Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3D

Orthogroup ID

OG0011572

Physical Location & Seq

Genomic Coordinates Forward (+)

3446013 .. 3452079

Gene Structure 6067 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3DG051400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1401 bp

ATGGGGGAATCAGTTGATCAGATGCTGCGTCAAGTGCGACAGGCAAAGGAACTTGGTGCTGACCTTGTTGAGATTCGGTTGGACTACATTAAGAACTTCAGTCCAAGACAAGATCTCGAAACTTTGATTAAGCGCAGCCCTTTGCCAACACTCGTCACTTACAGGCCAAAATGGGAAGGTGGTGAGTATGAAGGAGATGAAAATAAGCGACAAGAGGCACTCATTTTAGCCATGGAATTGGGAGCGGATTATATTGATGTTGAACTAAAGGTAGCAAATGACTTCTACAGTTCTATTCAAGGGAAGAAGCCAGAAAAGGTCAAAATCATAGTTTCTTCCCACAACTATGAGAATACTCCATCTGCTGAGGAAATTGGCAATCTTGTTGCAACGATACAAGCCATTGGAGCTGACATAGTCAAGGTCGCAACAACTGCCTTGGACATAACAGACAATGCAAGAATATTTCAAGTGCTAGCGCGTTCTCAAGTCCCAATGATAGGACTTTTGATGGGTGAGAAGGGTTTGATCTCTCGTGTACTTAGTGCAAAATATGGGTCATATGTCACATTTGGTACACTAGAGGCAGGTGAGGTATCAGCTCCTGGCCAGCCAACTGTAACGGATCTGTTGGAGTTATACAATTTTAGGCAGATTGGAGCCGATACCAAAGTACATGGTGTGATAGGAAATCCTATTGGTCACAGCAAAAGTCCTCATCTTTACAATGCAGCATTTAAAGCCAATAACTTCAATGGAATTTATCTGCCATTGCTGGTTGATAGCGTTGCAAACTTTATCAACACCTATAACTCCCCTGATTGGGTTGGATACAGTTACACAATTCCTCACAAAGAAGCTGGATTCAAATGTTGTGATGAGATCGATCCTAATGCCCTGGCAATAGGAGCTATTAGTTGCATGATCAGGAACCCAACTGATGGGAAGTTAAAGGGCTATAATGTTGACTATCTTGGAGCAATTGCAGCTATTGAGGAAGGACTTCGAGGATTAGGATTGAACGGTTCAAGTAATGGATCTGGTTCCCCATTAGCTGGTAGGTTATTTGTGGTCATGGGAGCTGGTGGTGCTGGAAAGGCACTTGCATATGGTGGAAAACAAAAGGGAGCAAGAGTTGTCGTTGCCAATCGCTCATTTGACAAAGCCAAGATACTGGCCGACAAAGTTGGAGGAGAAGCTATTACTCTTGCTGAGTTGGCAAACTTCCATCCAGAGGATGGTATGGTTCTTGCAAATACCACATCTGTTGGAATGAAACCAAGAACTGATCAAACACCCATCCCAAAGGTTTGTCCACCGTCACATTCTATAGTTATTTGTGCAGTTGTCAATTTGATGAAAGATCAAGTTTCTAGAATTTTATCTATATGCTGCAATTAA

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

466

Amino Acids

50.12

Weight (kDa)

6.22

Isoelectric Point (pI)

23.26

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DHquinase_I	PF01487	1 - 214	1.2e-67	Type I 3-dehydroquinase
Shikimate_dh_N	PF08501	228 - 306	8.6e-21	Shikimate dehydrogenase substrate binding domain
Shikimate_DH	PF01488	353 - 420	4.9e-06	Shikimate / quinate 5-dehydrogenase

