Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3D

Orthogroup ID

OG0002968

Physical Location & Seq

Genomic Coordinates Forward (+)

35875360 .. 35881274

Gene Structure 5915 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3DG326700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1098 bp

ATGTTCTCAAAAGGTTGCACACCAGATGTTGTTACATACACTACTGTTCTGAATGGGTATTGTCGACTTGGGAAGGTGGATCAAGCTAAAAAGATGCTTCAGCACATGTATAAGCATGGGTGCAAGCCAAATACTGTATCATATACGGCCATAATAAATGGGCTTTGTCATGGTGGGAACTTATTGGAGGCAAGGGAGATGATGAACATGAGTGAGGAAGAATGGTGGATACCAAATGCCATCACTTACAGTGTTCTGATGCATGGGTTCCGGAGGGAAGGGAAATTGGTTGAGGCTTGTGATATTGTCAAACAGATGATTAAAAAGGGACTTTTTCCTACCCCAATTGAAATTAATCTCTTAATTCAGTCTCTTTGCCAAGAGGGGAAGATGGATGAGGCTAAACATTTCATGGAGGAGTGTTTAAACAAAGGTTGTGCTGTTAATGTTGTCAATTTTACTACTGTTATTCATGGTTATTGTCAAAAAGATGACTTGGAAGCTGCTCTGTCATTGCTTGATGACATGTATCTCAGCAACAAACACGCAGATGCAGTAACTTATACAGCAGTGATCAATGCATTGGGAAAGAAGGGTAGAATACAAGAGGCAACAGAACTTATGATGAAGATGCTGGGTAAGGGTATTGACCCAACTCCCGTCACATACAGGACGATCATCCACTGGTATTGTAAGATGAATAGGGTGGCTGATTTGTTAAAATTATTGGAGAAGATGTTCTTGAGGCAGCGTTGCAAAACAACATATAATCAAGTGATTGAGAAGCTTTGTAGTTTTGGGAACTTTGAGGCTGCTGATAAACTATTGGGTAAGGTGTTGAGAACAGCTTCAAGAGTTGATGCTAAAACATGCCATGTTGTTATGGATGGTTATTTGAGAAAAGAGGTTCCTCTATTAGCATACAAAGTGGCTTGTCGAATGTTCAATCGGAATCTGATTCCTGATTTAAAGTTGTGTCAGAAGGTGACCAAGAGATTGATGCTAGAAGGATACTCCAAAGAGGCAGACAACCTTATGCTACGGTTTGTTGAGCGTGGATGCATATCAAACCAACTTCAGGAACATCTGGAAAGCTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0003006 GO:0003674 GO:0003676 GO:0003723 GO:0003824 GO:0004518 GO:0004519 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0006139 GO:0006725 GO:0006807 GO:0007275 GO:0008150 GO:0008152 GO:0009451 GO:0009507 GO:0009536 GO:0009790 GO:0009791 GO:0009793 GO:0009987 GO:0010154 GO:0016070 GO:0016787 GO:0016788 GO:0022414 GO:0032501 GO:0032502 GO:0034641 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043412 GO:0044237 GO:0044238 GO:0044424 GO:0044444 GO:0044464 GO:0046483 GO:0048316 GO:0048608 GO:0048731 GO:0048856 GO:0061458 GO:0071704 GO:0090304 GO:0090305 GO:0097159 GO:1901360 GO:1901363

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PPR PPR_1 PPR_2 PPR_3

Protein Analysis

365

Amino Acids

41.64

Weight (kDa)

8.8

Isoelectric Point (pI)

30.36

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_3	PF13812	3 - 53	6.5e-11	Pentatricopeptide repeat domain
PPR_1	PF12854	4 - 36	8.5e-14	PPR repeat
PPR_2	PF13041	8 - 57	8.1e-20	PPR repeat family
PPR	PF01535	11 - 41	8.1e-08	PPR repeat
PPR_1	PF12854	39 - 69	1.1e-08	PPR repeat
PPR_2	PF13041	78 - 114	6.8e-06	PPR repeat family
TPR_24	PF23276	80 - 173	1.5e-06	Fungal tetratrico peptide repeats
PPR_1	PF12854	144 - 176	1.6e-08	PPR repeat
PPR_2	PF13041	149 - 195	7.5e-12	PPR repeat family
PPR_3	PF13812	171 - 232	5.1e-07	Pentatricopeptide repeat domain
PPR_1	PF12854	183 - 211	5.1e-06	PPR repeat
PPR_2	PF13041	184 - 232	1.6e-13	PPR repeat family
PPR	PF01535	186 - 216	3.8e-07	PPR repeat
PPR_1	PF12854	214 - 246	4.2e-07	PPR repeat

