Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000003

Orthogroup ID

OG0003456

Physical Location & Seq

Genomic Coordinates Reverse (-)

43595826 .. 43600252

Gene Structure 4427 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_3G00249830.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 924 bp

ATGAGAGTTACCGAGTGGGTAGTTTCCAAAAATGGAAGCTACCACACATCTTTTTATGGGGTATTGTATGACTTGATTAAGCTCTATGTTGTGATTTATATTGCTTTCATCGATAATGCTGGAAATTTGCTCCCTGATGACTCATTTGGGATAATGATAGGAAATGGCAAGTTATTTTATGAATATATGAATGTGCTTGCCAAAATTCTTTTAAGGAGTGTTAGTAAGGAGCGGCTGATGAGTTCAAATGTTAGCATAATGGATACAATTGTTGCTGCATTATGTGGAGAGAGCATCAAGATGGATGGAGTTGGAATTTCGTTTTTAATTTTGTTGCTTGCAATTCATAGTACAAAGTTTAAGAGAGAAGCTGCAAGTATAATACATATCTGGGCATCTCTTATTGATCATCAGATGGTGGACTGGAATGTTATATATGCCTTGATGTATGAAGAGAGATTCATTATTGAGTTTTCTGAGCAAAGAAAAGACAGGGAACTTGAAGCTTTGAAATGTGTCTCTCTGGTTATAGAAGTTCATGGTTCTACTATGAGGAGAGGTTTATCTATTCTTGTCTTGCGAAATGCAGTTGTCAATGTATATGGCCAGTGGGGTTATAAAGTTCATGCATATCAGATGTTCAAATTGATTGAATCTAAAGATGTTGTGTCTTGGACGAGTATGATATCTTGTTATGTTCATAATGGGCCTGCAAGTGAGGCTCTTGAACTTTGTCGGCTCATGAAAGAAGTAAATGTTAAACCTGATTTCCAGGCTTATGGGATGCATGGTCATGGCAAGGAAGCCATTGATTTATTCAAGAGGATGGAAGACCAAAAGATTGTTCCAGATCATATTATGTTTTGGGCTCAAGTCTTTTACATTAAGGGTCAAATGGAAACTGATGATAGGCTTGCAAACTAA

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:0005737 GO:0006139 GO:0006396 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009451 GO:0009507 GO:0009536 GO:0009987 GO:0010467 GO:0016070 GO:0016787 GO:0016788 GO:0031425 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: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

307

Amino Acids

35.24

Weight (kDa)

6.37

Isoelectric Point (pI)

30.69

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	220 - 260	3.4e-07	PPR repeat family
PPR	PF01535	223 - 252	4.2e-07	PPR repeat

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0003456)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_1g23542
rosa_chinensis	RchiOBHm_Chr1g0323881 RchiOBHm_Chr1g0363301 RchiOBHm_Chr3g0488451 RchiOBHm_Chr4g0387101 RchiOBHm_Chr4g0387111 RchiOBHm_Chr4g0402531
rosa_laevigata	RLG00000000633 RLG00000003072 RLG00000011416 RLG00000019029 RLG00000026076 RLG00000036164
rosa_multiflora	Rmu_co8181938.1_g000002 Rmu_co8182286.1_g000002 Rmu_sc0000103.1_g000012 Rmu_sc0001207.1_g000051 Rmu_sc0003615.1_g000003 Rmu_sc0004695.1_g000012 Rmu_sc0006098.1_g000005 Rmu_sc0007104.1_g000004 Rmu_sc0022560.1_g000001
rosa_roxburghii	Rroxscaffold_3G00249830 Rroxscaffold_3G00250680 Rroxscaffold_4G00290730 Rroxscaffold_4G00291010 Rroxscaffold_5G00369410 Rroxscaffold_7G00179280
rosa_rugosa	Rorug07G0054300
rosa_samantha	Rh1BG312100 Rh1CG327200 Rh1DG343700 Rh3BG375900 Rh5BG126700 Rh7AG071200 Rh7DG076500

