Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0011572

Physical Location & Seq

Genomic Coordinates Forward (+)

3446237 .. 3451414

Gene Structure 5178 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG049400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1491 bp

ATGACTCTCAGCAGTATTCCGTTGGCTACGTCGGATCTTCAAATCGGTCATGGAGCTCGAAGAAATTCGACACTAATCTGTGCGCCGGTAATGGGGGAATCAGTTGATCAGATGCTGCGTCAAGTGCGACAGGCAAAGGAACTTGGTGCTGACCTTGTTGAGATTCGGTTGGACTACATTAAGAACTTCAGTCCAAGACAAGATCTCGAAACTTTGATTAAGCGCAGCCCTTTGCCAACACTCGTCACTTACAGGCCAAAATGGGAAGGTGGTGAGTATGAAGGAGATGAAAATAAGCGACAAGAGGCACTCATTTTAGCCATGGAATTGGGAGCGGATTATATTGATGTTGAACTAAAGGTAGCAAATGACTTCTACAGTTCTATTCAAGGGAAGAAGCCAGAAAAGGTCAAAATCATAGTTTCTTCCCACAACTATGAGAATACTCCATCTGCTGAGGAAATTGGCAATCTTGTTGCAACGATACAAGCCATTGGAGCTGACATAGTCAAGGTCGCAACAACTGCCTTGGACATAACAGACAATGCAAGAATATTTCAAGTGCTAGCGCGTTCTCAAGTCCCAATGATAGGACTTTTGATGGGTGAGAAGGGTTTGATCTCTCGTGTACTTAGTGCAAAATATGGGTCATATGTCACATTTGGTACACTAGAGGCAGGTGAGGTATCAGCTCCTGGCCAGCCAACTGTAACGGATCTGTTGGAGTTATACAATTTTAGGCAGATTGGAGCCGATACCAAAGTACATGGTGTGATAGGAAATCCTATTGGTCACAGCAAAAGTCCTCATCTTTACAATGCAGCATTTAAAGCCAATAACTTCAATGGAATTTATCTGCCATTGCTGGTTGATAGCGTTGCAAACTTTATCAACACCTATAACTCCCCTGATTGGGTTGGATACAGTTACACAATTCCTCACAAAGAAGCTGGATTCAAATGTTGTGATGAGATCGATCCTAATGCCCTGGCAATAGGAGCTATTAGTTGCATGATCAGGAACCCAACTGATGGGAAGTTAAAGGGCTATAATGTTGACTATCTTGGAGCAATTGCAGCTATTGAGGAAGGACTTCGAGGATTAGGATTGAACGGTTCAAGTAATGGATCTGGTTCCCCATTAGCTGGTAGGTTATTTGTGGTCATGGGAGCTGGTGGTGCTGGAAAGGCACTTGCATATGGTGGAAAACAAAAGGGAGCAAGAGTTGTCGTTGCCAATCGCTCATTTGACAAAGCCAAGATACTGGCCGACAAAGTTGGAGGAGAAGCTATTACTCTTGCTGAGTTGGCAAACTTCCATCCAGAGGATGGTATGGTTCTTGCAAATACCACATCTGTTGGAATGAAACCAAGAACTGATCAAACACCCATCCCAAAGGTTTGTCCACCGTCACATTCTATAGTTATTTGTGCAGTTGTCAATTTGATGAAAGATCAAGTTTCTAGAATTTTATCTATATGCTGCAATTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0003006 GO:0003674 GO:0003824 GO:0004764 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0006082 GO:0007275 GO:0008150 GO:0008152 GO:0009058 GO:0009423 GO:0009507 GO:0009532 GO:0009536 GO:0009570 GO:0009790 GO:0009791 GO:0009793 GO:0009987 GO:0010154 GO:0016053 GO:0016491 GO:0016614 GO:0016616 GO:0019632 GO:0019752 GO:0022414 GO:0032501 GO:0032502 GO:0032787 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043436 GO:0043648 GO:0043650 GO:0044237 GO:0044249 GO:0044281 GO:0044283 GO:0044422 GO:0044424 GO:0044434 GO:0044435 GO:0044444 GO:0044446 GO:0044464 GO:0046394 GO:0046417 GO:0048316 GO:0048608 GO:0048731 GO:0048856 GO:0055114 GO:0061458 GO:0071704 GO:1901576 GO:1901615

