Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1B

Orthogroup ID

OG0004347

Physical Location & Seq

Genomic Coordinates Forward (+)

2978917 .. 2981465

Gene Structure 2549 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1BG022700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1389 bp

ATGGAGCTCCACCTCCTCCGCTCCACTGTCTCCACCCCAACTCTGTACCCTGACCGCACCCACAAGCCAAACCCACCAATCCAGTGTCTCCGTTCGTCAAAACGGAGCTCCGGCCCGAAGGAACTCTCACGGATTCTGAGAACCGAGGCTGCTGTTAAAAACATTGAGAGGAAAGCAAACTCCAACAAGTACAATAACCTTTGGCCGAAGGCTGTCTTGGAGGCCTTGGATGAGGCTGTTGCCAACAATCTCTGGGAGACTGCTCTTAAGATATTTGGACTACTGCGTAAGCAACATTGGTATGAGCCGAGATGCCAAACTTATGCTAAATTGTTCATGATGCTTGGAAAGTGCAAGCAACCTGAGCAAGCTGGCTTACTTTTCGAGCTCATGTTAACTGATGGGCTCAAACCAACTGTTGACGTCTACACAGCTCTTGTTAGTGTTTATGGCAAAAGTGGCCTCTTTGACAAGGCATTCTCTACTGTTGATGATATGAAGTCAATTTCCGACTGCAAACCAGATGTGTATACATATTCAATTCTTATCCATTGCTGCACTAAATTCTGTCGCTATGATCTGATCGAGCAAGTTCTGGCTGAGATGTCATATCTGGGAATTGGATGTAACACAGTCATATACAATACTCTTATCGATGGATATGGTAAAGCTGAAATGTTTGAACTGATGGAGGACTCATTGACAGATATGATTGAAAGTGGCAGCTGCCTTCCTGATGTTTTCACATTCAATTCTTTTCTTGGCGCTTATGGGAAAAGTGGGCAGATAGACAAGATGGAGAAGTGGTATGATGAATTTCAGCTAATGGGAATAAAGCCAGACCTTAAGACATTTAATGTCCTGATTAAATCATATGGGAAAGCAAGAATGTATGAAAAGATGGGATCTGTTATGGAGTTTATGGAGAAAAGGTATTTCACCTCAACTGTTGTTACTTATAACATAGTAATTGAGGTATTTGGGAAAGCTGGAAATATTGTGAAGATGGAGGAATACTTCAGAAAAATGAAGCACCAAGGAATGAAGCCTAGCTCTATTACTTATTGTTCCCTCGTTAGTGCGTACAGCAAAGCTGGGAATATAAATAAAGTTGATTCCATTTTGAGGCAAGTAGAGAATTCAGATGTTATACTTGATACAGCTTTTTTCAACTGTATTATTAGTGCTTATGGTCGGGCTGGTGATATAAATAAGATGGGTGAATTATTTTTGACCATGGAAGAGAAAAAATGTGTTCCTGATCATATCACCTTTGCTACCATGATCCAAGCCTGCAATGCACTAGGCATGACTGCGGCTGTCGAAGATTTAAAAAACAGGATGATTACCACCAATGACAGTTCAGGCACAAGGTTGATTGGATTCTAG

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

462

Amino Acids

52.31

Weight (kDa)

8.08

Isoelectric Point (pI)

39.76

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	138 - 187	2.3e-12	PPR repeat family
PPR_3	PF13812	164 - 223	3.8e-07	Pentatricopeptide repeat domain
PPR_2	PF13041	245 - 293	2e-11	PPR repeat family
PPR_3	PF13812	271 - 329	1.3e-07	Pentatricopeptide repeat domain
TPR_24	PF23276	303 - 408	1.6e-08	Fungal tetratrico peptide repeats
PPR_2	PF13041	316 - 364	5.4e-11	PPR repeat family
PPR	PF01535	318 - 347	5.5e-06	PPR repeat
PPR_3	PF13812	373 - 432	3.9e-07	Pentatricopeptide repeat domain
PPR_2	PF13041	386 - 432	1.5e-10	PPR repeat family

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Align Labels (Cladogram)

