Rh5DG194600

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5D
OG0000258
Physical Location & Seq
Reverse (-)
21592645 .. 21593194
550 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5DG194600.1

Sequence Viewer

Length: 369 bp
ATGGATGCTGCTATGACCAACACCAAGATCCCAGATGTTTCCAAGATCGATGTTTTCAATGGCTCGTTCTTCAAAAGATGGCAAGAAAGAGTCTTCTCTGCTCTTGATGTCATGAACCTGGCACATTATCTCACGAAGGCCAAGCCCAAGGAAGGTAGCGAGAATTATAACAAAGAGTTGGCTGAATGGGAGAAAGGTAACAAAATTTGTAGGCATACTATTCTGAGCACACTTTCAAATGAGCTTTTTGATATATATTGTGCCTACAAGACTACTGCTGAAATTTGGGAGATTCTCACAAAAAAGTACATGACTGAACATGCTGGGACCAAAAATATGCAATTGGGAATTTTCTTAAATTTCAAATGA
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

122

Amino Acids

14.2

Weight (kDa)

8.49

Isoelectric Point (pI)

24.56

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 37 - 121 7e-08 gag-polypeptide of LTR copia-type
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
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: OG0000258)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G00980
fragaria_vesca FvH4_1g25682 FvH4_2g13961 FvH4_2g20162 FvH4_2g24753 FvH4_3g12191 FvH4_3g12632 FvH4_3g16171 FvH4_4g05871 FvH4_4g05873 FvH4_4g10121 FvH4_4g15488 FvH4_4g23911 FvH4_4g27782 FvH4_5g08912 FvH4_5g23001 FvH4_5g24552 FvH4_5g32801 FvH4_5g32802 FvH4_6g05093 FvH4_6g19722 FvH4_6g20391 FvH4_6g33792 FvH4_7g01381 FvH4_7g16761 FvH4_7g16761 FvH4_7g16761
malus_domestica MD01G1082500.v1.1 MD15G1436400.v1.1
prunus_persica Prupe.2G021400_v2.0.a1 Prupe.2G052400_v2.0.a1 Prupe.2G065000_v2.0.a1 Prupe.2G187700_v2.0.a1 Prupe.2G187800_v2.0.a1 Prupe.2G189900_v2.0.a1 Prupe.2G191300_v2.0.a1 Prupe.2G191700_v2.0.a1 Prupe.4G265600_v2.0.a1 Prupe.7G014200_v2.0.a1 Prupe.7G039000_v2.0.a1
pyrus_communis pycom01g05590 pycom01g05910 pycom02g12230 pycom02g25840 pycom03g15580 pycom04g04480 pycom05g09230 pycom05g23350 pycom05g23360 pycom07g08380 pycom09g01980 pycom09g01990 pycom11g18190 pycom11g18200 pycom11g21580 pycom13g04160 pycom15g25800 pycom16g16210 pycom16g17230 pycom16g24560 pycom16g25700 pycom17g11020
rosa_chinensis RchiOBHm_Chr1g0359981 RchiOBHm_Chr2g0151961 RchiOBHm_Chr2g0171331 RchiOBHm_Chr5g0081471 RchiOBHm_Chr6g0283031 RchiOBHm_Chr7g0197111 RchiOBHm_Chr7g0222601
rosa_laevigata RLG00000027843 RLG00000027845 RLG00000030065
rosa_multiflora Rmu_sc0000381.1_g000031 Rmu_sc0001179.1_g000035 Rmu_sc0001616.1_g000046 Rmu_sc0001851.1_g000032 Rmu_sc0002152.1_g000013 Rmu_sc0004031.1_g000015 Rmu_sc0004645.1_g000003 Rmu_sc0007393.1_g000001 Rmu_sc0008949.1_g000003 Rmu_sc0009799.1_g000011 Rmu_sc0011614.1_g000001 Rmu_sc0011699.1_g000009 Rmu_sc0019280.1_g000001 Rmu_sc0023984.1_g000001 Rmu_ssc0000050.1_g000036
rosa_roxburghii Rroxscaffold_1G00022650 Rroxscaffold_1G00033480 Rroxscaffold_3G00270250 Rroxscaffold_4G00296600 Rroxscaffold_4G00296760 Rroxscaffold_6G00409840
rosa_rugosa Rorug01G0273800 Rorug01G0273900 Rorug01G0274000
rosa_samantha Rh1AG287300 Rh1AG288100 Rh1BG253000 Rh1BG253500 Rh1BG399800 Rh1CG270400 Rh1CG271000 Rh1DG282000 Rh1DG282500 Rh4DG126500 Rh5DG194600 Rh5DG461100
rosa_wichuraiana Rw0G009130 Rw1G002590 Rw1G008490 Rw1G012210 Rw1G014290 Rw1G014490 Rw1G025510 Rw2G025840 Rw2G026170 Rw2G036510 Rw3G003050 Rw4G009270 Rw5G002350 Rw5G013930 Rw5G019500 Rw5G025890 Rw5G029960 Rw5G032360 Rw6G009890 Rw6G015670 Rw6G015860 Rw7G010030 Rw7G032600 Rw7G032770

