Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3D

Orthogroup ID

OG0006670

Physical Location & Seq

Genomic Coordinates Forward (+)

29719741 .. 29725685

Gene Structure 5945 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3DG288200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1173 bp

ATGGGTTTACTCAACTCTCCTCCACTCGCGCGCCGTCTTGCTCTGGCGGCGTTCACCCAACCTCGCCTCTCTTCTCTACTCAGAGGAAGAAGACACACGACGGCGACTTGTAGTGGTGAATGTGCTGCTCCGCTGGATTATGATGATAATGACGATGCTAAAGCGAGGGACAAAGATGCTGCTCTGCATTTGGCTCTCTCACGGCTCTCTGGCGATTTCGGGCACGAATCCATGTTGTCCCTGCCGCGGTTTTTTCGCTCGAGGCGGGCGCCTGTTATCTCCACTGGCTCCTTGAAGCTTGATATAGCTTTGGGGACTGGAGGATTGCCAAAGGGAAGAATTGTTGAGATTTATGGGCAGGAAGCATCTGGCAAGACTACGCTCGCACTTCACATCGTCAAGGAAGCCCAAAAGCTTGGAGGGTATTGTGCATATCTGGATGTAGAGAATGCGTTGGACCCTTCACTTGCAGAATCGATGGGTGTAAACACAGAAAACCTTCTCGTTTCGCATCCCAATTCTGCTGAAAATGTGCTGAATGTGGTTGACACTCTGACTAAAAGTGGTTCCTTGGATGTAATTGTTGTGGATAGTGTAGCTGCTCTGGTCCCCCAGTGTGAACTTGATGTTGCAATTGGTAGTGCATACCCAGACGCTCAGTCAAGAATAATGACCCAAGCACTACGAAAAATTCATTCTTCATTAAGCCATTCTCAAGCACTTGTTGTTTTTATAAATCAGGTTAGATCAAGTCCAAACTCAGGGCAAGGTTTTGGACCTGTGGATGAGGTCACCTGTGGTGGAAATGCCTTGAGATTCTATGCAGCAGTTCGATTGAGAATAAAAAGAACCCAGTTGCTTAAGACTGAAGATCAGATTACAGGTCTTGGAATTTCTGTGCAAGTGGTGAAAAATAAATTGGCACTTGCAATGAAGAAGGCTGATCTGGGGATACAGTTTGGTAGAGGGTTATGCTGTGAATCTGAGGTATTGCAATTGGCTTGCGAACATGGGGTCATTGCGAAAGATGGAAGCAACTACCACATAGGAAGAAAGGTTTTTAGTAATGTACATTCAGCAGAACAGTATTTGGCTAAAAATGATGATATTTTGAATAAGATAGTTAGGATCTTGAGGCAAACTTTATTTGAAAAAGATAGTCAATTTAGGTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000002 GO:0000150 GO:0000217 GO:0000400 GO:0000724 GO:0000725 GO:0000730 GO:0003674 GO:0003676 GO:0003677 GO:0003690 GO:0003697 GO:0003824 GO:0005488 GO:0006139 GO:0006259 GO:0006281 GO:0006302 GO:0006310 GO:0006312 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0006996 GO:0007005 GO:0008094 GO:0008150 GO:0008152 GO:0009266 GO:0009314 GO:0009408 GO:0009628 GO:0009987 GO:0010212 GO:0016043 GO:0016462 GO:0016787 GO:0016817 GO:0016818 GO:0016887 GO:0017111 GO:0022607 GO:0033554 GO:0034622 GO:0034641 GO:0042148 GO:0042623 GO:0043170 GO:0043933 GO:0044085 GO:0044237 GO:0044238 GO:0044260 GO:0045003 GO:0046483 GO:0050896 GO:0051716 GO:0065003 GO:0065004 GO:0071704 GO:0071824 GO:0071840 GO:0090304 GO:0090735 GO:0097159 GO:0140097 GO:1901360 GO:1901363

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Glyco_hydro_17 RecA

Protein Analysis

390

Amino Acids

42.15

Weight (kDa)

8.7

Isoelectric Point (pI)

39.19

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RecA_N	PF00154	61 - 324	1.8e-87	RecA N-terminal domain
Rad51	PF08423	92 - 284	1.8e-10	Rad51
ATPase	PF06745	94 - 167	3.2e-06	KaiC

