Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000007

Orthogroup ID

OG0003287

Physical Location & Seq

Genomic Coordinates Forward (+)

64596180 .. 64598210

Gene Structure 2031 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_7G00214090.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 651 bp

ATGCATGGTACTTTGACTCCGGGTGCAGCAACACGTGTGGTAGTAACTAGTAAGTCATGTTTCTCTATTTTGAATGAAGCATTTCGCACTGTTGTGAGGTTTGGTAATAATTCTACTAATGTTATATGGGAAAGGGTGCTATTCATATTAGAACTAAAACTGATCATATATATTAAAATCATTTTAAATGTGTTTTATGTCTCTAATTTGAAGTGTAATTTGTTGAGTATCGGTCAGCTTCAAGAGAAGGGATATGTGTCCACAATCAGAAAAGTTGCTTGTAAAATTTATGATCCACAAAGGAGCCTAATTGCTCATGTTAATATGACTCCAAATAAGCTGTCTCCGCAGCTAATCAAGAGTGTTCATTCCTGCCGTATAACCGAGATGAAAGATCCAACATGGCTTTGGCATTTTCGCTATGGTCATTTGAATTTTAATGGATTGAATTCACTATTATCAGAAGAAGATAGTTACCAGTTTTCCTCAAATCTGTCCTCCCTCCAAAAGAAAAAGCCTAGAGAGCTCAAGAGGGAGCAGTGCCATCAGGCCTTACCCGTAGCCGGCGTGGGATACCAATCCGTAGTCTTGGATCGTCATCTCGATCAATATGCTGTTTTTGGATGCATGTACGTAGCAGACGAAGTGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Retrotran_gag_2

Protein Analysis

216

Amino Acids

24.68

Weight (kDa)

9.32

Isoelectric Point (pI)

41.17

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Pol_BBD	PF22936	9 - 85	1e-09	Pol polyprotein, beta-barrel domain
gag_pre-integrs	PF13976	123 - 162	4e-08	GAG-pre-integrase domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Align Labels (Cladogram)

Image

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Publication-ready

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0003287)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G11591
fragaria_vesca	FvH4_2g20411 FvH4_2g29931 FvH4_3g14181 FvH4_4g00781 FvH4_4g12541 FvH4_5g22143 FvH4_7g24581
pyrus_communis	pycom04g03170 pycom05g18080 pycom12g05030 pycom13g18540
rosa_chinensis	RchiOBHm_Chr1g0313681 RchiOBHm_Chr1g0344501 RchiOBHm_Chr2g0157511
rosa_laevigata	RLG00000008144 RLG00000008360
rosa_multiflora	Rmu_sc0003765.1_g000035 Rmu_sc0004343.1_g000026 Rmu_sc0006087.1_g000011
rosa_roxburghii	Rroxscaffold_1G00038680 Rroxscaffold_3G00247490 Rroxscaffold_4G00315330 Rroxscaffold_5G00355970 Rroxscaffold_7G00214090
rosa_rugosa	Rorug04G0109300 Rorug04G0109400
rosa_samantha	Rh1AG403200 Rh4AG167500 Rh4BG164600 Rh4CG179400 Rh4DG162300
rosa_wichuraiana	Rw4G013620 Rw4G013850 Rw4G013950 Rw6G038170