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 168
AclWI GGATC 1 cut(s) 22
AcsI RAATTY 4 cut(s) 204, 282, 348, 358
AfaI GTAC 1 cut(s) 308
AfiI CCNNNNNNNGG 1 cut(s) 152
AgsI TTSAA 4 cut(s) 58, 73, 237, 364
AjnI CCWGG 1 cut(s) 117
AluBI AGCT 1 cut(s) 244
AluI AGCT 1 cut(s) 244
Alw21I GWGCWC 1 cut(s) 230
AlwI GGATC 1 cut(s) 22
AoxI GGCC 1 cut(s) 138
ApeKI GCWGC 1 cut(s) 8
ApoI RAATTY 4 cut(s) 204, 282, 348, 358
AspS9I GGNCC 1 cut(s) 327
AvaII GGWCC 1 cut(s) 327
BbsI GAAGAC 1 cut(s) 85
Bbv12I GWGCWC 1 cut(s) 230
BccI CCATC 1 cut(s) 72
BciT130I CCWGG 1 cut(s) 119
BisI GCNGC 1 cut(s) 9
BlsI GCNGC 1 cut(s) 10
Bme1390I CCNGG 1 cut(s) 119
Bme18I GGWCC 1 cut(s) 327
BmgT120I GGNCC 1 cut(s) 327
BmiI GGNNCC 1 cut(s) 328
BmrFI CCNGG 1 cut(s) 119
BpiI GAAGAC 1 cut(s) 85
Bsa29I ATCGAT 1 cut(s) 48
BsaJI CCNNGG 1 cut(s) 147
Bsc4I CCNNNNNNNGG 1 cut(s) 152
BseBI CCWGG 1 cut(s) 119
BseCI ATCGAT 1 cut(s) 48
BseDI CCNNGG 1 cut(s) 147
BseGI GGATG 1 cut(s) 10
BseLI CCNNNNNNNGG 1 cut(s) 152
BseMII CTCAG 1 cut(s) 215
BseYI CCCAGC 1 cut(s) 323
BshFI GGCC 1 cut(s) 140
BshVI ATCGAT 1 cut(s) 48
BsiHKAI GWGCWC 1 cut(s) 230
BslFI GGGAC 1 cut(s) 340
BslI CCNNNNNNNGG 1 cut(s) 152
BsmFI GGGAC 1 cut(s) 340
BsnI GGCC 1 cut(s) 140
Bsp1286I GDGCHC 1 cut(s) 230
Bsp143I GATC 2 cut(s) 27, 45
BspANI GGCC 1 cut(s) 140
BspCNI CTCAG 1 cut(s) 216
BspDI ATCGAT 1 cut(s) 48
BspHI TCATGA 1 cut(s) 111
BspLI GGNNCC 1 cut(s) 328
BspPI GGATC 1 cut(s) 22
BssECI CCNNGG 1 cut(s) 147
BssMI GATC 2 cut(s) 27, 45
BssT1I CCWWGG 1 cut(s) 147
Bst2UI CCWGG 1 cut(s) 119
BstDEI CTNAG 1 cut(s) 224
BstF5I GGATG 1 cut(s) 10
BstKTI GATC 2 cut(s) 30, 48
BstMBI GATC 2 cut(s) 27, 45
BstNI CCWGG 1 cut(s) 119
BstNSI RCATGY 1 cut(s) 323
BstSCI CCNGG 1 cut(s) 117
BstV2I GAAGAC 1 cut(s) 85
BstX2I RGATCY 1 cut(s) 27
BstYI RGATCY 1 cut(s) 27
Bsu15I ATCGAT 1 cut(s) 48
BsuRI GGCC 1 cut(s) 140
BsuTUI ATCGAT 1 cut(s) 48
BtsCI GGATG 1 cut(s) 10
CciI TCATGA 1 cut(s) 111
Cfr13I GGNCC 1 cut(s) 327
ClaI ATCGAT 1 cut(s) 48
Csp6I GTAC 1 cut(s) 307
CviAII CATG 3 cut(s) 112, 310, 320
CviJI RGCY 5 cut(s) 63, 140, 145, 182, 244
CviKI_1 RGCY 5 cut(s) 63, 140, 145, 182, 244
CviQI GTAC 1 cut(s) 307
DdeI CTNAG 1 cut(s) 224
DpnI GATC 2 cut(s) 29, 47
DpnII GATC 2 cut(s) 27, 45
