Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3D

Orthogroup ID

OG0007908

Physical Location & Seq

Genomic Coordinates Reverse (-)

24604621 .. 24606934

Gene Structure 2314 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3DG250000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 816 bp

ATGGAGCTTGCTCTCAGCTTAGGCGATGCTCCAAAGCAGTTTCTCTTCCTTGACAAAACCCCAAGCATGGGTAGCAACAAGGATCTAGGGTTTTGCATGGCCCTAGGAAGCAGGGAAAGCCGTGAAGGTTATGATCAAGAAGATGAGAGTAGTCGAAGAAGAAGAAGGGTTTCATCAGATCCACCTATTCAGCTCAATCTCTTGCCTTCTGCCCCGGTTATGAAGACTTCTTCTCAGCTTCGCTTCCCCTGGCTCACTGATAACTTGGCAGTGTCCGAACCGGCCGGTCTAGATGAACCAGGAAAGGGGCTGGATGTAAATCGGTTCCCCTTGGTGGCGGGTACGGCCGATGAGGCAGAAGACGCTGCGGCGCAGCTCTCTTCTCCGAACAGCACCGTGTCGTCGTTCCAGATGGATTTCGGTGTTAGGAGAAGCAAGAGAGACTTGGATTTGGAGGTGCTCGAGACGGAGAGAGCGAGTTCAAGAGCGAGTGACGACGACGAGAACGGGTCGACTCGGAAGAAACTCAGGCTCTCCAAGGACCAATCGGCTTTTCTTGAAGAGAGCTTCAAAGAACACAGCACCTTAAATCCCAAGCAAAAAATAGCTCTGGCAAAACAGTTAAATCTTCGTCCCCGCCAAGTGGAAGTGTGGTTTCAGAATCGAAGAGCAAGGTATTTTTATTTTCCTTACTCCATTTGTATTTATTTTCATTGTTTAAATAAATCTAAGAAAACCGATTACTGTTGTATTAATATTCGGGGCACTGTTCATATGTACAAATGGAATTATTTTGTTGCTTGTATTGTTTGGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003700 GO:0006355 GO:0008150 GO:0009889 GO:0010468 GO:0010556 GO:0019219 GO:0019222 GO:0031323 GO:0031326 GO:0050789 GO:0050794 GO:0051171 GO:0051252 GO:0060255 GO:0065007 GO:0080090 GO:0140110 GO:1903506 GO:2000112 GO:2001141

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

HALZ HD-ZIP_N Homeobox

Protein Analysis

271

Amino Acids

30.9

Weight (kDa)

8.46

Isoelectric Point (pI)

63.61

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
HD-ZIP_N	PF04618	27 - 147	6.8e-08	HD-ZIP protein N terminus
Homeodomain	PF00046	173 - 225	2.4e-15	Homeodomain

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

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

Orthologous Genes (Group: OG0007908)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G06710 AT5G06710 AT5G06710 AT5G06710
fragaria_vesca	FvH4_6g22050
malus_domestica	MD01G1069700.v1.1 MD12G1055800.v1.1 MD14G1056200.v1.1 MD14G1056300.v1.1
prunus_persica	Prupe.7G079300_v2.0.a1 Prupe.7G079300_v2.0.a1
pyrus_communis	pycom12g04870 pycom14g04600
rosa_chinensis	RchiOBHm_Chr3g0479361
rosa_laevigata	RLG00000023581
rosa_multiflora	Rmu_sc0006763.1_g000001 Rmu_sc0033237.1_g000001
rosa_roxburghii	Rroxscaffold_6G00402380
rosa_rugosa	Rorug03G0174600
rosa_samantha	Rh3AG225900 Rh3BG258600 Rh3CG254200 Rh3DG250000
rosa_wichuraiana	Rw3G020170