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: 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)	578
Acc36I	ACCTGC	1 cut(s)	578
AccB7I	CCANNNNNTGG	3 cut(s)	941, 1055, 1238
AccBSI	CCGCTC	1 cut(s)	245
AccII	CGCG	1 cut(s)	481
AciI	CCGC	1 cut(s)	245
AclWI	GGATC	3 cut(s)	633, 881, 1045
AcoI	YGGCCR	2 cut(s)	607, 1176
AcsI	RAATTY	2 cut(s)	759, 1377
AcuI	CTGAAG	1 cut(s)	82
AfaI	GTAC	3 cut(s)	540, 577, 675
AfiI	CCNNNNNNNGG	7 cut(s)	500, 822, 823, 941, 1055, 1234, 1238
AgsI	TTSAA	7 cut(s)	263, 299, 470, 754, 868, 1021, 1029
AjnI	CCWGG	2 cut(s)	604, 897
AluBI	AGCT	8 cut(s)	410, 602, 860, 911, 989, 1055, 1082, 1199
AluI	AGCT	8 cut(s)	410, 602, 860, 911, 989, 1055, 1082, 1199
AlwI	GGATC	3 cut(s)	633, 881, 1045
AlwNI	CAGNNNCTG	2 cut(s)	25, 605
AoxI	GGCC	3 cut(s)	164, 607, 1176
ApeKI	GCWGC	5 cut(s)	25, 135, 731, 986, 1392
ApoI	RAATTY	2 cut(s)	759, 1377
ArsI	GACNNNNNNTTYG	2 cut(s)	542, 574
Asp700I	GAANNNNTTC	1 cut(s)	1002
AspLEI	GCGC	2 cut(s)	135, 481
AsuHPI	GGTGA	3 cut(s)	194, 527, 602
AsuNHI	GCTAGC	1 cut(s)	475
BaeI	ACNNNNGTAYC	2 cut(s)	657, 690
BalI	TGGCCA	1 cut(s)	609
BauI	CACGAG	1 cut(s)	534
BbvCI	CCTCAGC	1 cut(s)	366
BbvI	GCAGC	5 cut(s)	12, 147, 743, 998, 1379
BccI	CCATC	6 cut(s)	367, 505, 935, 1232, 1236, 1307
BcgI	CGANNNNNNTGC	2 cut(s)	875, 909
BciT130I	CCWGG	2 cut(s)	606, 899
BciVI	GTATCC	1 cut(s)	824
BclI	TGATCA	3 cut(s)	16, 924, 1288
BfaI	CTAG	3 cut(s)	476, 581, 1374
BfmI	CTRYAG	2 cut(s)	286, 1329
BfuAI	ACCTGC	1 cut(s)	578
BfuI	GTATCC	1 cut(s)	824
BglII	AGATCT	1 cut(s)	112
BisI	GCNGC	5 cut(s)	26, 136, 732, 987, 1393
BlsI	GCNGC	5 cut(s)	27, 137, 733, 988, 1394
Bme1390I	CCNGG	2 cut(s)	606, 899
BmiI	GGNNCC	3 cut(s)	661, 932, 1045
BmrFI	CCNGG	2 cut(s)	606, 899
BmsI	GCATC	1 cut(s)	12
BmtI	GCTAGC	1 cut(s)	479
Bpu10I	CCTNAGC	1 cut(s)	366
BpuEI	CTTGAG	1 cut(s)	471
Bsa29I	ATCGAT	1 cut(s)	885
BsaJI	CCNNGG	3 cut(s)	231, 438, 897
BsaXI	ACNNNNNCTCC	2 cut(s)	1119, 1149
Bsc4I	CCNNNNNNNGG	7 cut(s)	500, 822, 823, 941, 1055, 1234, 1238
Bse1I	ACTGG	1 cut(s)	1179
Bse3DI	GCAATG	1 cut(s)	770
BseBI	CCWGG	2 cut(s)	606, 899
BseCI	ATCGAT	1 cut(s)	885
BseDI	CCNNGG	3 cut(s)	231, 438, 897
