Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3B

Orthogroup ID

OG0004163

Physical Location & Seq

Genomic Coordinates Forward (+)

31325564 .. 31371443

Gene Structure 45880 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3BG309600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1305 bp

ATGGCAACGGCCTTCTCTTTTGCCCAAGCTGCTCTCTTCTCCAAAACCCCACTCTCTCTTCGCACCAATGCCCTCAGAACCTTAACCTTCTGCTTACCCTTCTCTTCTTCTTCTTCTTCCGCAGCTCTTGCCTCTGACAAGCCTCGCAGCAAGAAATGGAGGCACCCAGTAACTTCAGCAGCGCTCGAGCTCGGCGGCGTCAAGATTGCTAGAGATGATGTGTTGAGGGATGACCCCACAAACAATGTTCCGGATACGATTTTTGCAAAGCTCGGAATGCAACTGCATAGAAGAGACCAGCACCCACTTGGAATTCTCAAGAATGCTATCTACGAATACTTCGACACCAATTACTCGAACAAGTTTGATAAGTTCGATGATCTTTGCCCACTTGTATCTGTTAAAGAGAATTTTGATGATGTATTAGTTCCTGCTGATCATGTAAGTCGAAGCTATAATGATACATACTATGTGGACTCTCAAACCGTTTTGAGGTGCCATACAAGTGCTCATCAGGCAGAGTTATTGAGAAGAGGACACACTCATTTCCTTGTAACTGGAGATGTGTACCGTAGGGATTCCATTGACTCTACACATTACCCTGTGTTCCATCAGATGGAAGGCGTGCGTGTTTTTTCTCCAGAAGATTGGGCAGCATCTGGGACAGATGCAACATCTTATGTAGCTGAGGACTTGAAGAAATGTCTTGAGGGTCTGGCACGCCACCTATTTGGTGCTGTGGAGATGCGCTGGGTTGATACATACTTTCCATTTACCAATCCATCATTTGAACTTGAGATTTTCTTTCAGGAAAAGTGGTTGGAGGTTTTGGGTTGCGGAGTAACAGAACAAGAAATATTGAAGAGAAGTGGGAAAACAGACAATATTGCTTGGGCTTTCGGACTTGGATTGGAGCGGCTGGCAATGGTTCTATTTGACATCCCTGATATTCGCCTTTTCTGGTCAACTGATGAGAGGTTTACCTCTCAGTTTTTGAAGGGGCAGCTGGGAGTCAAGTTCAAGCCATATTCAAAGTATCCTCCGTGTTACAAAGATGTTAGTTTTTGGATCAGTGAATCTTTCACCGAAAACAATTTATGTGAAGTTGTTAGAGAGGTTGCTGGAGATCTTGCTGAGGAGGTGCAATTGATAGACAATTTCACAAACAAGAAAGGAATGACCAGTCACTGTTACAGGATTGCTTATAGGTCTATGGAGCGATCACTTACAGACGAGGAAGTCAATAAATTGCAGGGTACTGTAAGGGAGTTGGTTGAGAGCAAGTTGAAGGTTATCTTGAGATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003824 GO:0004812 GO:0004826 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005739 GO:0006082 GO:0006139 GO:0006399 GO:0006412 GO:0006418 GO:0006432 GO:0006518 GO:0006520 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009507 GO:0009532 GO:0009536 GO:0009570 GO:0009987 GO:0010467 GO:0016020 GO:0016070 GO:0016874 GO:0016875 GO:0019538 GO:0019752 GO:0034641 GO:0034645 GO:0034660 GO:0043038 GO:0043039 GO:0043043 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043436 GO:0043603 GO:0043604 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044267 GO:0044271 GO:0044281 GO:0044422 GO:0044424 GO:0044434 GO:0044435 GO:0044444 GO:0044446 GO:0044464 GO:0046483 GO:0071704 GO:0090304 GO:0140098 GO:0140101 GO:1901360 GO:1901564 GO:1901566 GO:1901576

