Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr1

Orthogroup ID

OG0005460

Physical Location & Seq

Genomic Coordinates Forward (+)

3870462 .. 3874293

Gene Structure 3832 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000000687

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1389 bp

ATGCAGCTGATTCAGTTGCTGCTGCACTTGCGGTTGGTGCTGACTGCTGAGGCTGCAGAAACAGCTCAAGAAAGTGATGGCCGATGTGGTTTAATTGTGTCAGCTGATGTGTTACGAGAATACACAGAAGCTGTTGTTGCAGCCTGTGATGCTGCCCAGGAAAGATGGGCAAAACTACTTGGGGTTCATGCTCTTCTTCATCCTAAGTTGAGATTACAGGAGTCTTTTAGCATATATGACATCATGCAAGAGTTTATAACTGCTACAGAGAAGATGGGGGCAAAGCAGGGATTTAGTATTAGAGGAACACTACAGTCACAGGCCAAAGCCTTCCTCGATTTTTGGCGCGAATCACGAATGACAAAAATTAAGGCAGTTCTTGACCAAGAAGCATGGGTGGAAGTAGATGTTCCTGATGGATTTCTGGTTATTGTCACTTCATTATTTTGTTCTGAAGCATTGGGAACCGAGAACCTGGATGCTGTTCATGGTAGTACCGAAACAAGCTACACTGAGGTGGCCACAAGCAACAATAGTTCACATGTGGTGGATACAGGGCCATCATTTACAGAACAGCACATTAACCGAACTGATTCTACTGAATTATCTACGGATATGACCGGAAAGGATAAGTCTACATATGCTCCCGGAGCTGAAAAGAATAAGGCTGGTGTTACCAATTCTGTGGCTCAGAACAGCCACAGCAATATGAAGGAGAGAGGAAAGTCAACTTCCAAAACCATTTTGTGCAAAGGTGTTGGTTTTCATATGGTAAACTGGTTAGTTTCTTTGTTTCACTCTGTTTGTTTTTTTCCTTTCTTATATCTACTTGTCTCATTTTCCTGCTATATGTCTGCCAATACTCTATTTTTCGTAATGCTAATGCTGTATTTGGAGTTTTGTTCTGTTGTATGTTGTCAGATCGAGTACATTGATATGTCCAACTTTGTTTCCTCAGAAGTTATTCTTAGAGGTTGTTCATTGTTGTTGAAACTTTTAAAATCATATGTGGTATTGCAGGTATCTGGTCTGAAGTTGATAACTTCTAAACACTTGGCCTTGGCAAGTCAAGTCATCAGTTTCGCAGATGCTATTATTCGTGGCAAATTCATTTTTCTGAAAGTTCCTGAGACAAGAAAGGCAATGTTGCTAGCTGAAATTGATCAAGTAGCTCAGGATTATAAGGTTCATAAAGATGAAATTTATACAAAGCTGGTTCAGATCATGGTTGTTATGGCCTTACTCTCCAACTCCTTGCCAGGAAGGAATTATATCTGTGAGATTTTAATCCTAGCTAAAAATCATTTTCACGCTAGAGTTCAGCACACACCACAAGCCAAGTACAGAGATTTGGGTCAGAAGCTAGTTAAGTGCTGTTGTGAACTGTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000139 GO:0000149 GO:0000938 GO:0001894 GO:0003674 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005737 GO:0005794 GO:0005802 GO:0006810 GO:0006892 GO:0006896 GO:0006996 GO:0007010 GO:0007034 GO:0007041 GO:0008150 GO:0009507 GO:0009536 GO:0009987 GO:0012505 GO:0016020 GO:0016043 GO:0016192 GO:0016197 GO:0016482 GO:0019905 GO:0031090 GO:0031410 GO:0031974 GO:0031981 GO:0031982 GO:0031984 GO:0032501 GO:0032588 GO:0032991 GO:0040008 GO:0042147 GO:0042592 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044431 GO:0044433 GO:0044444 GO:0044446 GO:0044464 GO:0045103 GO:0045104 GO:0046907 GO:0048193 GO:0048471 GO:0048871 GO:0048872 GO:0048873 GO:0050789 GO:0050879 GO:0050881 GO:0051179 GO:0051234 GO:0051641 GO:0051649 GO:0060052 GO:0060249 GO:0065007 GO:0065008 GO:0070013 GO:0071840 GO:0097708 GO:0098588 GO:0098791 GO:0099023

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Vps54

Protein Analysis

463

Amino Acids

51.57

Weight (kDa)

6.7

Isoelectric Point (pI)

31.66

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Vps54	PF07928	339 - 409	4.8e-15	Vps54-like protein

