Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000001

Orthogroup ID

OG0001340

Physical Location & Seq

Genomic Coordinates Forward (+)

59420341 .. 59427544

Gene Structure 7204 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_1G00041540.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 822 bp

ATGGCTCATAGGACCAATCAACTGCCCTTCTTCTCGCTGCTGTACCGTGTGGTGATATGTAGGAGTACCTGTGTGGTGACATGTGGGAGTACCTGTGTGGCGAAATACTCTCCGTGTGGTGACATGTGGGGGTACCTGTGTGGCGAAATACTCCCCGTGTGTGTGCTGCAAGTCACTTGGTCCCATCCAGCTGAGGGTTATTTGAAGATAAATTACGATGGTGCCTATACTGTGAGGAAGGGAGGTTTAGGTGTGGTTGCTTGGGATACGAAGGGACGTTTTGTGGCAGCAAAGTGCTGGTTGGTTAATGTTGAATCGGAGGACGATGTGGTGGCAATGGAGGAGAGGTTTGCTTCTACTTCATGGTTTAACAAAGAGAAACTAAAGACCAACTTTTACAAACTCCAAAAAGGTTCAGATTTTATTGACAATCACTTAGATCGGGTGAAGATAGCTTGTGATCAGTTGGCTACCGTAGGGGTTCATATGACCGATGAAGACATAGTTGCCTCTGTTCTTCTTAGTTTGCCATTAGACTATATTACCATGAAAACTATAATTAGGGCTAAGCATGACCCCATTTCAATACAAGAGTTAAGGTCTCTTTTGCTCATTGCTGAAGCTGAACTTAAAGAAATTGACAAGTCTATTTCTGCTCCCGCAAGTCTTCCTTTGTCACCACCGAATGCAATGGTTGCATATAATGTACTACCTACTTTGCCTACTAGTAATGAGTATATTGGTGTTCATTGTGGATCTCCTACTTTGAAGCATGAAGCACTGCCATTTTTCTTCACTAGTTGCTATGGTTGCACAAAATAA

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 gag_pre-integrs

Protein Analysis

273

Amino Acids

30.31

Weight (kDa)

6.38

Isoelectric Point (pI)

34.28

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Retrotran_gag_2	PF14223	113 - 211	2.4e-10	gag-polypeptide of LTR copia-type

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

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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: OG0001340)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_5g05651 FvH4_5g06481
malus_domestica	MD04G1150100.v1.1
rosa_chinensis	RchiOBHm_Chr1g0366871 RchiOBHm_Chr2g0112811 RchiOBHm_Chr5g0022021 RchiOBHm_Chr5g0050161 RchiOBHm_Chr7g0178931
rosa_laevigata	RLG00000030270 RLG00000030274 RLG00000030285 RLG00000030289
rosa_multiflora	Rmu_sc0000206.1_g000011 Rmu_sc0000539.1_g000041 Rmu_sc0001706.1_g000020 Rmu_sc0002245.1_g000029 Rmu_sc0002935.1_g000016 Rmu_sc0002952.1_g000016 Rmu_sc0002952.1_g000017 Rmu_sc0003371.1_g000005 Rmu_sc0004193.1_g000005 Rmu_sc0004359.1_g000018 Rmu_sc0006422.1_g000014 Rmu_sc0007594.1_g000001 Rmu_sc0010925.1_g000018 Rmu_sc0013146.1_g000003 Rmu_sc0031630.1_g000002 Rmu_sc0033466.1_g000001 Rmu_ssc0000079.1_g000006 Rmu_ssc0000423.1_g000006
rosa_roxburghii	Rroxscaffold_1G00004520 Rroxscaffold_1G00005520 Rroxscaffold_1G00041540 Rroxscaffold_1G00045310 Rroxscaffold_5G00361650 Rroxscaffold_6G00388920 Rroxscaffold_6G00405980 Rroxscaffold_6G00410140 Rroxscaffold_6G00423840 Rroxscaffold_7G00200050
rosa_rugosa	Rorug02G0433500 Rorug02G0433600 Rorug02G0433600 Rorug02G0433700 Rorug04G0166100.1 Rorug05G0053500 Rorug06G0481300
rosa_samantha	Rh1CG036200 Rh4AG051700 Rh4BG049000 Rh4CG055700
rosa_wichuraiana	Rw0G022690 Rw1G035930 Rw4G004120

