Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1D

Orthogroup ID

OG0001350

Physical Location & Seq

Genomic Coordinates Forward (+)

16513279 .. 16517076

Gene Structure 3798 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1DG088500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 456 bp

ATGGGGATGAAGGGCACTGGGAAATGGACTGAAGGAGGAGAGGGAGAGCAAGAAGGAGGAGACTATCCAGGCCATAGATTGCACAAATGGAGTATTCCAGAAACAGCGGAAGTTGCAGTGTCTGTGGCTCATTTCCCTGCAAGTCAGGCAACCGAAACAGGCATAGCCAAGGCTCCACCTATCTCCGGAGCACCTAATTCAGGTCCCCTGAATATGTTTCCGCAGGAAGCACTGTCTGGTGCTGGTGTTGGTGCTGGTGCACTTGGATCCCTCGACTTCCTTAGAAACAATCATTTCCAAATGTTGCGCTCAATGTTACAAGCCAACCCACAAATTTTACAGCCCATGCTGCAGGAACTTGGAAAGCAAAACCCACAGCTTTTAAGATTAATTCAGGAGCACCATGTCGAGTTCCTTCAGTTAATAAATGAACCTCTTGAGGGTTCTGAAGGGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005737 GO:0031593 GO:0032182 GO:0043130 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044464 GO:0044877 GO:0070628 GO:0140030

KEGG Pathways

Metabolic & Signaling

ko03420 ko04141 map03420 map04141

Pfam Domains

Protein Families

UBA XPC-binding ubiquitin

Protein Analysis

151

Amino Acids

16.16

Weight (kDa)

5.27

Isoelectric Point (pI)

46.9

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
XPC-binding	PF09280	91 - 145	4.7e-19	XPC-binding domain

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

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0001350)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G16190 AT1G16190 AT1G79650 AT1G79650 AT1G79650 AT1G79650
fragaria_vesca	FvH4_6g28060
malus_domestica	MD09G1229800.v1.1 MD17G1228500.v1.1
prunus_persica	Prupe.3G105900_v2.0.a1
pyrus_communis	pycom09g14830 pycom17g23110
rosa_chinensis	RchiOBHm_Chr1g0327471 RchiOBHm_Chr2g0131831
rosa_laevigata	RLG00000019212 RLG00000021652 RLG00000030713
rosa_multiflora	Rmu_sc0002700.1_g000003 Rmu_sc0003731.1_g000013 Rmu_ssc0000213.1_g000013
rosa_roxburghii	Rroxscaffold_1G00054010 Rroxscaffold_2G00112590 Rroxscaffold_2G00127890 Rroxscaffold_4G00302760 Rroxscaffold_5G00338170 Rroxscaffold_5G00341450 Rroxscaffold_5G00371080 Rroxscaffold_6G00390940 Rroxscaffold_6G00420830 Rroxscaffold_7G00196290 Rroxscaffold_7G00209730
rosa_rugosa	Rorug02G0107700 Rorug02G0299900 Rorug02G0300000 Rorug02G0300100 Rorug02G0476100
rosa_samantha	Rh1AG084200 Rh1CG081900 Rh1CG257900 Rh1DG088500 Rh2AG352100 Rh2BG359300 Rh2CG337700 Rh2DG376600 Rh4BG187800 Rh5AG270100 Rh5CG354000 Rh5CG379700 Rh6AG057900 Rh7AG341300 Rh7CG359200
rosa_wichuraiana	Rw1G006620 Rw2G028620

