Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0010225

Physical Location & Seq

Genomic Coordinates Reverse (-)

24490119 .. 24492334

Gene Structure 2216 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG236500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1032 bp

ATGTATAATAGTGCCCCGCCTATCAAATCGTGGCAAACAGAGTTGCCGTTAATGGATTCAAATACCCATCTCAATCTGGAGCACCAACAGCCCCACCACCAACCCAATTCTGGGTTGCTCCGATTTCGCTCTGCTCCGAGCTCAGTGTTCGCTGAGAACAACAACAACGCCGATTTGGGGGTCCATAAGGGAACTTTAATCGAGGGTGGTTCCGACTCCGACAGATTGTTCTCGAGATTCGTGAGCTACAGTCACAGTAACGACTCGGAATCGTGGCCGTCGAGTTTCCAGGAGTTCGAGGACAAATCTACGGTGACGGAGGCGGCTGTGACGGCGAGTCGTATGAGCTCACAGCATCAGCAGCAGGGGTTTCCTGGTCTTCCACCTCATTATCCGAGACAGAACTCGTTTGGGAGTGGTAATGGCTCTTATGGGTTGGTGGGTTCGGCTGCAGTGGAACATCACCCGCAAGCCAAGACTGTTACTTCCAATCTTGTTCGGCAGAGTAGTTCTCCTGCTGGGCTTTTCTCCAACAACACCTCTGTTCAAAATGGATTCCCATTTGGAGCTTGGAATGATCCATCAAATTTTGCCGATAATTTAAGTGGCATGAGAAGAGACCAAGATAATGACCAGAAGTTATTCTCTGCTACTCAGAATGGTGATCTTGGGAACCGGATTCATATATTATCCCACCACTTGAGTTTACCAAAAAATTCAGCAGAAGTTGCCATGGAAAAGTTCCTCCAACTCCAAGATTCTGTACCTTGCAAAGTTAGAGCAAAGCGAGGTTGTGCCACTCATCCTCGAAGCATTGCAGAAAGGGTGAGAAGAACACGGATTAGTGAACGAATGAGGAAGCTACAAGAGCTTGTGCCGAACATGGACAAGCAAACAAATACAGCAGACATGTTGGACTTGGCTGTTGATTATATTAAAGAACTTCAGAAACAGTTCAAGAGTCTTAGCGATGTTCGAGCCAACTGCAAGTGTTTGAGTATGCAGAAGCCCGTTCAAAATCAGATAGTTTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0000976 GO:0000981 GO:0001046 GO:0001047 GO:0001067 GO:0001228 GO:0003006 GO:0003674 GO:0003676 GO:0003677 GO:0003690 GO:0003700 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006139 GO:0006351 GO:0006355 GO:0006357 GO:0006366 GO:0006725 GO:0006807 GO:0007275 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009314 GO:0009416 GO:0009628 GO:0009648 GO:0009791 GO:0009889 GO:0009891 GO:0009893 GO:0009987 GO:0010228 GO:0010467 GO:0010468 GO:0010556 GO:0010557 GO:0010604 GO:0010628 GO:0016070 GO:0018130 GO:0019219 GO:0019222 GO:0019438 GO:0022414 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0032501 GO:0032502 GO:0032774 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043565 GO:0044212 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044424 GO:0044464 GO:0045893 GO:0045935 GO:0045944 GO:0046483 GO:0048518 GO:0048522 GO:0048573 GO:0048608 GO:0048731 GO:0048856 GO:0050789 GO:0050794 GO:0050896 GO:0051171 GO:0051173 GO:0051252 GO:0051254 GO:0060255 GO:0061458 GO:0065007 GO:0071704 GO:0080090 GO:0090304 GO:0097159 GO:0097659 GO:0140110 GO:1901360 GO:1901362 GO:1901363 GO:1901576 GO:1902680 GO:1903506 GO:1903508 GO:1990837 GO:2000112 GO:2001141

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

HLH

Protein Analysis

343

Amino Acids

38.17

Weight (kDa)

8.63

Isoelectric Point (pI)

48.22

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
HLH	PF00010	271 - 316	6.8e-10	Helix-loop-helix DNA-binding domain

