Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4D

Orthogroup ID

OG0016608

Physical Location & Seq

Genomic Coordinates Forward (+)

52746390 .. 52749214

Gene Structure 2825 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4DG305500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 798 bp

ATGGCTCCCGTGGCTCCTCTCCCTTACTCTCTCGCCGATCGTGACATTCAGGCAATTGTTGACGCTTATAAGGATGAGCCTGGTAACCCTAAATATGCTTTTAAGCATCTGTTGTTTAGTGTAACTGATCCGCAGTTTAGGGTGAAGCCTGCTGGTGTATCGGATATAATGTGGGCAGAGGCTATGGGGAAGCTTGAAGGTCTATCAAGTACTGACAGAGAACGGCTGTGGCCTGAGCTTGTTCAGGGTTTTAAGGATCTTTCACAACGCCTGAAGCTCCAAGATGAAGTCATACTTTCAGATGCTGAGAGACTGCAAATGACCCAAAGCAACGTGAAGATGCTTCAAAGACATTTTCAAGCTGACACTATTCCTCGGATTGAAAGAATGAGACAGAAAGAGCAAGGTCTTGAAAGGCGCCTGTTGAGGGTAATGAGAATACTGGAGGCACTAGAGGGCAAAGGTTTCCGATTGCCTTTAATGAAAGGGGAAGCTGAGTTGGCTGAGAAGTTAGCTTCAATAACTAGACAGTTGAAAGGACCTGGAGCTGAGCTTTCTAGCAGGGTACAAAACCTGCGAACTATATCCCGAGTCCAGGCAAATTCTATTGGTGCTGGTGGTTTTGTTTCTCTTCCAGGATCAACCAAAATACATGAACAGAGTCTTGCTGATATGCAAGAGGTCTTACAACAACAGACTGAGGCTATTGCAAGACTTGGCAATGTTTTGAAGCGTGATATTAGGGATATGGAGATTATAATGGCTGAGGATCCAGACACTACAGATAATATGTGTTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0005198 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005635 GO:0005643 GO:0005730 GO:0006606 GO:0006607 GO:0006810 GO:0006886 GO:0006913 GO:0006996 GO:0006997 GO:0006999 GO:0008104 GO:0008150 GO:0009987 GO:0012505 GO:0015031 GO:0015833 GO:0016043 GO:0017038 GO:0017056 GO:0031967 GO:0031974 GO:0031975 GO:0031981 GO:0032991 GO:0033036 GO:0033365 GO:0034504 GO:0034613 GO:0036228 GO:0042886 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043933 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0044613 GO:0045184 GO:0046907 GO:0051169 GO:0051170 GO:0051179 GO:0051234 GO:0051641 GO:0051649 GO:0070013 GO:0070727 GO:0071702 GO:0071705 GO:0071840 GO:0072594 GO:0072657 GO:0090435

KEGG Pathways

Metabolic & Signaling

ko03013 map03013

Pfam Domains

Protein Families

Nup54

Protein Analysis

265

Amino Acids

29.88

Weight (kDa)

6.37

Isoelectric Point (pI)

36.39

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Nup54	PF13874	49 - 193	1e-32	Nucleoporin complex subunit 54

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Orthologous Genes (Group: OG0016608)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G24310
fragaria_vesca	FvH4_4g23970
malus_domestica	MD13G1116800.v1.1 MD16G1117500.v1.1
prunus_persica	Prupe.1G228700_v2.0.a1
pyrus_communis	pycom13g10140 pycom16g10070
rosa_chinensis	RchiOBHm_Chr4g0430621
rosa_laevigata	RLG00000006962
rosa_multiflora	Rmu_sc0000131.1_g000016
rosa_roxburghii	Rroxscaffold_5G00372370
rosa_rugosa	Rorug04G0244800
rosa_samantha	Rh4DG305500
rosa_wichuraiana	Rw4G026100

