Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3B

Orthogroup ID

OG0005462

Physical Location & Seq

Genomic Coordinates Reverse (-)

44278885 .. 44286202

Gene Structure 7318 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3BG362800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 978 bp

ATGAAAGCAGAGGGTAGAATCAGAATTGAAAAAGGTAGAAGCTGCAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCACGATTTCCCGCCACTTTTGCCGTCTGAAGAATCGAAGATGCTGTGGGTAGACAAGTACAGACCCAAAACCCTAGACCAGGCAATGGTCCACCAAGACACGGCGCAAAACCTCAAGAAACTTGTCGCGGAGCAGGACTGCCCCCATTTGCTCTTTTACGGGCCTTCCGGCTCCGGCAAGAAAACCCTAATCATCGCCCTTATTCGTCAGATTTTCGGACCCAGCGCCGACAAGGTGAAGGTGGAAAACAGGACATGGAAAGTTGATGCTGGGAGTAGAACCATTGACATAGAGCTGACTACATTATCAAGCACCAATCACATTGAACTCAACCCCAGTGATGCAGGCTTTCAGGACAGATACATTGTTCAAGAGATAATTAAGGAAATGGCTAAAAATAGACCCATCGACACAAAAGGGAAAAAAGGATATAAAATCTTGGTGTTGAATGAAGTTGACAAACTTTCAAGAGAAGCACAGCATTCTCTTCGAAGAACTATGGAGAAATATAGTGCTTATTGCCGCCTAATACTATGTTGTAACAGTTCTTCAAAGGTGACTGAAGCAATCCGATCACGGTGTCTAAATGTGCGAATAAATGCACCAACAGATGAACAGATTGTTAAGGCATTGGAGTTCATTGGAAAGAAAGAAGGGCTTCAACTTCCTTCTGGATTTGCTGCTCATATAGCTGAAAAATCAAACAGGAGCTTAAGGAGAGCTATATTGTCTCTAGAAACTTGTCATGTTCAACAGTATCCCTTTACAAGTAACCAAATAATTCCCTCAATGGATTGGGAGGAATATGTTTCAGAAATTGTATCTGATATAATGAAGGAGCAGAGTCCGAAAAGGTTTTCTACATCCTACAATAATTGCCTATATTTCAGCCTTTTCTGTTAG

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

325

Amino Acids

37.38

Weight (kDa)

9.01

Isoelectric Point (pI)

49.36

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Rad17	PF03215	36 - 99	4.9e-06	Rad17 P-loop domain
DNA_pol3_delta2	PF13177	57 - 226	1.5e-12	DNA polymerase III, delta subunit
AAA	PF00004	75 - 220	1.2e-06	ATPase family associated with various cellular activities (AAA)
RCF1-5-like_lid	PF21960	235 - 273	4.4e-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)