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	512
AciI	CCGC	3 cut(s)	338, 368, 637
AclWI	GGATC	2 cut(s)	90, 173
AcoI	YGGCCR	2 cut(s)	282, 345
AfaI	GTAC	2 cut(s)	343, 779
AfiI	CCNNNNNNNGG	5 cut(s)	67, 68, 305, 334, 643
AgsI	TTSAA	3 cut(s)	483, 560, 571
AjnI	CCWGG	2 cut(s)	248, 298
AjuI	GAANNNNNNNTTGG	2 cut(s)	537, 569
AluBI	AGCT	7 cut(s)	7, 18, 193, 238, 376, 567, 608
AluI	AGCT	7 cut(s)	7, 18, 193, 238, 376, 567, 608
Alw21I	GWGCWC	1 cut(s)	462
Alw26I	GTCTC	2 cut(s)	435, 458
AlwI	GGATC	2 cut(s)	90, 173
Ama87I	CYCGRG	1 cut(s)	461
AoxI	GGCC	3 cut(s)	99, 282, 345
ApeKI	GCWGC	2 cut(s)	365, 373
AseI	ATTAAT	1 cut(s)	753
Asp700I	GAANNNNTTC	1 cut(s)	169
AspA2I	CCTAGG	1 cut(s)	103
AspLEI	GCGC	1 cut(s)	373
AspS9I	GGNCC	2 cut(s)	100, 541
AsuC2I	CCSGG	1 cut(s)	215
AvaI	CYCGRG	1 cut(s)	461
AvaII	GGWCC	1 cut(s)	541
AvrII	CCTAGG	1 cut(s)	103
BaeGI	GKGCMC	1 cut(s)	767
BbsI	GAAGAC	2 cut(s)	230, 366
Bbv12I	GWGCWC	1 cut(s)	462
BbvI	GCAGC	2 cut(s)	352, 385
BccI	CCATC	1 cut(s)	406
BceAI	ACGGC	2 cut(s)	105, 360
BciT130I	CCWGG	2 cut(s)	250, 300
BclI	TGATCA	1 cut(s)	133
BcnI	CCSGG	1 cut(s)	215
BcoDI	GTCTC	2 cut(s)	435, 458
BfaI	CTAG	3 cut(s)	86, 104, 290
BglI	GCCNNNNNGGC	1 cut(s)	353
BisI	GCNGC	3 cut(s)	366, 369, 374
BlnI	CCTAGG	1 cut(s)	103
BlsI	GCNGC	3 cut(s)	367, 370, 375
Bme1390I	CCNGG	3 cut(s)	215, 250, 300
Bme18I	GGWCC	1 cut(s)	541
BmeT110I	CYCGRG	1 cut(s)	461
BmgT120I	GGNCC	2 cut(s)	100, 541
BmiI	GGNNCC	1 cut(s)	326
BmrFI	CCNGG	3 cut(s)	215, 250, 300
BmsI	GCATC	1 cut(s)	16
BpiI	GAAGAC	2 cut(s)	230, 366
Bpu10I	CCTNAGC	1 cut(s)	19
BpuMI	CCSGG	1 cut(s)	215
BsaBI	GATNNNNATC	1 cut(s)	318
BsaJI	CCNNGG	5 cut(s)	103, 213, 248, 330, 537
Bsc4I	CCNNNNNNNGG	5 cut(s)	67, 68, 305, 334, 643
Bse118I	RCCGGY	2 cut(s)	280, 284
Bse8I	GATNNNNATC	1 cut(s)	318
BseBI	CCWGG	2 cut(s)	250, 300
BseDI	CCNNGG	5 cut(s)	103, 213, 248, 330, 537
BseGI	GGATG	1 cut(s)	319
BseJI	GATNNNNATC	1 cut(s)	318
BseLI	CCNNNNNNNGG	5 cut(s)	67, 68, 305, 334, 643
BseMII	CTCAG	3 cut(s)	28, 248, 541
BseSI	GKGCMC	1 cut(s)	767
BseX3I	CGGCCG	2 cut(s)	282, 345
BseXI	GCAGC	2 cut(s)	352, 385
Bsh1285I	CGRYCG	2 cut(s)	285, 348