KEGG Pathways

Metabolic & Signaling

ko00970 map00970

Pfam Domains

Protein Families

FDX-ACB tRNA-synt_2d

Protein Analysis

434

Amino Acids

49.6

Weight (kDa)

5.99

Isoelectric Point (pI)

38.84

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
tRNA-synt_2d	PF01409	100 - 331	9.8e-49	tRNA synthetases class II core domain (F)
FDX-ACB	PF03147	344 - 434	1.4e-21	Ferredoxin-fold anticodon binding domain

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: OG0004163)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G58140
fragaria_vesca	FvH4_3g12680 FvH4_3g12680 FvH4_3g12680
malus_domestica	MD05G1248600.v1.1 MD10G1229100.v1.1
prunus_persica	Prupe.4G115500_v2.0.a1
pyrus_communis	pycom05g22530 pycom10g19270
rosa_chinensis	RchiOBHm_Chr3g0486261 RchiOBHm_Chr5g0020641
rosa_laevigata	RLG00000023089 RLG00000032549
rosa_multiflora	Rmu_sc0001857.1_g000018 Rmu_sc0005607.1_g000020 Rmu_sc0005842.1_g000003 Rmu_sc0007661.1_g000010
rosa_roxburghii	Rroxscaffold_1G00057630 Rroxscaffold_6G00395930
rosa_rugosa	Rorug03G0224300 Rorug03G0224400 Rorug03G0224500 Rorug05G0062200
rosa_samantha	Rh3AG274300 Rh3BG309600 Rh3CG308800 Rh5AG151900 Rh5BG151600 Rh5CG162900 Rh5DG150800
rosa_wichuraiana	Rw0G022550 Rw3G024320 Rw5G013460

