Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4A

Orthogroup ID

OG0005126

Physical Location & Seq

Genomic Coordinates Reverse (-)

40962175 .. 40967440

Gene Structure 5266 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4AG161000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1080 bp

ATGAGCAAGTCTTCTGCAGGGGAAGGTTCATCCTCAAAAGCGAAAGCCGGACCCTCGCAGCCGGCCGAAACTTCATTTAAGCGCAAGCGTGGAGTCTTCCAAAAAGAATTGCAGCACATGATGTATGGTTTCGGAGATGATCCCAATCCTCTTCCGGAGAGTGTGGCTCTCATGGAGGACATAGTGGTTGAATACATTACAGATTTGGTACATAAAGCCCAAGATACTGGATCAAATAGGGGAAAGCTATCAGTGGAGGATTTTCTCTACCTAATCCGCAAGGGATGCGTTACCTCTGTTCCCAAACATTCTATTGATGTTGTCCCAATACAGATAGTGTGTCACAAGACCAGTGATGATAAGGACTTTAATGATGACAAGGTTTTCAGATGTTTATGGAGAAATGCTCAGCAAGTAATTGAATCTACAAAGTCCTGTCCGCCCAGTGCAATAAAATATCAGAATAACTTTTGTGTTTTCATACGTGAGGTTTTGAGAAACAGTTCTGACCTCTTGACAGATGATGAAAAGGATTTCATCGAGTCGTTTACTTCGATGTCAGATGATAGTCAGAGGCTATTTGTTCAGCTTTATACACGGAAAGAGACAGGGAATACATCTTGCTTTGAAACAAATAAACTATCCGATGATGATATTAAGGAGATTTTGGATTTGCTCACTGTATCTATTGGCATCACCTTTGCAGACTTTCTTTTAGAGATCGTCTCATTAAACTCTATACCACATCCATTACTACCTAGTATGGTTTTGCATAGAACAGGATCCTGTGTTAGGATATCTTCAAATGCAGAGTCCCTTATCTGGCGTGCTGAGGATCTCTCAGCATTTCTACTGGTGGATTTGGGAATAATCAAGTATCCAACTTACAAGTGCATAGCTTCAGAACAAATTTTCTCAGCTCGAGATGACTTGCTTGGCTATGAAGAGGTGTCCTTTTATCTCTATGCAAAAGTATTGATGCCCACGCTTGCCTTTACTATATCTAATGGTTTTGCTTTGCAGGCTATTGAAGTGGCACAAATAGTTGATGAAAGCAACACTGGATTCGTCTTAAAGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0000280 GO:0003674 GO:0003676 GO:0003677 GO:0003824 GO:0004518 GO:0004519 GO:0004520 GO:0004527 GO:0004536 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006139 GO:0006259 GO:0006281 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0006996 GO:0007049 GO:0007059 GO:0007127 GO:0007129 GO:0008150 GO:0008152 GO:0008409 GO:0009987 GO:0016043 GO:0016787 GO:0016788 GO:0016888 GO:0016893 GO:0017108 GO:0022402 GO:0022414 GO:0033554 GO:0034641 GO:0036297 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044237 GO:0044238 GO:0044260 GO:0044424 GO:0044464 GO:0045132 GO:0045143 GO:0046483 GO:0048256 GO:0048285 GO:0050896 GO:0051276 GO:0051321 GO:0051716 GO:0061982 GO:0070192 GO:0070336 GO:0071704 GO:0071840 GO:0090304 GO:0090305 GO:0097159 GO:0098813 GO:0140013 GO:0140097 GO:1901360 GO:1901363 GO:1903046

KEGG Pathways

Metabolic & Signaling

ko03460 map03460

Pfam Domains

Protein Families

HIRAN VRR_NUC

Protein Analysis

359

Amino Acids

40.19

Weight (kDa)

5.01

Isoelectric Point (pI)

38.61

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TFIID-18kDa	PF02269	32 - 94	1.5e-19	Transcription initiation factor IID, 18kD subunit
FAN1_HTH	PF21315	153 - 222	8.4e-08	FAN1, HTH domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

Font Size (px)

Line Width

Align Labels (Cladogram)

