Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3C

Orthogroup ID

OG0006670

Physical Location & Seq

Genomic Coordinates Forward (+)

29811711 .. 29817913

Gene Structure 6203 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3CG292500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 942 bp

ATGTTGTCCCTGCCGCGGTTTTTTCGCTCGAGGCGGGCGCCTGTTATCTCCACTGGCTCCTTGAAGCTTGATATAGCTTTGGGGACTGGAGGATTGCCAAAGGGAAGAATTGTTGAGATTTATGGGCAGGAAGCATCTGGCAAGACTACGCTCGCACTTCACATCGTCAAGGAAGCCCAAAAGCTTGGAGGGTATTGTGCATATCTGGATGTAGAGAATGCATTGGACCCTTCACTTGCAGAATCGATGGGTGTAAACACAGAAAACCTTCTCATTTCGCATCCCAATTCTGCTGAAAATGTGCTGAATGTGGTCGACACTCTGACTAAAAGTGGTTCCTTGGATGTAATTGTTGTGGATAGTGTAGCTGCTCTGGTCCCCCAGTGTGAACTTGATGTTGCAATTGGTAGTGCATACCCAGACGCTCAGTCAAGAATAATGACCCAAGCACTACGAAAAATTCATTCTTCATTAAGCCATTCTCAAGCACTTGTTGTTTTTATAAATCAGGTTAGATCAAGTCCAAACTCAGGGCAAGGTTTTGGACCTGTGGATGAGGTCACCTGTGGTGGAAATGCCTTGAGATTCTATGCAGCAGTTCGATTGAGAATAAAAAGAACCCAGTTGCTTAAGACTGAAGATCAGATTACAGGTCTTGGGATTTCTGTGCAAGTGGTGAAAAATAAATTGGCACTTGCAATGAAGAAGGCTGATCTGGGGATACAGTTTGGTAGAGGGTTGTGCTGTGAATCTGAGGTATTGCAATTGGCTTGCGAACATGGGGTCATTGCAAAAGATGGAAGCAACTACCACATAGGAAGAAAGGTTTTTAGTAATGTACATTCAGCAGAACAGTATTTGGCTAAAAATGATGATATTTTGAATAAGATAGTTAGGATCTTGAGGCAAACTTTATTTGAAAAAGATAGTCAATTTAGGTAG

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

313

Amino Acids

33.9

Weight (kDa)

8.83

Isoelectric Point (pI)

35.97

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RecA_N	PF00154	14 - 247	1.8e-84	RecA N-terminal domain
Rad51	PF08423	15 - 208	1.3e-10	Rad51
ATPase	PF06745	17 - 75	3.9e-06	KaiC

