Rw5G032360

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr5
OG0000258
Physical Location & Seq
Reverse (-)
54663392 .. 54664222
831 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw5G032360.1

Sequence Viewer

Length: 831 bp
ATGGATCAATCTGTATCTACCATGAAGAATCATGTGGAGAAACCTGAGAAATTCAAGGGCTCTGACTTCAAATGCTGGCAACAGAAGATGTTGTTTTACTTGACAACTCTTCATGTGGCAAATGTTCTCACAACCGAGGCTCCCAAGGCTTTACCGGAAGGAGAAGGAGAAGGAGATGATGTTCCAACTGATGCTCAAAAGGCCGATATAGAGTCCTGGGCAAATAATGAGTTTCTGTGCAGGAATTACATCCTCAATGCCTTAGACAATTCCTTGTATGATATTTATTCGTCATTCAAAACAGCAAAGGAATTATGGGAGTCATTGGACAATAAGTATAAGACTGAAGTTGCTTGTTCAAAGAAGTTTGTCATTGGCAAGTTTCTGAATTACAAGATAGTTGATGCCAAATCTATTGTCAAGCAAGTGGAGGAACTCCAAGTCATTGTTCATGAGTTTGATGAAGAAGGTATGGGACTGAACTCGAATTTTCTTGTTGGTTCTGTTATTGAAAAATTACCTCCTTCATGGAAAGATTTCAAGGTTTATCTGAAACATCTAACTGAGGACATGAATTTTGAGCAATTGGTTCTGAAACTTCGTGTTGAAGAGGATCACCGGAAGAATGAAAGGGCTGATGCTATGGAGCCAAATGTAAACATGATTGGAGGAAGTCCATCAAAGGCCAAGTTTCAGAAAAAAAAAAGGCAAGAATGCTGCTACCAAACCAACTCTTGCTGCTGCAAAGAAGCCACTCGCCCCACAAAAGACCAAAGCCTTCAAAAAGCCACAAACTGGTGGATGTTGGGTGTGTGGCAAACCAGGGCATAG
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

276

Amino Acids

31.86

Weight (kDa)

6.27

Isoelectric Point (pI)