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

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Orthologous Genes (Group: OG0010225)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G42280 AT2G42280 AT2G42280
fragaria_vesca	FvH4_6g22880 FvH4_6g22880
malus_domestica	MD12G1062600.v1.1 MD14G1063300.v1.1
prunus_persica	Prupe.7G071500_v2.0.a1
pyrus_communis	pycom12g05530 pycom14g05110
rosa_chinensis	RchiOBHm_Chr3g0480621
rosa_laevigata	RLG00000023464
rosa_multiflora	Rmu_sc0002752.1_g000005
rosa_roxburghii	Rroxscaffold_6G00401200
rosa_rugosa	Rorug03G0184300 Rorug03G0184400
rosa_samantha	Rh3AG236500 Rh3BG269400 Rh3CG266100 Rh3DG261900
rosa_wichuraiana	Rw3G021190

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AciI	CCGC	3 cut(s)	17, 323, 467
AclWI	GGATC	1 cut(s)	572
AcoI	YGGCCR	1 cut(s)	275
AcsI	RAATTY	2 cut(s)	586, 715
AcuI	CTGAAG	1 cut(s)	929
AfaI	GTAC	1 cut(s)	765
AfiI	CCNNNNNNNGG	3 cut(s)	110, 111, 177
AflIII	ACRYGT	1 cut(s)	909
AgsI	TTSAA	4 cut(s)	60, 548, 958, 1016
AhdI	GACNNNNNGTC	1 cut(s)	336
AjnI	CCWGG	2 cut(s)	288, 373
AluBI	AGCT	6 cut(s)	141, 246, 348, 569, 862, 871
AluI	AGCT	6 cut(s)	141, 246, 348, 569, 862, 871
Alw21I	GWGCWC	3 cut(s)	84, 143, 350
Alw26I	GTCTC	2 cut(s)	391, 612
AlwI	GGATC	1 cut(s)	572
Ama87I	CYCGRG	1 cut(s)	232
AoxI	GGCC	1 cut(s)	275
ApeKI	GCWGC	2 cut(s)	361, 449
ApoI	RAATTY	2 cut(s)	586, 715
Asp700I	GAANNNNTTC	2 cut(s)	641, 953
AspS9I	GGNCC	1 cut(s)	181
AsuHPI	GGTGA	4 cut(s)	325, 455, 674, 838
AvaI	CYCGRG	1 cut(s)	232
AvaII	GGWCC	1 cut(s)	181
BaeGI	GKGCMC	1 cut(s)	16
BanII	GRGCYC	2 cut(s)	143, 350
BbsI	GAAGAC	1 cut(s)	371
Bbv12I	GWGCWC	3 cut(s)	84, 143, 350
BbvI	GCAGC	2 cut(s)	373, 436
BccI	CCATC	2 cut(s)	75, 589
BceAI	ACGGC	3 cut(s)	31, 262, 348
BcgI	CGANNNNNNTGC	2 cut(s)	966, 1000
BciT130I	CCWGG	2 cut(s)	290, 375
BcoDI	GTCTC	2 cut(s)	391, 612
BfmI	CTRYAG	2 cut(s)	247, 450
BisI	GCNGC	3 cut(s)	324, 362, 450
BlsI	GCNGC	3 cut(s)	325, 363, 451
Bme1390I	CCNGG	2 cut(s)	290, 375
Bme18I	GGWCC	1 cut(s)	181
BmeRI	GACNNNNNGTC	1 cut(s)	336
BmeT110I	CYCGRG	1 cut(s)	232
BmgT120I	GGNCC	1 cut(s)	181
BmiI	GGNNCC	3 cut(s)	182, 211, 674
BmrFI	CCNGG	2 cut(s)	290, 375
BmsI	GCATC	1 cut(s)	364
