Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1D

Orthogroup ID

OG0001472

Physical Location & Seq

Genomic Coordinates Reverse (-)

15433829 .. 15434605

Gene Structure 777 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1DG083800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 777 bp

ATGGACCTGTTTGAGGAAATGATCTCAAAGGATCAGATATTGCCTGATGTGCTAACGTACAACATTTTGATTAATGGTTTTTGCCGTGGTGGGAAAGTTAATAGGGCAAGGAAGATATTGGATTTTATGAAGAGCAAAGGATGCAACCCAAATGTATTCAATTACTCAGCTCTGATGAATGGATTCTGTAAGGAGGAAAGATTGGAGGAGACCAAGGAGCTTTTGGATGAAATGAAGATCTTTGGTTTCAAACCAGATACAGTTGTCTACACTTTAATTGATTGCTACTGTAGGACTGGGAGAGTTGACGAAGCGATAGAGTTGCTCAAAGAGATGAAAGAAAGACGGTGCAAAGCTGAAACTGTGACTTTCAATGTGATACTTGGAGGATTATGTAGAGAAGGAAGAATTGAGGATAAGCTTGAGATGCTGGACAAACTTCCTTATGAGGGTATCTATCTGAATAAGGGAAGTTACAGGATTGTGTTGAATTCCTTGTGTCAGAAAGGCAAACTAAACAAAGCTAAAGAGTTGTTGAGATTGATGATGGGTAGGGGGTTTGTACTACATTATGCAACTTCAAACGAGTTGCTAGTTAGCCTTTGTGAGGCTGGAATGGCAGATGATGCAACTATGGTTTTATTTGGATTGGTGGAGTTGGGTTTCAAACCACTGCCTGATTCCTGGGCTCTTTTTGTTGAATCAATTTGCAGAGAAAGAAAGTTGCTGCCTGCATTTGAACTGCTCGATGAATTAGTTAATGAAGAGTTTGATTAA

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_1 PPR_2 PPR_3

Protein Analysis

258

Amino Acids

29.61

Weight (kDa)

5.21

Isoelectric Point (pI)

23.74

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	1 - 29	9.7e-07	PPR repeat family
PPR_long	PF17177	1 - 147	3.7e-06	Pentacotripeptide-repeat region of PRORP
PPR_3	PF13812	4 - 62	8.6e-12	Pentatricopeptide repeat domain
PPR_1	PF12854	13 - 44	5.7e-13	PPR repeat
PPR_2	PF13041	15 - 64	7.6e-18	PPR repeat family
PPR	PF01535	19 - 48	2.6e-08	PPR repeat
PPR_1	PF12854	46 - 79	1.8e-11	PPR repeat
PPR_2	PF13041	50 - 91	7.9e-10	PPR repeat family
PPR	PF01535	55 - 83	8e-06	PPR repeat
PPR_3	PF13812	74 - 129	3.4e-10	Pentatricopeptide repeat domain
PPR_1	PF12854	82 - 113	3.1e-11	PPR repeat
PPR_2	PF13041	91 - 133	9.4e-14	PPR repeat family
PPR	PF01535	91 - 117	4.4e-09	PPR repeat
PPR_2	PF13041	121 - 168	1.1e-08	PPR repeat family
PPR_1	PF12854	151 - 182	6.3e-06	PPR repeat

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Orthologous Genes (Group: OG0001472)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G12615
fragaria_vesca	FvH4_3g40110
malus_domestica	MD04G1014300.v1.1 MD04G1014400.v1.1 MD04G1015100.v1.1 MD04G1015700.v1.1 MD04G1015800.v1.1 MD04G1015900.v1.1 MD04G1016200.v1.1 MD04G1021600.v1.1 MD05G1145400.v1.1 MD07G1093000.v1.1 MD10G1069200.v1.1 MD11G1128800.v1.1
prunus_persica	Prupe.1G160300_v2.0.a1 Prupe.1G162600_v2.0.a1 Prupe.1G166700_v2.0.a1 Prupe.1G167000_v2.0.a1 Prupe.6G346200_v2.0.a1
pyrus_communis	pycom04g01130 pycom04g01150 pycom04g01200 pycom04g01740 pycom04g01770 pycom04g10990
rosa_chinensis	RchiOBHm_Chr4g0414121 RchiOBHm_Chr7g0237341
rosa_laevigata	RLG00000008171 RLG00000008172 RLG00000036265
rosa_multiflora	Rmu_co8044332.1_g000001 Rmu_co8232951.1_g000001 Rmu_sc0003264.1_g000004 Rmu_sc0012180.1_g000010 Rmu_sc0012322.1_g000001 Rmu_sc0029476.1_g000001
rosa_roxburghii	Rroxscaffold_1G00018610 Rroxscaffold_5G00358060 Rroxscaffold_5G00358070 Rroxscaffold_5G00358080
rosa_rugosa	Rorug04G0125800 Rorug04G0125900 Rorug04G0126000
rosa_samantha	Rh1DG083800 Rh3BG179700 Rh3DG195400 Rh4AG184400 Rh4BG183800 Rh4DG179700 Rh7BG314900
rosa_wichuraiana	Rw4G015690

