Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5A

Orthogroup ID

OG0004646

Physical Location & Seq

Genomic Coordinates Reverse (-)

72930301 .. 72931360

Gene Structure 1060 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5AG422400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 405 bp

ATGCAGGAGCGGTTGCCTGAAGGATTGCCCTCTGATTGGCAGGCGATCAAAAAAACCCGAAAGAGTGGCAAATCTGCCGGGCAGGTTGATAAGTACTACATCAGCCCGGAAGGGAGGACCCTTCGATCACTGCCAGAAGTGGAACAGTTTCTCGAAACACATAAAGTGGAAGAGAGACAAATTAAAGATGAAGAAGATAGATCAGATCCGGAGAGCATGAAGAGCATCCCGGCGGAGGAGGATATGACCGGCCTATGCTTCAAGGACGAGGCTTGGCTGCAAACATTCCCTCTGGATCGCAATATGGTATTCGAGTACTTCGCCTTGTCTCCTTTTTATGACTGCAACCAACAACTCCGCAAAGCTCCGTTCACCCATTCGACCTCTCTTGCCTCTCACAAATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0001128 GO:0003674 GO:0003712 GO:0003713 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005667 GO:0006139 GO:0006351 GO:0006352 GO:0006355 GO:0006357 GO:0006366 GO:0006367 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009889 GO:0009891 GO:0009893 GO:0009987 GO:0010467 GO:0010468 GO:0010556 GO:0010557 GO:0010604 GO:0016043 GO:0016070 GO:0016591 GO:0016592 GO:0018130 GO:0019219 GO:0019222 GO:0019438 GO:0022607 GO:0030880 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0034622 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0043933 GO:0044085 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0044798 GO:0045935 GO:0046483 GO:0048518 GO:0048522 GO:0050789 GO:0050794 GO:0051123 GO:0051171 GO:0051173 GO:0051252 GO:0051254 GO:0055029 GO:0060255 GO:0061695 GO:0065003 GO:0065004 GO:0065007 GO:0070013 GO:0070847 GO:0070897 GO:0071704 GO:0071824 GO:0071840 GO:0080090 GO:0090304 GO:0090575 GO:0097659 GO:0140110 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1902680 GO:1903506 GO:1903508 GO:1990234 GO:2000112 GO:2001141

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Med6

Protein Analysis

134

Amino Acids

15.6

Weight (kDa)

5.27

Isoelectric Point (pI)

65.4

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
MBD	PF01429	9 - 61	1.4e-14	Methyl-CpG binding domain
Med6	PF04934	85 - 119	9.8e-08	MED6 mediator sub complex component

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready

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Orthologous Genes (Group: OG0004646)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G21350 AT3G21350
fragaria_vesca	FvH4_6g32730
malus_domestica	MD14G1079700.v1.1
prunus_persica	Prupe.3G054900_v2.0.a1
pyrus_communis	pycom14g06830
rosa_chinensis	RchiOBHm_Chr2g0141751 RchiOBHm_Chr5g0064381
rosa_laevigata	RLG00000019933 RLG00000035719
rosa_roxburghii	Rroxscaffold_1G00016640 Rroxscaffold_1G00016650 Rroxscaffold_2G00103900
rosa_rugosa	Rorug02G0368600 Rorug02G0368800 Rorug05G0364200
rosa_samantha	Rh2AG420200 Rh2BG429600 Rh2BG430900 Rh2CG407400 Rh2DG439500 Rh2DG440600 Rh5AG422400 Rh5BG438300 Rh5CG460800 Rh5CG460900 Rh5CG461000 Rh5DG451200 Rh5DG451300 Rh5DG451400
rosa_wichuraiana	Rw2G034460

