Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5A

Orthogroup ID

OG0001972

Physical Location & Seq

Genomic Coordinates Forward (+)

56442269 .. 56455746

Gene Structure 13478 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5AG344000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 729 bp

ATGGTTTCCCTTCTCTCACTTTCTCACAATTTCTTCTCCAAAGGGTATTTGTCTGTGAGCCCAAGTCAGAGGTCAGTTTGTCGCTCTGTGGTTTGTGAGGCTGCTCCAACCAAGAGGCTTGATTATGTTGAAAAGCGAGCTCGCCAGGTTGAGAAAAGGCGCATTTACAACAAGTCTAAAAAGTCTGAGATCAAAACCAGGTTGAGATCAAAACCAGGAGATAGAGGAGGTTCAGAGGCAGAGGAAGTCCCCGATCTGGTGTGTCAGACTGTCAGCTCGACAACTTCCAGCGCATGGTCGATACCTTCACCACCTTTCGATGGAAGTGCCATCAGGTCGATTATACGCAATGGAGCGAGGGCTGAAGATTCCTCAGAACAAGTGCACAAGACCACCAATTCCCTCATGATTTCACTCATGAAGCAGCTTGAAAAGCTTGAACAGAAGCAGAAGTATGCGGCTTGGAAAGCAGCAGATATAAGGAAAGCTGTGAAAGAAGGAAGGAAACCTCAAGCTGGCCCCTCTGCAGATTCGGCAGAGATTGCAAAGTTTCTGGGCATTATGAATACAATAGACACAGAAGCCATCCAAGTAACTAACGATATACAACTGATTGATTCCATTGCTGAAAAGCAAGCTCAAATATTCTCTGAAGATTGCAAATTGTTTCGTGCTGATGTTCAGATTCAAGCTATATATCCATTACCGAATGTTTCTAAGCTGGAGTAG

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

242

Amino Acids

26.89

Weight (kDa)

9.37

Isoelectric Point (pI)

49.83

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Plant_NMP1	PF06694	197 - 242	1.1e-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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Align Labels (Cladogram)

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Publication-ready

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Orthologous Genes (Group: OG0001972)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G15190
fragaria_vesca	FvH4_3g19430
malus_domestica	MD03G1232600.v1.1 MD11G1253300.v1.1
prunus_persica	Prupe.4G176000_v2.0.a1
pyrus_communis	pycom03g17940 pycom11g22450
rosa_chinensis	RchiOBHm_Chr5g0032711
rosa_laevigata	RLG00000022904 RLG00000033418
rosa_multiflora	Rmu_sc0002292.1_g000007 Rmu_ssc0000242.1_g000013
rosa_roxburghii	Rroxscaffold_1G00047390 Rroxscaffold_1G00047850 Rroxscaffold_2G00126870
rosa_rugosa	Rorug01G0128400 Rorug04G0017100 Rorug05G0133200 Rorug05G0268300 Rorug05G0268400 Rorug05G0268500
rosa_samantha	Rh1DG018700 Rh1DG018800 Rh2AG155500 Rh2BG161800 Rh2BG417900 Rh2DG161100 Rh4CG241300 Rh4CG241400 Rh4DG279300 Rh5AG225700 Rh5AG312200 Rh5AG344000 Rh5AG482400 Rh5AG537200 Rh5BG226900 Rh5BG388200 Rh5BG503200 Rh5CG214800 Rh5CG254500 Rh5CG275300 Rh5CG360900 Rh5CG526500 Rh5DG231500
rosa_wichuraiana	Rw5G020690