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: OG0005460)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G19490 AT4G19490
fragaria_vesca	FvH4_6g01010 FvH4_6g01010 FvH4_6g01010
malus_domestica	MD04G1237800.v1.1 MD12G1256000.v1.1
prunus_persica	Prupe.6G356900_v2.0.a1 Prupe.6G356900_v2.0.a1 Prupe.6G356900_v2.0.a1 Prupe.6G356900_v2.0.a1
pyrus_communis	pycom04g21100 pycom12g23480
rosa_chinensis	RchiOBHm_Chr3g0448451
rosa_laevigata	RLG00000000687 RLG00000025905
rosa_multiflora	Rmu_sc0003308.1_g000012 Rmu_sc0011979.1_g000005
rosa_roxburghii	Rroxscaffold_6G00426680
rosa_rugosa	Rorug02G0612500 Rorug02G0612600 Rorug02G0612600 Rorug07G0334800
rosa_samantha	Rh3AG012000 Rh3BG011800 Rh3CG011500 Rh3DG012200 Rh7BG461900
rosa_wichuraiana	Rw3G000930

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	2 cut(s)	257, 1182
Acc36I	ACCTGC	1 cut(s)	1009
AccI	GTMKAC	1 cut(s)	635
AccII	CGCG	1 cut(s)	348
AciI	CCGC	1 cut(s)	31
AcoI	YGGCCR	2 cut(s)	79, 519
AcsI	RAATTY	2 cut(s)	1106, 1200
AcuI	CTGAAG	2 cut(s)	474, 1052
AfaI	GTAC	3 cut(s)	496, 929, 1343
AflIII	ACRYGT	1 cut(s)	541
AgsI	TTSAA	1 cut(s)	991
AjnI	CCWGG	3 cut(s)	156, 474, 1258
AleI	CACNNNNGTG	1 cut(s)	515
Alw26I	GTCTC	2 cut(s)	838, 1124
AlwNI	CAGNNNCTG	2 cut(s)	19, 131
AoxI	GGCC	6 cut(s)	79, 321, 519, 557, 1056, 1236
ApeKI	GCWGC	6 cut(s)	4, 19, 22, 53, 140, 152
ApoI	RAATTY	2 cut(s)	1106, 1200
Asp700I	GAANNNNTTC	2 cut(s)	592, 963
AspLEI	GCGC	1 cut(s)	348
AspS9I	GGNCC	1 cut(s)	557
AsuC2I	CCSGG	1 cut(s)	648
AsuNHI	GCTAGC	1 cut(s)	1150
BalI	TGGCCA	1 cut(s)	521
BbvCI	CCTCAGC	1 cut(s)	48
BbvI	GCAGC	6 cut(s)	6, 9, 16, 40, 139, 152
BccI	CCATC	5 cut(s)	71, 159, 268, 410, 568
BciT130I	CCWGG	3 cut(s)	158, 476, 1260
BciVI	GTATCC	1 cut(s)	544
BclI	TGATCA	1 cut(s)	1162
BcnI	CCSGG	1 cut(s)	648
BcoDI	GTCTC	2 cut(s)	838, 1124
BfaI	CTAG	4 cut(s)	1151, 1292, 1314, 1364
BfmI	CTRYAG	4 cut(s)	54, 264, 311, 1385
BfuAI	ACCTGC	1 cut(s)	1009
BfuI	GTATCC	1 cut(s)	544
BisI	GCNGC	6 cut(s)	5, 20, 23, 54, 141, 153
BlsI	GCNGC	6 cut(s)	6, 21, 24, 55, 142, 154
Bme1390I	CCNGG	4 cut(s)	158, 476, 648, 1260
BmgT120I	GGNCC	1 cut(s)	557
BmiI	GGNNCC	1 cut(s)	466
BmrFI	CCNGG	4 cut(s)	158, 476, 648, 1260
BmsI	GCATC	3 cut(s)	139, 469, 1078
BmtI	GCTAGC	1 cut(s)	1154
Bpu10I	CCTNAGC	2 cut(s)	48, 1173
BpuEI	CTTGAG	1 cut(s)	51
BpuMI	CCSGG	1 cut(s)	648
BsaBI	GATNNNNATC	1 cut(s)	1286
BsaJI	CCNNGG	2 cut(s)	156, 1059
BsaWI	WCCGGW	1 cut(s)	620