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	2 cut(s)	69, 758
Acc36I	ACCTGC	1 cut(s)	582
AccB1I	GGYRCC	1 cut(s)	417
AciI	CCGC	1 cut(s)	131
AclWI	GGATC	5 cut(s)	122, 264, 646, 764, 777
AcsI	RAATTY	1 cut(s)	601
AcuI	CTGAAG	1 cut(s)	293
AcyI	GRCGYC	1 cut(s)	418
AfaI	GTAC	2 cut(s)	211, 567
AfiI	CCNNNNNNNGG	2 cut(s)	427, 595
AgsI	TTSAA	8 cut(s)	197, 347, 359, 383, 413, 519, 535, 730
AjnI	CCWGG	4 cut(s)	79, 541, 594, 634
AluBI	AGCT	8 cut(s)	193, 238, 277, 362, 494, 515, 548, 553
AluI	AGCT	8 cut(s)	193, 238, 277, 362, 494, 515, 548, 553
Alw26I	GTCTC	2 cut(s)	304, 385
AlwI	GGATC	5 cut(s)	122, 264, 646, 764, 777
AlwNI	CAGNNNCTG	1 cut(s)	305
Ama87I	CYCGRG	1 cut(s)	588
AoxI	GGCC	1 cut(s)	230
ApoI	RAATTY	1 cut(s)	601
AspLEI	GCGC	1 cut(s)	420
AspS9I	GGNCC	1 cut(s)	539
AsuHPI	GGTGA	1 cut(s)	154
AvaI	CYCGRG	1 cut(s)	588
AvaII	GGWCC	1 cut(s)	539
BamHI	GGATCC	1 cut(s)	769
BanI	GGYRCC	1 cut(s)	417
BbvCI	CCTCAGC	1 cut(s)	765
BceAI	ACGGC	1 cut(s)	239
BciT130I	CCWGG	4 cut(s)	81, 543, 596, 636
BcoDI	GTCTC	2 cut(s)	304, 385
BfaI	CTAG	3 cut(s)	452, 525, 558
BfmI	CTRYAG	1 cut(s)	780
BfoI	RGCGCY	1 cut(s)	421
BfuAI	ACCTGC	1 cut(s)	582
BlpI	GCTNAGC	1 cut(s)	549
BmcAI	AGTACT	1 cut(s)	211
Bme1390I	CCNGG	4 cut(s)	81, 543, 596, 636
Bme18I	GGWCC	1 cut(s)	539
BmeT110I	CYCGRG	1 cut(s)	588
BmgT120I	GGNCC	1 cut(s)	539
BmiI	GGNNCC	4 cut(s)	6, 15, 419, 771
BmrFI	CCNGG	4 cut(s)	81, 543, 596, 636
BmsI	GCATC	3 cut(s)	115, 292, 330
BpmI	CTGGAG	2 cut(s)	464, 564
Bpu10I	CCTNAGC	2 cut(s)	234, 765
Bpu1102I	GCTNAGC	1 cut(s)	549
BsaHI	GRCGYC	1 cut(s)	418
BsaJI	CCNNGG	2 cut(s)	9, 374
Bsc4I	CCNNNNNNNGG	2 cut(s)	427, 595
Bse1I	ACTGG	1 cut(s)	447
Bse3DI	GCAATG	1 cut(s)	727
BseBI	CCWGG	4 cut(s)	81, 543, 596, 636
BseDI	CCNNGG	2 cut(s)	9, 374
BseGI	GGATG	1 cut(s)	79
BseLI	CCNNNNNNNGG	2 cut(s)	427, 595
BseMI	GCAATG	1 cut(s)	727
BseMII	CTCAG	7 cut(s)	225, 297, 486, 495, 540, 690, 756
BseNI	ACTGG	1 cut(s)	447
BseRI	GAGGAG	1 cut(s)	6
Bsh1285I	CGRYCG	1 cut(s)	40
BshFI	GGCC	1 cut(s)	232
BshNI	GGYRCC	1 cut(s)	417
BsiEI	CGRYCG	1 cut(s)	40
BsiHKCI	CYCGRG	1 cut(s)	588
BslI	CCNNNNNNNGG	2 cut(s)	427, 595
BsmAI	GTCTC	2 cut(s)	304, 385
BsnI	GGCC	1 cut(s)	232
BsoBI	CYCGRG	1 cut(s)	588
Bsp143I	GATC	5 cut(s)	37, 127, 256, 638, 769
Bsp1720I	GCTNAGC	1 cut(s)	549
BspACI	CCGC	1 cut(s)	131
BspANI	GGCC	1 cut(s)	232
BspCNI	CTCAG	7 cut(s)	226, 298, 487, 496, 541, 691, 757
BspLI	GGNNCC	4 cut(s)	6, 15, 419, 771
BspMI	ACCTGC	1 cut(s)	582
BspPI	GGATC	5 cut(s)	122, 264, 646, 764, 777
