Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4C

Orthogroup ID

OG0002801

Physical Location & Seq

Genomic Coordinates Forward (+)

69546188 .. 69553244

Gene Structure 7057 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4CG465400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 720 bp

ATGGGAAGCGGGTCAATCAAATCGAACCCAACAAGGTCGAGGAAGAGGGTGGAGGCCACGGCGGAGGACTCGACTGGGCCTTCTCTCCTTCGCGGCAAAGATGGCAGTGCTTTTGCCAGATGCGATGGGTGCCAAAAGAATGTCCCAGTGGCGCTCATAAGCTTTCACAATTGTAGCCTCGATGCCAAAATCAAGACCAACCTGGAGGCTCAAGTCGTGGAAAAGCCCAGTGAAGTGACTAAGAAGCCTCCCACAGAGAGGAAGAAATCCAGTACATCGTCACAACCAAATGCCAAGAGAGCCAAGACTGACAAAGCAAAGAAGAGCAAGGATCCAAATGCACCCAAGCGCCCTCTCACTGCCTTCTTCCTTTTCATGAATGATTTTAGGAAAGCCTACAAGGAAGCTAATCCTGATTCCAAGGGTGTTAAGATGGTTGCAAAGGAGGGTGGTGAAAAGTGGAAACTTATGACTGATGAGGAGAAGAAGCCTTATATGGACAAAGCTGCTGAGCTTAAAGATGAGTTCAAAAAGACCATAGAGACTGAAGCTGATGATGCTGAAGTAAGTTTCACTATTGTTCATTCTCAAACCAGTCTGCCATTCTTGGATGTATTATTCTGGTTGCTATTTTCTTATTTTTTTTTTGAATTTCTTTTGTGGTTATTCAGGGTGAAGCTGAAGATGTTTCAGAAAAGGAAGTGCCAGAGAAGGAAGTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000741 GO:0003674 GO:0003676 GO:0003677 GO:0003700 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006355 GO:0006996 GO:0006997 GO:0007275 GO:0008150 GO:0009553 GO:0009559 GO:0009561 GO:0009889 GO:0009987 GO:0010197 GO:0010468 GO:0010556 GO:0016043 GO:0019219 GO:0019222 GO:0030154 GO:0031323 GO:0031326 GO:0032501 GO:0032502 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044464 GO:0048229 GO:0048284 GO:0048856 GO:0048869 GO:0050789 GO:0050794 GO:0051171 GO:0051252 GO:0060255 GO:0065007 GO:0071840 GO:0080090 GO:0097159 GO:0140110 GO:1901363 GO:1903506 GO:2000112 GO:2001141

KEGG Pathways

Metabolic & Signaling

ko03410 ko04140 ko04217 map03410 map04140 map04217

Pfam Domains

Protein Families

HMG_box

Protein Analysis

239

Amino Acids

27.25

Weight (kDa)

9.73

Isoelectric Point (pI)

38.98

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
HMG_box_2	PF09011	112 - 181	1.9e-13	HMG-box domain
HMG_box	PF00505	115 - 180	1.8e-18	HMG (high mobility group) box
HMG_WDHD1	PF24815	118 - 168	1.2e-14	WDHD1 HMG box

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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Tree File

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Publication-ready

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Orthologous Genes (Group: OG0002801)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G23420 AT5G23420
fragaria_vesca	FvH4_4g14340 FvH4_4g25270 FvH4_4g37280 FvH4_5g24080 FvH4_7g08880
malus_domestica	MD00G1127400.v1.1 MD13G1001900.v1.1
prunus_persica	Prupe.1G350700_v2.0.a1
pyrus_communis	pycom13g00150 pycom16g00050
rosa_chinensis	RchiOBHm_Chr4g0447101
rosa_laevigata	RLG00000005605 RLG00000017187 RLG00000019927 RLG00000024815
rosa_multiflora	Rmu_co7979696.1_g000001 Rmu_sc0010825.1_g000009 Rmu_ssc0000178.1_g000012
rosa_roxburghii	Rroxscaffold_2G00150280 Rroxscaffold_5G00357540 Rroxscaffold_5G00387440
rosa_rugosa	Rorug02G0403700 Rorug04G0378200 Rorug07G0307000
rosa_samantha	Rh1BG046400 Rh2AG305400 Rh2BG280600 Rh2DG275400 Rh2DG329200 Rh4AG439300 Rh4BG448400 Rh4CG465400 Rh4DG446800 Rh5BG556800 Rh5CG579600 Rh7DG482600
rosa_wichuraiana	Rw4G037580

