Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1D

Orthogroup ID

OG0005468

Physical Location & Seq

Genomic Coordinates Forward (+)

38381105 .. 38382431

Gene Structure 1327 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1DG193700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1122 bp

ATGAGAGGTGAAGGATTTACTCCTGATACGTGTACGTTAAACACGCTGATGCATTCGCATTGCAATGCAGGAAACTTAGAGGAAGCATTTAAGGTTTTCACAATGATGTCAGAGTTACAGGTCCCTCCAGATTCAGCTACATACAGCGTTTTGATACGCAGTTTGTGTCAACGAAGGGATTATGGTAAAGCTGAGGAGTTGTTTGATGAGCTATCCAAGAAACAAATCTTGTTAAGTGATCGTGGCTGTACACCTGTTGTTGCCTCTTACAAATCTATCTTTGAGTACTTATGTAGTAATGGGAGAACTAAGAAAGCAGATGAAGTGTTTAGGCAGCTACTGAAAAGAGGAACACAAGATCCTCCATCCTACAAGACTTTGATCATGGGCCACTGTAGGGAAGGAACATTCGAAGCTGGGTACAAACTTCTAGTCTTGATGCTTAGAAGGGATTTTGTTCCTGATGTCGAGATTTATGATTCCTTGATTGATGGTCTGTTGGAAAAGGGTAAGCCCCTTCTTGCACAACAGACTCTAGAGAAGATGCTGAAGAGCTCTCATCTCCCAGAAACATCTACTTTCCATTCTATACTGGCAGCTCTTTTAGAAATGCATTGTGCCCGTGAATCTGCAAGCTTTGTTCTTTTAATGTTGGAGAAAAACATTAGACAAAATATTAACTTCTCAACAGATCTTATAAGGCTTCTTTTCAGTGAGGGATTGCGAGATAAAGCATTTGAGATTGTAGGGATGCTGTATGATAACGGATACTCGATTAAAATAGAAGAAGTGGTCAGTTTCCTTTACCAGAGCAGAAAGCTAATAGAGGCATGTGAAATATTGCGATTTAGTCTGCGGAAGCAAGAAAATGTCAGTATTGATATATTTGACCAAGTTATATTAGGGCTATGTAATATCAATAAGCTTCGAGAAGCATTTGGCTTGTACCATGAACTAATTGAGAATGGCGACCACCAGCAGTTGCCGTGCTTACATCATTTAAAGTCTTCCCTAGAGGTTGCAGGTAGATCAGTTGAAGCTGACTTTGTCTCTAAAAGAATGCCAAAACATCAGCTGGTGAACAAATCTGGGAAGTCAAGACCTCAACTGAAACCAATATAG

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

Chal_sti_synt_C Chal_sti_synt_N PPR PPR_1 PPR_2 PPR_3

Protein Analysis

373

Amino Acids

42.54

Weight (kDa)

7.15

Isoelectric Point (pI)

51.54

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PPR_3	PF13812	2 - 53	8.4e-07	Pentatricopeptide repeat domain
PPR_1	PF12854	5 - 36	3.1e-10	PPR repeat
PPR_2	PF13041	8 - 57	2.7e-16	PPR repeat family
PPR_1	PF12854	41 - 70	2.6e-06	PPR repeat

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0005468)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G02060
fragaria_vesca	FvH4_7g09470 FvH4_7g09470 FvH4_7g09470 FvH4_7g09470 FvH4_7g09470 FvH4_7g09470 FvH4_7g09470 FvH4_7g09470 FvH4_7g09470
malus_domestica	MD02G1218600.v1.1
prunus_persica	Prupe.2G122500_v2.0.a1
pyrus_communis	pycom12652g00050
rosa_chinensis	RchiOBHm_Chr1g0346171
rosa_laevigata	RLG00000028810
rosa_multiflora	Rmu_sc0003809.1_g000024
rosa_roxburghii	Rroxscaffold_4G00308800
rosa_rugosa	Rorug01G0178600
rosa_samantha	Rh1AG197700 Rh1BG162900 Rh1BG163000 Rh1BG163800 Rh1CG182800 Rh1DG193600 Rh1DG193700 Rh1DG194800
rosa_wichuraiana	Rw1G016310 Rw1G016590 Rw1G016620