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AasI	GACNNNNNNGTC	1 cut(s)	1238
AccB1I	GGYRCC	2 cut(s)	162, 495
AccB7I	CCANNNNNTGG	1 cut(s)	616
AccBSI	CCGCTC	1 cut(s)	916
AccIII	TCCGGA	1 cut(s)	250
AciI	CCGC	4 cut(s)	120, 195, 837, 916
AclWI	GGATC	1 cut(s)	1076
AcsI	RAATTY	2 cut(s)	312, 409
AcuI	CTGAAG	1 cut(s)	159
AcyI	GRCGYC	1 cut(s)	198
AfaI	GTAC	2 cut(s)	569, 1258
AfeI	AGCGCT	1 cut(s)	183
AfiI	CCNNNNNNNGG	2 cut(s)	492, 616
AgsI	TTSAA	7 cut(s)	697, 791, 862, 997, 1021, 1032, 1288
AluBI	AGCT	7 cut(s)	29, 125, 190, 271, 453, 686, 1006
AluI	AGCT	7 cut(s)	29, 125, 190, 271, 453, 686, 1006
Alw21I	GWGCWC	2 cut(s)	192, 511
Alw26I	GTCTC	1 cut(s)	288
AlwI	GGATC	1 cut(s)	1076
AlwNI	CAGNNNCTG	2 cut(s)	659, 1188
Ama87I	CYCGRG	1 cut(s)	185
Aor13HI	TCCGGA	1 cut(s)	250
Aor51HI	AGCGCT	1 cut(s)	183
AoxI	GGCC	1 cut(s)	9
ApeKI	GCWGC	6 cut(s)	29, 122, 147, 179, 653, 1003
ApoI	RAATTY	2 cut(s)	312, 409
AspLEI	GCGC	2 cut(s)	184, 750
AsuHPI	GGTGA	1 cut(s)	1075
AvaI	CYCGRG	1 cut(s)	185
BanI	GGYRCC	2 cut(s)	162, 495
BanII	GRGCYC	1 cut(s)	192
Bbv12I	GWGCWC	2 cut(s)	192, 511
BbvCI	CCTCAGC	2 cut(s)	687, 1134
BbvI	GCAGC	6 cut(s)	16, 134, 159, 191, 665, 1015
BccI	CCATC	3 cut(s)	610, 618, 790
BceAI	ACGGC	1 cut(s)	24
BciVI	GTATCC	2 cut(s)	247, 1047
BclI	TGATCA	1 cut(s)	436
BcoDI	GTCTC	1 cut(s)	288
BfaI	CTAG	1 cut(s)	210
BfoI	RGCGCY	1 cut(s)	185
BfuI	GTATCC	2 cut(s)	247, 1047
BglII	AGATCT	1 cut(s)	1126
BisI	GCNGC	8 cut(s)	30, 123, 148, 180, 196, 654, 917, 1004
BlsI	GCNGC	8 cut(s)	31, 124, 149, 181, 197, 655, 918, 1005
BmeT110I	CYCGRG	1 cut(s)	185
BmiI	GGNNCC	2 cut(s)	164, 497
BmrI	ACTGGG	1 cut(s)	161
BmsI	GCATC	3 cut(s)	658, 665, 735
BmuI	ACTGGG	1 cut(s)	161
BpmI	CTGGAG	3 cut(s)	579, 624, 1143
Bpu10I	CCTNAGC	2 cut(s)	687, 1134
BpuEI	CTTGAG	3 cut(s)	302, 728, 815
BsaHI	GRCGYC	1 cut(s)	198
BsaI	GGTCTC	1 cut(s)	288
BsaWI	WCCGGW	1 cut(s)	250
Bsc4I	CCNNNNNNNGG	2 cut(s)	492, 616
Bse1I	ACTGG	3 cut(s)	167, 562, 1182
Bse3DI	GCAATG	1 cut(s)	930
BseAI	TCCGGA	1 cut(s)	250
BseGI	GGATG	2 cut(s)	235, 939
BseLI	CCNNNNNNNGG	2 cut(s)	492, 616
BseMI	GCAATG	1 cut(s)	930
BseMII	CTCAG	4 cut(s)	88, 678, 1001, 1125
BseNI	ACTGG	3 cut(s)	167, 562, 1182
BseRI	GAGGAG	1 cut(s)	1151
BseXI	GCAGC	6 cut(s)	16, 134, 159, 191, 665, 1015