Image

Tree File

Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready

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

Orthologous Genes (Group: OG0005126)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G02680
fragaria_vesca	FvH4_5g39500 FvH4_6g14960
malus_domestica	MD02G1287100.v1.1 MD02G1287200.v1.1
prunus_persica	Prupe.2G036200_v2.0.a1
pyrus_communis	pycom02g24340
rosa_chinensis	RchiOBHm_Chr4g0410491 RchiOBHm_Chr7g0241821
rosa_laevigata	RLG00000000541 RLG00000008420
rosa_multiflora	Rmu_co8297743.1_g000001 Rmu_sc0001865.1_g000010 Rmu_sc0007471.1_g000001 Rmu_sc0016181.1_g000002
rosa_roxburghii	Rroxscaffold_3G00218640 Rroxscaffold_5G00355320
rosa_rugosa	Rorug04G0114100 Rorug07G0347400 Rorug07G0347500
rosa_samantha	Rh4AG161000 Rh4BG160600 Rh4CG173300 Rh4DG156600 Rh7AG501800 Rh7BG473200 Rh7CG518300 Rh7DG487100
rosa_wichuraiana	Rw4G013450 Rw7G042420

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccIII	TCCGGA	1 cut(s)	154
AciI	CCGC	2 cut(s)	277, 440
AclWI	GGATC	5 cut(s)	134, 238, 777, 790, 843
AcoI	YGGCCR	1 cut(s)	63
AcsI	RAATTY	1 cut(s)	909
AcuI	CTGAAG	1 cut(s)	885
AfaI	GTAC	1 cut(s)	210
AfiI	CCNNNNNNNGG	2 cut(s)	792, 822
AgsI	TTSAA	5 cut(s)	191, 422, 629, 804, 1031
AluBI	AGCT	4 cut(s)	247, 589, 899, 920
AluI	AGCT	4 cut(s)	247, 589, 899, 920
Alw26I	GTCTC	2 cut(s)	599, 730
AlwI	GGATC	5 cut(s)	134, 238, 777, 790, 843
Ama87I	CYCGRG	1 cut(s)	921
Aor13HI	TCCGGA	1 cut(s)	154
AoxI	GGCC	1 cut(s)	63
ApeKI	GCWGC	2 cut(s)	58, 112
ApoI	RAATTY	1 cut(s)	909
ArsI	GACNNNNNNTTYG	2 cut(s)	797, 829
Asp700I	GAANNNNTTC	1 cut(s)	502
AspLEI	GCGC	1 cut(s)	84
AspS9I	GGNCC	1 cut(s)	50
AsuHPI	GGTGA	1 cut(s)	688
AvaI	CYCGRG	1 cut(s)	921
AvaII	GGWCC	1 cut(s)	50
BamHI	GGATCC	1 cut(s)	782
BbsI	GAAGAC	2 cut(s)	3, 88
BbvCI	CCTCAGC	1 cut(s)	831
BbvI	GCAGC	2 cut(s)	70, 124
BciVI	GTATCC	1 cut(s)	888
BcoDI	GTCTC	2 cut(s)	599, 730
BfaI	CTAG	1 cut(s)	759
BfmI	CTRYAG	1 cut(s)	15
BfuI	GTATCC	1 cut(s)	888
BisI	GCNGC	2 cut(s)	59, 113
BlpI	GCTNAGC	1 cut(s)	408
BlsI	GCNGC	2 cut(s)	60, 114
Bme18I	GGWCC	1 cut(s)	50
BmeT110I	CYCGRG	1 cut(s)	921
BmgT120I	GGNCC	1 cut(s)	50
BmiI	GGNNCC	2 cut(s)	52, 784
BmrI	ACTGGG	1 cut(s)	438
