Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr2A

Orthogroup ID

OG0007987

Physical Location & Seq

Genomic Coordinates Forward (+)

71710092 .. 71714298

Gene Structure 4207 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh2AG495800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1779 bp

ATGCCTCAAGCCCTTTTCTTGAAGCCCTTCATTTCCGCTCCTTTGGATAATTGGAGTAAATTGAAAGAATGCACAAATTCTATAGGTGCCAATGTGAAGATGCGTGGAAGACTGGAGGTGGTTTGTATGGGAATGCTGGCACCAAGAAAGTTCTTGCAGAAAAGAAAGAAAGTGGAGGTTTTTAAAGACGTTGGCGATGAGGCTGACCAGAAGAACTGGAGGAGACTGATGAATGAAATTGAAGAGAAGGGTTCTGCTGTTGCAGTGCTCAAAAGCGAAAAGCTCAAAAACAAGACGATTCCTAAGGATCTTGTTCTTGGAACGTTGGTTAGATTCAAGCAATTGAGGAAATGGAACCTTGTCGGTGAGATTCTTGAATGGCTTCAGACTCAGGACTGGTGGGACTTCAGCGAAATGGATTTTCTGATGCTTATAACAGCTTATGGAAAGCAAGGCAAATTCAACAGGGCTGAGAAGGTTTTAAGCTTGTTGAATGAAAAGGGCTATGCACCAAGTGTAATATCACATACTGCTCTTATGGAAGCATATGGAAAAGGAGGCCGATACAACAATGCTGAAGCAATATTTCGAAGAATGCAGTCTTCAGGGCCTGAACCATCTGCTGTGACATATCAAATCATACTAAAAATATTTGTTGAGGGCTGCAAGTTTAAGGAAGCTGAAGAAATCTTTGAGACCCTTTTGGATGAGGAAAAGTCACCTTTAAAGCCAGACCAAAAGATGTTCCACATGATGATCTATATGTTTAAGAAGGCTGGAAGTTATGAAAAAGCTCGTAAGATGTTTGCAGTGATGACTGAGAGAGGGGTTCGGCAATCAACAGTTACTTATAATAGCCTAATGTCGTTTGAAACTAACTACAAGGAAGTATCAAAGATGTACAACCAGATGCAAAGAGCTGGTCTCCGACCTGACGTTGTGAGTTATGCCTTACTCATTAATGCTTATGGGAAAGCTAGAAGAGAGGAAGAAGCCTTAGCTGTTTTTGAGGAAATGCTTGATGCTGGTGTCAGACCTACCCGCAAAGCATACAATATTTTGCTCGACGCATTTGCAGTATCAGGAATGGTGGACCAAGCTCGAACTGTTTTTAAAAGCATGAGAAGGGACAGGTATGAACCCGATATATACTCGTATACCACTATGCTGTCAGCTTATGTAAATGCACCCGACATGGAAGGTGCTGAAAAATTCTTCACAAGACTAAAGCAAGATGGATTCAAACCCAATGTCGTCACTTATGGGACCTTAATCAAAGGTTATGCTAAGACAAATGATATTGAGAAGATGATGGAGAAATATGAGGAAATGCAGGCATGTGGGGTCAAACCAAATCAAACTATCTTGACAACCATAATGGATGCGTATGGCAAGAACATTGATTTTGGGAGTGCTGTTGTTTGGTACAAGGAAATGGAATCCTGCAGGCTTACTCCTGATCAGAAAGCAAAGAATATCCTTTTATCTTTGGCAAAAACTGTAGAAGAACAACAGTTAGCAAACCAAATTTTAGGATATTTGGATAATACTAGCAATGAACAAGGACTTGGTCGTTTATCAATCTCTGTTGAGCAGAATGATGAGGATGAAGACAATTACGAAGATGATGAAGACGACGATGACAGTTATGATGAGGAAGTCGATGGTCCTTCACAGGTCACTTCATCATATGATGATGAACAAGAAAGTGAGCTGGTTTATTTAAATGCTGATAGTGAAAAAAACCTCGATGACTTACTTACAGTGGCTGAATTGTAA