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready

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Orthologous Genes (Group: OG0002968)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G30290 AT1G30290
fragaria_vesca	FvH4_3g05050 FvH4_3g05050 FvH4_3g05050 FvH4_3g05050 FvH4_3g05050 FvH4_3g05050 FvH4_3g05050 FvH4_3g05050
malus_domestica	MD10G1258300.v1.1
prunus_persica	Prupe.4G085500_v2.0.a1 Prupe.4G085500_v2.0.a1
pyrus_communis	pycom05g26000 pycom10g21460
rosa_chinensis	RchiOBHm_Chr3g0490541 RchiOBHm_Chr3g0490551 RchiOBHm_Chr5g0014911
rosa_laevigata	RLG00000022885 RLG00000032150
rosa_multiflora	Rmu_sc0003862.1_g000007 Rmu_sc0013610.1_g000002
rosa_roxburghii	Rroxscaffold_1G00061660 Rroxscaffold_6G00393420
rosa_rugosa	Rorug03G0243900 Rorug05G0021400
rosa_samantha	Rh3AG293300 Rh3AG293400 Rh3BG329800 Rh3CG327300 Rh3CG327400 Rh3DG326700 Rh5AG117100 Rh5BG114100 Rh5CG125600 Rh5DG113500
rosa_wichuraiana	Rw3G025970 Rw5G010080