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	698
Acc36I	ACCTGC	1 cut(s)	1013
AciI	CCGC	1 cut(s)	856
AclWI	GGATC	1 cut(s)	353
AcuI	CTGAAG	1 cut(s)	569
AfaI	GTAC	5 cut(s)	34, 250, 287, 422, 947
AfiI	CCNNNNNNNGG	1 cut(s)	397
AflIII	ACRYGT	1 cut(s)	29
AgsI	TTSAA	1 cut(s)	1037
AloI	GAACNNNNNNTCC	2 cut(s)	343, 375
Alw21I	GWGCWC	1 cut(s)	557
Alw26I	GTCTC	1 cut(s)	1054
AlwI	GGATC	1 cut(s)	353
AlwNI	CAGNNNCTG	1 cut(s)	340
AoxI	GGCC	1 cut(s)	388
ApeKI	GCWGC	2 cut(s)	334, 596
ArsI	GACNNNNNNTTYG	2 cut(s)	417, 449
AspS9I	GGNCC	2 cut(s)	121, 388
AsuHPI	GGTGA	2 cut(s)	20, 1090
AsuII	TTCGAA	1 cut(s)	411
AvaII	GGWCC	1 cut(s)	121
BaeGI	GKGCMC	1 cut(s)	622
BanII	GRGCYC	1 cut(s)	557
BbsI	GAAGAC	1 cut(s)	999
Bbv12I	GWGCWC	1 cut(s)	557
BbvCI	CCTCAGC	1 cut(s)	192
BbvI	GCAGC	2 cut(s)	346, 608
BccI	CCATC	2 cut(s)	373, 485
BceAI	ACGGC	1 cut(s)	970
BciVI	GTATCC	1 cut(s)	761
BclI	TGATCA	1 cut(s)	381
BcoDI	GTCTC	1 cut(s)	1054
BfaI	CTAG	3 cut(s)	431, 536, 1013
BfmI	CTRYAG	1 cut(s)	394
BfuAI	ACCTGC	1 cut(s)	1013
BfuI	GTATCC	1 cut(s)	761
BglII	AGATCT	1 cut(s)	691
BisI	GCNGC	2 cut(s)	335, 597
BlsI	GCNGC	2 cut(s)	336, 598
BmcAI	AGTACT	1 cut(s)	287
Bme18I	GGWCC	1 cut(s)	121
BmgT120I	GGNCC	2 cut(s)	121, 388
BmiI	GGNNCC	1 cut(s)	123
BmsI	GCATC	4 cut(s)	39, 429, 534, 741
BpiI	GAAGAC	1 cut(s)	999
BpmI	CTGGAG	1 cut(s)	111
Bpu10I	CCTNAGC	1 cut(s)	192
Bpu14I	TTCGAA	1 cut(s)	411
BsaAI	YACGTR	1 cut(s)	30
Bsc4I	CCNNNNNNNGG	1 cut(s)	397
Bse1I	ACTGG	1 cut(s)	597
Bse3DI	GCAATG	2 cut(s)	58, 70
BseGI	GGATG	2 cut(s)	365, 756
BseLI	CCNNNNNNNGG	1 cut(s)	397
BseMI	GCAATG	2 cut(s)	58, 70
BseMII	CTCAG	1 cut(s)	183
BseNI	ACTGG	1 cut(s)	597
BseRI	GAGGAG	1 cut(s)	209
BseSI	GKGCMC	1 cut(s)	622
BseXI	GCAGC	2 cut(s)	346, 608
BseYI	CCCAGC	1 cut(s)	416
BshFI	GGCC	1 cut(s)	390
BsiHKAI	GWGCWC	1 cut(s)	557
BslFI	GGGAC	1 cut(s)	107
BslI	CCNNNNNNNGG	1 cut(s)	397
BsmAI	GTCTC	1 cut(s)	1054
BsmFI	GGGAC	1 cut(s)	107
