Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0002968

Physical Location & Seq

Genomic Coordinates Forward (+)

35558046 .. 35560949

Gene Structure 2904 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG293300.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1260 bp

ATGGCTTCCGGTGGGGATAACATCTCTGTTACTAAAGGCGTTGTTTCTAGGGTTGAACCTACACAATATGTTCACGGTGCAACCCAGCTTATGGCAATACAGATCGATGCAGCAATAAATCCCGGGAATAGTGGTAGCCCAGCAATCATGGGAAATAAAGTTGCTGGTTTTGCTTTCCAAAACCTTTCTGGTGCAGAGAATATTGGTTATATAATTCCTGTTCCTGTAATAAAGCATTTTATTGCTGGAGTTGAAGAAAGAGGTAAATATTATGGAGATGGAGATGAAGATGAATATCGAGACCCTTTGGTGAGAGAGGTTTGTAGGTTAATTGAGCTTAGAACAGCTTGGACGCCAAAGTTTGAAGGTGAATTAAGGCACTTGTTACGAAGCTTGAAGCCAAAGCAGGTTTGTGCTGTTTTCAAGTCTCAGGCTGATGAAAGAGTTGCTTTGGAGGTTTTCTACTGGGCTGATAGGCAGTGGAGGTATAAGCATGACCCGATTGTGTACTATGCAATGCTTGAGGTGCTTAGTAAGACCAAGTTGTGCCAAGGTGCTAGGAGGATTCTTAGGTTAATGGCCCGTAGGCGGATTGAGCTTCGTTCTGAAGCTTTTGGTCATGTGATGGTGTCATATAGTCAAGCGGGCAAGTTAAGACATGCGTTGCGTGTGTTGACTTTGATGCAGAAAGCGGGGCTTGAGCTTGATTTGTCAATGTGTAATACTGCAATTTATGTTTTGGTGAAAGGTAATAAGTTAGAGAAGGCGTTGAGGACCTTGGAAAGGATGAAGCTTGTTGGGATTGCACCAAATGTTGTCACTTATAACTGTTTGATAAAGGGGTATTGTGATTTGCATCGTGTAGAAGATGCAATCCAGGTGATTGATGAAATGCCGATGAAGGGGTGTGCTCCTGATAAAGTTAGTTATTATACTGTCATGAATTTCCTTTGTAAGGAGAAGAGGGTCAAAGAAGTGAGGGACTTGATGGAGAAGATGATCAAGGATGGTGGGTTATTACCAGACCAGGTCACTTATAGTAATCTTGTCCATGTGCTTTGTAAGCACGGCTATGGTGATGAGGCACTTGAATTTTTAAGGGAAGCCGAAGAGAGGGGATTTCGGTTTGATAAGGTTGGGTATAGTGCAATTGTACATTCATTTTGTAAGGATGGTAGGATTGACATGGCAAAAGAAATTGTTAGTGAAATGTTCTCAAAAGGTTGCACACAGATGTTGTTACATACAGTACTGTTCTGA

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

419

Amino Acids

47.46

Weight (kDa)

8.79

Isoelectric Point (pI)

30.65

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TPR_24	PF23276	178 - 264	8.8e-07	Fungal tetratrico peptide repeats
PPR_3	PF13812	224 - 282	2.1e-12	Pentatricopeptide repeat domain
PPR_2	PF13041	238 - 284	1.1e-11	PPR repeat family
PPR_1	PF12854	267 - 298	5.1e-12	PPR repeat
PPR_2	PF13041	270 - 319	1.8e-16	PPR repeat family
PPR	PF01535	273 - 303	2.2e-07	PPR repeat
PPR_2	PF13041	308 - 355	5.2e-09	PPR repeat family
PPR_1	PF12854	338 - 368	4.3e-08	PPR repeat
PPR_2	PF13041	341 - 389	3.3e-08	PPR repeat family
PPR	PF01535	344 - 374	4.4e-06	PPR repeat
PPR_1	PF12854	372 - 404	1.6e-06	PPR repeat

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)