BmsI	GCATC	3 cut(s)	275, 702, 969
BmuI	ACTGGG	1 cut(s)	438
BpiI	GAAGAC	2 cut(s)	3, 88
BplI	GAGNNNNNCTC	8 cut(s)	151, 183, 391, 423, 710, 742, 824, 856
Bpu10I	CCTNAGC	1 cut(s)	831
Bpu1102I	GCTNAGC	1 cut(s)	408
BsaAI	YACGTR	1 cut(s)	485
BsaBI	GATNNNNATC	1 cut(s)	144
BsaWI	WCCGGW	1 cut(s)	154
Bsc4I	CCNNNNNNNGG	2 cut(s)	792, 822
Bse118I	RCCGGY	1 cut(s)	61
Bse1I	ACTGG	5 cut(s)	232, 351, 444, 858, 1066
Bse8I	GATNNNNATC	1 cut(s)	144
BseAI	TCCGGA	1 cut(s)	154
BseGI	GGATG	3 cut(s)	29, 290, 745
BseJI	GATNNNNATC	1 cut(s)	144
BseLI	CCNNNNNNNGG	2 cut(s)	792, 822
BseMII	CTCAG	4 cut(s)	422, 822, 855, 930
BseNI	ACTGG	5 cut(s)	232, 351, 444, 858, 1066
BseX3I	CGGCCG	1 cut(s)	63
BseXI	GCAGC	2 cut(s)	70, 124
Bsh1285I	CGRYCG	1 cut(s)	66
BshFI	GGCC	1 cut(s)	65
BsiEI	CGRYCG	1 cut(s)	66
BsiHKCI	CYCGRG	1 cut(s)	921
BsiSI	CCGG	3 cut(s)	48, 62, 155
BslFI	GGGAC	2 cut(s)	308, 799
BslI	CCNNNNNNNGG	2 cut(s)	792, 822
BsmAI	GTCTC	2 cut(s)	599, 730
BsmBI	CGTCTC	1 cut(s)	730
BsmFI	GGGAC	2 cut(s)	308, 799
BsnI	GGCC	1 cut(s)	65
BsoBI	CYCGRG	1 cut(s)	921
Bsp13I	TCCGGA	1 cut(s)	154
Bsp143I	GATC	5 cut(s)	139, 230, 720, 782, 835
Bsp1720I	GCTNAGC	1 cut(s)	408
BspACI	CCGC	2 cut(s)	277, 440
BspANI	GGCC	1 cut(s)	65
BspCNI	CTCAG	4 cut(s)	421, 823, 854, 929
BspEI	TCCGGA	1 cut(s)	154
BspLI	GGNNCC	2 cut(s)	52, 784
BspMAI	CTGCAG	1 cut(s)	19
BspPI	GGATC	5 cut(s)	134, 238, 777, 790, 843
BsrFI	RCCGGY	1 cut(s)	61
BsrI	ACTGG	5 cut(s)	232, 351, 444, 858, 1066
BssAI	RCCGGY	1 cut(s)	61
BssMI	GATC	5 cut(s)	139, 230, 720, 782, 835
Bst4CI	ACNGT	2 cut(s)	503, 682
Bst6I	CTCTTC	2 cut(s)	156, 939
BstAPI	GCANNNNNTGC	1 cut(s)	285
BstBAI	YACGTR	1 cut(s)	485
BstC8I	GCNNGC	5 cut(s)	63, 86, 828, 990, 1023
BstDEI	CTNAG	4 cut(s)	408, 831, 841, 916
BstENI	CCTNNNNNAGG	1 cut(s)	790
BstF5I	GGATG	3 cut(s)	29, 290, 745
BstHHI	GCGC	1 cut(s)	84
BstKTI	GATC	5 cut(s)	142, 233, 723, 785, 838
BstMAI	GTCTC	2 cut(s)	599, 730
BstMBI	GATC	5 cut(s)	139, 230, 720, 782, 835
BstMCI	CGRYCG	1 cut(s)	66
BstMWI	GCNNNNNNNGC	2 cut(s)	285, 1022
BstSFI	CTRYAG	1 cut(s)	15
BstV1I	GCAGC	2 cut(s)	70, 124
BstV2I	GAAGAC	2 cut(s)	3, 88
BstX2I	RGATCY	2 cut(s)	782, 835
BstXI	CCANNNNNNTGG	1 cut(s)	227
BstYI	RGATCY	2 cut(s)	782, 835
