Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1D

Orthogroup ID

OG0002972

Physical Location & Seq

Genomic Coordinates Reverse (-)

19650855 .. 19653167

Gene Structure 2313 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1DG105100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1098 bp

ATGCTACCGTTGTGTGAACCCTCTCTAGTAGCGGCTTTAATACAAAAATGCACCGCCATAAACTCGCTCAGGGAAGCGCGTCGACTCCACGCGCTTCTCCTAACCACCACAACCGTCAGCTCGCGCTCTGTGTTCCTGTACAACAATGTGCTATCTATGTATGCACGGTGCGGCTCGCTAGGAGATGCACGCAAGGTGTTAGACGAAATGCCTCAAAGAAGTCTTGTTTCGTTCAATGCGCTGGCTGCAGCCTATTCCCGGAGTTCAGACACTGCCGGTTTGGCATTGACATTGCTAAAACAAATGGGAGTTGAATGTCTCAGGCCAAATGTTTCGACTTTCACGAGTGTGATACAAGCGTCATGTAATCTTGAGGATTGGTTGGTTGGCTCTTTGGTTCATGCACAAGTTGTGAAATGTGGGTTCTTGAATGAAGTGCATCTTCAGACAGCTCTGCTTGGGATGTATTCCAGCTGTGGGGATTTGGTATCTGCTAGCAGAGTTTTCGGAGGAATGGTTGATAGAGATGTTGTGGCTTGGAATTCGATGATTTTCGGGTATTTGAAGAATGGTAAGAACAAGGAAGGGCTTCATTTGTTTGATGGTATGTTGAGGACTGGAGTTATTCCTACTCAGTTCACATATTCAATGGTTTTGAATGTGTGTAGCAGATTGAGATATTTGAATCGGGGGAAAATCATCCATGCCCGAGTCATAGTTTCAAGCACACATGCTGATTTGGCTTTGGAGAATTCACTGCTTGATATGTATCGTAACTCTGGTGACACCCAAGCAGCTTTTAGTGTGTTTAATAAAATGGACAGCCCGGATTTGGTTTCATGGAACACAATGATTTCTGGGTATTCAGAAAATGAGGATGGAGAAAAGGCGATGAATTTGTTTGCCCGGTTGAAAAGATTGTGTTATCTTAAACCAGATGAATATACTTATGCAGCTATCATATCTGCAGCAGGTACATACCTTGCTTCTGACTATGGTAAGCTTCTTCATGCTCAAGTCATAAAAGTAGGACTCGAGAAGAGTATATTTGTAGGAACTGCACTAGTGTCTGTACTTCAAGAACAGCGAAACGGATAG

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

LRRNT_2 LRR_8 PPR PPR_2

Protein Analysis

365

Amino Acids

40.07

Weight (kDa)

8.65

Isoelectric Point (pI)

34.91

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	175 - 223	3.2e-13	PPR repeat family
PPR	PF01535	178 - 207	6.2e-06	PPR repeat
PPR_2	PF13041	276 - 323	1.6e-10	PPR repeat family
PPR	PF01535	279 - 306	1.6e-06	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: OG0002972)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G50420 AT3G50420
fragaria_vesca	FvH4_1g14840
malus_domestica	MD06G1092000.v1.1 MD15G1276000.v1.1
prunus_persica	Prupe.7G142000_v2.0.a1
pyrus_communis	pycom06g08800 pycom15g23890
rosa_chinensis	RchiOBHm_Chr1g0329891 RchiOBHm_Chr2g0103801
rosa_laevigata	RLG00000017261 RLG00000017264 RLG00000029855 RLG00000029861
rosa_multiflora	Rmu_sc0000112.1_g000010 Rmu_sc0000112.1_g000024 Rmu_sc0000112.1_g000025 Rmu_sc0002081.1_g000002 Rmu_sc0002081.1_g000010 Rmu_sc0006774.1_g000014
rosa_roxburghii	Rroxscaffold_2G00139300 Rroxscaffold_2G00139350 Rroxscaffold_4G00320530
rosa_rugosa	Rorug01G0084100 Rorug02G0117300
rosa_samantha	Rh1AG102000 Rh1BG081200 Rh1CG097500 Rh1DG105100 Rh2AG166400 Rh2BG173600 Rh2CG172300 Rh2DG171800
rosa_wichuraiana	Rw0G002030 Rw0G006910 Rw1G008070 Rw1G008120 Rw2G013030

