Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr2D

Orthogroup ID

OG0014443

Physical Location & Seq

Genomic Coordinates Forward (+)

12046898 .. 12048130

Gene Structure 1233 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh2DG143100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 828 bp

ATGGTGGTGTGGACGGCTATGGTTACTGGTTATGCCCAGAATTCGATGCCGAAAGAGGCCTTGGATTGCTTTGAGAGAATGCGAGGTGCTGGTGTAGGGCTTGATGAGGTTACATTGCTCGGGGTCATTTCGGCTTGTGCACAATTGGGTGCTTCCAGGTATGCTAATTGGGTTCGAGACATTGCTGAGGAATCTGGTTTTGGGGCAACTCAGAATGTGCTTGTGGGATCTGCATTGATAGATATGTTCTCCAAGTGTGGGAGCTTGGATGATGCATACAATATTTTTCAGGGGATGAAGCAAAGGAATGTGTTTTCTTATAGCTCAATGATTTGGGGATTTGCAGTGCATGGAAATGCCAATGCAGCGATAGGATTGTTTCATGAGATGCTGACCACTGATGTAAGGCCGAACTGGGTTACTTTTATAGGTGTGCTAACTGCCTGCAGCCACGCGGGGATGGTTGATCAAGGTGAAACGAGTCACCCCAAATACAACAAGATTAAGAAGGCGTTGGAGGATCTTCTAAACAGATTGCAGGATCGTGGCTATAGGCCAAACCTAAATTCGGTGGATTATGATGTGGGGGATGAAGAAAAGATGCGTATATTGATGGCTCATAGCGAAAAACTGGCTTTGGCATACGCATTGCTCTACGCAGATTCTGGTTCCACCATTAAGATCGCCAAGAACATAAGGATTTGTGAAGACTGTCATGCCTTCATGTGTGGTGCATCACGGGTTACAGGAAGGCATATTATTGTCAGAGATAACATGAGATTCCACCACTTCGAAAATGGGACTTGTAATTGCGGCAACTTTTGGTGA

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

DYW_deaminase PPR PPR_2

Protein Analysis

275

Amino Acids

30.49

Weight (kDa)

6.3

Isoelectric Point (pI)

25.33

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	2 - 47	1.5e-06	PPR repeat family
PPR	PF01535	2 - 32	1.1e-07	PPR repeat
PPR_2	PF13041	102 - 150	5.7e-09	PPR repeat family
DYW_deaminase	PF14432	183 - 275	3.9e-41	DYW family of nucleic acid deaminases

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0014443)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G44230 AT5G44230
fragaria_vesca	FvH4_1g12540
malus_domestica	MD15G1252800.v1.1
prunus_persica	Prupe.7G161300_v2.0.a1
pyrus_communis	pycom15g22270
rosa_chinensis	RchiOBHm_Chr2g0100491
rosa_laevigata	RLG00000016976
rosa_multiflora	Rmu_sc0000528.1_g000023 Rmu_sc0020397.1_g000001
rosa_roxburghii	Rroxscaffold_2G00142190
rosa_rugosa	Rorug02G0088600
rosa_samantha	Rh2AG138300 Rh2BG141300 Rh2CG143500 Rh2DG143100
rosa_wichuraiana	Rw2G010810

