Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6D

Orthogroup ID

OG0000235

Physical Location & Seq

Genomic Coordinates Forward (+)

10532411 .. 10533608

Gene Structure 1198 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6DG090100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 816 bp

ATGGGGAGGAAAATACTCAGGGAAGTTACTGAGAAGAAGAGGCCTACCTTCTTCCAGCTTATTCATCCTCGTCTCACAACTGAACATCTGAGAATCCCACCTAAATTCACCCTGAAGTACATTGCAAAAGATCTGTCTGAAAGGGCAACGTTGAAATTGGAGCGATCTTCAGAGTGTTCATGGAGTGTGATAGTGAGGAAATCAGGAAGAGATGTGTATTTCAAGGATGGGTGGCAGGAGTTCTTGAGAGATAACTCCTTGGGTGACAAAGAATTCTTAGTGTTCATCTACGATGGAAAAATGCGATTCAGCGTAAAGATTTTCAACAAGAATGGGTGTGAGAGAATGGATTTCCATAACATAAAAGCACATCAAAACTCCACAGTTTCTAAGAGTACTAAAAGGCCTAGGGGTAGACCAAGAAAATGTAGCAAAGCCAATTCAGCTGATAAAGAGGTCAAAGAAGTAGAAGAAGAAGAAGAAGAAGAAGAAGAAGATTACAATGACAACCCTGCTCAGGAATATGCTGAATTGTTTGAATCTGAAGTCCGCCAGTTTACAAGCACCATTTATGTACCTCACAATGTGTCAATCCCGAAAAGCTTCTCTACAGAGTATCTTTCTTCGGGTGAGGTCTCCCTGAGAAACTCAAAGGGGAAAGAATGGGTAGTGAAAATTGTCGATTCGAATGGAAAACTCTGCTTTTCTGCAGGTTGGAAGGCTTTTGCAGAAGCCAACCAAATCAAGTTCCATGATGTATGCACGTTTCAGCTTGTGAGTGAAAAGAGATTGGTAGTTCACATTTGTAGGAAGTGA

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:0016553 GO:0016554 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

Protein Analysis

271

Amino Acids

31.66

Weight (kDa)

9.07

Isoelectric Point (pI)

44.47

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
B3	PF02362	23 - 111	4.6e-17	B3 DNA binding domain
B3	PF02362	195 - 271	7.9e-17	B3 DNA binding domain

