Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1C

Orthogroup ID

OG0000643

Physical Location & Seq

Genomic Coordinates Reverse (-)

33714722 .. 33717386

Gene Structure 2665 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1CG152300.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 444 bp

ATGATGTTTCAGAGCTGGAACAAAGGCTTACAGAACAATCAAAGATACTCTCAAGTCTTCAACAACAGGTTGATGATTTGGCATCAAAGGCATGATGTTTCTGAGCTGGAGCAAAAGCTTACAGAACAATCAAAGATACTCTCAAGTCTTCAACAAAAGGTTGATGATTTGGCATCAAAGCATGCTTACAACCCAGATGAGGAGTATGCAGAGGTAGAATCCAGATTGCGTTCACATTTGGAATCTTTTCTAGAAACTGCAAGATCATTCAATATGATTTACACCATGGATATACGTCCCTGGACACACATGATGGAGGTACCCCAGCTCCATGGGTTCGGGCCAGCTGCCAATCGCTTGTTGGAGGCATATAATGATGCTTTTGAAGGTATGTCATTGATAATCAAACTATATGTGAATTCATTTCTTCCCAGCACATCTTGA

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

147

Amino Acids

17.32

Weight (kDa)

5.84

Isoelectric Point (pI)

52.47

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Plant_NMP1	PF06694	31 - 126	8.8e-50	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)
Acc65I	GGTACC	1 cut(s)	319
AccB1I	GGYRCC	1 cut(s)	319
AcsI	RAATTY	1 cut(s)	418
AfaI	GTAC	1 cut(s)	321
AfiI	CCNNNNNNNGG	1 cut(s)	199
AgsI	TTSAA	4 cut(s)	61, 152, 271, 386
AjnI	CCWGG	1 cut(s)	299
AluBI	AGCT	5 cut(s)	15, 106, 118, 328, 347
AluI	AGCT	5 cut(s)	15, 106, 118, 328, 347
AoxI	GGCC	1 cut(s)	341
ApeKI	GCWGC	1 cut(s)	347
ApoI	RAATTY	1 cut(s)	418
Asp700I	GAANNNNTTC	1 cut(s)	246
Asp718I	GGTACC	1 cut(s)	319
AspS9I	GGNCC	1 cut(s)	341
BanI	GGYRCC	1 cut(s)	319
BbsI	GAAGAC	2 cut(s)	49, 140
BbvI	GCAGC	1 cut(s)	334
BccI	CCATC	1 cut(s)	307
BciT130I	CCWGG	1 cut(s)	301
BfaI	CTAG	1 cut(s)	251
BisI	GCNGC	1 cut(s)	348
BlsI	GCNGC	1 cut(s)	349
Bme1390I	CCNGG	1 cut(s)	301
BmgT120I	GGNCC	1 cut(s)	341
BmiI	GGNNCC	1 cut(s)	321
BmrFI	CCNGG	1 cut(s)	301
BmsI	GCATC	3 cut(s)	91, 182, 367
BpiI	GAAGAC	2 cut(s)	49, 140
BpmI	CTGGAG	1 cut(s)	128
BpuEI	CTTGAG	2 cut(s)	36, 127
BsaJI	CCNNGG	3 cut(s)	285, 299, 331
BsaXI	ACNNNNNCTCC	2 cut(s)	312, 342
Bsc4I	CCNNNNNNNGG	1 cut(s)	199
BseBI	CCWGG	1 cut(s)	301
BseDI	CCNNGG	3 cut(s)	285, 299, 331
BseLI	CCNNNNNNNGG	1 cut(s)	199
BseMII	CTCAG	1 cut(s)	93
BseRI	GAGGAG	1 cut(s)	215
BseXI	GCAGC	1 cut(s)	334
BseYI	CCCAGC	2 cut(s)	324, 431
BshFI	GGCC	1 cut(s)	343
BshNI	GGYRCC	1 cut(s)	319
BslFI	GGGAC	1 cut(s)	282
BslI	CCNNNNNNNGG	1 cut(s)	199
BsmFI	GGGAC	1 cut(s)	282
BsnI	GGCC	1 cut(s)	343
Bsp143I	GATC	1 cut(s)	263
Bsp19I	CCATGG	2 cut(s)	285, 331
BspANI	GGCC	1 cut(s)	343
BspCNI	CTCAG	1 cut(s)	94
BspLI	GGNNCC	1 cut(s)	321
BspT107I	GGYRCC	1 cut(s)	319
BssECI	CCNNGG	3 cut(s)	285, 299, 331
BssMI	GATC	1 cut(s)	263
BssT1I	CCWWGG	2 cut(s)	285, 331
Bst2UI	CCWGG	1 cut(s)	301
BstC8I	GCNNGC	2 cut(s)	183, 345
BstDEI	CTNAG	1 cut(s)	102
BstDSI	CCRYGG	2 cut(s)	285, 331
BstKTI	GATC	1 cut(s)	266
BstMBI	GATC	1 cut(s)	263
BstMWI	GCNNNNNNNGC	1 cut(s)	88
BstNI	CCWGG	1 cut(s)	301
BstNSI	RCATGY	1 cut(s)	185
BstSCI	CCNGG	1 cut(s)	299
BstV1I	GCAGC	1 cut(s)	334
BstV2I	GAAGAC	2 cut(s)	49, 140