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

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0006670)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G10140
fragaria_vesca	FvH4_6g24630 FvH4_6g24630 FvH4_6g24630 FvH4_6g24630
malus_domestica	MD08G1164600.v1.1
prunus_persica	Prupe.7G052200_v2.0.a1
pyrus_communis	pycom12654g00020
rosa_chinensis	RchiOBHm_Chr3g0483971
rosa_laevigata	RLG00000015036 RLG00000023245 RLG00000030551 RLG00000032361
rosa_multiflora	Rmu_sc0001190.1_g000001 Rmu_sc0001527.1_g000019 Rmu_sc0003477.1_g000015 Rmu_sc0020880.1_g000007 Rmu_ssc0000295.1_g000053
rosa_roxburghii	Rroxscaffold_6G00397920
rosa_rugosa	Rorug03G0209800
rosa_samantha	Rh3AG258000 Rh3BG295100 Rh3CG292500 Rh3DG288200 Rh6AG313300
rosa_wichuraiana	Rw6G027080

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	734
AccB1I	GGYRCC	1 cut(s)	268
AccII	CGCG	3 cut(s)	29, 31, 247
AciI	CCGC	5 cut(s)	47, 131, 245, 247, 265
AclWI	GGATC	1 cut(s)	1136
AcsI	RAATTY	2 cut(s)	690, 891
AcuI	CTGAAG	1 cut(s)	888
AcyI	GRCGYC	1 cut(s)	269
AfaI	GTAC	1 cut(s)	1071
AfiI	CCNNNNNNNGG	2 cut(s)	246, 761
AflII	CTTAAG	1 cut(s)	860
AgsI	TTSAA	3 cut(s)	295, 1114, 1151
AhdI	GACNNNNNGTC	1 cut(s)	658
AjuI	GAANNNNNNNTTGG	2 cut(s)	902, 934
AluBI	AGCT	4 cut(s)	298, 308, 415, 599
AluI	AGCT	4 cut(s)	298, 308, 415, 599
AlwI	GGATC	1 cut(s)	1136
Ama87I	CYCGRG	1 cut(s)	259
ApeKI	GCWGC	4 cut(s)	125, 179, 599, 824
ApoI	RAATTY	2 cut(s)	690, 891
ArsI	GACNNNNNNTTYG	2 cut(s)	999, 1031
Asp700I	GAANNNNTTC	1 cut(s)	498
AspLEI	GCGC	3 cut(s)	31, 33, 271
AspS9I	GGNCC	3 cut(s)	457, 607, 776
AsuHPI	GGTGA	4 cut(s)	46, 128, 784, 919
AvaI	CYCGRG	1 cut(s)	259
AvaII	GGWCC	3 cut(s)	457, 607, 776
BaeGI	GKGCMC	1 cut(s)	225
BanI	GGYRCC	1 cut(s)	268
BbsI	GAAGAC	1 cut(s)	97
BbvI	GCAGC	4 cut(s)	112, 166, 586, 836
BccI	CCATC	2 cut(s)	472, 1022
BceAI	ACGGC	3 cut(s)	18, 117, 218
BciVI	GTATCC	1 cut(s)	945
BfoI	RGCGCY	1 cut(s)	272
BfrI	CTTAAG	1 cut(s)	860
BfuI	GTATCC	1 cut(s)	945
BisI	GCNGC	6 cut(s)	48, 126, 180, 245, 600, 825
BlsI	GCNGC	6 cut(s)	49, 127, 181, 246, 601, 826
Bme18I	GGWCC	3 cut(s)	457, 607, 776
BmeRI	GACNNNNNGTC	1 cut(s)	658
BmeT110I	CYCGRG	1 cut(s)	259
BmgT120I	GGNCC	3 cut(s)	457, 607, 776
BmiI	GGNNCC	5 cut(s)	270, 289, 459, 568, 609
BmrI	ACTGGG	2 cut(s)	607, 847
BmsI	GCATC	4 cut(s)	145, 166, 374, 520
BmuI	ACTGGG	2 cut(s)	607, 847
BpiI	GAAGAC	1 cut(s)	97
BpmI	CTGGAG	1 cut(s)	339
BpuEI	CTTGAG	3 cut(s)	699, 832, 1153