BsaXI	ACNNNNNCTCC	2 cut(s)	628, 658
Bse1I	ACTGG	1 cut(s)	782
Bse3DI	GCAATG	1 cut(s)	1149
Bse8I	GATNNNNATC	1 cut(s)	1286
BseBI	CCWGG	3 cut(s)	158, 476, 1260
BseDI	CCNNGG	2 cut(s)	156, 1059
BseGI	GGATG	2 cut(s)	199, 484
BseJI	GATNNNNATC	1 cut(s)	1286
BseMI	GCAATG	1 cut(s)	1149
BseMII	CTCAG	6 cut(s)	39, 504, 704, 969, 1119, 1187
BseNI	ACTGG	1 cut(s)	782
BseXI	GCAGC	6 cut(s)	6, 9, 16, 40, 139, 152
BsgI	GTGCAG	1 cut(s)	8
Bsh1236I	CGCG	1 cut(s)	348
BshFI	GGCC	6 cut(s)	81, 323, 521, 559, 1058, 1238
BsiSI	CCGG	2 cut(s)	621, 648
BsmAI	GTCTC	2 cut(s)	838, 1124
BsnI	GGCC	6 cut(s)	81, 323, 521, 559, 1058, 1238
Bsp143I	GATC	3 cut(s)	921, 1162, 1221
BspACI	CCGC	1 cut(s)	31
BspANI	GGCC	6 cut(s)	81, 323, 521, 559, 1058, 1238
BspCNI	CTCAG	6 cut(s)	40, 505, 703, 968, 1120, 1186
BspFNI	CGCG	1 cut(s)	348
BspLI	GGNNCC	1 cut(s)	466
BspMAI	CTGCAG	1 cut(s)	58
BspMI	ACCTGC	1 cut(s)	1009
BspOI	GCTAGC	1 cut(s)	1154
BspQI	GCTCTTC	1 cut(s)	198
BsrDI	GCAATG	1 cut(s)	1149
BsrI	ACTGG	1 cut(s)	782
BssECI	CCNNGG	2 cut(s)	156, 1059
BssMI	GATC	3 cut(s)	921, 1162, 1221
BssT1I	CCWWGG	1 cut(s)	1059
Bst2UI	CCWGG	3 cut(s)	158, 476, 1260
Bst4CI	ACNGT	2 cut(s)	315, 1386
Bst6I	CTCTTC	1 cut(s)	198
BstC8I	GCNNGC	1 cut(s)	1152
BstDEI	CTNAG	8 cut(s)	48, 204, 513, 690, 955, 968, 1128, 1173
BstF5I	GGATG	2 cut(s)	199, 484
BstFNI	CGCG	1 cut(s)	348
BstHHI	GCGC	1 cut(s)	348
BstKTI	GATC	3 cut(s)	924, 1165, 1224
BstMAI	GTCTC	2 cut(s)	838, 1124
BstMBI	GATC	3 cut(s)	921, 1162, 1221
BstMWI	GCNNNNNNNGC	7 cut(s)	28, 37, 53, 62, 137, 149, 650
BstNI	CCWGG	3 cut(s)	158, 476, 1260
BstNSI	RCATGY	1 cut(s)	545
BstSCI	CCNGG	4 cut(s)	156, 474, 646, 1258
BstSFI	CTRYAG	4 cut(s)	54, 264, 311, 1385
BstUI	CGCG	1 cut(s)	348
BstV1I	GCAGC	6 cut(s)	6, 9, 16, 40, 139, 152
BstXI	CCANNNNNNTGG	1 cut(s)	685
BsuI	GTATCC	1 cut(s)	544
BsuRI	GGCC	6 cut(s)	81, 323, 521, 559, 1058, 1238
BtsCI	GGATG	2 cut(s)	199, 484
BtsIMutI	CAGTG	1 cut(s)	510
BveI	ACCTGC	1 cut(s)	1009
Cac8I	GCNNGC	1 cut(s)	1152
CaiI	CAGNNNCTG	2 cut(s)	19, 131
CfoI	GCGC	1 cut(s)	348
Cfr13I	GGNCC	1 cut(s)	557
Csp6I	GTAC	3 cut(s)	495, 928, 1342
CviAII	CATG	6 cut(s)	188, 244, 393, 488, 542, 1225
CviQI	GTAC	3 cut(s)	495, 928, 1342
DdeI	CTNAG	8 cut(s)	48, 204, 513, 690, 955, 968, 1128, 1173
DpnI	GATC	3 cut(s)	923, 1164, 1223
DpnII	GATC	3 cut(s)	921, 1162, 1221
DraI	TTTAAA	1 cut(s)	999
EaeI	YGGCCR	2 cut(s)	79, 519
Eam1104I	CTCTTC	1 cut(s)	198
