Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3D

Orthogroup ID

OG0005462

Physical Location & Seq

Genomic Coordinates Reverse (-)

44937179 .. 44944393

Gene Structure 7215 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3DG362200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 864 bp

ATGCTGTGGGTAGACAAGTACAGACCCAAAACCCTCGACCAGGCAATGGTCCACCAAGACACGGCGCAAAACCTCAAGAAACTTGTCGCGGAGCAGGACTGCCCCCATTTGCTCTTTTACGGGCCTTCCGGCTCCGGCAAGAAAACCCTAATCATCGCCCTTATTCGTCAGATTTTCGGACCCAGCGCCGACAAGGTGAAGGTGGAAAACAGGACATGGAAAGTTGATGCTGGGAGTAGAACCATTGACATAGAGCTGACTACATTATCAAGCACCAATCACATTGAACTCAACCCCAGTGATGCAGGCTTTCAGGACAGATACATTGTTCAAGAGATAATTAAGGAAATGGCTAAAAATAGACCCATTGACACAAAAGGGAAAAAAGGATATAAAATCTTGGTGTTGAATGAAGTTGACAAACTTTCAAGAGAAGCACAGCATTCTCTTCGAAGAACTATGGAGAAATATAGTGCTTATTGCCGCCTAATACTATGCTGTAACAGTTCTTCAAAGGTGACTGAAGCAATCCGATCACGGTGTCTAAATGTGCGAATAAATGCACCAACAGATGAACAGATTGTTAAGGCATTGGAGTTCATTGGAAAGAAAGAAGGGCTTCAACTTCCTTCTGGATTTGCTGCTCATATAGCTGAAAAATCAAACAGGAGCTTAAGGAGAGCTATATTGTCTCTAGAAACTTGTCATGTTCAACAGTATCCCTTTACAAGTAACCAAATAATTCCCTCAATGGATTGGGAGGAATATGTTTCAGAAATTGTATCTGATATAATGAAGGAGCAGAGTCCGAAAAGGTTTTCTACATCCTACAATAATTGCCTATATTTCAGCCTTTTCTGTTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005657 GO:0005663 GO:0005694 GO:0006139 GO:0006259 GO:0006260 GO:0006261 GO:0006275 GO:0006281 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009889 GO:0009891 GO:0009893 GO:0009987 GO:0010556 GO:0010557 GO:0010604 GO:0019219 GO:0019222 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0031390 GO:0032991 GO:0033554 GO:0034641 GO:0034645 GO:0043085 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0044093 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044422 GO:0044424 GO:0044427 GO:0044446 GO:0044464 GO:0045935 GO:0046483 GO:0048518 GO:0048522 GO:0050789 GO:0050790 GO:0050794 GO:0050896 GO:0051052 GO:0051054 GO:0051171 GO:0051173 GO:0051338 GO:0051347 GO:0051716 GO:0060255 GO:0065007 GO:0065009 GO:0071704 GO:0080090 GO:0090304 GO:0090329 GO:1900262 GO:1900264 GO:1901360 GO:1901576 GO:2000112 GO:2000278 GO:2000573

KEGG Pathways

Metabolic & Signaling

ko03030 ko03420 ko03430 map03030 map03420 map03430

Pfam Domains

Protein Families

DNA_pol3_delta2

Protein Analysis

287

Amino Acids

32.76

Weight (kDa)

8.99

Isoelectric Point (pI)

44.9

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DNA_pol3_delta2	PF13177	19 - 188	1e-12	DNA polymerase III, delta subunit
AAA	PF00004	37 - 182	8.6e-07	ATPase family associated with various cellular activities (AAA)
RCF1-5-like_lid	PF21960	197 - 235	3.7e-10	RCF1/5-like, AAA+ ATPase lid domain

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

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Orthologous Genes (Group: OG0005462)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G27740
fragaria_vesca	FvH4_1g23560 FvH4_2g04970 FvH4_2g04970 FvH4_2g04970
malus_domestica	MD04G1041000.v1.1 MD04G1041300.v1.1 MD12G1011300.v1.1
prunus_persica	Prupe.1G194700_v2.0.a1 Prupe.1G194700_v2.0.a1 Prupe.4G268900_v2.0.a1 Prupe.4G268900_v2.0.a1 Prupe.7G013300_v2.0.a1 Prupe.7G013300_v2.0.a1 Prupe.7G013300_v2.0.a1
pyrus_communis	pycom12g00880
rosa_chinensis	RchiOBHm_Chr3g0496081
rosa_laevigata	RLG00000022564
rosa_multiflora	Rmu_sc0002392.1_g000001
rosa_roxburghii	Rroxscaffold_6G00389580
rosa_rugosa	Rorug03G0279300 Rorug03G0279400 Rorug03G0279400 Rorug03G0279400 Rorug03G0279500
rosa_samantha	Rh3AG326500 Rh3BG362800 Rh3DG362200
rosa_wichuraiana	Rw3G028590

