Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0002968

Physical Location & Seq

Genomic Coordinates Forward (+)

35561422 .. 35561994

Gene Structure 573 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG293400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 573 bp

ATGTATCTCAGCAACAAACACGCAGATGCAGTAACTTATACAGCAGTGATTAATGCATTGGGAAAGAAGGGTAGAATACAAGAGGCAACAGAACTTATGATGAAGATGCTGGGTAAGGGTATTGACCCGACTCCAGTCACATACAGGACGATCATCCACTGGTATTGTAAGTTGAATAGGGTGGATGATATGTTAAAATTATTGGAGAAGATGTTCTTGAGGCAACGTTGCAAAACAACATATAATCAAGTGATTGAGAAGCTTTGTAGTTTTGGAAACTTTGAGGCTGCTGATAAACTATTGGGTAAGGTGTTGAGAACAGCTTCAAGAGTTGATGCTGAAACATGCCATGTTGTTATGGATGGTTATTTGAGAAAAGAGGTTCCTCTATTAGCATACAAAGTGGCTTGTCGAATGTTCAATCGGAATCTGATTCCTGATTTAAAGTTGTGTCAGAATGTGACCAAGAGATTGATGCTAGAAGGATACTCCAAAGAGGCAGACAACCTTATGTTACGGTTTGTTGAGCGTGGATGCATATCAAACCAACTTCAGGAACATCTGGAAAGCTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0003006 GO:0003674 GO:0003676 GO:0003723 GO:0003824 GO:0004518 GO:0004519 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0006139 GO:0006725 GO:0006807 GO:0007275 GO:0008150 GO:0008152 GO:0009451 GO:0009507 GO:0009536 GO:0009790 GO:0009791 GO:0009793 GO:0009987 GO:0010154 GO:0016070 GO:0016787 GO:0016788 GO:0022414 GO:0032501 GO:0032502 GO:0034641 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043412 GO:0044237 GO:0044238 GO:0044424 GO:0044444 GO:0044464 GO:0046483 GO:0048316 GO:0048608 GO:0048731 GO:0048856 GO:0061458 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

190

Amino Acids

21.94

Weight (kDa)

9.23

Isoelectric Point (pI)

20.94

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_1	PF12854	8 - 36	2e-06	PPR repeat
PPR_2	PF13041	9 - 53	6e-12	PPR repeat family
PPR_3	PF13812	9 - 55	5.9e-06	Pentatricopeptide repeat domain
PPR	PF01535	11 - 41	1.5e-07	PPR repeat
PPR_1	PF12854	39 - 71	2.2e-08	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: OG0002968)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G30290 AT1G30290
fragaria_vesca	FvH4_3g05050 FvH4_3g05050 FvH4_3g05050 FvH4_3g05050 FvH4_3g05050 FvH4_3g05050 FvH4_3g05050 FvH4_3g05050
malus_domestica	MD10G1258300.v1.1
prunus_persica	Prupe.4G085500_v2.0.a1 Prupe.4G085500_v2.0.a1
pyrus_communis	pycom05g26000 pycom10g21460
rosa_chinensis	RchiOBHm_Chr3g0490541 RchiOBHm_Chr3g0490551 RchiOBHm_Chr5g0014911
rosa_laevigata	RLG00000022885 RLG00000032150
rosa_multiflora	Rmu_sc0003862.1_g000007 Rmu_sc0013610.1_g000002
rosa_roxburghii	Rroxscaffold_1G00061660 Rroxscaffold_6G00393420
rosa_rugosa	Rorug03G0243900 Rorug05G0021400
rosa_samantha	Rh3AG293300 Rh3AG293400 Rh3BG329800 Rh3CG327300 Rh3CG327400 Rh3DG326700 Rh5AG117100 Rh5BG114100 Rh5CG125600 Rh5DG113500
rosa_wichuraiana	Rw3G025970 Rw5G010080