BseGI	GGATG	3 cut(s)	1228, 1243, 1299
BseLI	CCNNNNNNNGG	7 cut(s)	500, 822, 823, 941, 1055, 1234, 1238
BseMI	GCAATG	1 cut(s)	770
BseMII	CTCAG	2 cut(s)	357, 1203
BseNI	ACTGG	1 cut(s)	1179
BseRI	GAGGAG	1 cut(s)	1206
BseXI	GCAGC	5 cut(s)	12, 147, 743, 998, 1379
BsgI	GTGCAG	1 cut(s)	1362
Bsh1236I	CGCG	1 cut(s)	481
BshFI	GGCC	3 cut(s)	166, 609, 1178
BshVI	ATCGAT	1 cut(s)	885
BslFI	GGGAC	1 cut(s)	476
BslI	CCNNNNNNNGG	7 cut(s)	500, 822, 823, 941, 1055, 1234, 1238
BsmFI	GGGAC	1 cut(s)	476
BsnI	GGCC	3 cut(s)	166, 609, 1178
Bsp19I	CCATGG	1 cut(s)	231
BspACI	CCGC	1 cut(s)	245
BspANI	GGCC	3 cut(s)	166, 609, 1178
BspCNI	CTCAG	2 cut(s)	358, 1204
BspDI	ATCGAT	1 cut(s)	885
BspFNI	CGCG	1 cut(s)	481
BspLI	GGNNCC	3 cut(s)	661, 932, 1045
BspMI	ACCTGC	1 cut(s)	578
BspOI	GCTAGC	1 cut(s)	479
BspPI	GGATC	3 cut(s)	633, 881, 1045
BsrBI	CCGCTC	1 cut(s)	245
BsrDI	GCAATG	1 cut(s)	770
BsrI	ACTGG	1 cut(s)	1179
BssECI	CCNNGG	3 cut(s)	231, 438, 897
BssSI	CACGAG	1 cut(s)	534
BssT1I	CCWWGG	2 cut(s)	231, 438
Bst2BI	CACGAG	1 cut(s)	534
Bst2UI	CCWGG	2 cut(s)	606, 899
Bst4CI	ACNGT	5 cut(s)	290, 619, 836, 1025, 1320
BstAPI	GCANNNNNTGC	1 cut(s)	434
BstC8I	GCNNGC	2 cut(s)	477, 611
BstDEI	CTNAG	3 cut(s)	366, 542, 1212
BstDSI	CCRYGG	1 cut(s)	231
BstF5I	GGATG	3 cut(s)	1228, 1243, 1299
BstFNI	CGCG	1 cut(s)	481
BstHHI	GCGC	2 cut(s)	135, 481
BstMWI	GCNNNNNNNGC	9 cut(s)	34, 407, 434, 740, 908, 986, 1088, 1097, 1217
BstNI	CCWGG	2 cut(s)	606, 899
BstSCI	CCNGG	2 cut(s)	604, 897
BstSFI	CTRYAG	2 cut(s)	286, 1329
BstUI	CGCG	1 cut(s)	481
BstV1I	GCAGC	5 cut(s)	12, 147, 743, 998, 1379
BstX2I	RGATCY	3 cut(s)	112, 625, 1037
BstXI	CCANNNNNNTGG	2 cut(s)	238, 1174
BstYI	RGATCY	3 cut(s)	112, 625, 1037
Bsu15I	ATCGAT	1 cut(s)	885
BsuI	GTATCC	1 cut(s)	824
BsuRI	GGCC	3 cut(s)	166, 609, 1178
BsuTUI	ATCGAT	1 cut(s)	885
BtgI	CCRYGG	1 cut(s)	231
BtsCI	GGATG	3 cut(s)	1228, 1243, 1299
BveI	ACCTGC	1 cut(s)	578
Cac8I	GCNNGC	2 cut(s)	477, 611
CaiI	CAGNNNCTG	2 cut(s)	25, 605
CfoI	GCGC	2 cut(s)	135, 481
ClaI	ATCGAT	1 cut(s)	885
CseI	GACGC	1 cut(s)	17
Csp6I	GTAC	3 cut(s)	539, 576, 674
CspCI	CAANNNNNGTGG	2 cut(s)	1249, 1284
CviAII	CATG	4 cut(s)	232, 677, 922, 1075