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc36I	ACCTGC	1 cut(s)	73
AccBSI	CCGCTC	1 cut(s)	10
AccIII	TCCGGA	1 cut(s)	208
AciI	CCGC	3 cut(s)	10, 233, 358
AclWI	GGATC	2 cut(s)	200, 303
AcuI	CTGAAG	1 cut(s)	39
AfaI	GTAC	2 cut(s)	95, 317
AfiI	CCNNNNNNNGG	2 cut(s)	36, 235
AgsI	TTSAA	1 cut(s)	262
AluBI	AGCT	1 cut(s)	365
AluI	AGCT	1 cut(s)	365
Alw26I	GTCTC	2 cut(s)	169, 333
AlwI	GGATC	2 cut(s)	200, 303
Aor13HI	TCCGGA	1 cut(s)	208
AoxI	GGCC	1 cut(s)	250
ApeKI	GCWGC	1 cut(s)	277
Asp700I	GAANNNNTTC	1 cut(s)	147
AspS9I	GGNCC	1 cut(s)	117
AsuC2I	CCSGG	3 cut(s)	79, 107, 230
AsuHPI	GGTGA	1 cut(s)	364
AvaII	GGWCC	1 cut(s)	117
BbvI	GCAGC	1 cut(s)	264
BcnI	CCSGG	3 cut(s)	79, 107, 230
BcoDI	GTCTC	2 cut(s)	169, 333
BfuAI	ACCTGC	1 cut(s)	73
BisI	GCNGC	1 cut(s)	278
BlsI	GCNGC	1 cut(s)	279
BmcAI	AGTACT	2 cut(s)	95, 317
Bme1390I	CCNGG	3 cut(s)	79, 107, 230
Bme18I	GGWCC	1 cut(s)	117
BmgT120I	GGNCC	1 cut(s)	117
BmiI	GGNNCC	1 cut(s)	119
BmrFI	CCNGG	3 cut(s)	79, 107, 230
BmsI	GCATC	1 cut(s)	234
BpuMI	CCSGG	3 cut(s)	79, 107, 230
BsaWI	WCCGGW	1 cut(s)	208
Bsc4I	CCNNNNNNNGG	2 cut(s)	36, 235
Bse118I	RCCGGY	1 cut(s)	248
BseAI	TCCGGA	1 cut(s)	208
BseGI	GGATG	1 cut(s)	225
BseLI	CCNNNNNNNGG	2 cut(s)	36, 235
BseRI	GAGGAG	1 cut(s)	251
BseXI	GCAGC	1 cut(s)	264
BshFI	GGCC	1 cut(s)	252
BsiSI	CCGG	5 cut(s)	78, 107, 209, 230, 249
BslI	CCNNNNNNNGG	2 cut(s)	36, 235
BsmAI	GTCTC	2 cut(s)	169, 333
BsnI	GGCC	1 cut(s)	252
Bsp13I	TCCGGA	1 cut(s)	208
Bsp143I	GATC	5 cut(s)	45, 125, 200, 205, 295
BspACI	CCGC	3 cut(s)	10, 233, 358
BspANI	GGCC	1 cut(s)	252
BspEI	TCCGGA	1 cut(s)	208
BspLI	GGNNCC	1 cut(s)	119
BspMI	ACCTGC	1 cut(s)	73
BspPI	GGATC	2 cut(s)	200, 303
BspQI	GCTCTTC	1 cut(s)	215
BsrBI	CCGCTC	1 cut(s)	10
BsrFI	RCCGGY	1 cut(s)	248
BssAI	RCCGGY	1 cut(s)	248
BssMI	GATC	5 cut(s)	45, 125, 200, 205, 295
Bst4CI	ACNGT	1 cut(s)	147
Bst6I	CTCTTC	2 cut(s)	165, 215
BstC8I	GCNNGC	1 cut(s)	42
BstF5I	GGATG	1 cut(s)	225
BstKTI	GATC	5 cut(s)	48, 128, 203, 208, 298
BstMAI	GTCTC	2 cut(s)	169, 333
BstMBI	GATC	5 cut(s)	45, 125, 200, 205, 295
BstMWI	GCNNNNNNNGC	1 cut(s)	222
BstSCI	CCNGG	3 cut(s)	77, 105, 228
BstV1I	GCAGC	1 cut(s)	264
BstX2I	RGATCY	1 cut(s)	205
BstYI	RGATCY	1 cut(s)	205
BsuRI	GGCC	1 cut(s)	252
BtsCI	GGATG	1 cut(s)	225
BtsI	GCAGTG	1 cut(s)	128
BtsIMutI	CAGTG	1 cut(s)	128
BveI	ACCTGC	1 cut(s)	73
Cac8I	GCNNGC	1 cut(s)	42
Cfr10I	RCCGGY	1 cut(s)	248
Cfr13I	GGNCC	1 cut(s)	117
Csp6I	GTAC	2 cut(s)	94, 316
CviAII	CATG	1 cut(s)	217
CviJI	RGCY	5 cut(s)	105, 252, 272, 277, 365
CviKI_1	RGCY	5 cut(s)	105, 252, 272, 277, 365
CviQI	GTAC	2 cut(s)	94, 316
DpnI	GATC	5 cut(s)	47, 127, 202, 207, 297
DpnII	GATC	5 cut(s)	45, 125, 200, 205, 295
