Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0000930

Physical Location & Seq

Genomic Coordinates Reverse (-)

88118881 .. 88122218

Gene Structure 3338 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG574400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 609 bp

ATGGCAGAACCAGGGTTGGAGGGCAGCGGAAGCCAACCTGTAGATCTCAAGCAACATCCTTCTGGGATCGTCCCTACTCTTCAGAATATTGTGTCCACAGTCAATTTGGACTGCAAATTGGATCTTAAGGCCATTGCGTTGCAAGCTCGTAATGCAGAATACAATCCCAAGCGTTTTGCAGCTGTGATTATGAGAATAAGAGAACCGAAAACTACTGCACTGATATTTGCATCTGGTAAAATGGTTTGTACAGGAGCTAAGAGTGAAGTACAATCAAAATTGGCAGCACGGAAGTATGCTCGAATCATTCAGAAACTTGGTTTTCCTGCCAAGTTCAAGGACTTTAAAATCCAGAACATAGTTGGTTCTTGTGATGTTAAATTCCCCATAAGACTCGAAGGTCTGGCATATTCCCACGGTGCCTTCTCAAGTTATGAACCAGAGCTGTTCCCTGGCTTGATTTATCGAATGAAACAACCAAAGATTGTGCTTCTTATCTTTGTGTCTGGAAAAATTGTTCTCACGGGAGCAAAGGTAAGAGGTGAGACATACGAAGCCTTTGAGAACATATACCCAGTTCTTACAGAATTCAGGAAAAATCAGCAGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044464

KEGG Pathways

Metabolic & Signaling

ko03022 ko05016 ko05165 ko05166 ko05168 ko05169 ko05203 map03022 map05016 map05165 map05166 map05168 map05169 map05203

Pfam Domains

Protein Families

TBP

Protein Analysis

202

Amino Acids

22.42

Weight (kDa)

9.68

Isoelectric Point (pI)

36.32

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TBP	PF00352	25 - 106	1.9e-33	Transcription factor TFIID (or TATA-binding protein, TBP)
TBP	PF00352	114 - 197	1.5e-32	Transcription factor TFIID (or TATA-binding protein, TBP)

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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Publication-ready

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

Orthologous Genes (Group: OG0000930)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G55520 AT1G55520 AT1G55520 AT1G55520 AT3G13445 AT3G13445
fragaria_vesca	FvH4_1g28010 FvH4_1g28010 FvH4_1g28010 FvH4_1g28010 FvH4_1g28010 FvH4_1g28010 FvH4_1g28010 FvH4_3g32401 FvH4_3g32450 FvH4_3g45850 FvH4_3g45850 FvH4_4g21060 FvH4_6g12030
malus_domestica	MD03G1002100.v1.1 MD11G1002100.v1.1 MD12G1002700.v1.1 MD12G1176800.v1.1 MD14G1002000.v1.1
prunus_persica	Prupe.6G001900_v2.0.a1 Prupe.6G001900_v2.0.a1 Prupe.6G001900_v2.0.a1 Prupe.6G001900_v2.0.a1 Prupe.6G001900_v2.0.a1 Prupe.7G002800_v2.0.a1 Prupe.7G002800_v2.0.a1
pyrus_communis	pycom11g00190 pycom12g16680
rosa_chinensis	RchiOBHm_Chr3g0463861 RchiOBHm_Chr3g0497421 RchiOBHm_Chr5g0083961
rosa_laevigata	RLG00000022465 RLG00000024749 RLG00000035285 RLG00000037068
rosa_multiflora	Rmu_sc0004796.1_g000003
rosa_roxburghii	Rroxscaffold_1G00000660 Rroxscaffold_6G00388060 Rroxscaffold_6G00416240
rosa_rugosa	Rorug03G0068600 Rorug03G0292900 Rorug05G0488000 Rorug05G0488100
rosa_samantha	Rh3AG125700 Rh3AG336400 Rh3BG129800 Rh3BG374500 Rh3CG132300 Rh3CG370600 Rh3DG130900 Rh3DG371500 Rh3DG372800 Rh5AG540800 Rh5BG565800 Rh5CG587700 Rh5DG574400
rosa_wichuraiana	Rw3G010610 Rw3G029570 Rw5G050290

