Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0000874

Physical Location & Seq

Genomic Coordinates Forward (+)

12704731 .. 12706479

Gene Structure 1749 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG143700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 855 bp

ATGGCGAAGCGAACCAACCACCTCTGTACCAATCCCAATTCCGATCCGAACCAACCACCCCAAGATGACGATTCCCTCATAACCCAAGTCCTCCGACCCAATGAGAAAGACTGGAACTTTGACCAACTCCACACCCTCCTCTTCCCCAACTCAACCTCTCCTTCTTTTCGCTCCCTTTTCCTCATCACTCGCCGCCTCGACGCTCCCTCCAAAGCCCTCAAATTCTTCGATTACGTCACCGAAAACGTGGCCGAAACCCCTCCAGGATCCAAGGCTCTGCTCTCCTCCGCATTCCAGGCCCTTCTGGAGCTCACATTGCGGGAGCCCACCTCGGAAAAGAAGCTCTTTGAGCTTTACAAGATAGCCAAGGACCGGAATGTCCCGCTGAATCTCAAGGCCGCAGGTCTGCTTGTTCGGTCCATGGGCGCGGCTGGGATGGAGGACGAGGCTCTCACAGTGTTTAACGAGCTTCATTTGGGGTTGAAAACTTCTCATATTCGCAATGTGATGGGTGGTGCTGTAGAAGCTGCTTCGTGCAATGCGCTTTTGACAGCTTTGGGAAGAGCTAATGATTTTAAGAGGATGAGTGAGCTTATGGCGAAGATGGAAGAGATGGGCATTAAGCCCGATGTTATAACTTTTGGTATTCTTATTAATCGGTTAGGCAAGTCTAGGAGAATAGATGCTGCCTTGGAGGTGTTTGAAAAGATGAGTGGAGGGGTAAAGGGGGTTTCAGTTGAACCAGATGTGATCGTCTATAACACTCTGATTGATGGACTTTGCAAAGTGGGAAGGCAGGAAGAAGGATTGCTTAAGGATAATAGGGAGAAAGAAAGGCCATTGGTAGGCCCTTAG

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

ko03018 map03018

Pfam Domains

Protein Families

PPR PPR_1 PPR_2 PPR_3

Protein Analysis

284

Amino Acids

31.44

Weight (kDa)

6.92

Isoelectric Point (pI)

43.79

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	177 - 222	5.8e-10	PPR repeat family
PPR_3	PF13812	178 - 223	9.6e-08	Pentatricopeptide repeat domain
PPR_1	PF12854	205 - 238	2.8e-09	PPR repeat
PPR_2	PF13041	217 - 262	4.7e-07	PPR repeat family
PPR_1	PF12854	246 - 265	6.6e-08	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)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0000874)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G61520 AT5G28370 AT5G28460
fragaria_vesca	FvH4_5g03011 FvH4_5g03011 FvH4_5g32150 FvH4_5g32150 FvH4_5g32150 FvH4_5g32150 FvH4_5g32150 FvH4_7g15360
malus_domestica	MD01G1071400.v1.1 MD07G1131300.v1.1
prunus_persica	Prupe.2G177500_v2.0.a1
pyrus_communis	pycom01g10040 pycom04g02360 pycom07g12830
rosa_chinensis	RchiOBHm_Chr1g0357681 RchiOBHm_Chr3g0468501 RchiOBHm_Chr5g0017031 RchiOBHm_Chr7g0228211 RchiOBHm_Chr7g0228281 RchiOBHm_Chr7g0228291
rosa_laevigata	RLG00000001577 RLG00000005833 RLG00000009015 RLG00000009124 RLG00000012161 RLG00000028007 RLG00000028484
rosa_multiflora	Rmu_sc0001062.1_g000004 Rmu_sc0001626.1_g000014 Rmu_sc0001626.1_g000015 Rmu_sc0002582.1_g000009 Rmu_sc0003490.1_g000025 Rmu_sc0003490.1_g000026 Rmu_sc0004842.1_g000011 Rmu_sc0004842.1_g000012 Rmu_sc0004842.1_g000020 Rmu_ssc0000425.1_g000002
rosa_roxburghii	Rroxscaffold_3G00231300 Rroxscaffold_4G00298600 Rroxscaffold_6G00429570
rosa_rugosa	Rorug01G0257700 Rorug02G0051500 Rorug02G0572600 Rorug07G0246900.1 Rorug07G0247000 Rorug07G0247000
rosa_samantha	Rh1AG271700 Rh1BG238800 Rh1CG255600 Rh1DG267200 Rh3AG143700 Rh3BG166200 Rh3BG166300 Rh5AG043600 Rh7AG400900 Rh7AG401200 Rh7BG382400 Rh7CG420000 Rh7DG396900 Rh7DG397300
rosa_wichuraiana	Rw1G024230 Rw7G033300 Rw7G033330