BstXI	CCANNNNNNTGG	1 cut(s)	332
BsuRI	GGCC	1 cut(s)	343
BtgI	CCRYGG	2 cut(s)	285, 331
Cac8I	GCNNGC	2 cut(s)	183, 345
Cfr13I	GGNCC	1 cut(s)	341
Csp6I	GTAC	1 cut(s)	320
CviAII	CATG	5 cut(s)	92, 182, 286, 310, 332
CviJI	RGCY	7 cut(s)	15, 27, 106, 118, 328, 343, 347
CviKI_1	RGCY	7 cut(s)	15, 27, 106, 118, 328, 343, 347
CviQI	GTAC	1 cut(s)	320
DdeI	CTNAG	1 cut(s)	102
DpnI	GATC	1 cut(s)	265
DpnII	GATC	1 cut(s)	263
Eco130I	CCWWGG	2 cut(s)	285, 331
EcoRI	GAATTC	1 cut(s)	418
EcoRII	CCWGG	1 cut(s)	299
EcoT14I	CCWWGG	2 cut(s)	285, 331
ErhI	CCWWGG	2 cut(s)	285, 331
FaeI	CATG	5 cut(s)	95, 185, 289, 313, 335
FaqI	GGGAC	1 cut(s)	282
FatI	CATG	5 cut(s)	91, 181, 285, 309, 331
Fnu4HI	GCNGC	1 cut(s)	348
Fsp4HI	GCNGC	1 cut(s)	348
FspBI	CTAG	1 cut(s)	251
GluI	GCNGC	1 cut(s)	348
GsaI	CCCAGC	2 cut(s)	328, 435
GsuI	CTGGAG	1 cut(s)	128
HaeIII	GGCC	1 cut(s)	343
Hin1II	CATG	5 cut(s)	95, 185, 289, 313, 335
HindIII	AAGCTT	1 cut(s)	116
HinfI	GANTC	2 cut(s)	218, 242
Hpy166II	GTNNAC	1 cut(s)	233
Hpy188I	TCNGA	2 cut(s)	12, 103
Hpy188III	TCNNGA	3 cut(s)	222, 251, 441
Hpy8I	GTNNAC	1 cut(s)	233
HpyAV	CCTTC	1 cut(s)	380
HpyCH4IV	ACGT	1 cut(s)	295
HpyCH4V	TGCA	2 cut(s)	209, 260
HpyF10VI	GCNNNNNNNGC	1 cut(s)	88
HpyF3I	CTNAG	1 cut(s)	102
HpySE526I	ACGT	1 cut(s)	295
Hsp92II	CATG	5 cut(s)	95, 185, 289, 313, 335
KpnI	GGTACC	1 cut(s)	323
Kzo9I	GATC	1 cut(s)	263
LmnI	GCTCC	2 cut(s)	109, 333
LpnPI	CCDG	8 cut(s)	52, 92, 207, 235, 286, 313, 338, 357
Lsp1109I	GCAGC	1 cut(s)	334
LweI	GCATC	3 cut(s)	91, 182, 367
MaeI	CTAG	1 cut(s)	251
MaeII	ACGT	1 cut(s)	295
MalI	GATC	1 cut(s)	265
MboI	GATC	1 cut(s)	263
MboII	GAAGA	3 cut(s)	49, 140, 419
MluCI	AATT	1 cut(s)	418
MmeI	TCCRAC	1 cut(s)	342
MnlI	CCTC	4 cut(s)	193, 205, 310, 358
MroXI	GAANNNNTTC	1 cut(s)	246
MspA1I	CMGCKG	1 cut(s)	347
MspR9I	CCNGG	1 cut(s)	301
MvaI	CCWGG	1 cut(s)	301
MwoI	GCNNNNNNNGC	1 cut(s)	88
NcoI	CCATGG	2 cut(s)	285, 331
NdeII	GATC	1 cut(s)	263
NlaIII	CATG	5 cut(s)	95, 185, 289, 313, 335
NlaIV	GGNNCC	1 cut(s)	321
NspI	RCATGY	1 cut(s)	185
PaeI	GCATGC	1 cut(s)	185
PdmI	GAANNNNTTC	1 cut(s)	246
PfeI	GAWTC	2 cut(s)	218, 242
PkrI	GCNGC	1 cut(s)	349
Psp6I	CCWGG	1 cut(s)	299
PspFI	CCCAGC	2 cut(s)	324, 431
PspGI	CCWGG	1 cut(s)	299
PspN4I	GGNNCC	1 cut(s)	321
PspPI	GGNCC	1 cut(s)	341
PvuII	CAGCTG	1 cut(s)	347
RsaI	GTAC	1 cut(s)	321
RsaNI	GTAC	1 cut(s)	320
SatI	GCNGC	1 cut(s)	348
Sau3AI	GATC	1 cut(s)	263
Sau96I	GGNCC	1 cut(s)	341
ScrFI	CCNGG	1 cut(s)	301
SfaNI	GCATC	3 cut(s)	91, 182, 367
SmlI	CTYRAG	2 cut(s)	51, 142
SmoI	CTYRAG	2 cut(s)	51, 142
SphI	GCATGC	1 cut(s)	185
Sse9I	AATT	1 cut(s)	418
SspMI	CTAG	1 cut(s)	251
StyD4I	CCNGG	1 cut(s)	299
StyI	CCWWGG	2 cut(s)	285, 331
TaiI	ACGT	1 cut(s)	298
TasI	AATT	1 cut(s)	418
TfiI	GAWTC	2 cut(s)	218, 242
TseI	GCWGC	1 cut(s)	347
TspDTI	ATGAA	1 cut(s)	411
XapI	RAATTY	1 cut(s)	418
XbaI	TCTAGA	1 cut(s)	250
XceI	RCATGY	1 cut(s)	185
XcmI	CCANNNNNNNNNTGG	1 cut(s)	358
XmnI	GAANNNNTTC	1 cut(s)	246
XspI	CTAG	1 cut(s)	251

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