Bsa29I	ATCGAT	1 cut(s)	476
BsaHI	GRCGYC	1 cut(s)	269
BsaJI	CCNNGG	2 cut(s)	245, 570
Bsc4I	CCNNNNNNNGG	2 cut(s)	246, 761
Bse1I	ACTGG	4 cut(s)	289, 322, 613, 853
Bse3DI	GCAATG	2 cut(s)	936, 1017
BseCI	ATCGAT	1 cut(s)	476
BseDI	CCNNGG	2 cut(s)	245, 570
BseGI	GGATG	4 cut(s)	445, 511, 580, 790
BseLI	CCNNNNNNNGG	2 cut(s)	246, 761
BseMI	GCAATG	2 cut(s)	936, 1017
BseMII	CTCAG	4 cut(s)	94, 671, 774, 975
BseNI	ACTGG	4 cut(s)	289, 322, 613, 853
BsePI	GCGCGC	1 cut(s)	29
BseRI	GAGGAG	1 cut(s)	9
BseSI	GKGCMC	1 cut(s)	225
BseXI	GCAGC	4 cut(s)	112, 166, 586, 836
Bsh1236I	CGCG	3 cut(s)	29, 31, 247
BshNI	GGYRCC	1 cut(s)	268
BshVI	ATCGAT	1 cut(s)	476
BsiHKCI	CYCGRG	1 cut(s)	259
BslFI	GGGAC	4 cut(s)	182, 223, 328, 593
BslI	CCNNNNNNNGG	2 cut(s)	246, 761
BsmFI	GGGAC	4 cut(s)	182, 223, 328, 593
BsmI	GAATGC	1 cut(s)	454
BsoBI	CYCGRG	1 cut(s)	259
Bsp1286I	GDGCHC	1 cut(s)	225
Bsp1407I	TGTACA	1 cut(s)	1069
Bsp143I	GATC	4 cut(s)	746, 871, 943, 1128
BspACI	CCGC	5 cut(s)	47, 131, 245, 247, 265
BspCNI	CTCAG	4 cut(s)	93, 670, 773, 976
BspDI	ATCGAT	1 cut(s)	476
BspFNI	CGCG	3 cut(s)	29, 31, 247
BspLI	GGNNCC	5 cut(s)	270, 289, 459, 568, 609
BspPI	GGATC	1 cut(s)	1136
BspT107I	GGYRCC	1 cut(s)	268
BspTI	CTTAAG	1 cut(s)	860
BsrDI	GCAATG	2 cut(s)	936, 1017
BsrGI	TGTACA	1 cut(s)	1069
BsrI	ACTGG	4 cut(s)	289, 322, 613, 853
BssECI	CCNNGG	2 cut(s)	245, 570
BssHII	GCGCGC	1 cut(s)	29
BssMI	GATC	4 cut(s)	746, 871, 943, 1128
BssNI	GRCGYC	1 cut(s)	269
BssT1I	CCWWGG	1 cut(s)	570
Bst4CI	ACNGT	2 cut(s)	957, 1086
Bst6I	CTCTTC	1 cut(s)	76
BstACI	GRCGYC	1 cut(s)	269
BstAFI	CTTAAG	1 cut(s)	860
BstAUI	TGTACA	1 cut(s)	1069
BstC8I	GCNNGC	4 cut(s)	31, 267, 384, 1003
BstDEI	CTNAG	4 cut(s)	80, 657, 760, 984
BstDSI	CCRYGG	1 cut(s)	245
BstEII	GGTNACC	1 cut(s)	790
BstF5I	GGATG	4 cut(s)	445, 511, 580, 790
BstFNI	CGCG	3 cut(s)	29, 31, 247
BstH2I	RGCGCY	1 cut(s)	272
BstHHI	GCGC	3 cut(s)	31, 33, 271
BstKTI	GATC	4 cut(s)	749, 874, 946, 1131
BstMBI	GATC	4 cut(s)	746, 871, 943, 1128
BstMWI	GCNNNNNNNGC	1 cut(s)	47
BstPI	GGTNACC	1 cut(s)	790
BstSLI	GKGCMC	1 cut(s)	225
BstUI	CGCG	3 cut(s)	29, 31, 247
BstV1I	GCAGC	4 cut(s)	112, 166, 586, 836
BstV2I	GAAGAC	1 cut(s)	97
BstX2I	RGATCY	1 cut(s)	1128
BstXI	CCANNNNNNTGG	1 cut(s)	416
BstYI	RGATCY	1 cut(s)	1128
Bsu15I	ATCGAT	1 cut(s)	476
BsuI	GTATCC	1 cut(s)	945
BsuTUI	ATCGAT	1 cut(s)	476
BtgI	CCRYGG	1 cut(s)	245
BtsCI	GGATG	4 cut(s)	445, 511, 580, 790
BtsIMutI	CAGTG	2 cut(s)	282, 620