BseYI	CCCAGC	2 cut(s)	750, 1006
BshFI	GGCC	1 cut(s)	11
BshNI	GGYRCC	2 cut(s)	162, 495
BsiHKAI	GWGCWC	2 cut(s)	192, 511
BsiHKCI	CYCGRG	1 cut(s)	185
BsiSI	CCGG	1 cut(s)	251
BslFI	GGGAC	1 cut(s)	676
BslI	CCNNNNNNNGG	2 cut(s)	492, 616
BsmAI	GTCTC	1 cut(s)	288
BsmFI	GGGAC	1 cut(s)	676
BsmI	GAATGC	2 cut(s)	282, 328
BsnI	GGCC	1 cut(s)	11
Bso31I	GGTCTC	1 cut(s)	288
BsoBI	CYCGRG	1 cut(s)	185
Bsp1286I	GDGCHC	2 cut(s)	192, 511
Bsp13I	TCCGGA	1 cut(s)	250
Bsp143I	GATC	5 cut(s)	379, 436, 1068, 1126, 1220
BspACI	CCGC	4 cut(s)	120, 195, 837, 916
BspANI	GGCC	1 cut(s)	11
BspCNI	CTCAG	4 cut(s)	87, 679, 1000, 1126
BspEI	TCCGGA	1 cut(s)	250
BspLI	GGNNCC	2 cut(s)	164, 497
BspPI	GGATC	1 cut(s)	1076
BspT107I	GGYRCC	2 cut(s)	162, 495
BspTNI	GGTCTC	1 cut(s)	288
BsrBI	CCGCTC	1 cut(s)	916
BsrDI	GCAATG	1 cut(s)	930
BsrI	ACTGG	3 cut(s)	167, 562, 1182
BssMI	GATC	5 cut(s)	379, 436, 1068, 1126, 1220
BssNI	GRCGYC	1 cut(s)	198
Bst4CI	ACNGT	4 cut(s)	487, 572, 1190, 1261
Bst6I	CTCTTC	6 cut(s)	41, 63, 109, 286, 526, 857
BstACI	GRCGYC	1 cut(s)	198
BstAPI	GCANNNNNTGC	1 cut(s)	128
BstC8I	GCNNGC	3 cut(s)	626, 721, 921
BstDEI	CTNAG	4 cut(s)	74, 687, 987, 1134
BstF5I	GGATG	2 cut(s)	235, 939
BstH2I	RGCGCY	1 cut(s)	185
BstHHI	GCGC	2 cut(s)	184, 750
BstKTI	GATC	5 cut(s)	382, 439, 1071, 1129, 1223
BstMAI	GTCTC	1 cut(s)	288
BstMBI	GATC	5 cut(s)	379, 436, 1068, 1126, 1220
BstMWI	GCNNNNNNNGC	4 cut(s)	29, 128, 277, 515
BstV1I	GCAGC	6 cut(s)	16, 134, 159, 191, 665, 1015
BstX2I	RGATCY	1 cut(s)	1126
BstXI	CCANNNNNNTGG	2 cut(s)	648, 731
BstYI	RGATCY	1 cut(s)	1126
BsuI	GTATCC	2 cut(s)	247, 1047
BsuRI	GGCC	1 cut(s)	11
BtsCI	GGATG	2 cut(s)	235, 939
BtsIMutI	CAGTG	2 cut(s)	1078, 1186
Cac8I	GCNNGC	3 cut(s)	626, 721, 921
CaiI	CAGNNNCTG	2 cut(s)	659, 1188
CfoI	GCGC	2 cut(s)	184, 750
CseI	GACGC	1 cut(s)	187
Csp6I	GTAC	2 cut(s)	568, 1257
CviAII	CATG	1 cut(s)	440
CviQI	GTAC	2 cut(s)	568, 1257
DdeI	CTNAG	4 cut(s)	74, 687, 987, 1134
DpnI	GATC	5 cut(s)	381, 438, 1070, 1128, 1222
DpnII	GATC	5 cut(s)	379, 436, 1068, 1126, 1220
DrdI	GACNNNNNNGTC	1 cut(s)	1238
DseDI	GACNNNNNNGTC	1 cut(s)	1238
Eam1104I	CTCTTC	6 cut(s)	41, 63, 109, 286, 526, 857
EarI	CTCTTC	6 cut(s)	41, 63, 109, 286, 526, 857
Ecl136II	GAGCTC	1 cut(s)	190
Eco24I	GRGCYC	1 cut(s)	192