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc65I	GGTACC	1 cut(s)	132
AccB1I	GGYRCC	2 cut(s)	132, 221
AciI	CCGC	1 cut(s)	660
AclWI	GGATC	1 cut(s)	763
AcuI	CTGAAG	1 cut(s)	639
AfaI	GTAC	5 cut(s)	44, 67, 91, 134, 708
AfiI	CCNNNNNNNGG	1 cut(s)	194
AflIII	ACRYGT	2 cut(s)	80, 123
AgsI	TTSAA	4 cut(s)	205, 314, 585, 769
AhlI	ACTAGT	2 cut(s)	725, 797
AluBI	AGCT	3 cut(s)	191, 455, 623
AluI	AGCT	3 cut(s)	191, 455, 623
Alw26I	GTCTC	1 cut(s)	606
AlwI	GGATC	1 cut(s)	763
ApeKI	GCWGC	3 cut(s)	37, 166, 287
Asp718I	GGTACC	1 cut(s)	132
AspS9I	GGNCC	2 cut(s)	12, 180
AsuHPI	GGTGA	5 cut(s)	64, 88, 131, 457, 669
AvaII	GGWCC	2 cut(s)	12, 180
BaeI	ACNNNNGTAYC	2 cut(s)	124, 157
BanI	GGYRCC	2 cut(s)	132, 221
BarI	GAAGNNNNNNTAC	2 cut(s)	197, 229
BbsI	GAAGAC	2 cut(s)	504, 659
BbvCI	CCTCAGC	1 cut(s)	192
BbvI	GCAGC	3 cut(s)	24, 153, 299
BccI	CCATC	2 cut(s)	192, 212
BciVI	GTATCC	1 cut(s)	259
BclI	TGATCA	1 cut(s)	460
BcoDI	GTCTC	1 cut(s)	606
BcuI	ACTAGT	2 cut(s)	725, 797
BfaI	CTAG	2 cut(s)	726, 798
BfuI	GTATCC	1 cut(s)	259
BisI	GCNGC	3 cut(s)	38, 167, 288
BlpI	GCTNAGC	1 cut(s)	567
BlsI	GCNGC	3 cut(s)	39, 168, 289
Bme18I	GGWCC	2 cut(s)	12, 180
BmgT120I	GGNCC	2 cut(s)	12, 180
BmiI	GGNNCC	3 cut(s)	134, 182, 223
BpiI	GAAGAC	2 cut(s)	504, 659
Bpu10I	CCTNAGC	1 cut(s)	192
Bpu1102I	GCTNAGC	1 cut(s)	567
BsaI	GGTCTC	1 cut(s)	606
BsaXI	ACNNNNNCTCC	6 cut(s)	55, 79, 85, 109, 332, 362
Bsc4I	CCNNNNNNNGG	1 cut(s)	194
Bse3DI	GCAATG	3 cut(s)	342, 612, 696
BseGI	GGATG	1 cut(s)	184
BseLI	CCNNNNNNNGG	1 cut(s)	194
BseMI	GCAATG	3 cut(s)	342, 612, 696
BseMII	CTCAG	1 cut(s)	183
BseRI	GAGGAG	1 cut(s)	356
BseXI	GCAGC	3 cut(s)	24, 153, 299
BshNI	GGYRCC	2 cut(s)	132, 221
BslFI	GGGAC	2 cut(s)	166, 288
BslI	CCNNNNNNNGG	1 cut(s)	194
BsmAI	GTCTC	1 cut(s)	606
BsmFI	GGGAC	2 cut(s)	166, 288
BsmI	GAATGC	1 cut(s)	691
Bso31I	GGTCTC	1 cut(s)	606
Bsp143I	GATC	3 cut(s)	439, 460, 755
Bsp1720I	GCTNAGC	1 cut(s)	567
BspACI	CCGC	1 cut(s)	660
BspCNI	CTCAG	1 cut(s)	184
BspLI	GGNNCC	3 cut(s)	134, 182, 223
BspPI	GGATC	1 cut(s)	763
BspT107I	GGYRCC	2 cut(s)	132, 221