BshFI	GGCC	3 cut(s)	101, 284, 347
BsiEI	CGRYCG	2 cut(s)	285, 348
BsiHKAI	GWGCWC	1 cut(s)	462
BsiHKCI	CYCGRG	1 cut(s)	461
BsiSI	CCGG	3 cut(s)	215, 281, 285
BslFI	GGGAC	1 cut(s)	618
BslI	CCNNNNNNNGG	5 cut(s)	67, 68, 305, 334, 643
BsmAI	GTCTC	2 cut(s)	435, 458
BsmBI	CGTCTC	1 cut(s)	458
BsmFI	GGGAC	1 cut(s)	618
BsnI	GGCC	3 cut(s)	101, 284, 347
BsoBI	CYCGRG	1 cut(s)	461
Bsp1286I	GDGCHC	2 cut(s)	462, 767
Bsp1407I	TGTACA	1 cut(s)	777
Bsp143I	GATC	3 cut(s)	82, 133, 178
BspACI	CCGC	3 cut(s)	338, 368, 637
BspANI	GGCC	3 cut(s)	101, 284, 347
BspCNI	CTCAG	3 cut(s)	27, 247, 540
BspLI	GGNNCC	1 cut(s)	326
BspPI	GGATC	2 cut(s)	90, 173
BspQI	GCTCTTC	1 cut(s)	661
BsrFI	RCCGGY	2 cut(s)	280, 284
BsrGI	TGTACA	1 cut(s)	777
BssAI	RCCGGY	2 cut(s)	280, 284
BssECI	CCNNGG	5 cut(s)	103, 213, 248, 330, 537
BssMI	GATC	3 cut(s)	82, 133, 178
BssT1I	CCWWGG	3 cut(s)	103, 330, 537
Bst2UI	CCWGG	2 cut(s)	250, 300
Bst4CI	ACNGT	4 cut(s)	397, 621, 746, 769
Bst6I	CTCTTC	4 cut(s)	50, 385, 555, 661
BstAUI	TGTACA	1 cut(s)	777
BstC8I	GCNNGC	1 cut(s)	9
BstDEI	CTNAG	5 cut(s)	14, 19, 234, 527, 729
BstF5I	GGATG	1 cut(s)	319
BstHHI	GCGC	1 cut(s)	373
BstKTI	GATC	3 cut(s)	85, 136, 181
BstMAI	GTCTC	2 cut(s)	435, 458
BstMBI	GATC	3 cut(s)	82, 133, 178
BstMCI	CGRYCG	2 cut(s)	285, 348
BstMWI	GCNNNNNNNGC	5 cut(s)	72, 117, 344, 353, 362
BstNI	CCWGG	2 cut(s)	250, 300
BstSCI	CCNGG	3 cut(s)	213, 248, 298
BstSLI	GKGCMC	1 cut(s)	767
BstV1I	GCAGC	2 cut(s)	352, 385
BstV2I	GAAGAC	2 cut(s)	230, 366
BstX2I	RGATCY	2 cut(s)	82, 178
BstYI	RGATCY	2 cut(s)	82, 178
BstZI	CGGCCG	2 cut(s)	282, 345
BsuRI	GGCC	3 cut(s)	101, 284, 347
BtgZI	GCGATG	1 cut(s)	39
BtsCI	GGATG	1 cut(s)	319
BtsI	GCAGTG	1 cut(s)	276
BtsIMutI	CAGTG	3 cut(s)	255, 276, 765
Cac8I	GCNNGC	1 cut(s)	9
CfoI	GCGC	1 cut(s)	373
Cfr10I	RCCGGY	2 cut(s)	280, 284
Cfr13I	GGNCC	2 cut(s)	100, 541
CseI	GACGC	1 cut(s)	371
Csp6I	GTAC	2 cut(s)	342, 778
CviAII	CATG	2 cut(s)	67, 97
CviQI	GTAC	2 cut(s)	342, 778
DdeI	CTNAG	5 cut(s)	14, 19, 234, 527, 729
DpnI	GATC	3 cut(s)	84, 135, 180
DpnII	GATC	3 cut(s)	82, 133, 178
DraI	TTTAAA	1 cut(s)	720
EaeI	YGGCCR	2 cut(s)	282, 345
EagI	CGGCCG	2 cut(s)	282, 345