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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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)	503
AccB1I	GGYRCC	1 cut(s)	37
AccI	GTMKAC	1 cut(s)	315
AccII	CGCG	1 cut(s)	16
AciI	CCGC	3 cut(s)	14, 16, 34
AclWI	GGATC	1 cut(s)	905
AcsI	RAATTY	1 cut(s)	459
AcuI	CTGAAG	1 cut(s)	657
AcyI	GRCGYC	1 cut(s)	38
AfaI	GTAC	1 cut(s)	840
AfiI	CCNNNNNNNGG	2 cut(s)	15, 530
AflII	CTTAAG	1 cut(s)	629
AgsI	TTSAA	3 cut(s)	64, 883, 920
AhdI	GACNNNNNGTC	1 cut(s)	427
AjuI	GAANNNNNNNTTGG	2 cut(s)	671, 703
AluBI	AGCT	4 cut(s)	67, 77, 184, 368
AluI	AGCT	4 cut(s)	67, 77, 184, 368
AlwI	GGATC	1 cut(s)	905
Ama87I	CYCGRG	1 cut(s)	28
ApeKI	GCWGC	2 cut(s)	368, 593
ApoI	RAATTY	1 cut(s)	459
ArsI	GACNNNNNNTTYG	2 cut(s)	768, 800
Asp700I	GAANNNNTTC	1 cut(s)	267
AspLEI	GCGC	1 cut(s)	40
AspS9I	GGNCC	3 cut(s)	226, 376, 545
AsuHPI	GGTGA	2 cut(s)	553, 688
AvaI	CYCGRG	1 cut(s)	28
AvaII	GGWCC	3 cut(s)	226, 376, 545
BanI	GGYRCC	1 cut(s)	37
BbvI	GCAGC	2 cut(s)	355, 605
BccI	CCATC	2 cut(s)	241, 791
BciVI	GTATCC	1 cut(s)	714
BfoI	RGCGCY	1 cut(s)	41
BfrI	CTTAAG	1 cut(s)	629
BfuI	GTATCC	1 cut(s)	714
BisI	GCNGC	3 cut(s)	14, 369, 594
BlsI	GCNGC	3 cut(s)	15, 370, 595
Bme18I	GGWCC	3 cut(s)	226, 376, 545
BmeRI	GACNNNNNGTC	1 cut(s)	427
BmeT110I	CYCGRG	1 cut(s)	28
BmgT120I	GGNCC	3 cut(s)	226, 376, 545
BmiI	GGNNCC	5 cut(s)	39, 58, 228, 337, 378
BmrI	ACTGGG	2 cut(s)	376, 616
BmsI	GCATC	2 cut(s)	143, 289
BmuI	ACTGGG	2 cut(s)	376, 616
BpmI	CTGGAG	1 cut(s)	108
BpuEI	CTTGAG	3 cut(s)	468, 601, 922
Bsa29I	ATCGAT	1 cut(s)	245
BsaHI	GRCGYC	1 cut(s)	38
BsaJI	CCNNGG	2 cut(s)	14, 339
Bsc4I	CCNNNNNNNGG	2 cut(s)	15, 530
Bse1I	ACTGG	4 cut(s)	58, 91, 382, 622
Bse3DI	GCAATG	2 cut(s)	705, 786
BseCI	ATCGAT	1 cut(s)	245
BseDI	CCNNGG	2 cut(s)	14, 339
BseGI	GGATG	4 cut(s)	214, 280, 349, 559
BseLI	CCNNNNNNNGG	2 cut(s)	15, 530
BseMI	GCAATG	2 cut(s)	705, 786
BseMII	CTCAG	3 cut(s)	440, 543, 744
BseNI	ACTGG	4 cut(s)	58, 91, 382, 622
BseXI	GCAGC	2 cut(s)	355, 605
Bsh1236I	CGCG	1 cut(s)	16
BshNI	GGYRCC	1 cut(s)	37
BshVI	ATCGAT	1 cut(s)	245
BsiHKCI	CYCGRG	1 cut(s)	28
BslFI	GGGAC	2 cut(s)	97, 362
BslI	CCNNNNNNNGG	2 cut(s)	15, 530
BsmFI	GGGAC	2 cut(s)	97, 362
BsmI	GAATGC	1 cut(s)	223
BsoBI	CYCGRG	1 cut(s)	28
Bsp1407I	TGTACA	1 cut(s)	838
Bsp143I	GATC	4 cut(s)	515, 640, 712, 897
BspACI	CCGC	3 cut(s)	14, 16, 34
BspCNI	CTCAG	3 cut(s)	439, 542, 745
BspDI	ATCGAT	1 cut(s)	245
BspFNI	CGCG	1 cut(s)	16
BspLI	GGNNCC	5 cut(s)	39, 58, 228, 337, 378
BspPI	GGATC	1 cut(s)	905
BspT107I	GGYRCC	1 cut(s)	37
BspTI	CTTAAG	1 cut(s)	629
BsrDI	GCAATG	2 cut(s)	705, 786
BsrGI	TGTACA	1 cut(s)	838
BsrI	ACTGG	4 cut(s)	58, 91, 382, 622