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	46
AccI	GTMKAC	1 cut(s)	12
AccII	CGCG	1 cut(s)	89
AciI	CCGC	2 cut(s)	89, 484
AcuI	CTGAAG	1 cut(s)	543
AfaI	GTAC	1 cut(s)	20
AfiI	CCNNNNNNNGG	3 cut(s)	40, 46, 61
AflII	CTTAAG	1 cut(s)	673
AgsI	TTSAA	7 cut(s)	287, 332, 409, 429, 513, 623, 713
AjnI	CCWGG	1 cut(s)	39
AluBI	AGCT	4 cut(s)	256, 653, 672, 683
AluI	AGCT	4 cut(s)	256, 653, 672, 683
Alw26I	GTCTC	1 cut(s)	696
AoxI	GGCC	1 cut(s)	122
ApeKI	GCWGC	1 cut(s)	641
Asp700I	GAANNNNTTC	1 cut(s)	618
AspLEI	GCGC	2 cut(s)	67, 188
AspS9I	GGNCC	3 cut(s)	49, 122, 179
AsuHPI	GGTGA	2 cut(s)	208, 529
AsuII	TTCGAA	1 cut(s)	451
AvaII	GGWCC	2 cut(s)	49, 179
BarI	GAAGNNNNNNTAC	2 cut(s)	493, 525
BbvI	GCAGC	1 cut(s)	628
BceAI	ACGGC	1 cut(s)	78
BcgI	CGANNNNNNTGC	2 cut(s)	431, 465
BciT130I	CCWGG	1 cut(s)	41
BciVI	GTATCC	1 cut(s)	729
BcoDI	GTCTC	1 cut(s)	696
BfaI	CTAG	1 cut(s)	695
BfoI	RGCGCY	1 cut(s)	189
BfrI	CTTAAG	1 cut(s)	673
BfuI	GTATCC	1 cut(s)	729
BisI	GCNGC	2 cut(s)	484, 642
BlsI	GCNGC	2 cut(s)	485, 643
Bme1390I	CCNGG	1 cut(s)	41
Bme18I	GGWCC	2 cut(s)	49, 179
BmgT120I	GGNCC	3 cut(s)	49, 122, 179
BmiI	GGNNCC	2 cut(s)	133, 181
BmrFI	CCNGG	1 cut(s)	41
BmrI	ACTGGG	1 cut(s)	291
BmsI	GCATC	2 cut(s)	217, 292
BmuI	ACTGGG	1 cut(s)	291
Bpu14I	TTCGAA	1 cut(s)	451
BpuEI	CTTGAG	1 cut(s)	59
Bsc4I	CCNNNNNNNGG	3 cut(s)	40, 46, 61
Bse1I	ACTGG	1 cut(s)	297
Bse3DI	GCAATG	1 cut(s)	51
BseBI	CCWGG	1 cut(s)	41
BseGI	GGATG	1 cut(s)	824
BseLI	CCNNNNNNNGG	3 cut(s)	40, 46, 61
BseMI	GCAATG	1 cut(s)	51
BseNI	ACTGG	1 cut(s)	297
BseXI	GCAGC	1 cut(s)	628
BseYI	CCCAGC	2 cut(s)	182, 230
Bsh1236I	CGCG	1 cut(s)	89
BshFI	GGCC	1 cut(s)	124
BsiSI	CCGG	2 cut(s)	129, 135
BslI	CCNNNNNNNGG	3 cut(s)	40, 46, 61
BsmAI	GTCTC	1 cut(s)	696
BsmI	GAATGC	1 cut(s)	442
BsnI	GGCC	1 cut(s)	124
Bsp119I	TTCGAA	1 cut(s)	451
Bsp143I	GATC	1 cut(s)	533
BspACI	CCGC	2 cut(s)	89, 484
BspANI	GGCC	1 cut(s)	124
BspFNI	CGCG	1 cut(s)	89
BspLI	GGNNCC	2 cut(s)	133, 181
BspT104I	TTCGAA	1 cut(s)	451
BspTI	CTTAAG	1 cut(s)	673
BsrDI	GCAATG	1 cut(s)	51
BsrI	ACTGG	1 cut(s)	297
BssMI	GATC	1 cut(s)	533
Bst2UI	CCWGG	1 cut(s)	41
Bst4CI	ACNGT	3 cut(s)	506, 540, 717