BpiI	GAAGAC	1 cut(s)	371
BplI	GAGNNNNNCTC	2 cut(s)	496, 528
BpmI	CTGGAG	1 cut(s)	98
BpuEI	CTTGAG	1 cut(s)	721
BsaI	GGTCTC	1 cut(s)	612
BsaJI	CCNNGG	1 cut(s)	732
BsaWI	WCCGGW	1 cut(s)	675
Bsc4I	CCNNNNNNNGG	3 cut(s)	110, 111, 177
Bse3DI	GCAATG	1 cut(s)	813
BseBI	CCWGG	2 cut(s)	290, 375
BseDI	CCNNGG	1 cut(s)	732
BseGI	GGATG	1 cut(s)	802
BseLI	CCNNNNNNNGG	3 cut(s)	110, 111, 177
BseMI	GCAATG	1 cut(s)	813
BseMII	CTCAG	3 cut(s)	144, 156, 668
BseSI	GKGCMC	1 cut(s)	16
BseXI	GCAGC	2 cut(s)	373, 436
BseYI	CCCAGC	1 cut(s)	518
BshFI	GGCC	1 cut(s)	277
BsiHKAI	GWGCWC	3 cut(s)	84, 143, 350
BsiHKCI	CYCGRG	1 cut(s)	232
BsiSI	CCGG	1 cut(s)	676
BslI	CCNNNNNNNGG	3 cut(s)	110, 111, 177
BsmAI	GTCTC	2 cut(s)	391, 612
BsnI	GGCC	1 cut(s)	277
Bso31I	GGTCTC	1 cut(s)	612
BsoBI	CYCGRG	1 cut(s)	232
Bsp1286I	GDGCHC	4 cut(s)	16, 84, 143, 350
Bsp143I	GATC	2 cut(s)	577, 664
Bsp19I	CCATGG	1 cut(s)	732
BspACI	CCGC	3 cut(s)	17, 323, 467
BspANI	GGCC	1 cut(s)	277
BspCNI	CTCAG	3 cut(s)	145, 155, 667
BspLI	GGNNCC	3 cut(s)	182, 211, 674
BspMAI	CTGCAG	1 cut(s)	454
BspPI	GGATC	1 cut(s)	572
BspTNI	GGTCTC	1 cut(s)	612
BsrDI	GCAATG	1 cut(s)	813
BssECI	CCNNGG	1 cut(s)	732
BssMI	GATC	2 cut(s)	577, 664
BssT1I	CCWWGG	1 cut(s)	732
Bst2UI	CCWGG	2 cut(s)	290, 375
Bst4CI	ACNGT	5 cut(s)	251, 257, 313, 481, 954
Bst6I	CTCTTC	1 cut(s)	610
BstAPI	GCANNNNNTGC	1 cut(s)	728
BstC8I	GCNNGC	1 cut(s)	471
BstDEI	CTNAG	4 cut(s)	142, 153, 654, 965
BstDSI	CCRYGG	1 cut(s)	732
BstF5I	GGATG	1 cut(s)	802
BstKTI	GATC	2 cut(s)	580, 667
BstMAI	GTCTC	2 cut(s)	391, 612
BstMBI	GATC	2 cut(s)	577, 664
BstMWI	GCNNNNNNNGC	5 cut(s)	88, 332, 361, 728, 868
BstNI	CCWGG	2 cut(s)	290, 375
BstNSI	RCATGY	1 cut(s)	913
BstSCI	CCNGG	2 cut(s)	288, 373
BstSFI	CTRYAG	2 cut(s)	247, 450
BstSLI	GKGCMC	1 cut(s)	16
BstV1I	GCAGC	2 cut(s)	373, 436
BstV2I	GAAGAC	1 cut(s)	371
BsuRI	GGCC	1 cut(s)	277
BtgI	CCRYGG	1 cut(s)	732
BtgZI	GCGATG	1 cut(s)	984
BtsCI	GGATG	1 cut(s)	802
BtsI	GCAGTG	1 cut(s)	459
BtsIMutI	CAGTG	2 cut(s)	150, 459
Cac8I	GCNNGC	1 cut(s)	471
Cfr13I	GGNCC	1 cut(s)	181
Csp6I	GTAC	1 cut(s)	764
CviAII	CATG	4 cut(s)	610, 733, 883, 910
CviQI	GTAC	1 cut(s)	764
DdeI	CTNAG	4 cut(s)	142, 153, 654, 965
