Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr6

Orthogroup ID

OG0004347

Physical Location & Seq

Genomic Coordinates Reverse (-)

40667328 .. 40674075

Gene Structure 6748 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000029578

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1314 bp

ATGGAGCTCCACCTCCTCCGCTCCACTGTTTCCACCCCAACTCTGTACCCTGGCCGCACCCACAAGCCAAACCCACCAATCCAGTGTCTCCGTTCATCAAAACGGAGCTCCGGCCCGAAGGAACTCTCTCGGATTCTGAGAACCGAGGCTGCTGTTAAAAACATTGAGAGGAAAGCAAACTCCAACAAGTACAATAACCTCTGGCCTAAGATATTTGGACTACTGCGTAAGCAACAATGGTATGAGCCAAGATGCCAAACTTACGCTAAATTGTTCATGATGCTTGGAAAGTGCAAGCAACCTGAGCAGGCTGGCTTACTTTTCGAGCTCATGTTAACTGATGGGCTCAAACCAACTGTTGACGTCTACACAGCTCTTGTTAGTGTTTATGGCAAAAGTGGCCTCTTTGACAAGGCATTCTCTACTGTTGATGATATGAAGTCAATTTCTAACTGCAAACCAGATGTATATACATATTCAATTCTTATAAATTGCTGCACCAAATTCAGTCGCTATGATCTGATTGAGCAAGTTCTGGCTGAAATGTCATATCTGGGAATTGGATGTAACACAGTCATATACAATACTCTTATCGATGGATATGGTAAAGCTGAGATGTTTGAACTGATGGAGGACTCATTGACAGATATGATTGAAAGTGGCAGCTGCCTTCCTGATGTTTTCACATTCAATTCTTTTCTTGGCGCTTATGGGAAAAGTGGGCAGATAGACAAGATGGAGAAGTGGTATGATGAATTTCAGCTAATGGGAATAAAGCCAGACCTTAAGACATTTAATGTCCTGATTAAATCATATGGGAAAGCAAGAATGTATGAAAAGATGGGATCTGTTATGGAGTTTATGGAGAAAGGTTATTTCACCCCAACTGTTGTTACTTATAACATAGTAATTGAGGTATTTGGGAAAGCTGGAAATATTGTGAAGATGGAGGAATACTTCAGAAAAATGAAGCACCAAGGAATGAAGCCTAGCTCTATTACTTATTGTTCCCTCGTTAGTGCGTACAGCAAAGCTGGGAATATAAATAAAGTTGATTCCATTTTGAGGCAAGTAGAGAATTCAGATGTTATACTTGATACAGCTTTTTTCAACTGTATTGTTAGTGCTTATGGTCGGGCTGGTGATATAAATAAGATGGGTGAATTATTTTTGACCATGGAAGAGAAAAAATGTGTTCCTGATCATATCACCTTTGCTACCATGATCCAAGCCTGCAATGCACTAGGCATGACTGCAGCTGTCGAAGATTTAAAAAACAGGATGATTACCACCAATGACAGTTCAGGTATCTAA

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

PPR PPR_2 PPR_3

Protein Analysis

438

Amino Acids

49.37

Weight (kDa)

8.53

Isoelectric Point (pI)

40.84

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	118 - 167	2.7e-13	PPR repeat family
PPR_3	PF13812	144 - 203	9.7e-07	Pentatricopeptide repeat domain
PPR_2	PF13041	190 - 231	1.3e-06	PPR repeat family
PPR_2	PF13041	225 - 273	1.9e-11	PPR repeat family
PPR_3	PF13812	251 - 309	1.4e-09	Pentatricopeptide repeat domain
PPR_2	PF13041	264 - 305	4e-07	PPR repeat family
TPR_24	PF23276	283 - 388	4.1e-07	Fungal tetratrico peptide repeats
PPR_2	PF13041	295 - 344	1.2e-11	PPR repeat family
PPR	PF01535	298 - 327	5.1e-06	PPR repeat
PPR_3	PF13812	353 - 412	1.5e-06	Pentatricopeptide repeat domain
PPR_2	PF13041	366 - 412	1.6e-09	PPR repeat family