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)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0000235)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_1g22700 FvH4_2g06920 FvH4_2g06920 FvH4_2g06960 FvH4_2g06960 FvH4_2g06960 FvH4_2g06960 FvH4_2g06970 FvH4_2g06970 FvH4_2g07230 FvH4_2g07231 FvH4_2g07231 FvH4_2g07240 FvH4_2g07290 FvH4_2g07290 FvH4_2g07290 FvH4_2g07290 FvH4_2g07290 FvH4_2g07290 FvH4_2g07290 FvH4_2g07290 FvH4_2g07290 FvH4_2g07300 FvH4_2g07300 FvH4_2g07300 FvH4_2g07300 FvH4_2g07300 FvH4_2g07300 FvH4_2g07300 FvH4_2g07300 FvH4_2g07300 FvH4_2g07300 FvH4_4g19990 FvH4_4g19990 FvH4_4g19990 FvH4_4g20070
malus_domestica	MD05G1072700.v1.1
prunus_persica	Prupe.8G113100_v2.0.a1
pyrus_communis	pycom05g06500 pycom10g06950
rosa_chinensis	RchiOBHm_Chr4g0425711 RchiOBHm_Chr6g0259241 RchiOBHm_Chr6g0259251 RchiOBHm_Chr6g0259321 RchiOBHm_Chr6g0259331 RchiOBHm_Chr6g0259781 RchiOBHm_Chr6g0259791 RchiOBHm_Chr6g0259811 RchiOBHm_Chr6g0259881 RchiOBHm_Chr6g0259931
rosa_laevigata	RLG00000007345 RLG00000014500 RLG00000014501 RLG00000014505 RLG00000014506 RLG00000014507 RLG00000014539 RLG00000014540 RLG00000014545 RLG00000014546
rosa_multiflora	Rmu_co8137334.1_g000001 Rmu_co8454279.1_g000001 Rmu_co8476373.1_g000001 Rmu_sc0001078.1_g000001 Rmu_sc0003958.1_g000011 Rmu_sc0009049.1_g000001 Rmu_sc0009049.1_g000009 Rmu_sc0010546.1_g000001 Rmu_sc0011974.1_g000002 Rmu_sc0011974.1_g000003 Rmu_sc0033846.1_g000001 Rmu_sc0036999.1_g000001 Rmu_ssc0000052.1_g000015
rosa_roxburghii	Rroxscaffold_5G00367690 Rroxscaffold_7G00206530 Rroxscaffold_7G00206540 Rroxscaffold_7G00206560 Rroxscaffold_7G00206570 Rroxscaffold_7G00207020 Rroxscaffold_7G00207030 Rroxscaffold_7G00207150 Rroxscaffold_7G00207160 Rroxscaffold_7G00207170 Rroxscaffold_7G00207270
rosa_rugosa	Rorug04G0205300 Rorug05G0586300 Rorug05G0586400 Rorug05G0586500 Rorug05G0586600 Rorug05G0586700 Rorug05G0587300 Rorug05G0587400 Rorug05G0587500 Rorug05G0587600 Rorug05G0590500 Rorug05G0590600 Rorug05G0591200 Rorug05G0591300 Rorug05G0591400 Rorug05G0591500
rosa_samantha	Rh4AG262200 Rh4BG268500 Rh4CG279700 Rh4DG264100 Rh6AG103100 Rh6AG103600 Rh6AG107100 Rh6AG107200 Rh6AG107700 Rh6BG095400 Rh6BG095500 Rh6BG095900 Rh6BG096000 Rh6BG096800 Rh6BG102600 Rh6BG102700 Rh6BG102800 Rh6BG103800 Rh6CG092300 Rh6CG092400 Rh6CG092800 Rh6CG092900 Rh6CG096200 Rh6CG096300 Rh6CG096800 Rh6CG097100 Rh6DG086300 Rh6DG086400 Rh6DG086700 Rh6DG086800 Rh6DG090000 Rh6DG090100 Rh6DG090500 Rh6DG090800
rosa_wichuraiana	Rw4G022670 Rw6G008900 Rw6G008940 Rw6G009250 Rw6G009280 Rw6G009330