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	267
AclWI	GGATC	1 cut(s)	39
AcsI	RAATTY	1 cut(s)	490
AfaI	GTAC	2 cut(s)	59, 564
AfiI	CCNNNNNNNGG	3 cut(s)	13, 449, 607
AgsI	TTSAA	8 cut(s)	160, 250, 373, 490, 582, 667, 701, 740
AjnI	CCWGG	1 cut(s)	683
AluBI	AGCT	5 cut(s)	170, 220, 356, 421, 524
AluI	AGCT	5 cut(s)	170, 220, 356, 421, 524
Alw26I	GTCTC	1 cut(s)	203
AlwI	GGATC	1 cut(s)	39
ApeKI	GCWGC	1 cut(s)	727
ApoI	RAATTY	1 cut(s)	490
AseI	ATTAAT	1 cut(s)	72
Asp700I	GAANNNNTTC	1 cut(s)	182
AspS9I	GGNCC	1 cut(s)	4
AvaII	GGWCC	1 cut(s)	4
BaeI	ACNNNNGTAYC	2 cut(s)	249, 282
BanII	GRGCYC	1 cut(s)	691
BbvI	GCAGC	1 cut(s)	714
BccI	CCATC	1 cut(s)	541
BceAI	ACGGC	1 cut(s)	69
BcgI	CGANNNNNNTGC	2 cut(s)	304, 338
BciT130I	CCWGG	1 cut(s)	685
BcoDI	GTCTC	1 cut(s)	203
BfaI	CTAG	1 cut(s)	593
BfmI	CTRYAG	1 cut(s)	289
BglII	AGATCT	1 cut(s)	237
BisI	GCNGC	1 cut(s)	728
BlsI	GCNGC	1 cut(s)	729
Bme1390I	CCNGG	1 cut(s)	685
Bme18I	GGWCC	1 cut(s)	4
BmgT120I	GGNCC	1 cut(s)	4
BmrFI	CCNGG	1 cut(s)	685
BmrI	ACTGGG	1 cut(s)	306
BmsI	GCATC	3 cut(s)	131, 417, 616
BmuI	ACTGGG	1 cut(s)	306
BpuEI	CTTGAG	1 cut(s)	443
BsaI	GGTCTC	1 cut(s)	203
BsaJI	CCNNGG	3 cut(s)	85, 213, 684
Bsc4I	CCNNNNNNNGG	3 cut(s)	13, 449, 607
Bse1I	ACTGG	1 cut(s)	301
BseBI	CCWGG	1 cut(s)	685
BseDI	CCNNGG	3 cut(s)	85, 213, 684
BseGI	GGATG	2 cut(s)	146, 232
BseLI	CCNNNNNNNGG	3 cut(s)	13, 449, 607
BseMII	CTCAG	1 cut(s)	180
BseNI	ACTGG	1 cut(s)	301
BseRI	GAGGAG	1 cut(s)	221
BseXI	GCAGC	1 cut(s)	714
BslI	CCNNNNNNNGG	3 cut(s)	13, 449, 607
BsmAI	GTCTC	1 cut(s)	203
Bso31I	GGTCTC	1 cut(s)	203
Bsp1286I	GDGCHC	1 cut(s)	691
Bsp143I	GATC	3 cut(s)	21, 31, 237
BspCNI	CTCAG	1 cut(s)	179
BspPI	GGATC	1 cut(s)	39
BspQI	GCTCTTC	1 cut(s)	125
BspTNI	GGTCTC	1 cut(s)	203
BsrI	ACTGG	1 cut(s)	301
BssECI	CCNNGG	3 cut(s)	85, 213, 684
BssMI	GATC	3 cut(s)	21, 31, 237
BssT1I	CCWWGG	1 cut(s)	213
Bst2UI	CCWGG	1 cut(s)	685
Bst4CI	ACNGT	4 cut(s)	262, 290, 348, 364
Bst6I	CTCTTC	2 cut(s)	125, 759
BstAPI	GCANNNNNTGC	2 cut(s)	141, 626
BstC8I	GCNNGC	1 cut(s)	732
BstDEI	CTNAG	1 cut(s)	166
