Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr7D

Orthogroup ID

OG0006117

Physical Location & Seq

Genomic Coordinates Reverse (-)

54742631 .. 54746944

Gene Structure 4314 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh7DG398500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 993 bp

ATGGGCAAAGAAGGGGTGAAGGCTGATGCTGATTGTTTTCATTCTTTGTTTGAGTTGTGTGGGAATTCGACGTCGCTAGAGAATGGAAAGAAAGTTCATGATTTCTTTTTGCAGTCTACATGTAGGGGTAATAGGGACTTGAGCCATAAAGTAATCGAAATGTATGGAAAATGTGGAAGCATGACTGATGCCAGGAGAGTGTTTGATCACCTGCTTGAGAAGAACATTGATTCTTGGCATTTGATGATAAACTGGTATGCGGAGAACGGGTTAGGGGATGATGGGTTGAACATGTTTGAGTTGATGAGGGAGCAAGGTTTGAAACCCAATTCGGAAACATTCCTTGCAGTCTTTTCGGCTTGTGCCAGTGCAGATGCTGTTGAAGAAGCATTTATACATTTTGAGTCGATGAAAACTGATTACGGATTTGATCCTGTAGTGGAGCATTATTTGGGGATTCTTGATGTACTTGGAAAATGCGGTCATCTGAATGAAACAGTTGATTATATTGAGAAGCTCCCATTTGAGCCGACTGTGACAGTTTGGGAGGCATTGAGGAATTATGCCCAGGTTCATGGAGATATTGATCTTGAAGATCACGCTGAGGAGTTAATGGTTGCTCTTGACCCGTCAAAGGCTGGTAAGATTCCAACTCCACCACCTAGAAAGCGTGGTGCTATTTGCATGCTTGATGGGAAGAACAGAACCAGTGCGTTTAAAAATCCCACATTGTACAAGGATTGTGAAAAGTTAAAGGCTCTCAATTCGATGAGAGGAGAGGGTTATGTTCCAGACACAAGATATGTTCTTCATGACATTGACCAGGAGGCTAAGGAGCAAGCACTGCTCTATCACAGTGAGCTTTTGGCAATCGCATATGGCCTGATTGGTACTCCGGCAAGACACCTCTTAGGATCATTAACAACCTCCGTGTCTGTGGTGACTGCCACAGTGCCATTAAGATCATGTCCAAGATTGTTGGAAGGCAATTAA

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:0005739 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

DYW_deaminase PPR PPR_2

Protein Analysis

330

Amino Acids

36.81

Weight (kDa)

5.31

Isoelectric Point (pI)

32.15

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	75 - 122	4.2e-08	PPR repeat family
DYW_deaminase	PF14432	261 - 302	1.1e-09	DYW family of nucleic acid deaminases

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: OG0006117)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G15690
fragaria_vesca	FvH4_2g06150
malus_domestica	MD05G1080000.v1.1
prunus_persica	Prupe.8G123800_v2.0.a1
pyrus_communis	pycom05g07310 pycom10g07740
rosa_chinensis	RchiOBHm_Chr6g0257041 RchiOBHm_Chr7g0228581
rosa_laevigata	RLG00000001553 RLG00000014672
rosa_multiflora	Rmu_sc0008871.1_g000003 Rmu_sc0011334.1_g000001 Rmu_sc0019183.1_g000001
rosa_roxburghii	Rroxscaffold_3G00231050 Rroxscaffold_7G00208450
rosa_rugosa	Rorug05G0575600 Rorug07G0250600
rosa_samantha	Rh6AG093700 Rh6BG084500 Rh6CG081200 Rh6DG076600 Rh7AG402800 Rh7BG383700 Rh7CG422100 Rh7DG398500
rosa_wichuraiana	Rw6G008060 Rw7G033470