KEGG Pathways

Metabolic & Signaling

ko00400 ko01100 ko01110 ko01130 ko01230 map00400 map01100 map01110 map01130 map01230

Pfam Domains

Protein Families

DHquinase_I Shikimate_DH Shikimate_dh_N

Protein Analysis

496

Amino Acids

53.23

Weight (kDa)

6.48

Isoelectric Point (pI)

25.19

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DHquinase_I	PF01487	27 - 244	5.4e-70	Type I 3-dehydroquinase
Shikimate_dh_N	PF08501	258 - 336	9.5e-21	Shikimate dehydrogenase substrate binding domain
Shikimate_DH	PF01488	383 - 450	5.4e-06	Shikimate / quinate 5-dehydrogenase

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: OG0011572)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_6g04670 FvH4_6g04670 FvH4_6g04670
malus_domestica	MD04G1213800.v1.1 MD12G1228800.v1.1
prunus_persica	Prupe.6G334000_v2.0.a1 Prupe.6G334000_v2.0.a1
pyrus_communis	pycom04g18930 pycom12g21340
rosa_chinensis	RchiOBHm_Chr3g0453141
rosa_laevigata	RLG00000025534
rosa_multiflora	Rmu_sc0007132.1_g000006 Rmu_sc0013481.1_g000002
rosa_roxburghii	Rroxscaffold_6G00430200
rosa_rugosa	Rorug02G0646800
rosa_samantha	Rh3AG049400 Rh3BG050600 Rh3CG050800 Rh3DG051400
rosa_wichuraiana	Rw3G003790