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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)
AanI	TTATAA	1 cut(s)	825
Acc36I	ACCTGC	1 cut(s)	397
AccB7I	CCANNNNNTGG	1 cut(s)	91
AciI	CCGC	3 cut(s)	589, 644, 692
AcsI	RAATTY	2 cut(s)	943, 1091
AcuI	CTGAAG	1 cut(s)	627
AcyI	GRCGYC	1 cut(s)	353
AfaI	GTAC	3 cut(s)	509, 1155, 1251
AfiI	CCNNNNNNNGG	6 cut(s)	91, 588, 783, 902, 955, 1113
AgsI	TTSAA	6 cut(s)	56, 254, 365, 397, 424, 1091
AjnI	CCWGG	2 cut(s)	876, 1026
AluBI	AGCT	8 cut(s)	88, 337, 347, 393, 598, 611, 703, 793
AluI	AGCT	8 cut(s)	88, 337, 347, 393, 598, 611, 703, 793
Alw21I	GWGCWC	1 cut(s)	913
Alw26I	GTCTC	2 cut(s)	294, 432
Ama87I	CYCGRG	1 cut(s)	122
AoxI	GGCC	1 cut(s)	579
ApeKI	GCWGC	1 cut(s)	110
ApoI	RAATTY	2 cut(s)	943, 1091
AspS9I	GGNCC	2 cut(s)	580, 774
AsuC2I	CCSGG	2 cut(s)	123, 124
AsuHPI	GGTGA	5 cut(s)	322, 380, 754, 892, 1088
AvaI	CYCGRG	1 cut(s)	122
AvaII	GGWCC	1 cut(s)	774
Bbv12I	GWGCWC	1 cut(s)	913
BbvI	GCAGC	1 cut(s)	122
BccI	CCATC	5 cut(s)	272, 619, 982, 1001, 1166
BceAI	ACGGC	1 cut(s)	1084
BciT130I	CCWGG	2 cut(s)	878, 1028
BclI	TGATCA	1 cut(s)	999
BcnI	CCSGG	2 cut(s)	123, 124
BcoDI	GTCTC	2 cut(s)	294, 432
BfaI	CTAG	2 cut(s)	48, 558
BfuAI	ACCTGC	1 cut(s)	397
BisI	GCNGC	1 cut(s)	111
BlsI	GCNGC	1 cut(s)	112
BmcAI	AGTACT	1 cut(s)	1251
Bme1390I	CCNGG	4 cut(s)	123, 124, 878, 1028
Bme18I	GGWCC	1 cut(s)	774
BmeT110I	CYCGRG	1 cut(s)	122
BmgT120I	GGNCC	2 cut(s)	580, 774
BmrFI	CCNGG	4 cut(s)	123, 124, 878, 1028
BmrI	ACTGGG	1 cut(s)	475
BmsI	GCATC	4 cut(s)	97, 672, 859, 865
BmuI	ACTGGG	1 cut(s)	475
BpmI	CTGGAG	1 cut(s)	267
BpuEI	CTTGAG	2 cut(s)	542, 719
BpuMI	CCSGG	2 cut(s)	123, 124
Bsa29I	ATCGAT	1 cut(s)	105
BsaBI	GATNNNNATC	2 cut(s)	294, 855
BsaHI	GRCGYC	1 cut(s)	353
BsaI	GGTCTC	1 cut(s)	294
BsaJI	CCNNGG	3 cut(s)	122, 550, 777
BsaWI	WCCGGW	1 cut(s)	8
Bsc4I	CCNNNNNNNGG	6 cut(s)	91, 588, 783, 902, 955, 1113
Bse1I	ACTGG	1 cut(s)	470
Bse3DI	GCAATG	1 cut(s)	522
Bse8I	GATNNNNATC	2 cut(s)	294, 855
BseBI	CCWGG	2 cut(s)	878, 1028
BseCI	ATCGAT	1 cut(s)	105
BseDI	CCNNGG	3 cut(s)	122, 550, 777
BseGI	GGATG	3 cut(s)	792, 1012, 1177
BseJI	GATNNNNATC	2 cut(s)	294, 855
BseLI	CCNNNNNNNGG	6 cut(s)	91, 588, 783, 902, 955, 1113
BseMI	GCAATG	1 cut(s)	522
BseMII	CTCAG	1 cut(s)	443