43.12

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 53 - 211 1.6e-24 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)
AccB7I CCANNNNNTGG 1 cut(s) 795
AclWI GGATC 2 cut(s) 12, 621
AcsI RAATTY 3 cut(s) 50, 487, 574
AcuI CTGAAG 1 cut(s) 366
AfiI CCNNNNNNNGG 1 cut(s) 795
AgsI TTSAA 8 cut(s) 55, 70, 298, 360, 512, 541, 608, 782
AjnI CCWGG 2 cut(s) 215, 821
AjuI GAANNNNNNNTTGG 2 cut(s) 432, 464
AloI GAACNNNNNNTCC 2 cut(s) 165, 197
AlwI GGATC 2 cut(s) 12, 621
AoxI GGCC 2 cut(s) 201, 684
ApeKI GCWGC 3 cut(s) 717, 738, 741
ApoI RAATTY 3 cut(s) 50, 487, 574
ArsI GACNNNNNNTTYG 4 cut(s) 402, 434, 560, 592
Asp700I GAANNNNTTC 1 cut(s) 536
AsuHPI GGTGA 1 cut(s) 608
BanII GRGCYC 1 cut(s) 62
BbvI GCAGC 3 cut(s) 704, 725, 728
BccI CCATC 1 cut(s) 685
BciT130I CCWGG 2 cut(s) 217, 823
BisI GCNGC 3 cut(s) 718, 739, 742
BlsI GCNGC 3 cut(s) 719, 740, 743
Bme1390I CCNGG 2 cut(s) 217, 823
BmiI GGNNCC 2 cut(s) 141, 648
BmrFI CCNGG 2 cut(s) 217, 823
BmsI GCATC 3 cut(s) 181, 394, 628
BsaJI CCNNGG 4 cut(s) 135, 144, 216, 822
BsaWI WCCGGW 2 cut(s) 154, 618
BsaXI ACNNNNNCTCC 4 cut(s) 124, 154, 165, 195
Bsc4I CCNNNNNNNGG 1 cut(s) 795
Bse1I ACTGG 1 cut(s) 800
BseBI CCWGG 2 cut(s) 217, 823
BseDI CCNNGG 4 cut(s) 135, 144, 216, 822
BseGI GGATG 2 cut(s) 249, 807
BseLI CCNNNNNNNGG 1 cut(s) 795
BseMII CTCAG 2 cut(s) 36, 555
BseNI ACTGG 1 cut(s) 800
BseXI GCAGC 3 cut(s) 704, 725, 728
BsgI GTGCAG 1 cut(s) 259
BshFI GGCC 2 cut(s) 203, 686
BsiSI CCGG 2 cut(s) 155, 619
BslFI GGGAC 1 cut(s) 489
BslI CCNNNNNNNGG 1 cut(s) 795
BsmFI GGGAC 1 cut(s) 489
BsmI GAATGC 1 cut(s) 719
BsnI GGCC 2 cut(s) 203, 686
Bsp1286I GDGCHC 1 cut(s) 62
Bsp143I GATC 2 cut(s) 4, 613
BspANI GGCC 2 cut(s) 203, 686
BspCNI CTCAG 2 cut(s) 37, 556
BspHI TCATGA 1 cut(s) 451
BspLI GGNNCC 2 cut(s) 141, 648
BspPI GGATC 2 cut(s) 12, 621
BsrI ACTGG 1 cut(s) 800
BssECI CCNNGG 4 cut(s) 135, 144, 216, 822
BssMI GATC 2 cut(s) 4, 613
BssT1I CCWWGG 1 cut(s) 144
Bst2UI CCWGG 2 cut(s) 217, 823
Bst6I CTCTTC 2 cut(s) 114, 603
BstC8I GCNNGC 1 cut(s) 77
BstDEI CTNAG 3 cut(s) 45, 262, 564
BstF5I GGATG 2 cut(s) 249, 807
BstKTI GATC 2 cut(s) 7, 616
BstMBI GATC 2 cut(s) 4, 613
BstMWI GCNNNNNNNGC 2 cut(s) 146, 200
BstNI CCWGG 2 cut(s) 217, 823
BstSCI CCNGG 2 cut(s) 215, 821
BstV1I GCAGC 3 cut(s) 704, 725, 728
BsuRI GGCC 2 cut(s) 203, 686
BtsCI GGATG 2 cut(s) 249, 807
Cac8I GCNNGC 1 cut(s) 77
CciI TCATGA 1 cut(s) 451
CviAII CATG 7 cut(s) 22, 32, 113, 452, 528, 571, 661
DdeI CTNAG 3 cut(s) 45, 262, 564
DpnI GATC 2 cut(s) 6, 615
DpnII GATC 2 cut(s) 4, 613
Eam1104I CTCTTC 2 cut(s) 114, 603
EarI CTCTTC 2 cut(s) 114, 603
Eco130I CCWWGG 1 cut(s) 144
Eco24I GRGCYC 1 cut(s) 62
Eco57I CTGAAG 1 cut(s) 366
EcoRII CCWGG 2 cut(s) 215, 821
EcoT14I CCWWGG 1 cut(s) 144