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	668
Acc36I	ACCTGC	1 cut(s)	668
AccB7I	CCANNNNNTGG	3 cut(s)	1031, 1145, 1328
AccBSI	CCGCTC	1 cut(s)	335
AccII	CGCG	1 cut(s)	571
AciI	CCGC	1 cut(s)	335
AclWI	GGATC	4 cut(s)	42, 723, 971, 1135
AcoI	YGGCCR	2 cut(s)	697, 1266
AcsI	RAATTY	3 cut(s)	64, 849, 1467
AcuI	CTGAAG	1 cut(s)	172
AfaI	GTAC	3 cut(s)	630, 667, 765
AfiI	CCNNNNNNNGG	8 cut(s)	92, 590, 912, 913, 1031, 1145, 1324, 1328
AgsI	TTSAA	8 cut(s)	41, 353, 389, 560, 844, 958, 1111, 1119
AjnI	CCWGG	2 cut(s)	694, 987
AluBI	AGCT	9 cut(s)	56, 500, 692, 950, 1001, 1079, 1145, 1172, 1289
AluI	AGCT	9 cut(s)	56, 500, 692, 950, 1001, 1079, 1145, 1172, 1289
Alw21I	GWGCWC	1 cut(s)	58
AlwI	GGATC	4 cut(s)	42, 723, 971, 1135
AlwNI	CAGNNNCTG	2 cut(s)	115, 695
AoxI	GGCC	3 cut(s)	254, 697, 1266
ApeKI	GCWGC	5 cut(s)	115, 225, 821, 1076, 1482
ApoI	RAATTY	3 cut(s)	64, 849, 1467
ArsI	GACNNNNNNTTYG	2 cut(s)	632, 664
Asp700I	GAANNNNTTC	2 cut(s)	64, 1092
AspLEI	GCGC	3 cut(s)	85, 225, 571
AsuHPI	GGTGA	3 cut(s)	284, 617, 692
AsuNHI	GCTAGC	1 cut(s)	565
BaeI	ACNNNNGTAYC	2 cut(s)	747, 780
BalI	TGGCCA	1 cut(s)	699
BanII	GRGCYC	1 cut(s)	58
BauI	CACGAG	1 cut(s)	624
Bbv12I	GWGCWC	1 cut(s)	58
BbvCI	CCTCAGC	1 cut(s)	456
BbvI	GCAGC	5 cut(s)	102, 237, 833, 1088, 1469
BccI	CCATC	6 cut(s)	457, 595, 1025, 1322, 1326, 1397
BcgI	CGANNNNNNTGC	2 cut(s)	965, 999
BciT130I	CCWGG	2 cut(s)	696, 989
BciVI	GTATCC	1 cut(s)	914
BclI	TGATCA	3 cut(s)	106, 1014, 1378
BfaI	CTAG	3 cut(s)	566, 671, 1464
BfmI	CTRYAG	2 cut(s)	376, 1419
BfuAI	ACCTGC	1 cut(s)	668
BfuI	GTATCC	1 cut(s)	914
BglII	AGATCT	1 cut(s)	202
BisI	GCNGC	5 cut(s)	116, 226, 822, 1077, 1483
BlsI	GCNGC	5 cut(s)	117, 227, 823, 1078, 1484
Bme1390I	CCNGG	2 cut(s)	696, 989
BmiI	GGNNCC	3 cut(s)	751, 1022, 1135
BmrFI	CCNGG	2 cut(s)	696, 989
BmsI	GCATC	1 cut(s)	102
BmtI	GCTAGC	1 cut(s)	569
Bpu10I	CCTNAGC	1 cut(s)	456
BpuEI	CTTGAG	1 cut(s)	561
Bsa29I	ATCGAT	1 cut(s)	975
BsaJI	CCNNGG	3 cut(s)	321, 528, 987
BsaXI	ACNNNNNCTCC	2 cut(s)	1209, 1239
Bsc4I	CCNNNNNNNGG	8 cut(s)	92, 590, 912, 913, 1031, 1145, 1324, 1328
Bse118I	RCCGGY	1 cut(s)	85
Bse1I	ACTGG	1 cut(s)	1269
Bse3DI	GCAATG	1 cut(s)	860
BseBI	CCWGG	2 cut(s)	696, 989
BseCI	ATCGAT	1 cut(s)	975
BseDI	CCNNGG	3 cut(s)	321, 528, 987
BseGI	GGATG	3 cut(s)	1318, 1333, 1389
BseLI	CCNNNNNNNGG	8 cut(s)	92, 590, 912, 913, 1031, 1145, 1324, 1328