BseNI	ACTGG	1 cut(s)	470
BseXI	GCAGC	1 cut(s)	122
BseYI	CCCAGC	2 cut(s)	84, 139
BsgI	GTGCAG	1 cut(s)	213
BshFI	GGCC	1 cut(s)	581
BshVI	ATCGAT	1 cut(s)	105
BsiHKAI	GWGCWC	1 cut(s)	913
BsiHKCI	CYCGRG	1 cut(s)	122
BsiSI	CCGG	2 cut(s)	9, 123
BslFI	GGGAC	1 cut(s)	995
BslI	CCNNNNNNNGG	6 cut(s)	91, 588, 783, 902, 955, 1113
BsmAI	GTCTC	2 cut(s)	294, 432
BsmFI	GGGAC	1 cut(s)	995
BsnI	GGCC	1 cut(s)	581
Bso31I	GGTCTC	1 cut(s)	294
BsoBI	CYCGRG	1 cut(s)	122
Bsp1286I	GDGCHC	1 cut(s)	913
Bsp1407I	TGTACA	1 cut(s)	1153
Bsp143I	GATC	2 cut(s)	102, 999
BspACI	CCGC	3 cut(s)	589, 644, 692
BspANI	GGCC	1 cut(s)	581
BspCNI	CTCAG	1 cut(s)	442
BspDI	ATCGAT	1 cut(s)	105
BspHI	TCATGA	1 cut(s)	939
BspMI	ACCTGC	1 cut(s)	397
BspTNI	GGTCTC	1 cut(s)	294
BsrDI	GCAATG	1 cut(s)	522
BsrGI	TGTACA	1 cut(s)	1153
BsrI	ACTGG	1 cut(s)	470
BssECI	CCNNGG	3 cut(s)	122, 550, 777
BssMI	GATC	2 cut(s)	102, 999
BssNI	GRCGYC	1 cut(s)	353
BssT1I	CCWWGG	2 cut(s)	550, 777
Bst2UI	CCWGG	2 cut(s)	878, 1028
Bst4CI	ACNGT	5 cut(s)	77, 830, 937, 1249, 1254
Bst6I	CTCTTC	2 cut(s)	956, 1104
BstACI	GRCGYC	1 cut(s)	353
BstAUI	TGTACA	1 cut(s)	1153
BstC8I	GCNNGC	1 cut(s)	646
BstDEI	CTNAG	4 cut(s)	338, 429, 530, 569
BstENI	CCTNNNNNAGG	2 cut(s)	781, 953
BstF5I	GGATG	3 cut(s)	792, 1012, 1177
BstKTI	GATC	2 cut(s)	105, 1002
BstMAI	GTCTC	2 cut(s)	294, 432
BstMBI	GATC	2 cut(s)	102, 999
BstMWI	GCNNNNNNNGC	4 cut(s)	170, 526, 595, 1063
BstNI	CCWGG	2 cut(s)	878, 1028
BstNSI	RCATGY	1 cut(s)	662
BstSCI	CCNGG	4 cut(s)	121, 122, 876, 1026
BstV1I	GCAGC	1 cut(s)	122
Bsu15I	ATCGAT	1 cut(s)	105
BsuRI	GGCC	1 cut(s)	581
BsuTUI	ATCGAT	1 cut(s)	105
BtsCI	GGATG	3 cut(s)	792, 1012, 1177
BtsI	GCAGTG	1 cut(s)	485
BtsIMutI	CAGTG	1 cut(s)	485
BveI	ACCTGC	1 cut(s)	397
Cac8I	GCNNGC	1 cut(s)	646
CciI	TCATGA	1 cut(s)	939
Cfr13I	GGNCC	2 cut(s)	580, 774
Cfr9I	CCCGGG	1 cut(s)	122
ClaI	ATCGAT	1 cut(s)	105
CseI	GACGC	1 cut(s)	361
CsiI	ACCWGGT	1 cut(s)	1026
Csp6I	GTAC	3 cut(s)	508, 1154, 1250
CspCI	CAANNNNNGTGG	2 cut(s)	991, 1026
CviAII	CATG	7 cut(s)	148, 494, 620, 659, 940, 1052, 1186
CviQI	GTAC	3 cut(s)	508, 1154, 1250
DdeI	CTNAG	4 cut(s)	338, 429, 530, 569
DpnI	GATC	2 cut(s)	104, 1001
DpnII	GATC	2 cut(s)	102, 999
Eam1104I	CTCTTC	2 cut(s)	956, 1104
EarI	CTCTTC	2 cut(s)	956, 1104
