Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0005462

Physical Location & Seq

Genomic Coordinates Reverse (-)

46287521 .. 46294185

Gene Structure 6665 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG326500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1020 bp

ATGGTCCACCAAGACACGGCGCAAAACCTCAAGAAACTTGTCGCAGAGCAGGACTGCCCCCATTTGCTCTTTTACGGGCCTTCCGGCTCCGGCAAGAAAACCCTAATCATTGCCCTTATTCGTCAGATTTTCGGACCCAGCGCCGACAAGGTGAAGGTGGAAAACAGGACATGGAAAGTTGATGCTGGGAGTAGAACCATTGACATAGAGCTGACTACATTATCAAGCACCAATCACATTGAACTCAACCCCAGTGATGCAGGCTTTCAGGACAGATACATTGTTCAAGAGATAATTAAGGAAATGGCTAAAAATAGACCCATTGACACAAAAGGGAAAAAAGGATATAAAATCTTGGTGTTGAATGAAGTTGACAAACTTTCAAGAGAAGCACAGCATTCTCTTCGAAGAACTATGGAGAAATATAGTGCTTATTGCCGCCTAATACTATGCTGTAACAGTTCTTCAAAGGTGACTGAAGCAATCCGATCACGGTGTCTAAATGTGCGAATAAATGCACCAACAGATGAACAGATTGTTAAGGCATTGGAGTTCATTGGAAAGAAAGAAGGGCTTCAACTTCCTTCTGGATTTGCTGCTCATATAGCTGAAAAATCAAACAGGAGCTTAAGGAGAGCTATATTGTCTCTAGAAACTTGTCATGTTCAACAGTATCCCTTTACAAGTAACCAAATAATTCCCTCAATGGATTGGGAGGAATATGTTTCAGAAATTGTATCTGATATAATGAAGGAGCAGAGTCCGAAAAGGCTTTATCTGGTGCGGCAAAAGTTGTATGAGCTACTTGTTAATTGTATCCCTCCAGAGATCATTCTTAAGAGGCTGCTTTATGAGTTATTGAAGAAATTGGATGCAGAATTGAAGCATGAGGTCTGCCATTGGGCAGCATATTATGAACATAGGATGCGTCTTGGGCAGAAAGCCATATTTCACCTCGAAGCGTTCGTGGCCAAGTTCATGAGTATTTATAAGGCTTTCCTCATTGCAGCATTTGGCTAA

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

339

Amino Acids

38.89

Weight (kDa)

9.15

Isoelectric Point (pI)