BstZI	CGGCCG	1 cut(s)	63
BsuI	GTATCC	1 cut(s)	888
BsuRI	GGCC	1 cut(s)	65
BtsCI	GGATG	3 cut(s)	29, 290, 745
BtsIMutI	CAGTG	5 cut(s)	258, 358, 451, 678, 1059
Cac8I	GCNNGC	5 cut(s)	63, 86, 828, 990, 1023
CfoI	GCGC	1 cut(s)	84
Cfr10I	RCCGGY	1 cut(s)	61
Cfr13I	GGNCC	1 cut(s)	50
Csp6I	GTAC	1 cut(s)	209
CviAII	CATG	2 cut(s)	118, 172
CviQI	GTAC	1 cut(s)	209
DdeI	CTNAG	4 cut(s)	408, 831, 841, 916
DpnI	GATC	5 cut(s)	141, 232, 722, 784, 837
DpnII	GATC	5 cut(s)	139, 230, 720, 782, 835
EaeI	YGGCCR	1 cut(s)	63
EagI	CGGCCG	1 cut(s)	63
Eam1104I	CTCTTC	2 cut(s)	156, 939
EarI	CTCTTC	2 cut(s)	156, 939
EciI	GGCGGA	1 cut(s)	429
EclXI	CGGCCG	1 cut(s)	63
Eco32I	GATATC	1 cut(s)	798
Eco47I	GGWCC	1 cut(s)	50
Eco52I	CGGCCG	1 cut(s)	63
Eco57I	CTGAAG	1 cut(s)	885
Eco88I	CYCGRG	1 cut(s)	921
EcoNI	CCTNNNNNAGG	1 cut(s)	790
EcoRV	GATATC	1 cut(s)	798
Esp3I	CGTCTC	1 cut(s)	730
FaeI	CATG	2 cut(s)	121, 175
FaqI	GGGAC	2 cut(s)	308, 799
FatI	CATG	2 cut(s)	117, 171
Fnu4HI	GCNGC	2 cut(s)	59, 113
FokI	GGATG	3 cut(s)	16, 297, 732
Fsp4HI	GCNGC	2 cut(s)	59, 113
FspBI	CTAG	1 cut(s)	759
GlaI	GCGC	1 cut(s)	83
GluI	GCNGC	2 cut(s)	59, 113
HaeIII	GGCC	1 cut(s)	65
HapII	CCGG	3 cut(s)	48, 62, 155
HhaI	GCGC	1 cut(s)	84
Hin1II	CATG	2 cut(s)	121, 175
Hin6I	GCGC	1 cut(s)	82
HinP1I	GCGC	1 cut(s)	82
HinfI	GANTC	5 cut(s)	93, 422, 542, 812, 1065
HpaII	CCGG	3 cut(s)	48, 62, 155
HphI	GGTGA	1 cut(s)	688
Hpy166II	GTNNAC	1 cut(s)	549
Hpy188I	TCNGA	8 cut(s)	134, 389, 462, 508, 562, 573, 646, 904
Hpy188III	TCNNGA	3 cut(s)	155, 514, 923
Hpy8I	GTNNAC	1 cut(s)	549
HpyAV	CCTTC	1 cut(s)	17
HpyCH4III	ACNGT	2 cut(s)	503, 682
HpyCH4IV	ACGT	1 cut(s)	484
HpyCH4V	TGCA	9 cut(s)	17, 112, 449, 704, 772, 809, 894, 968, 1021
HpyF10VI	GCNNNNNNNGC	2 cut(s)	285, 1022
HpyF3I	CTNAG	4 cut(s)	408, 831, 841, 916
HpySE526I	ACGT	1 cut(s)	484
Hsp92II	CATG	2 cut(s)	121, 175
HspAI	GCGC	1 cut(s)	82
Kpn2I	TCCGGA	1 cut(s)	154
KroI	GCCGGC	1 cut(s)	61
KroNI	GCCGGC	1 cut(s)	63
Kzo9I	GATC	5 cut(s)	139, 230, 720, 782, 835
Lsp1109I	GCAGC	2 cut(s)	70, 124
LweI	GCATC	3 cut(s)	275, 702, 969
MaeI	CTAG	1 cut(s)	759
MaeII	ACGT	1 cut(s)	484
MaeIII	GTNAC	2 cut(s)	289, 341
MalI	GATC	5 cut(s)	141, 232, 722, 784, 837