Restriction Enzyme Sites

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Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc36I	ACCTGC	1 cut(s)	701
AccI	GTMKAC	1 cut(s)	415
AciI	CCGC	1 cut(s)	550
AclI	AACGTT	1 cut(s)	149
AcsI	RAATTY	2 cut(s)	104, 272
AcuI	CTGAAG	3 cut(s)	134, 153, 564
AdeI	CACNNNGTG	1 cut(s)	586
AfaI	GTAC	3 cut(s)	119, 397, 576
AfiI	CCNNNNNNNGG	1 cut(s)	517
AgsI	TTSAA	4 cut(s)	154, 223, 325, 539
AluBI	AGCT	4 cut(s)	58, 446, 603, 772
AluI	AGCT	4 cut(s)	58, 446, 603, 772
Alw26I	GTCTC	2 cut(s)	77, 640
AoxI	GGCC	2 cut(s)	41, 404
ApoI	RAATTY	2 cut(s)	104, 272
ArsI	GACNNNNNNTTYG	2 cut(s)	119, 151
Asp700I	GAANNNNTTC	1 cut(s)	602
AspA2I	CCTAGG	1 cut(s)	407
AsuHPI	GGTGA	3 cut(s)	100, 275, 641
AsuII	TTCGAA	1 cut(s)	686
AvrII	CCTAGG	1 cut(s)	407
BccI	CCATC	2 cut(s)	221, 287
BcoDI	GTCTC	2 cut(s)	77, 640
BfaI	CTAG	1 cut(s)	408
BfmI	CTRYAG	2 cut(s)	609, 708
BfuAI	ACCTGC	1 cut(s)	701
BglII	AGATCT	1 cut(s)	130
BlnI	CCTAGG	1 cut(s)	407
BmcAI	AGTACT	1 cut(s)	397
Bpu10I	CCTNAGC	1 cut(s)	516
Bpu14I	TTCGAA	1 cut(s)	686
BpuEI	CTTGAG	1 cut(s)	265
BsaI	GGTCTC	1 cut(s)	640
BsaJI	CCNNGG	2 cut(s)	258, 407
Bsc4I	CCNNNNNNNGG	1 cut(s)	517
Bse1I	ACTGG	1 cut(s)	553
Bse3DI	GCAATG	1 cut(s)	120
BseDI	CCNNGG	2 cut(s)	258, 407
BseGI	GGATG	2 cut(s)	64, 232
BseLI	CCNNNNNNNGG	1 cut(s)	517
BseMI	GCAATG	1 cut(s)	120
BseMII	CTCAG	5 cut(s)	21, 31, 80, 530, 632
BseNI	ACTGG	1 cut(s)	553
BshFI	GGCC	2 cut(s)	43, 406
BslI	CCNNNNNNNGG	1 cut(s)	517
BsmAI	GTCTC	2 cut(s)	77, 640
BsmBI	CGTCTC	1 cut(s)	77
BsnI	GGCC	2 cut(s)	43, 406
Bso31I	GGTCTC	1 cut(s)	640
Bsp119I	TTCGAA	1 cut(s)	686
Bsp143I	GATC	2 cut(s)	130, 164
BspACI	CCGC	1 cut(s)	550
BspANI	GGCC	2 cut(s)	43, 406
BspCNI	CTCAG	5 cut(s)	22, 30, 81, 529, 633
BspMAI	CTGCAG	1 cut(s)	712
BspMI	ACCTGC	1 cut(s)	701
BspT104I	TTCGAA	1 cut(s)	686
BspTNI	GGTCTC	1 cut(s)	640
BsrDI	GCAATG	1 cut(s)	120
BsrI	ACTGG	1 cut(s)	553
BssECI	CCNNGG	2 cut(s)	258, 407
BssMI	GATC	2 cut(s)	130, 164
BssT1I	CCWWGG	2 cut(s)	258, 407
Bst4CI	ACNGT	1 cut(s)	385
Bst6I	CTCTTC	2 cut(s)	32, 202
BstBI	TTCGAA	1 cut(s)	686
BstDEI	CTNAG	7 cut(s)	17, 30, 89, 277, 390, 516, 641
BstF5I	GGATG	2 cut(s)	64, 232
BstKTI	GATC	2 cut(s)	133, 167
BstMAI	GTCTC	2 cut(s)	77, 640
BstMBI	GATC	2 cut(s)	130, 164
BstMWI	GCNNNNNNNGC	1 cut(s)	443
BstSFI	CTRYAG	2 cut(s)	609, 708
BstX2I	RGATCY	1 cut(s)	130
BstYI	RGATCY	1 cut(s)	130
BsuRI	GGCC	2 cut(s)	43, 406
BtsCI	GGATG	2 cut(s)	64, 232
BveI	ACCTGC	1 cut(s)	701
Csp6I	GTAC	3 cut(s)	118, 396, 575
CviAII	CATG	2 cut(s)	180, 752
CviJI	RGCY	9 cut(s)	43, 58, 406, 437, 446, 603, 722, 734, 772
CviKI_1	RGCY	9 cut(s)	43, 58, 406, 437, 446, 603, 722, 734, 772
CviQI	GTAC	3 cut(s)	118, 396, 575
DdeI	CTNAG	7 cut(s)	17, 30, 89, 277, 390, 516, 641
DpnI	GATC	2 cut(s)	132, 166
DpnII	GATC	2 cut(s)	130, 164
DraIII	CACNNNGTG	1 cut(s)	586
