Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1D

Orthogroup ID

OG0000530

Physical Location & Seq

Genomic Coordinates Forward (+)

36352240 .. 36356049

Gene Structure 3810 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1DG178800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 939 bp

ATGCCTGCGATGGGATTTGTGCCCAATGTGGTGACTTTTACTACCATTTTGGGTGGTTATGTGTCGCGGCGCGATATGGTTGGTGCCAAGAGGGTGTTTGGTGAGATTTTGGACAGAGGGTGGTTTCCTGATGTGACTACATATACCATATTGATGGATGGGTATGTGAAGCAGGGGAAGCTGGTTGAGGCTATTAAGGTTATGGATGAGATGGAGGACAATGGGATTTGCGCCAATGAGGTTACTTATGGGGTTATGATTGAAGGTTATTGCAAGGAAAAGAAGTCGGGCGAAGCGGTTAATTTGCTTGATGATATGGTGCAGAAGAGGTATATACCGAGCTCGGCACTCTGTTGTAAGGTGATTGATGTTTTTTGTTGCGAAGGGAAGGTGGAGGATGCTTGTGAACTGTGGAAAAGGCTTTTGAAGAAGAATTGCACGCCGGATAATGCAGTATTGGGCACACTCATATACTGGCTTTGTAAGAAGGGAGAAGTGTGGAAAGCCAGGAGTTTGTTTGATCAGTTTGAGACGAGTGAGCCTCCGGATGTCATGACTTACAACGTGCTTATTTCTGGAATGTGTGAAGTGGGGGAGTTGTGTGAGGCAGGGAGGTTGTGGGATGACATGGTGGAGAAAGGTTATTCTCCGAATTCTTTTACATATAATGTATTGATCAAAGGATTCTGTAAGATTGGAAAAGCAAAGGAGGGAATTAGGATTTTGGACGAGATGTTCGAAAAAGGCTGTTTGCCAAACAAGTCTACTTATGCTATGTTGATTGAGGGGCTCTGCGACTCAGGAGAGGAAGCTGAAATCACTAGAGTAATATCTATGGCAATGTCAAGTGGAGACATTGACAGTGATTCCTGGGATCTTTTCCTTACTAAGGTTGGGGAAAGTGTTCTAAACAGAATACTACTGGAGAATGCTGATTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003676 GO:0003723 GO:0003824 GO:0004518 GO:0004519 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0006139 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009451 GO:0009987 GO:0016070 GO:0016787 GO:0016788 GO:0034641 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043412 GO:0044237 GO:0044238 GO:0044424 GO:0044464 GO:0046483 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

312

Amino Acids

34.89

Weight (kDa)

4.71

Isoelectric Point (pI)