Eam1104I	CTCTTC	4 cut(s)	50, 385, 555, 661
EarI	CTCTTC	4 cut(s)	50, 385, 555, 661
EclXI	CGGCCG	2 cut(s)	282, 345
Eco130I	CCWWGG	3 cut(s)	103, 330, 537
Eco47I	GGWCC	1 cut(s)	541
Eco52I	CGGCCG	2 cut(s)	282, 345
Eco88I	CYCGRG	1 cut(s)	461
EcoRII	CCWGG	2 cut(s)	248, 298
EcoT14I	CCWWGG	3 cut(s)	103, 330, 537
ErhI	CCWWGG	3 cut(s)	103, 330, 537
Esp3I	CGTCTC	1 cut(s)	458
FaeI	CATG	2 cut(s)	70, 100
FaiI	YATR	6 cut(s)	68, 98, 132, 221, 774, 776
FalI	AAGNNNNNCTT	2 cut(s)	428, 460
FaqI	GGGAC	1 cut(s)	618
FatI	CATG	2 cut(s)	66, 96
FauI	CCCGC	2 cut(s)	331, 644
FauNDI	CATATG	1 cut(s)	774
FbaI	TGATCA	1 cut(s)	133
FblI	GTMKAC	1 cut(s)	512
Fnu4HI	GCNGC	3 cut(s)	366, 369, 374
FokI	GGATG	1 cut(s)	326
Fsp4HI	GCNGC	3 cut(s)	366, 369, 374
FspBI	CTAG	3 cut(s)	86, 104, 290
GlaI	GCGC	1 cut(s)	372
GluI	GCNGC	3 cut(s)	366, 369, 374
HaeIII	GGCC	3 cut(s)	101, 284, 347
HapII	CCGG	3 cut(s)	215, 281, 285
HgaI	GACGC	1 cut(s)	371
HhaI	GCGC	1 cut(s)	373
Hin1II	CATG	2 cut(s)	70, 100
Hin6I	GCGC	1 cut(s)	371
HinP1I	GCGC	1 cut(s)	371
HincII	GTYRAC	1 cut(s)	513
HindII	GTYRAC	1 cut(s)	513
HinfI	GANTC	2 cut(s)	514, 661
HpaII	CCGG	3 cut(s)	215, 281, 285
Hpy166II	GTNNAC	1 cut(s)	513
Hpy188I	TCNGA	5 cut(s)	178, 277, 387, 519, 660
Hpy188III	TCNNGA	6 cut(s)	137, 290, 409, 463, 483, 557
Hpy8I	GTNNAC	1 cut(s)	513
Hpy99I	CGWCG	3 cut(s)	406, 500, 503
HpyAV	CCTTC	3 cut(s)	119, 159, 216
HpyCH4III	ACNGT	4 cut(s)	397, 621, 746, 769
HpyCH4V	TGCA	1 cut(s)	96
HpyF10VI	GCNNNNNNNGC	5 cut(s)	72, 117, 344, 353, 362
HpyF3I	CTNAG	5 cut(s)	14, 19, 234, 527, 729
Hsp92II	CATG	2 cut(s)	70, 100
HspAI	GCGC	1 cut(s)	371
Ksp22I	TGATCA	1 cut(s)	133
Kzo9I	GATC	3 cut(s)	82, 133, 178
LguI	GCTCTTC	1 cut(s)	661
LmnI	GCTCC	2 cut(s)	4, 34
Lsp1109I	GCAGC	2 cut(s)	352, 385
LweI	GCATC	1 cut(s)	16
MaeI	CTAG	3 cut(s)	86, 104, 290
MaeIII	GTNAC	1 cut(s)	491
MalI	GATC	3 cut(s)	84, 135, 180
MboI	GATC	3 cut(s)	82, 133, 178
MflI	RGATCY	2 cut(s)	82, 178
MhlI	GDGCHC	2 cut(s)	462, 767
MluCI	AATT	1 cut(s)	787
MlyI	GAGTC	1 cut(s)	508
MnlI	CCTC	2 cut(s)	346, 448
MroXI	GAANNNNTTC	1 cut(s)	169
MseI	TTAA	4 cut(s)	587, 623, 719, 753
MspI	CCGG	3 cut(s)	215, 281, 285
