Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4D

Orthogroup ID

OG0000310

Physical Location & Seq

Genomic Coordinates Forward (+)

12588055 .. 12588408

Gene Structure 354 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4DG083500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 354 bp

ATGGAGAAGCCGATCTACGACACTGTCGACGAGGACAAGTACGACGCGATCATCGCCAAGAGCCGCGAGGAGTTCGGGGACTTCATCGAGGATGACGACGGCCTAGGATACCGCGACGACGGCGAGGAAGAGGACTGGACCCGCCGCGGGCTTCCGACGTCGTCGGATGAATCAGACAGCGATATGAGGCCCAGGAGGAGGAAAAAGGTGGAGAAGAAGGAGAAGGAGAAGGAGCCGCGGCACAAAAAGCCCAATTCGTCGCTTACGGCGGCGGCGGCGATGATGGGGAAGCAGAGGCTTTCGTCGATGTTCACGTCTTCAGTGTTTAAAAAAAGTAGGGATCGCTGCTATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000228 GO:0000428 GO:0000726 GO:0003674 GO:0003824 GO:0003887 GO:0003896 GO:0003899 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005657 GO:0005658 GO:0005694 GO:0006139 GO:0006259 GO:0006260 GO:0006261 GO:0006269 GO:0006270 GO:0006271 GO:0006272 GO:0006273 GO:0006281 GO:0006302 GO:0006303 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0007275 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009653 GO:0009965 GO:0009987 GO:0010016 GO:0016070 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019438 GO:0022616 GO:0030880 GO:0030894 GO:0031974 GO:0031981 GO:0032501 GO:0032502 GO:0032774 GO:0032991 GO:0032993 GO:0033554 GO:0034061 GO:0034062 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043596 GO:0043601 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044427 GO:0044428 GO:0044446 GO:0044454 GO:0044464 GO:0046483 GO:0048366 GO:0048367 GO:0048731 GO:0048827 GO:0048856 GO:0050896 GO:0051716 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0071897 GO:0090304 GO:0097747 GO:0099402 GO:0140097 GO:0140098 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1905392 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03030 map00230 map00240 map01100 map03030

Pfam Domains

Protein Families

DNA_pol_B DNA_pol_B_exo1 DNA_pol_alpha_N zf-DNA_Pol

Protein Analysis

117

Amino Acids

13.66

Weight (kDa)

5.58

Isoelectric Point (pI)

53.89

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DNA_pol_alpha_N	PF12254	2 - 46	2.6e-13	DNA polymerase alpha subunit p180 N terminal

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: OG0000310)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G67100 AT5G67100
fragaria_vesca	FvH4_1g20001 FvH4_1g22730 FvH4_1g22730 FvH4_1g22730 FvH4_6g13861 FvH4_6g33603
malus_domestica	MD02G1174100.v1.1 MD02G1174200.v1.1 MD02G1174400.v1.1 MD15G1285400.v1.1
prunus_persica	Prupe.7G131600_v2.0.a1
pyrus_communis	pycom02g14040 pycom02g14050 pycom02g14060 pycom02g14070 pycom15g24830 pycom15g24840
rosa_chinensis	RchiOBHm_Chr2g0109901 RchiOBHm_Chr2g0117021 RchiOBHm_Chr2g0168121 RchiOBHm_Chr4g0394581
rosa_laevigata	RLG00000001621 RLG00000001943 RLG00000003450 RLG00000006116 RLG00000006535 RLG00000008147 RLG00000009121 RLG00000010680 RLG00000013987 RLG00000017585 RLG00000017603 RLG00000017638 RLG00000017923 RLG00000018320 RLG00000021520 RLG00000022613 RLG00000022614 RLG00000023966 RLG00000025998 RLG00000027760 RLG00000033421
rosa_multiflora	Rmu_co7985806.1_g000001 Rmu_co8250293.1_g000001 Rmu_co8353517.1_g000001 Rmu_sc0000697.1_g000011 Rmu_sc0000776.1_g000079 Rmu_sc0001023.1_g000057 Rmu_sc0001266.1_g000019 Rmu_sc0002711.1_g000010 Rmu_sc0002731.1_g000005 Rmu_sc0003002.1_g000047 Rmu_sc0003030.1_g000002 Rmu_sc0003672.1_g000003 Rmu_sc0004168.1_g000062 Rmu_sc0004180.1_g000003 Rmu_sc0009205.1_g000008 Rmu_sc0011259.1_g000001 Rmu_sc0011259.1_g000002 Rmu_sc0027274.1_g000001
rosa_roxburghii	Rroxscaffold_1G00023520 Rroxscaffold_2G00104450 Rroxscaffold_2G00126810 Rroxscaffold_2G00144870 Rroxscaffold_4G00315680 Rroxscaffold_4G00331480 Rroxscaffold_7G00182820
rosa_rugosa	Rorug02G0209600 Rorug04G0130600 Rorug04G0130600 Rorug04G0130700 Rorug05G0230000
rosa_samantha	Rh1AG170000 Rh1CG157700 Rh1CG385600 Rh2AG215100 Rh2AG265500 Rh2BG277300 Rh2CG217600 Rh2CG217700 Rh2DG220600 Rh2DG272800 Rh2DG291800 Rh3AG215700 Rh3BG271700 Rh3DG075200 Rh3DG242600 Rh4AG115400 Rh4AG138100 Rh4AG333600 Rh4BG115100 Rh4BG366300 Rh4CG125400 Rh4CG380400 Rh4DG083500 Rh4DG113200 Rh4DG192900 Rh4DG246300 Rh5AG075000 Rh5BG482300 Rh5CG181200 Rh5CG247200 Rh5CG506900 Rh5DG167600 Rh5DG202900 Rh6AG000500 Rh6AG213400 Rh6BG335800 Rh6CG255700 Rh7AG337500 Rh7BG404500 Rh7BG461500 Rh7CG355600
rosa_wichuraiana	Rw0G019110 Rw2G020950

