Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0010004

Physical Location & Seq

Genomic Coordinates Reverse (-)

25568834 .. 25573140

Gene Structure 4307 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG227000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 975 bp

ATGGCTTTGCTATTCACATGTAATTGGTACACTGCGAACAAGTCGATGGATGATCGTGCCTTTTGCAATGCTGATGGAGATTTCTTGATAGTCCCCCAATTAGGAAGGCTCTGGATCACTACAGAATGTGGAAGATTGATAGTTTCTCCTGGTGAAGTTGCTGTATTACCTCAAGGATTTAGATTTGCAGTAGATCTTCCTGATGGCCCTTCACGAGGTTATGTAGCTGAGGTTTTTGGCACCCATTTTCAACTCCCTGATCTTGGGCCAATAGGAGCTAATGGCCTTGCTGCTCCAAGGGATTTTCTTGTTCCCACAGCATGGTTTGAAAAAACTACCCGTCCAGGCTACATCATTATACAAAAATTTGGTGGAGAACTTTTTACTGCAAAGCAGGATTTCTCTCCATTTAATGTAGTTGCTTGGCATGGTAATTATGCTCCATATAAGTATGATCTGACGAAGTTCTGCCCATTCAACACAGTCTTGTTTGATCATGGTGATCCTTCTGTAAATACAGTATTGACAGCACCAACTGATAAACCTGGTGTTGCATTGCTGGATTTTGCCATTTTCCCTCCTCGATGGTTGGTTGCTGAGCATACATTCCGACCTCCATACTACCATCGTAATTGTATGAGTGAATTTATGGGACTCATTTACGGTGGATATGAGGCAAAAGCAGATGGGTTTCTTCCAGGTGGTGCAAGCCTCCATAGCTGCATGACTCCTCATGGTCCTGATACGAAGACATATGAGGCTACCATTTCACGCGGAAATGATGTAGGACCACAAAAAATAAGTGATACTATGGCTTTTATGTTCGAATCGTGTTTAGTCCCCCGAATTTGCTCATGGGCTCTTGAGTCTCCCTTCATAGATCATGACTATTACCAGTGCTGGATCGGACTAAGATCACACTTCACAGGCACAGGGGCAGATGCTAAAGATGGAGATATCCAGAATGGTCAGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003824 GO:0004411 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005829 GO:0006082 GO:0006520 GO:0006570 GO:0006572 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009056 GO:0009063 GO:0009072 GO:0009074 GO:0009987 GO:0016054 GO:0016491 GO:0016701 GO:0016702 GO:0018958 GO:0019336 GO:0019439 GO:0019752 GO:0032787 GO:0043436 GO:0044237 GO:0044238 GO:0044248 GO:0044281 GO:0044282 GO:0044424 GO:0044444 GO:0044464 GO:0046395 GO:0051213 GO:0055114 GO:0071704 GO:0072329 GO:1901360 GO:1901361 GO:1901564 GO:1901565 GO:1901575 GO:1901605 GO:1901606 GO:1901615 GO:1901616 GO:1901999 GO:1902000

KEGG Pathways

Metabolic & Signaling

ko00350 ko00643 ko01100 ko01120 map00350 map00643 map01100 map01120

Pfam Domains

Protein Families

HgmA

Protein Analysis

324

Amino Acids

35.92

Weight (kDa)

5.3

Isoelectric Point (pI)

37.08

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
HgmA_N	PF20510	8 - 153	3.2e-71	Homogentisate 1,2-dioxygenase N-terminal
HgmA_C	PF04209	155 - 308	2.2e-76	Homogentisate 1,2-dioxygenase C-terminal

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)

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Tree File

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Publication-ready

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Orthologous Genes (Group: OG0010004)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G54080 AT5G54080
fragaria_vesca	FvH4_3g19020 FvH4_3g19020 FvH4_3g19020
malus_domestica	MD03G1237300.v1.1 MD03G1237500.v1.1
prunus_persica	Prupe.4G172100_v2.0.a1
pyrus_communis	pycom03g18320
rosa_chinensis	RchiOBHm_Chr5g0031821
rosa_laevigata	RLG00000033349
rosa_multiflora	Rmu_co8454513.1_g000001 Rmu_sc0006847.1_g000029
rosa_roxburghii	Rroxscaffold_1G00048450
rosa_rugosa	Rorug05G0127800 Rorug05G0127900
rosa_samantha	Rh5AG222100 Rh5BG222100 Rh5CG245400 Rh5DG227000
rosa_wichuraiana	Rw5G020250