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc36I	ACCTGC	1 cut(s)	962
AccI	GTMKAC	1 cut(s)	82
AccII	CGCG	3 cut(s)	79, 92, 124
AciI	CCGC	3 cut(s)	32, 54, 171
AcsI	RAATTY	3 cut(s)	541, 751, 895
AcuI	CTGAAG	1 cut(s)	428
AfaI	GTAC	3 cut(s)	140, 976, 1074
AfiI	CCNNNNNNNGG	3 cut(s)	258, 477, 832
AhlI	ACTAGT	1 cut(s)	1063
AleI	CACNNNNGTG	1 cut(s)	347
AluBI	AGCT	6 cut(s)	120, 452, 474, 797, 956, 1003
AluI	AGCT	6 cut(s)	120, 452, 474, 797, 956, 1003
Alw26I	GTCTC	1 cut(s)	323
AlwNI	CAGNNNCTG	1 cut(s)	272
Ama87I	CYCGRG	2 cut(s)	708, 1034
AoxI	GGCC	1 cut(s)	323
ApeKI	GCWGC	5 cut(s)	245, 248, 794, 953, 968
ApoI	RAATTY	3 cut(s)	541, 751, 895
Asp700I	GAANNNNTTC	1 cut(s)	588
AspLEI	GCGC	4 cut(s)	79, 94, 126, 241
AsuC2I	CCSGG	3 cut(s)	259, 827, 907
AsuHPI	GGTGA	1 cut(s)	794
AsuNHI	GCTAGC	1 cut(s)	494
AvaI	CYCGRG	2 cut(s)	708, 1034
BaeI	ACNNNNGTAYC	2 cut(s)	344, 377
BauI	CACGAG	1 cut(s)	343
BbvI	GCAGC	5 cut(s)	232, 260, 806, 965, 980
BccI	CCATC	2 cut(s)	596, 872
BcgI	CGANNNNNNTGC	2 cut(s)	487, 521
BcnI	CCSGG	3 cut(s)	259, 827, 907
BcoDI	GTCTC	1 cut(s)	323
BcuI	ACTAGT	1 cut(s)	1063
BfaI	CTAG	4 cut(s)	26, 179, 495, 1064
BfmI	CTRYAG	2 cut(s)	246, 966
BfuAI	ACCTGC	1 cut(s)	962
BglI	GCCNNNNNGGC	1 cut(s)	281
BisI	GCNGC	7 cut(s)	33, 172, 246, 249, 795, 954, 969
BlsI	GCNGC	7 cut(s)	34, 173, 247, 250, 796, 955, 970
Bme1390I	CCNGG	3 cut(s)	259, 827, 907
BmeT110I	CYCGRG	2 cut(s)	708, 1034
BmrFI	CCNGG	3 cut(s)	259, 827, 907
BmsI	GCATC	2 cut(s)	175, 448
BmtI	GCTAGC	1 cut(s)	498
BpmI	CTGGAG	1 cut(s)	639
Bpu10I	CCTNAGC	1 cut(s)	68
BpuEI	CTTGAG	2 cut(s)	392, 999
BpuMI	CCSGG	3 cut(s)	259, 827, 907
BsaBI	GATNNNNATC	1 cut(s)	768
BsaXI	ACNNNNNCTCC	2 cut(s)	501, 531
Bsc4I	CCNNNNNNNGG	3 cut(s)	258, 477, 832
Bse118I	RCCGGY	1 cut(s)	275
Bse1I	ACTGG	1 cut(s)	622
Bse3DI	GCAATG	1 cut(s)	290
Bse8I	GATNNNNATC	1 cut(s)	768
BseGI	GGATG	3 cut(s)	468, 699, 883
BseJI	GATNNNNATC	1 cut(s)	768
BseLI	CCNNNNNNNGG	3 cut(s)	258, 477, 832
BseMI	GCAATG	1 cut(s)	290
