Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1D

Orthogroup ID

OG0007233

Physical Location & Seq

Genomic Coordinates Reverse (-)

3469127 .. 3473768

Gene Structure 4642 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1DG022600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 513 bp

ATGAACTTCACAGTTGTTAAGGCGGTTGCTACTCCAAATTCAGCCGTGGAATTACCATTGACTGCAGAAAATGTTGAAAGTGTATTAGATGAAATCCGGCCATATCTCATTTCTGATGGGGGGAATGTGGCATTACATGAAATTGATGGCAATATAGTGCGGTTAAAGCTACAAGGAGCATGTGGATCGTGTCCAAGTTCTGTTATGACAATGAAAATGGGTATTGAGCGACGTTTAATGGAAAAAATCCCTGAAATAGTTGCTGTGGAACCAATAGCAGATGAAGAAACAGGCCTTGAGCTGAATGAAGAAAATATAGAGAAGGTACTTGAAGAAATTAGACCCTACTTAGTAGGGGCAGCAGGTGGATCTCTAGAACTTGTGGCAATCGATGAGCCTATAGTCAAAGTCCGGATCACAGGTCCTGCTGCCGGGGTGATGACTGTTAGAGTTGCTGTCACACAGAAATTGCGTGAGAAAATCCCTACCATCGCAGCAGTTCAATTACTGTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0005198 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005886 GO:0006790 GO:0006950 GO:0006952 GO:0006996 GO:0008150 GO:0008152 GO:0009507 GO:0009532 GO:0009536 GO:0009570 GO:0009657 GO:0009658 GO:0009987 GO:0016020 GO:0016043 GO:0016226 GO:0022607 GO:0031163 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044085 GO:0044237 GO:0044422 GO:0044424 GO:0044434 GO:0044435 GO:0044444 GO:0044446 GO:0044464 GO:0050896 GO:0051186 GO:0071840 GO:0071944

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

NifU

Protein Analysis

170

Amino Acids

18.25

Weight (kDa)

4.71

Isoelectric Point (pI)

44.88

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
NifU	PF01106	25 - 90	1.3e-27	NifU-like domain
NifU	PF01106	106 - 167	2.6e-12	NifU-like domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0007233)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G49940 AT5G49940
fragaria_vesca	FvH4_7g01380 FvH4_7g01380 FvH4_7g01380 FvH4_7g01380 FvH4_7g01380
malus_domestica	MD08G1240400.v1.1 MD15G1433600.v1.1
prunus_persica	Prupe.1G577000_v2.0.a1
pyrus_communis	pycom08g20850 pycom15g38280
rosa_chinensis	RchiOBHm_Chr1g0317081
rosa_laevigata	RLG00000030628
rosa_multiflora	Rmu_co8218640.1_g000001 Rmu_sc0003689.1_g000019
rosa_roxburghii	Rroxscaffold_4G00330680
rosa_rugosa	Rorug01G0014300 Rorug01G0014400 Rorug01G0014500 Rorug01G0014600
rosa_samantha	Rh1AG025400 Rh1CG023800 Rh1DG022600
rosa_wichuraiana	Rw1G001770