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Tree File

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Publication-ready

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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	1 cut(s)	960
AatII	GACGTC	1 cut(s)	426
AccBSI	CCGCTC	1 cut(s)	21
AccI	GTMKAC	2 cut(s)	426, 530
AciI	CCGC	3 cut(s)	19, 55, 1316
AclWI	GGATC	2 cut(s)	913, 1279
AcoI	YGGCCR	1 cut(s)	203
AcsI	RAATTY	3 cut(s)	563, 815, 1138
AcuI	CTGAAG	1 cut(s)	1003
AcyI	GRCGYC	1 cut(s)	423
AfaI	GTAC	3 cut(s)	47, 191, 1085
AfiI	CCNNNNNNNGG	1 cut(s)	1125
AflII	CTTAAG	2 cut(s)	266, 845
AgsI	TTSAA	5 cut(s)	540, 683, 716, 751, 1171
AjuI	GAANNNNNNNTTGG	2 cut(s)	200, 232
Alw21I	GWGCWC	3 cut(s)	9, 110, 390
Alw26I	GTCTC	3 cut(s)	34, 92, 251
AlwI	GGATC	2 cut(s)	913, 1279
AoxI	GGCC	4 cut(s)	112, 203, 222, 460
ApeKI	GCWGC	4 cut(s)	149, 555, 723, 726
ApoI	RAATTY	3 cut(s)	563, 815, 1138
AspLEI	GCGC	1 cut(s)	767
AspS9I	GGNCC	1 cut(s)	113
AsuHPI	GGTGA	4 cut(s)	931, 1214, 1232, 1261
BanII	GRGCYC	4 cut(s)	9, 110, 390, 408
Bbv12I	GWGCWC	3 cut(s)	9, 110, 390
BbvI	GCAGC	4 cut(s)	136, 542, 713, 735
BccI	CCATC	7 cut(s)	395, 650, 682, 790, 895, 1000, 1210
BclI	TGATCA	1 cut(s)	1261
BcoDI	GTCTC	3 cut(s)	34, 92, 251
BfaI	CTAG	3 cut(s)	1050, 1304, 1387
BfoI	RGCGCY	1 cut(s)	768
BfrI	CTTAAG	2 cut(s)	266, 845
BisI	GCNGC	5 cut(s)	150, 556, 724, 727, 1317
BlsI	GCNGC	5 cut(s)	151, 557, 725, 728, 1318
BmgT120I	GGNCC	1 cut(s)	113
BmsI	GCATC	2 cut(s)	302, 330
Bpu10I	CCTNAGC	1 cut(s)	363
Bsa29I	ATCGAT	1 cut(s)	654
BsaHI	GRCGYC	1 cut(s)	423
BsaJI	CCNNGG	4 cut(s)	144, 225, 1036, 1236
BsaXI	ACNNNNNCTCC	4 cut(s)	791, 821, 917, 947
Bsc4I	CCNNNNNNNGG	1 cut(s)	1125
Bse1I	ACTGG	1 cut(s)	82
Bse3DI	GCAATG	2 cut(s)	550, 1303
BseCI	ATCGAT	1 cut(s)	654
BseDI	CCNNGG	4 cut(s)	144, 225, 1036, 1236
BseGI	GGATG	3 cut(s)	235, 629, 1347
BseLI	CCNNNNNNNGG	1 cut(s)	1125
BseMI	GCAATG	2 cut(s)	550, 1303
BseMII	CTCAG	3 cut(s)	128, 354, 591
BseNI	ACTGG	1 cut(s)	82
BseRI	GAGGAG	1 cut(s)	5
BseXI	GCAGC	4 cut(s)	136, 542, 713, 735
BseYI	CCCAGC	1 cut(s)	1094
BsgI	GTGCAG	1 cut(s)	541
BshFI	GGCC	4 cut(s)	114, 205, 224, 462
BshVI	ATCGAT	1 cut(s)	654
BsiHKAI	GWGCWC	3 cut(s)	9, 110, 390
BsiSI	CCGG	1 cut(s)	111
BslI	CCNNNNNNNGG	1 cut(s)	1125
