Rw3G003050

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr3
OG0000258
Physical Location & Seq
Forward (+)
2709187 .. 2711326
2140 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw3G003050.1

Sequence Viewer

Length: 843 bp
ATGGATCAATCTGTATCTACCATGAAGAATCATGTGGAGAAACCTGAGAAATTCAAGGGCTCTGACTTCAAACGCTGGCAACAGAAAATGTTGTTTTACTTGACAACTCTTCATGTGGCAAATGTTCTCACAACCGAGGCTCCCAAGGCTTTACCGGAAGGAGAAGGAGATGATGTTCCAACTGATGCTCAAAAGGCCGAAAATCAAAGGGCTATAGAGTCCTGGGCAAGTAATGAGTTTCTGTGCAGGAATTACATCCTCAATGCCTTAGACGATTCCTTGTATGATATTTATTCGTCATTCAAAACAGCAAAGGAATTATGGGAGTCATTGGACAATAAGTATAAAACTGAAGTTGCTTGTTCAAAGAAGTTTGTCATTGGCAAGTTTCTGAATTACAAGATGGTTGATGCCAAATCTGTTGTCAAGCAAGTGGAGGAACTCCAAGTCATTGTTCATGAGTTAGATGAAGAAGGTATGGGACTGAACTCGAATTTTCTTGTTGGTTCTGTTATTGAAAAATTACCTCCTTCATGGAAAGATTTCAAGGTTTATCTGAAACATCTAACTGAGGACATGACTTTTGAGCAATTGGTTCTGAAACTTCGTGTTGAAGAGGATCACCGGAAGAATGAAAGGGCTGATGCTATGGAGCCAAACGCAAACATGATTGGAGGAAGCCCATCAAAGGCCAAGTTTCAGAAAAACAAAGGCAAGAATGCTGCTACCAAACCAACTCTTGCTGCTGCAAAGAAGCCACTCGCCCCACAAAAGACCAAAGCCTTCAAAAAGCCACAAACTGGTGGATGTTGGGTAGAACTAAATTTGGACCAAAAACAATAG
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

280

Amino Acids

31.85

Weight (kDa)

8.49

Isoelectric Point (pI)