42.55

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DNA_pol3_delta2	PF13177	4 - 173	1.6e-12	DNA polymerase III, delta subunit
AAA	PF00004	22 - 167	1.3e-06	ATPase family associated with various cellular activities (AAA)
RCF1-5-like_lid	PF21960	182 - 220	4.7e-10	RCF1/5-like, AAA+ ATPase lid domain
RFC_C	PF22534	238 - 327	3.3e-31	Replication factor C subunit 3, C-terminal domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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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)
AanI	TTATAA	1 cut(s)	990
AciI	CCGC	2 cut(s)	439, 784
AcoI	YGGCCR	1 cut(s)	969
AcuI	CTGAAG	1 cut(s)	498
AfiI	CCNNNNNNNGG	1 cut(s)	16
AflII	CTTAAG	2 cut(s)	628, 836
AgsI	TTSAA	9 cut(s)	242, 287, 364, 384, 468, 578, 668, 862, 883
AluBI	AGCT	5 cut(s)	211, 608, 627, 638, 802
AluI	AGCT	5 cut(s)	211, 608, 627, 638, 802
Alw26I	GTCTC	1 cut(s)	651
AoxI	GGCC	2 cut(s)	77, 969
ApeKI	GCWGC	4 cut(s)	596, 844, 905, 1007
Asp700I	GAANNNNTTC	1 cut(s)	573
AspLEI	GCGC	2 cut(s)	22, 143
AspS9I	GGNCC	3 cut(s)	4, 77, 134
AsuHPI	GGTGA	3 cut(s)	163, 484, 944
AsuII	TTCGAA	1 cut(s)	406
AvaII	GGWCC	2 cut(s)	4, 134
BalI	TGGCCA	1 cut(s)	971
BarI	GAAGNNNNNNTAC	2 cut(s)	448, 480
BbvI	GCAGC	3 cut(s)	583, 831, 917
BceAI	ACGGC	1 cut(s)	33
BcgI	CGANNNNNNTGC	2 cut(s)	386, 420
BciVI	GTATCC	2 cut(s)	684, 827
BcoDI	GTCTC	1 cut(s)	651
BfaI	CTAG	1 cut(s)	650
BfoI	RGCGCY	1 cut(s)	144
BfrI	CTTAAG	2 cut(s)	628, 836
BfuI	GTATCC	2 cut(s)	684, 827
BisI	GCNGC	6 cut(s)	439, 597, 785, 845, 906, 1008
BlsI	GCNGC	6 cut(s)	440, 598, 786, 846, 907, 1009
Bme18I	GGWCC	2 cut(s)	4, 134
BmgT120I	GGNCC	3 cut(s)	4, 77, 134
BmiI	GGNNCC	2 cut(s)	88, 136
BmrI	ACTGGG	1 cut(s)	246
BmsI	GCATC	4 cut(s)	172, 247, 862, 915
BmuI	ACTGGG	1 cut(s)	246
BpmI	CTGGAG	1 cut(s)	807
Bpu14I	TTCGAA	1 cut(s)	406
BpuEI	CTTGAG	1 cut(s)	14
Bsc4I	CCNNNNNNNGG	1 cut(s)	16
Bse1I	ACTGG	1 cut(s)	252
Bse3DI	GCAATG	2 cut(s)	108, 1002
BseGI	GGATG	2 cut(s)	877, 930
BseLI	CCNNNNNNNGG	1 cut(s)	16
BseMI	GCAATG	2 cut(s)	108, 1002
BseNI	ACTGG	1 cut(s)	252
BseXI	GCAGC	3 cut(s)	583, 831, 917
BseYI	CCCAGC	2 cut(s)	137, 185
BshFI	GGCC	2 cut(s)	79, 971
BsiSI	CCGG	2 cut(s)	84, 90
BslI	CCNNNNNNNGG	1 cut(s)	16
BsmAI	GTCTC	1 cut(s)	651
BsmI	GAATGC	1 cut(s)	397
BsnI	GGCC	2 cut(s)	79, 971
Bsp119I	TTCGAA	1 cut(s)	406
Bsp143I	GATC	2 cut(s)	488, 828