Eco130I CCWWGG 1 cut(s) 147
Eco47I GGWCC 1 cut(s) 327
EcoRII CCWGG 1 cut(s) 117
EcoT14I CCWWGG 1 cut(s) 147
ErhI CCWWGG 1 cut(s) 147
FaeI CATG 3 cut(s) 115, 313, 323
FaiI YATR 9 cut(s) 14, 113, 168, 216, 254, 256, 311, 321, 338
FaqI GGGAC 1 cut(s) 340
FatI CATG 3 cut(s) 111, 309, 319
Fnu4HI GCNGC 1 cut(s) 9
FokI GGATG 1 cut(s) 17
Fsp4HI GCNGC 1 cut(s) 9
GluI GCNGC 1 cut(s) 9
GsaI CCCAGC 1 cut(s) 327
HaeIII GGCC 1 cut(s) 140
Hin1II CATG 3 cut(s) 115, 313, 323
HinfI GANTC 2 cut(s) 90, 292
Hpy188I TCNGA 1 cut(s) 225
Hpy188III TCNNGA 3 cut(s) 104, 112, 133
HpyAV CCTTC 2 cut(s) 130, 146
HpyCH4V TGCA 1 cut(s) 340
HpyF3I CTNAG 1 cut(s) 224
Hsp92II CATG 3 cut(s) 115, 313, 323
Kzo9I GATC 2 cut(s) 27, 45
LpnPI CCDG 4 cut(s) 45, 104, 131, 309
MaeIII GTNAC 1 cut(s) 197
MalI GATC 2 cut(s) 29, 47
MboI GATC 2 cut(s) 27, 45
MboII GAAGA 2 cut(s) 61, 85
MfeI CAATTG 1 cut(s) 341
MflI RGATCY 1 cut(s) 27
MhlI GDGCHC 1 cut(s) 230
MluCI AATT 6 cut(s) 163, 204, 282, 341, 348, 358
MlyI GAGTC 1 cut(s) 99
MseI TTAA 1 cut(s) 356
MspR9I CCNGG 1 cut(s) 119
MunI CAATTG 1 cut(s) 341
MvaI CCWGG 1 cut(s) 119
NdeII GATC 2 cut(s) 27, 45
NlaIII CATG 3 cut(s) 115, 313, 323
NlaIV GGNNCC 1 cut(s) 328
NspI RCATGY 1 cut(s) 323
PagI TCATGA 1 cut(s) 111
PfeI GAWTC 1 cut(s) 292
PkrI GCNGC 1 cut(s) 10
PleI GAGTC 1 cut(s) 98
PpsI GAGTC 1 cut(s) 98
PsiI TTATAA 1 cut(s) 168
Psp6I CCWGG 1 cut(s) 117
PspFI CCCAGC 1 cut(s) 323
PspGI CCWGG 1 cut(s) 117
PspN4I GGNNCC 1 cut(s) 328
PspPI GGNCC 1 cut(s) 327
PsuI RGATCY 1 cut(s) 27
RsaI GTAC 1 cut(s) 308
RsaNI GTAC 1 cut(s) 307
SaqAI TTAA 1 cut(s) 356
SatI GCNGC 1 cut(s) 9
Sau3AI GATC 2 cut(s) 27, 45
Sau96I GGNCC 1 cut(s) 327
SchI GAGTC 1 cut(s) 99
ScrFI CCNGG 1 cut(s) 119
SduI GDGCHC 1 cut(s) 230
SetI ASST 4 cut(s) 120, 157, 199, 246
SinI GGWCC 1 cut(s) 327
Sse9I AATT 6 cut(s) 163, 204, 282, 341, 348, 358
StyD4I CCNGG 1 cut(s) 117
StyI CCWWGG 1 cut(s) 147
TaqI TCGA 1 cut(s) 48
TasI AATT 6 cut(s) 163, 204, 282, 341, 348, 358
TatI WGTACW 1 cut(s) 306
TfiI GAWTC 1 cut(s) 292
Tru1I TTAA 1 cut(s) 356
Tru9I TTAA 1 cut(s) 356
TseI GCWGC 1 cut(s) 8
TspDTI ATGAA 1 cut(s) 128
VpaK11BI GGWCC 1 cut(s) 327
XapI RAATTY 4 cut(s) 204, 282, 348, 358
XceI RCATGY 1 cut(s) 323
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.