Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0000411

Physical Location & Seq

Genomic Coordinates Reverse (-)

67687858 .. 67688211

Gene Structure 354 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG424400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 354 bp

ATGAATGACGCATCGTCGTCCTTGTCGAAGGCGGCGGAGGAGGAGAGTGAGTGTTTGAGACTGTATTTCAAGGGGCTTGTGAGCGAGGAGAGGGTCAAGGACATGGATGTCATTGTGGCCGGGGTTGGGGTTGCCATTTGTGACGCTAGAGATAATCTGATTTTGGATGCCAAGAAGAATCTGGAGGCGTTTGGTGGTGGTGAGGTACTGAGCAATGAGGCTGCTGAGCTTGAGGCTCTTATTGAAGGGCTCAGTACAACTCTCACTCTGGACTTGAGAAATGTCACATTTTTCTGTGATAACAACAAGCTTTACCAATATGTGAGTTTTACTATTTTGCCATTCAAGTATTGA

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

117

Amino Acids

12.88

Weight (kDa)

4.39

Isoelectric Point (pI)

47.34

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RVT_3	PF13456	40 - 108	1.3e-09	Reverse transcriptase-like

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)

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Publication-ready

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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)
AasI	GACNNNNNNGTC	1 cut(s)	107
AciI	CCGC	2 cut(s)	32, 35
AcoI	YGGCCR	1 cut(s)	117
AfaI	GTAC	2 cut(s)	207, 256
AfiI	CCNNNNNNNGG	1 cut(s)	126
AgsI	TTSAA	3 cut(s)	70, 245, 346
AhdI	GACNNNNNGTC	1 cut(s)	13
AluBI	AGCT	2 cut(s)	229, 310
AluI	AGCT	2 cut(s)	229, 310
Alw26I	GTCTC	1 cut(s)	52
AoxI	GGCC	1 cut(s)	117
ApeKI	GCWGC	1 cut(s)	221
AsuC2I	CCSGG	1 cut(s)	121
AsuHPI	GGTGA	1 cut(s)	212
BanII	GRGCYC	1 cut(s)	252
BbvI	GCAGC	1 cut(s)	208
BcnI	CCSGG	1 cut(s)	121
BcoDI	GTCTC	1 cut(s)	52
BfaI	CTAG	1 cut(s)	147
BisI	GCNGC	2 cut(s)	33, 222
BlpI	GCTNAGC	1 cut(s)	225
BlsI	GCNGC	2 cut(s)	34, 223
Bme1390I	CCNGG	1 cut(s)	121
BmeRI	GACNNNNNGTC	1 cut(s)	13
BmrFI	CCNGG	1 cut(s)	121
BmsI	GCATC	2 cut(s)	20, 157
BpmI	CTGGAG	1 cut(s)	203
Bpu1102I	GCTNAGC	1 cut(s)	225
BpuEI	CTTGAG	2 cut(s)	251, 295
BpuMI	CCSGG	1 cut(s)	121
BsaJI	CCNNGG	1 cut(s)	120
BsaXI	ACNNNNNCTCC	2 cut(s)	35, 65
Bsc4I	CCNNNNNNNGG	1 cut(s)	126
Bse3DI	GCAATG	1 cut(s)	220
BseDI	CCNNGG	1 cut(s)	120
BseGI	GGATG	2 cut(s)	112, 172
BseLI	CCNNNNNNNGG	1 cut(s)	126
BseMI	GCAATG	1 cut(s)	220
BseMII	CTCAG	3 cut(s)	200, 216, 265
BseRI	GAGGAG	3 cut(s)	53, 56, 101
BseXI	GCAGC	1 cut(s)	208
BshFI	GGCC	1 cut(s)	119
BsiSI	CCGG	1 cut(s)	120
BslI	CCNNNNNNNGG	1 cut(s)	126
BsmAI	GTCTC	1 cut(s)	52
BsnI	GGCC	1 cut(s)	119
Bsp1286I	GDGCHC	1 cut(s)	252
Bsp1720I	GCTNAGC	1 cut(s)	225
BspACI	CCGC	2 cut(s)	32, 35
BspANI	GGCC	1 cut(s)	119
BspCNI	CTCAG	3 cut(s)	201, 217, 264
BsrDI	GCAATG	1 cut(s)	220
