Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1A

Orthogroup ID

OG0000643

Physical Location & Seq

Genomic Coordinates Reverse (-)

31213994 .. 31218318

Gene Structure 4325 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1AG162800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 381 bp

ATGATGTTTCAGAGCTGGAACAAAGGCTTACAGAACAATCAAAGATACTCTCAAGTCTTCAACAACAGGTTGATGATTTGGCATCAAAGGCATGATGTTTCTGAGCTGGAGCAAAAGCTTACAGAACAATCAAAGATACTCTCAAGTCTTCAACAAAAGGTTGATGATTTGGCATCAAAGGGAGGTTTTAGGCAGTTCCTAGGGAACTTGAGGAATCTTAGAGACTCACATGCTGCTCTTGCTGTTGGATCATCTGACTCGGTTGCTGGTGAGCCCTCTTCTGTCACAAGAATAATCTCAGAATGTGAATCTGCGTTGACATTCTTAAATCGTGACCTTGGAATTCTCTCGGCTTCCATTGCTCGAGAGCAAGGTGAATAG

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

126

Amino Acids

14.17

Weight (kDa)

6.84

Isoelectric Point (pI)

55.79

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Plant_NMP1	PF06694	31 - 61	2.5e-06	Plant nuclear matrix protein 1 (NMP1)
Plant_NMP1	PF06694	65 - 123	1.4e-23	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)