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	618
AccBSI	CCGCTC	1 cut(s)	232
AciI	CCGC	1 cut(s)	232
AcoI	YGGCCR	1 cut(s)	604
AcsI	RAATTY	3 cut(s)	124, 204, 315
AfaI	GTAC	1 cut(s)	352
AgsI	TTSAA	7 cut(s)	246, 503, 511, 643, 653, 728, 820
AjnI	CCWGG	1 cut(s)	771
AjuI	GAANNNNNNNTTGG	2 cut(s)	828, 860
AluBI	AGCT	4 cut(s)	39, 82, 371, 506
AluI	AGCT	4 cut(s)	39, 82, 371, 506
Alw26I	GTCTC	1 cut(s)	523
AoxI	GGCC	2 cut(s)	604, 707
ApeKI	GCWGC	2 cut(s)	275, 371
ApoI	RAATTY	3 cut(s)	124, 204, 315
AspS9I	GGNCC	1 cut(s)	707
BaeI	ACNNNNGTAYC	2 cut(s)	255, 288
BalI	TGGCCA	1 cut(s)	606
BanII	GRGCYC	1 cut(s)	871
BbsI	GAAGAC	1 cut(s)	837
BbvI	GCAGC	2 cut(s)	262, 358
BccI	CCATC	4 cut(s)	295, 299, 409, 820
BciT130I	CCWGG	1 cut(s)	773
BciVI	GTATCC	1 cut(s)	256
BclI	TGATCA	1 cut(s)	406
BcoDI	GTCTC	1 cut(s)	523
BfuI	GTATCC	1 cut(s)	256
BisI	GCNGC	3 cut(s)	233, 276, 372
BlsI	GCNGC	3 cut(s)	234, 277, 373
Bme1390I	CCNGG	1 cut(s)	773
BmgT120I	GGNCC	1 cut(s)	707
BmrFI	CCNGG	1 cut(s)	773
BmsI	GCATC	3 cut(s)	303, 404, 774
BpiI	GAAGAC	1 cut(s)	837
BpuEI	CTTGAG	1 cut(s)	855
Bsa29I	ATCGAT	1 cut(s)	111
BsaXI	ACNNNNNCTCC	2 cut(s)	208, 238
Bse1I	ACTGG	2 cut(s)	428, 607
BseBI	CCWGG	1 cut(s)	773
BseCI	ATCGAT	1 cut(s)	111
BseGI	GGATG	3 cut(s)	310, 789, 831
BseMII	CTCAG	1 cut(s)	468
BseNI	ACTGG	2 cut(s)	428, 607
BseRI	GAGGAG	1 cut(s)	568
BseXI	GCAGC	2 cut(s)	262, 358
BshFI	GGCC	2 cut(s)	606, 709
BshVI	ATCGAT	1 cut(s)	111
BsmAI	GTCTC	1 cut(s)	523
BsnI	GGCC	2 cut(s)	606, 709
Bsp1286I	GDGCHC	1 cut(s)	871
Bsp143I	GATC	2 cut(s)	406, 850
BspACI	CCGC	1 cut(s)	232
BspANI	GGCC	2 cut(s)	606, 709
BspCNI	CTCAG	1 cut(s)	469
BspDI	ATCGAT	1 cut(s)	111
BspHI	TCATGA	1 cut(s)	741
BsrBI	CCGCTC	1 cut(s)	232
BsrI	ACTGG	2 cut(s)	428, 607
BssMI	GATC	2 cut(s)	406, 850
Bst2UI	CCWGG	1 cut(s)	773
Bst6I	CTCTTC	1 cut(s)	447
BstC8I	GCNNGC	4 cut(s)	198, 339, 711, 915
BstDEI	CTNAG	1 cut(s)	477
BstF5I	GGATG	3 cut(s)	310, 789, 831
BstKTI	GATC	2 cut(s)	409, 853
