Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5A

Orthogroup ID

OG0000411

Physical Location & Seq

Genomic Coordinates Reverse (-)

68840919 .. 68847482

Gene Structure 6564 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5AG397500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 771 bp

ATGGAGGATCCAATCATGGATGATCATAGAGACGCAGAAGACCTCCAAGCCATTCTGGCGGAGCAGCGCAGAGAGCTCTTGGCAGCCAAAACCCTAGATTCCGACCTCGACATGGCATTCAATCTTCAAATGAAGGAAGCCCTCACCGCCTCTCCAACCCTCCTCCAGTACTCAGCAGTCTCCGCCGTACGAGGCCAAGAACGACCTCTTGGACCTCGCCGCAGCGTTCATGCTCGAGGACAGAGGTTTCCTCAGGAGTACGAGGACCACGAACGCAGCGTTTTGGAGGTGAAGAAACTGAAGACGGATCTCGACAGTCGGATTCACGACCAGAAGTTCGCGATCAACGTTTGTGACTTGCCGGAGGACTGCTGGAGGGAGTACGGAGACGAATATGAAAGGCCGTACTGTACGAATGGGTCGTCGTCTTCAAAAGATGGGTTGCAGACCGAGTGTTTGAGATTGTATTGCAAGGGTTTGATTATTGAAGAAGTGGTCAAGAATGTGAAGGTGGCGGTGGGTGGGATTGGGGTTGTGATTTGTGACCCGAGAGATAATCTGATTTTCGAGGCCAAGAAGAATCTAGAAGTGTTGATTGATGGCGAGATTATGAGCAATGAGGCTGTGGAGCTTGAGGCTCTCTGTGAAGGACTTAATCAAGCTCTCACACTGGACTTGAAAAATATCACCTTTTTCATTGATGACAACAAGCTTTACCAATATGTGAGTCTTAAAGCCTTTGTTCTTTTTTTACCTGTTTGGTCTAGTTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000151 GO:0000209 GO:0003674 GO:0003824 GO:0004842 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0006464 GO:0006807 GO:0008150 GO:0008152 GO:0009653 GO:0009893 GO:0009894 GO:0009896 GO:0009987 GO:0010604 GO:0016567 GO:0016740 GO:0019222 GO:0019538 GO:0019787 GO:0019899 GO:0030154 GO:0030162 GO:0030435 GO:0031323 GO:0031325 GO:0031329 GO:0031331 GO:0031624 GO:0032268 GO:0032270 GO:0032434 GO:0032436 GO:0032446 GO:0032502 GO:0032991 GO:0036211 GO:0042176 GO:0043170 GO:0043412 GO:0043934 GO:0044237 GO:0044238 GO:0044260 GO:0044267 GO:0044390 GO:0044424 GO:0044464 GO:0045732 GO:0045862 GO:0048518 GO:0048522 GO:0048646 GO:0048856 GO:0048869 GO:0050789 GO:0050794 GO:0051171 GO:0051173 GO:0051246 GO:0051247 GO:0060255 GO:0061136 GO:0061630 GO:0061659 GO:0065007 GO:0070647 GO:0071704 GO:0080090 GO:0140096 GO:1901564 GO:1901800 GO:1902494 GO:1903050 GO:1903052 GO:1903362 GO:1903364 GO:1990234 GO:2000058 GO:2000060

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

IBR RVT_3 zf-C3HC4

Protein Analysis

256

Amino Acids

29.08

Weight (kDa)

4.73

Isoelectric Point (pI)

51.77

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RVT_3	PF13456	171 - 243	1.1e-09	Reverse transcriptase-like

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

Font Size (px)

Line Width

Align Labels (Cladogram)