BseMI	GCAATG	1 cut(s)	860
BseMII	CTCAG	3 cut(s)	22, 447, 1293
BseNI	ACTGG	1 cut(s)	1269
BseRI	GAGGAG	1 cut(s)	1296
BseXI	GCAGC	5 cut(s)	102, 237, 833, 1088, 1469
BsgI	GTGCAG	1 cut(s)	1452
Bsh1236I	CGCG	1 cut(s)	571
BshFI	GGCC	3 cut(s)	256, 699, 1268
BshVI	ATCGAT	1 cut(s)	975
BsiHKAI	GWGCWC	1 cut(s)	58
BsiSI	CCGG	1 cut(s)	86
BslFI	GGGAC	1 cut(s)	566
BslI	CCNNNNNNNGG	8 cut(s)	92, 590, 912, 913, 1031, 1145, 1324, 1328
BsmFI	GGGAC	1 cut(s)	566
BsnI	GGCC	3 cut(s)	256, 699, 1268
Bsp1286I	GDGCHC	1 cut(s)	58
Bsp19I	CCATGG	1 cut(s)	321
BspACI	CCGC	1 cut(s)	335
BspANI	GGCC	3 cut(s)	256, 699, 1268
BspCNI	CTCAG	3 cut(s)	21, 448, 1294
BspDI	ATCGAT	1 cut(s)	975
BspFNI	CGCG	1 cut(s)	571
BspLI	GGNNCC	3 cut(s)	751, 1022, 1135
BspMI	ACCTGC	1 cut(s)	668
BspOI	GCTAGC	1 cut(s)	569
BspPI	GGATC	4 cut(s)	42, 723, 971, 1135
BsrBI	CCGCTC	1 cut(s)	335
BsrDI	GCAATG	1 cut(s)	860
BsrFI	RCCGGY	1 cut(s)	85
BsrI	ACTGG	1 cut(s)	1269
BssAI	RCCGGY	1 cut(s)	85
BssECI	CCNNGG	3 cut(s)	321, 528, 987
BssSI	CACGAG	1 cut(s)	624
BssT1I	CCWWGG	2 cut(s)	321, 528
Bst2BI	CACGAG	1 cut(s)	624
Bst2UI	CCWGG	2 cut(s)	696, 989
Bst4CI	ACNGT	5 cut(s)	380, 709, 926, 1115, 1410
BstAPI	GCANNNNNTGC	1 cut(s)	524
BstC8I	GCNNGC	2 cut(s)	567, 701
BstDEI	CTNAG	4 cut(s)	8, 456, 632, 1302
BstDSI	CCRYGG	1 cut(s)	321
BstF5I	GGATG	3 cut(s)	1318, 1333, 1389
BstFNI	CGCG	1 cut(s)	571
BstHHI	GCGC	3 cut(s)	85, 225, 571
BstMWI	GCNNNNNNNGC	9 cut(s)	124, 497, 524, 830, 998, 1076, 1178, 1187, 1307
BstNI	CCWGG	2 cut(s)	696, 989
BstSCI	CCNGG	2 cut(s)	694, 987
BstSFI	CTRYAG	2 cut(s)	376, 1419
BstUI	CGCG	1 cut(s)	571
BstV1I	GCAGC	5 cut(s)	102, 237, 833, 1088, 1469
BstX2I	RGATCY	4 cut(s)	34, 202, 715, 1127
BstXI	CCANNNNNNTGG	2 cut(s)	328, 1264
BstYI	RGATCY	4 cut(s)	34, 202, 715, 1127
Bsu15I	ATCGAT	1 cut(s)	975
BsuI	GTATCC	1 cut(s)	914
BsuRI	GGCC	3 cut(s)	256, 699, 1268
BsuTUI	ATCGAT	1 cut(s)	975
BtgI	CCRYGG	1 cut(s)	321
BtsCI	GGATG	3 cut(s)	1318, 1333, 1389
BveI	ACCTGC	1 cut(s)	668
Cac8I	GCNNGC	2 cut(s)	567, 701
CaiI	CAGNNNCTG	2 cut(s)	115, 695
CfoI	GCGC	3 cut(s)	85, 225, 571
Cfr10I	RCCGGY	1 cut(s)	85
ClaI	ATCGAT	1 cut(s)	975
CseI	GACGC	1 cut(s)	107
Csp6I	GTAC	3 cut(s)	629, 666, 764
CspCI	CAANNNNNGTGG	2 cut(s)	1339, 1374
CviAII	CATG	5 cut(s)	50, 322, 767, 1012, 1165
CviQI	GTAC	3 cut(s)	629, 666, 764
DdeI	CTNAG	4 cut(s)	8, 456, 632, 1302
DraI	TTTAAA	1 cut(s)	829