BstDSI	CCRYGG	1 cut(s)	85
BstENI	CCTNNNNNAGG	2 cut(s)	11, 605
BstF5I	GGATG	2 cut(s)	146, 232
BstKTI	GATC	3 cut(s)	24, 34, 240
BstMAI	GTCTC	1 cut(s)	203
BstMBI	GATC	3 cut(s)	21, 31, 237
BstMWI	GCNNNNNNNGC	5 cut(s)	49, 141, 427, 617, 626
BstNI	CCWGG	1 cut(s)	685
BstSCI	CCNGG	1 cut(s)	683
BstSFI	CTRYAG	1 cut(s)	289
BstV1I	GCAGC	1 cut(s)	714
BstX2I	RGATCY	1 cut(s)	237
BstYI	RGATCY	1 cut(s)	237
BtgI	CCRYGG	1 cut(s)	85
BtsCI	GGATG	2 cut(s)	146, 232
BtsI	GCAGTG	1 cut(s)	671
BtsIMutI	CAGTG	1 cut(s)	671
Cac8I	GCNNGC	1 cut(s)	732
Cfr13I	GGNCC	1 cut(s)	4
Csp6I	GTAC	2 cut(s)	58, 563
CviJI	RGCY	8 cut(s)	170, 220, 356, 421, 524, 600, 611, 689
CviKI_1	RGCY	8 cut(s)	170, 220, 356, 421, 524, 600, 611, 689
CviQI	GTAC	2 cut(s)	58, 563
DdeI	CTNAG	1 cut(s)	166
DpnI	GATC	3 cut(s)	23, 33, 239
DpnII	GATC	3 cut(s)	21, 31, 237
Eam1104I	CTCTTC	2 cut(s)	125, 759
EarI	CTCTTC	2 cut(s)	125, 759
Eco130I	CCWWGG	1 cut(s)	213
Eco24I	GRGCYC	1 cut(s)	691
Eco31I	GGTCTC	1 cut(s)	203
Eco47I	GGWCC	1 cut(s)	4
EcoNI	CCTNNNNNAGG	2 cut(s)	11, 605
EcoRI	GAATTC	1 cut(s)	490
EcoRII	CCWGG	1 cut(s)	683
EcoT14I	CCWWGG	1 cut(s)	213
EcoT38I	GRGCYC	1 cut(s)	691
ErhI	CCWWGG	1 cut(s)	213
FaiI	YATR	5 cut(s)	128, 394, 447, 573, 635
FblI	GTMKAC	1 cut(s)	267
Fnu4HI	GCNGC	1 cut(s)	728
FokI	GGATG	2 cut(s)	153, 239
FriOI	GRGCYC	1 cut(s)	691
Fsp4HI	GCNGC	1 cut(s)	728
FspBI	CTAG	1 cut(s)	593
GluI	GCNGC	1 cut(s)	728
HincII	GTYRAC	1 cut(s)	307
HindII	GTYRAC	1 cut(s)	307
HindIII	AAGCTT	1 cut(s)	419
HinfI	GANTC	3 cut(s)	183, 680, 701
Hpy166II	GTNNAC	2 cut(s)	268, 307
Hpy188I	TCNGA	4 cut(s)	36, 174, 462, 504
Hpy8I	GTNNAC	2 cut(s)	268, 307
HpyAV	CCTTC	1 cut(s)	395
HpyCH4III	ACNGT	4 cut(s)	262, 290, 348, 364
HpyCH4IV	ACGT	1 cut(s)	56
HpyCH4V	TGCA	6 cut(s)	144, 351, 575, 629, 711, 734
HpyF10VI	GCNNNNNNNGC	5 cut(s)	49, 141, 427, 617, 626
HpyF3I	CTNAG	1 cut(s)	166
HpySE526I	ACGT	1 cut(s)	56
Kzo9I	GATC	3 cut(s)	21, 31, 237
LguI	GCTCTTC	1 cut(s)	125
LmnI	GCTCC	1 cut(s)	217
Lsp1109I	GCAGC	1 cut(s)	714
LweI	GCATC	3 cut(s)	131, 417, 616
MaeI	CTAG	1 cut(s)	593
MaeII	ACGT	1 cut(s)	56