BsmAI	GTCTC	3 cut(s)	34, 92, 251
BsmI	GAATGC	1 cut(s)	476
BsnI	GGCC	4 cut(s)	114, 205, 224, 462
Bsp1286I	GDGCHC	4 cut(s)	9, 110, 390, 408
Bsp143I	GATC	5 cut(s)	577, 582, 905, 1261, 1284
Bsp19I	CCATGG	1 cut(s)	1236
BspACI	CCGC	3 cut(s)	19, 55, 1316
BspANI	GGCC	4 cut(s)	114, 205, 224, 462
BspCNI	CTCAG	3 cut(s)	129, 355, 592
BspDI	ATCGAT	1 cut(s)	654
BspHI	TCATGA	1 cut(s)	336
BspPI	GGATC	2 cut(s)	913, 1279
BspTI	CTTAAG	2 cut(s)	266, 845
BsrBI	CCGCTC	1 cut(s)	21
BsrDI	GCAATG	2 cut(s)	550, 1303
BsrI	ACTGG	1 cut(s)	82
BssECI	CCNNGG	4 cut(s)	144, 225, 1036, 1236
BssMI	GATC	5 cut(s)	577, 582, 905, 1261, 1284
BssNAI	GTATAC	1 cut(s)	531
BssNI	GRCGYC	1 cut(s)	423
BssT1I	CCWWGG	3 cut(s)	225, 1036, 1236
Bst1107I	GTATAC	1 cut(s)	531
Bst4CI	ACNGT	7 cut(s)	28, 418, 487, 634, 949, 1175, 1361
Bst6I	CTCTTC	1 cut(s)	1236
BstACI	GRCGYC	1 cut(s)	423
BstAFI	CTTAAG	2 cut(s)	266, 845
BstC8I	GCNNGC	4 cut(s)	356, 369, 373, 1294
BstDEI	CTNAG	3 cut(s)	137, 363, 600
BstDSI	CCRYGG	1 cut(s)	1236
BstF5I	GGATG	3 cut(s)	235, 629, 1347
BstH2I	RGCGCY	1 cut(s)	768
BstHHI	GCGC	1 cut(s)	767
BstKTI	GATC	5 cut(s)	580, 585, 908, 1264, 1287
BstMAI	GTCTC	3 cut(s)	34, 92, 251
BstMBI	GATC	5 cut(s)	577, 582, 905, 1261, 1284
BstMWI	GCNNNNNNNGC	3 cut(s)	364, 459, 1298
BstV1I	GCAGC	4 cut(s)	136, 542, 713, 735
BstX2I	RGATCY	1 cut(s)	905
BstYI	RGATCY	1 cut(s)	905
BstZ17I	GTATAC	1 cut(s)	531
Bsu15I	ATCGAT	1 cut(s)	654
BsuRI	GGCC	4 cut(s)	114, 205, 224, 462
BsuTUI	ATCGAT	1 cut(s)	654
BtgI	CCRYGG	1 cut(s)	1236
BtsCI	GGATG	3 cut(s)	235, 629, 1347
BtsIMutI	CAGTG	2 cut(s)	24, 89
Cac8I	GCNNGC	4 cut(s)	356, 369, 373, 1294
CciI	TCATGA	1 cut(s)	336
CfoI	GCGC	1 cut(s)	767
Cfr13I	GGNCC	1 cut(s)	113
ClaI	ATCGAT	1 cut(s)	654
Csp6I	GTAC	3 cut(s)	46, 190, 1084
CviAII	CATG	5 cut(s)	337, 391, 1237, 1282, 1309
CviQI	GTAC	3 cut(s)	46, 190, 1084
DdeI	CTNAG	3 cut(s)	137, 363, 600
DpnI	GATC	5 cut(s)	579, 584, 907, 1263, 1286
DpnII	GATC	5 cut(s)	577, 582, 905, 1261, 1284
DraI	TTTAAA	1 cut(s)	1332
EaeI	YGGCCR	1 cut(s)	203
Eam1104I	CTCTTC	1 cut(s)	1236
EarI	CTCTTC	1 cut(s)	1236
Ecl136II	GAGCTC	3 cut(s)	7, 108, 388
Eco130I	CCWWGG	3 cut(s)	225, 1036, 1236
Eco147I	AGGCCT	1 cut(s)	224
Eco24I	GRGCYC	4 cut(s)	9, 110, 390, 408
Eco53kI	GAGCTC	3 cut(s)	7, 108, 388