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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Orthologous Genes (Group: OG0004347)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G53170 AT3G53170 AT3G53170 AT3G53170
fragaria_vesca	FvH4_7g01420
malus_domestica	MD02G1305700.v1.1 MD02G1306000.v1.1
prunus_persica	Prupe.2G019900_v2.0.a1 Prupe.2G019900_v2.0.a1 Prupe.2G019900_v2.0.a1 Prupe.2G019900_v2.0.a1 Prupe.2G019900_v2.0.a1 Prupe.2G019900_v2.0.a1
pyrus_communis	pycom02g25620
rosa_chinensis	RchiOBHm_Chr1g0317271
rosa_laevigata	RLG00000029578 RLG00000030614 RLG00000030617
rosa_multiflora	Rmu_sc0005698.1_g000002 Rmu_sc0007593.1_g000003
rosa_roxburghii	Rroxscaffold_4G00327510 Rroxscaffold_4G00330560
rosa_rugosa	Rorug01G0015300 Rorug01G0015400 Rorug01G0015400
rosa_samantha	Rh1AG026400 Rh1BG022700 Rh1CG024600 Rh1CG049800 Rh1DG047300 Rh1DG054300
rosa_wichuraiana	Rw1G001840

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	2 cut(s)	488, 900
AatII	GACGTC	1 cut(s)	366
AccBSI	CCGCTC	1 cut(s)	21
AccI	GTMKAC	1 cut(s)	366
AciI	CCGC	2 cut(s)	19, 55
AclWI	GGATC	2 cut(s)	853, 1219
AcoI	YGGCCR	1 cut(s)	52
AcsI	RAATTY	3 cut(s)	503, 755, 1078
AcuI	CTGAAG	1 cut(s)	943
AcyI	GRCGYC	1 cut(s)	363
AfaI	GTAC	3 cut(s)	47, 191, 1025
AfiI	CCNNNNNNNGG	1 cut(s)	1065
AflII	CTTAAG	1 cut(s)	785
AgsI	TTSAA	5 cut(s)	480, 623, 656, 691, 1111
AjnI	CCWGG	1 cut(s)	49
Alw21I	GWGCWC	3 cut(s)	9, 110, 330
Alw26I	GTCTC	1 cut(s)	92
AlwI	GGATC	2 cut(s)	853, 1219
AoxI	GGCC	4 cut(s)	52, 112, 203, 400
ApeKI	GCWGC	5 cut(s)	149, 495, 663, 666, 1256
ApoI	RAATTY	3 cut(s)	503, 755, 1078
AspLEI	GCGC	1 cut(s)	707
AspS9I	GGNCC	1 cut(s)	113
AsuHPI	GGTGA	4 cut(s)	871, 1154, 1172, 1201
BanII	GRGCYC	4 cut(s)	9, 110, 330, 348
Bbv12I	GWGCWC	3 cut(s)	9, 110, 330
BbvI	GCAGC	5 cut(s)	136, 482, 653, 675, 1268
BccI	CCATC	7 cut(s)	335, 590, 622, 730, 835, 940, 1150
BciT130I	CCWGG	1 cut(s)	51
BclI	TGATCA	1 cut(s)	1201
BcoDI	GTCTC	1 cut(s)	92
BfaI	CTAG	2 cut(s)	990, 1244
BfmI	CTRYAG	1 cut(s)	1254
BfoI	RGCGCY	1 cut(s)	708
BfrI	CTTAAG	1 cut(s)	785
BisI	GCNGC	6 cut(s)	55, 150, 496, 664, 667, 1257
BlsI	GCNGC	6 cut(s)	56, 151, 497, 665, 668, 1258
Bme1390I	CCNGG	1 cut(s)	51
BmgT120I	GGNCC	1 cut(s)	113
BmrFI	CCNGG	1 cut(s)	51
BmsI	GCATC	2 cut(s)	242, 270
Bpu10I	CCTNAGC	1 cut(s)	303
Bsa29I	ATCGAT	1 cut(s)	594
BsaHI	GRCGYC	1 cut(s)	363
BsaJI	CCNNGG	4 cut(s)	49, 144, 976, 1176