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	635
AasI	GACNNNNNNGTC	1 cut(s)	377
Acc36I	ACCTGC	1 cut(s)	392
AccII	CGCG	1 cut(s)	428
AciI	CCGC	6 cut(s)	193, 288, 319, 383, 399, 428
AclWI	GGATC	3 cut(s)	38, 261, 274
AcoI	YGGCCR	1 cut(s)	249
AcsI	RAATTY	1 cut(s)	221
AfaI	GTAC	1 cut(s)	28
AfiI	CCNNNNNNNGG	2 cut(s)	372, 845
AflII	CTTAAG	1 cut(s)	812
AgsI	TTSAA	3 cut(s)	484, 704, 740
AjnI	CCWGG	2 cut(s)	262, 294
AluBI	AGCT	8 cut(s)	310, 343, 352, 469, 527, 554, 566, 592
AluI	AGCT	8 cut(s)	310, 343, 352, 469, 527, 554, 566, 592
Alw21I	GWGCWC	1 cut(s)	312
AlwI	GGATC	3 cut(s)	38, 261, 274
AoxI	GGCC	5 cut(s)	249, 297, 396, 836, 847
ApeKI	GCWGC	2 cut(s)	527, 686
ApoI	RAATTY	1 cut(s)	221
ArsI	GACNNNNNNTTYG	2 cut(s)	101, 133
AseI	ATTAAT	1 cut(s)	654
AspLEI	GCGC	2 cut(s)	428, 544
AspS9I	GGNCC	4 cut(s)	298, 370, 417, 848
AsuHPI	GGTGA	1 cut(s)	229
AvaII	GGWCC	2 cut(s)	370, 417
BaeI	ACNNNNGTAYC	2 cut(s)	10, 43
BamHI	GGATCC	1 cut(s)	266
BanII	GRGCYC	2 cut(s)	312, 327
Bbv12I	GWGCWC	1 cut(s)	312
BbvI	GCAGC	2 cut(s)	514, 673
BccI	CCATC	5 cut(s)	430, 502, 598, 607, 767
BciT130I	CCWGG	2 cut(s)	264, 296
BfaI	CTAG	1 cut(s)	672
BfmI	CTRYAG	1 cut(s)	519
BfrI	CTTAAG	1 cut(s)	812
BfuAI	ACCTGC	1 cut(s)	392
BisI	GCNGC	5 cut(s)	193, 399, 429, 528, 687
BlsI	GCNGC	5 cut(s)	194, 400, 430, 529, 688
Bme1390I	CCNGG	2 cut(s)	264, 296
Bme18I	GGWCC	2 cut(s)	370, 417
BmgT120I	GGNCC	4 cut(s)	298, 370, 417, 848
BmiI	GGNNCC	2 cut(s)	268, 324
BmrFI	CCNGG	2 cut(s)	264, 296
BmsI	GCATC	1 cut(s)	673
BplI	GAGNNNNNCTC	2 cut(s)	314, 346
BpmI	CTGGAG	2 cut(s)	246, 326
BpuEI	CTTGAG	1 cut(s)	377
BsaJI	CCNNGG	5 cut(s)	270, 330, 366, 420, 690
BsaWI	WCCGGW	1 cut(s)	372
BsaXI	ACNNNNNCTCC	2 cut(s)	191, 221
Bsc4I	CCNNNNNNNGG	2 cut(s)	372, 845
Bse1I	ACTGG	1 cut(s)	116
Bse3DI	GCAATG	3 cut(s)	314, 508, 544
BseBI	CCWGG	2 cut(s)	264, 296
BseDI	CCNNGG	5 cut(s)	270, 330, 366, 420, 690
BseGI	GGATG	2 cut(s)	441, 588
BseLI	CCNNNNNNNGG	2 cut(s)	372, 845
BseMI	GCAATG	3 cut(s)	314, 508, 544
BseNI	ACTGG	1 cut(s)	116
BseRI	GAGGAG	2 cut(s)	128, 274
BseXI	GCAGC	2 cut(s)	514, 673