BssECI	CCNNGG	2 cut(s)	14, 339
BssMI	GATC	4 cut(s)	515, 640, 712, 897
BssNI	GRCGYC	1 cut(s)	38
BssT1I	CCWWGG	1 cut(s)	339
Bst4CI	ACNGT	2 cut(s)	726, 855
BstACI	GRCGYC	1 cut(s)	38
BstAFI	CTTAAG	1 cut(s)	629
BstAUI	TGTACA	1 cut(s)	838
BstC8I	GCNNGC	3 cut(s)	36, 153, 772
BstDEI	CTNAG	3 cut(s)	426, 529, 753
BstDSI	CCRYGG	1 cut(s)	14
BstEII	GGTNACC	1 cut(s)	559
BstF5I	GGATG	4 cut(s)	214, 280, 349, 559
BstFNI	CGCG	1 cut(s)	16
BstH2I	RGCGCY	1 cut(s)	41
BstHHI	GCGC	1 cut(s)	40
BstKTI	GATC	4 cut(s)	518, 643, 715, 900
BstMBI	GATC	4 cut(s)	515, 640, 712, 897
BstPI	GGTNACC	1 cut(s)	559
BstUI	CGCG	1 cut(s)	16
BstV1I	GCAGC	2 cut(s)	355, 605
BstX2I	RGATCY	1 cut(s)	897
BstXI	CCANNNNNNTGG	1 cut(s)	185
BstYI	RGATCY	1 cut(s)	897
Bsu15I	ATCGAT	1 cut(s)	245
BsuI	GTATCC	1 cut(s)	714
BsuTUI	ATCGAT	1 cut(s)	245
BtgI	CCRYGG	1 cut(s)	14
BtsCI	GGATG	4 cut(s)	214, 280, 349, 559
BtsIMutI	CAGTG	2 cut(s)	51, 389
Cac8I	GCNNGC	3 cut(s)	36, 153, 772
CfoI	GCGC	1 cut(s)	40
Cfr13I	GGNCC	3 cut(s)	226, 376, 545
Cfr42I	CCGCGG	1 cut(s)	17
ClaI	ATCGAT	1 cut(s)	245
CseI	GACGC	1 cut(s)	431
Csp6I	GTAC	1 cut(s)	839
CviAII	CATG	1 cut(s)	779
CviQI	GTAC	1 cut(s)	839
DdeI	CTNAG	3 cut(s)	426, 529, 753
DinI	GGCGCC	1 cut(s)	39
DpnI	GATC	4 cut(s)	517, 642, 714, 899
DpnII	GATC	4 cut(s)	515, 640, 712, 897
DriI	GACNNNNNGTC	1 cut(s)	427
Eam1105I	GACNNNNNGTC	1 cut(s)	427
Eco130I	CCWWGG	1 cut(s)	339
Eco47I	GGWCC	3 cut(s)	226, 376, 545
Eco57I	CTGAAG	1 cut(s)	657
Eco88I	CYCGRG	1 cut(s)	28
Eco91I	GGTNACC	1 cut(s)	559
EcoO65I	GGTNACC	1 cut(s)	559
EcoT14I	CCWWGG	1 cut(s)	339
EcoT22I	ATGCAT	1 cut(s)	223
EgeI	GGCGCC	1 cut(s)	39
EheI	GGCGCC	1 cut(s)	39
ErhI	CCWWGG	1 cut(s)	339
FaeI	CATG	1 cut(s)	782
FaiI	YATR	8 cut(s)	74, 123, 202, 415, 503, 591, 780, 815
FaqI	GGGAC	2 cut(s)	97, 362
FatI	CATG	1 cut(s)	778
FauI	CCCGC	1 cut(s)	27
FblI	GTMKAC	1 cut(s)	315
Fnu4HI	GCNGC	3 cut(s)	14, 369, 594
FokI	GGATG	4 cut(s)	221, 267, 356, 566
Fsp4HI	GCNGC	3 cut(s)	14, 369, 594
GlaI	GCGC	1 cut(s)	39
GluI	GCNGC	3 cut(s)	14, 369, 594
GsuI	CTGGAG	1 cut(s)	108
HaeII	RGCGCY	1 cut(s)	41
HgaI	GACGC	1 cut(s)	431
HhaI	GCGC	1 cut(s)	40
Hin1I	GRCGYC	1 cut(s)	38
Hin1II	CATG	1 cut(s)	782
Hin6I	GCGC	1 cut(s)	38
HinP1I	GCGC	1 cut(s)	38
HincII	GTYRAC	1 cut(s)	316
HindII	GTYRAC	1 cut(s)	316
HindIII	AAGCTT	2 cut(s)	65, 182
HinfI	GANTC	3 cut(s)	242, 585, 749
HphI	GGTGA	2 cut(s)	553, 688
Hpy166II	GTNNAC	3 cut(s)	256, 316, 389
Hpy188I	TCNGA	3 cut(s)	324, 645, 754
Hpy188III	TCNNGA	3 cut(s)	206, 432, 901
Hpy8I	GTNNAC	3 cut(s)	256, 316, 389
HpyAV	CCTTC	3 cut(s)	240, 278, 700
HpyCH4III	ACNGT	2 cut(s)	726, 855
HpyF3I	CTNAG	3 cut(s)	426, 529, 753
Hsp92I	GRCGYC	1 cut(s)	38
Hsp92II	CATG	1 cut(s)	782