EcoT38I GRGCYC 1 cut(s) 62
ErhI CCWWGG 1 cut(s) 144
FaeI CATG 7 cut(s) 25, 35, 116, 455, 531, 574, 664
FaqI GGGAC 1 cut(s) 489
FatI CATG 7 cut(s) 21, 31, 112, 451, 527, 570, 660
Fnu4HI GCNGC 3 cut(s) 718, 739, 742
FokI GGATG 2 cut(s) 236, 814
FriOI GRGCYC 1 cut(s) 62
Fsp4HI GCNGC 3 cut(s) 718, 739, 742
GluI GCNGC 3 cut(s) 718, 739, 742
HaeIII GGCC 2 cut(s) 203, 686
HapII CCGG 2 cut(s) 155, 619
Hin1II CATG 7 cut(s) 25, 35, 116, 455, 531, 574, 664
HinfI GANTC 3 cut(s) 28, 212, 320
HpaII CCGG 2 cut(s) 155, 619
HphI GGTGA 1 cut(s) 608
Hpy166II GTNNAC 1 cut(s) 658
Hpy188I TCNGA 5 cut(s) 64, 387, 552, 594, 696
Hpy188III TCNNGA 1 cut(s) 452
Hpy8I GTNNAC 1 cut(s) 658
HpyAV CCTTC 6 cut(s) 152, 158, 164, 461, 534, 788
HpyCH4V TGCA 2 cut(s) 240, 744
HpyF10VI GCNNNNNNNGC 2 cut(s) 146, 200
HpyF3I CTNAG 3 cut(s) 45, 262, 564
Hsp92II CATG 7 cut(s) 25, 35, 116, 455, 531, 574, 664
Kzo9I GATC 2 cut(s) 4, 613
LmnI GCTCC 2 cut(s) 145, 646
LpnPI CCDG 9 cut(s) 57, 61, 168, 202, 226, 229, 632, 781, 808
Lsp1109I GCAGC 3 cut(s) 704, 725, 728
LweI GCATC 3 cut(s) 181, 394, 628
MalI GATC 2 cut(s) 6, 615
MboI GATC 2 cut(s) 4, 613
MboII GAAGA 6 cut(s) 37, 97, 101, 476, 620, 634
MfeI CAATTG 1 cut(s) 584
MhlI GDGCHC 1 cut(s) 62
MluCI AATT 9 cut(s) 50, 244, 268, 311, 388, 487, 515, 574, 584
MlyI GAGTC 2 cut(s) 221, 329
MmeI TCCRAC 1 cut(s) 209
MnlI CCTC 7 cut(s) 130, 263, 424, 531, 559, 604, 662
MroXI GAANNNNTTC 1 cut(s) 536
MspI CCGG 2 cut(s) 155, 619
MspR9I CCNGG 2 cut(s) 217, 823
MunI CAATTG 1 cut(s) 584
Mva1269I GAATGC 1 cut(s) 719
MvaI CCWGG 2 cut(s) 217, 823
MwoI GCNNNNNNNGC 2 cut(s) 146, 200
NdeII GATC 2 cut(s) 4, 613
NlaIII CATG 7 cut(s) 25, 35, 116, 455, 531, 574, 664
NlaIV GGNNCC 2 cut(s) 141, 648
PagI TCATGA 1 cut(s) 451
PctI GAATGC 1 cut(s) 719
PdmI GAANNNNTTC 1 cut(s) 536
PfeI GAWTC 1 cut(s) 28
PflMI CCANNNNNTGG 1 cut(s) 795
PkrI GCNGC 3 cut(s) 719, 740, 743
PleI GAGTC 2 cut(s) 220, 328
PpsI GAGTC 2 cut(s) 220, 328
Psp6I CCWGG 2 cut(s) 215, 821
PspGI CCWGG 2 cut(s) 215, 821
PspN4I GGNNCC 2 cut(s) 141, 648
SatI GCNGC 3 cut(s) 718, 739, 742
Sau3AI GATC 2 cut(s) 4, 613
SchI GAGTC 2 cut(s) 221, 329
ScrFI CCNGG 2 cut(s) 217, 823
SduI GDGCHC 1 cut(s) 62
SetI ASST 4 cut(s) 46, 472, 523, 546
SfaNI GCATC 3 cut(s) 181, 394, 628
Sse9I AATT 9 cut(s) 50, 244, 268, 311, 388, 487, 515, 574, 584
StyD4I CCNGG 2 cut(s) 215, 821
StyI CCWWGG 1 cut(s) 144
TaqI TCGA 1 cut(s) 485
TasI AATT 9 cut(s) 50, 244, 268, 311, 388, 487, 515, 574, 584
TfiI GAWTC 1 cut(s) 28
TseI GCWGC 3 cut(s) 717, 738, 741
TspDTI ATGAA 7 cut(s) 38, 101, 440, 477, 516, 587, 642
Van91I CCANNNNNTGG 1 cut(s) 795
XapI RAATTY 3 cut(s) 50, 487, 574
XmnI GAANNNNTTC 1 cut(s) 536
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.