Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1B

Orthogroup ID

OG0004806

Physical Location & Seq

Genomic Coordinates Forward (+)

9290210 .. 9295657

Gene Structure 5448 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1BG062800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 627 bp

ATGGAATCAGTGGAATCCTTGTATGGCATGTATAAGGAAAGACGTTTGGACGAAGCACTTGAGTTTCTTGCCAATATGGGTAAACTATTTCCCAGAGCTGTTGATAGGAGCTTTAGGATTTTAGGTTTCTGTGAGGAGGGTGCCACTGAGAATGCAAAGAAGGTCTATAATCAGATGATTGAGGAAAGGGCAGTCCCATGTGTTTTTATTTATGACTATCTAATCCATAGATTTTGCCAACAAGGGTGTGTTCGTCAAGCCTTTGAGCTTATGAATGAGATGATTGCTCATTGTTACTTTCCCGTTTCATCGATTTTCAATGTTCTGATTAACGGGTTTTGTGAGCAAGGAAAAGTTGGTAGTGCGCTAAAGCTCCTCGATGAGATGATTGGTAGAGGTTGTTTACCTGATATAGAAAGTTATAGTCATTTGGTAGGTGCTTTTTGCCAGAAGGGGGATTTTCAGAAAGCTTTAAAACTCGTTTTGCAAATGGTAGGAAAGGGTATCACTCCTGATTATTTCACATGGAACTCGTTGCTTCTTTGTTCAAGTCGAGAGACTGTATGGTTAAACAGCAAAAGTATGTTTTATGTGAATAATCAATTACGTTGTATTATTGAGGCTTAA

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

208

Amino Acids

23.87

Weight (kDa)

5.97

Isoelectric Point (pI)

32.7

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_long	PF17177	49 - 183	1.3e-08	Pentacotripeptide-repeat region of PRORP
PPR_2	PF13041	66 - 94	7.7e-06	PPR repeat family
PPR_1	PF12854	100 - 129	6.1e-09	PPR repeat
PPR_2	PF13041	103 - 150	1.9e-13	PPR repeat family
PPR	PF01535	105 - 134	7e-08	PPR repeat
PPR_3	PF13812	124 - 180	1.7e-07	Pentatricopeptide repeat domain
PPR_1	PF12854	132 - 165	4.6e-07	PPR repeat
PPR_2	PF13041	136 - 180	3.9e-10	PPR repeat family

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Orthologous Genes (Group: OG0004806)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G17525
fragaria_vesca	FvH4_7g03710 FvH4_7g03710 FvH4_7g03710
malus_domestica	MD05G1037900.v1.1 MD10G1041700.v1.1
prunus_persica	Prupe.2G066000_v2.0.a1
pyrus_communis	pycom05g02810 pycom10g02880
rosa_chinensis	RchiOBHm_Chr1g0326501 RchiOBHm_Chr1g0326531 RchiOBHm_Chr1g0326571 RchiOBHm_Chr1g0326581
rosa_laevigata	RLG00000005572 RLG00000006170 RLG00000023929 RLG00000030068
rosa_multiflora	Rmu_sc0001355.1_g000018
rosa_roxburghii	Rroxscaffold_2G00146300 Rroxscaffold_4G00323710 Rroxscaffold_4G00327680
rosa_rugosa	Rorug01G0061000
rosa_samantha	Rh1BG062600 Rh1BG062800 Rh1CG075400 Rh1DG082100 Rh1DG082200 Rh1DG082400 Rh7BG001800 Rh7DG001700
rosa_wichuraiana	Rw1G006130