EciI	GGCGGA	1 cut(s)	604
Eco130I	CCWWGG	2 cut(s)	550, 777
Eco31I	GGTCTC	1 cut(s)	294
Eco47I	GGWCC	1 cut(s)	774
Eco57I	CTGAAG	1 cut(s)	627
Eco88I	CYCGRG	1 cut(s)	122
EcoNI	CCTNNNNNAGG	2 cut(s)	781, 953
EcoO109I	RGGNCCY	1 cut(s)	774
EcoRII	CCWGG	2 cut(s)	876, 1026
EcoT14I	CCWWGG	2 cut(s)	550, 777
ErhI	CCWWGG	2 cut(s)	550, 777
FaeI	CATG	7 cut(s)	151, 497, 623, 662, 943, 1055, 1189
FalI	AAGNNNNNCTT	4 cut(s)	433, 465, 681, 713
FaqI	GGGAC	1 cut(s)	995
FatI	CATG	7 cut(s)	147, 493, 619, 658, 939, 1051, 1185
FauI	CCCGC	2 cut(s)	637, 685
FbaI	TGATCA	1 cut(s)	999
Fnu4HI	GCNGC	1 cut(s)	111
FokI	GGATG	3 cut(s)	799, 1019, 1184
Fsp4HI	GCNGC	1 cut(s)	111
FspBI	CTAG	2 cut(s)	48, 558
GluI	GCNGC	1 cut(s)	111
GsaI	CCCAGC	2 cut(s)	88, 143
GsuI	CTGGAG	1 cut(s)	267
HaeIII	GGCC	1 cut(s)	581
HapII	CCGG	2 cut(s)	9, 123
HgaI	GACGC	1 cut(s)	361
Hin1I	GRCGYC	1 cut(s)	353
Hin1II	CATG	7 cut(s)	151, 497, 623, 662, 943, 1055, 1189
HincII	GTYRAC	1 cut(s)	675
HindII	GTYRAC	1 cut(s)	675
HindIII	AAGCTT	3 cut(s)	391, 609, 791
HinfI	GANTC	1 cut(s)	565
HpaII	CCGG	2 cut(s)	9, 123
HphI	GGTGA	5 cut(s)	322, 380, 754, 892, 1088
Hpy166II	GTNNAC	3 cut(s)	73, 508, 675
Hpy188I	TCNGA	2 cut(s)	607, 1259
Hpy188III	TCNNGA	3 cut(s)	299, 914, 940
Hpy8I	GTNNAC	3 cut(s)	73, 508, 675
HpyAV	CCTTC	3 cut(s)	359, 757, 895
HpyCH4III	ACNGT	5 cut(s)	77, 830, 937, 1249, 1254
HpyF10VI	GCNNNNNNNGC	4 cut(s)	170, 526, 595, 1063
HpyF3I	CTNAG	4 cut(s)	338, 429, 530, 569
Hsp92I	GRCGYC	1 cut(s)	353
Hsp92II	CATG	7 cut(s)	151, 497, 623, 662, 943, 1055, 1189
Ksp22I	TGATCA	1 cut(s)	999
Kzo9I	GATC	2 cut(s)	102, 999
LmnI	GCTCC	1 cut(s)	916
Lsp1109I	GCAGC	1 cut(s)	122
LweI	GCATC	4 cut(s)	97, 672, 859, 865
MabI	ACCWGGT	1 cut(s)	1026
MaeI	CTAG	2 cut(s)	48, 558
MaeIII	GTNAC	5 cut(s)	28, 384, 817, 1030, 1239
MalI	GATC	2 cut(s)	104, 1001
MboI	GATC	2 cut(s)	102, 999
MboII	GAAGA	6 cut(s)	266, 299, 878, 973, 1006, 1121
MfeI	CAATTG	1 cut(s)	1149
MhlI	GDGCHC	1 cut(s)	913
MluCI	AATT	8 cut(s)	213, 330, 371, 729, 943, 1091, 1149, 1197
MseI	TTAA	5 cut(s)	329, 374, 575, 653, 1097
MslI	CAYNNNNRTG	2 cut(s)	1071, 1232
MspI	CCGG	2 cut(s)	9, 123
MspR9I	CCNGG	4 cut(s)	123, 124, 878, 1028
MunI	CAATTG	1 cut(s)	1149
MvaI	CCWGG	2 cut(s)	878, 1028