Eco31I	GGTCTC	1 cut(s)	288
Eco47III	AGCGCT	1 cut(s)	183
Eco53kI	GAGCTC	1 cut(s)	190
Eco57I	CTGAAG	1 cut(s)	159
Eco88I	CYCGRG	1 cut(s)	185
EcoICRI	GAGCTC	1 cut(s)	190
EcoRI	GAATTC	1 cut(s)	312
EcoT38I	GRGCYC	1 cut(s)	192
FaeI	CATG	1 cut(s)	443
FalI	AAGNNNNNCTT	1 cut(s)	1280
FaqI	GGGAC	1 cut(s)	676
FatI	CATG	1 cut(s)	439
FbaI	TGATCA	1 cut(s)	436
Fnu4HI	GCNGC	8 cut(s)	30, 123, 148, 180, 196, 654, 917, 1004
FokI	GGATG	2 cut(s)	242, 926
FriOI	GRGCYC	1 cut(s)	192
Fsp4HI	GCNGC	8 cut(s)	30, 123, 148, 180, 196, 654, 917, 1004
FspBI	CTAG	1 cut(s)	210
GlaI	GCGC	2 cut(s)	183, 749
GluI	GCNGC	8 cut(s)	30, 123, 148, 180, 196, 654, 917, 1004
GsaI	CCCAGC	2 cut(s)	754, 1010
GsuI	CTGGAG	3 cut(s)	579, 624, 1143
HaeII	RGCGCY	1 cut(s)	185
HaeIII	GGCC	1 cut(s)	11
HapII	CCGG	1 cut(s)	251
HgaI	GACGC	1 cut(s)	187
HhaI	GCGC	2 cut(s)	184, 750
Hin1I	GRCGYC	1 cut(s)	198
Hin1II	CATG	1 cut(s)	443
Hin6I	GCGC	2 cut(s)	182, 748
HinP1I	GCGC	2 cut(s)	182, 748
HincII	GTYRAC	1 cut(s)	966
HindII	GTYRAC	1 cut(s)	966
HinfI	GANTC	5 cut(s)	476, 578, 587, 1011, 1076
HpaII	CCGG	1 cut(s)	251
HphI	GGTGA	1 cut(s)	1075
Hpy166II	GTNNAC	4 cut(s)	475, 568, 966, 981
Hpy188I	TCNGA	5 cut(s)	77, 136, 275, 615, 902
Hpy188III	TCNNGA	7 cut(s)	202, 251, 319, 641, 707, 809, 1297
Hpy8I	GTNNAC	4 cut(s)	475, 568, 966, 981
HpyAV	CCTTC	6 cut(s)	22, 97, 109, 614, 991, 1282
HpyCH4III	ACNGT	4 cut(s)	487, 572, 1190, 1261
HpyCH4V	TGCA	6 cut(s)	266, 280, 286, 671, 1144, 1252
HpyF10VI	GCNNNNNNNGC	4 cut(s)	29, 128, 277, 515
HpyF3I	CTNAG	4 cut(s)	74, 687, 987, 1134
Hsp92I	GRCGYC	1 cut(s)	198
Hsp92II	CATG	1 cut(s)	443
HspAI	GCGC	2 cut(s)	182, 748
Kpn2I	TCCGGA	1 cut(s)	250
Ksp22I	TGATCA	1 cut(s)	436
Kzo9I	GATC	5 cut(s)	379, 436, 1068, 1126, 1220
LmnI	GCTCC	2 cut(s)	913, 1216
Lsp1109I	GCAGC	6 cut(s)	16, 134, 159, 191, 665, 1015
LweI	GCATC	3 cut(s)	658, 665, 735
MaeI	CTAG	1 cut(s)	210
MaeIII	GTNAC	6 cut(s)	169, 553, 841, 1046, 1184, 1190
MalI	GATC	5 cut(s)	381, 438, 1070, 1128, 1222
MbiI	CCGCTC	1 cut(s)	916
MboI	GATC	5 cut(s)	379, 436, 1068, 1126, 1220
MfeI	CAATTG	1 cut(s)	1145
MflI	RGATCY	1 cut(s)	1126
MhlI	GDGCHC	2 cut(s)	192, 511
MluCI	AATT	7 cut(s)	312, 349, 409, 1093, 1145, 1156, 1247
MlyI	GAGTC	3 cut(s)	470, 581, 1020
MmeI	TCCRAC	1 cut(s)	801