MspR9I	CCNGG	3 cut(s)	215, 250, 300
MvaI	CCWGG	2 cut(s)	250, 300
MwoI	GCNNNNNNNGC	5 cut(s)	72, 117, 344, 353, 362
NciI	CCSGG	1 cut(s)	215
NdeI	CATATG	1 cut(s)	774
NdeII	GATC	3 cut(s)	82, 133, 178
NlaIII	CATG	2 cut(s)	70, 100
NlaIV	GGNNCC	1 cut(s)	326
NmuCI	GTSAC	1 cut(s)	491
PaeR7I	CTCGAG	1 cut(s)	461
PciSI	GCTCTTC	1 cut(s)	661
PcsI	WCGNNNNNNNCGW	1 cut(s)	473
PdmI	GAANNNNTTC	1 cut(s)	169
PfeI	GAWTC	1 cut(s)	661
PkrI	GCNGC	3 cut(s)	367, 370, 375
PleI	GAGTC	1 cut(s)	508
PpsI	GAGTC	1 cut(s)	508
PshBI	ATTAAT	1 cut(s)	753
Psp6I	CCWGG	2 cut(s)	248, 298
PspGI	CCWGG	2 cut(s)	248, 298
PspN4I	GGNNCC	1 cut(s)	326
PspPI	GGNCC	2 cut(s)	100, 541
PsuI	RGATCY	2 cut(s)	82, 178
RsaI	GTAC	2 cut(s)	343, 779
RsaNI	GTAC	2 cut(s)	342, 778
SalI	GTCGAC	1 cut(s)	511
SapI	GCTCTTC	1 cut(s)	661
SaqAI	TTAA	4 cut(s)	587, 623, 719, 753
SatI	GCNGC	3 cut(s)	366, 369, 374
Sau3AI	GATC	3 cut(s)	82, 133, 178
Sau96I	GGNCC	2 cut(s)	100, 541
SchI	GAGTC	1 cut(s)	508
ScrFI	CCNGG	3 cut(s)	215, 250, 300
SduI	GDGCHC	2 cut(s)	462, 767
SfaNI	GCATC	1 cut(s)	16
Sfr274I	CTCGAG	1 cut(s)	461
SinI	GGWCC	1 cut(s)	541
SlaI	CTCGAG	1 cut(s)	461
SmlI	CTYRAG	1 cut(s)	461
SmoI	CTYRAG	1 cut(s)	461
Sse9I	AATT	1 cut(s)	787
SsiI	CCGC	3 cut(s)	338, 368, 637
SspI	AATATT	1 cut(s)	757
SspMI	CTAG	3 cut(s)	86, 104, 290
StyD4I	CCNGG	3 cut(s)	213, 248, 298
StyI	CCWWGG	3 cut(s)	103, 330, 537
TaaI	ACNGT	4 cut(s)	397, 621, 746, 769
TaqI	TCGA	4 cut(s)	154, 462, 512, 664
TasI	AATT	1 cut(s)	787
TatI	WGTACW	1 cut(s)	777
TauI	GCSGC	1 cut(s)	371
TfiI	GAWTC	1 cut(s)	661
Tru1I	TTAA	4 cut(s)	587, 623, 719, 753
Tru9I	TTAA	4 cut(s)	587, 623, 719, 753
TscAI	CASTG	3 cut(s)	262, 276, 772
TseFI	GTSAC	1 cut(s)	491
TseI	GCWGC	2 cut(s)	365, 373
Tsp45I	GTSAC	1 cut(s)	491
TspDTI	ATGAA	5 cut(s)	162, 236, 309, 701, 761
TspGWI	ACGGA	1 cut(s)	482
TspRI	CASTG	3 cut(s)	262, 276, 772
VpaK11BI	GGWCC	1 cut(s)	541
VspI	ATTAAT	1 cut(s)	753
XbaI	TCTAGA	1 cut(s)	289
XhoI	CTCGAG	1 cut(s)	461
XmaJI	CCTAGG	1 cut(s)	103
XmiI	GTMKAC	1 cut(s)	512
XmnI	GAANNNNTTC	1 cut(s)	169
XspI	CTAG	3 cut(s)	86, 104, 290

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