Bst6I	CTCTTC	1 cut(s)	453
BstAFI	CTTAAG	1 cut(s)	673
BstBI	TTCGAA	1 cut(s)	451
BstC8I	GCNNGC	1 cut(s)	307
BstENI	CCTNNNNNAGG	1 cut(s)	38
BstF5I	GGATG	1 cut(s)	824
BstFNI	CGCG	1 cut(s)	89
BstH2I	RGCGCY	1 cut(s)	189
BstHHI	GCGC	2 cut(s)	67, 188
BstKTI	GATC	1 cut(s)	536
BstMAI	GTCTC	1 cut(s)	696
BstMBI	GATC	1 cut(s)	533
BstMWI	GCNNNNNNNGC	1 cut(s)	650
BstNI	CCWGG	1 cut(s)	41
BstSCI	CCNGG	1 cut(s)	39
BstUI	CGCG	1 cut(s)	89
BstV1I	GCAGC	1 cut(s)	628
BsuI	GTATCC	1 cut(s)	729
BsuRI	GGCC	1 cut(s)	124
BtgZI	GCGATG	1 cut(s)	139
BtsCI	GGATG	1 cut(s)	824
BtsIMutI	CAGTG	1 cut(s)	304
Cac8I	GCNNGC	1 cut(s)	307
CfoI	GCGC	2 cut(s)	67, 188
Cfr13I	GGNCC	3 cut(s)	49, 122, 179
Csp6I	GTAC	1 cut(s)	19
CviAII	CATG	2 cut(s)	216, 707
CviQI	GTAC	1 cut(s)	19
DpnI	GATC	1 cut(s)	535
DpnII	GATC	1 cut(s)	533
Eam1104I	CTCTTC	1 cut(s)	453
EarI	CTCTTC	1 cut(s)	453
Eco47I	GGWCC	2 cut(s)	49, 179
Eco57I	CTGAAG	1 cut(s)	543
EcoNI	CCTNNNNNAGG	1 cut(s)	38
EcoRII	CCWGG	1 cut(s)	39
FaeI	CATG	2 cut(s)	219, 710
FalI	AAGNNNNNCTT	2 cut(s)	603, 635
FatI	CATG	2 cut(s)	215, 706
FblI	GTMKAC	1 cut(s)	12
Fnu4HI	GCNGC	2 cut(s)	484, 642
FokI	GGATG	1 cut(s)	811
Fsp4HI	GCNGC	2 cut(s)	484, 642
FspBI	CTAG	1 cut(s)	695
GlaI	GCGC	2 cut(s)	66, 187
GluI	GCNGC	2 cut(s)	484, 642
GsaI	CCCAGC	2 cut(s)	186, 234
HaeII	RGCGCY	1 cut(s)	189
HaeIII	GGCC	1 cut(s)	124
HapII	CCGG	2 cut(s)	129, 135
HhaI	GCGC	2 cut(s)	67, 188
Hin1II	CATG	2 cut(s)	219, 710
Hin6I	GCGC	2 cut(s)	65, 186
HinP1I	GCGC	2 cut(s)	65, 186
HincII	GTYRAC	1 cut(s)	418
HindII	GTYRAC	1 cut(s)	418
HinfI	GANTC	1 cut(s)	805
HpaII	CCGG	2 cut(s)	129, 135
HphI	GGTGA	2 cut(s)	208, 529
Hpy166II	GTNNAC	3 cut(s)	13, 52, 418
Hpy188I	TCNGA	6 cut(s)	171, 179, 533, 775, 787, 810
Hpy188III	TCNNGA	6 cut(s)	76, 314, 332, 429, 633, 695
Hpy8I	GTNNAC	3 cut(s)	13, 52, 418
HpyAV	CCTTC	5 cut(s)	135, 193, 608, 639, 790
HpyCH4III	ACNGT	3 cut(s)	506, 540, 717
HpyCH4V	TGCA	2 cut(s)	305, 563
HpyF10VI	GCNNNNNNNGC	1 cut(s)	650
Hsp92II	CATG	2 cut(s)	219, 710
HspAI	GCGC	2 cut(s)	65, 186
Kzo9I	GATC	1 cut(s)	533
LmnI	GCTCC	4 cut(s)	91, 137, 669, 799
Lsp1109I	GCAGC	1 cut(s)	628
LweI	GCATC	2 cut(s)	217, 292