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	64
AccIII	TCCGGA	1 cut(s)	270
AclWI	GGATC	1 cut(s)	87
AcoI	YGGCCR	1 cut(s)	147
AcuI	CTGAAG	2 cut(s)	83, 1061
AfiI	CCNNNNNNNGG	1 cut(s)	1078
AflIII	ACRYGT	2 cut(s)	105, 525
AgsI	TTSAA	3 cut(s)	350, 852, 946
AloI	GAACNNNNNNTCC	2 cut(s)	722, 754
AluBI	AGCT	5 cut(s)	86, 503, 787, 848, 1095
AluI	AGCT	5 cut(s)	86, 503, 787, 848, 1095
Alw26I	GTCTC	1 cut(s)	375
AlwI	GGATC	1 cut(s)	87
Aor13HI	TCCGGA	1 cut(s)	270
AoxI	GGCC	1 cut(s)	147
ApeKI	GCWGC	3 cut(s)	503, 748, 812
AseI	ATTAAT	1 cut(s)	354
Asp700I	GAANNNNTTC	2 cut(s)	737, 847
AsuHPI	GGTGA	1 cut(s)	997
BbvI	GCAGC	3 cut(s)	490, 760, 799
BccI	CCATC	3 cut(s)	248, 385, 881
BceAI	ACGGC	1 cut(s)	162
BciVI	GTATCC	2 cut(s)	222, 1004
BclI	TGATCA	1 cut(s)	573
BcoDI	GTCTC	1 cut(s)	375
BfaI	CTAG	2 cut(s)	1004, 1096
BfuI	GTATCC	2 cut(s)	222, 1004
BisI	GCNGC	3 cut(s)	504, 749, 813
BlsI	GCNGC	3 cut(s)	505, 750, 814
BmiI	GGNNCC	2 cut(s)	269, 909
BmsI	GCATC	7 cut(s)	84, 249, 541, 621, 850, 990, 1049
BpuEI	CTTGAG	1 cut(s)	763
BsaBI	GATNNNNATC	1 cut(s)	1063
BsaWI	WCCGGW	1 cut(s)	270
BsaXI	ACNNNNNCTCC	2 cut(s)	722, 752
Bsc4I	CCNNNNNNNGG	1 cut(s)	1078
Bse1I	ACTGG	1 cut(s)	689
Bse3DI	GCAATG	1 cut(s)	512
Bse8I	GATNNNNATC	1 cut(s)	1063
BseAI	TCCGGA	1 cut(s)	270
BseGI	GGATG	4 cut(s)	400, 678, 892, 1064
BseJI	GATNNNNATC	1 cut(s)	1063
BseLI	CCNNNNNNNGG	1 cut(s)	1078
BseMI	GCAATG	1 cut(s)	512
BseMII	CTCAG	1 cut(s)	547
BseNI	ACTGG	1 cut(s)	689
BseRI	GAGGAG	1 cut(s)	431
BseXI	GCAGC	3 cut(s)	490, 760, 799
BseYI	CCCAGC	1 cut(s)	634
BshFI	GGCC	1 cut(s)	149
BsiSI	CCGG	1 cut(s)	271
BslFI	GGGAC	1 cut(s)	342
BslI	CCNNNNNNNGG	1 cut(s)	1078
BsmAI	GTCTC	1 cut(s)	375
BsmFI	GGGAC	1 cut(s)	342
BsnI	GGCC	1 cut(s)	149
Bsp13I	TCCGGA	1 cut(s)	270
Bsp143I	GATC	3 cut(s)	79, 573, 675
BspANI	GGCC	1 cut(s)	149
BspCNI	CTCAG	1 cut(s)	546
BspEI	TCCGGA	1 cut(s)	270
BspLI	GGNNCC	2 cut(s)	269, 909
BspPI	GGATC	1 cut(s)	87
BsrDI	GCAATG	1 cut(s)	512
BsrI	ACTGG	1 cut(s)	689
BssMI	GATC	3 cut(s)	79, 573, 675
Bst4CI	ACNGT	5 cut(s)	46, 136, 251, 466, 1044
BstC8I	GCNNGC	1 cut(s)	125
BstDEI	CTNAG	1 cut(s)	533
BstEII	GGTNACC	1 cut(s)	985
BstF5I	GGATG	4 cut(s)	400, 678, 892, 1064
BstKTI	GATC	3 cut(s)	82, 576, 678
BstMAI	GTCTC	1 cut(s)	375
BstMBI	GATC	3 cut(s)	79, 573, 675
BstNSI	RCATGY	3 cut(s)	109, 529, 873
BstPI	GGTNACC	1 cut(s)	985
BstV1I	GCAGC	3 cut(s)	490, 760, 799
BsuI	GTATCC	2 cut(s)	222, 1004
BsuRI	GGCC	1 cut(s)	149
BtsCI	GGATG	4 cut(s)	400, 678, 892, 1064
BtsI	GCAGTG	1 cut(s)	576
BtsIMutI	CAGTG	3 cut(s)	256, 576, 682
Cac8I	GCNNGC	1 cut(s)	125
CspCI	CAANNNNNGTGG	2 cut(s)	671, 706
DdeI	CTNAG	1 cut(s)	533
DpnI	GATC	3 cut(s)	81, 575, 677
DpnII	GATC	3 cut(s)	79, 573, 675
DraI	TTTAAA	2 cut(s)	426, 969
EaeI	YGGCCR	1 cut(s)	147
Eco57I	CTGAAG	2 cut(s)	83, 1061
Eco91I	GGTNACC	1 cut(s)	985
EcoO65I	GGTNACC	1 cut(s)	985
EcoT22I	ATGCAT	3 cut(s)	264, 583, 1064
FalI	AAGNNNNNCTT	2 cut(s)	725, 757
FaqI	GGGAC	1 cut(s)	342
FbaI	TGATCA	1 cut(s)	573
FblI	GTMKAC	1 cut(s)	64
Fnu4HI	GCNGC	3 cut(s)	504, 749, 813