HspAI	GCGC	1 cut(s)	38
KasI	GGCGCC	1 cut(s)	37
KspI	CCGCGG	1 cut(s)	17
Kzo9I	GATC	4 cut(s)	515, 640, 712, 897
LmnI	GCTCC	1 cut(s)	62
Lsp1109I	GCAGC	2 cut(s)	355, 605
LweI	GCATC	2 cut(s)	143, 289
MaeIII	GTNAC	1 cut(s)	559
MalI	GATC	4 cut(s)	517, 642, 714, 899
MboI	GATC	4 cut(s)	515, 640, 712, 897
MboII	GAAGA	5 cut(s)	117, 459, 650, 715, 831
MfeI	CAATTG	2 cut(s)	402, 764
MflI	RGATCY	1 cut(s)	897
MluCI	AATT	8 cut(s)	108, 286, 348, 402, 459, 686, 764, 932
Mly113I	GGCGCC	1 cut(s)	38
MnlI	CCTC	7 cut(s)	24, 83, 182, 550, 728, 748, 897
Mph1103I	ATGCAT	1 cut(s)	223
MroXI	GAANNNNTTC	1 cut(s)	267
MseI	TTAA	2 cut(s)	473, 630
MspA1I	CMGCKG	1 cut(s)	16
MspCI	CTTAAG	1 cut(s)	629
MunI	CAATTG	2 cut(s)	402, 764
Mva1269I	GAATGC	1 cut(s)	223
MvnI	CGCG	1 cut(s)	16
NarI	GGCGCC	1 cut(s)	38
NdeII	GATC	4 cut(s)	515, 640, 712, 897
NlaIII	CATG	1 cut(s)	782
NlaIV	GGNNCC	5 cut(s)	39, 58, 228, 337, 378
NmuCI	GTSAC	1 cut(s)	559
NsiI	ATGCAT	1 cut(s)	223
PaeR7I	CTCGAG	1 cut(s)	28
PctI	GAATGC	1 cut(s)	223
PdmI	GAANNNNTTC	1 cut(s)	267
PfeI	GAWTC	3 cut(s)	242, 585, 749
PkrI	GCNGC	3 cut(s)	15, 370, 595
PluTI	GGCGCC	1 cut(s)	41
PsiI	TTATAA	1 cut(s)	503
PspEI	GGTNACC	1 cut(s)	559
PspN4I	GGNNCC	5 cut(s)	39, 58, 228, 337, 378
PspPI	GGNCC	3 cut(s)	226, 376, 545
PspXI	VCTCGAGB	1 cut(s)	28
PsuI	RGATCY	1 cut(s)	897
RsaI	GTAC	1 cut(s)	840
RsaNI	GTAC	1 cut(s)	839
SacII	CCGCGG	1 cut(s)	17
SalI	GTCGAC	1 cut(s)	314
SaqAI	TTAA	2 cut(s)	473, 630
SatI	GCNGC	3 cut(s)	14, 369, 594
Sau3AI	GATC	4 cut(s)	515, 640, 712, 897
Sau96I	GGNCC	3 cut(s)	226, 376, 545
SfaNI	GCATC	2 cut(s)	143, 289
SfoI	GGCGCC	1 cut(s)	39
Sfr274I	CTCGAG	1 cut(s)	28
Sfr303I	CCGCGG	1 cut(s)	17
SgrBI	CCGCGG	1 cut(s)	17
SinI	GGWCC	3 cut(s)	226, 376, 545
SlaI	CTCGAG	1 cut(s)	28
SmlI	CTYRAG	5 cut(s)	28, 483, 580, 629, 901
SmoI	CTYRAG	5 cut(s)	28, 483, 580, 629, 901
Sse9I	AATT	8 cut(s)	108, 286, 348, 402, 459, 686, 764, 932
SsiI	CCGC	3 cut(s)	14, 16, 34
SspDI	GGCGCC	1 cut(s)	37
StyI	CCWWGG	1 cut(s)	339
TaaI	ACNGT	2 cut(s)	726, 855
TaqI	TCGA	4 cut(s)	29, 245, 315, 601
TasI	AATT	8 cut(s)	108, 286, 348, 402, 459, 686, 764, 932
TatI	WGTACW	1 cut(s)	838
TauI	GCSGC	1 cut(s)	16
TfiI	GAWTC	3 cut(s)	242, 585, 749
Tru1I	TTAA	2 cut(s)	473, 630
Tru9I	TTAA	2 cut(s)	473, 630
TscAI	CASTG	2 cut(s)	58, 389
TseFI	GTSAC	1 cut(s)	559
TseI	GCWGC	2 cut(s)	368, 593
Tsp45I	GTSAC	1 cut(s)	559
TspDTI	ATGAA	3 cut(s)	452, 459, 716
TspRI	CASTG	2 cut(s)	58, 389
Vha464I	CTTAAG	1 cut(s)	629
VpaK11BI	GGWCC	3 cut(s)	226, 376, 545
XapI	RAATTY	1 cut(s)	459
XhoI	CTCGAG	1 cut(s)	28
XmiI	GTMKAC	1 cut(s)	315
XmnI	GAANNNNTTC	1 cut(s)	267
Zsp2I	ATGCAT	1 cut(s)	223

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