35.77

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	8 - 57	2.6e-13	PPR repeat family
PPR_3	PF13812	32 - 90	1.2e-07	Pentatricopeptide repeat domain
PPR_1	PF12854	40 - 72	2.6e-09	PPR repeat
PPR_2	PF13041	43 - 92	2.2e-17	PPR repeat family
PPR	PF01535	47 - 76	1.3e-08	PPR repeat
PPR_1	PF12854	74 - 107	1.5e-08	PPR repeat
PPR_2	PF13041	79 - 115	1.5e-07	PPR repeat family
PPR	PF01535	81 - 109	1.5e-06	PPR repeat
PPR_2	PF13041	120 - 162	9.8e-07	PPR repeat family
PPR_2	PF13041	182 - 231	1.3e-19	PPR repeat family
PPR_1	PF12854	182 - 211	4.8e-08	PPR repeat
PPR_3	PF13812	182 - 229	4.1e-07	Pentatricopeptide repeat domain
PPR_3	PF13812	205 - 262	3e-09	Pentatricopeptide repeat domain
PPR_1	PF12854	213 - 245	7.3e-11	PPR repeat
PPR_2	PF13041	220 - 266	6.3e-15	PPR repeat family
PPR	PF01535	220 - 250	4e-08	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: OG0000530)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G16420 AT5G16420 AT5G16420 AT5G16420
fragaria_vesca	FvH4_7g08341 FvH4_7g08360
malus_domestica	MD02G1232100.v1.1 MD07G1081300.v1.1
prunus_persica	Prupe.2G106500_v2.0.a1
pyrus_communis	pycom02g20040
rosa_chinensis	RchiOBHm_Chr1g0340331 RchiOBHm_Chr1g0340431 RchiOBHm_Chr1g0340441 RchiOBHm_Chr1g0340491 RchiOBHm_Chr1g0340531 RchiOBHm_Chr1g0340541 RchiOBHm_Chr1g0340561 RchiOBHm_Chr1g0340621 RchiOBHm_Chr1g0340661 RchiOBHm_Chr1g0340691
rosa_laevigata	RLG00000029013 RLG00000029018 RLG00000029020 RLG00000029024 RLG00000029026 RLG00000029029 RLG00000029030 RLG00000029032 RLG00000029033
rosa_multiflora	Rmu_sc0000566.1_g000026 Rmu_sc0000566.1_g000034 Rmu_sc0000566.1_g000054 Rmu_sc0001836.1_g000016 Rmu_sc0001836.1_g000022 Rmu_sc0001836.1_g000023 Rmu_sc0001836.1_g000028 Rmu_sc0001836.1_g000058 Rmu_sc0001946.1_g000004 Rmu_sc0002595.1_g000001 Rmu_sc0002595.1_g000005 Rmu_sc0005167.1_g000003 Rmu_sc0005167.1_g000009 Rmu_sc0005167.1_g000018 Rmu_sc0024761.1_g000004
rosa_roxburghii	Rroxscaffold_4G00311170 Rroxscaffold_4G00311190 Rroxscaffold_4G00311250 Rroxscaffold_4G00315930 Rroxscaffold_4G00315960 Rroxscaffold_5G00353270
rosa_rugosa	Rorug01G0162000.1 Rorug01G0162500.1 Rorug01G0162800.1 Rorug01G0163000.1 Rorug01G0163400.1 Rorug01G0163700.1 Rorug01G0164100.1 Rorug01G0164300 Rorug05G0484800
rosa_samantha	Rh1AG177800 Rh1AG178000 Rh1AG178300 Rh1AG178600 Rh1AG178900 Rh1BG145300 Rh1BG145600 Rh1BG145800 Rh1BG145900 Rh1BG146000 Rh1BG146700 Rh1CG165100 Rh1CG165200 Rh1CG165400 Rh1CG165600 Rh1CG165700 Rh1CG165900 Rh1DG177500 Rh1DG177600 Rh1DG177800 Rh1DG177900 Rh1DG178000 Rh1DG178800
rosa_wichuraiana	Rw0G006210 Rw1G014800 Rw1G014890