BseMII	CTCAG	3 cut(s)	82, 334, 647
BseNI	ACTGG	1 cut(s)	622
BseXI	GCAGC	5 cut(s)	232, 260, 806, 965, 980
BsgI	GTGCAG	1 cut(s)	1044
Bsh1236I	CGCG	3 cut(s)	79, 92, 124
BshFI	GGCC	1 cut(s)	325
BsiHKCI	CYCGRG	2 cut(s)	708, 1034
BsiSI	CCGG	4 cut(s)	259, 276, 827, 907
BslI	CCNNNNNNNGG	3 cut(s)	258, 477, 832
BsmAI	GTCTC	1 cut(s)	323
BsnI	GGCC	1 cut(s)	325
BsoBI	CYCGRG	2 cut(s)	708, 1034
Bsp1407I	TGTACA	1 cut(s)	138
BspACI	CCGC	3 cut(s)	32, 54, 171
BspANI	GGCC	1 cut(s)	325
BspCNI	CTCAG	3 cut(s)	81, 333, 646
BspFNI	CGCG	3 cut(s)	79, 92, 124
BspMAI	CTGCAG	2 cut(s)	250, 970
BspMI	ACCTGC	1 cut(s)	962
BspOI	GCTAGC	1 cut(s)	498
BsrDI	GCAATG	1 cut(s)	290
BsrFI	RCCGGY	1 cut(s)	275
BsrGI	TGTACA	1 cut(s)	138
BsrI	ACTGG	1 cut(s)	622
BssAI	RCCGGY	1 cut(s)	275
BssSI	CACGAG	1 cut(s)	343
Bst2BI	CACGAG	1 cut(s)	343
Bst4CI	ACNGT	3 cut(s)	9, 115, 168
Bst6I	CTCTTC	1 cut(s)	1034
BstAUI	TGTACA	1 cut(s)	138
BstC8I	GCNNGC	5 cut(s)	122, 176, 190, 243, 496
BstDEI	CTNAG	3 cut(s)	68, 320, 633
BstF5I	GGATG	3 cut(s)	468, 699, 883
BstFNI	CGCG	3 cut(s)	79, 92, 124
BstHHI	GCGC	4 cut(s)	79, 94, 126, 241
BstMAI	GTCTC	1 cut(s)	323
BstMWI	GCNNNNNNNGC	3 cut(s)	245, 281, 740
BstNSI	RCATGY	1 cut(s)	734
BstSCI	CCNGG	3 cut(s)	257, 825, 905
BstSFI	CTRYAG	2 cut(s)	246, 966
BstUI	CGCG	3 cut(s)	79, 92, 124
BstV1I	GCAGC	5 cut(s)	232, 260, 806, 965, 980
BsuRI	GGCC	1 cut(s)	325
BtgZI	GCGATG	1 cut(s)	905
BtsCI	GGATG	3 cut(s)	468, 699, 883
BtsI	GCAGTG	2 cut(s)	270, 755
BtsIMutI	CAGTG	2 cut(s)	270, 755
BveI	ACCTGC	1 cut(s)	962
Cac8I	GCNNGC	5 cut(s)	122, 176, 190, 243, 496
CaiI	CAGNNNCTG	1 cut(s)	272
CfoI	GCGC	4 cut(s)	79, 94, 126, 241
Cfr10I	RCCGGY	1 cut(s)	275
CseI	GACGC	2 cut(s)	68, 348
Csp6I	GTAC	3 cut(s)	139, 975, 1073
CviAII	CATG	6 cut(s)	363, 401, 704, 731, 840, 1010
CviQI	GTAC	3 cut(s)	139, 975, 1073
DdeI	CTNAG	3 cut(s)	68, 320, 633
Eam1104I	CTCTTC	1 cut(s)	1034
EarI	CTCTTC	1 cut(s)	1034
Eco57I	CTGAAG	1 cut(s)	428
Eco88I	CYCGRG	2 cut(s)	708, 1034
EcoRI	GAATTC	2 cut(s)	541, 751