BstMAI	GTCTC	1 cut(s)	523
BstMBI	GATC	2 cut(s)	406, 850
BstMWI	GCNNNNNNNGC	1 cut(s)	719
BstNI	CCWGG	1 cut(s)	773
BstSCI	CCNGG	1 cut(s)	771
BstV1I	GCAGC	2 cut(s)	262, 358
BstV2I	GAAGAC	1 cut(s)	837
BstXI	CCANNNNNNTGG	1 cut(s)	779
Bsu15I	ATCGAT	1 cut(s)	111
BsuI	GTATCC	1 cut(s)	256
BsuRI	GGCC	2 cut(s)	606, 709
BsuTUI	ATCGAT	1 cut(s)	111
BtsCI	GGATG	3 cut(s)	310, 789, 831
BtsIMutI	CAGTG	1 cut(s)	614
Cac8I	GCNNGC	4 cut(s)	198, 339, 711, 915
CciI	TCATGA	1 cut(s)	741
Cfr13I	GGNCC	1 cut(s)	707
ClaI	ATCGAT	1 cut(s)	111
Csp6I	GTAC	1 cut(s)	351
CviAII	CATG	5 cut(s)	539, 626, 742, 788, 794
CviQI	GTAC	1 cut(s)	351
DdeI	CTNAG	1 cut(s)	477
DpnI	GATC	2 cut(s)	408, 852
DpnII	GATC	2 cut(s)	406, 850
EaeI	YGGCCR	1 cut(s)	604
Eam1104I	CTCTTC	1 cut(s)	447
EarI	CTCTTC	1 cut(s)	447
Eco24I	GRGCYC	1 cut(s)	871
Eco32I	GATATC	1 cut(s)	687
EcoRII	CCWGG	1 cut(s)	771
EcoRV	GATATC	1 cut(s)	687
EcoT22I	ATGCAT	2 cut(s)	631, 789
EcoT38I	GRGCYC	1 cut(s)	871
FaeI	CATG	5 cut(s)	542, 629, 745, 791, 797
FatI	CATG	5 cut(s)	538, 625, 741, 787, 793
FbaI	TGATCA	1 cut(s)	406
Fnu4HI	GCNGC	3 cut(s)	233, 276, 372
FokI	GGATG	3 cut(s)	317, 796, 838
FriOI	GRGCYC	1 cut(s)	871
Fsp4HI	GCNGC	3 cut(s)	233, 276, 372
GluI	GCNGC	3 cut(s)	233, 276, 372
HaeIII	GGCC	2 cut(s)	606, 709
Hin1II	CATG	5 cut(s)	542, 629, 745, 791, 797
HindIII	AAGCTT	1 cut(s)	504
HinfI	GANTC	3 cut(s)	140, 459, 653
Hpy166II	GTNNAC	1 cut(s)	421
Hpy188I	TCNGA	3 cut(s)	414, 478, 636
Hpy188III	TCNNGA	5 cut(s)	298, 725, 742, 820, 848
Hpy8I	GTNNAC	1 cut(s)	421
HpyCH4V	TGCA	8 cut(s)	278, 341, 374, 587, 629, 713, 787, 917
HpyF10VI	GCNNNNNNNGC	1 cut(s)	719
HpyF3I	CTNAG	1 cut(s)	477
Hsp92II	CATG	5 cut(s)	542, 629, 745, 791, 797
Ksp22I	TGATCA	1 cut(s)	406
Kzo9I	GATC	2 cut(s)	406, 850
LmnI	GCTCC	2 cut(s)	135, 229
Lsp1109I	GCAGC	2 cut(s)	262, 358
LweI	GCATC	3 cut(s)	303, 404, 774
MaeIII	GTNAC	1 cut(s)	7
MalI	GATC	2 cut(s)	408, 852
MbiI	CCGCTC	1 cut(s)	232
MboI	GATC	2 cut(s)	406, 850
