Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1A

Orthogroup ID

OG0000643

Physical Location & Seq

Genomic Coordinates Forward (+)

25978222 .. 25985059

Gene Structure 6838 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1AG137400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 789 bp

ATGTTTCTGAGCTGGAGCAGAAGCTTTCATAACAATACTCTCTTACATCTTCAACAAAAGGTTGATGATTTGGCATCAAAGCATGCTTACAACCCACATGAGGAGTATGCAGATGTGGAATCCACATTGCGTTCGCATTTGGAATCTTTTCTAGAAACTGCAAGATCATTCAATATGATTTACACCAAGGAAATACGTCCCTGGACACACATGATGGAGGTACCCCAGCTCCATGGGTTCGAGCCTGCAGCCAATCGCTTATTGGAGGCATATAAGATGCTTTTGAAGAAACCTGTCGAGGATAATGTTGAGAAGAAGAAGAAAAGGAAAGAGATAGGGGAGGAGAGTTATTATTCACCTGAATTCTGGCCACCAGTTTTAGGAAATTCACCTGTAACTTTCTTGACGTGTGCAAATCCAGTGAATTCTTCTCAGTATGTGAACACTGCTCCCTGTATTAAATCCAAAAGGTATGGTTATGCCGTTCTACGCTATATGTTCCTGGAAGATGTGGAGAATGGGTGCAGTATAGATTGGATGGGTATGTTCACTTCGATGCACGGAAAGGACGGAAACATTTTCTATCACGACATACACAATGAAGACCGAAACATTTCCTATCTAGACATACACAATGAACTGGTGTATGGCTTTGAGCTTGAATGGAATTACAGAGTCGATTGCCACGGTCGATGGAATTACACTTTTCGGGACGGAGGATATGACTGTTATCCGCGCAGCATCCGAGGTTTCTTTCAACTTGGTTGGACGGTGTTAATCGTGTTGTAG

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

262

Amino Acids

30.96

Weight (kDa)

6.06

Isoelectric Point (pI)

56.26

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Plant_NMP1	PF06694	10 - 96	1.1e-44	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