EarI	CTCTTC	1 cut(s)	198
Eco130I	CCWWGG	1 cut(s)	1059
Eco57I	CTGAAG	2 cut(s)	474, 1052
EcoRII	CCWGG	3 cut(s)	156, 474, 1258
EcoT14I	CCWWGG	1 cut(s)	1059
ErhI	CCWWGG	1 cut(s)	1059
FaeI	CATG	6 cut(s)	191, 247, 396, 491, 545, 1228
FalI	AAGNNNNNCTT	2 cut(s)	951, 983
FatI	CATG	6 cut(s)	187, 243, 392, 487, 541, 1224
FauNDI	CATATG	3 cut(s)	640, 768, 1006
FbaI	TGATCA	1 cut(s)	1162
FblI	GTMKAC	1 cut(s)	635
Fnu4HI	GCNGC	6 cut(s)	5, 20, 23, 54, 141, 153
FokI	GGATG	2 cut(s)	186, 491
Fsp4HI	GCNGC	6 cut(s)	5, 20, 23, 54, 141, 153
FspBI	CTAG	4 cut(s)	1151, 1292, 1314, 1364
GlaI	GCGC	1 cut(s)	347
GluI	GCNGC	6 cut(s)	5, 20, 23, 54, 141, 153
HaeIII	GGCC	6 cut(s)	81, 323, 521, 559, 1058, 1238
HapII	CCGG	2 cut(s)	621, 648
HhaI	GCGC	1 cut(s)	348
Hin1II	CATG	6 cut(s)	191, 247, 396, 491, 545, 1228
Hin6I	GCGC	1 cut(s)	346
HinP1I	GCGC	1 cut(s)	346
HincII	GTYRAC	1 cut(s)	729
HindII	GTYRAC	1 cut(s)	729
HinfI	GANTC	4 cut(s)	10, 221, 350, 593
HpaII	CCGG	2 cut(s)	621, 648
Hpy166II	GTNNAC	5 cut(s)	539, 636, 729, 775, 1382
Hpy188I	TCNGA	8 cut(s)	454, 693, 921, 958, 1032, 1119, 1221, 1359
Hpy188III	TCNNGA	6 cut(s)	68, 354, 380, 413, 1127, 1175
Hpy8I	GTNNAC	5 cut(s)	539, 636, 729, 775, 1382
HpyAV	CCTTC	3 cut(s)	340, 706, 1257
HpyCH4III	ACNGT	2 cut(s)	315, 1386
HpyCH4V	TGCA	7 cut(s)	4, 25, 56, 140, 247, 750, 1018
HpyF10VI	GCNNNNNNNGC	7 cut(s)	28, 37, 53, 62, 137, 149, 650
HpyF3I	CTNAG	8 cut(s)	48, 204, 513, 690, 955, 968, 1128, 1173
Hsp92II	CATG	6 cut(s)	191, 247, 396, 491, 545, 1228
HspAI	GCGC	1 cut(s)	346
Ksp22I	TGATCA	1 cut(s)	1162
Kzo9I	GATC	3 cut(s)	921, 1162, 1221
LguI	GCTCTTC	1 cut(s)	198
LmnI	GCTCC	2 cut(s)	649, 650
Lsp1109I	GCAGC	6 cut(s)	6, 9, 16, 40, 139, 152
LweI	GCATC	3 cut(s)	139, 469, 1078
MaeI	CTAG	4 cut(s)	1151, 1292, 1314, 1364
MaeIII	GTNAC	4 cut(s)	111, 315, 433, 673
MalI	GATC	3 cut(s)	923, 1164, 1223
MboI	GATC	3 cut(s)	921, 1162, 1221
MboII	GAAGA	3 cut(s)	185, 188, 283
MlsI	TGGCCA	1 cut(s)	521
MluCI	AATT	8 cut(s)	93, 366, 602, 679, 1106, 1158, 1200, 1267
MluNI	TGGCCA	1 cut(s)	521
MlyI	GAGTC	1 cut(s)	230
MmeI	TCCRAC	2 cut(s)	966, 1272
MnlI	CCTC	7 cut(s)	43, 296, 344, 508, 713, 964, 965
Mox20I	TGGCCA	1 cut(s)	521
MroXI	GAANNNNTTC	2 cut(s)	592, 963
MscI	TGGCCA	1 cut(s)	521
MseI	TTAA	6 cut(s)	92, 369, 582, 998, 1286, 1368
MslI	CAYNNNNRTG	3 cut(s)	515, 935, 1194
Msp20I	TGGCCA	1 cut(s)	521
MspA1I	CMGCKG	2 cut(s)	7, 104
MspI	CCGG	2 cut(s)	621, 648