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	219
AatII	GACGTC	1 cut(s)	74
Acc36I	ACCTGC	1 cut(s)	219
AccI	GTMKAC	1 cut(s)	116
AciI	CCGC	2 cut(s)	260, 480
AclWI	GGATC	2 cut(s)	425, 922
AcsI	RAATTY	1 cut(s)	64
AcyI	GRCGYC	1 cut(s)	71
AfaI	GTAC	3 cut(s)	468, 734, 892
AfiI	CCNNNNNNNGG	1 cut(s)	634
AflIII	ACRYGT	2 cut(s)	119, 291
AgsI	TTSAA	4 cut(s)	289, 322, 383, 593
AjnI	CCWGG	3 cut(s)	191, 567, 822
AloI	GAACNNNNNNTCC	2 cut(s)	78, 110
AluBI	AGCT	2 cut(s)	517, 862
AluI	AGCT	2 cut(s)	517, 862
AlwI	GGATC	2 cut(s)	425, 922
AlwNI	CAGNNNCTG	1 cut(s)	377
AoxI	GGCC	1 cut(s)	880
ApoI	RAATTY	1 cut(s)	64
AsuHPI	GGTGA	3 cut(s)	28, 200, 952
BarI	GAAGNNNNNNTAC	2 cut(s)	378, 410
BbvCI	CCTCAGC	1 cut(s)	603
BccI	CCATC	2 cut(s)	275, 686
BcgI	CGANNNNNNTGC	2 cut(s)	336, 370
BciT130I	CCWGG	3 cut(s)	193, 569, 824
BclI	TGATCA	1 cut(s)	205
BfaI	CTAG	2 cut(s)	77, 663
BfmI	CTRYAG	1 cut(s)	435
BfuAI	ACCTGC	1 cut(s)	219
Bme1390I	CCNGG	3 cut(s)	193, 569, 824
BmrFI	CCNGG	3 cut(s)	193, 569, 824
BmsI	GCATC	3 cut(s)	16, 178, 364
Bpu10I	CCTNAGC	2 cut(s)	603, 831
BpuEI	CTTGAG	2 cut(s)	160, 236
BsaBI	GATNNNNATC	1 cut(s)	585
BsaHI	GRCGYC	1 cut(s)	71
BsaJI	CCNNGG	1 cut(s)	567
BsaXI	ACNNNNNCTCC	2 cut(s)	254, 284
Bsc4I	CCNNNNNNNGG	1 cut(s)	634
Bse1I	ACTGG	3 cut(s)	257, 366, 708
Bse8I	GATNNNNATC	1 cut(s)	585
BseBI	CCWGG	3 cut(s)	193, 569, 824
BseDI	CCNNGG	1 cut(s)	567
BseGI	GGATG	1 cut(s)	283
BseJI	GATNNNNATC	1 cut(s)	585
BseLI	CCNNNNNNNGG	1 cut(s)	634
BseMII	CTCAG	1 cut(s)	594
BseNI	ACTGG	3 cut(s)	257, 366, 708
BseRI	GAGGAG	2 cut(s)	620, 789
BsgI	GTGCAG	1 cut(s)	390
BshFI	GGCC	1 cut(s)	882
BsiSI	CCGG	1 cut(s)	896
BslFI	GGGAC	1 cut(s)	149
BslI	CCNNNNNNNGG	1 cut(s)	634
BsmFI	GGGAC	1 cut(s)	149
BsnI	GGCC	1 cut(s)	882
Bsp1407I	TGTACA	1 cut(s)	732
Bsp143I	GATC	6 cut(s)	205, 430, 586, 595, 914, 962
BspACI	CCGC	2 cut(s)	260, 480
BspANI	GGCC	1 cut(s)	882
BspCNI	CTCAG	1 cut(s)	595
BspHI	TCATGA	2 cut(s)	97, 811
BspMI	ACCTGC	1 cut(s)	219
BspPI	GGATC	2 cut(s)	425, 922
BsrGI	TGTACA	1 cut(s)	732
BsrI	ACTGG	3 cut(s)	257, 366, 708
BssECI	CCNNGG	1 cut(s)	567
BssMI	GATC	6 cut(s)	205, 430, 586, 595, 914, 962
BssNI	GRCGYC	1 cut(s)	71
Bst2UI	CCWGG	3 cut(s)	193, 569, 824
Bst4CI	ACNGT	5 cut(s)	499, 535, 541, 857, 952
BstACI	GRCGYC	1 cut(s)	71
BstAPI	GCANNNNNTGC	1 cut(s)	844
BstAUI	TGTACA	1 cut(s)	732