BsmI	GAATGC	2 cut(s)	52, 1065
BsnI	GGCC	1 cut(s)	390
Bsp119I	TTCGAA	1 cut(s)	411
Bsp1286I	GDGCHC	2 cut(s)	557, 622
Bsp1407I	TGTACA	1 cut(s)	248
Bsp143I	GATC	5 cut(s)	238, 358, 381, 691, 1028
BspACI	CCGC	1 cut(s)	856
BspANI	GGCC	1 cut(s)	390
BspCNI	CTCAG	1 cut(s)	184
BspLI	GGNNCC	1 cut(s)	123
BspMI	ACCTGC	1 cut(s)	1013
BspPI	GGATC	1 cut(s)	353
BspQI	GCTCTTC	1 cut(s)	545
BspT104I	TTCGAA	1 cut(s)	411
BsrDI	GCAATG	2 cut(s)	58, 70
BsrGI	TGTACA	1 cut(s)	248
BsrI	ACTGG	1 cut(s)	597
BssMI	GATC	5 cut(s)	238, 358, 381, 691, 1028
Bst4CI	ACNGT	1 cut(s)	395
Bst6I	CTCTTC	1 cut(s)	545
BstAUI	TGTACA	1 cut(s)	248
BstBAI	YACGTR	1 cut(s)	30
BstBI	TTCGAA	1 cut(s)	411
BstC8I	GCNNGC	1 cut(s)	634
BstDEI	CTNAG	4 cut(s)	76, 192, 309, 443
BstF5I	GGATG	2 cut(s)	365, 756
BstKTI	GATC	5 cut(s)	241, 361, 384, 694, 1031
BstMAI	GTCTC	1 cut(s)	1054
BstMBI	GATC	5 cut(s)	238, 358, 381, 691, 1028
BstNSI	RCATGY	1 cut(s)	834
BstSFI	CTRYAG	1 cut(s)	394
BstSLI	GKGCMC	1 cut(s)	622
BstV1I	GCAGC	2 cut(s)	346, 608
BstV2I	GAAGAC	1 cut(s)	999
BstX2I	RGATCY	2 cut(s)	358, 691
BstYI	RGATCY	2 cut(s)	358, 691
BsuI	GTATCC	1 cut(s)	761
BsuRI	GGCC	1 cut(s)	390
BtsCI	GGATG	2 cut(s)	365, 756
BtsIMutI	CAGTG	2 cut(s)	391, 718
BveI	ACCTGC	1 cut(s)	1013
Cac8I	GCNNGC	1 cut(s)	634
CaiI	CAGNNNCTG	1 cut(s)	340
Cfr13I	GGNCC	2 cut(s)	121, 388
Csp6I	GTAC	5 cut(s)	33, 249, 286, 421, 946
CviAII	CATG	3 cut(s)	385, 831, 950
CviQI	GTAC	5 cut(s)	33, 249, 286, 421, 946
DdeI	CTNAG	4 cut(s)	76, 192, 309, 443
DpnI	GATC	5 cut(s)	240, 360, 383, 693, 1030
DpnII	GATC	5 cut(s)	238, 358, 381, 691, 1028
DraI	TTTAAA	1 cut(s)	1002
Eam1104I	CTCTTC	1 cut(s)	545
EarI	CTCTTC	1 cut(s)	545
Ecl136II	GAGCTC	1 cut(s)	555
Eco24I	GRGCYC	1 cut(s)	557
Eco47I	GGWCC	1 cut(s)	121
Eco53kI	GAGCTC	1 cut(s)	555
Eco57I	CTGAAG	1 cut(s)	569
EcoICRI	GAGCTC	1 cut(s)	555
EcoO109I	RGGNCCY	1 cut(s)	121
EcoT22I	ATGCAT	2 cut(s)	54, 615
EcoT38I	GRGCYC	1 cut(s)	557
FaeI	CATG	3 cut(s)	388, 834, 953