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AatII	GACGTC	1 cut(s)	161
AccI	GTMKAC	1 cut(s)	27
AccII	CGCG	5 cut(s)	47, 66, 114, 147, 238
AclWI	GGATC	1 cut(s)	348
AcuI	CTGAAG	1 cut(s)	303
AcyI	GRCGYC	1 cut(s)	158
AfaI	GTAC	1 cut(s)	41
AfiI	CCNNNNNNNGG	2 cut(s)	147, 198
AjiI	CACGTC	1 cut(s)	315
AjnI	CCWGG	1 cut(s)	191
AlwI	GGATC	1 cut(s)	348
AoxI	GGCC	2 cut(s)	100, 188
ApeKI	GCWGC	1 cut(s)	345
AspA2I	CCTAGG	1 cut(s)	103
AspS9I	GGNCC	2 cut(s)	138, 189
AvaII	GGWCC	1 cut(s)	138
AvrII	CCTAGG	1 cut(s)	103
BarI	GAAGNNNNNNTAC	1 cut(s)	31
BbsI	GAAGAC	1 cut(s)	309
BbvI	GCAGC	1 cut(s)	332
BccI	CCATC	1 cut(s)	277
BceAI	ACGGC	3 cut(s)	115, 136, 282
BciT130I	CCWGG	1 cut(s)	193
BciVI	GTATCC	1 cut(s)	101
BfaI	CTAG	1 cut(s)	104
BfuI	GTATCC	1 cut(s)	101
BisI	GCNGC	8 cut(s)	64, 145, 236, 239, 270, 273, 276, 346
BlnI	CCTAGG	1 cut(s)	103
BlsI	GCNGC	8 cut(s)	65, 146, 237, 240, 271, 274, 277, 347
Bme1390I	CCNGG	1 cut(s)	193
Bme18I	GGWCC	1 cut(s)	138
BmgBI	CACGTC	1 cut(s)	315
BmgT120I	GGNCC	2 cut(s)	138, 189
BmiI	GGNNCC	2 cut(s)	140, 234
BmrFI	CCNGG	1 cut(s)	193
BpiI	GAAGAC	1 cut(s)	309
BsaHI	GRCGYC	1 cut(s)	158
BsaJI	CCNNGG	4 cut(s)	103, 145, 191, 236
Bsc4I	CCNNNNNNNGG	2 cut(s)	147, 198
Bse1I	ACTGG	1 cut(s)	140
BseBI	CCWGG	1 cut(s)	193
BseDI	CCNNGG	4 cut(s)	103, 145, 191, 236
BseGI	GGATG	2 cut(s)	97, 172
BseLI	CCNNNNNNNGG	2 cut(s)	147, 198
BseNI	ACTGG	1 cut(s)	140
BseRI	GAGGAG	2 cut(s)	83, 211
BseXI	GCAGC	1 cut(s)	332
Bsh1236I	CGCG	5 cut(s)	47, 66, 114, 147, 238
BshFI	GGCC	2 cut(s)	102, 190
BslFI	GGGAC	1 cut(s)	92
BslI	CCNNNNNNNGG	2 cut(s)	147, 198
BsmFI	GGGAC	1 cut(s)	92
BsnI	GGCC	2 cut(s)	102, 190
Bsp143I	GATC	3 cut(s)	12, 48, 340
BspANI	GGCC	2 cut(s)	102, 190
BspFNI	CGCG	5 cut(s)	47, 66, 114, 147, 238
BspLI	GGNNCC	2 cut(s)	140, 234
BspPI	GGATC	1 cut(s)	348
BsrI	ACTGG	1 cut(s)	140
BssECI	CCNNGG	4 cut(s)	103, 145, 191, 236
BssMI	GATC	3 cut(s)	12, 48, 340
BssNI	GRCGYC	1 cut(s)	158
BssT1I	CCWWGG	1 cut(s)	103
Bst2UI	CCWGG	1 cut(s)	193
Bst4CI	ACNGT	1 cut(s)	25
Bst6I	CTCTTC	1 cut(s)	123