MroI	TCCGGA	1 cut(s)	250
MseI	TTAA	2 cut(s)	83, 402
MslI	CAYNNNNRTG	1 cut(s)	504
MspA1I	CMGCKG	1 cut(s)	1006
MspI	CCGG	1 cut(s)	251
MunI	CAATTG	1 cut(s)	1145
Mva1269I	GAATGC	2 cut(s)	282, 328
MwoI	GCNNNNNNNGC	4 cut(s)	29, 128, 277, 515
NdeII	GATC	5 cut(s)	379, 436, 1068, 1126, 1220
NlaIII	CATG	1 cut(s)	443
NlaIV	GGNNCC	2 cut(s)	164, 497
NmeAIII	GCCGAG	1 cut(s)	171
NmuCI	GTSAC	1 cut(s)	1184
PaeR7I	CTCGAG	1 cut(s)	185
PcsI	WCGNNNNNNNCGW	1 cut(s)	339
PctI	GAATGC	2 cut(s)	282, 328
PfeI	GAWTC	2 cut(s)	578, 1076
PflMI	CCANNNNNTGG	1 cut(s)	616
PkrI	GCNGC	8 cut(s)	31, 124, 149, 181, 197, 655, 918, 1005
PleI	GAGTC	3 cut(s)	470, 581, 1019
PpsI	GAGTC	3 cut(s)	470, 581, 1019
Psp124BI	GAGCTC	1 cut(s)	192
PspFI	CCCAGC	2 cut(s)	750, 1006
PspN4I	GGNNCC	2 cut(s)	164, 497
PspXI	VCTCGAGB	1 cut(s)	185
PstNI	CAGNNNCTG	2 cut(s)	659, 1188
PsuI	RGATCY	1 cut(s)	1126
PvuII	CAGCTG	1 cut(s)	1006
RsaI	GTAC	2 cut(s)	569, 1258
RsaNI	GTAC	2 cut(s)	568, 1257
RseI	CAYNNNNRTG	1 cut(s)	504
SacI	GAGCTC	1 cut(s)	192
SaqAI	TTAA	2 cut(s)	83, 402
SatI	GCNGC	8 cut(s)	30, 123, 148, 180, 196, 654, 917, 1004
Sau3AI	GATC	5 cut(s)	379, 436, 1068, 1126, 1220
SchI	GAGTC	3 cut(s)	470, 581, 1020
SduI	GDGCHC	2 cut(s)	192, 511
SfaNI	GCATC	3 cut(s)	658, 665, 735
Sfr274I	CTCGAG	1 cut(s)	185
SlaI	CTCGAG	1 cut(s)	185
SmiMI	CAYNNNNRTG	1 cut(s)	504
SmlI	CTYRAG	5 cut(s)	185, 317, 707, 794, 1297
SmoI	CTYRAG	5 cut(s)	185, 317, 707, 794, 1297
Sse9I	AATT	7 cut(s)	312, 349, 409, 1093, 1145, 1156, 1247
SsiI	CCGC	4 cut(s)	120, 195, 837, 916
SspI	AATATT	2 cut(s)	858, 886
SspMI	CTAG	1 cut(s)	210
SstI	GAGCTC	1 cut(s)	192
TaaI	ACNGT	4 cut(s)	487, 572, 1190, 1261
TaqI	TCGA	5 cut(s)	186, 342, 356, 375, 448
TasI	AATT	7 cut(s)	312, 349, 409, 1093, 1145, 1156, 1247
TauI	GCSGC	2 cut(s)	198, 919
TfiI	GAWTC	2 cut(s)	578, 1076
Tru1I	TTAA	2 cut(s)	83, 402
Tru9I	TTAA	2 cut(s)	83, 402
TscAI	CASTG	2 cut(s)	1078, 1193
TseFI	GTSAC	1 cut(s)	1184
TseI	GCWGC	6 cut(s)	29, 122, 147, 179, 653, 1003
Tsp45I	GTSAC	1 cut(s)	1184
TspGWI	ACGGA	1 cut(s)	1032
TspRI	CASTG	2 cut(s)	1078, 1193
Van91I	CCANNNNNTGG	1 cut(s)	616
XapI	RAATTY	2 cut(s)	312, 409
XcmI	CCANNNNNNNNNTGG	1 cut(s)	305
XhoI	CTCGAG	1 cut(s)	185
XspI	CTAG	1 cut(s)	210

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