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AciI	CCGC	1 cut(s)	347
AclWI	GGATC	3 cut(s)	287, 389, 600
AcsI	RAATTY	3 cut(s)	285, 433, 448
AcvI	CACGTG	1 cut(s)	35
AfaI	GTAC	2 cut(s)	10, 632
AfiI	CCNNNNNNNGG	1 cut(s)	563
AflIII	ACRYGT	2 cut(s)	32, 34
AgsI	TTSAA	5 cut(s)	73, 211, 242, 433, 448
AhlI	ACTAGT	1 cut(s)	47
AleI	CACNNNNGTG	1 cut(s)	92
AluBI	AGCT	4 cut(s)	238, 340, 352, 526
AluI	AGCT	4 cut(s)	238, 340, 352, 526
Alw21I	GWGCWC	1 cut(s)	528
Alw26I	GTCTC	2 cut(s)	205, 348
AlwI	GGATC	3 cut(s)	287, 389, 600
AoxI	GGCC	1 cut(s)	549
ApeKI	GCWGC	2 cut(s)	26, 349
ApoI	RAATTY	3 cut(s)	285, 433, 448
ArsI	GACNNNNNNTTYG	2 cut(s)	326, 358
Asp700I	GAANNNNTTC	1 cut(s)	81
AsuC2I	CCSGG	1 cut(s)	21
BanII	GRGCYC	1 cut(s)	528
BbrPI	CACGTG	1 cut(s)	35
Bbv12I	GWGCWC	1 cut(s)	528
BbvI	GCAGC	2 cut(s)	38, 361
BccI	CCATC	1 cut(s)	552
BceAI	ACGGC	1 cut(s)	360
BcgI	CGANNNNNNTGC	2 cut(s)	593, 627
BciVI	GTATCC	1 cut(s)	566
BclI	TGATCA	1 cut(s)	162
BcnI	CCSGG	1 cut(s)	21
BcoDI	GTCTC	2 cut(s)	205, 348
BcuI	ACTAGT	1 cut(s)	47
BfaI	CTAG	2 cut(s)	48, 519
BfuI	GTATCC	1 cut(s)	566
BisI	GCNGC	2 cut(s)	27, 350
BlsI	GCNGC	2 cut(s)	28, 351
Bme1390I	CCNGG	1 cut(s)	21
BmiI	GGNNCC	1 cut(s)	305
BmrFI	CCNGG	1 cut(s)	21
BmsI	GCATC	1 cut(s)	614
BpuEI	CTTGAG	1 cut(s)	512
BpuMI	CCSGG	1 cut(s)	21
BsaAI	YACGTR	2 cut(s)	35, 634
BsaBI	GATNNNNATC	2 cut(s)	577, 597
BsaXI	ACNNNNNCTCC	1 cut(s)	31
Bsc4I	CCNNNNNNNGG	1 cut(s)	563
Bse118I	RCCGGY	1 cut(s)	563
Bse1I	ACTGG	1 cut(s)	478
Bse8I	GATNNNNATC	2 cut(s)	577, 597
BseGI	GGATG	1 cut(s)	629
BseJI	GATNNNNATC	2 cut(s)	577, 597
BseLI	CCNNNNNNNGG	1 cut(s)	563
BseNI	ACTGG	1 cut(s)	478
BseXI	GCAGC	2 cut(s)	38, 361
BsgI	GTGCAG	1 cut(s)	45
BshFI	GGCC	1 cut(s)	551
BsiHKAI	GWGCWC	1 cut(s)	528
BsiSI	CCGG	2 cut(s)	20, 564
BslI	CCNNNNNNNGG	1 cut(s)	563
BsmAI	GTCTC	2 cut(s)	205, 348
BsnI	GGCC	1 cut(s)	551
Bsp1286I	GDGCHC	1 cut(s)	528
Bsp143I	GATC	5 cut(s)	162, 292, 394, 592, 604
BspACI	CCGC	1 cut(s)	347
BspANI	GGCC	1 cut(s)	551
BspLI	GGNNCC	1 cut(s)	305
BspPI	GGATC	3 cut(s)	287, 389, 600
BsrFI	RCCGGY	1 cut(s)	563
BsrI	ACTGG	1 cut(s)	478
BssAI	RCCGGY	1 cut(s)	563
BssMI	GATC	5 cut(s)	162, 292, 394, 592, 604
Bst4CI	ACNGT	1 cut(s)	91
BstBAI	YACGTR	2 cut(s)	35, 634
BstC8I	GCNNGC	1 cut(s)	565
BstF5I	GGATG	1 cut(s)	629
BstKTI	GATC	5 cut(s)	165, 295, 397, 595, 607
BstMAI	GTCTC	2 cut(s)	205, 348
BstMBI	GATC	5 cut(s)	162, 292, 394, 592, 604