MboI	GATC	5 cut(s)	139, 230, 720, 782, 835
MboII	GAAGA	5 cut(s)	3, 88, 143, 792, 956
MflI	RGATCY	2 cut(s)	782, 835
MluCI	AATT	3 cut(s)	107, 417, 909
MlyI	GAGTC	3 cut(s)	102, 551, 821
MmeI	TCCRAC	1 cut(s)	905
MroI	TCCGGA	1 cut(s)	154
MroNI	GCCGGC	1 cut(s)	61
MroXI	GAANNNNTTC	1 cut(s)	502
MseI	TTAA	5 cut(s)	78, 369, 657, 731, 1073
MspI	CCGG	3 cut(s)	48, 62, 155
MwoI	GCNNNNNNNGC	2 cut(s)	285, 1022
NaeI	GCCGGC	1 cut(s)	63
NdeII	GATC	5 cut(s)	139, 230, 720, 782, 835
NgoMIV	GCCGGC	1 cut(s)	61
NlaIII	CATG	2 cut(s)	121, 175
NlaIV	GGNNCC	2 cut(s)	52, 784
NmuCI	GTSAC	1 cut(s)	341
PaeR7I	CTCGAG	1 cut(s)	921
PcsI	WCGNNNNNNNCGW	1 cut(s)	551
PdiI	GCCGGC	1 cut(s)	63
PdmI	GAANNNNTTC	1 cut(s)	502
PfeI	GAWTC	2 cut(s)	422, 1065
PkrI	GCNGC	2 cut(s)	60, 114
PleI	GAGTC	3 cut(s)	101, 550, 820
PpsI	GAGTC	3 cut(s)	101, 550, 820
Ppu21I	YACGTR	1 cut(s)	485
PspN4I	GGNNCC	2 cut(s)	52, 784
PspPI	GGNCC	1 cut(s)	50
PstI	CTGCAG	1 cut(s)	19
PsuI	RGATCY	2 cut(s)	782, 835
RsaI	GTAC	1 cut(s)	210
RsaNI	GTAC	1 cut(s)	209
SaqAI	TTAA	5 cut(s)	78, 369, 657, 731, 1073
SatI	GCNGC	2 cut(s)	59, 113
Sau3AI	GATC	5 cut(s)	139, 230, 720, 782, 835
Sau96I	GGNCC	1 cut(s)	50
SchI	GAGTC	3 cut(s)	102, 551, 821
SfaNI	GCATC	3 cut(s)	275, 702, 969
SfcI	CTRYAG	1 cut(s)	15
Sfr274I	CTCGAG	1 cut(s)	921
SinI	GGWCC	1 cut(s)	50
SlaI	CTCGAG	1 cut(s)	921
SmlI	CTYRAG	1 cut(s)	921
SmoI	CTYRAG	1 cut(s)	921
Sse9I	AATT	3 cut(s)	107, 417, 909
SsiI	CCGC	2 cut(s)	277, 440
SspMI	CTAG	1 cut(s)	759
TaaI	ACNGT	2 cut(s)	503, 682
TaiI	ACGT	1 cut(s)	487
TaqI	TCGA	3 cut(s)	540, 554, 922
TasI	AATT	3 cut(s)	107, 417, 909
TfiI	GAWTC	2 cut(s)	422, 1065
Tru1I	TTAA	5 cut(s)	78, 369, 657, 731, 1073
Tru9I	TTAA	5 cut(s)	78, 369, 657, 731, 1073
TscAI	CASTG	5 cut(s)	258, 358, 451, 685, 1066
TseFI	GTSAC	1 cut(s)	341
TseI	GCWGC	2 cut(s)	58, 112
Tsp45I	GTSAC	1 cut(s)	341
TspDTI	ATGAA	7 cut(s)	18, 63, 469, 526, 540, 957, 1065
TspGWI	ACGGA	1 cut(s)	613
TspRI	CASTG	5 cut(s)	258, 358, 451, 685, 1066
VpaK11BI	GGWCC	1 cut(s)	50
XagI	CCTNNNNNAGG	1 cut(s)	790
XapI	RAATTY	1 cut(s)	909
XhoI	CTCGAG	1 cut(s)	921
XmnI	GAANNNNTTC	1 cut(s)	502
XspI	CTAG	1 cut(s)	759

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