CviQI	GTAC	3 cut(s)	539, 576, 674
DdeI	CTNAG	3 cut(s)	366, 542, 1212
DraI	TTTAAA	1 cut(s)	739
EaeI	YGGCCR	2 cut(s)	607, 1176
Eco130I	CCWWGG	2 cut(s)	231, 438
Eco57I	CTGAAG	1 cut(s)	82
EcoRII	CCWGG	2 cut(s)	604, 897
EcoT14I	CCWWGG	2 cut(s)	231, 438
ErhI	CCWWGG	2 cut(s)	231, 438
FaeI	CATG	4 cut(s)	235, 680, 925, 1078
FaqI	GGGAC	1 cut(s)	476
FatI	CATG	4 cut(s)	231, 676, 921, 1074
FauNDI	CATATG	2 cut(s)	562, 1108
FbaI	TGATCA	3 cut(s)	16, 924, 1288
Fnu4HI	GCNGC	5 cut(s)	26, 136, 732, 987, 1393
FokI	GGATG	3 cut(s)	1215, 1250, 1286
Fsp4HI	GCNGC	5 cut(s)	26, 136, 732, 987, 1393
FspBI	CTAG	3 cut(s)	476, 581, 1374
GlaI	GCGC	2 cut(s)	134, 480
GluI	GCNGC	5 cut(s)	26, 136, 732, 987, 1393
HaeIII	GGCC	3 cut(s)	166, 609, 1178
HgaI	GACGC	1 cut(s)	17
HhaI	GCGC	2 cut(s)	135, 481
Hin1II	CATG	4 cut(s)	235, 680, 925, 1078
Hin6I	GCGC	2 cut(s)	133, 479
HinP1I	GCGC	2 cut(s)	133, 479
HincII	GTYRAC	1 cut(s)	967
HindII	GTYRAC	1 cut(s)	967
HinfI	GANTC	3 cut(s)	8, 73, 864
HphI	GGTGA	3 cut(s)	194, 527, 602
Hpy166II	GTNNAC	4 cut(s)	539, 578, 967, 1316
Hpy188I	TCNGA	1 cut(s)	21
Hpy188III	TCNNGA	4 cut(s)	116, 928, 1232, 1374
Hpy8I	GTNNAC	4 cut(s)	539, 578, 967, 1316
HpyAV	CCTTC	4 cut(s)	170, 185, 514, 992
HpyCH4III	ACNGT	5 cut(s)	290, 619, 836, 1025, 1320
HpyF10VI	GCNNNNNNNGC	9 cut(s)	34, 407, 434, 740, 908, 986, 1088, 1097, 1217
HpyF3I	CTNAG	3 cut(s)	366, 542, 1212
Hsp92II	CATG	4 cut(s)	235, 680, 925, 1078
HspAI	GCGC	2 cut(s)	133, 479
Ksp22I	TGATCA	3 cut(s)	16, 924, 1288
LmnI	GCTCC	8 cut(s)	242, 407, 607, 659, 908, 977, 1079, 1127
Lsp1109I	GCAGC	5 cut(s)	12, 147, 743, 998, 1379
LweI	GCATC	1 cut(s)	12
MaeI	CTAG	3 cut(s)	476, 581, 1374
MaeIII	GTNAC	6 cut(s)	154, 565, 619, 701, 836, 1320
MbiI	CCGCTC	1 cut(s)	245
MboII	GAAGA	2 cut(s)	316, 327
MfeI	CAATTG	1 cut(s)	981
MflI	RGATCY	3 cut(s)	112, 625, 1037
MlsI	TGGCCA	1 cut(s)	609
MluCI	AATT	9 cut(s)	236, 372, 643, 759, 843, 981, 1351, 1377, 1396
MluNI	TGGCCA	1 cut(s)	609
MmeI	TCCRAC	5 cut(s)	60, 612, 808, 1168, 1249
Mox20I	TGGCCA	1 cut(s)	609
MroXI	GAANNNNTTC	1 cut(s)	1002
MscI	TGGCCA	1 cut(s)	609
MseI	TTAA	5 cut(s)	90, 129, 738, 950, 1399
MslI	CAYNNNNRTG	1 cut(s)	345
Msp20I	TGGCCA	1 cut(s)	609