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

592

Amino Acids

67.88

Weight (kDa)

5.11

Isoelectric Point (pI)

40.89

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_3	PF13812	139 - 185	9.9e-06	Pentatricopeptide repeat domain
TPR_24	PF23276	148 - 239	4e-07	Fungal tetratrico peptide repeats
PPR_2	PF13041	171 - 217	2.5e-08	PPR repeat family
PPR_long	PF17177	242 - 375	1.4e-08	Pentacotripeptide-repeat region of PRORP
PPR_3	PF13812	302 - 358	9.8e-12	Pentatricopeptide repeat domain
TPR_24	PF23276	303 - 406	3.6e-07	Fungal tetratrico peptide repeats
PPR_1	PF12854	308 - 339	1.2e-06	PPR repeat
PPR_2	PF13041	311 - 359	4.3e-12	PPR repeat family
PPR	PF01535	314 - 344	2e-06	PPR repeat
PPR_2	PF13041	350 - 394	2.8e-10	PPR repeat family
TPR_24	PF23276	351 - 443	8e-06	Fungal tetratrico peptide repeats
PPR_long	PF17177	364 - 482	3.9e-09	Pentacotripeptide-repeat region of PRORP
PPR_3	PF13812	370 - 428	2.8e-12	Pentatricopeptide repeat domain
PPR_2	PF13041	381 - 430	2.2e-13	PPR repeat family
PPR_3	PF13812	410 - 466	4.5e-08	Pentatricopeptide repeat domain
PPR_1	PF12854	412 - 444	3.3e-06	PPR repeat
PPR_2	PF13041	416 - 453	5.8e-09	PPR repeat family
PPR	PF01535	419 - 449	5.5e-06	PPR repeat

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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Orthologous Genes (Group: OG0007987)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G59040 AT3G59040
fragaria_vesca	FvH4_6g38970 FvH4_6g38970 FvH4_6g38970 FvH4_6g38970 FvH4_6g38970
malus_domestica	MD09G1145700.v1.1
prunus_persica	Prupe.3G180100_v2.0.a1
pyrus_communis	pycom09g06600
rosa_chinensis	RchiOBHm_Chr2g0152561
rosa_laevigata	RLG00000020646
rosa_multiflora	Rmu_co8487657.1_g000002 Rmu_sc0027676.1_g000001 Rmu_sc0027677.1_g000001
rosa_roxburghii	Rroxscaffold_2G00095600
rosa_rugosa	Rorug02G0434500
rosa_samantha	Rh2AG495800 Rh2BG507600 Rh2CG482000 Rh2DG518900
rosa_wichuraiana	Rw0G004830 Rw2G040790 Rw2G041270