EaeI	YGGCCR	2 cut(s)	697, 1266
Ecl136II	GAGCTC	1 cut(s)	56
Eco130I	CCWWGG	2 cut(s)	321, 528
Eco24I	GRGCYC	1 cut(s)	58
Eco53kI	GAGCTC	1 cut(s)	56
Eco57I	CTGAAG	1 cut(s)	172
EcoICRI	GAGCTC	1 cut(s)	56
EcoRII	CCWGG	2 cut(s)	694, 987
EcoT14I	CCWWGG	2 cut(s)	321, 528
EcoT38I	GRGCYC	1 cut(s)	58
ErhI	CCWWGG	2 cut(s)	321, 528
FaeI	CATG	5 cut(s)	53, 325, 770, 1015, 1168
FaqI	GGGAC	1 cut(s)	566
FatI	CATG	5 cut(s)	49, 321, 766, 1011, 1164
FauNDI	CATATG	2 cut(s)	652, 1198
FbaI	TGATCA	3 cut(s)	106, 1014, 1378
Fnu4HI	GCNGC	5 cut(s)	116, 226, 822, 1077, 1483
FokI	GGATG	3 cut(s)	1305, 1340, 1376
FriOI	GRGCYC	1 cut(s)	58
Fsp4HI	GCNGC	5 cut(s)	116, 226, 822, 1077, 1483
FspBI	CTAG	3 cut(s)	566, 671, 1464
GlaI	GCGC	3 cut(s)	84, 224, 570
GluI	GCNGC	5 cut(s)	116, 226, 822, 1077, 1483
HaeIII	GGCC	3 cut(s)	256, 699, 1268
HapII	CCGG	1 cut(s)	86
HgaI	GACGC	1 cut(s)	107
HhaI	GCGC	3 cut(s)	85, 225, 571
Hin1II	CATG	5 cut(s)	53, 325, 770, 1015, 1168
Hin6I	GCGC	3 cut(s)	83, 223, 569
HinP1I	GCGC	3 cut(s)	83, 223, 569
HincII	GTYRAC	1 cut(s)	1057
HindII	GTYRAC	1 cut(s)	1057
HinfI	GANTC	4 cut(s)	4, 98, 163, 954
HpaII	CCGG	1 cut(s)	86
HphI	GGTGA	3 cut(s)	284, 617, 692
Hpy166II	GTNNAC	4 cut(s)	629, 668, 1057, 1406
Hpy188I	TCNGA	2 cut(s)	34, 111
Hpy188III	TCNNGA	4 cut(s)	206, 1018, 1322, 1464
Hpy8I	GTNNAC	4 cut(s)	629, 668, 1057, 1406
Hpy99I	CGWCG	1 cut(s)	34
HpyAV	CCTTC	4 cut(s)	260, 275, 604, 1082
HpyCH4III	ACNGT	5 cut(s)	380, 709, 926, 1115, 1410
HpyCH4IV	ACGT	1 cut(s)	29
HpyF10VI	GCNNNNNNNGC	9 cut(s)	124, 497, 524, 830, 998, 1076, 1178, 1187, 1307
HpyF3I	CTNAG	4 cut(s)	8, 456, 632, 1302
HpySE526I	ACGT	1 cut(s)	29
Hsp92II	CATG	5 cut(s)	53, 325, 770, 1015, 1168
HspAI	GCGC	3 cut(s)	83, 223, 569
Ksp22I	TGATCA	3 cut(s)	106, 1014, 1378
LmnI	GCTCC	9 cut(s)	53, 332, 497, 697, 749, 998, 1067, 1169, 1217
Lsp1109I	GCAGC	5 cut(s)	102, 237, 833, 1088, 1469
LweI	GCATC	1 cut(s)	102
MaeI	CTAG	3 cut(s)	566, 671, 1464
MaeII	ACGT	1 cut(s)	29
MaeIII	GTNAC	6 cut(s)	244, 655, 709, 791, 926, 1410
MbiI	CCGCTC	1 cut(s)	335
MboII	GAAGA	4 cut(s)	29, 72, 406, 417
MfeI	CAATTG	1 cut(s)	1071
MflI	RGATCY	4 cut(s)	34, 202, 715, 1127
MhlI	GDGCHC	1 cut(s)	58
MlsI	TGGCCA	1 cut(s)	699
MluNI	TGGCCA	1 cut(s)	699
MmeI	TCCRAC	6 cut(s)	12, 150, 702, 898, 1258, 1339
Mox20I	TGGCCA	1 cut(s)	699
MroXI	GAANNNNTTC	2 cut(s)	64, 1092
MscI	TGGCCA	1 cut(s)	699