BsaXI	ACNNNNNCTCC	2 cut(s)	731, 761
Bsc4I	CCNNNNNNNGG	1 cut(s)	1065
Bse1I	ACTGG	1 cut(s)	82
Bse3DI	GCAATG	1 cut(s)	1243
BseBI	CCWGG	1 cut(s)	51
BseCI	ATCGAT	1 cut(s)	594
BseDI	CCNNGG	4 cut(s)	49, 144, 976, 1176
BseGI	GGATG	2 cut(s)	569, 1287
BseLI	CCNNNNNNNGG	1 cut(s)	1065
BseMI	GCAATG	1 cut(s)	1243
BseMII	CTCAG	3 cut(s)	128, 294, 603
BseNI	ACTGG	1 cut(s)	82
BseRI	GAGGAG	1 cut(s)	5
BseXI	GCAGC	5 cut(s)	136, 482, 653, 675, 1268
BseYI	CCCAGC	1 cut(s)	1034
BsgI	GTGCAG	1 cut(s)	481
BshFI	GGCC	4 cut(s)	54, 114, 205, 402
BshVI	ATCGAT	1 cut(s)	594
BsiHKAI	GWGCWC	3 cut(s)	9, 110, 330
BsiSI	CCGG	1 cut(s)	111
BslI	CCNNNNNNNGG	1 cut(s)	1065
BsmAI	GTCTC	1 cut(s)	92
BsmI	GAATGC	1 cut(s)	416
BsnI	GGCC	4 cut(s)	54, 114, 205, 402
Bsp1286I	GDGCHC	4 cut(s)	9, 110, 330, 348
Bsp143I	GATC	4 cut(s)	517, 845, 1201, 1224
Bsp19I	CCATGG	1 cut(s)	1176
BspACI	CCGC	2 cut(s)	19, 55
BspANI	GGCC	4 cut(s)	54, 114, 205, 402
BspCNI	CTCAG	3 cut(s)	129, 295, 604
BspDI	ATCGAT	1 cut(s)	594
BspHI	TCATGA	1 cut(s)	276
BspMAI	CTGCAG	1 cut(s)	1258
BspPI	GGATC	2 cut(s)	853, 1219
BspTI	CTTAAG	1 cut(s)	785
BsrBI	CCGCTC	1 cut(s)	21
BsrDI	GCAATG	1 cut(s)	1243
BsrI	ACTGG	1 cut(s)	82
BssECI	CCNNGG	4 cut(s)	49, 144, 976, 1176
BssMI	GATC	4 cut(s)	517, 845, 1201, 1224
BssNI	GRCGYC	1 cut(s)	363
BssT1I	CCWWGG	2 cut(s)	976, 1176
Bst2UI	CCWGG	1 cut(s)	51
Bst4CI	ACNGT	7 cut(s)	28, 358, 427, 574, 889, 1115, 1301
Bst6I	CTCTTC	1 cut(s)	1176
BstACI	GRCGYC	1 cut(s)	363
BstAFI	CTTAAG	1 cut(s)	785
BstC8I	GCNNGC	4 cut(s)	296, 309, 313, 1234
BstDEI	CTNAG	4 cut(s)	137, 207, 303, 612
BstDSI	CCRYGG	1 cut(s)	1176
BstF5I	GGATG	2 cut(s)	569, 1287
BstH2I	RGCGCY	1 cut(s)	708
BstHHI	GCGC	1 cut(s)	707
BstKTI	GATC	4 cut(s)	520, 848, 1204, 1227
BstMAI	GTCTC	1 cut(s)	92
BstMBI	GATC	4 cut(s)	517, 845, 1201, 1224
BstMWI	GCNNNNNNNGC	3 cut(s)	304, 399, 1238
BstNI	CCWGG	1 cut(s)	51
BstSCI	CCNGG	1 cut(s)	49
BstSFI	CTRYAG	1 cut(s)	1254
BstV1I	GCAGC	5 cut(s)	136, 482, 653, 675, 1268
BstX2I	RGATCY	1 cut(s)	845
BstYI	RGATCY	1 cut(s)	845
Bsu15I	ATCGAT	1 cut(s)	594
BsuRI	GGCC	4 cut(s)	54, 114, 205, 402
BsuTUI	ATCGAT	1 cut(s)	594
BtgI	CCRYGG	1 cut(s)	1176
BtsCI	GGATG	2 cut(s)	569, 1287
BtsIMutI	CAGTG	2 cut(s)	24, 89
Cac8I	GCNNGC	4 cut(s)	296, 309, 313, 1234
CciI	TCATGA	1 cut(s)	276
CfoI	GCGC	1 cut(s)	707
Cfr13I	GGNCC	1 cut(s)	113
ClaI	ATCGAT	1 cut(s)	594
Csp6I	GTAC	3 cut(s)	46, 190, 1024
CviAII	CATG	5 cut(s)	277, 331, 1177, 1222, 1249