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccIII	TCCGGA	1 cut(s)	185
AciI	CCGC	2 cut(s)	107, 221
AclWI	GGATC	2 cut(s)	261, 274
AcsI	RAATTY	1 cut(s)	333
AcuI	CTGAAG	2 cut(s)	51, 401
AfiI	CCNNNNNNNGG	3 cut(s)	185, 200, 440
AjnI	CCWGG	1 cut(s)	67
AluBI	AGCT	1 cut(s)	379
AluI	AGCT	1 cut(s)	379
Alw21I	GWGCWC	3 cut(s)	193, 262, 402
Alw26I	GTCTC	1 cut(s)	54
Alw44I	GTGCAC	1 cut(s)	258
AlwI	GGATC	2 cut(s)	261, 274
AlwNI	CAGNNNCTG	1 cut(s)	122
Aor13HI	TCCGGA	1 cut(s)	185
AoxI	GGCC	1 cut(s)	70
ApaLI	GTGCAC	1 cut(s)	258
ApeKI	GCWGC	1 cut(s)	349
ApoI	RAATTY	1 cut(s)	333
AseI	ATTAAT	1 cut(s)	389
AspLEI	GCGC	1 cut(s)	309
AspS9I	GGNCC	1 cut(s)	203
AvaII	GGWCC	1 cut(s)	203
BaeGI	GKGCMC	2 cut(s)	17, 262
BamHI	GGATCC	1 cut(s)	266
Bbv12I	GWGCWC	3 cut(s)	193, 262, 402
BbvI	GCAGC	1 cut(s)	336
BciT130I	CCWGG	1 cut(s)	69
BcoDI	GTCTC	1 cut(s)	54
BfmI	CTRYAG	1 cut(s)	350
BisI	GCNGC	1 cut(s)	350
BlsI	GCNGC	1 cut(s)	351
Bme1390I	CCNGG	1 cut(s)	69
Bme18I	GGWCC	1 cut(s)	203
BmgT120I	GGNCC	1 cut(s)	203
BmiI	GGNNCC	3 cut(s)	174, 205, 268
BmrFI	CCNGG	1 cut(s)	69
BmrI	ACTGGG	1 cut(s)	27
BmuI	ACTGGG	1 cut(s)	27
BsaJI	CCNNGG	1 cut(s)	168
BsaWI	WCCGGW	1 cut(s)	185
Bsc4I	CCNNNNNNNGG	3 cut(s)	185, 200, 440
Bse1I	ACTGG	1 cut(s)	22
BseAI	TCCGGA	1 cut(s)	185
BseBI	CCWGG	1 cut(s)	69
BseDI	CCNNGG	1 cut(s)	168
BseGI	GGATG	1 cut(s)	12
BseLI	CCNNNNNNNGG	3 cut(s)	185, 200, 440
BseNI	ACTGG	1 cut(s)	22
BseRI	GAGGAG	2 cut(s)	51, 72
BseSI	GKGCMC	2 cut(s)	17, 262
BseXI	GCAGC	1 cut(s)	336
BshFI	GGCC	1 cut(s)	72
BsiHKAI	GWGCWC	3 cut(s)	193, 262, 402
BsiSI	CCGG	1 cut(s)	186
BslFI	GGGAC	1 cut(s)	189
BslI	CCNNNNNNNGG	3 cut(s)	185, 200, 440
BsmAI	GTCTC	1 cut(s)	54
BsmFI	GGGAC	1 cut(s)	189
BsnI	GGCC	1 cut(s)	72
Bsp1286I	GDGCHC	4 cut(s)	17, 193, 262, 402
Bsp13I	TCCGGA	1 cut(s)	185
Bsp143I	GATC	1 cut(s)	266
BspACI	CCGC	2 cut(s)	107, 221
BspANI	GGCC	1 cut(s)	72
BspEI	TCCGGA	1 cut(s)	185
BspLI	GGNNCC	3 cut(s)	174, 205, 268
BspMAI	CTGCAG	1 cut(s)	354
BspPI	GGATC	2 cut(s)	261, 274
BsrI	ACTGG	1 cut(s)	22
BssECI	CCNNGG	1 cut(s)	168
BssMI	GATC	1 cut(s)	266
BssT1I	CCWWGG	1 cut(s)	168
Bst2UI	CCWGG	1 cut(s)	69
Bst4CI	ACNGT	1 cut(s)	234
BstDEI	CTNAG	1 cut(s)	281
BstENI	CCTNNNNNAGG	1 cut(s)	198
BstF5I	GGATG	1 cut(s)	12
BstHHI	GCGC	1 cut(s)	309
BstKTI	GATC	1 cut(s)	269
BstMAI	GTCTC	1 cut(s)	54
BstMBI	GATC	1 cut(s)	266
BstMWI	GCNNNNNNNGC	3 cut(s)	113, 146, 349
BstNI	CCWGG	1 cut(s)	69
BstSCI	CCNGG	1 cut(s)	67
BstSFI	CTRYAG	1 cut(s)	350
BstSLI	GKGCMC	2 cut(s)	17, 262
BstV1I	GCAGC	1 cut(s)	336
BstX2I	RGATCY	1 cut(s)	266
BstYI	RGATCY	1 cut(s)	266
BsuRI	GGCC	1 cut(s)	72
BtsCI	GGATG	1 cut(s)	12
BtsI	GCAGTG	1 cut(s)	123
BtsIMutI	CAGTG	3 cut(s)	15, 123, 230
CaiI	CAGNNNCTG	1 cut(s)	122
CfoI	GCGC	1 cut(s)	309
Cfr13I	GGNCC	1 cut(s)	203
CviAII	CATG	2 cut(s)	346, 404
CviJI	RGCY	7 cut(s)	72, 128, 167, 173, 323, 343, 379
CviKI_1	RGCY	7 cut(s)	72, 128, 167, 173, 323, 343, 379
DdeI	CTNAG	1 cut(s)	281
