Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4D

Orthogroup ID

OG0012829

Physical Location & Seq

Genomic Coordinates Forward (+)

59960356 .. 59963414

Gene Structure 3059 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4DG382100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 915 bp

ATGACTGGGAATGGGATGGCTTTTTTCCAAGCAAATTTCATGCTACAATCTCCTCACCATGAAGATCATCATGACCACCAACAGCCTCCCACTTCTCTGAATCCATTACTTCCTTCCTGCACACCTCAAGACTTTCATGGTGTTGCATCGTTCCTAGGGAAGCGGTCAATGTCATTTTCCGGGATTGAGTTGGGCACTGAAGAGGGTCATGGGGAAGATGATTTATCTGATGATGGGTCACAGGCCGGAGGGGAGAAGAAGAGGAGGCTAAACATGGAGCAAGTGAAGACACTTGAGAAGAACTTTGAGTTGGGGAACAAGCTTGAGCCTGAGAGGAAAATGCAGCTGGCTAGAGCTCTTGGTCTGCAGCCAAGACAGATTGCCATTTGGTTTCAGAACAGAAGAGCAAGGTGGAAGACAAAGCAGTTGGAGAAAGACTATGATATTCTCAAGAGACAGTTTGATGCTATCAAAGCTGACAATGAATCCCTCCAAGCTCAAAACCAAAAACTTCATGCAGAGATACAGGCACTAAAAAATAGAGAACCAGCAGAATCTATCAACCTGAATATAAAAGAGACAGAGGGTTCTTGCAGCAATAGAAGTGAAAACAACTCTGCAGAAATCAAGTTGGACATTTCAAGAACTCCTCCAGCTATTGACAGCCCTCTATCCTCTCATCAAAATCCAATTATTACAAGCAGATCCCTCTTTCCTACCTCTGCTGCTACTACTATAAGGCCTTCTGGAATACAACAACTCTTTCATCAAAACCCATCATCAAGGCCTGAGCTACTCCAATGCTCTCAGAAGATTGACCACATAGTCAAAGAAGAAAGCTTGAGCAACATGTTCTGTGGCATTGATGATCAGTCTGGGTTTTGGCCATGGTTGGAACAACACCAATTCAATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0001101 GO:0003006 GO:0003674 GO:0003676 GO:0003677 GO:0003700 GO:0005488 GO:0006355 GO:0007275 GO:0008150 GO:0009653 GO:0009719 GO:0009725 GO:0009739 GO:0009743 GO:0009744 GO:0009790 GO:0009791 GO:0009793 GO:0009889 GO:0009965 GO:0010016 GO:0010033 GO:0010154 GO:0010468 GO:0010556 GO:0019219 GO:0019222 GO:0022414 GO:0022622 GO:0031323 GO:0031326 GO:0032501 GO:0032502 GO:0033993 GO:0034285 GO:0042221 GO:0043565 GO:0048316 GO:0048364 GO:0048366 GO:0048367 GO:0048598 GO:0048608 GO:0048731 GO:0048825 GO:0048826 GO:0048827 GO:0048856 GO:0050789 GO:0050794 GO:0050896 GO:0051171 GO:0051252 GO:0060255 GO:0061458 GO:0065007 GO:0080022 GO:0080090 GO:0090698 GO:0097159 GO:0099402 GO:0140110 GO:1901363 GO:1901700 GO:1903506 GO:1905392 GO:2000112 GO:2001141

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

HALZ Homeobox

Protein Analysis

304

Amino Acids

34.45

Weight (kDa)

6.07

Isoelectric Point (pI)

66.56

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Homeodomain	PF00046	86 - 139	1.1e-15	Homeodomain
HALZ	PF02183	141 - 182	3.7e-18	Homeobox associated leucine zipper

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Align Labels (Cladogram)

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Publication-ready

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Orthologous Genes (Group: OG0012829)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G69780
fragaria_vesca	FvH4_4g31640
malus_domestica	MD13G1074800.v1.1 MD16G1076000.v1.1
prunus_persica	Prupe.1G271400_v2.0.a1 Prupe.1G271400_v2.0.a1
pyrus_communis	pycom13g06660 pycom16g06590
rosa_chinensis	RchiOBHm_Chr4g0440141
rosa_laevigata	RLG00000006202
rosa_multiflora	Rmu_sc0001685.1_g000019
rosa_roxburghii	Rroxscaffold_5G00381070
rosa_rugosa	Rorug04G0324700
rosa_samantha	Rh4AG375500 Rh4BG387900 Rh4CG402500 Rh4DG382100
rosa_wichuraiana	Rw4G032130