BspACI	CCGC	2 cut(s)	439, 784
BspANI	GGCC	2 cut(s)	79, 971
BspHI	TCATGA	1 cut(s)	978
BspLI	GGNNCC	2 cut(s)	88, 136
BspT104I	TTCGAA	1 cut(s)	406
BspTI	CTTAAG	2 cut(s)	628, 836
BsrDI	GCAATG	2 cut(s)	108, 1002
BsrI	ACTGG	1 cut(s)	252
BssMI	GATC	2 cut(s)	488, 828
Bst4CI	ACNGT	3 cut(s)	461, 495, 672
Bst6I	CTCTTC	1 cut(s)	408
BstAFI	CTTAAG	2 cut(s)	628, 836
BstBI	TTCGAA	1 cut(s)	406
BstC8I	GCNNGC	1 cut(s)	262
BstF5I	GGATG	2 cut(s)	877, 930
BstH2I	RGCGCY	1 cut(s)	144
BstHHI	GCGC	2 cut(s)	22, 143
BstKTI	GATC	2 cut(s)	491, 831
BstMAI	GTCTC	1 cut(s)	651
BstMBI	GATC	2 cut(s)	488, 828
BstMWI	GCNNNNNNNGC	3 cut(s)	605, 934, 968
BstV1I	GCAGC	3 cut(s)	583, 831, 917
BsuI	GTATCC	2 cut(s)	684, 827
BsuRI	GGCC	2 cut(s)	79, 971
BtsCI	GGATG	2 cut(s)	877, 930
BtsIMutI	CAGTG	1 cut(s)	259
Cac8I	GCNNGC	1 cut(s)	262
CciI	TCATGA	1 cut(s)	978
CfoI	GCGC	2 cut(s)	22, 143
Cfr13I	GGNCC	3 cut(s)	4, 77, 134
CseI	GACGC	1 cut(s)	917
CviAII	CATG	4 cut(s)	171, 662, 887, 979
DpnI	GATC	2 cut(s)	490, 830
DpnII	GATC	2 cut(s)	488, 828
EaeI	YGGCCR	1 cut(s)	969
Eam1104I	CTCTTC	1 cut(s)	408
EarI	CTCTTC	1 cut(s)	408
Eco47I	GGWCC	2 cut(s)	4, 134
Eco57I	CTGAAG	1 cut(s)	498
FaeI	CATG	4 cut(s)	174, 665, 890, 982
FalI	AAGNNNNNCTT	2 cut(s)	558, 590
FatI	CATG	4 cut(s)	170, 661, 886, 978
Fnu4HI	GCNGC	6 cut(s)	439, 597, 785, 845, 906, 1008
FokI	GGATG	2 cut(s)	884, 937
Fsp4HI	GCNGC	6 cut(s)	439, 597, 785, 845, 906, 1008
FspBI	CTAG	1 cut(s)	650
GlaI	GCGC	2 cut(s)	21, 142
GluI	GCNGC	6 cut(s)	439, 597, 785, 845, 906, 1008
GsaI	CCCAGC	2 cut(s)	141, 189
GsuI	CTGGAG	1 cut(s)	807
HaeII	RGCGCY	1 cut(s)	144
HaeIII	GGCC	2 cut(s)	79, 971
HapII	CCGG	2 cut(s)	84, 90
HgaI	GACGC	1 cut(s)	917
HhaI	GCGC	2 cut(s)	22, 143
Hin1II	CATG	4 cut(s)	174, 665, 890, 982
Hin6I	GCGC	2 cut(s)	20, 141
HinP1I	GCGC	2 cut(s)	20, 141
HincII	GTYRAC	1 cut(s)	373
HindII	GTYRAC	1 cut(s)	373
HinfI	GANTC	1 cut(s)	760
HpaII	CCGG	2 cut(s)	84, 90
HphI	GGTGA	3 cut(s)	163, 484, 944
Hpy166II	GTNNAC	2 cut(s)	7, 373
Hpy188I	TCNGA	6 cut(s)	126, 134, 488, 730, 742, 765
Hpy188III	TCNNGA	8 cut(s)	31, 269, 287, 384, 588, 650, 824, 979
Hpy8I	GTNNAC	2 cut(s)	7, 373
HpyAV	CCTTC	5 cut(s)	90, 148, 563, 594, 745
HpyCH4III	ACNGT	3 cut(s)	461, 495, 672
HpyCH4V	TGCA	4 cut(s)	260, 518, 875, 1007
HpyF10VI	GCNNNNNNNGC	3 cut(s)	605, 934, 968
Hsp92II	CATG	4 cut(s)	174, 665, 890, 982