MspR9I	CCNGG	2 cut(s)	606, 899
MunI	CAATTG	1 cut(s)	981
MvaI	CCWGG	2 cut(s)	606, 899
MvnI	CGCG	1 cut(s)	481
MwoI	GCNNNNNNNGC	9 cut(s)	34, 407, 434, 740, 908, 986, 1088, 1097, 1217
NcoI	CCATGG	1 cut(s)	231
NdeI	CATATG	2 cut(s)	562, 1108
NheI	GCTAGC	1 cut(s)	475
NlaIII	CATG	4 cut(s)	235, 680, 925, 1078
NlaIV	GGNNCC	3 cut(s)	661, 932, 1045
NmuCI	GTSAC	4 cut(s)	154, 565, 701, 1320
PaqCI	CACCTGC	1 cut(s)	578
PdmI	GAANNNNTTC	1 cut(s)	1002
PfeI	GAWTC	3 cut(s)	8, 73, 864
PflFI	GACNNNGTC	1 cut(s)	416
PflMI	CCANNNNNTGG	3 cut(s)	941, 1055, 1238
PkrI	GCNGC	5 cut(s)	27, 137, 733, 988, 1394
Psp6I	CCWGG	2 cut(s)	604, 897
PspGI	CCWGG	2 cut(s)	604, 897
PspN4I	GGNNCC	3 cut(s)	661, 932, 1045
PstNI	CAGNNNCTG	2 cut(s)	25, 605
PsuI	RGATCY	3 cut(s)	112, 625, 1037
PsyI	GACNNNGTC	1 cut(s)	416
RsaI	GTAC	3 cut(s)	540, 577, 675
RsaNI	GTAC	3 cut(s)	539, 576, 674
RseI	CAYNNNNRTG	1 cut(s)	345
SaqAI	TTAA	5 cut(s)	90, 129, 738, 950, 1399
SatI	GCNGC	5 cut(s)	26, 136, 732, 987, 1393
ScrFI	CCNGG	2 cut(s)	606, 899
SfaNI	GCATC	1 cut(s)	12
SfcI	CTRYAG	2 cut(s)	286, 1329
SmiMI	CAYNNNNRTG	1 cut(s)	345
SmlI	CTYRAG	1 cut(s)	486
SmoI	CTYRAG	1 cut(s)	486
Sse9I	AATT	9 cut(s)	236, 372, 643, 759, 843, 981, 1351, 1377, 1396
SsiI	CCGC	1 cut(s)	245
SspI	AATATT	1 cut(s)	465
SspMI	CTAG	3 cut(s)	476, 581, 1374
StyD4I	CCNGG	2 cut(s)	604, 897
StyI	CCWWGG	2 cut(s)	231, 438
TaaI	ACNGT	5 cut(s)	290, 619, 836, 1025, 1320
TaqI	TCGA	3 cut(s)	117, 885, 1006
TasI	AATT	9 cut(s)	236, 372, 643, 759, 843, 981, 1351, 1377, 1396
TatI	WGTACW	2 cut(s)	538, 673
TfiI	GAWTC	3 cut(s)	8, 73, 864
Tru1I	TTAA	5 cut(s)	90, 129, 738, 950, 1399
Tru9I	TTAA	5 cut(s)	90, 129, 738, 950, 1399
TseFI	GTSAC	4 cut(s)	154, 565, 701, 1320
TseI	GCWGC	5 cut(s)	25, 135, 731, 986, 1392
Tsp45I	GTSAC	4 cut(s)	154, 565, 701, 1320
TspDTI	ATGAA	4 cut(s)	204, 213, 1289, 1373
TspGWI	ACGGA	1 cut(s)	638
Tth111I	GACNNNGTC	1 cut(s)	416
Van91I	CCANNNNNTGG	3 cut(s)	941, 1055, 1238
XapI	RAATTY	2 cut(s)	759, 1377
XbaI	TCTAGA	1 cut(s)	1373
XcmI	CCANNNNNNNNNTGG	1 cut(s)	1235
XmnI	GAANNNNTTC	1 cut(s)	1002
XspI	CTAG	3 cut(s)	476, 581, 1374

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