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	239
AccB7I	CCANNNNNTGG	1 cut(s)	321
AccII	CGCG	1 cut(s)	774
AciI	CCGC	1 cut(s)	774
AclWI	GGATC	3 cut(s)	122, 497, 911
AcsI	RAATTY	3 cut(s)	365, 644, 846
AfaI	GTAC	1 cut(s)	29
AfiI	CCNNNNNNNGG	4 cut(s)	101, 215, 263, 321
AflIII	ACRYGT	1 cut(s)	17
AgsI	TTSAA	3 cut(s)	251, 329, 478
AjnI	CCWGG	4 cut(s)	148, 343, 544, 697
AluBI	AGCT	3 cut(s)	227, 278, 720
AluI	AGCT	3 cut(s)	227, 278, 720
Alw26I	GTCTC	1 cut(s)	873
AlwI	GGATC	3 cut(s)	122, 497, 911
AoxI	GGCC	3 cut(s)	205, 266, 283
ApeKI	GCWGC	2 cut(s)	290, 720
ApoI	RAATTY	3 cut(s)	365, 644, 846
AspS9I	GGNCC	4 cut(s)	206, 266, 737, 788
AsuHPI	GGTGA	2 cut(s)	164, 512
AsuII	TTCGAA	1 cut(s)	825
AvaII	GGWCC	2 cut(s)	737, 788
BanI	GGYRCC	1 cut(s)	239
BanII	GRGCYC	1 cut(s)	862
BauI	CACGAG	1 cut(s)	213
BbsI	GAAGAC	1 cut(s)	755
BbvCI	CCTCAGC	1 cut(s)	228
BbvI	GCAGC	2 cut(s)	277, 707
BccI	CCATC	7 cut(s)	40, 68, 197, 579, 633, 680, 944
BciT130I	CCWGG	4 cut(s)	150, 345, 546, 699
BclI	TGATCA	1 cut(s)	493
BcoDI	GTCTC	1 cut(s)	873
BfmI	CTRYAG	1 cut(s)	120
BglII	AGATCT	1 cut(s)	193
BisI	GCNGC	2 cut(s)	291, 721
BlpI	GCTNAGC	1 cut(s)	597
BlsI	GCNGC	2 cut(s)	292, 722
Bme1390I	CCNGG	4 cut(s)	150, 345, 546, 699
Bme18I	GGWCC	2 cut(s)	737, 788
BmgT120I	GGNCC	4 cut(s)	206, 266, 737, 788
BmiI	GGNNCC	1 cut(s)	241
BmrFI	CCNGG	4 cut(s)	150, 345, 546, 699
BmsI	GCATC	1 cut(s)	931
BpiI	GAAGAC	1 cut(s)	755
Bpu10I	CCTNAGC	1 cut(s)	228
Bpu1102I	GCTNAGC	1 cut(s)	597
Bpu14I	TTCGAA	1 cut(s)	825
BpuEI	CTTGAG	2 cut(s)	156, 884
BsaJI	CCNNGG	1 cut(s)	296
Bsc4I	CCNNNNNNNGG	4 cut(s)	101, 215, 263, 321
Bse1I	ACTGG	1 cut(s)	895
Bse3DI	GCAATG	2 cut(s)	73, 554
BseBI	CCWGG	4 cut(s)	150, 345, 546, 699
BseDI	CCNNGG	1 cut(s)	296
BseGI	GGATG	1 cut(s)	55
BseLI	CCNNNNNNNGG	4 cut(s)	101, 215, 263, 321
BseMI	GCAATG	2 cut(s)	73, 554
BseMII	CTCAG	2 cut(s)	219, 588
BseNI	ACTGG	1 cut(s)	895
BseRI	GAGGAG	2 cut(s)	570, 720
BseXI	GCAGC	2 cut(s)	277, 707
Bsh1236I	CGCG	1 cut(s)	774
BshFI	GGCC	3 cut(s)	207, 268, 285
BshNI	GGYRCC	1 cut(s)	239
BslFI	GGGAC	3 cut(s)	77, 666, 824
BslI	CCNNNNNNNGG	4 cut(s)	101, 215, 263, 321
BsmAI	GTCTC	1 cut(s)	873
BsmFI	GGGAC	3 cut(s)	77, 666, 824
BsnI	GGCC	3 cut(s)	207, 268, 285
Bsp119I	TTCGAA	1 cut(s)	825
Bsp1286I	GDGCHC	1 cut(s)	862
Bsp1720I	GCTNAGC	1 cut(s)	597
BspACI	CCGC	1 cut(s)	774
BspANI	GGCC	3 cut(s)	207, 268, 285
BspCNI	CTCAG	2 cut(s)	220, 589