BspT107I	GGYRCC	1 cut(s)	417
BsrDI	GCAATG	1 cut(s)	727
BsrI	ACTGG	1 cut(s)	447
BssECI	CCNNGG	2 cut(s)	9, 374
BssMI	GATC	5 cut(s)	37, 127, 256, 638, 769
BssNI	GRCGYC	1 cut(s)	418
Bst2UI	CCWGG	4 cut(s)	81, 543, 596, 636
Bst4CI	ACNGT	1 cut(s)	531
Bst6I	CTCTTC	1 cut(s)	636
BstACI	GRCGYC	1 cut(s)	418
BstC8I	GCNNGC	1 cut(s)	150
BstDEI	CTNAG	7 cut(s)	234, 306, 495, 504, 549, 699, 765
BstDSI	CCRYGG	1 cut(s)	9
BstEII	GGTNACC	1 cut(s)	83
BstF5I	GGATG	1 cut(s)	79
BstH2I	RGCGCY	1 cut(s)	421
BstHHI	GCGC	1 cut(s)	420
BstKTI	GATC	5 cut(s)	40, 130, 259, 641, 772
BstMAI	GTCTC	2 cut(s)	304, 385
BstMBI	GATC	5 cut(s)	37, 127, 256, 638, 769
BstMCI	CGRYCG	1 cut(s)	40
BstMWI	GCNNNNNNNGC	2 cut(s)	11, 500
BstNI	CCWGG	4 cut(s)	81, 543, 596, 636
BstPI	GGTNACC	1 cut(s)	83
BstSCI	CCNGG	4 cut(s)	79, 541, 594, 634
BstSFI	CTRYAG	1 cut(s)	780
BstX2I	RGATCY	2 cut(s)	256, 769
BstYI	RGATCY	2 cut(s)	256, 769
BsuRI	GGCC	1 cut(s)	232
BtgI	CCRYGG	1 cut(s)	9
BtsCI	GGATG	1 cut(s)	79
BveI	ACCTGC	1 cut(s)	582
Cac8I	GCNNGC	1 cut(s)	150
CaiI	CAGNNNCTG	1 cut(s)	305
CfoI	GCGC	1 cut(s)	420
Cfr13I	GGNCC	1 cut(s)	539
CseI	GACGC	1 cut(s)	71
Csp6I	GTAC	2 cut(s)	210, 566
CviAII	CATG	1 cut(s)	653
CviQI	GTAC	2 cut(s)	210, 566
DdeI	CTNAG	7 cut(s)	234, 306, 495, 504, 549, 699, 765
DinI	GGCGCC	1 cut(s)	419
DpnI	GATC	5 cut(s)	39, 129, 258, 640, 771
DpnII	GATC	5 cut(s)	37, 127, 256, 638, 769
Eam1104I	CTCTTC	1 cut(s)	636
EarI	CTCTTC	1 cut(s)	636
Eco47I	GGWCC	1 cut(s)	539
Eco57I	CTGAAG	1 cut(s)	293
Eco88I	CYCGRG	1 cut(s)	588
Eco91I	GGTNACC	1 cut(s)	83
EcoO109I	RGGNCCY	1 cut(s)	539
EcoO65I	GGTNACC	1 cut(s)	83
EcoRII	CCWGG	4 cut(s)	79, 541, 594, 634
EgeI	GGCGCC	1 cut(s)	419
EheI	GGCGCC	1 cut(s)	419
FaeI	CATG	1 cut(s)	656
FalI	AAGNNNNNCTT	2 cut(s)	279, 311
FatI	CATG	1 cut(s)	652
FokI	GGATG	1 cut(s)	86
FspBI	CTAG	3 cut(s)	452, 525, 558
GlaI	GCGC	1 cut(s)	419
GsuI	CTGGAG	2 cut(s)	464, 564
HaeII	RGCGCY	1 cut(s)	421
HaeIII	GGCC	1 cut(s)	232
HgaI	GACGC	1 cut(s)	71
HhaI	GCGC	1 cut(s)	420
Hin1I	GRCGYC	1 cut(s)	418
Hin1II	CATG	1 cut(s)	656
Hin6I	GCGC	1 cut(s)	418
HinP1I	GCGC	1 cut(s)	418
HincII	GTYRAC	1 cut(s)	61
HindII	GTYRAC	1 cut(s)	61
HindIII	AAGCTT	1 cut(s)	191
HinfI	GANTC	2 cut(s)	591, 661
HphI	GGTGA	1 cut(s)	154
Hpy166II	GTNNAC	1 cut(s)	61
Hpy188I	TCNGA	4 cut(s)	163, 301, 378, 470
Hpy188III	TCNNGA	4 cut(s)	41, 410, 588, 773
Hpy8I	GTNNAC	1 cut(s)	61
HpyAV	CCTTC	1 cut(s)	191
HpyCH4III	ACNGT	1 cut(s)	531
HpyCH4IV	ACGT	1 cut(s)	333
HpyCH4V	TGCA	3 cut(s)	316, 676, 710
HpyF10VI	GCNNNNNNNGC	2 cut(s)	11, 500