FaeI	CATG	6 cut(s)	366, 404, 707, 734, 843, 1013
FalI	AAGNNNNNCTT	2 cut(s)	426, 458
FatI	CATG	6 cut(s)	362, 400, 703, 730, 839, 1009
FblI	GTMKAC	1 cut(s)	82
Fnu4HI	GCNGC	7 cut(s)	33, 172, 246, 249, 795, 954, 969
FokI	GGATG	3 cut(s)	475, 686, 890
Fsp4HI	GCNGC	7 cut(s)	33, 172, 246, 249, 795, 954, 969
FspBI	CTAG	4 cut(s)	26, 179, 495, 1064
GlaI	GCGC	4 cut(s)	78, 93, 125, 240
GluI	GCNGC	7 cut(s)	33, 172, 246, 249, 795, 954, 969
GsuI	CTGGAG	1 cut(s)	639
HaeIII	GGCC	1 cut(s)	325
HapII	CCGG	4 cut(s)	259, 276, 827, 907
HgaI	GACGC	2 cut(s)	68, 348
HhaI	GCGC	4 cut(s)	79, 94, 126, 241
Hin1II	CATG	6 cut(s)	366, 404, 707, 734, 843, 1013
Hin6I	GCGC	4 cut(s)	77, 92, 124, 239
HinP1I	GCGC	4 cut(s)	77, 92, 124, 239
HincII	GTYRAC	1 cut(s)	83
HindII	GTYRAC	1 cut(s)	83
HindIII	AAGCTT	1 cut(s)	1001
HinfI	GANTC	4 cut(s)	84, 685, 711, 1032
HpaII	CCGG	4 cut(s)	259, 276, 827, 907
HphI	GGTGA	1 cut(s)	794
Hpy166II	GTNNAC	3 cut(s)	17, 83, 639
Hpy188I	TCNGA	5 cut(s)	268, 447, 509, 868, 991
Hpy188III	TCNNGA	5 cut(s)	343, 371, 427, 1036, 1079
Hpy8I	GTNNAC	3 cut(s)	17, 83, 639
Hpy99I	CGWCG	1 cut(s)	84
HpyAV	CCTTC	1 cut(s)	578
HpyCH4III	ACNGT	3 cut(s)	9, 115, 168
HpyCH4V	TGCA	9 cut(s)	51, 164, 188, 248, 404, 439, 953, 968, 1061
HpyF10VI	GCNNNNNNNGC	3 cut(s)	245, 281, 740
HpyF3I	CTNAG	3 cut(s)	68, 320, 633
Hsp92II	CATG	6 cut(s)	366, 404, 707, 734, 843, 1013
HspAI	GCGC	4 cut(s)	77, 92, 124, 239
Lsp1109I	GCAGC	5 cut(s)	232, 260, 806, 965, 980
LweI	GCATC	2 cut(s)	175, 448
MaeI	CTAG	4 cut(s)	26, 179, 495, 1064
MaeIII	GTNAC	2 cut(s)	773, 782
MboII	GAAGA	4 cut(s)	434, 577, 998, 1051
MluCI	AATT	3 cut(s)	541, 751, 895
MlyI	GAGTC	3 cut(s)	78, 720, 1026
MnlI	CCTC	6 cut(s)	31, 222, 367, 503, 606, 868
MroXI	GAANNNNTTC	1 cut(s)	588
MseI	TTAA	3 cut(s)	38, 810, 930
MslI	CAYNNNNRTG	1 cut(s)	347
MspA1I	CMGCKG	1 cut(s)	474
MspI	CCGG	4 cut(s)	259, 276, 827, 907
MspR9I	CCNGG	3 cut(s)	259, 827, 907
MvnI	CGCG	3 cut(s)	79, 92, 124
MwoI	GCNNNNNNNGC	3 cut(s)	245, 281, 740