MwoI	GCNNNNNNNGC	4 cut(s)	170, 526, 595, 1063
NciI	CCSGG	2 cut(s)	123, 124
NdeII	GATC	2 cut(s)	102, 999
NlaIII	CATG	7 cut(s)	151, 497, 623, 662, 943, 1055, 1189
NmuCI	GTSAC	2 cut(s)	817, 1030
NspI	RCATGY	1 cut(s)	662
PagI	TCATGA	1 cut(s)	939
PfeI	GAWTC	1 cut(s)	565
PflFI	GACNNNGTC	1 cut(s)	1028
PflMI	CCANNNNNTGG	1 cut(s)	91
PkrI	GCNGC	1 cut(s)	112
PpuMI	RGGWCCY	1 cut(s)	774
PsiI	TTATAA	1 cut(s)	825
Psp5II	RGGWCCY	1 cut(s)	774
Psp6I	CCWGG	2 cut(s)	876, 1026
PspFI	CCCAGC	2 cut(s)	84, 139
PspGI	CCWGG	2 cut(s)	876, 1026
PspPI	GGNCC	2 cut(s)	580, 774
PspPPI	RGGWCCY	1 cut(s)	774
PsyI	GACNNNGTC	1 cut(s)	1028
RsaI	GTAC	3 cut(s)	509, 1155, 1251
RsaNI	GTAC	3 cut(s)	508, 1154, 1250
RseI	CAYNNNNRTG	2 cut(s)	1071, 1232
SaqAI	TTAA	5 cut(s)	329, 374, 575, 653, 1097
SatI	GCNGC	1 cut(s)	111
Sau3AI	GATC	2 cut(s)	102, 999
Sau96I	GGNCC	2 cut(s)	580, 774
ScaI	AGTACT	1 cut(s)	1251
ScrFI	CCNGG	4 cut(s)	123, 124, 878, 1028
SduI	GDGCHC	1 cut(s)	913
SexAI	ACCWGGT	1 cut(s)	1026
SfaNI	GCATC	4 cut(s)	97, 672, 859, 865
SinI	GGWCC	1 cut(s)	774
SmaI	CCCGGG	1 cut(s)	124
SmiMI	CAYNNNNRTG	2 cut(s)	1071, 1232
SmlI	CTYRAG	2 cut(s)	521, 698
SmoI	CTYRAG	2 cut(s)	521, 698
Sse9I	AATT	8 cut(s)	213, 330, 371, 729, 943, 1091, 1149, 1197
SsiI	CCGC	3 cut(s)	589, 644, 692
SspI	AATATT	2 cut(s)	202, 269
SspMI	CTAG	2 cut(s)	48, 558
StyD4I	CCNGG	4 cut(s)	121, 122, 876, 1026
StyI	CCWWGG	2 cut(s)	550, 777
TaaI	ACNGT	5 cut(s)	77, 830, 937, 1249, 1254
TaqI	TCGA	2 cut(s)	105, 298
TasI	AATT	8 cut(s)	213, 330, 371, 729, 943, 1091, 1149, 1197
TatI	WGTACW	3 cut(s)	507, 1153, 1249
TfiI	GAWTC	1 cut(s)	565
Tru1I	TTAA	5 cut(s)	329, 374, 575, 653, 1097
Tru9I	TTAA	5 cut(s)	329, 374, 575, 653, 1097
TscAI	CASTG	1 cut(s)	485
TseFI	GTSAC	2 cut(s)	817, 1030
TseI	GCWGC	1 cut(s)	110
Tsp45I	GTSAC	2 cut(s)	817, 1030
TspDTI	ATGAA	8 cut(s)	300, 306, 453, 803, 903, 914, 956, 1149
TspMI	CCCGGG	1 cut(s)	122
TspRI	CASTG	1 cut(s)	485
Tth111I	GACNNNGTC	1 cut(s)	1028
Van91I	CCANNNNNTGG	1 cut(s)	91
VpaK11BI	GGWCC	1 cut(s)	774
XagI	CCTNNNNNAGG	2 cut(s)	781, 953
XapI	RAATTY	2 cut(s)	943, 1091
XceI	RCATGY	1 cut(s)	662
XcmI	CCANNNNNNNNNTGG	1 cut(s)	185
XmaI	CCCGGG	1 cut(s)	122
XspI	CTAG	2 cut(s)	48, 558
ZrmI	AGTACT	1 cut(s)	1251

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