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccII	CGCG	1 cut(s)	455
AciI	CCGC	2 cut(s)	455, 813
AclWI	GGATC	3 cut(s)	235, 528, 549
AcsI	RAATTY	2 cut(s)	40, 565
AfiI	CCNNNNNNNGG	2 cut(s)	258, 568
AjnI	CCWGG	1 cut(s)	155
AjuI	GAANNNNNNNTTGG	6 cut(s)	44, 76, 183, 215, 550, 582
AluBI	AGCT	2 cut(s)	264, 324
AluI	AGCT	2 cut(s)	264, 324
Alw21I	GWGCWC	1 cut(s)	142
Alw26I	GTCTC	1 cut(s)	171
Alw44I	GTGCAC	1 cut(s)	138
AlwI	GGATC	3 cut(s)	235, 528, 549
AlwNI	CAGNNNCTG	1 cut(s)	665
Ama87I	CYCGRG	1 cut(s)	119
AoxI	GGCC	3 cut(s)	57, 407, 554
ApaLI	GTGCAC	1 cut(s)	138
ApeKI	GCWGC	2 cut(s)	365, 447
ApoI	RAATTY	2 cut(s)	40, 565
AsuHPI	GGTGA	2 cut(s)	476, 485
AsuII	TTCGAA	1 cut(s)	792
AvaI	CYCGRG	1 cut(s)	119
BaeGI	GKGCMC	1 cut(s)	142
BbsI	GAAGAC	1 cut(s)	714
Bbv12I	GWGCWC	1 cut(s)	142
BbvCI	CCTCAGC	1 cut(s)	186
BbvI	GCAGC	2 cut(s)	377, 459
BccI	CCATC	2 cut(s)	454, 607
BceAI	ACGGC	1 cut(s)	30
BciT130I	CCWGG	1 cut(s)	157
BclI	TGATCA	1 cut(s)	466
BcoDI	GTCTC	1 cut(s)	171
BfmI	CTRYAG	2 cut(s)	445, 550
BisI	GCNGC	3 cut(s)	366, 448, 814
BlsI	GCNGC	3 cut(s)	367, 449, 815
Bme1390I	CCNGG	1 cut(s)	157
BmeT110I	CYCGRG	1 cut(s)	119
BmiI	GGNNCC	1 cut(s)	670
BmrFI	CCNGG	1 cut(s)	157
BmrI	ACTGGG	1 cut(s)	424
BmsI	GCATC	5 cut(s)	36, 262, 378, 591, 743
BmuI	ACTGGG	1 cut(s)	424
BpiI	GAAGAC	1 cut(s)	714
Bpu10I	CCTNAGC	1 cut(s)	186
Bpu14I	TTCGAA	1 cut(s)	792
BsaJI	CCNNGG	1 cut(s)	60
Bsc4I	CCNNNNNNNGG	2 cut(s)	258, 568
Bse1I	ACTGG	3 cut(s)	31, 419, 636
Bse3DI	GCAATG	3 cut(s)	113, 180, 647
BseBI	CCWGG	1 cut(s)	157
BseDI	CCNNGG	1 cut(s)	60
BseGI	GGATG	4 cut(s)	274, 300, 465, 595
BseLI	CCNNNNNNNGG	2 cut(s)	258, 568
BseMI	GCAATG	3 cut(s)	113, 180, 647
BseMII	CTCAG	2 cut(s)	177, 224
BseNI	ACTGG	3 cut(s)	31, 419, 636
BseSI	GKGCMC	1 cut(s)	142
BseXI	GCAGC	2 cut(s)	377, 459
Bsh1236I	CGCG	1 cut(s)	455
BshFI	GGCC	3 cut(s)	59, 409, 556
BsiHKAI	GWGCWC	1 cut(s)	142
BsiHKCI	CYCGRG	1 cut(s)	119
BslFI	GGGAC	1 cut(s)	814
BslI	CCNNNNNNNGG	2 cut(s)	258, 568
BsmAI	GTCTC	1 cut(s)	171
BsmFI	GGGAC	1 cut(s)	814
BsmI	GAATGC	1 cut(s)	84
BsnI	GGCC	3 cut(s)	59, 409, 556
BsoBI	CYCGRG	1 cut(s)	119
Bsp119I	TTCGAA	1 cut(s)	792
Bsp1286I	GDGCHC	1 cut(s)	142
Bsp143I	GATC	5 cut(s)	227, 466, 520, 541, 681
BspACI	CCGC	2 cut(s)	455, 813
BspANI	GGCC	3 cut(s)	59, 409, 556
BspCNI	CTCAG	2 cut(s)	178, 223
BspFNI	CGCG	1 cut(s)	455
BspHI	TCATGA	1 cut(s)	382
BspLI	GGNNCC	1 cut(s)	670
BspMAI	CTGCAG	1 cut(s)	449