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	353
Acc36I	ACCTGC	1 cut(s)	353
AccIII	TCCGGA	1 cut(s)	411
AciI	CCGC	2 cut(s)	23, 160
AclWI	GGATC	3 cut(s)	193, 376, 422
AcoI	YGGCCR	1 cut(s)	98
AcsI	RAATTY	1 cut(s)	37
AfaI	GTAC	1 cut(s)	327
AfiI	CCNNNNNNNGG	1 cut(s)	431
AgsI	TTSAA	3 cut(s)	77, 332, 503
AluBI	AGCT	2 cut(s)	169, 301
AluI	AGCT	2 cut(s)	169, 301
AlwI	GGATC	3 cut(s)	193, 376, 422
AlwNI	CAGNNNCTG	1 cut(s)	425
Aor13HI	TCCGGA	1 cut(s)	411
AoxI	GGCC	2 cut(s)	98, 292
ApeKI	GCWGC	3 cut(s)	359, 428, 494
ApoI	RAATTY	1 cut(s)	37
AspS9I	GGNCC	1 cut(s)	422
AsuC2I	CCSGG	1 cut(s)	433
AsuHPI	GGTGA	1 cut(s)	448
AvaII	GGWCC	1 cut(s)	422
BbvI	GCAGC	3 cut(s)	371, 415, 506
BccI	CCATC	3 cut(s)	110, 140, 497
BceAI	ACGGC	1 cut(s)	29
BcgI	CGANNNNNNTGC	2 cut(s)	168, 202
BcnI	CCSGG	1 cut(s)	433
BfaI	CTAG	1 cut(s)	374
BfmI	CTRYAG	2 cut(s)	63, 399
BfuAI	ACCTGC	1 cut(s)	353
BisI	GCNGC	3 cut(s)	360, 429, 495
BlsI	GCNGC	3 cut(s)	361, 430, 496
Bme1390I	CCNGG	1 cut(s)	433
Bme18I	GGWCC	1 cut(s)	422
BmgT120I	GGNCC	1 cut(s)	422
BmiI	GGNNCC	1 cut(s)	270
BmrFI	CCNGG	1 cut(s)	433
BpuEI	CTTGAG	1 cut(s)	317
BpuMI	CCSGG	1 cut(s)	433
Bsa29I	ATCGAT	1 cut(s)	390
BsaJI	CCNNGG	2 cut(s)	45, 432
BsaWI	WCCGGW	1 cut(s)	411
Bsc4I	CCNNNNNNNGG	1 cut(s)	431
BseAI	TCCGGA	1 cut(s)	411
BseCI	ATCGAT	1 cut(s)	390
BseDI	CCNNGG	2 cut(s)	45, 432
BseLI	CCNNNNNNNGG	1 cut(s)	431
BseXI	GCAGC	3 cut(s)	371, 415, 506
BshFI	GGCC	2 cut(s)	100, 294
BshVI	ATCGAT	1 cut(s)	390
BsiSI	CCGG	3 cut(s)	97, 412, 432
BslI	CCNNNNNNNGG	1 cut(s)	431
BsnI	GGCC	2 cut(s)	100, 294
Bsp13I	TCCGGA	1 cut(s)	411
Bsp143I	GATC	3 cut(s)	185, 368, 414
BspACI	CCGC	2 cut(s)	23, 160
BspANI	GGCC	2 cut(s)	100, 294
BspDI	ATCGAT	1 cut(s)	390
BspEI	TCCGGA	1 cut(s)	411
BspLI	GGNNCC	1 cut(s)	270
BspMAI	CTGCAG	1 cut(s)	67
BspMI	ACCTGC	1 cut(s)	353
BspPI	GGATC	3 cut(s)	193, 376, 422
BssECI	CCNNGG	2 cut(s)	45, 432
BssMI	GATC	3 cut(s)	185, 368, 414
Bst4CI	ACNGT	3 cut(s)	13, 445, 510
BstDEI	CTNAG	1 cut(s)	349
BstDSI	CCRYGG	1 cut(s)	45
BstKTI	GATC	3 cut(s)	188, 371, 417
BstMBI	GATC	3 cut(s)	185, 368, 414
BstMWI	GCNNNNNNNGC	1 cut(s)	166
BstNSI	RCATGY	1 cut(s)	183
BstSCI	CCNGG	1 cut(s)	431
BstSFI	CTRYAG	2 cut(s)	63, 399
BstV1I	GCAGC	3 cut(s)	371, 415, 506
BstX2I	RGATCY	1 cut(s)	368
BstYI	RGATCY	1 cut(s)	368
Bsu15I	ATCGAT	1 cut(s)	390
BsuRI	GGCC	2 cut(s)	100, 294
BsuTUI	ATCGAT	1 cut(s)	390
BtgI	CCRYGG	1 cut(s)	45
BtgZI	GCGATG	1 cut(s)	475
BveI	ACCTGC	1 cut(s)	353
CaiI	CAGNNNCTG	1 cut(s)	425
Cfr13I	GGNCC	1 cut(s)	422
ClaI	ATCGAT	1 cut(s)	390
Csp6I	GTAC	1 cut(s)	326
CviAII	CATG	2 cut(s)	137, 180
CviJI	RGCY	6 cut(s)	44, 100, 169, 294, 301, 397
CviKI_1	RGCY	6 cut(s)	44, 100, 169, 294, 301, 397
CviQI	GTAC	1 cut(s)	326
DdeI	CTNAG	1 cut(s)	349
DpnI	GATC	3 cut(s)	187, 370, 416
DpnII	GATC	3 cut(s)	185, 368, 414
EaeI	YGGCCR	1 cut(s)	98
Eco147I	AGGCCT	1 cut(s)	294
Eco47I	GGWCC	1 cut(s)	422
