Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1A

Orthogroup ID

OG0000643

Physical Location & Seq

Genomic Coordinates Reverse (-)

31387529 .. 31391788

Gene Structure 4260 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1AG163600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 474 bp

ATGGTGAAGAAGAATAAGTGGGAGCATGGAGGATTTGTATCGATGAGCAGATTCAGTCTATATATCCATTGCATGATGTTTCAGAGCTGGAACAAAGGCTTACAGAACAATCAAAGATACTCTCAAGTCTTCAACAACAGGTTGATGATTTGGCATCAAAGGCATGATGTTTCTGAGCTGGAGCAAAAGCTTACAGAACAATCAAAGATACTCTCAAGTCTTCAACAAAAGGTTGATGATTTGGCATCAAAGCATGCTTACAACCCAGATGAGGAGTATGCAGGGGTAGAATCCAGATTGCGTTCACATTTGGAATCTTTTCTAGAAACTGCAAGATCATTCAATATGATTTACACCAAGGATATACGTCCCTGGACACACATGATGGAGGTACCCCAGCTCCATGGGTTCGGGCCAGCTGCCAATCGCTTGTTGGAGGCATATAATGATGCTTTTGAAGGAACGTTGACTTAA

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

157

Amino Acids

18.53

Weight (kDa)

7.1

Isoelectric Point (pI)

52.91

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Plant_NMP1	PF06694	55 - 149	9.1e-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)