FokI	GGATG	4 cut(s)	407, 665, 899, 1071
Fsp4HI	GCNGC	3 cut(s)	504, 749, 813
FspBI	CTAG	2 cut(s)	1004, 1096
GluI	GCNGC	3 cut(s)	504, 749, 813
GsaI	CCCAGC	1 cut(s)	638
HaeIII	GGCC	1 cut(s)	149
HapII	CCGG	1 cut(s)	271
HincII	GTYRAC	1 cut(s)	65
HindII	GTYRAC	1 cut(s)	65
HindIII	AAGCTT	1 cut(s)	785
HinfI	GANTC	2 cut(s)	952, 958
HpaII	CCGG	1 cut(s)	271
HphI	GGTGA	1 cut(s)	997
Hpy166II	GTNNAC	1 cut(s)	65
Hpy188I	TCNGA	5 cut(s)	51, 258, 951, 957, 981
Hpy188III	TCNNGA	6 cut(s)	271, 742, 852, 962, 1079, 1088
Hpy8I	GTNNAC	1 cut(s)	65
HpyAV	CCTTC	5 cut(s)	67, 272, 586, 976, 1001
HpyCH4III	ACNGT	5 cut(s)	46, 136, 251, 466, 1044
HpyCH4V	TGCA	7 cut(s)	18, 123, 262, 554, 581, 756, 1062
HpyF3I	CTNAG	1 cut(s)	533
Kpn2I	TCCGGA	1 cut(s)	270
Ksp22I	TGATCA	1 cut(s)	573
Kzo9I	GATC	3 cut(s)	79, 573, 675
LpnPI	CCDG	8 cut(s)	36, 284, 620, 655, 670, 975, 1064, 1073
Lsp1109I	GCAGC	3 cut(s)	490, 760, 799
LweI	GCATC	7 cut(s)	84, 249, 541, 621, 850, 990, 1049
MaeI	CTAG	2 cut(s)	1004, 1096
MaeIII	GTNAC	4 cut(s)	31, 556, 661, 985
MalI	GATC	3 cut(s)	81, 575, 677
MboI	GATC	3 cut(s)	79, 573, 675
MboII	GAAGA	4 cut(s)	230, 400, 640, 745
MfeI	CAATTG	1 cut(s)	345
MluCI	AATT	6 cut(s)	284, 345, 351, 363, 454, 722
Mph1103I	ATGCAT	3 cut(s)	264, 583, 1064
MroI	TCCGGA	1 cut(s)	270
MroXI	GAANNNNTTC	2 cut(s)	737, 847
MseI	TTAA	7 cut(s)	321, 354, 362, 425, 444, 719, 968
MslI	CAYNNNNRTG	1 cut(s)	549
MspI	CCGG	1 cut(s)	271
MssI	GTTTAAAC	1 cut(s)	426
MunI	CAATTG	1 cut(s)	345
NdeII	GATC	3 cut(s)	79, 573, 675
NlaIV	GGNNCC	2 cut(s)	269, 909
NmuCI	GTSAC	2 cut(s)	661, 985
NsiI	ATGCAT	3 cut(s)	264, 583, 1064
NspI	RCATGY	3 cut(s)	109, 529, 873
PciI	ACATGT	2 cut(s)	105, 525
PdmI	GAANNNNTTC	2 cut(s)	737, 847
PfeI	GAWTC	2 cut(s)	952, 958
PkrI	GCNGC	3 cut(s)	505, 750, 814
PmeI	GTTTAAAC	1 cut(s)	426
PscI	ACATGT	2 cut(s)	105, 525
PshBI	ATTAAT	1 cut(s)	354
PspEI	GGTNACC	1 cut(s)	985
PspFI	CCCAGC	1 cut(s)	634
PspN4I	GGNNCC	2 cut(s)	269, 909
RseI	CAYNNNNRTG	1 cut(s)	549
SalI	GTCGAC	1 cut(s)	63
SaqAI	TTAA	7 cut(s)	321, 354, 362, 425, 444, 719, 968
SatI	GCNGC	3 cut(s)	504, 749, 813
Sau3AI	GATC	3 cut(s)	79, 573, 675
SfaNI	GCATC	7 cut(s)	84, 249, 541, 621, 850, 990, 1049
SmiMI	CAYNNNNRTG	1 cut(s)	549
SmlI	CTYRAG	1 cut(s)	742
SmoI	CTYRAG	1 cut(s)	742
Sse9I	AATT	6 cut(s)	284, 345, 351, 363, 454, 722
SspMI	CTAG	2 cut(s)	1004, 1096
TaaI	ACNGT	5 cut(s)	46, 136, 251, 466, 1044
TaqI	TCGA	2 cut(s)	64, 937
TasI	AATT	6 cut(s)	284, 345, 351, 363, 454, 722
TfiI	GAWTC	2 cut(s)	952, 958
Tru1I	TTAA	7 cut(s)	321, 354, 362, 425, 444, 719, 968
Tru9I	TTAA	7 cut(s)	321, 354, 362, 425, 444, 719, 968
TscAI	CASTG	3 cut(s)	256, 576, 689
TseFI	GTSAC	2 cut(s)	661, 985
TseI	GCWGC	3 cut(s)	503, 748, 812
Tsp45I	GTSAC	2 cut(s)	661, 985
TspDTI	ATGAA	5 cut(s)	218, 400, 461, 641, 713
TspRI	CASTG	3 cut(s)	256, 576, 689
VspI	ATTAAT	1 cut(s)	354
XceI	RCATGY	3 cut(s)	109, 529, 873
XmiI	GTMKAC	1 cut(s)	64
XmnI	GAANNNNTTC	2 cut(s)	737, 847
XspI	CTAG	2 cut(s)	1004, 1096
Zsp2I	ATGCAT	3 cut(s)	264, 583, 1064

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