FaqI	GGGAC	1 cut(s)	107
FatI	CATG	3 cut(s)	384, 830, 949
FbaI	TGATCA	1 cut(s)	381
Fnu4HI	GCNGC	2 cut(s)	335, 597
FokI	GGATG	2 cut(s)	352, 763
FriOI	GRGCYC	1 cut(s)	557
Fsp4HI	GCNGC	2 cut(s)	335, 597
FspBI	CTAG	3 cut(s)	431, 536, 1013
GluI	GCNGC	2 cut(s)	335, 597
GsaI	CCCAGC	1 cut(s)	420
GsuI	CTGGAG	1 cut(s)	111
HaeIII	GGCC	1 cut(s)	390
Hin1II	CATG	3 cut(s)	388, 834, 953
HincII	GTYRAC	1 cut(s)	170
HindII	GTYRAC	1 cut(s)	170
HindIII	AAGCTT	2 cut(s)	634, 923
HinfI	GANTC	4 cut(s)	131, 479, 532, 626
HphI	GGTGA	2 cut(s)	20, 1090
Hpy166II	GTNNAC	4 cut(s)	33, 170, 251, 1081
Hpy188I	TCNGA	1 cut(s)	112
Hpy188III	TCNNGA	8 cut(s)	23, 128, 436, 461, 469, 536, 929, 1098
Hpy8I	GTNNAC	4 cut(s)	33, 170, 251, 1081
HpyAV	CCTTC	5 cut(s)	5, 168, 395, 441, 527
HpyCH4III	ACNGT	1 cut(s)	395
HpyCH4IV	ACGT	2 cut(s)	29, 35
HpyCH4V	TGCA	7 cut(s)	52, 63, 68, 524, 613, 632, 1022
HpyF3I	CTNAG	4 cut(s)	76, 192, 309, 443
HpySE526I	ACGT	2 cut(s)	29, 35
Hsp92II	CATG	3 cut(s)	388, 834, 953
Ksp22I	TGATCA	1 cut(s)	381
Kzo9I	GATC	5 cut(s)	238, 358, 381, 691, 1028
LguI	GCTCTTC	1 cut(s)	545
Lsp1109I	GCAGC	2 cut(s)	346, 608
LweI	GCATC	4 cut(s)	39, 429, 534, 741
MaeI	CTAG	3 cut(s)	431, 536, 1013
MaeII	ACGT	2 cut(s)	29, 35
MaeIII	GTNAC	1 cut(s)	114
MalI	GATC	5 cut(s)	240, 360, 383, 693, 1030
MboI	GATC	5 cut(s)	238, 358, 381, 691, 1028
MboII	GAAGA	4 cut(s)	553, 562, 797, 999
MflI	RGATCY	2 cut(s)	358, 691
MhlI	GDGCHC	2 cut(s)	557, 622
MluCI	AATT	1 cut(s)	957
MlyI	GAGTC	1 cut(s)	526
MmeI	TCCRAC	2 cut(s)	480, 633
Mph1103I	ATGCAT	2 cut(s)	54, 615
MseI	TTAA	7 cut(s)	38, 90, 233, 647, 678, 777, 1001
MslI	CAYNNNNRTG	3 cut(s)	47, 63, 104
MspA1I	CMGCKG	1 cut(s)	1075
Mva1269I	GAATGC	2 cut(s)	52, 1065
NdeII	GATC	5 cut(s)	238, 358, 381, 691, 1028
NlaIII	CATG	3 cut(s)	388, 834, 953
NlaIV	GGNNCC	1 cut(s)	123
NsiI	ATGCAT	2 cut(s)	54, 615
NspI	RCATGY	1 cut(s)	834
NspV	TTCGAA	1 cut(s)	411
PciSI	GCTCTTC	1 cut(s)	545