Eam1104I	CTCTTC	2 cut(s)	32, 202
EarI	CTCTTC	2 cut(s)	32, 202
EciI	GGCGGA	1 cut(s)	539
Eco130I	CCWWGG	2 cut(s)	258, 407
Eco147I	AGGCCT	2 cut(s)	43, 406
Eco31I	GGTCTC	1 cut(s)	640
Eco57I	CTGAAG	3 cut(s)	134, 153, 564
EcoRI	GAATTC	1 cut(s)	272
EcoT14I	CCWWGG	2 cut(s)	258, 407
ErhI	CCWWGG	2 cut(s)	258, 407
Esp3I	CGTCTC	1 cut(s)	77
FaeI	CATG	2 cut(s)	183, 755
FaiI	YATR	7 cut(s)	181, 357, 362, 525, 573, 753, 760
FatI	CATG	2 cut(s)	179, 751
FblI	GTMKAC	1 cut(s)	415
FokI	GGATG	2 cut(s)	51, 239
FspBI	CTAG	1 cut(s)	408
HaeIII	GGCC	2 cut(s)	43, 406
Hin1II	CATG	2 cut(s)	183, 755
HindIII	AAGCTT	1 cut(s)	601
HinfI	GANTC	4 cut(s)	93, 306, 539, 683
HphI	GGTGA	3 cut(s)	100, 275, 641
Hpy166II	GTNNAC	3 cut(s)	416, 558, 799
Hpy188I	TCNGA	4 cut(s)	90, 139, 172, 544
Hpy188III	TCNNGA	4 cut(s)	204, 244, 518, 595
Hpy8I	GTNNAC	3 cut(s)	416, 558, 799
HpyAV	CCTTC	2 cut(s)	58, 712
HpyCH4III	ACNGT	1 cut(s)	385
HpyCH4IV	ACGT	2 cut(s)	149, 764
HpyCH4V	TGCA	4 cut(s)	125, 710, 728, 762
HpyF10VI	GCNNNNNNNGC	1 cut(s)	443
HpyF3I	CTNAG	7 cut(s)	17, 30, 89, 277, 390, 516, 641
HpySE526I	ACGT	2 cut(s)	149, 764
Hsp92II	CATG	2 cut(s)	183, 755
Kzo9I	GATC	2 cut(s)	130, 164
LmnI	GCTCC	1 cut(s)	160
MaeI	CTAG	1 cut(s)	408
MaeII	ACGT	2 cut(s)	149, 764
MaeIII	GTNAC	2 cut(s)	25, 263
MalI	GATC	2 cut(s)	132, 166
MboI	GATC	2 cut(s)	130, 164
MflI	RGATCY	1 cut(s)	130
MluCI	AATT	6 cut(s)	104, 155, 272, 439, 530, 675
MmeI	TCCRAC	1 cut(s)	695
MnlI	CCTC	6 cut(s)	33, 78, 189, 448, 588, 625
MroXI	GAANNNNTTC	1 cut(s)	602
MspA1I	CMGCKG	1 cut(s)	446
MwoI	GCNNNNNNNGC	1 cut(s)	443
NdeII	GATC	2 cut(s)	130, 164
NlaIII	CATG	2 cut(s)	183, 755
NmuCI	GTSAC	1 cut(s)	263
NspV	TTCGAA	1 cut(s)	686
PceI	AGGCCT	2 cut(s)	43, 406
PdmI	GAANNNNTTC	1 cut(s)	602
PfeI	GAWTC	4 cut(s)	93, 306, 539, 683
Psp1406I	AACGTT	1 cut(s)	149
PstI	CTGCAG	1 cut(s)	712
PsuI	RGATCY	1 cut(s)	130
PvuII	CAGCTG	1 cut(s)	446
RsaI	GTAC	3 cut(s)	119, 397, 576
RsaNI	GTAC	3 cut(s)	118, 396, 575
Sau3AI	GATC	2 cut(s)	130, 164
ScaI	AGTACT	1 cut(s)	397
SfcI	CTRYAG	2 cut(s)	609, 708
SfuI	TTCGAA	1 cut(s)	686
SmlI	CTYRAG	1 cut(s)	244
SmoI	CTYRAG	1 cut(s)	244
Sse9I	AATT	6 cut(s)	104, 155, 272, 439, 530, 675
SseBI	AGGCCT	2 cut(s)	43, 406
SsiI	CCGC	1 cut(s)	550
SspMI	CTAG	1 cut(s)	408
StuI	AGGCCT	2 cut(s)	43, 406
StyI	CCWWGG	2 cut(s)	258, 407
TaaI	ACNGT	1 cut(s)	385
TaiI	ACGT	2 cut(s)	152, 767
TaqI	TCGA	2 cut(s)	681, 686
TasI	AATT	6 cut(s)	104, 155, 272, 439, 530, 675
TatI	WGTACW	2 cut(s)	117, 395
TfiI	GAWTC	4 cut(s)	93, 306, 539, 683
TseFI	GTSAC	1 cut(s)	263
Tsp45I	GTSAC	1 cut(s)	263
TspDTI	ATGAA	3 cut(s)	53, 168, 274
XapI	RAATTY	2 cut(s)	104, 272
XmaJI	CCTAGG	1 cut(s)	407
XmiI	GTMKAC	1 cut(s)	415
XmnI	GAANNNNTTC	1 cut(s)	602
XspI	CTAG	1 cut(s)	408
ZrmI	AGTACT	1 cut(s)	397

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