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AasI	GACNNNNNNGTC	1 cut(s)	399
AccB1I	GGYRCC	1 cut(s)	419
AciI	CCGC	1 cut(s)	27
AclWI	GGATC	2 cut(s)	74, 129
AcsI	RAATTY	2 cut(s)	380, 587
AcuI	CTGAAG	1 cut(s)	65
AfaI	GTAC	2 cut(s)	250, 270
AflII	CTTAAG	1 cut(s)	125
AgsI	TTSAA	1 cut(s)	337
AjnI	CCWGG	2 cut(s)	10, 451
AloI	GAACNNNNNNTCC	2 cut(s)	501, 533
AluBI	AGCT	4 cut(s)	146, 182, 257, 445
AluI	AGCT	4 cut(s)	146, 182, 257, 445
Alw26I	GTCTC	1 cut(s)	539
AlwI	GGATC	2 cut(s)	74, 129
AoxI	GGCC	1 cut(s)	129
ApeKI	GCWGC	3 cut(s)	24, 179, 284
ApoI	RAATTY	2 cut(s)	380, 587
AsuHPI	GGTGA	1 cut(s)	554
BanI	GGYRCC	1 cut(s)	419
BbvI	GCAGC	3 cut(s)	36, 191, 296
BciT130I	CCWGG	2 cut(s)	12, 453
BcoDI	GTCTC	1 cut(s)	539
BfmI	CTRYAG	1 cut(s)	39
BfrI	CTTAAG	1 cut(s)	125
BglII	AGATCT	1 cut(s)	43
BisI	GCNGC	3 cut(s)	25, 180, 285
BlsI	GCNGC	3 cut(s)	26, 181, 286
Bme1390I	CCNGG	2 cut(s)	12, 453
BmiI	GGNNCC	1 cut(s)	421
BmrFI	CCNGG	2 cut(s)	12, 453
BmrI	ACTGGG	1 cut(s)	569
BmsI	GCATC	1 cut(s)	239
BmuI	ACTGGG	1 cut(s)	569
BpuEI	CTTGAG	2 cut(s)	32, 412
BsaJI	CCNNGG	3 cut(s)	11, 415, 451
BsaXI	ACNNNNNCTCC	2 cut(s)	519, 549
Bse1I	ACTGG	1 cut(s)	575
Bse3DI	GCAATG	1 cut(s)	132
BseBI	CCWGG	2 cut(s)	12, 453
BseDI	CCNNGG	3 cut(s)	11, 415, 451
BseGI	GGATG	1 cut(s)	55
BseMI	GCAATG	1 cut(s)	132
BseNI	ACTGG	1 cut(s)	575
BseXI	GCAGC	3 cut(s)	36, 191, 296
BsgI	GTGCAG	1 cut(s)	201
BshFI	GGCC	1 cut(s)	131
BshNI	GGYRCC	1 cut(s)	419
BslFI	GGGAC	1 cut(s)	56
BsmAI	GTCTC	1 cut(s)	539
BsmFI	GGGAC	1 cut(s)	56
BsnI	GGCC	1 cut(s)	131
Bsp1407I	TGTACA	1 cut(s)	248
Bsp143I	GATC	3 cut(s)	43, 66, 121
BspACI	CCGC	1 cut(s)	27
BspANI	GGCC	1 cut(s)	131
BspLI	GGNNCC	1 cut(s)	421
BspPI	GGATC	2 cut(s)	74, 129
BspT107I	GGYRCC	1 cut(s)	419
BspTI	CTTAAG	1 cut(s)	125
BsrDI	GCAATG	1 cut(s)	132
BsrGI	TGTACA	1 cut(s)	248
BsrI	ACTGG	1 cut(s)	575
BssECI	CCNNGG	3 cut(s)	11, 415, 451
BssMI	GATC	3 cut(s)	43, 66, 121
Bst2UI	CCWGG	2 cut(s)	12, 453
Bst4CI	ACNGT	2 cut(s)	100, 419
Bst6I	CTCTTC	1 cut(s)	84
BstAFI	CTTAAG	1 cut(s)	125
BstAUI	TGTACA	1 cut(s)	248
BstC8I	GCNNGC	1 cut(s)	144
BstDEI	CTNAG	1 cut(s)	258
BstDSI	CCRYGG	1 cut(s)	415
BstF5I	GGATG	1 cut(s)	55
BstKTI	GATC	3 cut(s)	46, 69, 124
BstMAI	GTCTC	1 cut(s)	539
BstMBI	GATC	3 cut(s)	43, 66, 121
BstMWI	GCNNNNNNNGC	3 cut(s)	30, 143, 152
BstNI	CCWGG	2 cut(s)	12, 453
BstSCI	CCNGG	2 cut(s)	10, 451
BstSFI	CTRYAG	1 cut(s)	39
BstV1I	GCAGC	3 cut(s)	36, 191, 296
BstX2I	RGATCY	2 cut(s)	43, 121
BstYI	RGATCY	2 cut(s)	43, 121
BsuRI	GGCC	1 cut(s)	131
BtgI	CCRYGG	1 cut(s)	415
BtsCI	GGATG	1 cut(s)	55
BtsIMutI	CAGTG	1 cut(s)	218
Cac8I	GCNNGC	1 cut(s)	144
Csp6I	GTAC	2 cut(s)	249, 269
CviJI	RGCY	8 cut(s)	33, 131, 146, 182, 257, 445, 456, 557
CviKI_1	RGCY	8 cut(s)	33, 131, 146, 182, 257, 445, 456, 557
CviQI	GTAC	2 cut(s)	249, 269
DdeI	CTNAG	1 cut(s)	258