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AasI	GACNNNNNNGTC	1 cut(s)	824
AciI	CCGC	1 cut(s)	163
AclWI	GGATC	1 cut(s)	699
AcoI	YGGCCR	1 cut(s)	884
AcsI	RAATTY	1 cut(s)	34
AcuI	CTGAAG	1 cut(s)	219
AflIII	ACRYGT	1 cut(s)	849
AgsI	TTSAA	2 cut(s)	642, 910
AjuI	GAANNNNNNNTTGG	2 cut(s)	293, 325
AluBI	AGCT	8 cut(s)	322, 346, 356, 476, 497, 656, 793, 840
AluI	AGCT	8 cut(s)	322, 346, 356, 476, 497, 656, 793, 840
Alw21I	GWGCWC	1 cut(s)	358
Alw26I	GTCTC	2 cut(s)	448, 572
AlwI	GGATC	1 cut(s)	699
AoxI	GGCC	4 cut(s)	243, 740, 785, 884
ApeKI	GCWGC	4 cut(s)	343, 367, 594, 725
ApoI	RAATTY	1 cut(s)	34
AspA2I	CCTAGG	1 cut(s)	154
AsuC2I	CCSGG	1 cut(s)	181
AsuHPI	GGTGA	1 cut(s)	47
AvrII	CCTAGG	1 cut(s)	154
BaeGI	GKGCMC	1 cut(s)	197
BalI	TGGCCA	1 cut(s)	886
BanII	GRGCYC	1 cut(s)	358
BbsI	GAAGAC	2 cut(s)	293, 422
Bbv12I	GWGCWC	1 cut(s)	358
BbvI	GCAGC	4 cut(s)	355, 379, 606, 712
BccI	CCATC	3 cut(s)	10, 227, 784
BclI	TGATCA	1 cut(s)	868
BcnI	CCSGG	1 cut(s)	181
BcoDI	GTCTC	2 cut(s)	448, 572
BfaI	CTAG	2 cut(s)	155, 351
BfmI	CTRYAG	2 cut(s)	365, 618
BisI	GCNGC	4 cut(s)	344, 368, 595, 726
BlnI	CCTAGG	1 cut(s)	154
BlsI	GCNGC	4 cut(s)	345, 369, 596, 727
Bme1390I	CCNGG	1 cut(s)	181
BmrFI	CCNGG	1 cut(s)	181
BmrI	ACTGGG	1 cut(s)	15
BmsI	GCATC	2 cut(s)	155, 454
BmuI	ACTGGG	1 cut(s)	15
BpiI	GAAGAC	2 cut(s)	293, 422
BpmI	CTGGAG	1 cut(s)	636
Bpu10I	CCTNAGC	1 cut(s)	789
BpuEI	CTTGAG	5 cut(s)	111, 314, 344, 434, 862
BpuMI	CCSGG	1 cut(s)	181
BsaJI	CCNNGG	2 cut(s)	154, 887
Bse1I	ACTGG	1 cut(s)	10
BseDI	CCNNGG	2 cut(s)	154, 887
BseGI	GGATG	1 cut(s)	21
BseMII	CTCAG	3 cut(s)	321, 780, 821
BseNI	ACTGG	1 cut(s)	10
BseRI	GAGGAG	3 cut(s)	42, 277, 639
BseSI	GKGCMC	1 cut(s)	197
BseXI	GCAGC	4 cut(s)	355, 379, 606, 712
BsgI	GTGCAG	1 cut(s)	103
BshFI	GGCC	4 cut(s)	245, 742, 787, 886
BsiHKAI	GWGCWC	1 cut(s)	358
BsiSI	CCGG	2 cut(s)	180, 246
BsmAI	GTCTC	2 cut(s)	448, 572
BsnI	GGCC	4 cut(s)	245, 742, 787, 886
Bsp1286I	GDGCHC	2 cut(s)	197, 358
Bsp143I	GATC	3 cut(s)	64, 704, 868
Bsp19I	CCATGG	1 cut(s)	887
BspACI	CCGC	1 cut(s)	163
BspANI	GGCC	4 cut(s)	245, 742, 787, 886
BspCNI	CTCAG	3 cut(s)	322, 781, 820
BspHI	TCATGA	1 cut(s)	70
BspMAI	CTGCAG	2 cut(s)	369, 622
BspPI	GGATC	1 cut(s)	699
BspQI	GCTCTTC	1 cut(s)	397
BsrI	ACTGG	1 cut(s)	10
BssECI	CCNNGG	2 cut(s)	154, 887
BssMI	GATC	3 cut(s)	64, 704, 868