EcoO109I	RGGNCCY	1 cut(s)	422
FaeI	CATG	2 cut(s)	140, 183
FaiI	YATR	7 cut(s)	103, 138, 155, 181, 206, 317, 401
FatI	CATG	2 cut(s)	136, 179
Fnu4HI	GCNGC	3 cut(s)	360, 429, 495
Fsp4HI	GCNGC	3 cut(s)	360, 429, 495
FspBI	CTAG	1 cut(s)	374
GluI	GCNGC	3 cut(s)	360, 429, 495
HaeIII	GGCC	2 cut(s)	100, 294
HapII	CCGG	3 cut(s)	97, 412, 432
Hin1II	CATG	2 cut(s)	140, 183
HpaII	CCGG	3 cut(s)	97, 412, 432
HphI	GGTGA	1 cut(s)	448
Hpy188I	TCNGA	1 cut(s)	115
Hpy188III	TCNNGA	2 cut(s)	374, 412
Hpy99I	CGWCG	1 cut(s)	234
HpyAV	CCTTC	1 cut(s)	316
HpyCH4III	ACNGT	3 cut(s)	13, 445, 510
HpyCH4IV	ACGT	1 cut(s)	232
HpyCH4V	TGCA	1 cut(s)	65
HpyF10VI	GCNNNNNNNGC	1 cut(s)	166
HpyF3I	CTNAG	1 cut(s)	349
HpySE526I	ACGT	1 cut(s)	232
Hsp92II	CATG	2 cut(s)	140, 183
Kpn2I	TCCGGA	1 cut(s)	411
Kzo9I	GATC	3 cut(s)	185, 368, 414
LmnI	GCTCC	1 cut(s)	176
LpnPI	CCDG	8 cut(s)	110, 264, 276, 348, 405, 425, 438, 445
Lsp1109I	GCAGC	3 cut(s)	371, 415, 506
MaeI	CTAG	1 cut(s)	374
MaeII	ACGT	1 cut(s)	232
MaeIII	GTNAC	1 cut(s)	457
MalI	GATC	3 cut(s)	187, 370, 416
MboI	GATC	3 cut(s)	185, 368, 414
MboII	GAAGA	3 cut(s)	296, 320, 344
MflI	RGATCY	1 cut(s)	368
MluCI	AATT	6 cut(s)	37, 50, 141, 336, 467, 503
MroI	TCCGGA	1 cut(s)	411
MseI	TTAA	3 cut(s)	18, 164, 236
MspI	CCGG	3 cut(s)	97, 412, 432
MspR9I	CCNGG	1 cut(s)	433
MwoI	GCNNNNNNNGC	1 cut(s)	166
NciI	CCSGG	1 cut(s)	433
NdeII	GATC	3 cut(s)	185, 368, 414
NlaIII	CATG	2 cut(s)	140, 183
NlaIV	GGNNCC	1 cut(s)	270
NmuCI	GTSAC	1 cut(s)	457
NspI	RCATGY	1 cut(s)	183
PaqCI	CACCTGC	1 cut(s)	353
PceI	AGGCCT	1 cut(s)	294
PkrI	GCNGC	3 cut(s)	361, 430, 496
PpuMI	RGGWCCY	1 cut(s)	422
Psp5II	RGGWCCY	1 cut(s)	422
PspN4I	GGNNCC	1 cut(s)	270
PspPI	GGNCC	1 cut(s)	422
PspPPI	RGGWCCY	1 cut(s)	422
PstI	CTGCAG	1 cut(s)	67
PstNI	CAGNNNCTG	1 cut(s)	425
PsuI	RGATCY	1 cut(s)	368
RsaI	GTAC	1 cut(s)	327
RsaNI	GTAC	1 cut(s)	326
SaqAI	TTAA	3 cut(s)	18, 164, 236
SatI	GCNGC	3 cut(s)	360, 429, 495
Sau3AI	GATC	3 cut(s)	185, 368, 414
Sau96I	GGNCC	1 cut(s)	422
ScrFI	CCNGG	1 cut(s)	433
SetI	ASST	6 cut(s)	171, 235, 303, 327, 367, 424
SfcI	CTRYAG	2 cut(s)	63, 399
SinI	GGWCC	1 cut(s)	422
SmlI	CTYRAG	1 cut(s)	296
SmoI	CTYRAG	1 cut(s)	296
Sse9I	AATT	6 cut(s)	37, 50, 141, 336, 467, 503
SseBI	AGGCCT	1 cut(s)	294
SsiI	CCGC	2 cut(s)	23, 160
SspMI	CTAG	1 cut(s)	374
StuI	AGGCCT	1 cut(s)	294
StyD4I	CCNGG	1 cut(s)	431
TaaI	ACNGT	3 cut(s)	13, 445, 510
TaiI	ACGT	1 cut(s)	235
TaqI	TCGA	1 cut(s)	390
TasI	AATT	6 cut(s)	37, 50, 141, 336, 467, 503
Tru1I	TTAA	3 cut(s)	18, 164, 236
Tru9I	TTAA	3 cut(s)	18, 164, 236
TseFI	GTSAC	1 cut(s)	457
TseI	GCWGC	3 cut(s)	359, 428, 494
Tsp45I	GTSAC	1 cut(s)	457
TspDTI	ATGAA	6 cut(s)	17, 105, 153, 227, 297, 321
VpaK11BI	GGWCC	1 cut(s)	422
XapI	RAATTY	1 cut(s)	37
XbaI	TCTAGA	1 cut(s)	373
XceI	RCATGY	1 cut(s)	183
XspI	CTAG	1 cut(s)	374

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