Eco57I	CTGAAG	1 cut(s)	1003
EcoICRI	GAGCTC	3 cut(s)	7, 108, 388
EcoRI	GAATTC	1 cut(s)	1138
EcoT14I	CCWWGG	3 cut(s)	225, 1036, 1236
EcoT38I	GRGCYC	4 cut(s)	9, 110, 390, 408
ErhI	CCWWGG	3 cut(s)	225, 1036, 1236
FaeI	CATG	5 cut(s)	340, 394, 1240, 1285, 1312
FalI	AAGNNNNNCTT	2 cut(s)	200, 232
FatI	CATG	5 cut(s)	336, 390, 1236, 1281, 1308
FauNDI	CATATG	1 cut(s)	874
FbaI	TGATCA	1 cut(s)	1261
FblI	GTMKAC	2 cut(s)	426, 530
Fnu4HI	GCNGC	5 cut(s)	150, 556, 724, 727, 1317
FokI	GGATG	3 cut(s)	242, 636, 1354
FriOI	GRGCYC	4 cut(s)	9, 110, 390, 408
Fsp4HI	GCNGC	5 cut(s)	150, 556, 724, 727, 1317
FspBI	CTAG	3 cut(s)	1050, 1304, 1387
GlaI	GCGC	1 cut(s)	766
GluI	GCNGC	5 cut(s)	150, 556, 724, 727, 1317
GsaI	CCCAGC	1 cut(s)	1098
HaeII	RGCGCY	1 cut(s)	768
HaeIII	GGCC	4 cut(s)	114, 205, 224, 462
HapII	CCGG	1 cut(s)	111
HhaI	GCGC	1 cut(s)	767
Hin1I	GRCGYC	1 cut(s)	423
Hin1II	CATG	5 cut(s)	340, 394, 1240, 1285, 1312
Hin6I	GCGC	1 cut(s)	765
HinP1I	GCGC	1 cut(s)	765
HincII	GTYRAC	2 cut(s)	396, 421
HindII	GTYRAC	2 cut(s)	396, 421
HinfI	GANTC	4 cut(s)	133, 695, 1115, 1383
HpaI	GTTAAC	1 cut(s)	396
HpaII	CCGG	1 cut(s)	111
HphI	GGTGA	4 cut(s)	931, 1214, 1232, 1261
Hpy166II	GTNNAC	4 cut(s)	396, 421, 427, 531
Hpy188I	TCNGA	5 cut(s)	138, 511, 582, 1022, 1144
Hpy188III	TCNNGA	4 cut(s)	337, 734, 862, 1259
Hpy8I	GTNNAC	4 cut(s)	396, 421, 427, 531
HpyAV	CCTTC	3 cut(s)	112, 202, 740
HpyCH4III	ACNGT	7 cut(s)	28, 418, 487, 634, 949, 1175, 1361
HpyCH4IV	ACGT	1 cut(s)	423
HpyCH4V	TGCA	5 cut(s)	354, 516, 558, 1296, 1301
HpyF10VI	GCNNNNNNNGC	3 cut(s)	364, 459, 1298
HpyF3I	CTNAG	3 cut(s)	137, 363, 600
HpySE526I	ACGT	1 cut(s)	423
Hsp92I	GRCGYC	1 cut(s)	423
Hsp92II	CATG	5 cut(s)	340, 394, 1240, 1285, 1312
HspAI	GCGC	1 cut(s)	765
Ksp22I	TGATCA	1 cut(s)	1261
KspAI	GTTAAC	1 cut(s)	396
Kzo9I	GATC	5 cut(s)	577, 582, 905, 1261, 1284
LmnI	GCTCC	5 cut(s)	4, 12, 26, 105, 113
Lsp1109I	GCAGC	4 cut(s)	136, 542, 713, 735
LweI	GCATC	2 cut(s)	302, 330
MaeI	CTAG	3 cut(s)	1050, 1304, 1387
MaeII	ACGT	1 cut(s)	423
MaeIII	GTNAC	2 cut(s)	626, 952
MalI	GATC	5 cut(s)	579, 584, 907, 1263, 1286
MbiI	CCGCTC	1 cut(s)	21
MboI	GATC	5 cut(s)	577, 582, 905, 1261, 1284
MboII	GAAGA	3 cut(s)	1015, 1253, 1337
MflI	RGATCY	1 cut(s)	905
MhlI	GDGCHC	4 cut(s)	9, 110, 390, 408