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	83
AccI	GTMKAC	1 cut(s)	764
AccII	CGCG	2 cut(s)	67, 72
AccIII	TCCGGA	1 cut(s)	544
AciI	CCGC	2 cut(s)	67, 296
AclWI	GGATC	1 cut(s)	882
AcsI	RAATTY	1 cut(s)	652
AfiI	CCNNNNNNNGG	2 cut(s)	11, 889
AgsI	TTSAA	2 cut(s)	263, 427
AjnI	CCWGG	2 cut(s)	506, 869
AloI	GAACNNNNNNTCC	2 cut(s)	719, 751
AluBI	AGCT	3 cut(s)	181, 342, 812
AluI	AGCT	3 cut(s)	181, 342, 812
Alw21I	GWGCWC	1 cut(s)	344
Alw26I	GTCTC	2 cut(s)	524, 846
AlwI	GGATC	1 cut(s)	882
Aor13HI	TCCGGA	1 cut(s)	544
ApoI	RAATTY	1 cut(s)	652
ArsI	GACNNNNNNTTYG	2 cut(s)	719, 751
Asp700I	GAANNNNTTC	1 cut(s)	903
AspLEI	GCGC	2 cut(s)	72, 233
AsuHPI	GGTGA	3 cut(s)	43, 113, 373
AsuII	TTCGAA	1 cut(s)	738
BaeGI	GKGCMC	2 cut(s)	24, 464
BanI	GGYRCC	1 cut(s)	83
BanII	GRGCYC	2 cut(s)	344, 792
Bbv12I	GWGCWC	1 cut(s)	344
BccI	CCATC	4 cut(s)	4, 148, 152, 205
BciT130I	CCWGG	2 cut(s)	508, 871
BclI	TGATCA	2 cut(s)	520, 675
BcoDI	GTCTC	2 cut(s)	524, 846
BfaI	CTAG	1 cut(s)	822
BisI	GCNGC	1 cut(s)	68
BlsI	GCNGC	1 cut(s)	69
Bme1390I	CCNGG	2 cut(s)	508, 871
BmiI	GGNNCC	1 cut(s)	85
BmrFI	CCNGG	2 cut(s)	508, 871
BmsI	GCATC	1 cut(s)	388
BplI	GAGNNNNNCTC	2 cut(s)	526, 558
Bpu14I	TTCGAA	1 cut(s)	738
BsaJI	CCNNGG	1 cut(s)	870
BsaWI	WCCGGW	1 cut(s)	544
Bsc4I	CCNNNNNNNGG	2 cut(s)	11, 889
Bse1I	ACTGG	2 cut(s)	479, 927
Bse3DI	GCAATG	1 cut(s)	846
BseAI	TCCGGA	1 cut(s)	544
BseBI	CCWGG	2 cut(s)	508, 871
BseDI	CCNNGG	1 cut(s)	870
BseGI	GGATG	5 cut(s)	163, 211, 403, 553, 628
BseLI	CCNNNNNNNGG	2 cut(s)	11, 889
BseMI	GCAATG	1 cut(s)	846
BseMII	CTCAG	1 cut(s)	813
BseNI	ACTGG	2 cut(s)	479, 927
BseSI	GKGCMC	2 cut(s)	24, 464
BsgI	GTGCAG	1 cut(s)	341
Bsh1236I	CGCG	2 cut(s)	67, 72
BshNI	GGYRCC	1 cut(s)	83
BsiHKAI	GWGCWC	1 cut(s)	344
BsiSI	CCGG	2 cut(s)	443, 545
BslI	CCNNNNNNNGG	2 cut(s)	11, 889
BsmAI	GTCTC	2 cut(s)	524, 846
BsmBI	CGTCTC	1 cut(s)	524
BsmI	GAATGC	1 cut(s)	934
Bsp119I	TTCGAA	1 cut(s)	738
Bsp1286I	GDGCHC	4 cut(s)	24, 344, 464, 792
Bsp13I	TCCGGA	1 cut(s)	544
Bsp143I	GATC	3 cut(s)	520, 675, 874
BspACI	CCGC	2 cut(s)	67, 296
BspCNI	CTCAG	1 cut(s)	812
BspEI	TCCGGA	1 cut(s)	544
BspFNI	CGCG	2 cut(s)	67, 72
BspHI	TCATGA	1 cut(s)	552
BspLI	GGNNCC	1 cut(s)	85
BspPI	GGATC	1 cut(s)	882
BspT104I	TTCGAA	1 cut(s)	738
BspT107I	GGYRCC	1 cut(s)	83
BsrDI	GCAATG	1 cut(s)	846