NciI	CCSGG	3 cut(s)	259, 827, 907
NheI	GCTAGC	1 cut(s)	494
NlaIII	CATG	6 cut(s)	366, 404, 707, 734, 843, 1013
NmuCI	GTSAC	1 cut(s)	782
NspI	RCATGY	1 cut(s)	734
OliI	CACNNNNGTG	1 cut(s)	347
PaeR7I	CTCGAG	1 cut(s)	1034
PcsI	WCGNNNNNNNCGW	1 cut(s)	341
PdmI	GAANNNNTTC	1 cut(s)	588
PfeI	GAWTC	1 cut(s)	685
PfoI	TCCNGGA	1 cut(s)	257
PkrI	GCNGC	7 cut(s)	34, 173, 247, 250, 796, 955, 970
PleI	GAGTC	3 cut(s)	78, 719, 1026
PpsI	GAGTC	3 cut(s)	78, 719, 1026
PstI	CTGCAG	2 cut(s)	250, 970
PstNI	CAGNNNCTG	1 cut(s)	272
PvuII	CAGCTG	1 cut(s)	474
RsaI	GTAC	3 cut(s)	140, 976, 1074
RsaNI	GTAC	3 cut(s)	139, 975, 1073
RseI	CAYNNNNRTG	1 cut(s)	347
SalI	GTCGAC	1 cut(s)	81
SaqAI	TTAA	3 cut(s)	38, 810, 930
SatI	GCNGC	7 cut(s)	33, 172, 246, 249, 795, 954, 969
SchI	GAGTC	3 cut(s)	78, 720, 1026
ScrFI	CCNGG	3 cut(s)	259, 827, 907
SetI	ASST	9 cut(s)	122, 198, 454, 476, 799, 958, 976, 984, 1005
SfaNI	GCATC	2 cut(s)	175, 448
SfcI	CTRYAG	2 cut(s)	246, 966
Sfr274I	CTCGAG	1 cut(s)	1034
SlaI	CTCGAG	1 cut(s)	1034
SmiMI	CAYNNNNRTG	1 cut(s)	347
SmlI	CTYRAG	3 cut(s)	371, 1014, 1034
SmoI	CTYRAG	3 cut(s)	371, 1014, 1034
SpeI	ACTAGT	1 cut(s)	1063
Sse9I	AATT	3 cut(s)	541, 751, 895
SsiI	CCGC	3 cut(s)	32, 54, 171
SspMI	CTAG	4 cut(s)	26, 179, 495, 1064
StyD4I	CCNGG	3 cut(s)	257, 825, 905
TaaI	ACNGT	3 cut(s)	9, 115, 168
TaqI	TCGA	4 cut(s)	82, 335, 545, 1035
TasI	AATT	3 cut(s)	541, 751, 895
TatI	WGTACW	2 cut(s)	138, 1072
TauI	GCSGC	2 cut(s)	35, 174
TfiI	GAWTC	1 cut(s)	685
Tru1I	TTAA	3 cut(s)	38, 810, 930
Tru9I	TTAA	3 cut(s)	38, 810, 930
TscAI	CASTG	2 cut(s)	277, 762
TseFI	GTSAC	1 cut(s)	782
TseI	GCWGC	5 cut(s)	245, 248, 794, 953, 968
Tsp45I	GTSAC	1 cut(s)	782
TspDTI	ATGAA	7 cut(s)	389, 447, 581, 828, 908, 954, 998
TspRI	CASTG	2 cut(s)	277, 762
XapI	RAATTY	3 cut(s)	541, 751, 895
XceI	RCATGY	1 cut(s)	734
XhoI	CTCGAG	1 cut(s)	1034
XmiI	GTMKAC	1 cut(s)	82
XmnI	GAANNNNTTC	1 cut(s)	588
XspI	CTAG	4 cut(s)	26, 179, 495, 1064

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