Cac8I	GCNNGC	4 cut(s)	31, 267, 384, 1003
CfoI	GCGC	3 cut(s)	31, 33, 271
Cfr13I	GGNCC	3 cut(s)	457, 607, 776
Cfr42I	CCGCGG	1 cut(s)	248
ClaI	ATCGAT	1 cut(s)	476
CseI	GACGC	1 cut(s)	662
Csp6I	GTAC	1 cut(s)	1070
CviAII	CATG	2 cut(s)	232, 1010
CviQI	GTAC	1 cut(s)	1070
DdeI	CTNAG	4 cut(s)	80, 657, 760, 984
DinI	GGCGCC	1 cut(s)	270
DpnI	GATC	4 cut(s)	748, 873, 945, 1130
DpnII	GATC	4 cut(s)	746, 871, 943, 1128
DriI	GACNNNNNGTC	1 cut(s)	658
Eam1104I	CTCTTC	1 cut(s)	76
Eam1105I	GACNNNNNGTC	1 cut(s)	658
EarI	CTCTTC	1 cut(s)	76
Eco130I	CCWWGG	1 cut(s)	570
Eco47I	GGWCC	3 cut(s)	457, 607, 776
Eco57I	CTGAAG	1 cut(s)	888
Eco88I	CYCGRG	1 cut(s)	259
Eco91I	GGTNACC	1 cut(s)	790
EcoO65I	GGTNACC	1 cut(s)	790
EcoT14I	CCWWGG	1 cut(s)	570
EgeI	GGCGCC	1 cut(s)	270
EheI	GGCGCC	1 cut(s)	270
ErhI	CCWWGG	1 cut(s)	570
FaeI	CATG	2 cut(s)	235, 1013
FaqI	GGGAC	4 cut(s)	182, 223, 328, 593
FatI	CATG	2 cut(s)	231, 1009
FauI	CCCGC	1 cut(s)	258
Fnu4HI	GCNGC	6 cut(s)	48, 126, 180, 245, 600, 825
FokI	GGATG	4 cut(s)	452, 498, 587, 797
Fsp4HI	GCNGC	6 cut(s)	48, 126, 180, 245, 600, 825
GlaI	GCGC	3 cut(s)	30, 32, 270
GluI	GCNGC	6 cut(s)	48, 126, 180, 245, 600, 825
GsuI	CTGGAG	1 cut(s)	339
HaeII	RGCGCY	1 cut(s)	272
HgaI	GACGC	1 cut(s)	662
HhaI	GCGC	3 cut(s)	31, 33, 271
Hin1I	GRCGYC	1 cut(s)	269
Hin1II	CATG	2 cut(s)	235, 1013
Hin6I	GCGC	3 cut(s)	29, 31, 269
HinP1I	GCGC	3 cut(s)	29, 31, 269
HincII	GTYRAC	1 cut(s)	547
HindII	GTYRAC	1 cut(s)	547
HindIII	AAGCTT	2 cut(s)	296, 413
HinfI	GANTC	4 cut(s)	227, 473, 816, 980
HphI	GGTGA	4 cut(s)	46, 128, 784, 919
Hpy166II	GTNNAC	5 cut(s)	8, 54, 487, 547, 620
Hpy188I	TCNGA	4 cut(s)	83, 555, 876, 985
Hpy188III	TCNNGA	3 cut(s)	437, 663, 1132
Hpy8I	GTNNAC	5 cut(s)	8, 54, 487, 547, 620
Hpy99I	CGWCG	1 cut(s)	103
HpyAV	CCTTC	3 cut(s)	471, 509, 931
HpyCH4III	ACNGT	2 cut(s)	957, 1086
HpyCH4V	TGCA	9 cut(s)	187, 431, 470, 632, 644, 824, 901, 929, 994
HpyF10VI	GCNNNNNNNGC	1 cut(s)	47
HpyF3I	CTNAG	4 cut(s)	80, 657, 760, 984
Hsp92I	GRCGYC	1 cut(s)	269
Hsp92II	CATG	2 cut(s)	235, 1013
HspAI	GCGC	3 cut(s)	29, 31, 269
KasI	GGCGCC	1 cut(s)	268
KspI	CCGCGG	1 cut(s)	248
Kzo9I	GATC	4 cut(s)	746, 871, 943, 1128
LmnI	GCTCC	2 cut(s)	133, 293
Lsp1109I	GCAGC	4 cut(s)	112, 166, 586, 836
LweI	GCATC	4 cut(s)	145, 166, 374, 520
MaeIII	GTNAC	1 cut(s)	790
MalI	GATC	4 cut(s)	748, 873, 945, 1130
MboI	GATC	4 cut(s)	746, 871, 943, 1128
MboII	GAAGA	8 cut(s)	63, 99, 102, 348, 690, 881, 946, 1062