DpnI	GATC	1 cut(s)	268
DpnII	GATC	1 cut(s)	266
Eco130I	CCWWGG	1 cut(s)	168
Eco47I	GGWCC	1 cut(s)	203
Eco57I	CTGAAG	2 cut(s)	51, 401
EcoNI	CCTNNNNNAGG	1 cut(s)	198
EcoO109I	RGGNCCY	1 cut(s)	203
EcoRII	CCWGG	1 cut(s)	67
EcoT14I	CCWWGG	1 cut(s)	168
ErhI	CCWWGG	1 cut(s)	168
FaeI	CATG	2 cut(s)	349, 407
FaiI	YATR	5 cut(s)	75, 164, 215, 347, 405
FaqI	GGGAC	1 cut(s)	189
FatI	CATG	2 cut(s)	345, 403
Fnu4HI	GCNGC	1 cut(s)	350
FokI	GGATG	1 cut(s)	19
Fsp4HI	GCNGC	1 cut(s)	350
GlaI	GCGC	1 cut(s)	308
GluI	GCNGC	1 cut(s)	350
HaeIII	GGCC	1 cut(s)	72
HapII	CCGG	1 cut(s)	186
HhaI	GCGC	1 cut(s)	309
Hin1II	CATG	2 cut(s)	349, 407
Hin6I	GCGC	1 cut(s)	307
HinP1I	GCGC	1 cut(s)	307
HpaII	CCGG	1 cut(s)	186
Hpy166II	GTNNAC	1 cut(s)	260
Hpy188I	TCNGA	1 cut(s)	448
Hpy188III	TCNNGA	4 cut(s)	98, 186, 395, 437
Hpy8I	GTNNAC	1 cut(s)	260
HpyAV	CCTTC	5 cut(s)	4, 26, 47, 425, 443
HpyCH4III	ACNGT	1 cut(s)	234
HpyCH4V	TGCA	5 cut(s)	82, 116, 140, 260, 352
HpyF10VI	GCNNNNNNNGC	3 cut(s)	113, 146, 349
HpyF3I	CTNAG	1 cut(s)	281
Hsp92II	CATG	2 cut(s)	349, 407
HspAI	GCGC	1 cut(s)	307
Kpn2I	TCCGGA	1 cut(s)	185
Kzo9I	GATC	1 cut(s)	266
LmnI	GCTCC	3 cut(s)	178, 188, 397
Lsp1109I	GCAGC	1 cut(s)	336
MaeIII	GTNAC	1 cut(s)	315
MalI	GATC	1 cut(s)	268
MboI	GATC	1 cut(s)	266
MflI	RGATCY	1 cut(s)	266
MhlI	GDGCHC	4 cut(s)	17, 193, 262, 402
MluCI	AATT	3 cut(s)	196, 333, 390
MnlI	CCTC	6 cut(s)	29, 34, 50, 281, 433, 444
MroI	TCCGGA	1 cut(s)	185
MseI	TTAA	3 cut(s)	383, 389, 422
MspA1I	CMGCKG	1 cut(s)	107
MspI	CCGG	1 cut(s)	186
MspR9I	CCNGG	1 cut(s)	69
MvaI	CCWGG	1 cut(s)	69
MwoI	GCNNNNNNNGC	3 cut(s)	113, 146, 349
NdeII	GATC	1 cut(s)	266
NlaIII	CATG	2 cut(s)	349, 407
NlaIV	GGNNCC	3 cut(s)	174, 205, 268
PkrI	GCNGC	1 cut(s)	351
PpuMI	RGGWCCY	1 cut(s)	203
PshBI	ATTAAT	1 cut(s)	389
Psp5II	RGGWCCY	1 cut(s)	203
Psp6I	CCWGG	1 cut(s)	67
PspGI	CCWGG	1 cut(s)	67
PspN4I	GGNNCC	3 cut(s)	174, 205, 268
PspPI	GGNCC	1 cut(s)	203
PspPPI	RGGWCCY	1 cut(s)	203
PstI	CTGCAG	1 cut(s)	354
PstNI	CAGNNNCTG	1 cut(s)	122
PsuI	RGATCY	1 cut(s)	266
SaqAI	TTAA	3 cut(s)	383, 389, 422
SatI	GCNGC	1 cut(s)	350
Sau3AI	GATC	1 cut(s)	266
Sau96I	GGNCC	1 cut(s)	203
ScrFI	CCNGG	1 cut(s)	69
SduI	GDGCHC	4 cut(s)	17, 193, 262, 402
SetI	ASST	5 cut(s)	181, 196, 205, 381, 436
SfcI	CTRYAG	1 cut(s)	350
SinI	GGWCC	1 cut(s)	203
SmlI	CTYRAG	1 cut(s)	437
SmoI	CTYRAG	1 cut(s)	437
Sse9I	AATT	3 cut(s)	196, 333, 390
SsiI	CCGC	2 cut(s)	107, 221
StyD4I	CCNGG	1 cut(s)	67
StyI	CCWWGG	1 cut(s)	168
TaaI	ACNGT	1 cut(s)	234
TaqI	TCGA	2 cut(s)	273, 408
TasI	AATT	3 cut(s)	196, 333, 390
Tru1I	TTAA	3 cut(s)	383, 389, 422
Tru9I	TTAA	3 cut(s)	383, 389, 422
TscAI	CASTG	3 cut(s)	22, 123, 237
TseI	GCWGC	1 cut(s)	349
TspDTI	ATGAA	2 cut(s)	23, 444
TspRI	CASTG	3 cut(s)	22, 123, 237
VneI	GTGCAC	1 cut(s)	258
VpaK11BI	GGWCC	1 cut(s)	203
VspI	ATTAAT	1 cut(s)	389
XagI	CCTNNNNNAGG	1 cut(s)	198
XapI	RAATTY	1 cut(s)	333

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