Image

Tree File

Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready

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

Orthologous Genes (Group: OG0000411)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G45470 AT3G45555 AT5G60250
fragaria_vesca	FvH4_3g33450 FvH4_3g33450 FvH4_3g33450 FvH4_3g33450 FvH4_3g33450 FvH4_3g33470 FvH4_3g33471 FvH4_3g33480 FvH4_3g33480
malus_domestica	MD03G1130800.v1.1 MD11G1125600.v1.1 MD11G1125700.v1.1 MD11G1125800.v1.1 MD11G1126100.v1.1 MD11G1152600.v1.1
prunus_persica	Prupe.6G094100_v2.0.a1 Prupe.6G094100_v2.0.a1 Prupe.6G094200_v2.0.a1 Prupe.6G094500_v2.0.a1 Prupe.6G094500_v2.0.a1 Prupe.6G115600_v2.0.a1 Prupe.6G115700_v2.0.a1 Prupe.6G115700_v2.0.a1 Prupe.6G115700_v2.0.a1 Prupe.6G115700_v2.0.a1
pyrus_communis	pycom11g10590 pycom11g10600 pycom11g10620 pycom11g10640 pycom11g12510
rosa_chinensis	RchiOBHm_Chr5g0060811 RchiOBHm_Chr5g0060821 RchiOBHm_Chr5g0060851 RchiOBHm_Chr5g0060881 RchiOBHm_Chr5g0060891
rosa_laevigata	RLG00000035404 RLG00000035405 RLG00000035407 RLG00000035408
rosa_multiflora	Rmu_sc0000420.1_g000048 Rmu_sc0000420.1_g000049 Rmu_sc0000727.1_g000006 Rmu_sc0000727.1_g000007 Rmu_sc0000727.1_g000024 Rmu_sc0000727.1_g000025 Rmu_sc0024212.1_g000001 Rmu_sc0024212.1_g000003 Rmu_sc0027900.1_g000003 Rmu_sc0030258.1_g000001
rosa_roxburghii	Rroxscaffold_1G00019780 Rroxscaffold_1G00019790 Rroxscaffold_1G00019800 Rroxscaffold_1G00019810 Rroxscaffold_1G00019820 Rroxscaffold_1G00019840 Rroxscaffold_1G00019850
rosa_rugosa	Rorug05G0334200 Rorug05G0334300 Rorug05G0334400 Rorug05G0334500 Rorug05G0334600 Rorug05G0334700
rosa_samantha	Rh4BG359600 Rh4CG373900 Rh5AG397000 Rh5AG397100 Rh5AG397200 Rh5AG397300 Rh5AG397400 Rh5AG397500 Rh5AG397600 Rh5AG397700 Rh5BG409300 Rh5BG409400 Rh5BG409800 Rh5BG409900 Rh5BG410000 Rh5BG410100 Rh5CG434100 Rh5CG434200 Rh5CG434600 Rh5CG434700 Rh5CG434800 Rh5CG434900 Rh5CG435000 Rh5DG424100 Rh5DG424200 Rh5DG424400 Rh5DG424500 Rh5DG424600 Rh5DG424800
rosa_wichuraiana	Rw5G037420 Rw5G037430 Rw5G037480 Rw5G037490 Rw5G037500