Image

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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)	160
AccI	GTMKAC	1 cut(s)	126
AccII	CGCG	1 cut(s)	203
AciI	CCGC	3 cut(s)	86, 203, 598
AcuI	CTGAAG	2 cut(s)	123, 657
AfaI	GTAC	1 cut(s)	134
AfiI	CCNNNNNNNGG	3 cut(s)	154, 160, 175
AflII	CTTAAG	1 cut(s)	787
AgsI	TTSAA	8 cut(s)	29, 401, 446, 523, 543, 627, 737, 827
AjnI	CCWGG	1 cut(s)	153
AluBI	AGCT	5 cut(s)	42, 370, 767, 786, 797
AluI	AGCT	5 cut(s)	42, 370, 767, 786, 797
Alw21I	GWGCWC	1 cut(s)	78
Alw26I	GTCTC	1 cut(s)	810
AoxI	GGCC	1 cut(s)	236
ApeKI	GCWGC	2 cut(s)	42, 755
Asp700I	GAANNNNTTC	1 cut(s)	732
AspLEI	GCGC	2 cut(s)	181, 302
AspS9I	GGNCC	3 cut(s)	163, 236, 293
AsuHPI	GGTGA	2 cut(s)	322, 643
AsuII	TTCGAA	1 cut(s)	565
AvaII	GGWCC	2 cut(s)	163, 293
BarI	GAAGNNNNNNTAC	2 cut(s)	607, 639
Bbv12I	GWGCWC	1 cut(s)	78
BbvI	GCAGC	2 cut(s)	29, 742
BccI	CCATC	1 cut(s)	488
BceAI	ACGGC	2 cut(s)	82, 192
BcgI	CGANNNNNNTGC	2 cut(s)	545, 579
BciT130I	CCWGG	1 cut(s)	155
BciVI	GTATCC	1 cut(s)	843
BcoDI	GTCTC	1 cut(s)	810
BfaI	CTAG	2 cut(s)	149, 809
BfmI	CTRYAG	1 cut(s)	43
BfoI	RGCGCY	1 cut(s)	303
BfrI	CTTAAG	1 cut(s)	787
BfuI	GTATCC	1 cut(s)	843
BisI	GCNGC	3 cut(s)	43, 598, 756
BlsI	GCNGC	3 cut(s)	44, 599, 757
Bme1390I	CCNGG	1 cut(s)	155
Bme18I	GGWCC	2 cut(s)	163, 293
BmgT120I	GGNCC	3 cut(s)	163, 236, 293
BmiI	GGNNCC	2 cut(s)	247, 295
BmrFI	CCNGG	1 cut(s)	155
BmrI	ACTGGG	1 cut(s)	405
BmsI	GCATC	3 cut(s)	105, 331, 406
BmuI	ACTGGG	1 cut(s)	405
Bpu14I	TTCGAA	1 cut(s)	565
BpuEI	CTTGAG	1 cut(s)	173
Bsc4I	CCNNNNNNNGG	3 cut(s)	154, 160, 175
Bse1I	ACTGG	1 cut(s)	411
Bse3DI	GCAATG	1 cut(s)	165
BseBI	CCWGG	1 cut(s)	155
BseGI	GGATG	1 cut(s)	938
BseLI	CCNNNNNNNGG	3 cut(s)	154, 160, 175
BseMI	GCAATG	1 cut(s)	165
BseNI	ACTGG	1 cut(s)	411
BseXI	GCAGC	2 cut(s)	29, 742
BseYI	CCCAGC	2 cut(s)	296, 344
Bsh1236I	CGCG	1 cut(s)	203
BshFI	GGCC	1 cut(s)	238
BsiHKAI	GWGCWC	1 cut(s)	78
BsiSI	CCGG	2 cut(s)	243, 249
BslI	CCNNNNNNNGG	3 cut(s)	154, 160, 175
BsmAI	GTCTC	1 cut(s)	810
BsmI	GAATGC	1 cut(s)	556
BsnI	GGCC	1 cut(s)	238
Bsp119I	TTCGAA	1 cut(s)	565
Bsp1286I	GDGCHC	1 cut(s)	78
Bsp143I	GATC	1 cut(s)	647
BspACI	CCGC	3 cut(s)	86, 203, 598
BspANI	GGCC	1 cut(s)	238
BspFNI	CGCG	1 cut(s)	203
BspLI	GGNNCC	2 cut(s)	247, 295
BspMAI	CTGCAG	1 cut(s)	47
BspT104I	TTCGAA	1 cut(s)	565
BspTI	CTTAAG	1 cut(s)	787
BsrDI	GCAATG	1 cut(s)	165