BseYI	CCCAGC	1 cut(s)	431
Bsh1236I	CGCG	1 cut(s)	428
BshFI	GGCC	5 cut(s)	251, 299, 398, 838, 849
BsiHKAI	GWGCWC	1 cut(s)	312
BsiSI	CCGG	1 cut(s)	373
BslFI	GGGAC	1 cut(s)	365
BslI	CCNNNNNNNGG	2 cut(s)	372, 845
BsmFI	GGGAC	1 cut(s)	365
BsmI	GAATGC	1 cut(s)	290
BsnI	GGCC	5 cut(s)	251, 299, 398, 838, 849
Bsp1286I	GDGCHC	2 cut(s)	312, 327
Bsp143I	GATC	3 cut(s)	43, 266, 750
Bsp19I	CCATGG	1 cut(s)	420
BspACI	CCGC	6 cut(s)	193, 288, 319, 383, 399, 428
BspANI	GGCC	5 cut(s)	251, 299, 398, 838, 849
BspFNI	CGCG	1 cut(s)	428
BspLI	GGNNCC	2 cut(s)	268, 324
BspMI	ACCTGC	1 cut(s)	392
BspPI	GGATC	3 cut(s)	38, 261, 274
BspQI	GCTCTTC	1 cut(s)	556
BspTI	CTTAAG	1 cut(s)	812
BsrDI	GCAATG	3 cut(s)	314, 508, 544
BsrI	ACTGG	1 cut(s)	116
BssECI	CCNNGG	5 cut(s)	270, 330, 366, 420, 690
BssMI	GATC	3 cut(s)	43, 266, 750
BssT1I	CCWWGG	4 cut(s)	270, 366, 420, 690
Bst2UI	CCWGG	2 cut(s)	264, 296
Bst4CI	ACNGT	1 cut(s)	457
Bst6I	CTCTTC	3 cut(s)	146, 556, 603
BstAFI	CTTAAG	1 cut(s)	812
BstDEI	CTNAG	1 cut(s)	852
BstDSI	CCRYGG	1 cut(s)	420
BstF5I	GGATG	2 cut(s)	441, 588
BstFNI	CGCG	1 cut(s)	428
BstHHI	GCGC	2 cut(s)	428, 544
BstKTI	GATC	3 cut(s)	46, 269, 753
BstMBI	GATC	3 cut(s)	43, 266, 750
BstMWI	GCNNNNNNNGC	4 cut(s)	296, 316, 349, 524
BstNI	CCWGG	2 cut(s)	264, 296
BstSCI	CCNGG	2 cut(s)	262, 294
BstSFI	CTRYAG	1 cut(s)	519
BstUI	CGCG	1 cut(s)	428
BstV1I	GCAGC	2 cut(s)	514, 673
BstX2I	RGATCY	1 cut(s)	266
BstYI	RGATCY	1 cut(s)	266
BsuRI	GGCC	5 cut(s)	251, 299, 398, 838, 849
BtgI	CCRYGG	1 cut(s)	420
BtsCI	GGATG	2 cut(s)	441, 588
BtsIMutI	CAGTG	1 cut(s)	462
BveI	ACCTGC	1 cut(s)	392
CfoI	GCGC	2 cut(s)	428, 544
Cfr13I	GGNCC	4 cut(s)	298, 370, 417, 848
CseI	GACGC	1 cut(s)	209
Csp6I	GTAC	1 cut(s)	27
CviAII	CATG	1 cut(s)	421
CviQI	GTAC	1 cut(s)	27
DdeI	CTNAG	1 cut(s)	852
DpnI	GATC	3 cut(s)	45, 268, 752
DpnII	GATC	3 cut(s)	43, 266, 750
DrdI	GACNNNNNNGTC	1 cut(s)	377
DseDI	GACNNNNNNGTC	1 cut(s)	377
EaeI	YGGCCR	1 cut(s)	249
Eam1104I	CTCTTC	3 cut(s)	146, 556, 603
EarI	CTCTTC	3 cut(s)	146, 556, 603
Ecl136II	GAGCTC	1 cut(s)	310