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccII	CGCG	1 cut(s)	341
AciI	CCGC	5 cut(s)	59, 147, 183, 220, 515
AclI	AACGTT	1 cut(s)	348
AclWI	GGATC	3 cut(s)	2, 15, 315
AcuI	CTGAAG	1 cut(s)	320
AfaI	GTAC	6 cut(s)	170, 189, 260, 383, 407, 412
AfiI	CCNNNNNNNGG	1 cut(s)	112
AgsI	TTSAA	5 cut(s)	121, 128, 432, 488, 679
AjuI	GAANNNNNNNTTGG	2 cut(s)	192, 224
AluBI	AGCT	4 cut(s)	76, 631, 662, 712
AluI	AGCT	4 cut(s)	76, 631, 662, 712
Alw21I	GWGCWC	1 cut(s)	78
Alw26I	GTCTC	3 cut(s)	24, 184, 381
AlwI	GGATC	3 cut(s)	2, 15, 315
Ama87I	CYCGRG	2 cut(s)	234, 547
AoxI	GGCC	3 cut(s)	193, 401, 570
ApeKI	GCWGC	4 cut(s)	64, 83, 222, 276
ArsI	GACNNNNNNTTYG	6 cut(s)	320, 352, 407, 439, 439, 471
AspLEI	GCGC	1 cut(s)	69
AspS9I	GGNCC	2 cut(s)	212, 265
AsuHPI	GGTGA	3 cut(s)	136, 301, 679
AvaI	CYCGRG	2 cut(s)	234, 547
AvaII	GGWCC	2 cut(s)	212, 265
AxyI	CCTNAGG	1 cut(s)	252
BamHI	GGATCC	1 cut(s)	7
BanII	GRGCYC	1 cut(s)	78
BbsI	GAAGAC	3 cut(s)	45, 308, 420
Bbv12I	GWGCWC	1 cut(s)	78
BbvI	GCAGC	4 cut(s)	76, 95, 234, 288
BccI	CCATC	2 cut(s)	431, 593
BceAI	ACGGC	2 cut(s)	170, 388
BclI	TGATCA	1 cut(s)	22
BcoDI	GTCTC	3 cut(s)	24, 184, 381
BfaI	CTAG	3 cut(s)	95, 584, 765
BglI	GCCNNNNNGGC	1 cut(s)	56
BisI	GCNGC	5 cut(s)	65, 84, 220, 223, 277
BlsI	GCNGC	5 cut(s)	66, 85, 221, 224, 278
BmcAI	AGTACT	1 cut(s)	170
Bme18I	GGWCC	2 cut(s)	212, 265
BmeT110I	CYCGRG	2 cut(s)	234, 547
BmgT120I	GGNCC	2 cut(s)	212, 265
BmiI	GGNNCC	1 cut(s)	9
BpiI	GAAGAC	3 cut(s)	45, 308, 420
BplI	GAGNNNNNCTC	2 cut(s)	235, 267
BpmI	CTGGAG	2 cut(s)	149, 394
BpuEI	CTTGAG	1 cut(s)	653
BsaXI	ACNNNNNCTCC	2 cut(s)	136, 166
Bsc4I	CCNNNNNNNGG	1 cut(s)	112
Bse1I	ACTGG	2 cut(s)	166, 675
Bse21I	CCTNAGG	1 cut(s)	252
Bse3DI	GCAATG	1 cut(s)	622
BseGI	GGATG	1 cut(s)	25
BseLI	CCNNNNNNNGG	1 cut(s)	112
BseMI	GCAATG	1 cut(s)	622
BseMII	CTCAG	2 cut(s)	186, 266
BseNI	ACTGG	2 cut(s)	166, 675
BseRI	GAGGAG	1 cut(s)	152
BseXI	GCAGC	4 cut(s)	76, 95, 234, 288
Bsh1236I	CGCG	1 cut(s)	341
BshFI	GGCC	3 cut(s)	195, 403, 572
BsiHKAI	GWGCWC	1 cut(s)	78
BsiHKCI	CYCGRG	2 cut(s)	234, 547
BsiSI	CCGG	1 cut(s)	362
BsiWI	CGTACG	1 cut(s)	187
BslI	CCNNNNNNNGG	1 cut(s)	112
BsmAI	GTCTC	3 cut(s)	24, 184, 381
BsmBI	CGTCTC	2 cut(s)	24, 381
BsmI	GAATGC	1 cut(s)	116
BsnI	GGCC	3 cut(s)	195, 403, 572
BsoBI	CYCGRG	2 cut(s)	234, 547
Bsp1286I	GDGCHC	1 cut(s)	78
Bsp143I	GATC	4 cut(s)	7, 22, 307, 342
Bsp68I	TCGCGA	1 cut(s)	341
BspACI	CCGC	5 cut(s)	59, 147, 183, 220, 515
BspANI	GGCC	3 cut(s)	195, 403, 572
BspCNI	CTCAG	2 cut(s)	185, 265
BspFNI	CGCG	1 cut(s)	341
BspLI	GGNNCC	1 cut(s)	9
