Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4C

Orthogroup ID

OG0002613

Physical Location & Seq

Genomic Coordinates Forward (+)

38010061 .. 38010984

Gene Structure 924 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4CG174000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 924 bp

ATGGGCTTTCCAGAGACTCGCGGGCGCGCCAAGACATTGCTTAACCGCTACGTTTCCGGCGACTCCGGCCCTCCTCCTCCGGCAGTCCTTCTCGATCGTTTGCTGGACTGCGCAGAGAGGTTTGGATTTGATTTTGATTCTTGGGTTTTCAGTTACTTGTTGAATAGCTATGTTAGAGCGAACCGAATAGGGGATGCTGTTGATTGCTTTAATAGAATGGTGGAGCTTGAGATATATGCTGGTGCTGGTGCTGGTGTTGAATATATGAACATTGTGTTGACGGCATTGGTTAGGAGGAATATGTTTGAGGAAGCACGAGACTTGTATGGTAAAATGGTTGAGAGAGGAGTTGGCGGTGATTGCGCCACTCTAAATGTCATGATGCGTGCTTGTTTGAAGGAGGGGAAGCCGGAGGAGTACTTTCGGAAGGCAAGGGGGAGAGGGATAGCAGCTGATGCCGCATTGTATGATGTGGCCATTGGGGCTGTTTGTAAGACTCCCGAATCGAGTTTGGCTTTGGTGTTGTTGGCTGAAATGAGAGAAATGGGGTGGGTTCCTTCCGCGCGTACGTACACTAGTGTGATTGGGGCGTGTGTGAAGCAGGGGAATATGGTGGAGGCGCTAAGGCTCAAGGATGAAATGGTGAGTTCTGGGGAATCGATTGATTTGGTTGTTGCTACCAGCTTGATGAAGGGTTATTGTGCGCAAGGGAAGTTGGATGCTGCTTTGGATTTGTTCAACATGATCATGCAGGATGGACTTATTCCTAACAGAATCACTCATGCAACTGTGATAGGATGCTGCTGTAAGAATGGGAACATGGAAAGGGCATATGAGCTTTACACCAAAATGAAACGGATGGGTATTTTGCCTGATGAGTTCATTGTGAATCATTTGGTGCGTGGATTTTTGAAATGTCGGTGA

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

307

Amino Acids

33.96

Weight (kDa)

7.44

Isoelectric Point (pI)

28.27

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_2	PF13041	89 - 133	1.2e-08	PPR repeat family
PPR_2	PF13041	152 - 200	3.9e-06	PPR repeat family
PPR	PF01535	190 - 218	1.9e-06	PPR repeat
PPR_3	PF13812	209 - 271	3.5e-07	Pentatricopeptide repeat domain
PPR_2	PF13041	222 - 270	1.2e-10	PPR repeat family
PPR_1	PF12854	252 - 285	6.2e-08	PPR repeat
PPR	PF01535	262 - 289	5.3e-07	PPR repeat
PPR_2	PF13041	263 - 304	5.3e-09	PPR repeat family

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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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: OG0002613)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G39230 AT3G54980 AT3G54980
fragaria_vesca	FvH4_5g25890 FvH4_5g25890 FvH4_5g25890
malus_domestica	MD04G1151000.v1.1 MD12G1164900.v1.1
prunus_persica	Prupe.6G275900_v2.0.a1 Prupe.6G275900_v2.0.a1
pyrus_communis	pycom04g13670 pycom12g15770
rosa_chinensis	RchiOBHm_Chr4g0410561 RchiOBHm_Chr4g0410571 RchiOBHm_Chr5g0071501 RchiOBHm_Chr6g0264781 RchiOBHm_Chr7g0216391 RchiOBHm_Chr7g0216401
rosa_laevigata	RLG00000002575 RLG00000002576 RLG00000002577 RLG00000031675
rosa_multiflora	Rmu_sc0000692.1_g000003 Rmu_sc0000692.1_g000005 Rmu_sc0006325.1_g000046
rosa_roxburghii	Rroxscaffold_159G00432870 Rroxscaffold_3G00243290 Rroxscaffold_4G00298080
rosa_rugosa	Rorug01G0081600 Rorug07G0160300
rosa_samantha	Rh2DG118300 Rh4CG174000 Rh4CG174100 Rh4CG174200 Rh7AG298700 Rh7AG298800 Rh7BG290300 Rh7BG290400
rosa_wichuraiana	Rw7G025370 Rw7G025380