Image

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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)	391
AccB1I	GGYRCC	1 cut(s)	391
AclI	AACGTT	1 cut(s)	464
AfaI	GTAC	1 cut(s)	393
AfiI	CCNNNNNNNGG	1 cut(s)	271
AgsI	TTSAA	4 cut(s)	133, 224, 343, 458
AjnI	CCWGG	1 cut(s)	371
AluBI	AGCT	5 cut(s)	87, 178, 190, 400, 419
AluI	AGCT	5 cut(s)	87, 178, 190, 400, 419
AoxI	GGCC	1 cut(s)	413
ApeKI	GCWGC	1 cut(s)	419
Asp700I	GAANNNNTTC	1 cut(s)	318
Asp718I	GGTACC	1 cut(s)	391
AspS9I	GGNCC	1 cut(s)	413
AsuHPI	GGTGA	1 cut(s)	16
BanI	GGYRCC	1 cut(s)	391
BbsI	GAAGAC	2 cut(s)	121, 212
BbvI	GCAGC	1 cut(s)	406
BccI	CCATC	1 cut(s)	379
BciT130I	CCWGG	1 cut(s)	373
BfaI	CTAG	1 cut(s)	323
BisI	GCNGC	1 cut(s)	420
BlsI	GCNGC	1 cut(s)	421
Bme1390I	CCNGG	1 cut(s)	373
BmgT120I	GGNCC	1 cut(s)	413
BmiI	GGNNCC	1 cut(s)	393
BmrFI	CCNGG	1 cut(s)	373
BmsI	GCATC	3 cut(s)	163, 254, 439
BpiI	GAAGAC	2 cut(s)	121, 212
BpmI	CTGGAG	1 cut(s)	200
BpuEI	CTTGAG	2 cut(s)	108, 199
Bsa29I	ATCGAT	1 cut(s)	41
BsaBI	GATNNNNATC	1 cut(s)	37
BsaJI	CCNNGG	3 cut(s)	357, 371, 403
BsaXI	ACNNNNNCTCC	4 cut(s)	21, 51, 384, 414
Bsc4I	CCNNNNNNNGG	1 cut(s)	271
Bse3DI	GCAATG	1 cut(s)	67
Bse8I	GATNNNNATC	1 cut(s)	37
BseBI	CCWGG	1 cut(s)	373
BseCI	ATCGAT	1 cut(s)	41
BseDI	CCNNGG	3 cut(s)	357, 371, 403
BseJI	GATNNNNATC	1 cut(s)	37
BseLI	CCNNNNNNNGG	1 cut(s)	271
BseMI	GCAATG	1 cut(s)	67
BseMII	CTCAG	1 cut(s)	165
BseRI	GAGGAG	1 cut(s)	287
BseXI	GCAGC	1 cut(s)	406
BseYI	CCCAGC	1 cut(s)	396
BshFI	GGCC	1 cut(s)	415
BshNI	GGYRCC	1 cut(s)	391
BshVI	ATCGAT	1 cut(s)	41
BslFI	GGGAC	1 cut(s)	354
BslI	CCNNNNNNNGG	1 cut(s)	271
BsmFI	GGGAC	1 cut(s)	354
BsnI	GGCC	1 cut(s)	415
Bsp143I	GATC	1 cut(s)	335
Bsp19I	CCATGG	1 cut(s)	403
BspANI	GGCC	1 cut(s)	415
BspCNI	CTCAG	1 cut(s)	166
BspDI	ATCGAT	1 cut(s)	41
BspLI	GGNNCC	1 cut(s)	393
BspT107I	GGYRCC	1 cut(s)	391
BsrDI	GCAATG	1 cut(s)	67
BssECI	CCNNGG	3 cut(s)	357, 371, 403
BssMI	GATC	1 cut(s)	335
BssT1I	CCWWGG	2 cut(s)	357, 403
Bst2UI	CCWGG	1 cut(s)	373
BstC8I	GCNNGC	2 cut(s)	255, 417
BstDEI	CTNAG	1 cut(s)	174
BstDSI	CCRYGG	1 cut(s)	403
BstKTI	GATC	1 cut(s)	338
BstMBI	GATC	1 cut(s)	335
BstMWI	GCNNNNNNNGC	1 cut(s)	160
BstNI	CCWGG	1 cut(s)	373
BstNSI	RCATGY	1 cut(s)	257
BstSCI	CCNGG	1 cut(s)	371
BstV1I	GCAGC	1 cut(s)	406
BstV2I	GAAGAC	2 cut(s)	121, 212
BstXI	CCANNNNNNTGG	1 cut(s)	404
Bsu15I	ATCGAT	1 cut(s)	41
BsuRI	GGCC	1 cut(s)	415
BsuTUI	ATCGAT	1 cut(s)	41
BtgI	CCRYGG	1 cut(s)	403
Cac8I	GCNNGC	2 cut(s)	255, 417
Cfr13I	GGNCC	1 cut(s)	413
ClaI	ATCGAT	1 cut(s)	41
Csp6I	GTAC	1 cut(s)	392
CviAII	CATG	6 cut(s)	26, 73, 164, 254, 382, 404
CviJI	RGCY	7 cut(s)	87, 99, 178, 190, 400, 415, 419
CviKI_1	RGCY	7 cut(s)	87, 99, 178, 190, 400, 415, 419
CviQI	GTAC	1 cut(s)	392