Restriction Enzyme Sites

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Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	2 cut(s)	434, 852
AccB1I	GGYRCC	2 cut(s)	86, 139
AccBSI	CCGCTC	1 cut(s)	38
AccI	GTMKAC	1 cut(s)	1157
AciI	CCGC	2 cut(s)	36, 1042
AclI	AACGTT	1 cut(s)	323
AclWI	GGATC	1 cut(s)	315
AcsI	RAATTY	4 cut(s)	76, 458, 1211, 1527
AcuI	CTGAAG	5 cut(s)	368, 391, 588, 597, 702
AdeI	CACNNNGTG	1 cut(s)	515
AfaI	GTAC	2 cut(s)	902, 1427
AgsI	TTSAA	9 cut(s)	22, 64, 242, 337, 377, 463, 493, 872, 1243
AjuI	GAANNNNNNNTTGG	2 cut(s)	1551, 1583
Alw21I	GWGCWC	1 cut(s)	270
Alw26I	GTCTC	3 cut(s)	217, 689, 929
AlwI	GGATC	1 cut(s)	315
AlwNI	CAGNNNCTG	2 cut(s)	611, 1769
AoxI	GGCC	2 cut(s)	559, 608
ApeKI	GCWGC	1 cut(s)	663
ApoI	RAATTY	4 cut(s)	76, 458, 1211, 1527
ArsI	GACNNNNNNTTYG	4 cut(s)	907, 939, 1236, 1268
AseI	ATTAAT	1 cut(s)	960
Asp700I	GAANNNNTTC	2 cut(s)	26, 381
AspS9I	GGNCC	4 cut(s)	608, 1093, 1266, 1667
AsuHPI	GGTGA	2 cut(s)	377, 711
AsuII	TTCGAA	1 cut(s)	589
AvaII	GGWCC	3 cut(s)	1093, 1266, 1667
AxyI	CCTNAGG	1 cut(s)	303
BanI	GGYRCC	2 cut(s)	86, 139
BbsI	GAAGAC	4 cut(s)	115, 594, 1617, 1638
Bbv12I	GWGCWC	1 cut(s)	270
BbvI	GCAGC	1 cut(s)	650
BccI	CCATC	4 cut(s)	625, 1229, 1306, 1658
BcgI	CGANNNNNNTGC	2 cut(s)	1055, 1089
BclI	TGATCA	1 cut(s)	1459
BcoDI	GTCTC	3 cut(s)	217, 689, 929
BfaI	CTAG	2 cut(s)	978, 1551
BfmI	CTRYAG	3 cut(s)	81, 1444, 1500
BisI	GCNGC	1 cut(s)	664
BlsI	GCNGC	1 cut(s)	665
Bme18I	GGWCC	3 cut(s)	1093, 1266, 1667
BmgT120I	GGNCC	4 cut(s)	608, 1093, 1266, 1667
BmiI	GGNNCC	4 cut(s)	88, 141, 356, 1267
BmsI	GCATC	5 cut(s)	90, 417, 900, 1012, 1372
BpiI	GAAGAC	4 cut(s)	115, 594, 1617, 1638
BplI	GAGNNNNNCTC	2 cut(s)	909, 941
BpmI	CTGGAG	2 cut(s)	134, 238
Bpu10I	CCTNAGC	1 cut(s)	997
Bpu14I	TTCGAA	1 cut(s)	589
BsaI	GGTCTC	2 cut(s)	689, 929
Bse1I	ACTGG	3 cut(s)	117, 221, 401
Bse21I	CCTNAGG	1 cut(s)	303
Bse3DI	GCAATG	1 cut(s)	1561
BseGI	GGATG	3 cut(s)	712, 1387, 1612
BseMI	GCAATG	1 cut(s)	1561
BseMII	CTCAG	3 cut(s)	404, 462, 810
BseNI	ACTGG	3 cut(s)	117, 221, 401
BseRI	GAGGAG	1 cut(s)	235
BseXI	GCAGC	1 cut(s)	650
BshFI	GGCC	2 cut(s)	561, 610
BshNI	GGYRCC	2 cut(s)	86, 139