BspPI	GGATC	3 cut(s)	2, 15, 315
BsrDI	GCAATG	1 cut(s)	622
BsrI	ACTGG	2 cut(s)	166, 675
BssMI	GATC	4 cut(s)	7, 22, 307, 342
Bst4CI	ACNGT	2 cut(s)	317, 410
BstDEI	CTNAG	2 cut(s)	172, 252
BstF5I	GGATG	1 cut(s)	25
BstFNI	CGCG	1 cut(s)	341
BstHHI	GCGC	1 cut(s)	69
BstKTI	GATC	4 cut(s)	10, 25, 310, 345
BstMAI	GTCTC	3 cut(s)	24, 184, 381
BstMBI	GATC	4 cut(s)	7, 22, 307, 342
BstMWI	GCNNNNNNNGC	4 cut(s)	56, 73, 146, 182
BstUI	CGCG	1 cut(s)	341
BstV1I	GCAGC	4 cut(s)	76, 95, 234, 288
BstV2I	GAAGAC	3 cut(s)	45, 308, 420
BstX2I	RGATCY	2 cut(s)	7, 307
BstYI	RGATCY	2 cut(s)	7, 307
Bsu36I	CCTNAGG	1 cut(s)	252
BsuRI	GGCC	3 cut(s)	195, 403, 572
BtsCI	GGATG	1 cut(s)	25
BtsIMutI	CAGTG	1 cut(s)	668
BtuMI	TCGCGA	1 cut(s)	341
CfoI	GCGC	1 cut(s)	69
Cfr13I	GGNCC	2 cut(s)	212, 265
CseI	GACGC	1 cut(s)	41
Csp6I	GTAC	6 cut(s)	169, 188, 259, 382, 406, 411
CviAII	CATG	3 cut(s)	16, 112, 230
CviQI	GTAC	6 cut(s)	169, 188, 259, 382, 406, 411
DdeI	CTNAG	2 cut(s)	172, 252
DpnI	GATC	4 cut(s)	9, 24, 309, 344
DpnII	GATC	4 cut(s)	7, 22, 307, 342
EciI	GGCGGA	2 cut(s)	74, 172
Ecl136II	GAGCTC	1 cut(s)	76
Eco24I	GRGCYC	1 cut(s)	78
Eco47I	GGWCC	2 cut(s)	212, 265
Eco53kI	GAGCTC	1 cut(s)	76
Eco57I	CTGAAG	1 cut(s)	320
Eco81I	CCTNAGG	1 cut(s)	252
Eco88I	CYCGRG	2 cut(s)	234, 547
EcoICRI	GAGCTC	1 cut(s)	76
EcoT38I	GRGCYC	1 cut(s)	78
Esp3I	CGTCTC	2 cut(s)	24, 381
FaeI	CATG	3 cut(s)	19, 115, 233
FaiI	YATR	7 cut(s)	17, 27, 113, 231, 396, 611, 723
FatI	CATG	3 cut(s)	15, 111, 229
FbaI	TGATCA	1 cut(s)	22
Fnu4HI	GCNGC	5 cut(s)	65, 84, 220, 223, 277
FokI	GGATG	1 cut(s)	32
FriOI	GRGCYC	1 cut(s)	78
Fsp4HI	GCNGC	5 cut(s)	65, 84, 220, 223, 277
FspBI	CTAG	3 cut(s)	95, 584, 765
GlaI	GCGC	1 cut(s)	68
GluI	GCNGC	5 cut(s)	65, 84, 220, 223, 277
GsuI	CTGGAG	2 cut(s)	149, 394
HaeIII	GGCC	3 cut(s)	195, 403, 572
HapII	CCGG	1 cut(s)	362
HgaI	GACGC	1 cut(s)	41
HhaI	GCGC	1 cut(s)	69
Hin1II	CATG	3 cut(s)	19, 115, 233
Hin6I	GCGC	1 cut(s)	67
HinP1I	GCGC	1 cut(s)	67
HindIII	AAGCTT	1 cut(s)	710
HinfI	GANTC	4 cut(s)	98, 322, 580, 727
HpaII	CCGG	1 cut(s)	362
HphI	GGTGA	3 cut(s)	136, 301, 679
Hpy188I	TCNGA	3 cut(s)	103, 321, 561
Hpy188III	TCNNGA	6 cut(s)	254, 311, 326, 340, 499, 584
Hpy99I	CGWCG	1 cut(s)	427
HpyAV	CCTTC	3 cut(s)	127, 502, 641
HpyCH4III	ACNGT	2 cut(s)	317, 410
HpyCH4IV	ACGT	1 cut(s)	348
HpyCH4V	TGCA	2 cut(s)	445, 471
HpyF10VI	GCNNNNNNNGC	4 cut(s)	56, 73, 146, 182
HpyF3I	CTNAG	2 cut(s)	172, 252
HpySE526I	ACGT	1 cut(s)	348
Hsp92II	CATG	3 cut(s)	19, 115, 233
HspAI	GCGC	1 cut(s)	67
Ksp22I	TGATCA	1 cut(s)	22