MfeI	CAATTG	2 cut(s)	633, 995
MflI	RGATCY	1 cut(s)	1128
MhlI	GDGCHC	1 cut(s)	225
MluCI	AATT	9 cut(s)	339, 517, 579, 633, 690, 891, 917, 995, 1163
Mly113I	GGCGCC	1 cut(s)	269
MmeI	TCCRAC	1 cut(s)	435
MroXI	GAANNNNTTC	1 cut(s)	498
MseI	TTAA	2 cut(s)	704, 861
MspA1I	CMGCKG	2 cut(s)	133, 247
MspCI	CTTAAG	1 cut(s)	860
MunI	CAATTG	2 cut(s)	633, 995
Mva1269I	GAATGC	1 cut(s)	454
MvnI	CGCG	3 cut(s)	29, 31, 247
MwoI	GCNNNNNNNGC	1 cut(s)	47
NarI	GGCGCC	1 cut(s)	269
NdeII	GATC	4 cut(s)	746, 871, 943, 1128
NlaIII	CATG	2 cut(s)	235, 1013
NlaIV	GGNNCC	5 cut(s)	270, 289, 459, 568, 609
NmuCI	GTSAC	1 cut(s)	790
PaeR7I	CTCGAG	1 cut(s)	259
PauI	GCGCGC	1 cut(s)	29
PctI	GAATGC	1 cut(s)	454
PdmI	GAANNNNTTC	1 cut(s)	498
PfeI	GAWTC	4 cut(s)	227, 473, 816, 980
PkrI	GCNGC	6 cut(s)	49, 127, 181, 246, 601, 826
PluTI	GGCGCC	1 cut(s)	272
PsiI	TTATAA	1 cut(s)	734
PspEI	GGTNACC	1 cut(s)	790
PspN4I	GGNNCC	5 cut(s)	270, 289, 459, 568, 609
PspPI	GGNCC	3 cut(s)	457, 607, 776
PspXI	VCTCGAGB	1 cut(s)	259
PsuI	RGATCY	1 cut(s)	1128
PteI	GCGCGC	1 cut(s)	29
RsaI	GTAC	1 cut(s)	1071
RsaNI	GTAC	1 cut(s)	1070
SacII	CCGCGG	1 cut(s)	248
SaqAI	TTAA	2 cut(s)	704, 861
SatI	GCNGC	6 cut(s)	48, 126, 180, 245, 600, 825
Sau3AI	GATC	4 cut(s)	746, 871, 943, 1128
Sau96I	GGNCC	3 cut(s)	457, 607, 776
SduI	GDGCHC	1 cut(s)	225
SfaNI	GCATC	4 cut(s)	145, 166, 374, 520
SfoI	GGCGCC	1 cut(s)	270
Sfr274I	CTCGAG	1 cut(s)	259
Sfr303I	CCGCGG	1 cut(s)	248
SgrBI	CCGCGG	1 cut(s)	248
SinI	GGWCC	3 cut(s)	457, 607, 776
SlaI	CTCGAG	1 cut(s)	259
SmlI	CTYRAG	5 cut(s)	259, 714, 811, 860, 1132
SmoI	CTYRAG	5 cut(s)	259, 714, 811, 860, 1132
Sse9I	AATT	9 cut(s)	339, 517, 579, 633, 690, 891, 917, 995, 1163
SsiI	CCGC	5 cut(s)	47, 131, 245, 247, 265
SspDI	GGCGCC	1 cut(s)	268
StyI	CCWWGG	1 cut(s)	570
TaaI	ACNGT	2 cut(s)	957, 1086
TaqI	TCGA	3 cut(s)	260, 476, 832
TasI	AATT	9 cut(s)	339, 517, 579, 633, 690, 891, 917, 995, 1163
TatI	WGTACW	1 cut(s)	1069
TauI	GCSGC	2 cut(s)	50, 247
TfiI	GAWTC	4 cut(s)	227, 473, 816, 980
Tru1I	TTAA	2 cut(s)	704, 861
Tru9I	TTAA	2 cut(s)	704, 861
TscAI	CASTG	2 cut(s)	289, 620
TseFI	GTSAC	1 cut(s)	790
TseI	GCWGC	4 cut(s)	125, 179, 599, 824
Tsp45I	GTSAC	1 cut(s)	790
TspDTI	ATGAA	3 cut(s)	683, 690, 947
TspRI	CASTG	2 cut(s)	289, 620
Vha464I	CTTAAG	1 cut(s)	860
VpaK11BI	GGWCC	3 cut(s)	457, 607, 776
XapI	RAATTY	2 cut(s)	690, 891
XhoI	CTCGAG	1 cut(s)	259
XmnI	GAANNNNTTC	1 cut(s)	498

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