DpnI	GATC	3 cut(s)	45, 68, 123
DpnII	GATC	3 cut(s)	43, 66, 121
DraI	TTTAAA	1 cut(s)	346
DrdI	GACNNNNNNGTC	1 cut(s)	399
DseDI	GACNNNNNNGTC	1 cut(s)	399
Eam1104I	CTCTTC	1 cut(s)	84
EarI	CTCTTC	1 cut(s)	84
Eco57I	CTGAAG	1 cut(s)	65
EcoRI	GAATTC	1 cut(s)	587
EcoRII	CCWGG	2 cut(s)	10, 451
FaiI	YATR	9 cut(s)	191, 297, 359, 389, 409, 435, 550, 569, 571
FaqI	GGGAC	1 cut(s)	56
Fnu4HI	GCNGC	3 cut(s)	25, 180, 285
FokI	GGATG	1 cut(s)	42
Fsp4HI	GCNGC	3 cut(s)	25, 180, 285
GluI	GCNGC	3 cut(s)	25, 180, 285
HaeIII	GGCC	1 cut(s)	131
HinfI	GANTC	2 cut(s)	303, 393
HphI	GGTGA	1 cut(s)	554
Hpy166II	GTNNAC	1 cut(s)	96
Hpy188I	TCNGA	2 cut(s)	84, 312
Hpy188III	TCNNGA	3 cut(s)	352, 507, 592
Hpy8I	GTNNAC	1 cut(s)	96
HpyAV	CCTTC	3 cut(s)	69, 392, 433
HpyCH4III	ACNGT	2 cut(s)	100, 419
HpyCH4V	TGCA	6 cut(s)	114, 142, 155, 179, 218, 230
HpyF10VI	GCNNNNNNNGC	3 cut(s)	30, 143, 152
HpyF3I	CTNAG	1 cut(s)	258
Kzo9I	GATC	3 cut(s)	43, 66, 121
LmnI	GCTCC	2 cut(s)	254, 527
Lsp1109I	GCAGC	3 cut(s)	36, 191, 296
LweI	GCATC	1 cut(s)	239
MalI	GATC	3 cut(s)	45, 68, 123
MboI	GATC	3 cut(s)	43, 66, 121
MboII	GAAGA	1 cut(s)	71
MflI	RGATCY	2 cut(s)	43, 121
MluCI	AATT	6 cut(s)	103, 116, 278, 380, 513, 587
MlyI	GAGTC	1 cut(s)	387
MnlI	CCTC	2 cut(s)	13, 533
MseI	TTAA	3 cut(s)	126, 345, 378
MspA1I	CMGCKG	2 cut(s)	27, 182
MspCI	CTTAAG	1 cut(s)	125
MspR9I	CCNGG	2 cut(s)	12, 453
MvaI	CCWGG	2 cut(s)	12, 453
MwoI	GCNNNNNNNGC	3 cut(s)	30, 143, 152
NdeII	GATC	3 cut(s)	43, 66, 121
NlaIV	GGNNCC	1 cut(s)	421
PfeI	GAWTC	1 cut(s)	303
PkrI	GCNGC	3 cut(s)	26, 181, 286
PleI	GAGTC	1 cut(s)	387
PpsI	GAGTC	1 cut(s)	387
Psp6I	CCWGG	2 cut(s)	10, 451
PspGI	CCWGG	2 cut(s)	10, 451
PspN4I	GGNNCC	1 cut(s)	421
PsuI	RGATCY	2 cut(s)	43, 121
PvuII	CAGCTG	1 cut(s)	182
RsaI	GTAC	2 cut(s)	250, 270
RsaNI	GTAC	2 cut(s)	249, 269
SaqAI	TTAA	3 cut(s)	126, 345, 378
SatI	GCNGC	3 cut(s)	25, 180, 285
Sau3AI	GATC	3 cut(s)	43, 66, 121
SchI	GAGTC	1 cut(s)	387
ScrFI	CCNGG	2 cut(s)	12, 453
SetI	ASST	8 cut(s)	40, 148, 184, 259, 403, 447, 537, 544
SfaNI	GCATC	1 cut(s)	239
SfcI	CTRYAG	1 cut(s)	39
SmlI	CTYRAG	3 cut(s)	47, 125, 427
SmoI	CTYRAG	3 cut(s)	47, 125, 427
Sse9I	AATT	6 cut(s)	103, 116, 278, 380, 513, 587
SsiI	CCGC	1 cut(s)	27
SspI	AATATT	1 cut(s)	88
StyD4I	CCNGG	2 cut(s)	10, 451
TaaI	ACNGT	2 cut(s)	100, 419
TaqI	TCGA	3 cut(s)	301, 396, 466
TasI	AATT	6 cut(s)	103, 116, 278, 380, 513, 587
TatI	WGTACW	2 cut(s)	248, 268
TfiI	GAWTC	1 cut(s)	303
Tru1I	TTAA	3 cut(s)	126, 345, 378
Tru9I	TTAA	3 cut(s)	126, 345, 378
TscAI	CASTG	1 cut(s)	225
TseI	GCWGC	3 cut(s)	24, 179, 284
TspDTI	ATGAA	2 cut(s)	450, 485
TspGWI	ACGGA	1 cut(s)	304
TspRI	CASTG	1 cut(s)	225
Vha464I	CTTAAG	1 cut(s)	125
XapI	RAATTY	2 cut(s)	380, 587
XcmI	CCANNNNNNNNNTGG	2 cut(s)	103, 359

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