BspPI	GGATC	3 cut(s)	235, 528, 549
BspT104I	TTCGAA	1 cut(s)	792
BsrDI	GCAATG	3 cut(s)	113, 180, 647
BsrI	ACTGG	3 cut(s)	31, 419, 636
BssECI	CCNNGG	1 cut(s)	60
BssMI	GATC	5 cut(s)	227, 466, 520, 541, 681
BssT1I	CCWWGG	1 cut(s)	60
Bst2UI	CCWGG	1 cut(s)	157
Bst4CI	ACNGT	1 cut(s)	713
BstBI	TTCGAA	1 cut(s)	792
BstC8I	GCNNGC	1 cut(s)	445
BstDEI	CTNAG	2 cut(s)	186, 210
BstF5I	GGATG	4 cut(s)	274, 300, 465, 595
BstFNI	CGCG	1 cut(s)	455
BstKTI	GATC	5 cut(s)	230, 469, 523, 544, 684
BstMAI	GTCTC	1 cut(s)	171
BstMBI	GATC	5 cut(s)	227, 466, 520, 541, 681
BstMWI	GCNNNNNNNGC	1 cut(s)	365
BstNI	CCWGG	1 cut(s)	157
BstSCI	CCNGG	1 cut(s)	155
BstSFI	CTRYAG	2 cut(s)	445, 550
BstSLI	GKGCMC	1 cut(s)	142
BstUI	CGCG	1 cut(s)	455
BstV1I	GCAGC	2 cut(s)	377, 459
BstV2I	GAAGAC	1 cut(s)	714
BstX2I	RGATCY	2 cut(s)	227, 520
BstYI	RGATCY	2 cut(s)	227, 520
BsuRI	GGCC	3 cut(s)	59, 409, 556
BtsCI	GGATG	4 cut(s)	274, 300, 465, 595
BtsI	GCAGTG	1 cut(s)	351
BtsIMutI	CAGTG	2 cut(s)	351, 396
Cac8I	GCNNGC	1 cut(s)	445
CaiI	CAGNNNCTG	1 cut(s)	665
CciI	TCATGA	1 cut(s)	382
CviAII	CATG	5 cut(s)	350, 383, 716, 724, 775
DdeI	CTNAG	2 cut(s)	186, 210
DpnI	GATC	5 cut(s)	229, 468, 522, 543, 683
DpnII	GATC	5 cut(s)	227, 466, 520, 541, 681
Eco130I	CCWWGG	1 cut(s)	60
Eco147I	AGGCCT	1 cut(s)	59
Eco88I	CYCGRG	1 cut(s)	119
EcoRI	GAATTC	1 cut(s)	40
EcoRII	CCWGG	1 cut(s)	155
EcoT14I	CCWWGG	1 cut(s)	60
EcoT22I	ATGCAT	1 cut(s)	277
ErhI	CCWWGG	1 cut(s)	60
FaeI	CATG	5 cut(s)	353, 386, 719, 727, 778
FaqI	GGGAC	1 cut(s)	814
FatI	CATG	5 cut(s)	349, 382, 715, 723, 774
FauI	CCCGC	1 cut(s)	448
FbaI	TGATCA	1 cut(s)	466
Fnu4HI	GCNGC	3 cut(s)	366, 448, 814
FokI	GGATG	4 cut(s)	281, 307, 472, 602
Fsp4HI	GCNGC	3 cut(s)	366, 448, 814
GluI	GCNGC	3 cut(s)	366, 448, 814
HaeIII	GGCC	3 cut(s)	59, 409, 556
Hin1II	CATG	5 cut(s)	353, 386, 719, 727, 778
HinfI	GANTC	4 cut(s)	191, 481, 662, 780
HphI	GGTGA	2 cut(s)	476, 485
Hpy166II	GTNNAC	2 cut(s)	12, 140
Hpy188I	TCNGA	2 cut(s)	213, 767
Hpy188III	TCNNGA	2 cut(s)	176, 383
Hpy8I	GTNNAC	2 cut(s)	12, 140
HpyAV	CCTTC	3 cut(s)	502, 730, 744
HpyCH4III	ACNGT	1 cut(s)	713
HpyCH4V	TGCA	9 cut(s)	140, 233, 275, 344, 349, 365, 447, 538, 734
HpyF10VI	GCNNNNNNNGC	1 cut(s)	365
HpyF3I	CTNAG	2 cut(s)	186, 210
Hsp92II	CATG	5 cut(s)	353, 386, 719, 727, 778
Ksp22I	TGATCA	1 cut(s)	466
Kzo9I	GATC	5 cut(s)	227, 466, 520, 541, 681
LmnI	GCTCC	1 cut(s)	261
Lsp1109I	GCAGC	2 cut(s)	377, 459