BspFNI	CGCG	1 cut(s)	774
BspHI	TCATGA	1 cut(s)	883
BspLI	GGNNCC	1 cut(s)	241
BspPI	GGATC	3 cut(s)	122, 497, 911
BspT104I	TTCGAA	1 cut(s)	825
BspT107I	GGYRCC	1 cut(s)	239
BsrDI	GCAATG	2 cut(s)	73, 554
BsrI	ACTGG	1 cut(s)	895
BssECI	CCNNGG	1 cut(s)	296
BssSI	CACGAG	1 cut(s)	213
BssT1I	CCWWGG	1 cut(s)	296
Bst2BI	CACGAG	1 cut(s)	213
Bst2UI	CCWGG	4 cut(s)	150, 345, 546, 699
Bst4CI	ACNGT	3 cut(s)	484, 520, 665
BstBI	TTCGAA	1 cut(s)	825
BstC8I	GCNNGC	1 cut(s)	709
BstDEI	CTNAG	3 cut(s)	228, 597, 911
BstENI	CCTNNNNNAGG	1 cut(s)	213
BstF5I	GGATG	1 cut(s)	55
BstFNI	CGCG	1 cut(s)	774
BstMAI	GTCTC	1 cut(s)	873
BstMWI	GCNNNNNNNGC	1 cut(s)	717
BstNI	CCWGG	4 cut(s)	150, 345, 546, 699
BstNSI	RCATGY	1 cut(s)	21
BstSCI	CCNGG	4 cut(s)	148, 343, 544, 697
BstSFI	CTRYAG	1 cut(s)	120
BstUI	CGCG	1 cut(s)	774
BstV1I	GCAGC	2 cut(s)	277, 707
BstV2I	GAAGAC	1 cut(s)	755
BstX2I	RGATCY	1 cut(s)	193
BstYI	RGATCY	1 cut(s)	193
BsuRI	GGCC	3 cut(s)	207, 268, 285
BtsCI	GGATG	1 cut(s)	55
BtsI	GCAGTG	1 cut(s)	30
BtsIMutI	CAGTG	2 cut(s)	30, 902
Cac8I	GCNNGC	1 cut(s)	709
CciI	TCATGA	1 cut(s)	883
Cfr13I	GGNCC	4 cut(s)	206, 266, 737, 788
CsiI	ACCWGGT	1 cut(s)	544
Csp6I	GTAC	1 cut(s)	28
CviAII	CATG	8 cut(s)	18, 321, 428, 497, 724, 734, 855, 884
CviQI	GTAC	1 cut(s)	28
DdeI	CTNAG	3 cut(s)	228, 597, 911
Eco130I	CCWWGG	1 cut(s)	296
Eco24I	GRGCYC	1 cut(s)	862
Eco32I	GATATC	1 cut(s)	958
Eco47I	GGWCC	2 cut(s)	737, 788
EcoNI	CCTNNNNNAGG	1 cut(s)	213
EcoRII	CCWGG	4 cut(s)	148, 343, 544, 697
EcoRV	GATATC	1 cut(s)	958
EcoT14I	CCWWGG	1 cut(s)	296
EcoT38I	GRGCYC	1 cut(s)	862
ErhI	CCWWGG	1 cut(s)	296
FaeI	CATG	8 cut(s)	21, 324, 431, 500, 727, 737, 858, 887
FaqI	GGGAC	3 cut(s)	77, 666, 824
FatI	CATG	8 cut(s)	17, 320, 427, 496, 723, 733, 854, 883
FauNDI	CATATG	1 cut(s)	754
FbaI	TGATCA	1 cut(s)	493
Fnu4HI	GCNGC	2 cut(s)	291, 721
FokI	GGATG	1 cut(s)	62
FriOI	GRGCYC	1 cut(s)	862
Fsp4HI	GCNGC	2 cut(s)	291, 721
GluI	GCNGC	2 cut(s)	291, 721
HaeIII	GGCC	3 cut(s)	207, 268, 285
Hin1II	CATG	8 cut(s)	21, 324, 431, 500, 727, 737, 858, 887
HinfI	GANTC	4 cut(s)	654, 727, 827, 866
HphI	GGTGA	2 cut(s)	164, 512
Hpy166II	GTNNAC	1 cut(s)	30
Hpy188I	TCNGA	3 cut(s)	459, 611, 908
Hpy188III	TCNNGA	8 cut(s)	85, 112, 200, 213, 740, 863, 884, 961
Hpy8I	GTNNAC	1 cut(s)	30
HpyAV	CCTTC	4 cut(s)	99, 219, 516, 883
HpyCH4III	ACNGT	3 cut(s)	484, 520, 665
HpyCH4V	TGCA	6 cut(s)	66, 188, 389, 554, 707, 723