BspTNI	GGTCTC	1 cut(s)	606
BsrDI	GCAATG	3 cut(s)	342, 612, 696
BssMI	GATC	3 cut(s)	439, 460, 755
Bst4CI	ACNGT	3 cut(s)	47, 232, 475
BstAPI	GCANNNNNTGC	1 cut(s)	695
BstDEI	CTNAG	4 cut(s)	192, 436, 521, 567
BstF5I	GGATG	1 cut(s)	184
BstKTI	GATC	3 cut(s)	442, 463, 758
BstMAI	GTCTC	1 cut(s)	606
BstMBI	GATC	3 cut(s)	439, 460, 755
BstMWI	GCNNNNNNNGC	2 cut(s)	695, 810
BstNSI	RCATGY	2 cut(s)	84, 127
BstV1I	GCAGC	3 cut(s)	24, 153, 299
BstV2I	GAAGAC	2 cut(s)	504, 659
BstX2I	RGATCY	1 cut(s)	755
BstYI	RGATCY	1 cut(s)	755
BsuI	GTATCC	1 cut(s)	259
BtsCI	GGATG	1 cut(s)	184
BtsI	GCAGTG	1 cut(s)	779
BtsIMutI	CAGTG	1 cut(s)	779
Cfr13I	GGNCC	2 cut(s)	12, 180
Csp6I	GTAC	5 cut(s)	43, 66, 90, 133, 707
CviAII	CATG	6 cut(s)	81, 124, 363, 547, 572, 773
CviJI	RGCY	6 cut(s)	5, 191, 455, 470, 566, 623
CviKI_1	RGCY	6 cut(s)	5, 191, 455, 470, 566, 623
CviQI	GTAC	5 cut(s)	43, 66, 90, 133, 707
DdeI	CTNAG	4 cut(s)	192, 436, 521, 567
DpnI	GATC	3 cut(s)	441, 462, 757
DpnII	GATC	3 cut(s)	439, 460, 755
Eco31I	GGTCTC	1 cut(s)	606
Eco47I	GGWCC	2 cut(s)	12, 180
Eco57I	CTGAAG	1 cut(s)	639
FaeI	CATG	6 cut(s)	84, 127, 366, 550, 575, 776
FalI	AAGNNNNNCTT	6 cut(s)	377, 409, 612, 644, 655, 687
FaqI	GGGAC	2 cut(s)	166, 288
FatI	CATG	6 cut(s)	80, 123, 362, 546, 571, 772
FauI	CCCGC	1 cut(s)	667
FauNDI	CATATG	1 cut(s)	486
FbaI	TGATCA	1 cut(s)	460
Fnu4HI	GCNGC	3 cut(s)	38, 167, 288
FokI	GGATG	1 cut(s)	171
Fsp4HI	GCNGC	3 cut(s)	38, 167, 288
FspBI	CTAG	2 cut(s)	726, 798
GluI	GCNGC	3 cut(s)	38, 167, 288
Hin1II	CATG	6 cut(s)	84, 127, 366, 550, 575, 776
HinfI	GANTC	1 cut(s)	314
HphI	GGTGA	5 cut(s)	64, 88, 131, 457, 669
Hpy188I	TCNGA	2 cut(s)	319, 418
HpyAV	CCTTC	3 cut(s)	37, 232, 265
HpyCH4III	ACNGT	3 cut(s)	47, 232, 475
HpyCH4IV	ACGT	1 cut(s)	277
HpyCH4V	TGCA	4 cut(s)	169, 689, 698, 813
HpyF10VI	GCNNNNNNNGC	2 cut(s)	695, 810
HpyF3I	CTNAG	4 cut(s)	192, 436, 521, 567
HpySE526I	ACGT	1 cut(s)	277
Hsp92II	CATG	6 cut(s)	84, 127, 366, 550, 575, 776
KpnI	GGTACC	1 cut(s)	136
Ksp22I	TGATCA	1 cut(s)	460
Kzo9I	GATC	3 cut(s)	439, 460, 755