BstC8I	GCNNGC	2 cut(s)	686, 840
BstDEI	CTNAG	3 cut(s)	603, 831, 910
BstF5I	GGATG	1 cut(s)	283
BstKTI	GATC	6 cut(s)	208, 433, 589, 598, 917, 965
BstMBI	GATC	6 cut(s)	205, 430, 586, 595, 914, 962
BstMWI	GCNNNNNNNGC	1 cut(s)	844
BstNI	CCWGG	3 cut(s)	193, 569, 824
BstNSI	RCATGY	3 cut(s)	123, 295, 688
BstSCI	CCNGG	3 cut(s)	191, 567, 822
BstSFI	CTRYAG	1 cut(s)	435
BstXI	CCANNNNNNTGG	1 cut(s)	575
BsuRI	GGCC	1 cut(s)	882
BtsCI	GGATG	1 cut(s)	283
BtsI	GCAGTG	1 cut(s)	842
BtsIMutI	CAGTG	5 cut(s)	373, 715, 842, 862, 957
BveI	ACCTGC	1 cut(s)	219
Cac8I	GCNNGC	2 cut(s)	686, 840
CaiI	CAGNNNCTG	1 cut(s)	377
CciI	TCATGA	2 cut(s)	97, 811
Csp6I	GTAC	3 cut(s)	467, 733, 891
CviAII	CATG	8 cut(s)	98, 120, 181, 292, 575, 685, 812, 966
CviQI	GTAC	3 cut(s)	467, 733, 891
DdeI	CTNAG	3 cut(s)	603, 831, 910
DpnI	GATC	6 cut(s)	207, 432, 588, 597, 916, 964
DpnII	GATC	6 cut(s)	205, 430, 586, 595, 914, 962
DraI	TTTAAA	1 cut(s)	718
EcoRI	GAATTC	1 cut(s)	64
EcoRII	CCWGG	3 cut(s)	191, 567, 822
FaeI	CATG	8 cut(s)	101, 123, 184, 295, 578, 688, 815, 969
FaqI	GGGAC	1 cut(s)	149
FatI	CATG	8 cut(s)	97, 119, 180, 291, 574, 684, 811, 965
FauNDI	CATATG	1 cut(s)	877
FbaI	TGATCA	1 cut(s)	205
FblI	GTMKAC	1 cut(s)	116
FokI	GGATG	1 cut(s)	290
FspBI	CTAG	2 cut(s)	77, 663
HaeIII	GGCC	1 cut(s)	882
HapII	CCGG	1 cut(s)	896
Hin1I	GRCGYC	1 cut(s)	71
Hin1II	CATG	8 cut(s)	101, 123, 184, 295, 578, 688, 815, 969
HinfI	GANTC	4 cut(s)	230, 404, 457, 646
HpaII	CCGG	1 cut(s)	896
HphI	GGTGA	3 cut(s)	28, 200, 952
Hpy166II	GTNNAC	1 cut(s)	117
Hpy188I	TCNGA	2 cut(s)	334, 489
Hpy188III	TCNNGA	6 cut(s)	98, 461, 590, 623, 791, 812
Hpy8I	GTNNAC	1 cut(s)	117
Hpy99I	CGWCG	2 cut(s)	73, 76
HpyAV	CCTTC	3 cut(s)	5, 13, 977
HpyCH4III	ACNGT	5 cut(s)	499, 535, 541, 857, 952
HpyCH4IV	ACGT	1 cut(s)	71
HpyCH4V	TGCA	4 cut(s)	112, 347, 371, 684
HpyF10VI	GCNNNNNNNGC	1 cut(s)	844
HpyF3I	CTNAG	3 cut(s)	603, 831, 910
HpySE526I	ACGT	1 cut(s)	71
Hsp92I	GRCGYC	1 cut(s)	71
Hsp92II	CATG	8 cut(s)	101, 123, 184, 295, 578, 688, 815, 969
Ksp22I	TGATCA	1 cut(s)	205
Kzo9I	GATC	6 cut(s)	205, 430, 586, 595, 914, 962
LmnI	GCTCC	4 cut(s)	310, 442, 522, 835
LweI	GCATC	3 cut(s)	16, 178, 364
MaeI	CTAG	2 cut(s)	77, 663
MaeII	ACGT	1 cut(s)	71
MaeIII	GTNAC	2 cut(s)	535, 940
MalI	GATC	6 cut(s)	207, 432, 588, 597, 916, 964
MboI	GATC	6 cut(s)	205, 430, 586, 595, 914, 962