BstMWI	GCNNNNNNNGC	2 cut(s)	346, 523
BstNSI	RCATGY	1 cut(s)	631
BstSCI	CCNGG	1 cut(s)	19
BstSNI	TACGTA	1 cut(s)	634
BstV1I	GCAGC	2 cut(s)	38, 361
BstX2I	RGATCY	1 cut(s)	394
BstYI	RGATCY	1 cut(s)	394
BsuI	GTATCC	1 cut(s)	566
BsuRI	GGCC	1 cut(s)	551
BtsCI	GGATG	1 cut(s)	629
BtsI	GCAGTG	1 cut(s)	545
BtsIMutI	CAGTG	2 cut(s)	87, 545
Cac8I	GCNNGC	1 cut(s)	565
Cfr10I	RCCGGY	1 cut(s)	563
Csp6I	GTAC	2 cut(s)	9, 631
CspCI	CAANNNNNGTGG	2 cut(s)	18, 53
CviAII	CATG	5 cut(s)	5, 57, 317, 402, 628
CviJI	RGCY	9 cut(s)	238, 306, 340, 352, 406, 517, 526, 551, 563
CviKI_1	RGCY	9 cut(s)	238, 306, 340, 352, 406, 517, 526, 551, 563
CviQI	GTAC	2 cut(s)	9, 631
DpnI	GATC	5 cut(s)	164, 294, 396, 594, 606
DpnII	GATC	5 cut(s)	162, 292, 394, 592, 604
DraI	TTTAAA	1 cut(s)	186
Ecl136II	GAGCTC	1 cut(s)	526
Eco105I	TACGTA	1 cut(s)	634
Eco147I	AGGCCT	1 cut(s)	551
Eco24I	GRGCYC	1 cut(s)	528
Eco53kI	GAGCTC	1 cut(s)	526
Eco72I	CACGTG	1 cut(s)	35
EcoICRI	GAGCTC	1 cut(s)	526
EcoRI	GAATTC	1 cut(s)	448
EcoT22I	ATGCAT	2 cut(s)	6, 629
EcoT38I	GRGCYC	1 cut(s)	528
FaeI	CATG	5 cut(s)	8, 60, 320, 405, 631
FatI	CATG	5 cut(s)	4, 56, 316, 401, 627
FbaI	TGATCA	1 cut(s)	162
Fnu4HI	GCNGC	2 cut(s)	27, 350
FokI	GGATG	1 cut(s)	636
FriOI	GRGCYC	1 cut(s)	528
Fsp4HI	GCNGC	2 cut(s)	27, 350
FspBI	CTAG	2 cut(s)	48, 519
GluI	GCNGC	2 cut(s)	27, 350
HaeIII	GGCC	1 cut(s)	551
HapII	CCGG	2 cut(s)	20, 564
Hin1II	CATG	5 cut(s)	8, 60, 320, 405, 631
HinfI	GANTC	2 cut(s)	16, 328
HpaII	CCGG	2 cut(s)	20, 564
Hpy166II	GTNNAC	1 cut(s)	261
Hpy188I	TCNGA	2 cut(s)	269, 463
Hpy188III	TCNNGA	4 cut(s)	242, 358, 529, 602
Hpy8I	GTNNAC	1 cut(s)	261
HpyAV	CCTTC	1 cut(s)	241
HpyCH4III	ACNGT	1 cut(s)	91
HpyCH4IV	ACGT	2 cut(s)	34, 633
HpyCH4V	TGCA	3 cut(s)	4, 26, 627
HpyF10VI	GCNNNNNNNGC	2 cut(s)	346, 523
HpySE526I	ACGT	2 cut(s)	34, 633
Hsp92II	CATG	5 cut(s)	8, 60, 320, 405, 631
KroI	GCCGGC	1 cut(s)	563
KroNI	GCCGGC	1 cut(s)	565
Ksp22I	TGATCA	1 cut(s)	162
Kzo9I	GATC	5 cut(s)	162, 292, 394, 592, 604
LmnI	GCTCC	2 cut(s)	303, 535
LpnPI	CCDG	5 cut(s)	33, 385, 491, 533, 577
Lsp1109I	GCAGC	2 cut(s)	38, 361
LweI	GCATC	1 cut(s)	614
MaeI	CTAG	2 cut(s)	48, 519
MaeII	ACGT	2 cut(s)	34, 633
MaeIII	GTNAC	2 cut(s)	43, 473
MalI	GATC	5 cut(s)	164, 294, 396, 594, 606
MboI	GATC	5 cut(s)	162, 292, 394, 592, 604
MboII	GAAGA	2 cut(s)	476, 479
MflI	RGATCY	1 cut(s)	394
MhlI	GDGCHC	1 cut(s)	528