CviQI	GTAC	3 cut(s)	46, 190, 1024
DdeI	CTNAG	4 cut(s)	137, 207, 303, 612
DpnI	GATC	4 cut(s)	519, 847, 1203, 1226
DpnII	GATC	4 cut(s)	517, 845, 1201, 1224
DraI	TTTAAA	1 cut(s)	1272
EaeI	YGGCCR	1 cut(s)	52
Eam1104I	CTCTTC	1 cut(s)	1176
EarI	CTCTTC	1 cut(s)	1176
Ecl136II	GAGCTC	3 cut(s)	7, 108, 328
Eco130I	CCWWGG	2 cut(s)	976, 1176
Eco24I	GRGCYC	4 cut(s)	9, 110, 330, 348
Eco53kI	GAGCTC	3 cut(s)	7, 108, 328
Eco57I	CTGAAG	1 cut(s)	943
EcoICRI	GAGCTC	3 cut(s)	7, 108, 328
EcoRI	GAATTC	1 cut(s)	1078
EcoRII	CCWGG	1 cut(s)	49
EcoT14I	CCWWGG	2 cut(s)	976, 1176
EcoT38I	GRGCYC	4 cut(s)	9, 110, 330, 348
ErhI	CCWWGG	2 cut(s)	976, 1176
FaeI	CATG	5 cut(s)	280, 334, 1180, 1225, 1252
FatI	CATG	5 cut(s)	276, 330, 1176, 1221, 1248
FauNDI	CATATG	1 cut(s)	814
FbaI	TGATCA	1 cut(s)	1201
FblI	GTMKAC	1 cut(s)	366
Fnu4HI	GCNGC	6 cut(s)	55, 150, 496, 664, 667, 1257
FokI	GGATG	2 cut(s)	576, 1294
FriOI	GRGCYC	4 cut(s)	9, 110, 330, 348
Fsp4HI	GCNGC	6 cut(s)	55, 150, 496, 664, 667, 1257
FspBI	CTAG	2 cut(s)	990, 1244
GlaI	GCGC	1 cut(s)	706
GluI	GCNGC	6 cut(s)	55, 150, 496, 664, 667, 1257
GsaI	CCCAGC	1 cut(s)	1038
HaeII	RGCGCY	1 cut(s)	708
HaeIII	GGCC	4 cut(s)	54, 114, 205, 402
HapII	CCGG	1 cut(s)	111
HhaI	GCGC	1 cut(s)	707
Hin1I	GRCGYC	1 cut(s)	363
Hin1II	CATG	5 cut(s)	280, 334, 1180, 1225, 1252
Hin6I	GCGC	1 cut(s)	705
HinP1I	GCGC	1 cut(s)	705
HincII	GTYRAC	2 cut(s)	336, 361
HindII	GTYRAC	2 cut(s)	336, 361
HinfI	GANTC	3 cut(s)	133, 635, 1055
HpaI	GTTAAC	1 cut(s)	336
HpaII	CCGG	1 cut(s)	111
HphI	GGTGA	4 cut(s)	871, 1154, 1172, 1201
Hpy166II	GTNNAC	3 cut(s)	336, 361, 367
Hpy188I	TCNGA	5 cut(s)	132, 138, 522, 962, 1084
Hpy188III	TCNNGA	4 cut(s)	277, 674, 802, 1199
Hpy8I	GTNNAC	3 cut(s)	336, 361, 367
HpyAV	CCTTC	2 cut(s)	112, 680
HpyCH4III	ACNGT	7 cut(s)	28, 358, 427, 574, 889, 1115, 1301
HpyCH4IV	ACGT	1 cut(s)	363
HpyCH4V	TGCA	6 cut(s)	294, 456, 498, 1236, 1241, 1256
HpyF10VI	GCNNNNNNNGC	3 cut(s)	304, 399, 1238
HpyF3I	CTNAG	4 cut(s)	137, 207, 303, 612
HpySE526I	ACGT	1 cut(s)	363
Hsp92I	GRCGYC	1 cut(s)	363
Hsp92II	CATG	5 cut(s)	280, 334, 1180, 1225, 1252
HspAI	GCGC	1 cut(s)	705
Ksp22I	TGATCA	1 cut(s)	1201
KspAI	GTTAAC	1 cut(s)	336
Kzo9I	GATC	4 cut(s)	517, 845, 1201, 1224
LmnI	GCTCC	5 cut(s)	4, 12, 26, 105, 113
Lsp1109I	GCAGC	5 cut(s)	136, 482, 653, 675, 1268
LweI	GCATC	2 cut(s)	242, 270
MaeI	CTAG	2 cut(s)	990, 1244
MaeII	ACGT	1 cut(s)	363
MaeIII	GTNAC	2 cut(s)	566, 892