BsiHKAI	GWGCWC	1 cut(s)	270
BslFI	GGGAC	3 cut(s)	416, 1142, 1279
BsmAI	GTCTC	3 cut(s)	217, 689, 929
BsmFI	GGGAC	3 cut(s)	416, 1142, 1279
BsmI	GAATGC	3 cut(s)	74, 138, 600
BsnI	GGCC	2 cut(s)	561, 610
Bso31I	GGTCTC	2 cut(s)	689, 929
Bsp119I	TTCGAA	1 cut(s)	589
Bsp1286I	GDGCHC	1 cut(s)	270
Bsp1407I	TGTACA	1 cut(s)	900
Bsp143I	GATC	3 cut(s)	307, 756, 1459
BspACI	CCGC	2 cut(s)	36, 1042
BspANI	GGCC	2 cut(s)	561, 610
BspCNI	CTCAG	3 cut(s)	403, 463, 811
BspLI	GGNNCC	4 cut(s)	88, 141, 356, 1267
BspMAI	CTGCAG	1 cut(s)	1448
BspPI	GGATC	1 cut(s)	315
BspT104I	TTCGAA	1 cut(s)	589
BspT107I	GGYRCC	2 cut(s)	86, 139
BspTNI	GGTCTC	2 cut(s)	689, 929
BsrBI	CCGCTC	1 cut(s)	38
BsrDI	GCAATG	1 cut(s)	1561
BsrGI	TGTACA	1 cut(s)	900
BsrI	ACTGG	3 cut(s)	117, 221, 401
BssMI	GATC	3 cut(s)	307, 756, 1459
BssNAI	GTATAC	1 cut(s)	1158
Bst1107I	GTATAC	1 cut(s)	1158
Bst4CI	ACNGT	6 cut(s)	844, 1108, 1501, 1515, 1646, 1765
Bst6I	CTCTTC	2 cut(s)	237, 976
BstAUI	TGTACA	1 cut(s)	900
BstBI	TTCGAA	1 cut(s)	589
BstC8I	GCNNGC	3 cut(s)	138, 1335, 1448
BstDEI	CTNAG	6 cut(s)	303, 390, 471, 819, 997, 1287
BstF5I	GGATG	3 cut(s)	712, 1387, 1612
BstKTI	GATC	3 cut(s)	310, 759, 1462
BstMAI	GTCTC	3 cut(s)	217, 689, 929
BstMBI	GATC	3 cut(s)	307, 756, 1459
BstNSI	RCATGY	1 cut(s)	1341
BstSFI	CTRYAG	3 cut(s)	81, 1444, 1500
BstV1I	GCAGC	1 cut(s)	650
BstV2I	GAAGAC	4 cut(s)	115, 594, 1617, 1638
BstX2I	RGATCY	1 cut(s)	307
BstYI	RGATCY	1 cut(s)	307
BstZ17I	GTATAC	1 cut(s)	1158
Bsu36I	CCTNAGG	1 cut(s)	303
BsuRI	GGCC	2 cut(s)	561, 610
BtgZI	GCGATG	1 cut(s)	210
BtsCI	GGATG	3 cut(s)	712, 1387, 1612
BtsI	GCAGTG	2 cut(s)	270, 816
BtsIMutI	CAGTG	3 cut(s)	270, 816, 1770
Cac8I	GCNNGC	3 cut(s)	138, 1335, 1448
CaiI	CAGNNNCTG	2 cut(s)	611, 1769
Cfr13I	GGNCC	4 cut(s)	608, 1093, 1266, 1667
CseI	GACGC	1 cut(s)	1076
Csp6I	GTAC	2 cut(s)	901, 1426
CviAII	CATG	4 cut(s)	751, 1120, 1195, 1338
CviQI	GTAC	2 cut(s)	901, 1426
DdeI	CTNAG	6 cut(s)	303, 390, 471, 819, 997, 1287
DpnI	GATC	3 cut(s)	309, 758, 1461
DpnII	GATC	3 cut(s)	307, 756, 1459
DraI	TTTAAA	4 cut(s)	184, 726, 1114, 1725
DraIII	CACNNNGTG	1 cut(s)	515
Eam1104I	CTCTTC	2 cut(s)	237, 976
EarI	CTCTTC	2 cut(s)	237, 976
Eco31I	GGTCTC	2 cut(s)	689, 929