Eam1104I	CTCTTC	2 cut(s)	165, 215
EarI	CTCTTC	2 cut(s)	165, 215
EciI	GGCGGA	1 cut(s)	248
Eco47I	GGWCC	1 cut(s)	117
Eco57I	CTGAAG	1 cut(s)	39
EcoO109I	RGGNCCY	1 cut(s)	117
FaeI	CATG	1 cut(s)	220
FaiI	YATR	6 cut(s)	162, 218, 245, 256, 305, 339
FatI	CATG	1 cut(s)	216
Fnu4HI	GCNGC	1 cut(s)	278
FokI	GGATG	1 cut(s)	212
Fsp4HI	GCNGC	1 cut(s)	278
GluI	GCNGC	1 cut(s)	278
HaeIII	GGCC	1 cut(s)	252
HapII	CCGG	5 cut(s)	78, 107, 209, 230, 249
Hin1II	CATG	1 cut(s)	220
HpaII	CCGG	5 cut(s)	78, 107, 209, 230, 249
HphI	GGTGA	1 cut(s)	364
Hpy166II	GTNNAC	1 cut(s)	372
Hpy188I	TCNGA	2 cut(s)	34, 205
Hpy188III	TCNNGA	3 cut(s)	152, 209, 293
Hpy8I	GTNNAC	1 cut(s)	372
HpyAV	CCTTC	3 cut(s)	14, 104, 131
HpyCH4III	ACNGT	1 cut(s)	147
HpyCH4V	TGCA	3 cut(s)	4, 280, 345
HpyF10VI	GCNNNNNNNGC	1 cut(s)	222
Hsp92II	CATG	1 cut(s)	220
Kpn2I	TCCGGA	1 cut(s)	208
Kzo9I	GATC	5 cut(s)	45, 125, 200, 205, 295
LguI	GCTCTTC	1 cut(s)	215
LmnI	GCTCC	2 cut(s)	7, 370
Lsp1109I	GCAGC	1 cut(s)	264
LweI	GCATC	1 cut(s)	234
MalI	GATC	5 cut(s)	47, 127, 202, 207, 297
MbiI	CCGCTC	1 cut(s)	10
MboI	GATC	5 cut(s)	45, 125, 200, 205, 295
MboII	GAAGA	4 cut(s)	182, 203, 206, 232
MflI	RGATCY	1 cut(s)	205
MluCI	AATT	1 cut(s)	180
MnlI	CCTC	8 cut(s)	40, 108, 229, 232, 262, 300, 394, 403
MroI	TCCGGA	1 cut(s)	208
MroXI	GAANNNNTTC	1 cut(s)	147
MseI	TTAA	1 cut(s)	183
MspI	CCGG	5 cut(s)	78, 107, 209, 230, 249
MspR9I	CCNGG	3 cut(s)	79, 107, 230
MwoI	GCNNNNNNNGC	1 cut(s)	222
NciI	CCSGG	3 cut(s)	79, 107, 230
NdeII	GATC	5 cut(s)	45, 125, 200, 205, 295
NlaIII	CATG	1 cut(s)	220
NlaIV	GGNNCC	1 cut(s)	119
PciSI	GCTCTTC	1 cut(s)	215
PdmI	GAANNNNTTC	1 cut(s)	147
PkrI	GCNGC	1 cut(s)	279
PpuMI	RGGWCCY	1 cut(s)	117
Psp5II	RGGWCCY	1 cut(s)	117
PspN4I	GGNNCC	1 cut(s)	119
PspPI	GGNCC	1 cut(s)	117
PspPPI	RGGWCCY	1 cut(s)	117
PsuI	RGATCY	1 cut(s)	205
RsaI	GTAC	2 cut(s)	95, 317
RsaNI	GTAC	2 cut(s)	94, 316
SapI	GCTCTTC	1 cut(s)	215
SaqAI	TTAA	1 cut(s)	183
SatI	GCNGC	1 cut(s)	278
Sau3AI	GATC	5 cut(s)	45, 125, 200, 205, 295
Sau96I	GGNCC	1 cut(s)	117
ScaI	AGTACT	2 cut(s)	95, 317
ScrFI	CCNGG	3 cut(s)	79, 107, 230
SetI	ASST	3 cut(s)	87, 367, 386
SfaNI	GCATC	1 cut(s)	234
SinI	GGWCC	1 cut(s)	117
Sse9I	AATT	1 cut(s)	180
SsiI	CCGC	3 cut(s)	10, 233, 358
StyD4I	CCNGG	3 cut(s)	77, 105, 228
TaaI	ACNGT	1 cut(s)	147
TaqI	TCGA	4 cut(s)	124, 153, 312, 380
TasI	AATT	1 cut(s)	180
TatI	WGTACW	2 cut(s)	93, 315
Tru1I	TTAA	1 cut(s)	183
Tru9I	TTAA	1 cut(s)	183
TscAI	CASTG	1 cut(s)	135
TseI	GCWGC	1 cut(s)	277
TspDTI	ATGAA	2 cut(s)	204, 233
TspGWI	ACGGA	1 cut(s)	357
TspRI	CASTG	1 cut(s)	135
VpaK11BI	GGWCC	1 cut(s)	117
XmnI	GAANNNNTTC	1 cut(s)	147
ZrmI	AGTACT	2 cut(s)	95, 317

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