MboII	GAAGA	5 cut(s)	232, 395, 605, 709, 800
MluCI	AATT	5 cut(s)	64, 328, 559, 763, 988
MlyI	GAGTC	1 cut(s)	413
MmeI	TCCRAC	2 cut(s)	674, 960
MnlI	CCTC	9 cut(s)	300, 541, 549, 598, 767, 772, 820, 917, 937
MseI	TTAA	6 cut(s)	611, 717, 752, 920, 959, 991
MslI	CAYNNNNRTG	1 cut(s)	489
MspI	CCGG	1 cut(s)	896
MspR9I	CCNGG	3 cut(s)	193, 569, 824
MvaI	CCWGG	3 cut(s)	193, 569, 824
MwoI	GCNNNNNNNGC	1 cut(s)	844
NdeI	CATATG	1 cut(s)	877
NdeII	GATC	6 cut(s)	205, 430, 586, 595, 914, 962
NlaIII	CATG	8 cut(s)	101, 123, 184, 295, 578, 688, 815, 969
NmuCI	GTSAC	2 cut(s)	535, 940
NspI	RCATGY	3 cut(s)	123, 295, 688
PaeI	GCATGC	1 cut(s)	688
PagI	TCATGA	2 cut(s)	97, 811
PaqCI	CACCTGC	1 cut(s)	219
PciI	ACATGT	2 cut(s)	119, 291
PfeI	GAWTC	3 cut(s)	230, 457, 646
PleI	GAGTC	1 cut(s)	412
PpsI	GAGTC	1 cut(s)	412
PscI	ACATGT	2 cut(s)	119, 291
Psp6I	CCWGG	3 cut(s)	191, 567, 822
PspGI	CCWGG	3 cut(s)	191, 567, 822
PstNI	CAGNNNCTG	1 cut(s)	377
RsaI	GTAC	3 cut(s)	468, 734, 892
RsaNI	GTAC	3 cut(s)	467, 733, 891
RseI	CAYNNNNRTG	1 cut(s)	489
SaqAI	TTAA	6 cut(s)	611, 717, 752, 920, 959, 991
Sau3AI	GATC	6 cut(s)	205, 430, 586, 595, 914, 962
SchI	GAGTC	1 cut(s)	413
ScrFI	CCNGG	3 cut(s)	193, 569, 824
SetI	ASST	9 cut(s)	74, 213, 319, 519, 573, 664, 864, 909, 929
SfaNI	GCATC	3 cut(s)	16, 178, 364
SfcI	CTRYAG	1 cut(s)	435
SmiMI	CAYNNNNRTG	1 cut(s)	489
SmlI	CTYRAG	2 cut(s)	139, 215
SmoI	CTYRAG	2 cut(s)	139, 215
SphI	GCATGC	1 cut(s)	688
Sse9I	AATT	5 cut(s)	64, 328, 559, 763, 988
SsiI	CCGC	2 cut(s)	260, 480
SspMI	CTAG	2 cut(s)	77, 663
StyD4I	CCNGG	3 cut(s)	191, 567, 822
TaaI	ACNGT	5 cut(s)	499, 535, 541, 857, 952
TaiI	ACGT	1 cut(s)	74
TaqI	TCGA	4 cut(s)	68, 156, 407, 767
TasI	AATT	5 cut(s)	64, 328, 559, 763, 988
TatI	WGTACW	2 cut(s)	466, 732
TfiI	GAWTC	3 cut(s)	230, 457, 646
Tru1I	TTAA	6 cut(s)	611, 717, 752, 920, 959, 991
Tru9I	TTAA	6 cut(s)	611, 717, 752, 920, 959, 991
TscAI	CASTG	5 cut(s)	373, 715, 849, 862, 957
TseFI	GTSAC	2 cut(s)	535, 940
Tsp45I	GTSAC	2 cut(s)	535, 940
TspDTI	ATGAA	6 cut(s)	29, 86, 425, 507, 563, 800
TspGWI	ACGGA	2 cut(s)	438, 919
TspRI	CASTG	5 cut(s)	373, 715, 849, 862, 957
XapI	RAATTY	1 cut(s)	64
XceI	RCATGY	3 cut(s)	123, 295, 688
XmiI	GTMKAC	1 cut(s)	116
XspI	CTAG	2 cut(s)	77, 663
ZraI	GACGTC	1 cut(s)	72

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