MspR9I	CCNGG	4 cut(s)	158, 476, 648, 1260
MvaI	CCWGG	3 cut(s)	158, 476, 1260
MvnI	CGCG	1 cut(s)	348
MwoI	GCNNNNNNNGC	7 cut(s)	28, 37, 53, 62, 137, 149, 650
NciI	CCSGG	1 cut(s)	648
NdeI	CATATG	3 cut(s)	640, 768, 1006
NdeII	GATC	3 cut(s)	921, 1162, 1221
NheI	GCTAGC	1 cut(s)	1150
NlaIII	CATG	6 cut(s)	191, 247, 396, 491, 545, 1228
NlaIV	GGNNCC	1 cut(s)	466
NmuCI	GTSAC	2 cut(s)	315, 433
NspI	RCATGY	1 cut(s)	545
OliI	CACNNNNGTG	1 cut(s)	515
PciI	ACATGT	1 cut(s)	541
PciSI	GCTCTTC	1 cut(s)	198
PdmI	GAANNNNTTC	2 cut(s)	592, 963
PfeI	GAWTC	3 cut(s)	10, 350, 593
PfoI	TCCNGGA	1 cut(s)	646
PkrI	GCNGC	6 cut(s)	6, 21, 24, 55, 142, 154
PleI	GAGTC	1 cut(s)	229
PpsI	GAGTC	1 cut(s)	229
PscI	ACATGT	1 cut(s)	541
PsiI	TTATAA	2 cut(s)	257, 1182
Psp6I	CCWGG	3 cut(s)	156, 474, 1258
PspGI	CCWGG	3 cut(s)	156, 474, 1258
PspN4I	GGNNCC	1 cut(s)	466
PspPI	GGNCC	1 cut(s)	557
PsrI	GAACNNNNNNTAC	2 cut(s)	580, 612
PstI	CTGCAG	1 cut(s)	58
PstNI	CAGNNNCTG	2 cut(s)	19, 131
PvuII	CAGCTG	2 cut(s)	7, 104
RsaI	GTAC	3 cut(s)	496, 929, 1343
RsaNI	GTAC	3 cut(s)	495, 928, 1342
RseI	CAYNNNNRTG	3 cut(s)	515, 935, 1194
SapI	GCTCTTC	1 cut(s)	198
SaqAI	TTAA	6 cut(s)	92, 369, 582, 998, 1286, 1368
SatI	GCNGC	6 cut(s)	5, 20, 23, 54, 141, 153
Sau3AI	GATC	3 cut(s)	921, 1162, 1221
Sau96I	GGNCC	1 cut(s)	557
SchI	GAGTC	1 cut(s)	230
ScrFI	CCNGG	4 cut(s)	158, 476, 648, 1260
SfaNI	GCATC	3 cut(s)	139, 469, 1078
SfcI	CTRYAG	4 cut(s)	54, 264, 311, 1385
SmiMI	CAYNNNNRTG	3 cut(s)	515, 935, 1194
SmlI	CTYRAG	1 cut(s)	66
SmoI	CTYRAG	1 cut(s)	66
Sse9I	AATT	8 cut(s)	93, 366, 602, 679, 1106, 1158, 1200, 1267
SsiI	CCGC	1 cut(s)	31
SspMI	CTAG	4 cut(s)	1151, 1292, 1314, 1364
StyD4I	CCNGG	4 cut(s)	156, 474, 646, 1258
StyI	CCWWGG	1 cut(s)	1059
TaaI	ACNGT	2 cut(s)	315, 1386
TaqI	TCGA	2 cut(s)	336, 924
TasI	AATT	8 cut(s)	93, 366, 602, 679, 1106, 1158, 1200, 1267
TatI	WGTACW	2 cut(s)	927, 1341
TfiI	GAWTC	3 cut(s)	10, 350, 593
Tru1I	TTAA	6 cut(s)	92, 369, 582, 998, 1286, 1368
Tru9I	TTAA	6 cut(s)	92, 369, 582, 998, 1286, 1368
TscAI	CASTG	1 cut(s)	517
TseFI	GTSAC	2 cut(s)	315, 433
TseI	GCWGC	6 cut(s)	4, 19, 22, 53, 140, 152
Tsp45I	GTSAC	2 cut(s)	315, 433
TspGWI	ACGGA	1 cut(s)	626
TspRI	CASTG	1 cut(s)	517
XapI	RAATTY	2 cut(s)	1106, 1200
XceI	RCATGY	1 cut(s)	545
XmiI	GTMKAC	1 cut(s)	635
XmnI	GAANNNNTTC	2 cut(s)	592, 963
XspI	CTAG	4 cut(s)	1151, 1292, 1314, 1364

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