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc16I	TGCGCA	2 cut(s)	112, 705
AccII	CGCG	4 cut(s)	21, 27, 563, 565
AciI	CCGC	5 cut(s)	21, 46, 354, 459, 561
AcoI	YGGCCR	1 cut(s)	474
AfaI	GTAC	3 cut(s)	419, 568, 572
AfiI	CCNNNNNNNGG	1 cut(s)	190
AgsI	TTSAA	5 cut(s)	163, 260, 397, 739, 913
AhlI	ACTAGT	1 cut(s)	575
AleI	CACNNNNGTG	1 cut(s)	578
AluBI	AGCT	5 cut(s)	168, 226, 452, 684, 838
AluI	AGCT	5 cut(s)	168, 226, 452, 684, 838
Alw26I	GTCTC	2 cut(s)	8, 312
AoxI	GGCC	2 cut(s)	67, 474
ApeKI	GCWGC	3 cut(s)	449, 722, 801
AscI	GGCGCGCC	1 cut(s)	25
AspLEI	GCGC	7 cut(s)	27, 29, 113, 365, 565, 622, 706
AspS9I	GGNCC	1 cut(s)	68
AsuHPI	GGTGA	2 cut(s)	368, 655
BalI	TGGCCA	1 cut(s)	476
BauI	CACGAG	1 cut(s)	315
BbvI	GCAGC	3 cut(s)	461, 709, 788
BccI	CCATC	2 cut(s)	749, 853
BceAI	ACGGC	1 cut(s)	297
BclI	TGATCA	1 cut(s)	744
BcoDI	GTCTC	2 cut(s)	8, 312
BcuI	ACTAGT	1 cut(s)	575
BfaI	CTAG	1 cut(s)	576
BfoI	RGCGCY	1 cut(s)	623
BglI	GCCNNNNNGGC	1 cut(s)	482
BisI	GCNGC	4 cut(s)	450, 459, 723, 802
BlsI	GCNGC	4 cut(s)	451, 460, 724, 803
BmcAI	AGTACT	1 cut(s)	419
BmgT120I	GGNCC	1 cut(s)	68
BmiI	GGNNCC	1 cut(s)	555
BmsI	GCATC	5 cut(s)	184, 372, 445, 709, 788
Bpu10I	CCTNAGC	1 cut(s)	623
BpuEI	CTTGAG	2 cut(s)	248, 614
Bsa29I	ATCGAT	1 cut(s)	659
BsaAI	YACGTR	1 cut(s)	570
Bsc4I	CCNNNNNNNGG	1 cut(s)	190
Bse3DI	GCAATG	1 cut(s)	35
BseCI	ATCGAT	1 cut(s)	659
BseGI	GGATG	6 cut(s)	199, 640, 724, 760, 803, 864
BseLI	CCNNNNNNNGG	1 cut(s)	190
BseMI	GCAATG	1 cut(s)	35
BsePI	GCGCGC	1 cut(s)	25
BseRI	GAGGAG	4 cut(s)	63, 66, 360, 428
BseXI	GCAGC	3 cut(s)	461, 709, 788
Bsh1236I	CGCG	4 cut(s)	21, 27, 563, 565
Bsh1285I	CGRYCG	1 cut(s)	97
BshFI	GGCC	2 cut(s)	69, 476
BshVI	ATCGAT	1 cut(s)	659
BsiEI	CGRYCG	1 cut(s)	97
BsiSI	CCGG	4 cut(s)	57, 66, 80, 410
BsiWI	CGTACG	1 cut(s)	566
BslI	CCNNNNNNNGG	1 cut(s)	190
BsmAI	GTCTC	2 cut(s)	8, 312
BsnI	GGCC	2 cut(s)	69, 476
Bsp143I	GATC	2 cut(s)	94, 744
BspACI	CCGC	5 cut(s)	21, 46, 354, 459, 561
BspANI	GGCC	2 cut(s)	69, 476
BspDI	ATCGAT	1 cut(s)	659
BspFNI	CGCG	4 cut(s)	21, 27, 563, 565
BspHI	TCATGA	1 cut(s)	378
BspLI	GGNNCC	1 cut(s)	555
BsrDI	GCAATG	1 cut(s)	35
BssHII	GCGCGC	1 cut(s)	25
BssMI	GATC	2 cut(s)	94, 744
BssSI	CACGAG	1 cut(s)	315
Bst2BI	CACGAG	1 cut(s)	315
Bst4CI	ACNGT	1 cut(s)	790
BstAPI	GCANNNNNTGC	1 cut(s)	455
BstBAI	YACGTR	1 cut(s)	570
BstC8I	GCNNGC	3 cut(s)	23, 27, 387
BstDEI	CTNAG	1 cut(s)	623
BstF5I	GGATG	6 cut(s)	199, 640, 724, 760, 803, 864