PctI	GAATGC	2 cut(s)	52, 1065
PfeI	GAWTC	3 cut(s)	131, 479, 626
PflFI	GACNNNGTC	1 cut(s)	1046
PkrI	GCNGC	2 cut(s)	336, 598
PleI	GAGTC	1 cut(s)	526
PpsI	GAGTC	1 cut(s)	526
Ppu21I	YACGTR	1 cut(s)	30
PpuMI	RGGWCCY	1 cut(s)	121
PsiI	TTATAA	1 cut(s)	698
Psp124BI	GAGCTC	1 cut(s)	557
Psp5II	RGGWCCY	1 cut(s)	121
PspFI	CCCAGC	1 cut(s)	416
PspN4I	GGNNCC	1 cut(s)	123
PspPI	GGNCC	2 cut(s)	121, 388
PspPPI	RGGWCCY	1 cut(s)	121
PstNI	CAGNNNCTG	1 cut(s)	340
PsuI	RGATCY	2 cut(s)	358, 691
PsyI	GACNNNGTC	1 cut(s)	1046
PvuII	CAGCTG	1 cut(s)	1075
RsaI	GTAC	5 cut(s)	34, 250, 287, 422, 947
RsaNI	GTAC	5 cut(s)	33, 249, 286, 421, 946
RseI	CAYNNNNRTG	3 cut(s)	47, 63, 104
SacI	GAGCTC	1 cut(s)	557
SapI	GCTCTTC	1 cut(s)	545
SaqAI	TTAA	7 cut(s)	38, 90, 233, 647, 678, 777, 1001
SatI	GCNGC	2 cut(s)	335, 597
Sau3AI	GATC	5 cut(s)	238, 358, 381, 691, 1028
Sau96I	GGNCC	2 cut(s)	121, 388
ScaI	AGTACT	1 cut(s)	287
SchI	GAGTC	1 cut(s)	526
SduI	GDGCHC	2 cut(s)	557, 622
SfaNI	GCATC	4 cut(s)	39, 429, 534, 741
SfcI	CTRYAG	1 cut(s)	394
SfuI	TTCGAA	1 cut(s)	411
SinI	GGWCC	1 cut(s)	121
SmiMI	CAYNNNNRTG	3 cut(s)	47, 63, 104
Sse9I	AATT	1 cut(s)	957
SsiI	CCGC	1 cut(s)	856
SspI	AATATT	2 cut(s)	676, 840
SspMI	CTAG	3 cut(s)	431, 536, 1013
SstI	GAGCTC	1 cut(s)	557
TaaI	ACNGT	1 cut(s)	395
TaiI	ACGT	2 cut(s)	32, 38
TaqI	TCGA	4 cut(s)	411, 468, 773, 928
TasI	AATT	1 cut(s)	957
TatI	WGTACW	2 cut(s)	248, 285
TfiI	GAWTC	3 cut(s)	131, 479, 626
Tru1I	TTAA	7 cut(s)	38, 90, 233, 647, 678, 777, 1001
Tru9I	TTAA	7 cut(s)	38, 90, 233, 647, 678, 777, 1001
TscAI	CASTG	2 cut(s)	398, 718
TseI	GCWGC	2 cut(s)	334, 596
TspDTI	ATGAA	2 cut(s)	336, 966
TspGWI	ACGGA	1 cut(s)	780
TspRI	CASTG	2 cut(s)	398, 718
Tth111I	GACNNNGTC	1 cut(s)	1046
VpaK11BI	GGWCC	1 cut(s)	121
XbaI	TCTAGA	1 cut(s)	535
XceI	RCATGY	1 cut(s)	834
XspI	CTAG	3 cut(s)	431, 536, 1013
ZrmI	AGTACT	1 cut(s)	287
Zsp2I	ATGCAT	2 cut(s)	54, 615

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