HspAI	GCGC	2 cut(s)	20, 141
Kzo9I	GATC	2 cut(s)	488, 828
LmnI	GCTCC	3 cut(s)	92, 624, 754
Lsp1109I	GCAGC	3 cut(s)	583, 831, 917
LweI	GCATC	4 cut(s)	172, 247, 862, 915
MaeI	CTAG	1 cut(s)	650
MaeIII	GTNAC	3 cut(s)	455, 472, 686
MalI	GATC	2 cut(s)	490, 830
MboI	GATC	2 cut(s)	488, 828
MboII	GAAGA	4 cut(s)	395, 420, 456, 874
MlsI	TGGCCA	1 cut(s)	971
MluCI	AATT	6 cut(s)	294, 696, 732, 811, 866, 878
MluNI	TGGCCA	1 cut(s)	971
MlyI	GAGTC	1 cut(s)	769
MnlI	CCTC	8 cut(s)	38, 709, 712, 831, 834, 883, 965, 1010
Mox20I	TGGCCA	1 cut(s)	971
MroXI	GAANNNNTTC	1 cut(s)	573
MscI	TGGCCA	1 cut(s)	971
MseI	TTAA	5 cut(s)	297, 540, 629, 810, 837
Msp20I	TGGCCA	1 cut(s)	971
MspCI	CTTAAG	2 cut(s)	628, 836
MspI	CCGG	2 cut(s)	84, 90
Mva1269I	GAATGC	1 cut(s)	397
MwoI	GCNNNNNNNGC	3 cut(s)	605, 934, 968
NdeII	GATC	2 cut(s)	488, 828
NlaIII	CATG	4 cut(s)	174, 665, 890, 982
NlaIV	GGNNCC	2 cut(s)	88, 136
NmuCI	GTSAC	1 cut(s)	472
NspV	TTCGAA	1 cut(s)	406
PagI	TCATGA	1 cut(s)	978
PcsI	WCGNNNNNNNCGW	1 cut(s)	963
PctI	GAATGC	1 cut(s)	397
PdmI	GAANNNNTTC	1 cut(s)	573
PkrI	GCNGC	6 cut(s)	440, 598, 786, 846, 907, 1009
PleI	GAGTC	1 cut(s)	768
PpsI	GAGTC	1 cut(s)	768
PsiI	TTATAA	1 cut(s)	990
PspFI	CCCAGC	2 cut(s)	137, 185
PspN4I	GGNNCC	2 cut(s)	88, 136
PspPI	GGNCC	3 cut(s)	4, 77, 134
SaqAI	TTAA	5 cut(s)	297, 540, 629, 810, 837
SatI	GCNGC	6 cut(s)	439, 597, 785, 845, 906, 1008
Sau3AI	GATC	2 cut(s)	488, 828
Sau96I	GGNCC	3 cut(s)	4, 77, 134
SchI	GAGTC	1 cut(s)	769
SfaNI	GCATC	4 cut(s)	172, 247, 862, 915
SfuI	TTCGAA	1 cut(s)	406
SinI	GGWCC	2 cut(s)	4, 134
SmlI	CTYRAG	3 cut(s)	29, 628, 836
SmoI	CTYRAG	3 cut(s)	29, 628, 836
Sse9I	AATT	6 cut(s)	294, 696, 732, 811, 866, 878
SsiI	CCGC	2 cut(s)	439, 784
SspMI	CTAG	1 cut(s)	650
TaaI	ACNGT	3 cut(s)	461, 495, 672
TaqI	TCGA	2 cut(s)	406, 957
TasI	AATT	6 cut(s)	294, 696, 732, 811, 866, 878
TauI	GCSGC	2 cut(s)	441, 787
Tru1I	TTAA	5 cut(s)	297, 540, 629, 810, 837
Tru9I	TTAA	5 cut(s)	297, 540, 629, 810, 837
TscAI	CASTG	1 cut(s)	259
TseFI	GTSAC	1 cut(s)	472
TseI	GCWGC	4 cut(s)	596, 844, 905, 1007
Tsp45I	GTSAC	1 cut(s)	472
TspDTI	ATGAA	6 cut(s)	381, 543, 544, 764, 930, 967
TspRI	CASTG	1 cut(s)	259
Vha464I	CTTAAG	2 cut(s)	628, 836
VpaK11BI	GGWCC	2 cut(s)	4, 134
XbaI	TCTAGA	1 cut(s)	649
XmnI	GAANNNNTTC	1 cut(s)	573
XspI	CTAG	1 cut(s)	650

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