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	129
AccII	CGCG	1 cut(s)	93
AciI	CCGC	3 cut(s)	9, 62, 93
AclWI	GGATC	2 cut(s)	326, 339
AcsI	RAATTY	1 cut(s)	650
AcuI	CTGAAG	3 cut(s)	567, 582, 701
AfaI	GTAC	1 cut(s)	274
AfiI	CCNNNNNNNGG	1 cut(s)	258
AgsI	TTSAA	2 cut(s)	529, 650
AjnI	CCWGG	1 cut(s)	201
AluBI	AGCT	6 cut(s)	162, 407, 506, 514, 551, 679
AluI	AGCT	6 cut(s)	162, 407, 506, 514, 551, 679
Alw26I	GTCTC	1 cut(s)	536
AlwI	GGATC	2 cut(s)	326, 339
AoxI	GGCC	2 cut(s)	54, 77
ApeKI	GCWGC	1 cut(s)	506
ApoI	RAATTY	1 cut(s)	650
AspLEI	GCGC	2 cut(s)	154, 351
AspS9I	GGNCC	1 cut(s)	77
AsuHPI	GGTGA	2 cut(s)	464, 685
BamHI	GGATCC	1 cut(s)	331
BanI	GGYRCC	1 cut(s)	129
BbvI	GCAGC	1 cut(s)	493
BccI	CCATC	3 cut(s)	95, 119, 427
BceAI	ACGGC	1 cut(s)	75
BciT130I	CCWGG	1 cut(s)	203
BcoDI	GTCTC	1 cut(s)	536
BfoI	RGCGCY	2 cut(s)	155, 352
BisI	GCNGC	2 cut(s)	94, 507
BlpI	GCTNAGC	1 cut(s)	510
BlsI	GCNGC	2 cut(s)	95, 508
Bme1390I	CCNGG	1 cut(s)	203
BmgT120I	GGNCC	1 cut(s)	77
BmiI	GGNNCC	2 cut(s)	131, 333
BmrFI	CCNGG	1 cut(s)	203
BmrI	ACTGGG	3 cut(s)	84, 140, 222
BmsI	GCATC	3 cut(s)	110, 172, 547
BmuI	ACTGGG	3 cut(s)	84, 140, 222
BpmI	CTGGAG	1 cut(s)	224
Bpu1102I	GCTNAGC	1 cut(s)	510
BpuEI	CTTGAG	1 cut(s)	195
BsaJI	CCNNGG	2 cut(s)	57, 420
Bsc4I	CCNNNNNNNGG	1 cut(s)	258
Bse1I	ACTGG	5 cut(s)	79, 146, 228, 270, 594
BseBI	CCWGG	1 cut(s)	203
BseDI	CCNNGG	2 cut(s)	57, 420
BseGI	GGATG	1 cut(s)	616
BseLI	CCNNNNNNNGG	1 cut(s)	258
BseMII	CTCAG	1 cut(s)	501
BseNI	ACTGG	5 cut(s)	79, 146, 228, 270, 594
BseRI	GAGGAG	1 cut(s)	494
BseXI	GCAGC	1 cut(s)	493
Bsh1236I	CGCG	1 cut(s)	93
BshFI	GGCC	2 cut(s)	56, 79
BshNI	GGYRCC	1 cut(s)	129
BslFI	GGGAC	1 cut(s)	128
BslI	CCNNNNNNNGG	1 cut(s)	258
BsmAI	GTCTC	1 cut(s)	536
BsmFI	GGGAC	1 cut(s)	128
BsnI	GGCC	2 cut(s)	56, 79
Bsp143I	GATC	1 cut(s)	331
Bsp1720I	GCTNAGC	1 cut(s)	510
BspACI	CCGC	3 cut(s)	9, 62, 93
BspANI	GGCC	2 cut(s)	56, 79
BspCNI	CTCAG	1 cut(s)	502
BspFNI	CGCG	1 cut(s)	93
BspHI	TCATGA	1 cut(s)	375
BspLI	GGNNCC	2 cut(s)	131, 333
BspPI	GGATC	2 cut(s)	326, 339