Eco130I	CCWWGG	4 cut(s)	270, 366, 420, 690
Eco24I	GRGCYC	2 cut(s)	312, 327
Eco47I	GGWCC	2 cut(s)	370, 417
Eco53kI	GAGCTC	1 cut(s)	310
EcoICRI	GAGCTC	1 cut(s)	310
EcoO109I	RGGNCCY	2 cut(s)	298, 848
EcoRII	CCWGG	2 cut(s)	262, 294
EcoT14I	CCWWGG	4 cut(s)	270, 366, 420, 690
EcoT38I	GRGCYC	2 cut(s)	312, 327
ErhI	CCWWGG	4 cut(s)	270, 366, 420, 690
FaeI	CATG	1 cut(s)	424
FaiI	YATR	6 cut(s)	80, 422, 495, 596, 635, 759
FalI	AAGNNNNNCTT	4 cut(s)	329, 361, 795, 827
FaqI	GGGAC	1 cut(s)	365
FatI	CATG	1 cut(s)	420
FauI	CCCGC	2 cut(s)	312, 390
Fnu4HI	GCNGC	5 cut(s)	193, 399, 429, 528, 687
FokI	GGATG	2 cut(s)	448, 595
FriOI	GRGCYC	2 cut(s)	312, 327
Fsp4HI	GCNGC	5 cut(s)	193, 399, 429, 528, 687
FspBI	CTAG	1 cut(s)	672
GlaI	GCGC	2 cut(s)	427, 543
GluI	GCNGC	5 cut(s)	193, 399, 429, 528, 687
GsaI	CCCAGC	1 cut(s)	435
GsuI	CTGGAG	2 cut(s)	246, 326
HaeIII	GGCC	5 cut(s)	251, 299, 398, 838, 849
HapII	CCGG	1 cut(s)	373
HgaI	GACGC	1 cut(s)	209
HhaI	GCGC	2 cut(s)	428, 544
Hin1II	CATG	1 cut(s)	424
Hin6I	GCGC	2 cut(s)	426, 542
HinP1I	GCGC	2 cut(s)	426, 542
HinfI	GANTC	2 cut(s)	71, 388
HpaII	CCGG	1 cut(s)	373
HphI	GGTGA	1 cut(s)	229
Hpy188I	TCNGA	5 cut(s)	43, 48, 95, 334, 768
Hpy188III	TCNNGA	1 cut(s)	305
Hpy99I	CGWCG	1 cut(s)	203
HpyAV	CCTTC	4 cut(s)	171, 311, 786, 797
HpyCH4III	ACNGT	1 cut(s)	457
HpyCH4IV	ACGT	2 cut(s)	234, 246
HpyCH4V	TGCA	2 cut(s)	537, 783
HpyF10VI	GCNNNNNNNGC	4 cut(s)	296, 316, 349, 524
HpyF3I	CTNAG	1 cut(s)	852
HpySE526I	ACGT	2 cut(s)	234, 246
Hsp92II	CATG	1 cut(s)	424
HspAI	GCGC	2 cut(s)	426, 542
Kzo9I	GATC	3 cut(s)	43, 266, 750
LguI	GCTCTTC	1 cut(s)	556
LmnI	GCTCC	4 cut(s)	176, 208, 307, 322
Lsp1109I	GCAGC	2 cut(s)	514, 673
LweI	GCATC	1 cut(s)	673
MaeI	CTAG	1 cut(s)	672
MaeII	ACGT	2 cut(s)	234, 246
MaeIII	GTNAC	1 cut(s)	235
MalI	GATC	3 cut(s)	45, 268, 752
MboI	GATC	3 cut(s)	43, 266, 750
MboII	GAAGA	6 cut(s)	133, 217, 573, 613, 620, 812
MflI	RGATCY	1 cut(s)	266
MhlI	GDGCHC	2 cut(s)	312, 327
MluCI	AATT	2 cut(s)	37, 221
MmeI	TCCRAC	1 cut(s)	118
MseI	TTAA	5 cut(s)	462, 576, 621, 654, 813
MspA1I	CMGCKG	1 cut(s)	385
