Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5B

Orthogroup ID

OG0000930

Physical Location & Seq

Genomic Coordinates Reverse (-)

89553623 .. 89557018

Gene Structure 3396 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5BG565800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 501 bp

ATGGCAGAACCAGGGTTGGAGGGCAGCGGAAGCCAACCTGTAGATCTGAAGCAACATCCTTCTGGGATCGTCCCTACTCTTCAGAATATTGTGTCCACAGTCAATTTGGACTGCAAATTGGATCTTAAGGCCATTGCGTTGCAAGCTCGTAATGCAGAATACAATCCCAAGCGTTTTGCAGCTGTGATTATGAGAATAAGAGAACCGAAAACTACTGCACTGATATTTGCATCTGGTAAAATGGTTTGTACAGGAGCTAAGAGTGAAGTACAATCGAAATTGGCAGCACGGAAGTATGCTCGAATCATTCAGAAACTTGGTTTTCCTGCCAAGTTCAAGGACTTTAAAATCCAGAACATAGTTGGTTCTTGTGATGTTAAATTCCCCATAAGACTTGAAGGTCTGGCATATTCCCACGGTGCCTTCTCAAGTGTGAGTATACCTTTGTGTCTTGATGTGGTTGCTGTTGGATATCTAATCTTGGAACAAACTGTTTACTGA

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

166

Amino Acids

18.05

Weight (kDa)

9.43

Isoelectric Point (pI)

38.47

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TBP	PF00352	25 - 106	1.2e-33	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)

Image

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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
AccI	GTMKAC	1 cut(s)	439
AciI	CCGC	1 cut(s)	27
AclWI	GGATC	2 cut(s)	74, 129
AcsI	RAATTY	1 cut(s)	380
AcuI	CTGAAG	2 cut(s)	65, 68
AfaI	GTAC	2 cut(s)	250, 270
AflII	CTTAAG	1 cut(s)	125
AgsI	TTSAA	2 cut(s)	337, 398
AjnI	CCWGG	1 cut(s)	10
AluBI	AGCT	3 cut(s)	146, 182, 257
AluI	AGCT	3 cut(s)	146, 182, 257
AlwI	GGATC	2 cut(s)	74, 129
AoxI	GGCC	1 cut(s)	129
ApeKI	GCWGC	3 cut(s)	24, 179, 284
ApoI	RAATTY	1 cut(s)	380
BanI	GGYRCC	1 cut(s)	419
BbvI	GCAGC	3 cut(s)	36, 191, 296
BciT130I	CCWGG	1 cut(s)	12
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	1 cut(s)	12
BmiI	GGNNCC	1 cut(s)	421
BmrFI	CCNGG	1 cut(s)	12
BmsI	GCATC	1 cut(s)	239
BpuEI	CTTGAG	1 cut(s)	412
BsaJI	CCNNGG	2 cut(s)	11, 415
Bse3DI	GCAATG	1 cut(s)	132
BseBI	CCWGG	1 cut(s)	12
BseDI	CCNNGG	2 cut(s)	11, 415
BseGI	GGATG	1 cut(s)	55
BseMI	GCAATG	1 cut(s)	132
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
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
BssECI	CCNNGG	2 cut(s)	11, 415
BssMI	GATC	3 cut(s)	43, 66, 121
BssNAI	GTATAC	1 cut(s)	440
Bst1107I	GTATAC	1 cut(s)	440
Bst2UI	CCWGG	1 cut(s)	12
Bst4CI	ACNGT	3 cut(s)	100, 419, 493
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
BstMBI	GATC	3 cut(s)	43, 66, 121
BstMWI	GCNNNNNNNGC	3 cut(s)	30, 143, 152
BstNI	CCWGG	1 cut(s)	12
BstSCI	CCNGG	1 cut(s)	10
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
BstZ17I	GTATAC	1 cut(s)	440
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	5 cut(s)	33, 131, 146, 182, 257
CviKI_1	RGCY	5 cut(s)	33, 131, 146, 182, 257
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
Eco32I	GATATC	1 cut(s)	473
Eco57I	CTGAAG	2 cut(s)	65, 68
EcoRII	CCWGG	1 cut(s)	10
EcoRV	GATATC	1 cut(s)	473
FaiI	YATR	6 cut(s)	191, 297, 359, 389, 409, 440
FaqI	GGGAC	1 cut(s)	56
FblI	GTMKAC	1 cut(s)	439
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	1 cut(s)	303
Hpy166II	GTNNAC	3 cut(s)	96, 440, 496
Hpy188I	TCNGA	3 cut(s)	48, 84, 312
Hpy188III	TCNNGA	2 cut(s)	352, 452
Hpy8I	GTNNAC	3 cut(s)	96, 440, 496
HpyAV	CCTTC	3 cut(s)	69, 392, 433
HpyCH4III	ACNGT	3 cut(s)	100, 419, 493
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	1 cut(s)	254
LpnPI	CCDG	8 cut(s)	24, 48, 51, 219, 237, 339, 365, 389
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	4 cut(s)	103, 116, 278, 380
MmeI	TCCRAC	1 cut(s)	448
MnlI	CCTC	1 cut(s)	13
MseI	TTAA	3 cut(s)	126, 345, 378
MspA1I	CMGCKG	2 cut(s)	27, 182
MspCI	CTTAAG	1 cut(s)	125
MspR9I	CCNGG	1 cut(s)	12
MvaI	CCWGG	1 cut(s)	12
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
Psp6I	CCWGG	1 cut(s)	10
PspGI	CCWGG	1 cut(s)	10
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
ScrFI	CCNGG	1 cut(s)	12
SetI	ASST	6 cut(s)	40, 148, 184, 259, 403, 445
SfaNI	GCATC	1 cut(s)	239
SfcI	CTRYAG	1 cut(s)	39
SmlI	CTYRAG	2 cut(s)	125, 427
SmoI	CTYRAG	2 cut(s)	125, 427
Sse9I	AATT	4 cut(s)	103, 116, 278, 380
SsiI	CCGC	1 cut(s)	27
SspI	AATATT	1 cut(s)	88
StyD4I	CCNGG	1 cut(s)	10
TaaI	ACNGT	3 cut(s)	100, 419, 493
TaqI	TCGA	2 cut(s)	275, 301
TasI	AATT	4 cut(s)	103, 116, 278, 380
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
TspGWI	ACGGA	1 cut(s)	304
TspRI	CASTG	1 cut(s)	225
Vha464I	CTTAAG	1 cut(s)	125
XapI	RAATTY	1 cut(s)	380
XcmI	CCANNNNNNNNNTGG	2 cut(s)	103, 359
XmiI	GTMKAC	1 cut(s)	439

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