MaeI	CTAG	1 cut(s)	695
MaeIII	GTNAC	3 cut(s)	500, 517, 731
MalI	GATC	1 cut(s)	535
MboI	GATC	1 cut(s)	533
MboII	GAAGA	3 cut(s)	440, 465, 501
MluCI	AATT	4 cut(s)	339, 741, 777, 835
MlyI	GAGTC	1 cut(s)	814
MnlI	CCTC	4 cut(s)	44, 83, 754, 757
MroXI	GAANNNNTTC	1 cut(s)	618
MseI	TTAA	3 cut(s)	342, 585, 674
MspCI	CTTAAG	1 cut(s)	673
MspI	CCGG	2 cut(s)	129, 135
MspR9I	CCNGG	1 cut(s)	41
Mva1269I	GAATGC	1 cut(s)	442
MvaI	CCWGG	1 cut(s)	41
MvnI	CGCG	1 cut(s)	89
MwoI	GCNNNNNNNGC	1 cut(s)	650
NdeII	GATC	1 cut(s)	533
NlaIII	CATG	2 cut(s)	219, 710
NlaIV	GGNNCC	2 cut(s)	133, 181
NmuCI	GTSAC	1 cut(s)	517
NspV	TTCGAA	1 cut(s)	451
PctI	GAATGC	1 cut(s)	442
PdmI	GAANNNNTTC	1 cut(s)	618
PflMI	CCANNNNNTGG	1 cut(s)	46
PkrI	GCNGC	2 cut(s)	485, 643
PleI	GAGTC	1 cut(s)	813
PpsI	GAGTC	1 cut(s)	813
Psp6I	CCWGG	1 cut(s)	39
PspFI	CCCAGC	2 cut(s)	182, 230
PspGI	CCWGG	1 cut(s)	39
PspN4I	GGNNCC	2 cut(s)	133, 181
PspPI	GGNCC	3 cut(s)	49, 122, 179
RsaI	GTAC	1 cut(s)	20
RsaNI	GTAC	1 cut(s)	19
SaqAI	TTAA	3 cut(s)	342, 585, 674
SatI	GCNGC	2 cut(s)	484, 642
Sau3AI	GATC	1 cut(s)	533
Sau96I	GGNCC	3 cut(s)	49, 122, 179
SchI	GAGTC	1 cut(s)	814
ScrFI	CCNGG	1 cut(s)	41
SetI	ASST	9 cut(s)	75, 198, 204, 258, 519, 655, 674, 685, 818
SfaNI	GCATC	2 cut(s)	217, 292
SfuI	TTCGAA	1 cut(s)	451
SinI	GGWCC	2 cut(s)	49, 179
SmlI	CTYRAG	2 cut(s)	74, 673
SmoI	CTYRAG	2 cut(s)	74, 673
Sse9I	AATT	4 cut(s)	339, 741, 777, 835
SsiI	CCGC	2 cut(s)	89, 484
SspMI	CTAG	1 cut(s)	695
StyD4I	CCNGG	1 cut(s)	39
TaaI	ACNGT	3 cut(s)	506, 540, 717
TaqI	TCGA	2 cut(s)	36, 451
TasI	AATT	4 cut(s)	339, 741, 777, 835
TatI	WGTACW	1 cut(s)	18
TauI	GCSGC	1 cut(s)	486
Tru1I	TTAA	3 cut(s)	342, 585, 674
Tru9I	TTAA	3 cut(s)	342, 585, 674
TscAI	CASTG	1 cut(s)	304
TseFI	GTSAC	1 cut(s)	517
TseI	GCWGC	1 cut(s)	641
Tsp45I	GTSAC	1 cut(s)	517
TspDTI	ATGAA	4 cut(s)	426, 588, 589, 809
TspRI	CASTG	1 cut(s)	304
Van91I	CCANNNNNTGG	1 cut(s)	46
Vha464I	CTTAAG	1 cut(s)	673
VpaK11BI	GGWCC	2 cut(s)	49, 179
XagI	CCTNNNNNAGG	1 cut(s)	38
XbaI	TCTAGA	1 cut(s)	694
XmiI	GTMKAC	1 cut(s)	12
XmnI	GAANNNNTTC	1 cut(s)	618
XspI	CTAG	1 cut(s)	695

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