DdeI	CTNAG	1 cut(s)	174
DpnI	GATC	1 cut(s)	337
DpnII	GATC	1 cut(s)	335
Eco130I	CCWWGG	2 cut(s)	357, 403
EcoRII	CCWGG	1 cut(s)	371
EcoT14I	CCWWGG	2 cut(s)	357, 403
ErhI	CCWWGG	2 cut(s)	357, 403
FaeI	CATG	6 cut(s)	29, 76, 167, 257, 385, 407
FaqI	GGGAC	1 cut(s)	354
FatI	CATG	6 cut(s)	25, 72, 163, 253, 381, 403
Fnu4HI	GCNGC	1 cut(s)	420
Fsp4HI	GCNGC	1 cut(s)	420
FspBI	CTAG	1 cut(s)	323
GluI	GCNGC	1 cut(s)	420
GsaI	CCCAGC	1 cut(s)	400
GsuI	CTGGAG	1 cut(s)	200
HaeIII	GGCC	1 cut(s)	415
Hin1II	CATG	6 cut(s)	29, 76, 167, 257, 385, 407
HincII	GTYRAC	1 cut(s)	468
HindII	GTYRAC	1 cut(s)	468
HindIII	AAGCTT	1 cut(s)	188
HinfI	GANTC	3 cut(s)	51, 290, 314
HphI	GGTGA	1 cut(s)	16
Hpy166II	GTNNAC	2 cut(s)	305, 468
Hpy188I	TCNGA	2 cut(s)	84, 175
Hpy188III	TCNNGA	2 cut(s)	294, 323
Hpy8I	GTNNAC	2 cut(s)	305, 468
HpyAV	CCTTC	1 cut(s)	452
HpyCH4IV	ACGT	2 cut(s)	367, 464
HpyCH4V	TGCA	3 cut(s)	72, 281, 332
HpyF10VI	GCNNNNNNNGC	1 cut(s)	160
HpyF3I	CTNAG	1 cut(s)	174
HpySE526I	ACGT	2 cut(s)	367, 464
Hsp92II	CATG	6 cut(s)	29, 76, 167, 257, 385, 407
KpnI	GGTACC	1 cut(s)	395
Kzo9I	GATC	1 cut(s)	335
LmnI	GCTCC	3 cut(s)	22, 181, 405
Lsp1109I	GCAGC	1 cut(s)	406
LweI	GCATC	3 cut(s)	163, 254, 439
MaeI	CTAG	1 cut(s)	323
MaeII	ACGT	2 cut(s)	367, 464
MalI	GATC	1 cut(s)	337
MboI	GATC	1 cut(s)	335
MboII	GAAGA	4 cut(s)	19, 22, 121, 212
MmeI	TCCRAC	1 cut(s)	414
MnlI	CCTC	4 cut(s)	23, 265, 382, 430
MroXI	GAANNNNTTC	1 cut(s)	318
MseI	TTAA	1 cut(s)	472
MspA1I	CMGCKG	1 cut(s)	419
MspR9I	CCNGG	1 cut(s)	373
MvaI	CCWGG	1 cut(s)	373
MwoI	GCNNNNNNNGC	1 cut(s)	160
NcoI	CCATGG	1 cut(s)	403
NdeII	GATC	1 cut(s)	335
NlaIII	CATG	6 cut(s)	29, 76, 167, 257, 385, 407
NlaIV	GGNNCC	1 cut(s)	393
NspI	RCATGY	1 cut(s)	257
PaeI	GCATGC	1 cut(s)	257
PdmI	GAANNNNTTC	1 cut(s)	318
PfeI	GAWTC	3 cut(s)	51, 290, 314
PkrI	GCNGC	1 cut(s)	421
Psp1406I	AACGTT	1 cut(s)	464
Psp6I	CCWGG	1 cut(s)	371
PspFI	CCCAGC	1 cut(s)	396
PspGI	CCWGG	1 cut(s)	371
PspN4I	GGNNCC	1 cut(s)	393
PspPI	GGNCC	1 cut(s)	413
PvuII	CAGCTG	1 cut(s)	419
RsaI	GTAC	1 cut(s)	393
RsaNI	GTAC	1 cut(s)	392
SaqAI	TTAA	1 cut(s)	472
SatI	GCNGC	1 cut(s)	420
Sau3AI	GATC	1 cut(s)	335
Sau96I	GGNCC	1 cut(s)	413
ScrFI	CCNGG	1 cut(s)	373
SfaNI	GCATC	3 cut(s)	163, 254, 439
SmlI	CTYRAG	2 cut(s)	123, 214
SmoI	CTYRAG	2 cut(s)	123, 214
SphI	GCATGC	1 cut(s)	257
SspMI	CTAG	1 cut(s)	323
StyD4I	CCNGG	1 cut(s)	371
StyI	CCWWGG	2 cut(s)	357, 403
TaiI	ACGT	2 cut(s)	370, 467
TaqI	TCGA	1 cut(s)	41
TfiI	GAWTC	3 cut(s)	51, 290, 314
Tru1I	TTAA	1 cut(s)	472
Tru9I	TTAA	1 cut(s)	472
TseI	GCWGC	1 cut(s)	419
XbaI	TCTAGA	1 cut(s)	322
XceI	RCATGY	1 cut(s)	257
XcmI	CCANNNNNNNNNTGG	1 cut(s)	430
XmnI	GAANNNNTTC	1 cut(s)	318
XspI	CTAG	1 cut(s)	323

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