BsrI	ACTGG	1 cut(s)	411
BssMI	GATC	1 cut(s)	647
Bst2UI	CCWGG	1 cut(s)	155
Bst4CI	ACNGT	3 cut(s)	620, 654, 831
Bst6I	CTCTTC	1 cut(s)	567
BstAFI	CTTAAG	1 cut(s)	787
BstBI	TTCGAA	1 cut(s)	565
BstC8I	GCNNGC	1 cut(s)	421
BstENI	CCTNNNNNAGG	1 cut(s)	152
BstF5I	GGATG	1 cut(s)	938
BstFNI	CGCG	1 cut(s)	203
BstH2I	RGCGCY	1 cut(s)	303
BstHHI	GCGC	2 cut(s)	181, 302
BstKTI	GATC	1 cut(s)	650
BstMAI	GTCTC	1 cut(s)	810
BstMBI	GATC	1 cut(s)	647
BstMWI	GCNNNNNNNGC	2 cut(s)	94, 764
BstNI	CCWGG	1 cut(s)	155
BstSCI	CCNGG	1 cut(s)	153
BstSFI	CTRYAG	1 cut(s)	43
BstUI	CGCG	1 cut(s)	203
BstV1I	GCAGC	2 cut(s)	29, 742
BsuI	GTATCC	1 cut(s)	843
BsuRI	GGCC	1 cut(s)	238
BtgZI	GCGATG	1 cut(s)	253
BtsCI	GGATG	1 cut(s)	938
BtsIMutI	CAGTG	1 cut(s)	418
Cac8I	GCNNGC	1 cut(s)	421
CfoI	GCGC	2 cut(s)	181, 302
Cfr13I	GGNCC	3 cut(s)	163, 236, 293
Csp6I	GTAC	1 cut(s)	133
CviAII	CATG	2 cut(s)	330, 821
CviQI	GTAC	1 cut(s)	133
DpnI	GATC	1 cut(s)	649
DpnII	GATC	1 cut(s)	647
Eam1104I	CTCTTC	1 cut(s)	567
EarI	CTCTTC	1 cut(s)	567
Eco47I	GGWCC	2 cut(s)	163, 293
Eco57I	CTGAAG	2 cut(s)	123, 657
EcoNI	CCTNNNNNAGG	1 cut(s)	152
EcoRII	CCWGG	1 cut(s)	153
FaeI	CATG	2 cut(s)	333, 824
FalI	AAGNNNNNCTT	2 cut(s)	717, 749
FatI	CATG	2 cut(s)	329, 820
FauI	CCCGC	1 cut(s)	93
FblI	GTMKAC	1 cut(s)	126
Fnu4HI	GCNGC	3 cut(s)	43, 598, 756
FokI	GGATG	1 cut(s)	925
Fsp4HI	GCNGC	3 cut(s)	43, 598, 756
FspBI	CTAG	2 cut(s)	149, 809
GlaI	GCGC	2 cut(s)	180, 301
GluI	GCNGC	3 cut(s)	43, 598, 756
GsaI	CCCAGC	2 cut(s)	300, 348
HaeII	RGCGCY	1 cut(s)	303
HaeIII	GGCC	1 cut(s)	238
HapII	CCGG	2 cut(s)	243, 249
HhaI	GCGC	2 cut(s)	181, 302
Hin1II	CATG	2 cut(s)	333, 824
Hin6I	GCGC	2 cut(s)	179, 300
HinP1I	GCGC	2 cut(s)	179, 300
HincII	GTYRAC	1 cut(s)	532
HindII	GTYRAC	1 cut(s)	532
HinfI	GANTC	3 cut(s)	18, 107, 919
HpaII	CCGG	2 cut(s)	243, 249
HphI	GGTGA	2 cut(s)	322, 643
Hpy166II	GTNNAC	3 cut(s)	127, 166, 532
Hpy188I	TCNGA	8 cut(s)	23, 103, 285, 293, 647, 889, 901, 924
Hpy188III	TCNNGA	6 cut(s)	190, 428, 446, 543, 747, 809
Hpy8I	GTNNAC	3 cut(s)	127, 166, 532
HpyAV	CCTTC	5 cut(s)	249, 307, 722, 753, 904
HpyCH4III	ACNGT	3 cut(s)	620, 654, 831
HpyCH4V	TGCA	3 cut(s)	45, 419, 677
HpyF10VI	GCNNNNNNNGC	2 cut(s)	94, 764
Hsp92II	CATG	2 cut(s)	333, 824
HspAI	GCGC	2 cut(s)	179, 300
Kzo9I	GATC	1 cut(s)	647
LmnI	GCTCC	4 cut(s)	205, 251, 783, 913
Lsp1109I	GCAGC	2 cut(s)	29, 742