MboII	GAAGA	2 cut(s)	464, 842
MfeI	CAATTG	1 cut(s)	267
MhlI	GDGCHC	1 cut(s)	871
MlsI	TGGCCA	1 cut(s)	606
MluCI	AATT	7 cut(s)	124, 204, 267, 315, 327, 342, 644
MluNI	TGGCCA	1 cut(s)	606
MlyI	GAGTC	1 cut(s)	134
MmeI	TCCRAC	1 cut(s)	292
MnlI	CCTC	4 cut(s)	546, 551, 712, 816
Mox20I	TGGCCA	1 cut(s)	606
Mph1103I	ATGCAT	2 cut(s)	631, 789
MscI	TGGCCA	1 cut(s)	606
MseI	TTAA	6 cut(s)	78, 212, 326, 360, 759, 885
MslI	CAYNNNNRTG	2 cut(s)	299, 792
Msp20I	TGGCCA	1 cut(s)	606
MspR9I	CCNGG	1 cut(s)	773
MunI	CAATTG	1 cut(s)	267
MvaI	CCWGG	1 cut(s)	773
MwoI	GCNNNNNNNGC	1 cut(s)	719
NdeII	GATC	2 cut(s)	406, 850
NlaIII	CATG	5 cut(s)	542, 629, 745, 791, 797
NsiI	ATGCAT	2 cut(s)	631, 789
PagI	TCATGA	1 cut(s)	741
PfeI	GAWTC	2 cut(s)	459, 653
PkrI	GCNGC	3 cut(s)	234, 277, 373
PleI	GAGTC	1 cut(s)	134
PpsI	GAGTC	1 cut(s)	134
PsiI	TTATAA	1 cut(s)	618
Psp6I	CCWGG	1 cut(s)	771
PspGI	CCWGG	1 cut(s)	771
PspPI	GGNCC	1 cut(s)	707
RsaI	GTAC	1 cut(s)	352
RsaNI	GTAC	1 cut(s)	351
RseI	CAYNNNNRTG	2 cut(s)	299, 792
SaqAI	TTAA	6 cut(s)	78, 212, 326, 360, 759, 885
SatI	GCNGC	3 cut(s)	233, 276, 372
Sau3AI	GATC	2 cut(s)	406, 850
Sau96I	GGNCC	1 cut(s)	707
SchI	GAGTC	1 cut(s)	134
ScrFI	CCNGG	1 cut(s)	773
SduI	GDGCHC	1 cut(s)	871
SetI	ASST	6 cut(s)	41, 84, 373, 508, 562, 766
SfaNI	GCATC	3 cut(s)	303, 404, 774
SmiMI	CAYNNNNRTG	2 cut(s)	299, 792
SmlI	CTYRAG	1 cut(s)	870
SmoI	CTYRAG	1 cut(s)	870
Sse9I	AATT	7 cut(s)	124, 204, 267, 315, 327, 342, 644
SsiI	CCGC	1 cut(s)	232
StyD4I	CCNGG	1 cut(s)	771
TaqI	TCGA	1 cut(s)	111
TasI	AATT	7 cut(s)	124, 204, 267, 315, 327, 342, 644
TatI	WGTACW	1 cut(s)	350
TauI	GCSGC	1 cut(s)	235
TfiI	GAWTC	2 cut(s)	459, 653
Tru1I	TTAA	6 cut(s)	78, 212, 326, 360, 759, 885
Tru9I	TTAA	6 cut(s)	78, 212, 326, 360, 759, 885
TscAI	CASTG	1 cut(s)	614
TseI	GCWGC	2 cut(s)	275, 371
TspRI	CASTG	1 cut(s)	614
XapI	RAATTY	3 cut(s)	124, 204, 315
Zsp2I	ATGCAT	2 cut(s)	631, 789

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