MluCI	AATT	7 cut(s)	109, 205, 217, 285, 309, 433, 448
MlyI	GAGTC	2 cut(s)	10, 322
MmeI	TCCRAC	1 cut(s)	422
MnlI	CCTC	5 cut(s)	90, 496, 508, 512, 525
Mph1103I	ATGCAT	2 cut(s)	6, 629
MroNI	GCCGGC	1 cut(s)	563
MroXI	GAANNNNTTC	1 cut(s)	81
MseI	TTAA	4 cut(s)	174, 185, 321, 438
MslI	CAYNNNNRTG	1 cut(s)	92
MspI	CCGG	2 cut(s)	20, 564
MspR9I	CCNGG	1 cut(s)	21
MwoI	GCNNNNNNNGC	2 cut(s)	346, 523
NaeI	GCCGGC	1 cut(s)	565
NciI	CCSGG	1 cut(s)	21
NdeII	GATC	5 cut(s)	162, 292, 394, 592, 604
NgoMIV	GCCGGC	1 cut(s)	563
NlaIII	CATG	5 cut(s)	8, 60, 320, 405, 631
NlaIV	GGNNCC	1 cut(s)	305
NsiI	ATGCAT	2 cut(s)	6, 629
NspI	RCATGY	1 cut(s)	631
OliI	CACNNNNGTG	1 cut(s)	92
PceI	AGGCCT	1 cut(s)	551
PcsI	WCGNNNNNNNCGW	1 cut(s)	639
PdiI	GCCGGC	1 cut(s)	565
PdmI	GAANNNNTTC	1 cut(s)	81
PkrI	GCNGC	2 cut(s)	28, 351
PleI	GAGTC	2 cut(s)	10, 322
PmaCI	CACGTG	1 cut(s)	35
PmlI	CACGTG	1 cut(s)	35
PpsI	GAGTC	2 cut(s)	10, 322
Ppu21I	YACGTR	2 cut(s)	35, 634
Psp124BI	GAGCTC	1 cut(s)	528
PspCI	CACGTG	1 cut(s)	35
PspN4I	GGNNCC	1 cut(s)	305
PsuI	RGATCY	1 cut(s)	394
RsaI	GTAC	2 cut(s)	10, 632
RsaNI	GTAC	2 cut(s)	9, 631
RseI	CAYNNNNRTG	1 cut(s)	92
SacI	GAGCTC	1 cut(s)	528
SaqAI	TTAA	4 cut(s)	174, 185, 321, 438
SatI	GCNGC	2 cut(s)	27, 350
Sau3AI	GATC	5 cut(s)	162, 292, 394, 592, 604
SchI	GAGTC	2 cut(s)	10, 322
ScrFI	CCNGG	1 cut(s)	21
SduI	GDGCHC	1 cut(s)	528
SetI	ASST	7 cut(s)	37, 101, 240, 342, 354, 528, 636
SfaNI	GCATC	1 cut(s)	614
SmiMI	CAYNNNNRTG	1 cut(s)	92
SmlI	CTYRAG	1 cut(s)	527
SmoI	CTYRAG	1 cut(s)	527
SnaBI	TACGTA	1 cut(s)	634
SpeI	ACTAGT	1 cut(s)	47
Sse9I	AATT	7 cut(s)	109, 205, 217, 285, 309, 433, 448
SseBI	AGGCCT	1 cut(s)	551
SsiI	CCGC	1 cut(s)	347
SspMI	CTAG	2 cut(s)	48, 519
SstI	GAGCTC	1 cut(s)	528
StuI	AGGCCT	1 cut(s)	551
StyD4I	CCNGG	1 cut(s)	19
TaaI	ACNGT	1 cut(s)	91
TaiI	ACGT	2 cut(s)	37, 636
TaqI	TCGA	1 cut(s)	603
TaqII	GACCGA	1 cut(s)	221
TasI	AATT	7 cut(s)	109, 205, 217, 285, 309, 433, 448
Tru1I	TTAA	4 cut(s)	174, 185, 321, 438
Tru9I	TTAA	4 cut(s)	174, 185, 321, 438
TscAI	CASTG	2 cut(s)	94, 545
TseI	GCWGC	2 cut(s)	26, 349
TspDTI	ATGAA	4 cut(s)	90, 133, 356, 404
TspGWI	ACGGA	1 cut(s)	571
TspRI	CASTG	2 cut(s)	94, 545
XapI	RAATTY	3 cut(s)	285, 433, 448
XceI	RCATGY	1 cut(s)	631
XcmI	CCANNNNNNNNNTGG	1 cut(s)	405
XmnI	GAANNNNTTC	1 cut(s)	81
XspI	CTAG	2 cut(s)	48, 519
Zsp2I	ATGCAT	2 cut(s)	6, 629

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