HpyF10VI	GCNNNNNNNGC	1 cut(s)	717
HpyF3I	CTNAG	3 cut(s)	228, 597, 911
Hsp92II	CATG	8 cut(s)	21, 324, 431, 500, 727, 737, 858, 887
Ksp22I	TGATCA	1 cut(s)	493
LmnI	GCTCC	3 cut(s)	275, 298, 445
Lsp1109I	GCAGC	2 cut(s)	277, 707
LweI	GCATC	1 cut(s)	931
MabI	ACCWGGT	1 cut(s)	544
MboII	GAAGA	4 cut(s)	144, 188, 686, 760
MflI	RGATCY	1 cut(s)	193
MhlI	GDGCHC	1 cut(s)	862
MluCI	AATT	7 cut(s)	22, 98, 365, 433, 631, 644, 846
MlyI	GAGTC	3 cut(s)	648, 721, 875
MmeI	TCCRAC	1 cut(s)	634
MseI	TTAA	1 cut(s)	411
MspR9I	CCNGG	4 cut(s)	150, 345, 546, 699
MvaI	CCWGG	4 cut(s)	150, 345, 546, 699
MvnI	CGCG	1 cut(s)	774
MwoI	GCNNNNNNNGC	1 cut(s)	717
NdeI	CATATG	1 cut(s)	754
NlaIII	CATG	8 cut(s)	21, 324, 431, 500, 727, 737, 858, 887
NlaIV	GGNNCC	1 cut(s)	241
NspI	RCATGY	1 cut(s)	21
NspV	TTCGAA	1 cut(s)	825
PagI	TCATGA	1 cut(s)	883
PciI	ACATGT	1 cut(s)	17
PfeI	GAWTC	1 cut(s)	827
PflMI	CCANNNNNTGG	1 cut(s)	321
PkrI	GCNGC	2 cut(s)	292, 722
PleI	GAGTC	3 cut(s)	648, 721, 874
PpsI	GAGTC	3 cut(s)	648, 721, 874
PscI	ACATGT	1 cut(s)	17
Psp6I	CCWGG	4 cut(s)	148, 343, 544, 697
PspGI	CCWGG	4 cut(s)	148, 343, 544, 697
PspN4I	GGNNCC	1 cut(s)	241
PspPI	GGNCC	4 cut(s)	206, 266, 737, 788
PsuI	RGATCY	1 cut(s)	193
RsaI	GTAC	1 cut(s)	29
RsaNI	GTAC	1 cut(s)	28
SaqAI	TTAA	1 cut(s)	411
SatI	GCNGC	2 cut(s)	291, 721
Sau96I	GGNCC	4 cut(s)	206, 266, 737, 788
SchI	GAGTC	3 cut(s)	648, 721, 875
ScrFI	CCNGG	4 cut(s)	150, 345, 546, 699
SduI	GDGCHC	1 cut(s)	862
SetI	ASST	9 cut(s)	172, 220, 229, 234, 280, 547, 616, 703, 722
SexAI	ACCWGGT	1 cut(s)	544
SfaNI	GCATC	1 cut(s)	931
SfcI	CTRYAG	1 cut(s)	120
SfuI	TTCGAA	1 cut(s)	825
SinI	GGWCC	2 cut(s)	737, 788
SmlI	CTYRAG	2 cut(s)	171, 863
SmoI	CTYRAG	2 cut(s)	171, 863
Sse9I	AATT	7 cut(s)	22, 98, 365, 433, 631, 644, 846
SsiI	CCGC	1 cut(s)	774
StyD4I	CCNGG	4 cut(s)	148, 343, 544, 697
StyI	CCWWGG	1 cut(s)	296
TaaI	ACNGT	3 cut(s)	484, 520, 665
TaqI	TCGA	3 cut(s)	44, 583, 825
TasI	AATT	7 cut(s)	22, 98, 365, 433, 631, 644, 846
TfiI	GAWTC	1 cut(s)	827
Tru1I	TTAA	1 cut(s)	411
Tru9I	TTAA	1 cut(s)	411
TscAI	CASTG	2 cut(s)	37, 902
TseI	GCWGC	2 cut(s)	290, 720
TspDTI	ATGAA	1 cut(s)	865
TspRI	CASTG	2 cut(s)	37, 902
Van91I	CCANNNNNTGG	1 cut(s)	321
VpaK11BI	GGWCC	2 cut(s)	737, 788
XagI	CCTNNNNNAGG	1 cut(s)	213
XapI	RAATTY	3 cut(s)	365, 644, 846
XceI	RCATGY	1 cut(s)	21

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