MlyI	GAGTC	1 cut(s)	689
MmeI	TCCRAC	2 cut(s)	207, 534
MseI	TTAA	7 cut(s)	156, 267, 395, 846, 855, 867, 1331
MslI	CAYNNNNRTG	1 cut(s)	300
MspA1I	CMGCKG	1 cut(s)	726
MspCI	CTTAAG	2 cut(s)	266, 845
MspI	CCGG	1 cut(s)	111
Mva1269I	GAATGC	1 cut(s)	476
MwoI	GCNNNNNNNGC	3 cut(s)	364, 459, 1298
NcoI	CCATGG	1 cut(s)	1236
NdeI	CATATG	1 cut(s)	874
NdeII	GATC	5 cut(s)	577, 582, 905, 1261, 1284
NlaIII	CATG	5 cut(s)	340, 394, 1240, 1285, 1312
NmeAIII	GCCGAG	1 cut(s)	333
PagI	TCATGA	1 cut(s)	336
PceI	AGGCCT	1 cut(s)	224
PctI	GAATGC	1 cut(s)	476
PfeI	GAWTC	3 cut(s)	133, 1115, 1383
PkrI	GCNGC	5 cut(s)	151, 557, 725, 728, 1318
PleI	GAGTC	1 cut(s)	689
PpsI	GAGTC	1 cut(s)	689
PsiI	TTATAA	1 cut(s)	960
Psp124BI	GAGCTC	3 cut(s)	9, 110, 390
PspFI	CCCAGC	1 cut(s)	1094
PspPI	GGNCC	1 cut(s)	113
PsuI	RGATCY	1 cut(s)	905
PvuII	CAGCTG	1 cut(s)	726
RsaI	GTAC	3 cut(s)	47, 191, 1085
RsaNI	GTAC	3 cut(s)	46, 190, 1084
RseI	CAYNNNNRTG	1 cut(s)	300
SacI	GAGCTC	3 cut(s)	9, 110, 390
SaqAI	TTAA	7 cut(s)	156, 267, 395, 846, 855, 867, 1331
SatI	GCNGC	5 cut(s)	150, 556, 724, 727, 1317
Sau3AI	GATC	5 cut(s)	577, 582, 905, 1261, 1284
Sau96I	GGNCC	1 cut(s)	113
SchI	GAGTC	1 cut(s)	689
SduI	GDGCHC	4 cut(s)	9, 110, 390, 408
SfaNI	GCATC	2 cut(s)	302, 330
SmiMI	CAYNNNNRTG	1 cut(s)	300
SmlI	CTYRAG	2 cut(s)	266, 845
SmoI	CTYRAG	2 cut(s)	266, 845
SseBI	AGGCCT	1 cut(s)	224
SsiI	CCGC	3 cut(s)	19, 55, 1316
SspI	AATATT	1 cut(s)	997
SspMI	CTAG	3 cut(s)	1050, 1304, 1387
SstI	GAGCTC	3 cut(s)	9, 110, 390
StuI	AGGCCT	1 cut(s)	224
StyI	CCWWGG	3 cut(s)	225, 1036, 1236
TaaI	ACNGT	7 cut(s)	28, 418, 487, 634, 949, 1175, 1361
TaiI	ACGT	1 cut(s)	426
TaqI	TCGA	4 cut(s)	384, 585, 654, 1323
TatI	WGTACW	1 cut(s)	189
TauI	GCSGC	1 cut(s)	1319
TfiI	GAWTC	3 cut(s)	133, 1115, 1383
Tru1I	TTAA	7 cut(s)	156, 267, 395, 846, 855, 867, 1331
Tru9I	TTAA	7 cut(s)	156, 267, 395, 846, 855, 867, 1331
TscAI	CASTG	2 cut(s)	31, 89
TseI	GCWGC	4 cut(s)	149, 555, 723, 726
TspDTI	ATGAA	6 cut(s)	325, 512, 828, 909, 1043, 1058
TspGWI	ACGGA	3 cut(s)	80, 118, 145
TspRI	CASTG	2 cut(s)	31, 89
Vha464I	CTTAAG	2 cut(s)	266, 845
XapI	RAATTY	3 cut(s)	563, 815, 1138
XmiI	GTMKAC	2 cut(s)	426, 530
XspI	CTAG	3 cut(s)	1050, 1304, 1387
ZraI	GACGTC	1 cut(s)	424

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