BstFNI	CGCG	4 cut(s)	21, 27, 563, 565
BstH2I	RGCGCY	1 cut(s)	623
BstHHI	GCGC	7 cut(s)	27, 29, 113, 365, 565, 622, 706
BstKTI	GATC	2 cut(s)	97, 747
BstMAI	GTCTC	2 cut(s)	8, 312
BstMBI	GATC	2 cut(s)	94, 744
BstMCI	CGRYCG	1 cut(s)	97
BstMWI	GCNNNNNNNGC	5 cut(s)	66, 360, 455, 458, 482
BstSNI	TACGTA	1 cut(s)	570
BstUI	CGCG	4 cut(s)	21, 27, 563, 565
BstV1I	GCAGC	3 cut(s)	461, 709, 788
Bsu15I	ATCGAT	1 cut(s)	659
BsuRI	GGCC	2 cut(s)	69, 476
BsuTUI	ATCGAT	1 cut(s)	659
BtsCI	GGATG	6 cut(s)	199, 640, 724, 760, 803, 864
Cac8I	GCNNGC	3 cut(s)	23, 27, 387
CciI	TCATGA	1 cut(s)	378
CfoI	GCGC	7 cut(s)	27, 29, 113, 365, 565, 622, 706
Cfr13I	GGNCC	1 cut(s)	68
ClaI	ATCGAT	1 cut(s)	659
Csp6I	GTAC	3 cut(s)	418, 567, 571
CviAII	CATG	5 cut(s)	379, 742, 748, 782, 820
CviQI	GTAC	3 cut(s)	418, 567, 571
DdeI	CTNAG	1 cut(s)	623
DpnI	GATC	2 cut(s)	96, 746
DpnII	GATC	2 cut(s)	94, 744
EaeI	YGGCCR	1 cut(s)	474
Eco105I	TACGTA	1 cut(s)	570
FaeI	CATG	5 cut(s)	382, 745, 751, 785, 823
FatI	CATG	5 cut(s)	378, 741, 747, 781, 819
FauI	CCCGC	1 cut(s)	14
FauNDI	CATATG	1 cut(s)	832
FbaI	TGATCA	1 cut(s)	744
Fnu4HI	GCNGC	4 cut(s)	450, 459, 723, 802
FokI	GGATG	6 cut(s)	206, 647, 731, 767, 810, 871
Fsp4HI	GCNGC	4 cut(s)	450, 459, 723, 802
FspBI	CTAG	1 cut(s)	576
FspI	TGCGCA	2 cut(s)	112, 705
GlaI	GCGC	7 cut(s)	26, 28, 112, 364, 564, 621, 705
GluI	GCNGC	4 cut(s)	450, 459, 723, 802
HaeII	RGCGCY	1 cut(s)	623
HaeIII	GGCC	2 cut(s)	69, 476
HapII	CCGG	4 cut(s)	57, 66, 80, 410
HhaI	GCGC	7 cut(s)	27, 29, 113, 365, 565, 622, 706
Hin1II	CATG	5 cut(s)	382, 745, 751, 785, 823
Hin6I	GCGC	7 cut(s)	25, 27, 111, 363, 563, 620, 704
HinP1I	GCGC	7 cut(s)	25, 27, 111, 363, 563, 620, 704
HincII	GTYRAC	1 cut(s)	279
HindII	GTYRAC	1 cut(s)	279
HinfI	GANTC	8 cut(s)	16, 62, 137, 496, 503, 656, 774, 889
HpaII	CCGG	4 cut(s)	57, 66, 80, 410
HphI	GGTGA	2 cut(s)	368, 655
Hpy166II	GTNNAC	2 cut(s)	279, 573
Hpy188I	TCNGA	1 cut(s)	426
Hpy188III	TCNNGA	4 cut(s)	11, 92, 379, 500
Hpy8I	GTNNAC	2 cut(s)	279, 573
HpyAV	CCTTC	5 cut(s)	98, 391, 421, 567, 685
HpyCH4III	ACNGT	1 cut(s)	790
HpyCH4IV	ACGT	2 cut(s)	51, 569
HpyCH4V	TGCA	2 cut(s)	751, 785
HpyF10VI	GCNNNNNNNGC	5 cut(s)	66, 360, 455, 458, 482
HpyF3I	CTNAG	1 cut(s)	623
HpySE526I	ACGT	2 cut(s)	51, 569
Hsp92II	CATG	5 cut(s)	382, 745, 751, 785, 823
HspAI	GCGC	7 cut(s)	25, 27, 111, 363, 563, 620, 704
Ksp22I	TGATCA	1 cut(s)	744
Kzo9I	GATC	2 cut(s)	94, 744
