Bme1390I	CCNGG	1 cut(s)	118
BmgT120I	GGNCC	1 cut(s)	158
BmiI	GGNNCC	1 cut(s)	138
BmrFI	CCNGG	1 cut(s)	118
BmsI	GCATC	1 cut(s)	183
BsaJI	CCNNGG	2 cut(s)	116, 148
BsaXI	ACNNNNNCTCC	2 cut(s)	129, 159
BseBI	CCWGG	1 cut(s)	118
BseDI	CCNNGG	2 cut(s)	116, 148
BseGI	GGATG	1 cut(s)	112
BseXI	GCAGC	1 cut(s)	176
BseYI	CCCAGC	1 cut(s)	141
BshFI	GGCC	1 cut(s)	160
BshNI	GGYRCC	1 cut(s)	136
BsnI	GGCC	1 cut(s)	160
Bsp143I	GATC	1 cut(s)	100
Bsp19I	CCATGG	1 cut(s)	148
BspANI	GGCC	1 cut(s)	160
BspLI	GGNNCC	1 cut(s)	138
BspMAI	CTGCAG	1 cut(s)	166
BspT107I	GGYRCC	1 cut(s)	136
BssECI	CCNNGG	2 cut(s)	116, 148
BssMI	GATC	1 cut(s)	100
BssT1I	CCWWGG	1 cut(s)	148
Bst2UI	CCWGG	1 cut(s)	118
BstC8I	GCNNGC	1 cut(s)	162
BstDSI	CCRYGG	1 cut(s)	148
BstF5I	GGATG	1 cut(s)	112
BstKTI	GATC	1 cut(s)	103
BstMBI	GATC	1 cut(s)	100
BstNI	CCWGG	1 cut(s)	118
BstSCI	CCNGG	1 cut(s)	116
BstSFI	CTRYAG	1 cut(s)	162
BstV1I	GCAGC	1 cut(s)	176
BstXI	CCANNNNNNTGG	2 cut(s)	149, 155
BsuRI	GGCC	1 cut(s)	160
BtgI	CCRYGG	1 cut(s)	148
BtsCI	GGATG	1 cut(s)	112
Cac8I	GCNNGC	1 cut(s)	162
Cfr13I	GGNCC	1 cut(s)	158
Csp6I	GTAC	1 cut(s)	137
CviAII	CATG	2 cut(s)	127, 149
CviJI	RGCY	3 cut(s)	145, 160, 167
CviKI_1	RGCY	3 cut(s)	145, 160, 167
CviQI	GTAC	1 cut(s)	137
DpnI	GATC	1 cut(s)	102
DpnII	GATC	1 cut(s)	100
Eco130I	CCWWGG	1 cut(s)	148
EcoRII	CCWGG	1 cut(s)	116
EcoT14I	CCWWGG	1 cut(s)	148
ErhI	CCWWGG	1 cut(s)	148
FaeI	CATG	2 cut(s)	130, 152
FaiI	YATR	5 cut(s)	128, 150, 187, 189, 208
FatI	CATG	2 cut(s)	126, 148
FbaI	TGATCA	1 cut(s)	100
Fnu4HI	GCNGC	1 cut(s)	165
FokI	GGATG	1 cut(s)	99
Fsp4HI	GCNGC	1 cut(s)	165
GluI	GCNGC	1 cut(s)	165
GsaI	CCCAGC	1 cut(s)	145
HaeIII	GGCC	1 cut(s)	160
Hin1II	CATG	2 cut(s)	130, 152
HphI	GGTGA	1 cut(s)	110
Hpy188III	TCNNGA	1 cut(s)	104
HpyAV	CCTTC	2 cut(s)	22, 196
HpyCH4V	TGCA	1 cut(s)	164
Hsp92II	CATG	2 cut(s)	130, 152
KpnI	GGTACC	1 cut(s)	140
Ksp22I	TGATCA	1 cut(s)	100
Kzo9I	GATC	1 cut(s)	100
LmnI	GCTCC	1 cut(s)	150
LpnPI	CCDG	4 cut(s)	103, 130, 155, 174
Lsp1109I	GCAGC	1 cut(s)	176
LweI	GCATC	1 cut(s)	183
MalI	GATC	1 cut(s)	102
MboI	GATC	1 cut(s)	100
MboII	GAAGA	1 cut(s)	62
MnlI	CCTC	5 cut(s)	3, 30, 56, 127, 175
MspR9I	CCNGG	1 cut(s)	118
MvaI	CCWGG	1 cut(s)	118
NcoI	CCATGG	1 cut(s)	148
NdeII	GATC	1 cut(s)	100
NlaIII	CATG	2 cut(s)	130, 152
NlaIV	GGNNCC	1 cut(s)	138
PkrI	GCNGC	1 cut(s)	166
Psp6I	CCWGG	1 cut(s)	116
PspFI	CCCAGC	1 cut(s)	141
PspGI	CCWGG	1 cut(s)	116
PspN4I	GGNNCC	1 cut(s)	138
PspPI	GGNCC	1 cut(s)	158
PstI	CTGCAG	1 cut(s)	166
RsaI	GTAC	1 cut(s)	138
RsaNI	GTAC	1 cut(s)	137
SatI	GCNGC	1 cut(s)	165
Sau3AI	GATC	1 cut(s)	100
Sau96I	GGNCC	1 cut(s)	158
ScrFI	CCNGG	1 cut(s)	118
SetI	ASST	5 cut(s)	41, 67, 138, 147, 207
SfaNI	GCATC	1 cut(s)	183
SfcI	CTRYAG	1 cut(s)	162
SgeI	CNNG	7 cut(s)	116, 129, 130, 139, 154, 161, 173
StyD4I	CCNGG	1 cut(s)	116
StyI	CCWWGG	1 cut(s)	148
TseI	GCWGC	1 cut(s)	164
TspDTI	ATGAA	1 cut(s)	17
XcmI	CCANNNNNNNNNTGG	1 cut(s)	175

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