DpnI	GATC	2 cut(s)	579, 666
DpnII	GATC	2 cut(s)	577, 664
DriI	GACNNNNNGTC	1 cut(s)	336
EaeI	YGGCCR	1 cut(s)	275
Eam1104I	CTCTTC	1 cut(s)	610
Eam1105I	GACNNNNNGTC	1 cut(s)	336
EarI	CTCTTC	1 cut(s)	610
Ecl136II	GAGCTC	2 cut(s)	141, 348
Eco130I	CCWWGG	1 cut(s)	732
Eco24I	GRGCYC	2 cut(s)	143, 350
Eco31I	GGTCTC	1 cut(s)	612
Eco47I	GGWCC	1 cut(s)	181
Eco53kI	GAGCTC	2 cut(s)	141, 348
Eco57I	CTGAAG	1 cut(s)	929
Eco88I	CYCGRG	1 cut(s)	232
EcoICRI	GAGCTC	2 cut(s)	141, 348
EcoRII	CCWGG	2 cut(s)	288, 373
EcoT14I	CCWWGG	1 cut(s)	732
EcoT38I	GRGCYC	2 cut(s)	143, 350
ErhI	CCWWGG	1 cut(s)	732
FaeI	CATG	4 cut(s)	613, 736, 886, 913
FatI	CATG	4 cut(s)	609, 732, 882, 909
FauI	CCCGC	2 cut(s)	24, 474
Fnu4HI	GCNGC	3 cut(s)	324, 362, 450
FokI	GGATG	1 cut(s)	789
FriOI	GRGCYC	2 cut(s)	143, 350
Fsp4HI	GCNGC	3 cut(s)	324, 362, 450
GluI	GCNGC	3 cut(s)	324, 362, 450
GsaI	CCCAGC	1 cut(s)	522
GsuI	CTGGAG	1 cut(s)	98
HaeIII	GGCC	1 cut(s)	277
HapII	CCGG	1 cut(s)	676
Hin1II	CATG	4 cut(s)	613, 736, 886, 913
HpaII	CCGG	1 cut(s)	676
HphI	GGTGA	4 cut(s)	325, 455, 674, 838
Hpy166II	GTNNAC	2 cut(s)	707, 848
Hpy188I	TCNGA	9 cut(s)	122, 138, 214, 220, 268, 396, 657, 948, 1023
Hpy188III	TCNNGA	5 cut(s)	77, 232, 234, 241, 958
Hpy8I	GTNNAC	2 cut(s)	707, 848
Hpy99I	CGWCG	1 cut(s)	283
HpyCH4III	ACNGT	5 cut(s)	251, 257, 313, 481, 954
HpyCH4V	TGCA	5 cut(s)	452, 771, 818, 987, 1003
HpyF10VI	GCNNNNNNNGC	5 cut(s)	88, 332, 361, 728, 868
HpyF3I	CTNAG	4 cut(s)	142, 153, 654, 965
Hsp92II	CATG	4 cut(s)	613, 736, 886, 913
Kzo9I	GATC	2 cut(s)	577, 664
LmnI	GCTCC	4 cut(s)	79, 123, 139, 566
Lsp1109I	GCAGC	2 cut(s)	373, 436
LweI	GCATC	1 cut(s)	364
MaeIII	GTNAC	5 cut(s)	251, 257, 313, 328, 481
MalI	GATC	2 cut(s)	579, 666
MboI	GATC	2 cut(s)	577, 664
MboII	GAAGA	3 cut(s)	371, 627, 843
MhlI	GDGCHC	4 cut(s)	16, 84, 143, 350
MluCI	AATT	4 cut(s)	106, 586, 598, 715
MlyI	GAGTC	4 cut(s)	209, 257, 346, 970
MmeI	TCCRAC	5 cut(s)	237, 243, 555, 772, 894
MnlI	CCTC	9 cut(s)	196, 292, 313, 396, 550, 755, 782, 816, 849
MroXI	GAANNNNTTC	2 cut(s)	641, 953
MseI	TTAA	4 cut(s)	50, 197, 602, 936
MspI	CCGG	1 cut(s)	676
MspR9I	CCNGG	2 cut(s)	290, 375
MvaI	CCWGG	2 cut(s)	290, 375