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	294
AciI	CCGC	1 cut(s)	458
AcuI	CTGAAG	2 cut(s)	384, 672
AfiI	CCNNNNNNNGG	4 cut(s)	256, 294, 320, 515
AgsI	TTSAA	4 cut(s)	131, 431, 440, 689
AjnI	CCWGG	3 cut(s)	144, 197, 214
AluBI	AGCT	9 cut(s)	140, 276, 427, 436, 488, 515, 638, 692, 721
AluI	AGCT	9 cut(s)	140, 276, 427, 436, 488, 515, 638, 692, 721
Alw21I	GWGCWC	2 cut(s)	142, 387
Alw44I	GTGCAC	1 cut(s)	383
AoxI	GGCC	1 cut(s)	517
ApaLI	GTGCAC	1 cut(s)	383
ApeKI	GCWGC	3 cut(s)	101, 424, 470
AspLEI	GCGC	2 cut(s)	162, 293
AspS9I	GGNCC	1 cut(s)	518
AsuHPI	GGTGA	1 cut(s)	300
BaeGI	GKGCMC	1 cut(s)	387
BanII	GRGCYC	2 cut(s)	62, 142
Bbv12I	GWGCWC	2 cut(s)	142, 387
BbvI	GCAGC	3 cut(s)	88, 436, 482
BccI	CCATC	3 cut(s)	314, 338, 593
BcgI	CGANNNNNNTGC	2 cut(s)	308, 342
BciT130I	CCWGG	3 cut(s)	146, 199, 216
BfmI	CTRYAG	1 cut(s)	525
BisI	GCNGC	4 cut(s)	102, 425, 459, 471
BlsI	GCNGC	4 cut(s)	103, 426, 460, 472
Bme1390I	CCNGG	3 cut(s)	146, 199, 216
BmgT120I	GGNCC	1 cut(s)	518
BmiI	GGNNCC	1 cut(s)	520
BmrFI	CCNGG	3 cut(s)	146, 199, 216
BpuEI	CTTGAG	1 cut(s)	495
Bsc4I	CCNNNNNNNGG	4 cut(s)	256, 294, 320, 515
Bse3DI	GCAATG	2 cut(s)	355, 621
BseBI	CCWGG	3 cut(s)	146, 199, 216
BseGI	GGATG	1 cut(s)	585
BseLI	CCNNNNNNNGG	4 cut(s)	256, 294, 320, 515
BseMI	GCAATG	2 cut(s)	355, 621
BseMII	CTCAG	2 cut(s)	177, 387
BseRI	GAGGAG	1 cut(s)	240
BseSI	GKGCMC	1 cut(s)	387
BseXI	GCAGC	3 cut(s)	88, 436, 482
BshFI	GGCC	1 cut(s)	519
BsiHKAI	GWGCWC	2 cut(s)	142, 387
BslFI	GGGAC	1 cut(s)	233
BslI	CCNNNNNNNGG	4 cut(s)	256, 294, 320, 515
BsmFI	GGGAC	1 cut(s)	233
BsnI	GGCC	1 cut(s)	519
Bsp1286I	GDGCHC	3 cut(s)	62, 142, 387
Bsp143I	GATC	3 cut(s)	189, 206, 253
BspACI	CCGC	1 cut(s)	458
BspANI	GGCC	1 cut(s)	519
BspCNI	CTCAG	2 cut(s)	178, 386
BspHI	TCATGA	2 cut(s)	405, 417
BspLI	GGNNCC	1 cut(s)	520
BspMAI	CTGCAG	1 cut(s)	529
BsrDI	GCAATG	2 cut(s)	355, 621
BssMI	GATC	3 cut(s)	189, 206, 253
Bst2UI	CCWGG	3 cut(s)	146, 199, 216
Bst4CI	ACNGT	1 cut(s)	271
BstAPI	GCANNNNNTGC	1 cut(s)	542
BstC8I	GCNNGC	4 cut(s)	138, 142, 517, 636
BstDEI	CTNAG	3 cut(s)	186, 373, 717
BstF5I	GGATG	1 cut(s)	585
BstHHI	GCGC	2 cut(s)	162, 293
BstKTI	GATC	3 cut(s)	192, 209, 256
BstMBI	GATC	3 cut(s)	189, 206, 253
BstMWI	GCNNNNNNNGC	4 cut(s)	433, 467, 533, 542
BstNI	CCWGG	3 cut(s)	146, 199, 216
BstSCI	CCNGG	3 cut(s)	144, 197, 214
BstSFI	CTRYAG	1 cut(s)	525
BstSLI	GKGCMC	1 cut(s)	387
BstV1I	GCAGC	3 cut(s)	88, 436, 482
BsuRI	GGCC	1 cut(s)	519
BtsCI	GGATG	1 cut(s)	585
Cac8I	GCNNGC	4 cut(s)	138, 142, 517, 636
CciI	TCATGA	2 cut(s)	405, 417
CfoI	GCGC	2 cut(s)	162, 293
Cfr13I	GGNCC	1 cut(s)	518
CsiI	ACCWGGT	1 cut(s)	197
CviAII	CATG	3 cut(s)	294, 406, 418
DdeI	CTNAG	3 cut(s)	186, 373, 717
DpnI	GATC	3 cut(s)	191, 208, 255
DpnII	GATC	3 cut(s)	189, 206, 253
Ecl136II	GAGCTC	1 cut(s)	140