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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)
AclWI	GGATC	1 cut(s)	256
AcsI	RAATTY	1 cut(s)	342
AgsI	TTSAA	2 cut(s)	61, 152
AluBI	AGCT	3 cut(s)	15, 106, 118
AluI	AGCT	3 cut(s)	15, 106, 118
Alw26I	GTCTC	1 cut(s)	216
AlwI	GGATC	1 cut(s)	256
Ama87I	CYCGRG	1 cut(s)	363
ApeKI	GCWGC	1 cut(s)	233
ApoI	RAATTY	1 cut(s)	342
AspA2I	CCTAGG	1 cut(s)	199
AsuHPI	GGTGA	1 cut(s)	281
AvaI	CYCGRG	1 cut(s)	363
AvrII	CCTAGG	1 cut(s)	199
BanII	GRGCYC	1 cut(s)	276
BbsI	GAAGAC	2 cut(s)	49, 140
BbvI	GCAGC	1 cut(s)	220
BcoDI	GTCTC	1 cut(s)	216
BfaI	CTAG	1 cut(s)	200
BisI	GCNGC	1 cut(s)	234
BlnI	CCTAGG	1 cut(s)	199
BlsI	GCNGC	1 cut(s)	235
BmeT110I	CYCGRG	1 cut(s)	363
BmsI	GCATC	2 cut(s)	91, 182
BpiI	GAAGAC	2 cut(s)	49, 140
BpmI	CTGGAG	1 cut(s)	128
BpuEI	CTTGAG	3 cut(s)	36, 127, 229
BsaJI	CCNNGG	2 cut(s)	199, 337
Bse3DI	GCAATG	1 cut(s)	357
BseDI	CCNNGG	2 cut(s)	199, 337
BseMI	GCAATG	1 cut(s)	357
BseMII	CTCAG	2 cut(s)	93, 312
BseXI	GCAGC	1 cut(s)	220
BsiHKCI	CYCGRG	1 cut(s)	363
BsmAI	GTCTC	1 cut(s)	216
BsoBI	CYCGRG	1 cut(s)	363
Bsp1286I	GDGCHC	1 cut(s)	276
Bsp143I	GATC	1 cut(s)	248
BspCNI	CTCAG	2 cut(s)	94, 311
BspPI	GGATC	1 cut(s)	256
BsrDI	GCAATG	1 cut(s)	357
BssECI	CCNNGG	2 cut(s)	199, 337
BssMI	GATC	1 cut(s)	248
BssT1I	CCWWGG	2 cut(s)	199, 337
Bst6I	CTCTTC	1 cut(s)	283
BstDEI	CTNAG	3 cut(s)	102, 218, 298
BstKTI	GATC	1 cut(s)	251
BstMAI	GTCTC	1 cut(s)	216
BstMBI	GATC	1 cut(s)	248
BstMWI	GCNNNNNNNGC	3 cut(s)	88, 239, 359
BstNSI	RCATGY	1 cut(s)	233
BstV1I	GCAGC	1 cut(s)	220
BstV2I	GAAGAC	2 cut(s)	49, 140
CviAII	CATG	2 cut(s)	92, 230
CviJI	RGCY	6 cut(s)	15, 27, 106, 118, 274, 353
CviKI_1	RGCY	6 cut(s)	15, 27, 106, 118, 274, 353
DdeI	CTNAG	3 cut(s)	102, 218, 298
DpnI	GATC	1 cut(s)	250
DpnII	GATC	1 cut(s)	248
Eam1104I	CTCTTC	1 cut(s)	283
EarI	CTCTTC	1 cut(s)	283
Eco130I	CCWWGG	2 cut(s)	199, 337
Eco24I	GRGCYC	1 cut(s)	276
Eco88I	CYCGRG	1 cut(s)	363
EcoRI	GAATTC	1 cut(s)	342
EcoT14I	CCWWGG	2 cut(s)	199, 337
EcoT38I	GRGCYC	1 cut(s)	276
ErhI	CCWWGG	2 cut(s)	199, 337
FaeI	CATG	2 cut(s)	95, 233
FaiI	YATR	2 cut(s)	93, 231
FatI	CATG	2 cut(s)	91, 229
Fnu4HI	GCNGC	1 cut(s)	234
FriOI	GRGCYC	1 cut(s)	276
Fsp4HI	GCNGC	1 cut(s)	234
FspBI	CTAG	1 cut(s)	200
GluI	GCNGC	1 cut(s)	234
GsuI	CTGGAG	1 cut(s)	128
Hin1II	CATG	2 cut(s)	95, 233
HincII	GTYRAC	1 cut(s)	318
HindII	GTYRAC	1 cut(s)	318
HindIII	AAGCTT	1 cut(s)	116
HinfI	GANTC	4 cut(s)	214, 224, 257, 308
HphI	GGTGA	1 cut(s)	281
Hpy166II	GTNNAC	1 cut(s)	318
Hpy188I	TCNGA	4 cut(s)	12, 103, 256, 301
Hpy188III	TCNNGA	2 cut(s)	332, 365
Hpy8I	GTNNAC	1 cut(s)	318
HpyF10VI	GCNNNNNNNGC	3 cut(s)	88, 239, 359
HpyF3I	CTNAG	3 cut(s)	102, 218, 298
Hsp92II	CATG	2 cut(s)	95, 233
Kzo9I	GATC	1 cut(s)	248
LmnI	GCTCC	1 cut(s)	109
LpnPI	CCDG	3 cut(s)	52, 92, 252
Lsp1109I	GCAGC	1 cut(s)	220
LweI	GCATC	2 cut(s)	91, 182
MaeI	CTAG	1 cut(s)	200
MaeIII	GTNAC	2 cut(s)	283, 332
MalI	GATC	1 cut(s)	250
MboI	GATC	1 cut(s)	248
MboII	GAAGA	3 cut(s)	49, 140, 270
MhlI	GDGCHC	1 cut(s)	276
MluCI	AATT	1 cut(s)	342
MlyI	GAGTC	2 cut(s)	218, 251
MmeI	TCCRAC	1 cut(s)	226
MnlI	CCTC	3 cut(s)	176, 204, 286
MseI	TTAA	1 cut(s)	326
MwoI	GCNNNNNNNGC	3 cut(s)	88, 239, 359
NdeII	GATC	1 cut(s)	248
NlaIII	CATG	2 cut(s)	95, 233
NmeAIII	GCCGAG	1 cut(s)	329
NmuCI	GTSAC	2 cut(s)	283, 332
NspI	RCATGY	1 cut(s)	233
PaeR7I	CTCGAG	1 cut(s)	363
PfeI	GAWTC	2 cut(s)	214, 308
PkrI	GCNGC	1 cut(s)	235
PleI	GAGTC	2 cut(s)	218, 251
PpsI	GAGTC	2 cut(s)	218, 251
SaqAI	TTAA	1 cut(s)	326
SatI	GCNGC	1 cut(s)	234
Sau3AI	GATC	1 cut(s)	248
SchI	GAGTC	2 cut(s)	218, 251
SduI	GDGCHC	1 cut(s)	276
SetI	ASST	8 cut(s)	17, 71, 108, 120, 162, 187, 339, 376
SfaNI	GCATC	2 cut(s)	91, 182
Sfr274I	CTCGAG	1 cut(s)	363
SlaI	CTCGAG	1 cut(s)	363
SmlI	CTYRAG	4 cut(s)	51, 142, 208, 363
SmoI	CTYRAG	4 cut(s)	51, 142, 208, 363
Sse9I	AATT	1 cut(s)	342
SspMI	CTAG	1 cut(s)	200
StyI	CCWWGG	2 cut(s)	199, 337
TaqI	TCGA	1 cut(s)	364
TasI	AATT	1 cut(s)	342
TfiI	GAWTC	2 cut(s)	214, 308
Tru1I	TTAA	1 cut(s)	326
Tru9I	TTAA	1 cut(s)	326
TseFI	GTSAC	2 cut(s)	283, 332
TseI	GCWGC	1 cut(s)	233
Tsp45I	GTSAC	2 cut(s)	283, 332
XapI	RAATTY	1 cut(s)	342
XceI	RCATGY	1 cut(s)	233
XhoI	CTCGAG	1 cut(s)	363
XmaJI	CCTAGG	1 cut(s)	199
XspI	CTAG	1 cut(s)	200

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