LweI	GCATC	5 cut(s)	36, 262, 378, 591, 743
MaeIII	GTNAC	5 cut(s)	22, 109, 418, 482, 742
MalI	GATC	5 cut(s)	229, 468, 522, 543, 683
MboI	GATC	5 cut(s)	227, 466, 520, 541, 681
MboII	GAAGA	3 cut(s)	515, 605, 719
MfeI	CAATTG	1 cut(s)	143
MflI	RGATCY	2 cut(s)	227, 520
MhlI	GDGCHC	1 cut(s)	142
MluCI	AATT	5 cut(s)	40, 143, 166, 565, 808
MlyI	GAGTC	1 cut(s)	490
MmeI	TCCRAC	1 cut(s)	495
MnlI	CCTC	5 cut(s)	49, 77, 100, 181, 511
Mph1103I	ATGCAT	1 cut(s)	277
MseI	TTAA	2 cut(s)	504, 678
MslI	CAYNNNNRTG	1 cut(s)	354
MspR9I	CCNGG	1 cut(s)	157
MunI	CAATTG	1 cut(s)	143
Mva1269I	GAATGC	1 cut(s)	84
MvaI	CCWGG	1 cut(s)	157
MvnI	CGCG	1 cut(s)	455
MwoI	GCNNNNNNNGC	1 cut(s)	365
NdeII	GATC	5 cut(s)	227, 466, 520, 541, 681
NlaIII	CATG	5 cut(s)	353, 386, 719, 727, 778
NlaIV	GGNNCC	1 cut(s)	670
NmuCI	GTSAC	1 cut(s)	482
NsiI	ATGCAT	1 cut(s)	277
NspV	TTCGAA	1 cut(s)	792
PagI	TCATGA	1 cut(s)	382
PceI	AGGCCT	1 cut(s)	59
PctI	GAATGC	1 cut(s)	84
PfeI	GAWTC	3 cut(s)	191, 662, 780
PkrI	GCNGC	3 cut(s)	367, 449, 815
PleI	GAGTC	1 cut(s)	489
PpsI	GAGTC	1 cut(s)	489
Psp6I	CCWGG	1 cut(s)	155
PspGI	CCWGG	1 cut(s)	155
PspN4I	GGNNCC	1 cut(s)	670
PstI	CTGCAG	1 cut(s)	449
PstNI	CAGNNNCTG	1 cut(s)	665
PsuI	RGATCY	2 cut(s)	227, 520
RseI	CAYNNNNRTG	1 cut(s)	354
SaqAI	TTAA	2 cut(s)	504, 678
SatI	GCNGC	3 cut(s)	366, 448, 814
Sau3AI	GATC	5 cut(s)	227, 466, 520, 541, 681
SchI	GAGTC	1 cut(s)	490
ScrFI	CCNGG	1 cut(s)	157
SduI	GDGCHC	1 cut(s)	142
SetI	ASST	8 cut(s)	88, 111, 161, 266, 326, 433, 475, 564
SfaNI	GCATC	5 cut(s)	36, 262, 378, 591, 743
SfcI	CTRYAG	2 cut(s)	445, 550
SfuI	TTCGAA	1 cut(s)	792
SmiMI	CAYNNNNRTG	1 cut(s)	354
Sse9I	AATT	5 cut(s)	40, 143, 166, 565, 808
SseBI	AGGCCT	1 cut(s)	59
SsiI	CCGC	2 cut(s)	455, 813
SspI	AATATT	1 cut(s)	283
StuI	AGGCCT	1 cut(s)	59
StyD4I	CCNGG	1 cut(s)	155
StyI	CCWWGG	1 cut(s)	60
TaaI	ACNGT	1 cut(s)	713
TaqI	TCGA	3 cut(s)	44, 175, 792
TasI	AATT	5 cut(s)	40, 143, 166, 565, 808
TauI	GCSGC	1 cut(s)	816
TfiI	GAWTC	3 cut(s)	191, 662, 780
Tru1I	TTAA	2 cut(s)	504, 678
Tru9I	TTAA	2 cut(s)	504, 678
TscAI	CASTG	2 cut(s)	351, 403
TseFI	GTSAC	1 cut(s)	482
TseI	GCWGC	2 cut(s)	365, 447
Tsp45I	GTSAC	1 cut(s)	482
TspDTI	ATGAA	4 cut(s)	311, 371, 606, 712
TspRI	CASTG	2 cut(s)	351, 403
VneI	GTGCAC	1 cut(s)	138
XapI	RAATTY	2 cut(s)	40, 565
XcmI	CCANNNNNNNNNTGG	1 cut(s)	794
Zsp2I	ATGCAT	1 cut(s)	277

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