Kzo9I	GATC	4 cut(s)	7, 22, 307, 342
LmnI	GCTCC	2 cut(s)	61, 628
LpnPI	CCDG	7 cut(s)	41, 179, 239, 344, 358, 375, 656
Lsp1109I	GCAGC	4 cut(s)	76, 95, 234, 288
MaeI	CTAG	3 cut(s)	95, 584, 765
MaeII	ACGT	1 cut(s)	348
MaeIII	GTNAC	2 cut(s)	353, 542
MalI	GATC	4 cut(s)	9, 24, 309, 344
MboI	GATC	4 cut(s)	7, 22, 307, 342
MboII	GAAGA	7 cut(s)	50, 116, 304, 313, 420, 500, 589
MflI	RGATCY	2 cut(s)	7, 307
MhlI	GDGCHC	1 cut(s)	78
MlyI	GAGTC	1 cut(s)	736
MmeI	TCCRAC	3 cut(s)	126, 179, 299
MseI	TTAA	3 cut(s)	654, 732, 769
MspI	CCGG	1 cut(s)	362
Mva1269I	GAATGC	1 cut(s)	116
MvnI	CGCG	1 cut(s)	341
MwoI	GCNNNNNNNGC	4 cut(s)	56, 73, 146, 182
NdeII	GATC	4 cut(s)	7, 22, 307, 342
NlaIII	CATG	3 cut(s)	19, 115, 233
NlaIV	GGNNCC	1 cut(s)	9
NmuCI	GTSAC	2 cut(s)	353, 542
NruI	TCGCGA	1 cut(s)	341
PaeR7I	CTCGAG	1 cut(s)	234
PcsI	WCGNNNNNNNCGW	4 cut(s)	267, 276, 345, 419
PctI	GAATGC	1 cut(s)	116
PfeI	GAWTC	3 cut(s)	98, 322, 580
Pfl23II	CGTACG	1 cut(s)	187
PkrI	GCNGC	5 cut(s)	66, 85, 221, 224, 278
PleI	GAGTC	1 cut(s)	735
PpsI	GAGTC	1 cut(s)	735
Psp124BI	GAGCTC	1 cut(s)	78
Psp1406I	AACGTT	1 cut(s)	348
PspLI	CGTACG	1 cut(s)	187
PspN4I	GGNNCC	1 cut(s)	9
PspPI	GGNCC	2 cut(s)	212, 265
PspXI	VCTCGAGB	1 cut(s)	234
PsuI	RGATCY	2 cut(s)	7, 307
RruI	TCGCGA	1 cut(s)	341
RsaI	GTAC	6 cut(s)	170, 189, 260, 383, 407, 412
RsaNI	GTAC	6 cut(s)	169, 188, 259, 382, 406, 411
SacI	GAGCTC	1 cut(s)	78
SaqAI	TTAA	3 cut(s)	654, 732, 769
SatI	GCNGC	5 cut(s)	65, 84, 220, 223, 277
Sau3AI	GATC	4 cut(s)	7, 22, 307, 342
Sau96I	GGNCC	2 cut(s)	212, 265
ScaI	AGTACT	1 cut(s)	170
SchI	GAGTC	1 cut(s)	736
SduI	GDGCHC	1 cut(s)	78
Sfr274I	CTCGAG	1 cut(s)	234
SinI	GGWCC	2 cut(s)	212, 265
SlaI	CTCGAG	1 cut(s)	234
SmlI	CTYRAG	2 cut(s)	234, 632
SmoI	CTYRAG	2 cut(s)	234, 632
SsiI	CCGC	5 cut(s)	59, 147, 183, 220, 515
SspMI	CTAG	3 cut(s)	95, 584, 765
SstI	GAGCTC	1 cut(s)	78
TaaI	ACNGT	2 cut(s)	317, 410
TaiI	ACGT	1 cut(s)	351
TaqI	TCGA	4 cut(s)	108, 235, 312, 567
TaqII	GACCGA	1 cut(s)	464
TatI	WGTACW	1 cut(s)	168
TauI	GCSGC	1 cut(s)	222
TfiI	GAWTC	3 cut(s)	98, 322, 580
Tru1I	TTAA	3 cut(s)	654, 732, 769
Tru9I	TTAA	3 cut(s)	654, 732, 769
TscAI	CASTG	1 cut(s)	675
TseFI	GTSAC	2 cut(s)	353, 542
TseI	GCWGC	4 cut(s)	64, 83, 222, 276
Tsp45I	GTSAC	2 cut(s)	353, 542
TspDTI	ATGAA	4 cut(s)	146, 218, 411, 685
TspGWI	ACGGA	2 cut(s)	320, 399
TspRI	CASTG	1 cut(s)	675
VpaK11BI	GGWCC	2 cut(s)	212, 265
XbaI	TCTAGA	1 cut(s)	583
XhoI	CTCGAG	1 cut(s)	234
XspI	CTAG	3 cut(s)	95, 584, 765
ZrmI	AGTACT	1 cut(s)	170

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