HpyF3I	CTNAG	7 cut(s)	234, 306, 495, 504, 549, 699, 765
HpySE526I	ACGT	1 cut(s)	333
Hsp92I	GRCGYC	1 cut(s)	418
Hsp92II	CATG	1 cut(s)	656
HspAI	GCGC	1 cut(s)	418
KasI	GGCGCC	1 cut(s)	417
Kzo9I	GATC	5 cut(s)	37, 127, 256, 638, 769
LmnI	GCTCC	4 cut(s)	10, 19, 282, 545
LweI	GCATC	3 cut(s)	115, 292, 330
MaeI	CTAG	3 cut(s)	452, 525, 558
MaeII	ACGT	1 cut(s)	333
MaeIII	GTNAC	3 cut(s)	41, 83, 121
MalI	GATC	5 cut(s)	39, 129, 258, 640, 771
MboI	GATC	5 cut(s)	37, 127, 256, 638, 769
MboII	GAAGA	2 cut(s)	349, 623
MfeI	CAATTG	1 cut(s)	54
MflI	RGATCY	2 cut(s)	256, 769
MluCI	AATT	2 cut(s)	54, 601
Mly113I	GGCGCC	1 cut(s)	418
MlyI	GAGTC	2 cut(s)	600, 670
MnlI	CCTC	9 cut(s)	27, 172, 384, 420, 439, 448, 673, 694, 760
MseI	TTAA	3 cut(s)	102, 252, 479
MspR9I	CCNGG	4 cut(s)	81, 543, 596, 636
MunI	CAATTG	1 cut(s)	54
MvaI	CCWGG	4 cut(s)	81, 543, 596, 636
MwoI	GCNNNNNNNGC	2 cut(s)	11, 500
NarI	GGCGCC	1 cut(s)	418
NdeII	GATC	5 cut(s)	37, 127, 256, 638, 769
NlaIII	CATG	1 cut(s)	656
NlaIV	GGNNCC	4 cut(s)	6, 15, 419, 771
NmuCI	GTSAC	1 cut(s)	41
PfoI	TCCNGGA	1 cut(s)	634
Ple19I	CGATCG	1 cut(s)	40
PleI	GAGTC	2 cut(s)	599, 669
PluTI	GGCGCC	1 cut(s)	421
PpsI	GAGTC	2 cut(s)	599, 669
PpuMI	RGGWCCY	1 cut(s)	539
PsiI	TTATAA	2 cut(s)	69, 758
Psp5II	RGGWCCY	1 cut(s)	539
Psp6I	CCWGG	4 cut(s)	79, 541, 594, 634
PspEI	GGTNACC	1 cut(s)	83
PspGI	CCWGG	4 cut(s)	79, 541, 594, 634
PspN4I	GGNNCC	4 cut(s)	6, 15, 419, 771
PspPI	GGNCC	1 cut(s)	539
PspPPI	RGGWCCY	1 cut(s)	539
PstNI	CAGNNNCTG	1 cut(s)	305
PsuI	RGATCY	2 cut(s)	256, 769
PvuI	CGATCG	1 cut(s)	40
RsaI	GTAC	2 cut(s)	211, 567
RsaNI	GTAC	2 cut(s)	210, 566
SaqAI	TTAA	3 cut(s)	102, 252, 479
Sau3AI	GATC	5 cut(s)	37, 127, 256, 638, 769
Sau96I	GGNCC	1 cut(s)	539
ScaI	AGTACT	1 cut(s)	211
SchI	GAGTC	2 cut(s)	600, 670
ScrFI	CCNGG	4 cut(s)	81, 543, 596, 636
SfaNI	GCATC	3 cut(s)	115, 292, 330
SfcI	CTRYAG	1 cut(s)	780
SfoI	GGCGCC	1 cut(s)	419
SinI	GGWCC	1 cut(s)	539
Sse9I	AATT	2 cut(s)	54, 601
SsiI	CCGC	1 cut(s)	131
SspDI	GGCGCC	1 cut(s)	417
SspMI	CTAG	3 cut(s)	452, 525, 558
StyD4I	CCNGG	4 cut(s)	79, 541, 594, 634
TaaI	ACNGT	1 cut(s)	531
TaiI	ACGT	1 cut(s)	336
TasI	AATT	2 cut(s)	54, 601
TatI	WGTACW	1 cut(s)	209
Tru1I	TTAA	3 cut(s)	102, 252, 479
Tru9I	TTAA	3 cut(s)	102, 252, 479
TseFI	GTSAC	1 cut(s)	41
Tsp45I	GTSAC	1 cut(s)	41
TspDTI	ATGAA	3 cut(s)	300, 497, 669
VpaK11BI	GGWCC	1 cut(s)	539
XapI	RAATTY	1 cut(s)	601
XspI	CTAG	3 cut(s)	452, 525, 558
ZrmI	AGTACT	1 cut(s)	211

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