MwoI	GCNNNNNNNGC	5 cut(s)	88, 332, 361, 728, 868
NcoI	CCATGG	1 cut(s)	732
NdeII	GATC	2 cut(s)	577, 664
NlaIII	CATG	4 cut(s)	613, 736, 886, 913
NlaIV	GGNNCC	3 cut(s)	182, 211, 674
NmuCI	GTSAC	3 cut(s)	251, 313, 328
NspI	RCATGY	1 cut(s)	913
PaeR7I	CTCGAG	1 cut(s)	232
PciI	ACATGT	1 cut(s)	909
PcsI	WCGNNNNNNNCGW	1 cut(s)	278
PdmI	GAANNNNTTC	2 cut(s)	641, 953
PfeI	GAWTC	6 cut(s)	56, 237, 269, 555, 679, 758
PfoI	TCCNGGA	1 cut(s)	288
PkrI	GCNGC	3 cut(s)	325, 363, 451
PleI	GAGTC	4 cut(s)	209, 257, 345, 969
PpsI	GAGTC	4 cut(s)	209, 257, 345, 969
PscI	ACATGT	1 cut(s)	909
Psp124BI	GAGCTC	2 cut(s)	143, 350
Psp6I	CCWGG	2 cut(s)	288, 373
PspFI	CCCAGC	1 cut(s)	518
PspGI	CCWGG	2 cut(s)	288, 373
PspN4I	GGNNCC	3 cut(s)	182, 211, 674
PspPI	GGNCC	1 cut(s)	181
PstI	CTGCAG	1 cut(s)	454
RsaI	GTAC	1 cut(s)	765
RsaNI	GTAC	1 cut(s)	764
SacI	GAGCTC	2 cut(s)	143, 350
SaqAI	TTAA	4 cut(s)	50, 197, 602, 936
SatI	GCNGC	3 cut(s)	324, 362, 450
Sau3AI	GATC	2 cut(s)	577, 664
Sau96I	GGNCC	1 cut(s)	181
SchI	GAGTC	4 cut(s)	209, 257, 346, 970
ScrFI	CCNGG	2 cut(s)	290, 375
SduI	GDGCHC	4 cut(s)	16, 84, 143, 350
SfaNI	GCATC	1 cut(s)	364
SfcI	CTRYAG	2 cut(s)	247, 450
Sfr274I	CTCGAG	1 cut(s)	232
SinI	GGWCC	1 cut(s)	181
SlaI	CTCGAG	1 cut(s)	232
SmlI	CTYRAG	2 cut(s)	232, 700
SmoI	CTYRAG	2 cut(s)	232, 700
Sse9I	AATT	4 cut(s)	106, 586, 598, 715
SsiI	CCGC	3 cut(s)	17, 323, 467
SstI	GAGCTC	2 cut(s)	143, 350
StyD4I	CCNGG	2 cut(s)	288, 373
StyI	CCWWGG	1 cut(s)	732
TaaI	ACNGT	5 cut(s)	251, 257, 313, 481, 954
TaqI	TCGA	6 cut(s)	201, 233, 281, 297, 808, 976
TasI	AATT	4 cut(s)	106, 586, 598, 715
TauI	GCSGC	1 cut(s)	326
TfiI	GAWTC	6 cut(s)	56, 237, 269, 555, 679, 758
Tru1I	TTAA	4 cut(s)	50, 197, 602, 936
Tru9I	TTAA	4 cut(s)	50, 197, 602, 936
TscAI	CASTG	2 cut(s)	150, 459
TseFI	GTSAC	3 cut(s)	251, 313, 328
TseI	GCWGC	2 cut(s)	361, 449
Tsp45I	GTSAC	3 cut(s)	251, 313, 328
TspDTI	ATGAA	1 cut(s)	671
TspGWI	ACGGA	2 cut(s)	332, 853
TspRI	CASTG	2 cut(s)	150, 459
VpaK11BI	GGWCC	1 cut(s)	181
XapI	RAATTY	2 cut(s)	586, 715
XceI	RCATGY	1 cut(s)	913
XcmI	CCANNNNNNNNNTGG	2 cut(s)	107, 567
XhoI	CTCGAG	1 cut(s)	232
XmnI	GAANNNNTTC	2 cut(s)	641, 953

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