BspQI	GCTCTTC	1 cut(s)	317
BspT107I	GGYRCC	1 cut(s)	129
BsrI	ACTGG	5 cut(s)	79, 146, 228, 270, 594
BssECI	CCNNGG	2 cut(s)	57, 420
BssMI	GATC	1 cut(s)	331
BssT1I	CCWWGG	1 cut(s)	420
Bst2UI	CCWGG	1 cut(s)	203
Bst6I	CTCTTC	2 cut(s)	38, 317
BstDEI	CTNAG	2 cut(s)	240, 510
BstDSI	CCRYGG	1 cut(s)	57
BstF5I	GGATG	1 cut(s)	616
BstFNI	CGCG	1 cut(s)	93
BstH2I	RGCGCY	2 cut(s)	155, 352
BstHHI	GCGC	2 cut(s)	154, 351
BstKTI	GATC	1 cut(s)	334
BstMAI	GTCTC	1 cut(s)	536
BstMBI	GATC	1 cut(s)	331
BstMWI	GCNNNNNNNGC	4 cut(s)	102, 129, 299, 557
BstNI	CCWGG	1 cut(s)	203
BstSCI	CCNGG	1 cut(s)	201
BstUI	CGCG	1 cut(s)	93
BstV1I	GCAGC	1 cut(s)	493
BstX2I	RGATCY	1 cut(s)	331
BstYI	RGATCY	1 cut(s)	331
BsuRI	GGCC	2 cut(s)	56, 79
BtgI	CCRYGG	1 cut(s)	57
BtgZI	GCGATG	1 cut(s)	138
BtsCI	GGATG	1 cut(s)	616
BtsI	GCAGTG	2 cut(s)	112, 357
BtsIMutI	CAGTG	4 cut(s)	112, 153, 235, 357
CciI	TCATGA	1 cut(s)	375
CfoI	GCGC	2 cut(s)	154, 351
Cfr13I	GGNCC	1 cut(s)	77
Csp6I	GTAC	1 cut(s)	273
CviAII	CATG	1 cut(s)	376
CviQI	GTAC	1 cut(s)	273
DdeI	CTNAG	2 cut(s)	240, 510
DpnI	GATC	1 cut(s)	333
DpnII	GATC	1 cut(s)	331
Eam1104I	CTCTTC	2 cut(s)	38, 317
EarI	CTCTTC	2 cut(s)	38, 317
EciI	GGCGGA	1 cut(s)	77
Eco130I	CCWWGG	1 cut(s)	420
Eco57I	CTGAAG	3 cut(s)	567, 582, 701
EcoRII	CCWGG	1 cut(s)	201
EcoT14I	CCWWGG	1 cut(s)	420
ErhI	CCWWGG	1 cut(s)	420
FaeI	CATG	1 cut(s)	379
FaiI	YATR	6 cut(s)	158, 377, 470, 495, 497, 539
FaqI	GGGAC	1 cut(s)	128
FatI	CATG	1 cut(s)	375
FauI	CCCGC	1 cut(s)	2
Fnu4HI	GCNGC	2 cut(s)	94, 507
FokI	GGATG	1 cut(s)	623
Fsp4HI	GCNGC	2 cut(s)	94, 507
GlaI	GCGC	2 cut(s)	153, 350
GluI	GCNGC	2 cut(s)	94, 507
GsuI	CTGGAG	1 cut(s)	224
HaeII	RGCGCY	2 cut(s)	155, 352
HaeIII	GGCC	2 cut(s)	56, 79
HhaI	GCGC	2 cut(s)	154, 351
Hin1II	CATG	1 cut(s)	379
Hin6I	GCGC	2 cut(s)	152, 349
HinP1I	GCGC	2 cut(s)	152, 349
HindIII	AAGCTT	1 cut(s)	160
HinfI	GANTC	2 cut(s)	68, 416
HphI	GGTGA	2 cut(s)	464, 685
Hpy188I	TCNGA	1 cut(s)	693
Hpy188III	TCNNGA	3 cut(s)	193, 376, 413
HpyAV	CCTTC	4 cut(s)	90, 98, 373, 705
HpyCH4V	TGCA	2 cut(s)	341, 440