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AclI	AACGTT	1 cut(s)	226
AcuI	CTGAAG	1 cut(s)	536
AfiI	CCNNNNNNNGG	1 cut(s)	553
AgsI	TTSAA	3 cut(s)	175, 327, 421
AloI	GAACNNNNNNTCC	2 cut(s)	197, 229
AluBI	AGCT	3 cut(s)	262, 323, 570
AluI	AGCT	3 cut(s)	262, 323, 570
ApeKI	GCWGC	1 cut(s)	287
AseI	ATTAAT	1 cut(s)	51
Asp700I	GAANNNNTTC	2 cut(s)	212, 322
BbvI	GCAGC	1 cut(s)	274
BccI	CCATC	1 cut(s)	356
BciVI	GTATCC	1 cut(s)	479
BfaI	CTAG	2 cut(s)	479, 571
BfuI	GTATCC	1 cut(s)	479
BisI	GCNGC	1 cut(s)	288
BlsI	GCNGC	1 cut(s)	289
BmiI	GGNNCC	1 cut(s)	384
BmsI	GCATC	5 cut(s)	16, 96, 325, 465, 524
BoxI	GACNNNNGTC	1 cut(s)	134
BpmI	CTGGAG	1 cut(s)	117
BpuEI	CTTGAG	1 cut(s)	238
BsaBI	GATNNNNATC	1 cut(s)	538
BsaXI	ACNNNNNCTCC	2 cut(s)	197, 227
Bsc4I	CCNNNNNNNGG	1 cut(s)	553
Bse1I	ACTGG	2 cut(s)	134, 164
Bse8I	GATNNNNATC	1 cut(s)	538
BseGI	GGATG	4 cut(s)	153, 190, 367, 539
BseJI	GATNNNNATC	1 cut(s)	538
BseLI	CCNNNNNNNGG	1 cut(s)	553
BseMII	CTCAG	1 cut(s)	22
BseNI	ACTGG	2 cut(s)	134, 164
BseXI	GCAGC	1 cut(s)	274
BseYI	CCCAGC	1 cut(s)	109
BslI	CCNNNNNNNGG	1 cut(s)	553
Bsp143I	GATC	1 cut(s)	150
BspCNI	CTCAG	1 cut(s)	21
BspLI	GGNNCC	1 cut(s)	384
BsrI	ACTGG	2 cut(s)	134, 164
BssMI	GATC	1 cut(s)	150
Bst4CI	ACNGT	1 cut(s)	519
BstDEI	CTNAG	1 cut(s)	8
BstF5I	GGATG	4 cut(s)	153, 190, 367, 539
BstKTI	GATC	1 cut(s)	153
BstMBI	GATC	1 cut(s)	150
BstNSI	RCATGY	1 cut(s)	348
BstPAI	GACNNNNGTC	1 cut(s)	134
BstV1I	GCAGC	1 cut(s)	274
BsuI	GTATCC	1 cut(s)	479
BtsCI	GGATG	4 cut(s)	153, 190, 367, 539
BtsI	GCAGTG	1 cut(s)	51
BtsIMutI	CAGTG	2 cut(s)	51, 157
CspCI	CAANNNNNGTGG	2 cut(s)	146, 181
CviAII	CATG	2 cut(s)	345, 350
CviJI	RGCY	5 cut(s)	262, 287, 323, 407, 570
CviKI_1	RGCY	5 cut(s)	262, 287, 323, 407, 570
DdeI	CTNAG	1 cut(s)	8
DpnI	GATC	1 cut(s)	152
DpnII	GATC	1 cut(s)	150
DraI	TTTAAA	1 cut(s)	444
Eco57I	CTGAAG	1 cut(s)	536
EcoT22I	ATGCAT	2 cut(s)	58, 539
FaeI	CATG	2 cut(s)	348, 353
FalI	AAGNNNNNCTT	2 cut(s)	200, 232
FatI	CATG	2 cut(s)	344, 349
Fnu4HI	GCNGC	1 cut(s)	288
FokI	GGATG	4 cut(s)	140, 197, 374, 546
Fsp4HI	GCNGC	1 cut(s)	288
FspBI	CTAG	2 cut(s)	479, 571
GluI	GCNGC	1 cut(s)	288
GsaI	CCCAGC	1 cut(s)	113
GsuI	CTGGAG	1 cut(s)	117
Hin1II	CATG	2 cut(s)	348, 353
HindIII	AAGCTT	1 cut(s)	260