BssECI	CCNNGG	1 cut(s)	120
Bst4CI	ACNGT	1 cut(s)	63
BstDEI	CTNAG	3 cut(s)	209, 225, 251
BstF5I	GGATG	2 cut(s)	112, 172
BstMAI	GTCTC	1 cut(s)	52
BstSCI	CCNGG	1 cut(s)	119
BstV1I	GCAGC	1 cut(s)	208
BsuRI	GGCC	1 cut(s)	119
BtsCI	GGATG	2 cut(s)	112, 172
CseI	GACGC	2 cut(s)	17, 152
Csp6I	GTAC	2 cut(s)	206, 255
CviAII	CATG	1 cut(s)	103
CviJI	RGCY	7 cut(s)	76, 119, 221, 229, 236, 250, 310
CviKI_1	RGCY	7 cut(s)	76, 119, 221, 229, 236, 250, 310
CviQI	GTAC	2 cut(s)	206, 255
DdeI	CTNAG	3 cut(s)	209, 225, 251
DrdI	GACNNNNNNGTC	1 cut(s)	107
DriI	GACNNNNNGTC	1 cut(s)	13
DseDI	GACNNNNNNGTC	1 cut(s)	107
EaeI	YGGCCR	1 cut(s)	117
Eam1105I	GACNNNNNGTC	1 cut(s)	13
EciI	GGCGGA	1 cut(s)	50
Eco24I	GRGCYC	1 cut(s)	252
EcoT38I	GRGCYC	1 cut(s)	252
FaeI	CATG	1 cut(s)	106
FaiI	YATR	2 cut(s)	104, 321
FatI	CATG	1 cut(s)	102
Fnu4HI	GCNGC	2 cut(s)	33, 222
FokI	GGATG	2 cut(s)	119, 179
FriOI	GRGCYC	1 cut(s)	252
Fsp4HI	GCNGC	2 cut(s)	33, 222
FspBI	CTAG	1 cut(s)	147
GluI	GCNGC	2 cut(s)	33, 222
GsuI	CTGGAG	1 cut(s)	203
HaeIII	GGCC	1 cut(s)	119
HapII	CCGG	1 cut(s)	120
HgaI	GACGC	2 cut(s)	17, 152
Hin1II	CATG	1 cut(s)	106
HindIII	AAGCTT	1 cut(s)	308
HinfI	GANTC	1 cut(s)	178
HpaII	CCGG	1 cut(s)	120
HphI	GGTGA	1 cut(s)	212
Hpy188I	TCNGA	1 cut(s)	159
Hpy188III	TCNNGA	2 cut(s)	182, 269
Hpy99I	CGWCG	1 cut(s)	19
HpyAV	CCTTC	2 cut(s)	22, 239
HpyCH4III	ACNGT	1 cut(s)	63
HpyF3I	CTNAG	3 cut(s)	209, 225, 251
Hsp92II	CATG	1 cut(s)	106
LpnPI	CCDG	3 cut(s)	133, 167, 254
Lsp1109I	GCAGC	1 cut(s)	208
LweI	GCATC	2 cut(s)	20, 157
MaeI	CTAG	1 cut(s)	147
MaeIII	GTNAC	2 cut(s)	140, 283
MboII	GAAGA	1 cut(s)	187
MhlI	GDGCHC	1 cut(s)	252
MnlI	CCTC	8 cut(s)	31, 34, 79, 84, 178, 196, 211, 226
MspI	CCGG	1 cut(s)	120
MspR9I	CCNGG	1 cut(s)	121
NciI	CCSGG	1 cut(s)	121
NlaIII	CATG	1 cut(s)	106
NmuCI	GTSAC	2 cut(s)	140, 283
PcsI	WCGNNNNNNNCGW	1 cut(s)	23
PfeI	GAWTC	1 cut(s)	178
PkrI	GCNGC	2 cut(s)	34, 223
RsaI	GTAC	2 cut(s)	207, 256
RsaNI	GTAC	2 cut(s)	206, 255
SatI	GCNGC	2 cut(s)	33, 222
ScrFI	CCNGG	1 cut(s)	121
SduI	GDGCHC	1 cut(s)	252
SetI	ASST	3 cut(s)	207, 231, 312
SfaNI	GCATC	2 cut(s)	20, 157
SmlI	CTYRAG	2 cut(s)	230, 274
SmoI	CTYRAG	2 cut(s)	230, 274
SsiI	CCGC	2 cut(s)	32, 35
SspMI	CTAG	1 cut(s)	147
StyD4I	CCNGG	1 cut(s)	119
TaaI	ACNGT	1 cut(s)	63
TaqI	TCGA	1 cut(s)	26
TatI	WGTACW	1 cut(s)	254
TauI	GCSGC	1 cut(s)	35
TfiI	GAWTC	1 cut(s)	178
TseFI	GTSAC	2 cut(s)	140, 283
TseI	GCWGC	1 cut(s)	221
Tsp45I	GTSAC	2 cut(s)	140, 283
TspDTI	ATGAA	1 cut(s)	17
XcmI	CCANNNNNNNNNTGG	1 cut(s)	178
XspI	CTAG	1 cut(s)	147

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