MalI	GATC	4 cut(s)	519, 847, 1203, 1226
MbiI	CCGCTC	1 cut(s)	21
MboI	GATC	4 cut(s)	517, 845, 1201, 1224
MboII	GAAGA	3 cut(s)	955, 1193, 1277
MflI	RGATCY	1 cut(s)	845
MhlI	GDGCHC	4 cut(s)	9, 110, 330, 348
MlyI	GAGTC	1 cut(s)	629
MmeI	TCCRAC	1 cut(s)	207
MseI	TTAA	6 cut(s)	156, 335, 786, 795, 807, 1271
MspA1I	CMGCKG	2 cut(s)	666, 1259
MspCI	CTTAAG	1 cut(s)	785
MspI	CCGG	1 cut(s)	111
MspR9I	CCNGG	1 cut(s)	51
Mva1269I	GAATGC	1 cut(s)	416
MvaI	CCWGG	1 cut(s)	51
MwoI	GCNNNNNNNGC	3 cut(s)	304, 399, 1238
NcoI	CCATGG	1 cut(s)	1176
NdeI	CATATG	1 cut(s)	814
NdeII	GATC	4 cut(s)	517, 845, 1201, 1224
NlaIII	CATG	5 cut(s)	280, 334, 1180, 1225, 1252
PagI	TCATGA	1 cut(s)	276
PctI	GAATGC	1 cut(s)	416
PfeI	GAWTC	2 cut(s)	133, 1055
PkrI	GCNGC	6 cut(s)	56, 151, 497, 665, 668, 1258
PleI	GAGTC	1 cut(s)	629
PpsI	GAGTC	1 cut(s)	629
PsiI	TTATAA	2 cut(s)	488, 900
Psp124BI	GAGCTC	3 cut(s)	9, 110, 330
Psp6I	CCWGG	1 cut(s)	49
PspFI	CCCAGC	1 cut(s)	1034
PspGI	CCWGG	1 cut(s)	49
PspPI	GGNCC	1 cut(s)	113
PstI	CTGCAG	1 cut(s)	1258
PsuI	RGATCY	1 cut(s)	845
PvuII	CAGCTG	2 cut(s)	666, 1259
RsaI	GTAC	3 cut(s)	47, 191, 1025
RsaNI	GTAC	3 cut(s)	46, 190, 1024
SacI	GAGCTC	3 cut(s)	9, 110, 330
SaqAI	TTAA	6 cut(s)	156, 335, 786, 795, 807, 1271
SatI	GCNGC	6 cut(s)	55, 150, 496, 664, 667, 1257
Sau3AI	GATC	4 cut(s)	517, 845, 1201, 1224
Sau96I	GGNCC	1 cut(s)	113
SchI	GAGTC	1 cut(s)	629
ScrFI	CCNGG	1 cut(s)	51
SduI	GDGCHC	4 cut(s)	9, 110, 330, 348
SfaNI	GCATC	2 cut(s)	242, 270
SfcI	CTRYAG	1 cut(s)	1254
SmlI	CTYRAG	1 cut(s)	785
SmoI	CTYRAG	1 cut(s)	785
SsiI	CCGC	2 cut(s)	19, 55
SspI	AATATT	1 cut(s)	937
SspMI	CTAG	2 cut(s)	990, 1244
SstI	GAGCTC	3 cut(s)	9, 110, 330
StyD4I	CCNGG	1 cut(s)	49
StyI	CCWWGG	2 cut(s)	976, 1176
TaaI	ACNGT	7 cut(s)	28, 358, 427, 574, 889, 1115, 1301
TaiI	ACGT	1 cut(s)	366
TaqI	TCGA	3 cut(s)	324, 594, 1263
TatI	WGTACW	1 cut(s)	189
TauI	GCSGC	1 cut(s)	57
TfiI	GAWTC	2 cut(s)	133, 1055
Tru1I	TTAA	6 cut(s)	156, 335, 786, 795, 807, 1271
Tru9I	TTAA	6 cut(s)	156, 335, 786, 795, 807, 1271
TscAI	CASTG	2 cut(s)	31, 89
TseI	GCWGC	5 cut(s)	149, 495, 663, 666, 1256
TspDTI	ATGAA	7 cut(s)	84, 265, 452, 768, 849, 983, 998
TspGWI	ACGGA	2 cut(s)	80, 118
TspRI	CASTG	2 cut(s)	31, 89
Vha464I	CTTAAG	1 cut(s)	785
XapI	RAATTY	3 cut(s)	503, 755, 1078
XmiI	GTMKAC	1 cut(s)	366
XspI	CTAG	2 cut(s)	990, 1244
ZraI	GACGTC	1 cut(s)	364

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