BssT1I	CCWWGG	2 cut(s)	154, 887
Bst4CI	ACNGT	1 cut(s)	459
Bst6I	CTCTTC	3 cut(s)	195, 254, 397
BstC8I	GCNNGC	1 cut(s)	348
BstDEI	CTNAG	3 cut(s)	330, 789, 807
BstDSI	CCRYGG	1 cut(s)	887
BstF5I	GGATG	1 cut(s)	21
BstKTI	GATC	3 cut(s)	67, 707, 871
BstMAI	GTCTC	2 cut(s)	448, 572
BstMBI	GATC	3 cut(s)	64, 704, 868
BstMWI	GCNNNNNNNGC	1 cut(s)	473
BstNSI	RCATGY	1 cut(s)	853
BstSCI	CCNGG	1 cut(s)	179
BstSFI	CTRYAG	2 cut(s)	365, 618
BstSLI	GKGCMC	1 cut(s)	197
BstV1I	GCAGC	4 cut(s)	355, 379, 606, 712
BstV2I	GAAGAC	2 cut(s)	293, 422
BstX2I	RGATCY	1 cut(s)	704
BstYI	RGATCY	1 cut(s)	704
BsuRI	GGCC	4 cut(s)	245, 742, 787, 886
BtgI	CCRYGG	1 cut(s)	887
BtsCI	GGATG	1 cut(s)	21
BtsIMutI	CAGTG	1 cut(s)	195
Cac8I	GCNNGC	1 cut(s)	348
CciI	TCATGA	1 cut(s)	70
CviAII	CATG	9 cut(s)	40, 59, 71, 137, 209, 274, 515, 850, 888
DdeI	CTNAG	3 cut(s)	330, 789, 807
DpnI	GATC	3 cut(s)	66, 706, 870
DpnII	GATC	3 cut(s)	64, 704, 868
DrdI	GACNNNNNNGTC	1 cut(s)	824
DseDI	GACNNNNNNGTC	1 cut(s)	824
EaeI	YGGCCR	1 cut(s)	884
Eam1104I	CTCTTC	3 cut(s)	195, 254, 397
EarI	CTCTTC	3 cut(s)	195, 254, 397
Ecl136II	GAGCTC	1 cut(s)	356
Eco130I	CCWWGG	2 cut(s)	154, 887
Eco147I	AGGCCT	2 cut(s)	742, 787
Eco24I	GRGCYC	1 cut(s)	358
Eco53kI	GAGCTC	1 cut(s)	356
Eco57I	CTGAAG	1 cut(s)	219
EcoICRI	GAGCTC	1 cut(s)	356
EcoT14I	CCWWGG	2 cut(s)	154, 887
EcoT38I	GRGCYC	1 cut(s)	358
ErhI	CCWWGG	2 cut(s)	154, 887
FaeI	CATG	9 cut(s)	43, 62, 74, 140, 212, 277, 518, 853, 891
FatI	CATG	9 cut(s)	39, 58, 70, 136, 208, 273, 514, 849, 887
FbaI	TGATCA	1 cut(s)	868
Fnu4HI	GCNGC	4 cut(s)	344, 368, 595, 726
FokI	GGATG	1 cut(s)	28
FriOI	GRGCYC	1 cut(s)	358
Fsp4HI	GCNGC	4 cut(s)	344, 368, 595, 726
FspBI	CTAG	2 cut(s)	155, 351
GluI	GCNGC	4 cut(s)	344, 368, 595, 726
GsuI	CTGGAG	1 cut(s)	636
HaeIII	GGCC	4 cut(s)	245, 742, 787, 886
HapII	CCGG	2 cut(s)	180, 246
Hin1II	CATG	9 cut(s)	43, 62, 74, 140, 212, 277, 518, 853, 891
HindIII	AAGCTT	2 cut(s)	320, 838
HinfI	GANTC	3 cut(s)	100, 485, 554
HpaII	CCGG	2 cut(s)	180, 246
HphI	GGTGA	1 cut(s)	47
Hpy188I	TCNGA	4 cut(s)	99, 229, 396, 810
Hpy188III	TCNNGA	5 cut(s)	71, 128, 451, 642, 747
HpyAV	CCTTC	2 cut(s)	123, 753
HpyCH4III	ACNGT	1 cut(s)	459
HpyCH4V	TGCA	7 cut(s)	120, 146, 343, 367, 518, 594, 620
HpyF10VI	GCNNNNNNNGC	1 cut(s)	473
HpyF3I	CTNAG	3 cut(s)	330, 789, 807