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	140
AfiI	CCNNNNNNNGG	1 cut(s)	454
AgsI	TTSAA	2 cut(s)	319, 549
AluBI	AGCT	5 cut(s)	98, 111, 268, 373, 470
AluI	AGCT	5 cut(s)	98, 111, 268, 373, 470
Alw26I	GTCTC	1 cut(s)	551
AspLEI	GCGC	1 cut(s)	367
BanI	GGYRCC	1 cut(s)	140
BcoDI	GTCTC	1 cut(s)	551
BmiI	GGNNCC	1 cut(s)	142
BpuEI	CTTGAG	1 cut(s)	80
Bsa29I	ATCGAT	1 cut(s)	311
Bsc4I	CCNNNNNNNGG	1 cut(s)	454
BseCI	ATCGAT	1 cut(s)	311
BseLI	CCNNNNNNNGG	1 cut(s)	454
BseMII	CTCAG	1 cut(s)	138
BseRI	GAGGAG	2 cut(s)	149, 365
BshNI	GGYRCC	1 cut(s)	140
BshVI	ATCGAT	1 cut(s)	311
BslFI	GGGAC	1 cut(s)	179
BslI	CCNNNNNNNGG	1 cut(s)	454
BsmAI	GTCTC	1 cut(s)	551
BsmFI	GGGAC	1 cut(s)	179
BsmI	GAATGC	1 cut(s)	157
BspCNI	CTCAG	1 cut(s)	139
BspDI	ATCGAT	1 cut(s)	311
BspLI	GGNNCC	1 cut(s)	142
BspT107I	GGYRCC	1 cut(s)	140
Bst4CI	ACNGT	1 cut(s)	562
BstDEI	CTNAG	1 cut(s)	147
BstHHI	GCGC	1 cut(s)	367
BstMAI	GTCTC	1 cut(s)	551
BstNSI	RCATGY	1 cut(s)	31
Bsu15I	ATCGAT	1 cut(s)	311
BsuTUI	ATCGAT	1 cut(s)	311
BtsIMutI	CAGTG	2 cut(s)	15, 144
CfoI	GCGC	1 cut(s)	367
ClaI	ATCGAT	1 cut(s)	311
CviAII	CATG	3 cut(s)	28, 198, 525
CviJI	RGCY	7 cut(s)	98, 111, 260, 268, 373, 470, 623
CviKI_1	RGCY	7 cut(s)	98, 111, 260, 268, 373, 470, 623
DdeI	CTNAG	1 cut(s)	147
DraI	TTTAAA	1 cut(s)	474
FaeI	CATG	3 cut(s)	31, 201, 528
FaqI	GGGAC	1 cut(s)	179
FatI	CATG	3 cut(s)	27, 197, 524
GlaI	GCGC	1 cut(s)	366
HhaI	GCGC	1 cut(s)	367
Hin1II	CATG	3 cut(s)	31, 201, 528
Hin6I	GCGC	1 cut(s)	365
HinP1I	GCGC	1 cut(s)	365
HindIII	AAGCTT	1 cut(s)	468
HinfI	GANTC	2 cut(s)	5, 14
Hpy166II	GTNNAC	2 cut(s)	83, 404
Hpy188I	TCNGA	3 cut(s)	174, 327, 465
Hpy188III	TCNNGA	2 cut(s)	512, 554
Hpy8I	GTNNAC	2 cut(s)	83, 404
HpyAV	CCTTC	2 cut(s)	154, 445
HpyCH4III	ACNGT	1 cut(s)	562
HpyCH4IV	ACGT	2 cut(s)	43, 607
HpyCH4V	TGCA	2 cut(s)	155, 487
HpyF3I	CTNAG	1 cut(s)	147
HpySE526I	ACGT	2 cut(s)	43, 607
Hsp92II	CATG	3 cut(s)	31, 201, 528
HspAI	GCGC	1 cut(s)	365
LmnI	GCTCC	2 cut(s)	108, 378
LpnPI	CCDG	4 cut(s)	106, 420, 461, 525
MaeII	ACGT	2 cut(s)	43, 607
MaeIII	GTNAC	1 cut(s)	293
MluCI	AATT	1 cut(s)	602
MnlI	CCTC	6 cut(s)	127, 130, 175, 386, 389, 613
MseI	TTAA	4 cut(s)	330, 473, 569, 625
Mva1269I	GAATGC	1 cut(s)	157
NlaIII	CATG	3 cut(s)	31, 201, 528
NlaIV	GGNNCC	1 cut(s)	142
NspI	RCATGY	1 cut(s)	31
PctI	GAATGC	1 cut(s)	157
PfeI	GAWTC	2 cut(s)	5, 14
PspN4I	GGNNCC	1 cut(s)	142
SaqAI	TTAA	4 cut(s)	330, 473, 569, 625
SmlI	CTYRAG	1 cut(s)	59
SmoI	CTYRAG	1 cut(s)	59
Sse9I	AATT	1 cut(s)	602
TaaI	ACNGT	1 cut(s)	562
TaiI	ACGT	2 cut(s)	46, 610
TaqI	TCGA	3 cut(s)	311, 378, 553
TasI	AATT	1 cut(s)	602
TfiI	GAWTC	2 cut(s)	5, 14
Tru1I	TTAA	4 cut(s)	330, 473, 569, 625
Tru9I	TTAA	4 cut(s)	330, 473, 569, 625
TscAI	CASTG	2 cut(s)	15, 151
TspDTI	ATGAA	2 cut(s)	287, 297
TspRI	CASTG	2 cut(s)	15, 151
XceI	RCATGY	1 cut(s)	31

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