Eco47I	GGWCC	3 cut(s)	1093, 1266, 1667
Eco57I	CTGAAG	5 cut(s)	368, 391, 588, 597, 702
Eco81I	CCTNAGG	1 cut(s)	303
EcoO109I	RGGNCCY	2 cut(s)	608, 1266
FaeI	CATG	4 cut(s)	754, 1123, 1198, 1341
FaqI	GGGAC	3 cut(s)	416, 1142, 1279
FatI	CATG	4 cut(s)	750, 1119, 1194, 1337
FauI	CCCGC	1 cut(s)	1049
FauNDI	CATATG	2 cut(s)	547, 1690
FbaI	TGATCA	1 cut(s)	1459
FblI	GTMKAC	1 cut(s)	1157
Fnu4HI	GCNGC	1 cut(s)	664
FokI	GGATG	3 cut(s)	719, 1394, 1619
Fsp4HI	GCNGC	1 cut(s)	664
FspBI	CTAG	2 cut(s)	978, 1551
GluI	GCNGC	1 cut(s)	664
GsuI	CTGGAG	2 cut(s)	134, 238
HaeIII	GGCC	2 cut(s)	561, 610
HgaI	GACGC	1 cut(s)	1076
Hin1II	CATG	4 cut(s)	754, 1123, 1198, 1341
HindIII	AAGCTT	1 cut(s)	484
HinfI	GANTC	6 cut(s)	298, 333, 370, 388, 1239, 1439
HphI	GGTGA	2 cut(s)	377, 711
Hpy166II	GTNNAC	2 cut(s)	1093, 1158
Hpy188I	TCNGA	5 cut(s)	387, 426, 929, 1034, 1464
Hpy188III	TCNNGA	6 cut(s)	19, 374, 392, 1083, 1366, 1457
Hpy8I	GTNNAC	2 cut(s)	1093, 1158
Hpy99I	CGWCG	2 cut(s)	1070, 1640
HpyAV	CCTTC	7 cut(s)	37, 241, 469, 766, 1119, 1193, 1680
HpyCH4III	ACNGT	6 cut(s)	844, 1108, 1501, 1515, 1646, 1765
HpyCH4IV	ACGT	3 cut(s)	189, 323, 936
HpyF3I	CTNAG	6 cut(s)	303, 390, 471, 819, 997, 1287
HpySE526I	ACGT	3 cut(s)	189, 323, 936
Hsp92II	CATG	4 cut(s)	754, 1123, 1198, 1341
Ksp22I	TGATCA	1 cut(s)	1459
Kzo9I	GATC	3 cut(s)	307, 756, 1459
LmnI	GCTCC	1 cut(s)	43
Lsp1109I	GCAGC	1 cut(s)	650
LweI	GCATC	5 cut(s)	90, 417, 900, 1012, 1372
MaeI	CTAG	2 cut(s)	978, 1551
MaeII	ACGT	3 cut(s)	189, 323, 936
MaeIII	GTNAC	5 cut(s)	625, 717, 844, 1255, 1678
MalI	GATC	3 cut(s)	309, 758, 1461
MbiI	CCGCTC	1 cut(s)	38
MboI	GATC	3 cut(s)	307, 756, 1459
MfeI	CAATTG	1 cut(s)	341
MflI	RGATCY	1 cut(s)	307
MhlI	GDGCHC	1 cut(s)	270
MlyI	GAGTC	1 cut(s)	382
MmeI	TCCRAC	1 cut(s)	952
MroXI	GAANNNNTTC	2 cut(s)	26, 381
MseI	TTAA	9 cut(s)	183, 482, 672, 725, 768, 960, 1113, 1271, 1724
MunI	CAATTG	1 cut(s)	341
Mva1269I	GAATGC	3 cut(s)	74, 138, 600
NdeI	CATATG	2 cut(s)	547, 1690
NdeII	GATC	3 cut(s)	307, 756, 1459
NlaIII	CATG	4 cut(s)	754, 1123, 1198, 1341
NlaIV	GGNNCC	4 cut(s)	88, 141, 356, 1267
NmuCI	GTSAC	4 cut(s)	625, 717, 1255, 1678
NspI	RCATGY	1 cut(s)	1341