HinfI	GANTC	3 cut(s)	130, 427, 433
Hpy188I	TCNGA	3 cut(s)	426, 432, 456
Hpy188III	TCNNGA	5 cut(s)	217, 327, 437, 554, 563
HpyAV	CCTTC	2 cut(s)	61, 476
HpyCH4III	ACNGT	1 cut(s)	519
HpyCH4IV	ACGT	1 cut(s)	226
HpyCH4V	TGCA	4 cut(s)	29, 56, 231, 537
HpyF3I	CTNAG	1 cut(s)	8
HpySE526I	ACGT	1 cut(s)	226
Hsp92II	CATG	2 cut(s)	348, 353
Kzo9I	GATC	1 cut(s)	150
LpnPI	CCDG	7 cut(s)	95, 130, 145, 147, 450, 539, 548
Lsp1109I	GCAGC	1 cut(s)	274
LweI	GCATC	5 cut(s)	16, 96, 325, 465, 524
MaeI	CTAG	2 cut(s)	479, 571
MaeII	ACGT	1 cut(s)	226
MaeIII	GTNAC	4 cut(s)	31, 136, 460, 513
MalI	GATC	1 cut(s)	152
MboI	GATC	1 cut(s)	150
MboII	GAAGA	2 cut(s)	115, 220
MluCI	AATT	1 cut(s)	197
MlyI	GAGTC	1 cut(s)	124
MnlI	CCTC	6 cut(s)	76, 213, 277, 373, 396, 490
Mph1103I	ATGCAT	2 cut(s)	58, 539
MroXI	GAANNNNTTC	2 cut(s)	212, 322
MseI	TTAA	3 cut(s)	51, 194, 443
MslI	CAYNNNNRTG	1 cut(s)	24
NdeII	GATC	1 cut(s)	150
NlaIII	CATG	2 cut(s)	348, 353
NlaIV	GGNNCC	1 cut(s)	384
NmuCI	GTSAC	2 cut(s)	136, 460
NsiI	ATGCAT	2 cut(s)	58, 539
NspI	RCATGY	1 cut(s)	348
PdmI	GAANNNNTTC	2 cut(s)	212, 322
PfeI	GAWTC	2 cut(s)	427, 433
PkrI	GCNGC	1 cut(s)	289
PleI	GAGTC	1 cut(s)	124
PpsI	GAGTC	1 cut(s)	124
PshAI	GACNNNNGTC	1 cut(s)	134
PshBI	ATTAAT	1 cut(s)	51
Psp1406I	AACGTT	1 cut(s)	226
PspFI	CCCAGC	1 cut(s)	109
PspN4I	GGNNCC	1 cut(s)	384
RseI	CAYNNNNRTG	1 cut(s)	24
SaqAI	TTAA	3 cut(s)	51, 194, 443
SatI	GCNGC	1 cut(s)	288
Sau3AI	GATC	1 cut(s)	150
SchI	GAGTC	1 cut(s)	124
SetI	ASST	7 cut(s)	229, 264, 312, 325, 384, 510, 572
SfaNI	GCATC	5 cut(s)	16, 96, 325, 465, 524
SmiMI	CAYNNNNRTG	1 cut(s)	24
SmlI	CTYRAG	1 cut(s)	217
SmoI	CTYRAG	1 cut(s)	217
Sse9I	AATT	1 cut(s)	197
SspMI	CTAG	2 cut(s)	479, 571
TaaI	ACNGT	1 cut(s)	519
TaiI	ACGT	1 cut(s)	229
TaqI	TCGA	1 cut(s)	412
TasI	AATT	1 cut(s)	197
TfiI	GAWTC	2 cut(s)	427, 433
Tru1I	TTAA	3 cut(s)	51, 194, 443
Tru9I	TTAA	3 cut(s)	51, 194, 443
TscAI	CASTG	2 cut(s)	51, 164
TseFI	GTSAC	2 cut(s)	136, 460
TseI	GCWGC	1 cut(s)	287
Tsp45I	GTSAC	2 cut(s)	136, 460
TspDTI	ATGAA	1 cut(s)	116
TspRI	CASTG	2 cut(s)	51, 164
VspI	ATTAAT	1 cut(s)	51
XceI	RCATGY	1 cut(s)	348
XmnI	GAANNNNTTC	2 cut(s)	212, 322
XspI	CTAG	2 cut(s)	479, 571
Zsp2I	ATGCAT	2 cut(s)	58, 539

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