BsrI	ACTGG	2 cut(s)	479, 927
BssECI	CCNNGG	1 cut(s)	870
BssMI	GATC	3 cut(s)	520, 675, 874
Bst2UI	CCWGG	2 cut(s)	508, 871
Bst4CI	ACNGT	2 cut(s)	411, 863
Bst6I	CTCTTC	1 cut(s)	320
BstBI	TTCGAA	1 cut(s)	738
BstC8I	GCNNGC	2 cut(s)	6, 440
BstDEI	CTNAG	2 cut(s)	799, 888
BstENI	CCTNNNNNAGG	1 cut(s)	887
BstF5I	GGATG	5 cut(s)	163, 211, 403, 553, 628
BstFNI	CGCG	2 cut(s)	67, 72
BstHHI	GCGC	2 cut(s)	72, 233
BstKTI	GATC	3 cut(s)	523, 678, 877
BstMAI	GTCTC	2 cut(s)	524, 846
BstMBI	GATC	3 cut(s)	520, 675, 874
BstMWI	GCNNNNNNNGC	1 cut(s)	178
BstNI	CCWGG	2 cut(s)	508, 871
BstSCI	CCNGG	2 cut(s)	506, 869
BstSLI	GKGCMC	2 cut(s)	24, 464
BstUI	CGCG	2 cut(s)	67, 72
BstX2I	RGATCY	1 cut(s)	874
BstXI	CCANNNNNNTGG	1 cut(s)	154
BstYI	RGATCY	1 cut(s)	874
BtgZI	GCGATG	1 cut(s)	23
BtsCI	GGATG	5 cut(s)	163, 211, 403, 553, 628
BtsIMutI	CAGTG	1 cut(s)	868
Cac8I	GCNNGC	2 cut(s)	6, 440
CciI	TCATGA	1 cut(s)	552
CfoI	GCGC	2 cut(s)	72, 233
CviAII	CATG	2 cut(s)	553, 628
DdeI	CTNAG	2 cut(s)	799, 888
DpnI	GATC	3 cut(s)	522, 677, 876
DpnII	GATC	3 cut(s)	520, 675, 874
Eam1104I	CTCTTC	1 cut(s)	320
EarI	CTCTTC	1 cut(s)	320
Ecl136II	GAGCTC	1 cut(s)	342
Eco24I	GRGCYC	2 cut(s)	344, 792
Eco53kI	GAGCTC	1 cut(s)	342
EcoICRI	GAGCTC	1 cut(s)	342
EcoNI	CCTNNNNNAGG	1 cut(s)	887
EcoRI	GAATTC	1 cut(s)	652
EcoRII	CCWGG	2 cut(s)	506, 869
EcoT38I	GRGCYC	2 cut(s)	344, 792
Esp3I	CGTCTC	1 cut(s)	524
FaeI	CATG	2 cut(s)	556, 631
FatI	CATG	2 cut(s)	552, 627
FbaI	TGATCA	2 cut(s)	520, 675
FblI	GTMKAC	1 cut(s)	764
Fnu4HI	GCNGC	1 cut(s)	68
FokI	GGATG	5 cut(s)	170, 218, 410, 560, 635
FriOI	GRGCYC	2 cut(s)	344, 792
Fsp4HI	GCNGC	1 cut(s)	68
FspBI	CTAG	1 cut(s)	822
GlaI	GCGC	2 cut(s)	71, 232
GluI	GCNGC	1 cut(s)	68
HapII	CCGG	2 cut(s)	443, 545
HhaI	GCGC	2 cut(s)	72, 233
Hin1II	CATG	2 cut(s)	556, 631
Hin6I	GCGC	2 cut(s)	70, 231
HinP1I	GCGC	2 cut(s)	70, 231
HinfI	GANTC	3 cut(s)	684, 797, 866
HpaII	CCGG	2 cut(s)	443, 545
HphI	GGTGA	3 cut(s)	43, 113, 373
Hpy166II	GTNNAC	2 cut(s)	407, 765
Hpy188I	TCNGA	1 cut(s)	651
Hpy188III	TCNNGA	5 cut(s)	128, 545, 553, 576, 801
Hpy8I	GTNNAC	2 cut(s)	407, 765
HpyAV	CCTTC	4 cut(s)	257, 377, 382, 481
HpyCH4III	ACNGT	2 cut(s)	411, 863
HpyCH4IV	ACGT	1 cut(s)	564
HpyCH4V	TGCA	4 cut(s)	273, 322, 438, 452
HpyF10VI	GCNNNNNNNGC	1 cut(s)	178
HpyF3I	CTNAG	2 cut(s)	799, 888
HpySE526I	ACGT	1 cut(s)	564