BstACI	GRCGYC	1 cut(s)	158
BstC8I	GCNNGC	1 cut(s)	149
BstDSI	CCRYGG	2 cut(s)	145, 236
BstF5I	GGATG	2 cut(s)	97, 172
BstFNI	CGCG	5 cut(s)	47, 66, 114, 147, 238
BstKTI	GATC	3 cut(s)	15, 51, 343
BstMBI	GATC	3 cut(s)	12, 48, 340
BstMWI	GCNNNNNNNGC	4 cut(s)	53, 120, 247, 275
BstNI	CCWGG	1 cut(s)	193
BstSCI	CCNGG	1 cut(s)	191
BstUI	CGCG	5 cut(s)	47, 66, 114, 147, 238
BstV1I	GCAGC	1 cut(s)	332
BstV2I	GAAGAC	1 cut(s)	309
BsuI	GTATCC	1 cut(s)	101
BsuRI	GGCC	2 cut(s)	102, 190
BtgI	CCRYGG	2 cut(s)	145, 236
BtgZI	GCGATG	2 cut(s)	37, 293
BtrI	CACGTC	1 cut(s)	315
BtsCI	GGATG	2 cut(s)	97, 172
BtsIMutI	CAGTG	2 cut(s)	21, 327
Cac8I	GCNNGC	1 cut(s)	149
Cfr13I	GGNCC	2 cut(s)	138, 189
Cfr42I	CCGCGG	2 cut(s)	148, 239
CseI	GACGC	1 cut(s)	53
Csp6I	GTAC	1 cut(s)	40
CviJI	RGCY	8 cut(s)	10, 63, 102, 151, 190, 235, 250, 298
CviKI_1	RGCY	8 cut(s)	10, 63, 102, 151, 190, 235, 250, 298
CviQI	GTAC	1 cut(s)	40
DpnI	GATC	3 cut(s)	14, 50, 342
DpnII	GATC	3 cut(s)	12, 48, 340
DraI	TTTAAA	1 cut(s)	328
Eam1104I	CTCTTC	1 cut(s)	123
EarI	CTCTTC	1 cut(s)	123
Eco130I	CCWWGG	1 cut(s)	103
Eco47I	GGWCC	1 cut(s)	138
Eco57I	CTGAAG	1 cut(s)	303
EcoRII	CCWGG	1 cut(s)	191
EcoT14I	CCWWGG	1 cut(s)	103
ErhI	CCWWGG	1 cut(s)	103
FaiI	YATR	1 cut(s)	185
FaqI	GGGAC	1 cut(s)	92
FauI	CCCGC	2 cut(s)	140, 149
FblI	GTMKAC	1 cut(s)	27
Fnu4HI	GCNGC	8 cut(s)	64, 145, 236, 239, 270, 273, 276, 346
FokI	GGATG	2 cut(s)	104, 179
Fsp4HI	GCNGC	8 cut(s)	64, 145, 236, 239, 270, 273, 276, 346
FspBI	CTAG	1 cut(s)	104
GluI	GCNGC	8 cut(s)	64, 145, 236, 239, 270, 273, 276, 346
HaeIII	GGCC	2 cut(s)	102, 190
HgaI	GACGC	1 cut(s)	53
Hin1I	GRCGYC	1 cut(s)	158
HincII	GTYRAC	1 cut(s)	28
HindII	GTYRAC	1 cut(s)	28
HinfI	GANTC	1 cut(s)	170
Hpy166II	GTNNAC	2 cut(s)	28, 312
Hpy188I	TCNGA	3 cut(s)	156, 166, 175
Hpy8I	GTNNAC	2 cut(s)	28, 312
HpyAV	CCTTC	3 cut(s)	211, 217, 223
HpyCH4III	ACNGT	1 cut(s)	25
HpyCH4IV	ACGT	2 cut(s)	158, 314
HpyF10VI	GCNNNNNNNGC	4 cut(s)	53, 120, 247, 275
HpySE526I	ACGT	2 cut(s)	158, 314
Hsp92I	GRCGYC	1 cut(s)	158