Hsp92II	CATG	9 cut(s)	43, 62, 74, 140, 212, 277, 518, 853, 891
Ksp22I	TGATCA	1 cut(s)	868
Kzo9I	GATC	3 cut(s)	64, 704, 868
LguI	GCTCTTC	1 cut(s)	397
LmnI	GCTCC	1 cut(s)	277
Lsp1109I	GCAGC	4 cut(s)	355, 379, 606, 712
LweI	GCATC	2 cut(s)	155, 454
MaeI	CTAG	2 cut(s)	155, 351
MaeIII	GTNAC	1 cut(s)	237
MalI	GATC	3 cut(s)	66, 706, 870
MboI	GATC	3 cut(s)	64, 704, 868
MfeI	CAATTG	1 cut(s)	910
MflI	RGATCY	1 cut(s)	704
MhlI	GDGCHC	2 cut(s)	197, 358
MlsI	TGGCCA	1 cut(s)	886
MluCI	AATT	4 cut(s)	34, 690, 905, 910
MluNI	TGGCCA	1 cut(s)	886
MmeI	TCCRAC	3 cut(s)	408, 612, 873
Mox20I	TGGCCA	1 cut(s)	886
MscI	TGGCCA	1 cut(s)	886
Msp20I	TGGCCA	1 cut(s)	886
MspA1I	CMGCKG	1 cut(s)	346
MspI	CCGG	2 cut(s)	180, 246
MspR9I	CCNGG	1 cut(s)	181
MunI	CAATTG	1 cut(s)	910
MwoI	GCNNNNNNNGC	1 cut(s)	473
NciI	CCSGG	1 cut(s)	181
NcoI	CCATGG	1 cut(s)	887
NdeII	GATC	3 cut(s)	64, 704, 868
NlaIII	CATG	9 cut(s)	43, 62, 74, 140, 212, 277, 518, 853, 891
NmuCI	GTSAC	1 cut(s)	237
NspI	RCATGY	1 cut(s)	853
PagI	TCATGA	1 cut(s)	70
PceI	AGGCCT	2 cut(s)	742, 787
PciI	ACATGT	1 cut(s)	849
PciSI	GCTCTTC	1 cut(s)	397
PfeI	GAWTC	3 cut(s)	100, 485, 554
PfoI	TCCNGGA	1 cut(s)	179
PkrI	GCNGC	4 cut(s)	345, 369, 596, 727
PscI	ACATGT	1 cut(s)	849
Psp124BI	GAGCTC	1 cut(s)	358
PstI	CTGCAG	2 cut(s)	369, 622
PsuI	RGATCY	1 cut(s)	704
PvuII	CAGCTG	1 cut(s)	346
SacI	GAGCTC	1 cut(s)	358
SapI	GCTCTTC	1 cut(s)	397
SatI	GCNGC	4 cut(s)	344, 368, 595, 726
Sau3AI	GATC	3 cut(s)	64, 704, 868
ScrFI	CCNGG	1 cut(s)	181
SduI	GDGCHC	2 cut(s)	197, 358
SfaNI	GCATC	2 cut(s)	155, 454
SfcI	CTRYAG	2 cut(s)	365, 618
SmlI	CTYRAG	5 cut(s)	126, 293, 323, 449, 841
SmoI	CTYRAG	5 cut(s)	126, 293, 323, 449, 841
Sse9I	AATT	4 cut(s)	34, 690, 905, 910
SseBI	AGGCCT	2 cut(s)	742, 787
SsiI	CCGC	1 cut(s)	163
SspMI	CTAG	2 cut(s)	155, 351
SstI	GAGCTC	1 cut(s)	358
StuI	AGGCCT	2 cut(s)	742, 787
StyD4I	CCNGG	1 cut(s)	179
StyI	CCWWGG	2 cut(s)	154, 887
TaaI	ACNGT	1 cut(s)	459
TasI	AATT	4 cut(s)	34, 690, 905, 910
TfiI	GAWTC	3 cut(s)	100, 485, 554
TscAI	CASTG	1 cut(s)	202
TseFI	GTSAC	1 cut(s)	237
TseI	GCWGC	4 cut(s)	343, 367, 594, 725
Tsp45I	GTSAC	1 cut(s)	237
TspDTI	ATGAA	6 cut(s)	28, 75, 125, 498, 503, 755
TspRI	CASTG	1 cut(s)	202
XapI	RAATTY	1 cut(s)	34
XceI	RCATGY	1 cut(s)	853
XmaJI	CCTAGG	1 cut(s)	154
XspI	CTAG	2 cut(s)	155, 351

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