Eco24I	GRGCYC	2 cut(s)	62, 142
Eco53kI	GAGCTC	1 cut(s)	140
Eco57I	CTGAAG	2 cut(s)	384, 672
EcoICRI	GAGCTC	1 cut(s)	140
EcoRII	CCWGG	3 cut(s)	144, 197, 214
EcoT38I	GRGCYC	2 cut(s)	62, 142
FaeI	CATG	3 cut(s)	297, 409, 421
FaqI	GGGAC	1 cut(s)	233
FatI	CATG	3 cut(s)	293, 405, 417
Fnu4HI	GCNGC	4 cut(s)	102, 425, 459, 471
FokI	GGATG	1 cut(s)	572
FriOI	GRGCYC	2 cut(s)	62, 142
Fsp4HI	GCNGC	4 cut(s)	102, 425, 459, 471
GlaI	GCGC	2 cut(s)	161, 292
GluI	GCNGC	4 cut(s)	102, 425, 459, 471
HaeIII	GGCC	1 cut(s)	519
HhaI	GCGC	2 cut(s)	162, 293
Hin1II	CATG	3 cut(s)	297, 409, 421
Hin6I	GCGC	2 cut(s)	160, 291
HinP1I	GCGC	2 cut(s)	160, 291
HindIII	AAGCTT	1 cut(s)	434
HinfI	GANTC	4 cut(s)	368, 530, 617, 685
HphI	GGTGA	1 cut(s)	300
Hpy166II	GTNNAC	1 cut(s)	385
Hpy188I	TCNGA	7 cut(s)	69, 187, 235, 267, 376, 652, 684
Hpy188III	TCNNGA	2 cut(s)	406, 418
Hpy8I	GTNNAC	1 cut(s)	385
HpyAV	CCTTC	4 cut(s)	20, 315, 491, 495
HpyCH4III	ACNGT	1 cut(s)	271
HpyCH4V	TGCA	4 cut(s)	385, 527, 545, 660
HpyF10VI	GCNNNNNNNGC	4 cut(s)	433, 467, 533, 542
HpyF3I	CTNAG	3 cut(s)	186, 373, 717
Hsp92II	CATG	3 cut(s)	297, 409, 421
HspAI	GCGC	2 cut(s)	160, 291
Kzo9I	GATC	3 cut(s)	189, 206, 253
LmnI	GCTCC	2 cut(s)	109, 353
Lsp1109I	GCAGC	3 cut(s)	88, 436, 482
MabI	ACCWGGT	1 cut(s)	197
MaeIII	GTNAC	1 cut(s)	592
MalI	GATC	3 cut(s)	191, 208, 255
MboI	GATC	3 cut(s)	189, 206, 253
MboII	GAAGA	3 cut(s)	25, 377, 665
MhlI	GDGCHC	3 cut(s)	62, 142, 387
MluCI	AATT	3 cut(s)	28, 397, 662
MmeI	TCCRAC	1 cut(s)	131
MspR9I	CCNGG	3 cut(s)	146, 199, 216
MvaI	CCWGG	3 cut(s)	146, 199, 216
MwoI	GCNNNNNNNGC	4 cut(s)	433, 467, 533, 542
NdeII	GATC	3 cut(s)	189, 206, 253
NlaIII	CATG	3 cut(s)	297, 409, 421
NlaIV	GGNNCC	1 cut(s)	520
PagI	TCATGA	2 cut(s)	405, 417
PfeI	GAWTC	4 cut(s)	368, 530, 617, 685
PflMI	CCANNNNNTGG	1 cut(s)	294
PkrI	GCNGC	4 cut(s)	103, 426, 460, 472
Psp124BI	GAGCTC	1 cut(s)	142
Psp6I	CCWGG	3 cut(s)	144, 197, 214
PspGI	CCWGG	3 cut(s)	144, 197, 214
PspN4I	GGNNCC	1 cut(s)	520
PspPI	GGNCC	1 cut(s)	518
PstI	CTGCAG	1 cut(s)	529
SacI	GAGCTC	1 cut(s)	142
SatI	GCNGC	4 cut(s)	102, 425, 459, 471
Sau3AI	GATC	3 cut(s)	189, 206, 253
Sau96I	GGNCC	1 cut(s)	518
ScrFI	CCNGG	3 cut(s)	146, 199, 216
SduI	GDGCHC	3 cut(s)	62, 142, 387
SexAI	ACCWGGT	1 cut(s)	197
SfcI	CTRYAG	1 cut(s)	525
SmlI	CTYRAG	1 cut(s)	510
SmoI	CTYRAG	1 cut(s)	510
Sse9I	AATT	3 cut(s)	28, 397, 662
SsiI	CCGC	1 cut(s)	458
SspI	AATATT	1 cut(s)	645
SstI	GAGCTC	1 cut(s)	142
StyD4I	CCNGG	3 cut(s)	144, 197, 214
TaaI	ACNGT	1 cut(s)	271
TaqI	TCGA	4 cut(s)	278, 299, 318, 338
TasI	AATT	3 cut(s)	28, 397, 662
TauI	GCSGC	1 cut(s)	461
TfiI	GAWTC	4 cut(s)	368, 530, 617, 685
TseI	GCWGC	3 cut(s)	101, 424, 470
TspDTI	ATGAA	2 cut(s)	434, 578
Van91I	CCANNNNNTGG	1 cut(s)	294
VneI	GTGCAC	1 cut(s)	383

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