KspI	CCGCGG	2 cut(s)	148, 239
Kzo9I	GATC	3 cut(s)	12, 48, 340
LmnI	GCTCC	1 cut(s)	232
LpnPI	CCDG	3 cut(s)	121, 178, 205
Lsp1109I	GCAGC	1 cut(s)	332
MaeI	CTAG	1 cut(s)	104
MaeII	ACGT	2 cut(s)	158, 314
MalI	GATC	3 cut(s)	14, 50, 342
MboI	GATC	3 cut(s)	12, 48, 340
MboII	GAAGA	3 cut(s)	140, 226, 309
MluCI	AATT	1 cut(s)	253
MmeI	TCCRAC	2 cut(s)	144, 179
MnlI	CCTC	9 cut(s)	25, 61, 82, 118, 124, 180, 189, 192, 288
MseI	TTAA	1 cut(s)	327
MspA1I	CMGCKG	2 cut(s)	147, 238
MspR9I	CCNGG	1 cut(s)	193
MvaI	CCWGG	1 cut(s)	193
MvnI	CGCG	5 cut(s)	47, 66, 114, 147, 238
MwoI	GCNNNNNNNGC	4 cut(s)	53, 120, 247, 275
NdeII	GATC	3 cut(s)	12, 48, 340
NlaIV	GGNNCC	2 cut(s)	140, 234
PcsI	WCGNNNNNNNCGW	3 cut(s)	24, 93, 311
PfeI	GAWTC	1 cut(s)	170
PflFI	GACNNNGTC	2 cut(s)	23, 160
PkrI	GCNGC	8 cut(s)	65, 146, 237, 240, 271, 274, 277, 347
Psp6I	CCWGG	1 cut(s)	191
PspGI	CCWGG	1 cut(s)	191
PspN4I	GGNNCC	2 cut(s)	140, 234
PspPI	GGNCC	2 cut(s)	138, 189
PsyI	GACNNNGTC	2 cut(s)	23, 160
RsaI	GTAC	1 cut(s)	41
RsaNI	GTAC	1 cut(s)	40
SacII	CCGCGG	2 cut(s)	148, 239
SalI	GTCGAC	1 cut(s)	26
SaqAI	TTAA	1 cut(s)	327
SatI	GCNGC	8 cut(s)	64, 145, 236, 239, 270, 273, 276, 346
Sau3AI	GATC	3 cut(s)	12, 48, 340
Sau96I	GGNCC	2 cut(s)	138, 189
ScrFI	CCNGG	1 cut(s)	193
SetI	ASST	3 cut(s)	161, 210, 317
Sfr303I	CCGCGG	2 cut(s)	148, 239
SgrBI	CCGCGG	2 cut(s)	148, 239
SinI	GGWCC	1 cut(s)	138
Sse9I	AATT	1 cut(s)	253
SspMI	CTAG	1 cut(s)	104
StyD4I	CCNGG	1 cut(s)	191
StyI	CCWWGG	1 cut(s)	103
TaaI	ACNGT	1 cut(s)	25
TaiI	ACGT	2 cut(s)	161, 317
TaqI	TCGA	3 cut(s)	27, 87, 305
TasI	AATT	1 cut(s)	253
TauI	GCSGC	7 cut(s)	66, 147, 238, 241, 272, 275, 278
TfiI	GAWTC	1 cut(s)	170
Tru1I	TTAA	1 cut(s)	327
Tru9I	TTAA	1 cut(s)	327
TscAI	CASTG	2 cut(s)	28, 327
TseI	GCWGC	1 cut(s)	345
TspDTI	ATGAA	2 cut(s)	73, 183
TspRI	CASTG	2 cut(s)	28, 327
Tth111I	GACNNNGTC	2 cut(s)	23, 160
VpaK11BI	GGWCC	1 cut(s)	138
XmaJI	CCTAGG	1 cut(s)	103
XmiI	GTMKAC	1 cut(s)	27
XspI	CTAG	1 cut(s)	104
ZraI	GACGTC	1 cut(s)	159

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