NspV	TTCGAA	1 cut(s)	589
PctI	GAATGC	3 cut(s)	74, 138, 600
PdmI	GAANNNNTTC	2 cut(s)	26, 381
PfeI	GAWTC	5 cut(s)	298, 333, 370, 1239, 1439
PflFI	GACNNNGTC	1 cut(s)	1569
PkrI	GCNGC	1 cut(s)	665
PleI	GAGTC	1 cut(s)	382
PpsI	GAGTC	1 cut(s)	382
PpuMI	RGGWCCY	1 cut(s)	1266
PshBI	ATTAAT	1 cut(s)	960
PsiI	TTATAA	2 cut(s)	434, 852
Psp1406I	AACGTT	1 cut(s)	323
Psp5II	RGGWCCY	1 cut(s)	1266
PspN4I	GGNNCC	4 cut(s)	88, 141, 356, 1267
PspPI	GGNCC	4 cut(s)	608, 1093, 1266, 1667
PspPPI	RGGWCCY	1 cut(s)	1266
PstI	CTGCAG	1 cut(s)	1448
PstNI	CAGNNNCTG	2 cut(s)	611, 1769
PsuI	RGATCY	1 cut(s)	307
PsyI	GACNNNGTC	1 cut(s)	1569
RsaI	GTAC	2 cut(s)	902, 1427
RsaNI	GTAC	2 cut(s)	901, 1426
SaqAI	TTAA	9 cut(s)	183, 482, 672, 725, 768, 960, 1113, 1271, 1724
SatI	GCNGC	1 cut(s)	664
Sau3AI	GATC	3 cut(s)	307, 756, 1459
Sau96I	GGNCC	4 cut(s)	608, 1093, 1266, 1667
SbfI	CCTGCAGG	1 cut(s)	1448
SchI	GAGTC	1 cut(s)	382
SdaI	CCTGCAGG	1 cut(s)	1448
SduI	GDGCHC	1 cut(s)	270
SfaNI	GCATC	5 cut(s)	90, 417, 900, 1012, 1372
SfcI	CTRYAG	3 cut(s)	81, 1444, 1500
SfuI	TTCGAA	1 cut(s)	589
SinI	GGWCC	3 cut(s)	1093, 1266, 1667
SmiI	ATTTAAAT	1 cut(s)	1725
SmlI	CTYRAG	1 cut(s)	6
SmoI	CTYRAG	1 cut(s)	6
Sse8387I	CCTGCAGG	1 cut(s)	1448
SsiI	CCGC	2 cut(s)	36, 1042
SspI	AATATT	3 cut(s)	585, 651, 1057
SspMI	CTAG	2 cut(s)	978, 1551
SwaI	ATTTAAAT	1 cut(s)	1725
TaaI	ACNGT	6 cut(s)	844, 1108, 1501, 1515, 1646, 1765
TaiI	ACGT	3 cut(s)	192, 326, 939
TaqI	TCGA	5 cut(s)	589, 1065, 1102, 1662, 1749
TatI	WGTACW	1 cut(s)	900
TfiI	GAWTC	5 cut(s)	298, 333, 370, 1239, 1439
Tru1I	TTAA	9 cut(s)	183, 482, 672, 725, 768, 960, 1113, 1271, 1724
Tru9I	TTAA	9 cut(s)	183, 482, 672, 725, 768, 960, 1113, 1271, 1724
TscAI	CASTG	3 cut(s)	270, 816, 1770
TseFI	GTSAC	4 cut(s)	625, 717, 1255, 1678
TseI	GCWGC	1 cut(s)	663
Tsp45I	GTSAC	4 cut(s)	625, 717, 1255, 1678
TspRI	CASTG	3 cut(s)	270, 816, 1770
Tth111I	GACNNNGTC	1 cut(s)	1569
VpaK11BI	GGWCC	3 cut(s)	1093, 1266, 1667
VspI	ATTAAT	1 cut(s)	960
XapI	RAATTY	4 cut(s)	76, 458, 1211, 1527
XceI	RCATGY	1 cut(s)	1341
XmiI	GTMKAC	1 cut(s)	1157
XmnI	GAANNNNTTC	2 cut(s)	26, 381
XspI	CTAG	2 cut(s)	978, 1551

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