Hsp92II	CATG	2 cut(s)	556, 631
HspAI	GCGC	2 cut(s)	70, 231
Kpn2I	TCCGGA	1 cut(s)	544
Ksp22I	TGATCA	2 cut(s)	520, 675
Kzo9I	GATC	3 cut(s)	520, 675, 874
LweI	GCATC	1 cut(s)	388
MaeI	CTAG	1 cut(s)	822
MaeII	ACGT	1 cut(s)	564
MaeIII	GTNAC	3 cut(s)	31, 133, 241
MalI	GATC	3 cut(s)	522, 677, 876
MboI	GATC	3 cut(s)	520, 675, 874
MboII	GAAGA	3 cut(s)	337, 439, 442
MflI	RGATCY	1 cut(s)	874
MhlI	GDGCHC	4 cut(s)	24, 344, 464, 792
MluCI	AATT	4 cut(s)	301, 433, 652, 714
MlyI	GAGTC	1 cut(s)	791
MroI	TCCGGA	1 cut(s)	544
MroXI	GAANNNNTTC	1 cut(s)	903
MseI	TTAA	2 cut(s)	195, 300
MslI	CAYNNNNRTG	1 cut(s)	152
MspI	CCGG	2 cut(s)	443, 545
MspR9I	CCNGG	2 cut(s)	508, 871
Mva1269I	GAATGC	1 cut(s)	934
MvaI	CCWGG	2 cut(s)	508, 871
MvnI	CGCG	2 cut(s)	67, 72
MwoI	GCNNNNNNNGC	1 cut(s)	178
NdeII	GATC	3 cut(s)	520, 675, 874
NlaIII	CATG	2 cut(s)	556, 631
NlaIV	GGNNCC	1 cut(s)	85
NmeAIII	GCCGAG	1 cut(s)	323
NmuCI	GTSAC	2 cut(s)	31, 133
NspV	TTCGAA	1 cut(s)	738
PagI	TCATGA	1 cut(s)	552
PcsI	WCGNNNNNNNCGW	1 cut(s)	735
PctI	GAATGC	1 cut(s)	934
PdmI	GAANNNNTTC	1 cut(s)	903
PfeI	GAWTC	2 cut(s)	684, 866
PkrI	GCNGC	1 cut(s)	69
PleI	GAGTC	1 cut(s)	791
PpsI	GAGTC	1 cut(s)	791
Psp124BI	GAGCTC	1 cut(s)	344
Psp6I	CCWGG	2 cut(s)	506, 869
PspGI	CCWGG	2 cut(s)	506, 869
PspN4I	GGNNCC	1 cut(s)	85
PsuI	RGATCY	1 cut(s)	874
RseI	CAYNNNNRTG	1 cut(s)	152
SacI	GAGCTC	1 cut(s)	344
SaqAI	TTAA	2 cut(s)	195, 300
SatI	GCNGC	1 cut(s)	68
Sau3AI	GATC	3 cut(s)	520, 675, 874
SchI	GAGTC	1 cut(s)	791
ScrFI	CCNGG	2 cut(s)	508, 871
SduI	GDGCHC	4 cut(s)	24, 344, 464, 792
SfaNI	GCATC	1 cut(s)	388
SfuI	TTCGAA	1 cut(s)	738
SmiMI	CAYNNNNRTG	1 cut(s)	152
Sse9I	AATT	4 cut(s)	301, 433, 652, 714
SsiI	CCGC	2 cut(s)	67, 296
SspMI	CTAG	1 cut(s)	822
SstI	GAGCTC	1 cut(s)	344
StyD4I	CCNGG	2 cut(s)	506, 869
TaaI	ACNGT	2 cut(s)	411, 863
TaiI	ACGT	1 cut(s)	567
TaqI	TCGA	1 cut(s)	738
TasI	AATT	4 cut(s)	301, 433, 652, 714
TauI	GCSGC	1 cut(s)	70
TfiI	GAWTC	2 cut(s)	684, 866
Tru1I	TTAA	2 cut(s)	195, 300
Tru9I	TTAA	2 cut(s)	195, 300
TscAI	CASTG	1 cut(s)	868
TseFI	GTSAC	2 cut(s)	31, 133
Tsp45I	GTSAC	2 cut(s)	31, 133
TspRI	CASTG	1 cut(s)	868
XagI	CCTNNNNNAGG	1 cut(s)	887
XapI	RAATTY	1 cut(s)	652
XmiI	GTMKAC	1 cut(s)	764
XmnI	GAANNNNTTC	1 cut(s)	903
XspI	CTAG	1 cut(s)	822

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