MseI	TTAA	5 cut(s)	180, 219, 828, 1040, 1489
MslI	CAYNNNNRTG	1 cut(s)	435
Msp20I	TGGCCA	1 cut(s)	699
MspI	CCGG	1 cut(s)	86
MspR9I	CCNGG	2 cut(s)	696, 989
MunI	CAATTG	1 cut(s)	1071
MvaI	CCWGG	2 cut(s)	696, 989
MvnI	CGCG	1 cut(s)	571
MwoI	GCNNNNNNNGC	9 cut(s)	124, 497, 524, 830, 998, 1076, 1178, 1187, 1307
NcoI	CCATGG	1 cut(s)	321
NdeI	CATATG	2 cut(s)	652, 1198
NheI	GCTAGC	1 cut(s)	565
NlaIII	CATG	5 cut(s)	53, 325, 770, 1015, 1168
NlaIV	GGNNCC	3 cut(s)	751, 1022, 1135
NmuCI	GTSAC	4 cut(s)	244, 655, 791, 1410
PaqCI	CACCTGC	1 cut(s)	668
PdmI	GAANNNNTTC	2 cut(s)	64, 1092
PfeI	GAWTC	3 cut(s)	98, 163, 954
PflFI	GACNNNGTC	1 cut(s)	506
PflMI	CCANNNNNTGG	3 cut(s)	1031, 1145, 1328
PkrI	GCNGC	5 cut(s)	117, 227, 823, 1078, 1484
Psp124BI	GAGCTC	1 cut(s)	58
Psp6I	CCWGG	2 cut(s)	694, 987
PspGI	CCWGG	2 cut(s)	694, 987
PspN4I	GGNNCC	3 cut(s)	751, 1022, 1135
PstNI	CAGNNNCTG	2 cut(s)	115, 695
PsuI	RGATCY	4 cut(s)	34, 202, 715, 1127
PsyI	GACNNNGTC	1 cut(s)	506
RsaI	GTAC	3 cut(s)	630, 667, 765
RsaNI	GTAC	3 cut(s)	629, 666, 764
RseI	CAYNNNNRTG	1 cut(s)	435
SacI	GAGCTC	1 cut(s)	58
SaqAI	TTAA	5 cut(s)	180, 219, 828, 1040, 1489
SatI	GCNGC	5 cut(s)	116, 226, 822, 1077, 1483
ScrFI	CCNGG	2 cut(s)	696, 989
SduI	GDGCHC	1 cut(s)	58
SfaNI	GCATC	1 cut(s)	102
SfcI	CTRYAG	2 cut(s)	376, 1419
SmiMI	CAYNNNNRTG	1 cut(s)	435
SmlI	CTYRAG	1 cut(s)	576
SmoI	CTYRAG	1 cut(s)	576
SsiI	CCGC	1 cut(s)	335
SspI	AATATT	1 cut(s)	555
SspMI	CTAG	3 cut(s)	566, 671, 1464
SstI	GAGCTC	1 cut(s)	58
StyD4I	CCNGG	2 cut(s)	694, 987
StyI	CCWWGG	2 cut(s)	321, 528
TaaI	ACNGT	5 cut(s)	380, 709, 926, 1115, 1410
TaiI	ACGT	1 cut(s)	32
TaqI	TCGA	5 cut(s)	58, 68, 207, 975, 1096
TaqII	GACCGA	1 cut(s)	35
TatI	WGTACW	2 cut(s)	628, 763
TfiI	GAWTC	3 cut(s)	98, 163, 954
Tru1I	TTAA	5 cut(s)	180, 219, 828, 1040, 1489
Tru9I	TTAA	5 cut(s)	180, 219, 828, 1040, 1489
TseFI	GTSAC	4 cut(s)	244, 655, 791, 1410
TseI	GCWGC	5 cut(s)	115, 225, 821, 1076, 1482
Tsp45I	GTSAC	4 cut(s)	244, 655, 791, 1410
TspDTI	ATGAA	4 cut(s)	294, 303, 1379, 1463
TspGWI	ACGGA	2 cut(s)	9, 728
Tth111I	GACNNNGTC	1 cut(s)	506
Van91I	CCANNNNNTGG	3 cut(s)	1031, 1145, 1328
XapI	RAATTY	3 cut(s)	64, 849, 1467
XbaI	TCTAGA	1 cut(s)	1463
XcmI	CCANNNNNNNNNTGG	1 cut(s)	1325
XmnI	GAANNNNTTC	2 cut(s)	64, 1092
XspI	CTAG	3 cut(s)	566, 671, 1464

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