LweI	GCATC	3 cut(s)	105, 331, 406
MaeI	CTAG	2 cut(s)	149, 809
MaeIII	GTNAC	3 cut(s)	614, 631, 845
MalI	GATC	1 cut(s)	649
MboI	GATC	1 cut(s)	647
MboII	GAAGA	5 cut(s)	116, 124, 554, 579, 615
MhlI	GDGCHC	1 cut(s)	78
MluCI	AATT	5 cut(s)	24, 453, 855, 891, 949
MlyI	GAGTC	1 cut(s)	928
MnlI	CCTC	4 cut(s)	4, 197, 868, 871
MroXI	GAANNNNTTC	1 cut(s)	732
MseI	TTAA	3 cut(s)	456, 699, 788
MspCI	CTTAAG	1 cut(s)	787
MspI	CCGG	2 cut(s)	243, 249
MspR9I	CCNGG	1 cut(s)	155
Mva1269I	GAATGC	1 cut(s)	556
MvaI	CCWGG	1 cut(s)	155
MvnI	CGCG	1 cut(s)	203
MwoI	GCNNNNNNNGC	2 cut(s)	94, 764
NdeII	GATC	1 cut(s)	647
NlaIII	CATG	2 cut(s)	333, 824
NlaIV	GGNNCC	2 cut(s)	247, 295
NmuCI	GTSAC	1 cut(s)	631
NspV	TTCGAA	1 cut(s)	565
PctI	GAATGC	1 cut(s)	556
PdmI	GAANNNNTTC	1 cut(s)	732
PfeI	GAWTC	2 cut(s)	18, 107
PflMI	CCANNNNNTGG	1 cut(s)	160
PkrI	GCNGC	3 cut(s)	44, 599, 757
PleI	GAGTC	1 cut(s)	927
PpsI	GAGTC	1 cut(s)	927
Psp6I	CCWGG	1 cut(s)	153
PspFI	CCCAGC	2 cut(s)	296, 344
PspGI	CCWGG	1 cut(s)	153
PspN4I	GGNNCC	2 cut(s)	247, 295
PspPI	GGNCC	3 cut(s)	163, 236, 293
PstI	CTGCAG	1 cut(s)	47
RsaI	GTAC	1 cut(s)	134
RsaNI	GTAC	1 cut(s)	133
SaqAI	TTAA	3 cut(s)	456, 699, 788
SatI	GCNGC	3 cut(s)	43, 598, 756
Sau3AI	GATC	1 cut(s)	647
Sau96I	GGNCC	3 cut(s)	163, 236, 293
SchI	GAGTC	1 cut(s)	928
ScrFI	CCNGG	1 cut(s)	155
SduI	GDGCHC	1 cut(s)	78
SfaNI	GCATC	3 cut(s)	105, 331, 406
SfcI	CTRYAG	1 cut(s)	43
SfuI	TTCGAA	1 cut(s)	565
SinI	GGWCC	2 cut(s)	163, 293
SmlI	CTYRAG	2 cut(s)	188, 787
SmoI	CTYRAG	2 cut(s)	188, 787
Sse9I	AATT	5 cut(s)	24, 453, 855, 891, 949
SsiI	CCGC	3 cut(s)	86, 203, 598
SspMI	CTAG	2 cut(s)	149, 809
StyD4I	CCNGG	1 cut(s)	153
TaaI	ACNGT	3 cut(s)	620, 654, 831
TaqI	TCGA	3 cut(s)	110, 483, 565
TasI	AATT	5 cut(s)	24, 453, 855, 891, 949
TatI	WGTACW	1 cut(s)	132
TauI	GCSGC	1 cut(s)	600
TfiI	GAWTC	2 cut(s)	18, 107
Tru1I	TTAA	3 cut(s)	456, 699, 788
Tru9I	TTAA	3 cut(s)	456, 699, 788
TscAI	CASTG	1 cut(s)	418
TseFI	GTSAC	1 cut(s)	631
TseI	GCWGC	2 cut(s)	42, 755
Tsp45I	GTSAC	1 cut(s)	631
TspDTI	ATGAA	5 cut(s)	17, 540, 702, 703, 923
TspRI	CASTG	1 cut(s)	418
Van91I	CCANNNNNTGG	1 cut(s)	160
Vha464I	CTTAAG	1 cut(s)	787
VpaK11BI	GGWCC	2 cut(s)	163, 293
XagI	CCTNNNNNAGG	1 cut(s)	152
XbaI	TCTAGA	1 cut(s)	808
XmiI	GTMKAC	1 cut(s)	126
XmnI	GAANNNNTTC	1 cut(s)	732
XspI	CTAG	2 cut(s)	149, 809

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