LmnI	GCTCC	1 cut(s)	223
Lsp1109I	GCAGC	3 cut(s)	461, 709, 788
LweI	GCATC	5 cut(s)	184, 372, 445, 709, 788
MaeI	CTAG	1 cut(s)	576
MaeII	ACGT	2 cut(s)	51, 569
MaeIII	GTNAC	1 cut(s)	152
MalI	GATC	2 cut(s)	96, 746
MboI	GATC	2 cut(s)	94, 744
MlsI	TGGCCA	1 cut(s)	476
MluNI	TGGCCA	1 cut(s)	476
MlyI	GAGTC	3 cut(s)	10, 56, 490
MmeI	TCCRAC	1 cut(s)	696
Mox20I	TGGCCA	1 cut(s)	476
MscI	TGGCCA	1 cut(s)	476
MseI	TTAA	2 cut(s)	42, 210
MslI	CAYNNNNRTG	3 cut(s)	578, 746, 848
Msp20I	TGGCCA	1 cut(s)	476
MspA1I	CMGCKG	1 cut(s)	452
MspI	CCGG	4 cut(s)	57, 66, 80, 410
MvnI	CGCG	4 cut(s)	21, 27, 563, 565
MwoI	GCNNNNNNNGC	5 cut(s)	66, 360, 455, 458, 482
NdeI	CATATG	1 cut(s)	832
NdeII	GATC	2 cut(s)	94, 744
NlaIII	CATG	5 cut(s)	382, 745, 751, 785, 823
NlaIV	GGNNCC	1 cut(s)	555
NsbI	TGCGCA	2 cut(s)	112, 705
OliI	CACNNNNGTG	1 cut(s)	578
PagI	TCATGA	1 cut(s)	378
PalAI	GGCGCGCC	1 cut(s)	25
PauI	GCGCGC	1 cut(s)	25
PcsI	WCGNNNNNNNCGW	1 cut(s)	57
PfeI	GAWTC	5 cut(s)	137, 503, 656, 774, 889
Pfl23II	CGTACG	1 cut(s)	566
PkrI	GCNGC	4 cut(s)	451, 460, 724, 803
Ple19I	CGATCG	1 cut(s)	97
PleI	GAGTC	3 cut(s)	10, 56, 490
PpsI	GAGTC	3 cut(s)	10, 56, 490
Ppu21I	YACGTR	1 cut(s)	570
PspLI	CGTACG	1 cut(s)	566
PspN4I	GGNNCC	1 cut(s)	555
PspPI	GGNCC	1 cut(s)	68
PteI	GCGCGC	1 cut(s)	25
PvuI	CGATCG	1 cut(s)	97
PvuII	CAGCTG	1 cut(s)	452
RsaI	GTAC	3 cut(s)	419, 568, 572
RsaNI	GTAC	3 cut(s)	418, 567, 571
RseI	CAYNNNNRTG	3 cut(s)	578, 746, 848
SaqAI	TTAA	2 cut(s)	42, 210
SatI	GCNGC	4 cut(s)	450, 459, 723, 802
Sau3AI	GATC	2 cut(s)	94, 744
Sau96I	GGNCC	1 cut(s)	68
ScaI	AGTACT	1 cut(s)	419
SchI	GAGTC	3 cut(s)	10, 56, 490
SetI	ASST	8 cut(s)	54, 122, 170, 228, 454, 572, 686, 840
SfaNI	GCATC	5 cut(s)	184, 372, 445, 709, 788
SgsI	GGCGCGCC	1 cut(s)	25
SmiMI	CAYNNNNRTG	3 cut(s)	578, 746, 848
SmlI	CTYRAG	2 cut(s)	227, 629
SmoI	CTYRAG	2 cut(s)	227, 629
SnaBI	TACGTA	1 cut(s)	570
SpeI	ACTAGT	1 cut(s)	575
SsiI	CCGC	5 cut(s)	21, 46, 354, 459, 561
SspMI	CTAG	1 cut(s)	576
TaaI	ACNGT	1 cut(s)	790
TaiI	ACGT	2 cut(s)	54, 572
TaqI	TCGA	3 cut(s)	93, 506, 659
TatI	WGTACW	1 cut(s)	417
TauI	GCSGC	1 cut(s)	461
TfiI	GAWTC	5 cut(s)	137, 503, 656, 774, 889
Tru1I	TTAA	2 cut(s)	42, 210
Tru9I	TTAA	2 cut(s)	42, 210
TseI	GCWGC	3 cut(s)	449, 722, 801
TspDTI	ATGAA	5 cut(s)	281, 651, 704, 866, 871
TspGWI	ACGGA	1 cut(s)	871
XspI	CTAG	1 cut(s)	576
ZrmI	AGTACT	1 cut(s)	419

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