MspCI	CTTAAG	1 cut(s)	812
MspI	CCGG	1 cut(s)	373
MspR9I	CCNGG	2 cut(s)	264, 296
Mva1269I	GAATGC	1 cut(s)	290
MvaI	CCWGG	2 cut(s)	264, 296
MvnI	CGCG	1 cut(s)	428
MwoI	GCNNNNNNNGC	4 cut(s)	296, 316, 349, 524
NcoI	CCATGG	1 cut(s)	420
NdeII	GATC	3 cut(s)	43, 266, 750
NlaIII	CATG	1 cut(s)	424
NlaIV	GGNNCC	2 cut(s)	268, 324
NmuCI	GTSAC	1 cut(s)	235
PciSI	GCTCTTC	1 cut(s)	556
PctI	GAATGC	1 cut(s)	290
PfeI	GAWTC	2 cut(s)	71, 388
PfoI	TCCNGGA	1 cut(s)	262
PkrI	GCNGC	5 cut(s)	194, 400, 430, 529, 688
PshBI	ATTAAT	1 cut(s)	654
PsiI	TTATAA	1 cut(s)	635
Psp124BI	GAGCTC	1 cut(s)	312
Psp6I	CCWGG	2 cut(s)	262, 294
PspFI	CCCAGC	1 cut(s)	431
PspGI	CCWGG	2 cut(s)	262, 294
PspN4I	GGNNCC	2 cut(s)	268, 324
PspPI	GGNCC	4 cut(s)	298, 370, 417, 848
PsuI	RGATCY	1 cut(s)	266
RsaI	GTAC	1 cut(s)	28
RsaNI	GTAC	1 cut(s)	27
SacI	GAGCTC	1 cut(s)	312
SapI	GCTCTTC	1 cut(s)	556
SaqAI	TTAA	5 cut(s)	462, 576, 621, 654, 813
SatI	GCNGC	5 cut(s)	193, 399, 429, 528, 687
Sau3AI	GATC	3 cut(s)	43, 266, 750
Sau96I	GGNCC	4 cut(s)	298, 370, 417, 848
ScrFI	CCNGG	2 cut(s)	264, 296
SduI	GDGCHC	2 cut(s)	312, 327
SfaNI	GCATC	1 cut(s)	673
SfcI	CTRYAG	1 cut(s)	519
SinI	GGWCC	2 cut(s)	370, 417
SmlI	CTYRAG	2 cut(s)	392, 812
SmoI	CTYRAG	2 cut(s)	392, 812
Sse9I	AATT	2 cut(s)	37, 221
SsiI	CCGC	6 cut(s)	193, 288, 319, 383, 399, 428
SspMI	CTAG	1 cut(s)	672
SstI	GAGCTC	1 cut(s)	312
StyD4I	CCNGG	2 cut(s)	262, 294
StyI	CCWWGG	4 cut(s)	270, 366, 420, 690
TaaI	ACNGT	1 cut(s)	457
TaiI	ACGT	2 cut(s)	237, 249
TaqI	TCGA	2 cut(s)	198, 228
TaqII	GACCGA	1 cut(s)	405
TasI	AATT	2 cut(s)	37, 221
TauI	GCSGC	3 cut(s)	195, 401, 431
TfiI	GAWTC	2 cut(s)	71, 388
Tru1I	TTAA	5 cut(s)	462, 576, 621, 654, 813
Tru9I	TTAA	5 cut(s)	462, 576, 621, 654, 813
TscAI	CASTG	1 cut(s)	462
TseFI	GTSAC	1 cut(s)	235
TseI	GCWGC	2 cut(s)	527, 686
Tsp45I	GTSAC	1 cut(s)	235
TspDTI	ATGAA	1 cut(s)	461
TspRI	CASTG	1 cut(s)	462
Vha464I	CTTAAG	1 cut(s)	812
VpaK11BI	GGWCC	2 cut(s)	370, 417
VspI	ATTAAT	1 cut(s)	654
XapI	RAATTY	1 cut(s)	221
XspI	CTAG	1 cut(s)	672

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