HpyF10VI	GCNNNNNNNGC	4 cut(s)	102, 129, 299, 557
HpyF3I	CTNAG	2 cut(s)	240, 510
Hsp92II	CATG	1 cut(s)	379
HspAI	GCGC	2 cut(s)	152, 349
Kzo9I	GATC	1 cut(s)	331
LguI	GCTCTTC	1 cut(s)	317
Lsp1109I	GCAGC	1 cut(s)	493
LweI	GCATC	3 cut(s)	110, 172, 547
MaeIII	GTNAC	2 cut(s)	235, 279
MalI	GATC	1 cut(s)	333
MboI	GATC	1 cut(s)	331
MboII	GAAGA	6 cut(s)	55, 274, 334, 358, 496, 694
MfeI	CAATTG	1 cut(s)	169
MflI	RGATCY	1 cut(s)	331
MluCI	AATT	2 cut(s)	169, 650
MlyI	GAGTC	1 cut(s)	62
MseI	TTAA	2 cut(s)	429, 516
MspR9I	CCNGG	1 cut(s)	203
MunI	CAATTG	1 cut(s)	169
MvaI	CCWGG	1 cut(s)	203
MvnI	CGCG	1 cut(s)	93
MwoI	GCNNNNNNNGC	4 cut(s)	102, 129, 299, 557
NdeII	GATC	1 cut(s)	331
NlaIII	CATG	1 cut(s)	379
NlaIV	GGNNCC	2 cut(s)	131, 333
NmuCI	GTSAC	2 cut(s)	235, 279
PagI	TCATGA	1 cut(s)	375
PciSI	GCTCTTC	1 cut(s)	317
PfeI	GAWTC	1 cut(s)	416
PkrI	GCNGC	2 cut(s)	95, 508
PleI	GAGTC	1 cut(s)	62
PpsI	GAGTC	1 cut(s)	62
Psp6I	CCWGG	1 cut(s)	201
PspGI	CCWGG	1 cut(s)	201
PspN4I	GGNNCC	2 cut(s)	131, 333
PspPI	GGNCC	1 cut(s)	77
PsuI	RGATCY	1 cut(s)	331
RsaI	GTAC	1 cut(s)	274
RsaNI	GTAC	1 cut(s)	273
SapI	GCTCTTC	1 cut(s)	317
SaqAI	TTAA	2 cut(s)	429, 516
SatI	GCNGC	2 cut(s)	94, 507
Sau3AI	GATC	1 cut(s)	331
Sau96I	GGNCC	1 cut(s)	77
SchI	GAGTC	1 cut(s)	62
ScrFI	CCNGG	1 cut(s)	203
SetI	ASST	8 cut(s)	38, 164, 204, 409, 508, 516, 553, 681
SfaNI	GCATC	3 cut(s)	110, 172, 547
SmlI	CTYRAG	1 cut(s)	210
SmoI	CTYRAG	1 cut(s)	210
Sse9I	AATT	2 cut(s)	169, 650
SsiI	CCGC	3 cut(s)	9, 62, 93
StyD4I	CCNGG	1 cut(s)	201
StyI	CCWWGG	1 cut(s)	420
TaqI	TCGA	4 cut(s)	23, 38, 71, 180
TasI	AATT	2 cut(s)	169, 650
TatI	WGTACW	1 cut(s)	272
TauI	GCSGC	1 cut(s)	96
TfiI	GAWTC	1 cut(s)	416
Tru1I	TTAA	2 cut(s)	429, 516
Tru9I	TTAA	2 cut(s)	429, 516
TscAI	CASTG	4 cut(s)	112, 153, 235, 364
TseFI	GTSAC	2 cut(s)	235, 279
TseI	GCWGC	1 cut(s)	506
Tsp45I	GTSAC	2 cut(s)	235, 279
TspDTI	ATGAA	3 cut(s)	364, 392, 572
TspRI	CASTG	4 cut(s)	112, 153, 235, 364
XapI	RAATTY	1 cut(s)	650

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