LmnI	GCTCC	1 cut(s)	661
LpnPI	CCDG	5 cut(s)	82, 106, 149, 201, 283
Lsp1109I	GCAGC	3 cut(s)	24, 153, 299
MaeI	CTAG	2 cut(s)	726, 798
MaeII	ACGT	1 cut(s)	277
MaeIII	GTNAC	4 cut(s)	76, 119, 172, 675
MalI	GATC	3 cut(s)	441, 462, 757
MboI	GATC	3 cut(s)	439, 460, 755
MboII	GAAGA	7 cut(s)	22, 217, 460, 509, 509, 659, 784
MflI	RGATCY	1 cut(s)	755
MluCI	AATT	3 cut(s)	211, 558, 636
MnlI	CCTC	7 cut(s)	187, 228, 236, 313, 334, 339, 520
MseI	TTAA	4 cut(s)	306, 369, 596, 630
MspA1I	CMGCKG	1 cut(s)	191
Mva1269I	GAATGC	1 cut(s)	691
MwoI	GCNNNNNNNGC	2 cut(s)	695, 810
NdeI	CATATG	1 cut(s)	486
NdeII	GATC	3 cut(s)	439, 460, 755
NlaIII	CATG	6 cut(s)	84, 127, 366, 550, 575, 776
NlaIV	GGNNCC	3 cut(s)	134, 182, 223
NmuCI	GTSAC	4 cut(s)	76, 119, 172, 675
NspI	RCATGY	2 cut(s)	84, 127
PciI	ACATGT	2 cut(s)	80, 123
PctI	GAATGC	1 cut(s)	691
PfeI	GAWTC	1 cut(s)	314
PkrI	GCNGC	3 cut(s)	39, 168, 289
PscI	ACATGT	2 cut(s)	80, 123
PspN4I	GGNNCC	3 cut(s)	134, 182, 223
PspPI	GGNCC	2 cut(s)	12, 180
PsuI	RGATCY	1 cut(s)	755
PvuII	CAGCTG	1 cut(s)	191
RsaI	GTAC	5 cut(s)	44, 67, 91, 134, 708
RsaNI	GTAC	5 cut(s)	43, 66, 90, 133, 707
SaqAI	TTAA	4 cut(s)	306, 369, 596, 630
SatI	GCNGC	3 cut(s)	38, 167, 288
Sau3AI	GATC	3 cut(s)	439, 460, 755
Sau96I	GGNCC	2 cut(s)	12, 180
SinI	GGWCC	2 cut(s)	12, 180
SpeI	ACTAGT	2 cut(s)	725, 797
Sse9I	AATT	3 cut(s)	211, 558, 636
SsiI	CCGC	1 cut(s)	660
SspMI	CTAG	2 cut(s)	726, 798
TaaI	ACNGT	3 cut(s)	47, 232, 475
TaiI	ACGT	1 cut(s)	280
TaqII	GACCGA	1 cut(s)	506
TasI	AATT	3 cut(s)	211, 558, 636
TatI	WGTACW	1 cut(s)	706
TfiI	GAWTC	1 cut(s)	314
Tru1I	TTAA	4 cut(s)	306, 369, 596, 630
Tru9I	TTAA	4 cut(s)	306, 369, 596, 630
TscAI	CASTG	1 cut(s)	786
TseFI	GTSAC	4 cut(s)	76, 119, 172, 675
TseI	GCWGC	3 cut(s)	37, 166, 287
Tsp45I	GTSAC	4 cut(s)	76, 119, 172, 675
TspDTI	ATGAA	6 cut(s)	351, 473, 510, 563, 737, 789
TspGWI	ACGGA	1 cut(s)	102
TspRI	CASTG	1 cut(s)	786
VpaK11BI	GGWCC	2 cut(s)	12, 180
XceI	RCATGY	2 cut(s)	84, 127
XspI	CTAG	2 cut(s)	726, 798

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