Tree File

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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)	220
AccB1I	GGYRCC	1 cut(s)	220
AccII	CGCG	1 cut(s)	736
AciI	CCGC	1 cut(s)	734
AcoI	YGGCCR	1 cut(s)	368
AcsI	RAATTY	3 cut(s)	362, 385, 424
AfaI	GTAC	1 cut(s)	222
AfiI	CCNNNNNNNGG	2 cut(s)	100, 380
AflIII	ACRYGT	1 cut(s)	407
AgsI	TTSAA	5 cut(s)	53, 172, 286, 662, 758
AjiI	CACGTC	1 cut(s)	408
AjnI	CCWGG	2 cut(s)	200, 501
AluBI	AGCT	4 cut(s)	12, 24, 229, 658
AluI	AGCT	4 cut(s)	12, 24, 229, 658
AoxI	GGCC	1 cut(s)	368
ApeKI	GCWGC	2 cut(s)	248, 738
ApoI	RAATTY	3 cut(s)	362, 385, 424
Asp700I	GAANNNNTTC	2 cut(s)	147, 613
Asp718I	GGTACC	1 cut(s)	220
AspLEI	GCGC	1 cut(s)	738
AsuHPI	GGTGA	2 cut(s)	348, 381
BalI	TGGCCA	1 cut(s)	370
BanI	GGYRCC	1 cut(s)	220
BarI	GAAGNNNNNNTAC	2 cut(s)	535, 567
BbsI	GAAGAC	1 cut(s)	609
BbvI	GCAGC	2 cut(s)	260, 750
BccI	CCATC	3 cut(s)	208, 532, 687
BceAI	ACGGC	1 cut(s)	467
BciT130I	CCWGG	2 cut(s)	202, 503
BfaI	CTAG	2 cut(s)	152, 623
BfmI	CTRYAG	1 cut(s)	246
BisI	GCNGC	2 cut(s)	249, 739
BlsI	GCNGC	2 cut(s)	250, 740
Bme1390I	CCNGG	2 cut(s)	202, 503
BmgBI	CACGTC	1 cut(s)	408
BmiI	GGNNCC	1 cut(s)	222
BmrFI	CCNGG	2 cut(s)	202, 503
BmsI	GCATC	4 cut(s)	83, 267, 546, 750
BpiI	GAAGAC	1 cut(s)	609
BpmI	CTGGAG	1 cut(s)	34
BsaJI	CCNNGG	5 cut(s)	186, 200, 232, 685, 745
BsaXI	ACNNNNNCTCC	4 cut(s)	213, 243, 506, 536
Bsc4I	CCNNNNNNNGG	2 cut(s)	100, 380
Bse1I	ACTGG	3 cut(s)	374, 419, 645
Bse3DI	GCAATG	1 cut(s)	125
BseBI	CCWGG	2 cut(s)	202, 503
BseDI	CCNNGG	5 cut(s)	186, 200, 232, 685, 745
BseGI	GGATG	2 cut(s)	543, 741
BseLI	CCNNNNNNNGG	2 cut(s)	100, 380
BseMI	GCAATG	1 cut(s)	125
BseMII	CTCAG	1 cut(s)	446
BseNI	ACTGG	3 cut(s)	374, 419, 645
BseRI	GAGGAG	2 cut(s)	116, 356
BseXI	GCAGC	2 cut(s)	260, 750
BseYI	CCCAGC	1 cut(s)	225
BsgI	GTGCAG	1 cut(s)	544
Bsh1236I	CGCG	1 cut(s)	736
Bsh1285I	CGRYCG	1 cut(s)	691
BshFI	GGCC	1 cut(s)	370
BshNI	GGYRCC	1 cut(s)	220
BsiEI	CGRYCG	1 cut(s)	691
BslFI	GGGAC	2 cut(s)	183, 725
BslI	CCNNNNNNNGG	2 cut(s)	100, 380
BsmFI	GGGAC	2 cut(s)	183, 725
BsnI	GGCC	1 cut(s)	370
Bsp143I	GATC	1 cut(s)	164
Bsp19I	CCATGG	1 cut(s)	232
BspACI	CCGC	1 cut(s)	734
BspANI	GGCC	1 cut(s)	370
BspCNI	CTCAG	1 cut(s)	445
BspFNI	CGCG	1 cut(s)	736
BspLI	GGNNCC	1 cut(s)	222
BspMAI	CTGCAG	1 cut(s)	250
BspT107I	GGYRCC	1 cut(s)	220