MaeIII	GTNAC	2 cut(s)	364, 473
MalI	GATC	3 cut(s)	23, 33, 239
MboI	GATC	3 cut(s)	21, 31, 237
MboII	GAAGA	5 cut(s)	124, 142, 247, 417, 776
MflI	RGATCY	1 cut(s)	237
MhlI	GDGCHC	1 cut(s)	691
MluCI	AATT	6 cut(s)	160, 276, 408, 490, 705, 752
MnlI	CCTC	7 cut(s)	7, 187, 199, 380, 406, 442, 601
MroXI	GAANNNNTTC	1 cut(s)	182
MseI	TTAA	5 cut(s)	72, 99, 275, 759, 775
MspR9I	CCNGG	1 cut(s)	685
MvaI	CCWGG	1 cut(s)	685
MwoI	GCNNNNNNNGC	5 cut(s)	49, 141, 427, 617, 626
NdeII	GATC	3 cut(s)	21, 31, 237
NmuCI	GTSAC	1 cut(s)	364
PciSI	GCTCTTC	1 cut(s)	125
PdmI	GAANNNNTTC	1 cut(s)	182
PfeI	GAWTC	3 cut(s)	183, 680, 701
PkrI	GCNGC	1 cut(s)	729
PshBI	ATTAAT	1 cut(s)	72
Psp6I	CCWGG	1 cut(s)	683
PspGI	CCWGG	1 cut(s)	683
PspPI	GGNCC	1 cut(s)	4
PsuI	RGATCY	1 cut(s)	237
RsaI	GTAC	2 cut(s)	59, 564
RsaNI	GTAC	2 cut(s)	58, 563
SapI	GCTCTTC	1 cut(s)	125
SaqAI	TTAA	5 cut(s)	72, 99, 275, 759, 775
SatI	GCNGC	1 cut(s)	728
Sau3AI	GATC	3 cut(s)	21, 31, 237
Sau96I	GGNCC	1 cut(s)	4
ScrFI	CCNGG	1 cut(s)	685
SduI	GDGCHC	1 cut(s)	691
SetI	ASST	7 cut(s)	9, 59, 172, 222, 358, 423, 526
SfaNI	GCATC	3 cut(s)	131, 417, 616
SfcI	CTRYAG	1 cut(s)	289
SinI	GGWCC	1 cut(s)	4
SmlI	CTYRAG	1 cut(s)	422
SmoI	CTYRAG	1 cut(s)	422
Sse9I	AATT	6 cut(s)	160, 276, 408, 490, 705, 752
SspMI	CTAG	1 cut(s)	593
StyD4I	CCNGG	1 cut(s)	683
StyI	CCWWGG	1 cut(s)	213
TaaI	ACNGT	4 cut(s)	262, 290, 348, 364
TaiI	ACGT	1 cut(s)	59
TaqI	TCGA	1 cut(s)	747
TasI	AATT	6 cut(s)	160, 276, 408, 490, 705, 752
TatI	WGTACW	1 cut(s)	562
TfiI	GAWTC	3 cut(s)	183, 680, 701
Tru1I	TTAA	5 cut(s)	72, 99, 275, 759, 775
Tru9I	TTAA	5 cut(s)	72, 99, 275, 759, 775
TscAI	CASTG	1 cut(s)	678
TseFI	GTSAC	1 cut(s)	364
TseI	GCWGC	1 cut(s)	727
Tsp45I	GTSAC	1 cut(s)	364
TspDTI	ATGAA	7 cut(s)	143, 191, 243, 248, 350, 765, 777
TspRI	CASTG	1 cut(s)	678
VpaK11BI	GGWCC	1 cut(s)	4
VspI	ATTAAT	1 cut(s)	72
XagI	CCTNNNNNAGG	2 cut(s)	11, 605
XapI	RAATTY	1 cut(s)	490
XcmI	CCANNNNNNNNNTGG	1 cut(s)	220
XmiI	GTMKAC	1 cut(s)	267
XmnI	GAANNNNTTC	1 cut(s)	182
XspI	CTAG	1 cut(s)	593

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