BsrDI	GCAATG	1 cut(s)	125
BsrI	ACTGG	3 cut(s)	374, 419, 645
BssECI	CCNNGG	5 cut(s)	186, 200, 232, 685, 745
BssMI	GATC	1 cut(s)	164
BssT1I	CCWWGG	2 cut(s)	186, 232
Bst2UI	CCWGG	2 cut(s)	202, 503
Bst4CI	ACNGT	3 cut(s)	689, 728, 772
BstC8I	GCNNGC	2 cut(s)	84, 246
BstDEI	CTNAG	2 cut(s)	8, 432
BstDSI	CCRYGG	2 cut(s)	232, 685
BstF5I	GGATG	2 cut(s)	543, 741
BstFNI	CGCG	1 cut(s)	736
BstHHI	GCGC	1 cut(s)	738
BstKTI	GATC	1 cut(s)	167
BstMBI	GATC	1 cut(s)	164
BstMCI	CGRYCG	1 cut(s)	691
BstNI	CCWGG	2 cut(s)	202, 503
BstNSI	RCATGY	1 cut(s)	86
BstSCI	CCNGG	2 cut(s)	200, 501
BstSFI	CTRYAG	1 cut(s)	246
BstUI	CGCG	1 cut(s)	736
BstV1I	GCAGC	2 cut(s)	260, 750
BstV2I	GAAGAC	1 cut(s)	609
BstXI	CCANNNNNNTGG	1 cut(s)	233
BsuRI	GGCC	1 cut(s)	370
BtgI	CCRYGG	2 cut(s)	232, 685
BtrI	CACGTC	1 cut(s)	408
BtsCI	GGATG	2 cut(s)	543, 741
BtsI	GCAGTG	1 cut(s)	444
BtsIMutI	CAGTG	2 cut(s)	426, 444
Cac8I	GCNNGC	2 cut(s)	84, 246
CfoI	GCGC	1 cut(s)	738
Csp6I	GTAC	1 cut(s)	221
CviAII	CATG	4 cut(s)	83, 98, 211, 233
CviJI	RGCY	8 cut(s)	12, 24, 229, 244, 251, 370, 651, 658
CviKI_1	RGCY	8 cut(s)	12, 24, 229, 244, 251, 370, 651, 658
CviQI	GTAC	1 cut(s)	221
DdeI	CTNAG	2 cut(s)	8, 432
DpnI	GATC	1 cut(s)	166
DpnII	GATC	1 cut(s)	164
EaeI	YGGCCR	1 cut(s)	368
Eco130I	CCWWGG	2 cut(s)	186, 232
EcoRI	GAATTC	2 cut(s)	362, 424
EcoRII	CCWGG	2 cut(s)	200, 501
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	2 cut(s)	183, 725
FatI	CATG	4 cut(s)	82, 97, 210, 232
Fnu4HI	GCNGC	2 cut(s)	249, 739
FokI	GGATG	2 cut(s)	550, 728
Fsp4HI	GCNGC	2 cut(s)	249, 739
FspBI	CTAG	2 cut(s)	152, 623
GlaI	GCGC	1 cut(s)	737
GluI	GCNGC	2 cut(s)	249, 739
GsaI	CCCAGC	1 cut(s)	229
GsuI	CTGGAG	1 cut(s)	34
HaeIII	GGCC	1 cut(s)	370
HhaI	GCGC	1 cut(s)	738
Hin1II	CATG	4 cut(s)	86, 101, 214, 236
Hin6I	GCGC	1 cut(s)	736
HinP1I	GCGC	1 cut(s)	736
HindIII	AAGCTT	1 cut(s)	22
HinfI	GANTC	3 cut(s)	119, 143, 675
HphI	GGTGA	2 cut(s)	348, 381
Hpy166II	GTNNAC	2 cut(s)	442, 549
Hpy188I	TCNGA	2 cut(s)	9, 746
Hpy188III	TCNNGA	5 cut(s)	152, 403, 587, 623, 710
Hpy8I	GTNNAC	2 cut(s)	442, 549
HpyCH4III	ACNGT	3 cut(s)	689, 728, 772
HpyCH4IV	ACGT	2 cut(s)	196, 407
HpyCH4V	TGCA	6 cut(s)	110, 161, 248, 413, 525, 559
HpyF3I	CTNAG	2 cut(s)	8, 432
HpySE526I	ACGT	2 cut(s)	196, 407
Hsp92II	CATG	4 cut(s)	86, 101, 214, 236
HspAI	GCGC	1 cut(s)	736
KpnI	GGTACC	1 cut(s)	224
Kzo9I	GATC	1 cut(s)	164
LmnI	GCTCC	3 cut(s)	15, 234, 454
Lsp1109I	GCAGC	2 cut(s)	260, 750
LweI	GCATC	4 cut(s)	83, 267, 546, 750
MaeI	CTAG	2 cut(s)	152, 623
MaeII	ACGT	2 cut(s)	196, 407
MaeIII	GTNAC	1 cut(s)	394
MalI	GATC	1 cut(s)	166
MboI	GATC	1 cut(s)	164
MboII	GAAGA	8 cut(s)	41, 298, 325, 328, 331, 420, 518, 614
MlsI	TGGCCA	1 cut(s)	370
MluCI	AATT	5 cut(s)	362, 385, 424, 667, 697
MluNI	TGGCCA	1 cut(s)	370
MlyI	GAGTC	1 cut(s)	684
MmeI	TCCRAC	1 cut(s)	746
MnlI	CCTC	7 cut(s)	94, 211, 259, 292, 334, 710, 740
Mox20I	TGGCCA	1 cut(s)	370
MroXI	GAANNNNTTC	2 cut(s)	147, 613
MscI	TGGCCA	1 cut(s)	370
MseI	TTAA	2 cut(s)	459, 776
MslI	CAYNNNNRTG	1 cut(s)	554
Msp20I	TGGCCA	1 cut(s)	370
MspR9I	CCNGG	2 cut(s)	202, 503
MvaI	CCWGG	2 cut(s)	202, 503
MvnI	CGCG	1 cut(s)	736
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, 613
PfeI	GAWTC	2 cut(s)	119, 143
PfoI	TCCNGGA	1 cut(s)	501
PkrI	GCNGC	2 cut(s)	250, 740
PleI	GAGTC	1 cut(s)	683
PpsI	GAGTC	1 cut(s)	683
Psp6I	CCWGG	2 cut(s)	200, 501
PspFI	CCCAGC	1 cut(s)	225
PspGI	CCWGG	2 cut(s)	200, 501
PspN4I	GGNNCC	1 cut(s)	222
PstI	CTGCAG	1 cut(s)	250
RsaI	GTAC	1 cut(s)	222
RsaNI	GTAC	1 cut(s)	221
RseI	CAYNNNNRTG	1 cut(s)	554
SaqAI	TTAA	2 cut(s)	459, 776
SatI	GCNGC	2 cut(s)	249, 739
Sau3AI	GATC	1 cut(s)	164
SchI	GAGTC	1 cut(s)	684
ScrFI	CCNGG	2 cut(s)	202, 503
SfaNI	GCATC	4 cut(s)	83, 267, 546, 750
SfcI	CTRYAG	1 cut(s)	246
SmiMI	CAYNNNNRTG	1 cut(s)	554
SphI	GCATGC	1 cut(s)	86
Sse9I	AATT	5 cut(s)	362, 385, 424, 667, 697
SsiI	CCGC	1 cut(s)	734
SspMI	CTAG	2 cut(s)	152, 623
StyD4I	CCNGG	2 cut(s)	200, 501
StyI	CCWWGG	2 cut(s)	186, 232
TaaI	ACNGT	3 cut(s)	689, 728, 772
TaiI	ACGT	2 cut(s)	199, 410
TaqI	TCGA	5 cut(s)	240, 297, 554, 678, 691
TaqII	GACCGA	1 cut(s)	621
TasI	AATT	5 cut(s)	362, 385, 424, 667, 697
TfiI	GAWTC	2 cut(s)	119, 143
Tru1I	TTAA	2 cut(s)	459, 776
Tru9I	TTAA	2 cut(s)	459, 776
TscAI	CASTG	2 cut(s)	426, 451
TseI	GCWGC	2 cut(s)	248, 738
TspDTI	ATGAA	3 cut(s)	17, 615, 651
TspGWI	ACGGA	3 cut(s)	576, 585, 729
TspRI	CASTG	2 cut(s)	426, 451
XapI	RAATTY	3 cut(s)	362, 385, 424
XbaI	TCTAGA	2 cut(s)	151, 622
XceI	RCATGY	1 cut(s)	86
XcmI	CCANNNNNNNNNTGG	1 cut(s)	259
XmnI	GAANNNNTTC	2 cut(s)	147, 613
XspI	CTAG	2 cut(s)	152, 623

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