42.89

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 63 - 213 3.5e-27 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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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) 800
AclWI GGATC 2 cut(s) 12, 627
AcsI RAATTY 3 cut(s) 50, 493, 823
AcuI CTGAAG 1 cut(s) 372
AfiI CCNNNNNNNGG 2 cut(s) 688, 800
AgsI TTSAA 8 cut(s) 55, 70, 304, 366, 518, 547, 614, 787
AjnI CCWGG 1 cut(s) 221
AjuI GAANNNNNNNTTGG 2 cut(s) 438, 470
AloI GAACNNNNNNTCC 2 cut(s) 159, 191
AlwI GGATC 2 cut(s) 12, 627
AoxI GGCC 2 cut(s) 195, 690
ApeKI GCWGC 3 cut(s) 722, 743, 746
ApoI RAATTY 3 cut(s) 50, 493, 823
ArsI GACNNNNNNTTYG 4 cut(s) 408, 440, 566, 598
Asp700I GAANNNNTTC 1 cut(s) 542
AspS9I GGNCC 1 cut(s) 829
AsuHPI GGTGA 1 cut(s) 614
AvaII GGWCC 1 cut(s) 829
BanII GRGCYC 1 cut(s) 62
BbvI GCAGC 3 cut(s) 709, 730, 733
BccI CCATC 2 cut(s) 397, 691
BciT130I CCWGG 1 cut(s) 223
BfmI CTRYAG 1 cut(s) 213
BisI GCNGC 3 cut(s) 723, 744, 747
BlsI GCNGC 3 cut(s) 724, 745, 748
Bme1390I CCNGG 1 cut(s) 223
Bme18I GGWCC 1 cut(s) 829
BmgT120I GGNCC 1 cut(s) 829
BmiI GGNNCC 2 cut(s) 141, 654
BmrFI CCNGG 1 cut(s) 223
BmsI GCATC 3 cut(s) 175, 400, 634
BsaJI CCNNGG 3 cut(s) 135, 144, 222
BsaWI WCCGGW 2 cut(s) 154, 624
BsaXI ACNNNNNCTCC 4 cut(s) 124, 154, 159, 189
Bsc4I CCNNNNNNNGG 2 cut(s) 688, 800
Bse1I ACTGG 1 cut(s) 805
BseBI CCWGG 1 cut(s) 223
BseDI CCNNGG 3 cut(s) 135, 144, 222
BseGI GGATG 2 cut(s) 255, 812
BseLI CCNNNNNNNGG 2 cut(s) 688, 800
BseMII CTCAG 2 cut(s) 36, 561
BseNI ACTGG 1 cut(s) 805
BseXI GCAGC 3 cut(s) 709, 730, 733
BsgI GTGCAG 1 cut(s) 265
BshFI GGCC 2 cut(s) 197, 692
BsiSI CCGG 2 cut(s) 155, 625
BslFI GGGAC 1 cut(s) 495
BslI CCNNNNNNNGG 2 cut(s) 688, 800
BsmFI GGGAC 1 cut(s) 495
BsmI GAATGC 1 cut(s) 724
BsnI GGCC 2 cut(s) 197, 692
Bsp1286I GDGCHC 1 cut(s) 62
Bsp143I GATC 2 cut(s) 4, 619
BspANI GGCC 2 cut(s) 197, 692
BspCNI CTCAG 2 cut(s) 37, 562
BspHI TCATGA 1 cut(s) 457
BspLI GGNNCC 2 cut(s) 141, 654
BspPI GGATC 2 cut(s) 12, 627
BsrI ACTGG 1 cut(s) 805
BssECI CCNNGG 3 cut(s) 135, 144, 222
BssMI GATC 2 cut(s) 4, 619
BssT1I CCWWGG 1 cut(s) 144
Bst2UI CCWGG 1 cut(s) 223
Bst6I CTCTTC 2 cut(s) 114, 609
BstC8I GCNNGC 1 cut(s) 77
BstDEI CTNAG 3 cut(s) 45, 268, 570
BstF5I GGATG 2 cut(s) 255, 812
BstKTI GATC 2 cut(s) 7, 622
BstMBI GATC 2 cut(s) 4, 619
BstMWI GCNNNNNNNGC 2 cut(s) 146, 194
BstNI CCWGG 1 cut(s) 223
BstSCI CCNGG 1 cut(s) 221
BstSFI CTRYAG 1 cut(s) 213
BstV1I GCAGC 3 cut(s) 709, 730, 733
BsuRI GGCC 2 cut(s) 197, 692
BtsCI GGATG 2 cut(s) 255, 812
Cac8I GCNNGC 1 cut(s) 77
CciI TCATGA 1 cut(s) 457
Cfr13I GGNCC 1 cut(s) 829
CviAII CATG 7 cut(s) 22, 32, 113, 458, 534, 577, 667
DdeI CTNAG 3 cut(s) 45, 268, 570
DpnI GATC 2 cut(s) 6, 621
DpnII GATC 2 cut(s) 4, 619
Eam1104I CTCTTC 2 cut(s) 114, 609
EarI CTCTTC 2 cut(s) 114, 609
Eco130I CCWWGG 1 cut(s) 144
Eco24I GRGCYC 1 cut(s) 62
Eco47I GGWCC 1 cut(s) 829
Eco57I CTGAAG 1 cut(s) 372
EcoRII CCWGG 1 cut(s) 221
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, 461, 537, 580, 670
FaqI GGGAC 1 cut(s) 495
FatI CATG 7 cut(s) 21, 31, 112, 457, 533, 576, 666
Fnu4HI GCNGC 3 cut(s) 723, 744, 747
FokI GGATG 2 cut(s) 242, 819
FriOI GRGCYC 1 cut(s) 62
Fsp4HI GCNGC 3 cut(s) 723, 744, 747
GluI GCNGC 3 cut(s) 723, 744, 747
HaeIII GGCC 2 cut(s) 197, 692
HapII CCGG 2 cut(s) 155, 625
Hin1II CATG 7 cut(s) 25, 35, 116, 461, 537, 580, 670
HinfI GANTC 4 cut(s) 28, 218, 275, 326
HpaII CCGG 2 cut(s) 155, 625
HphI GGTGA 1 cut(s) 614
Hpy188I TCNGA 5 cut(s) 64, 393, 558, 600, 702
Hpy188III TCNNGA 1 cut(s) 458
HpyAV CCTTC 5 cut(s) 152, 158, 467, 540, 793
HpyCH4V TGCA 2 cut(s) 246, 749
HpyF10VI GCNNNNNNNGC 2 cut(s) 146, 194
HpyF3I CTNAG 3 cut(s) 45, 268, 570
Hsp92II CATG 7 cut(s) 25, 35, 116, 461, 537, 580, 670
Kzo9I GATC 2 cut(s) 4, 619
LmnI GCTCC 2 cut(s) 145, 652
LpnPI CCDG 8 cut(s) 57, 61, 168, 208, 232, 235, 638, 786
Lsp1109I GCAGC 3 cut(s) 709, 730, 733
LweI GCATC 3 cut(s) 175, 400, 634
MalI GATC 2 cut(s) 6, 621
MboI GATC 2 cut(s) 4, 619
MboII GAAGA 5 cut(s) 37, 101, 482, 626, 640
MfeI CAATTG 1 cut(s) 590
MhlI GDGCHC 1 cut(s) 62
MluCI AATT 8 cut(s) 50, 250, 317, 394, 493, 521, 590, 823
MlyI GAGTC 2 cut(s) 227, 335
MmeI TCCRAC 1 cut(s) 203
MnlI CCTC 7 cut(s) 130, 269, 430, 537, 565, 610, 668
MroXI GAANNNNTTC 1 cut(s) 542
MspI CCGG 2 cut(s) 155, 625
MspR9I CCNGG 1 cut(s) 223
MunI CAATTG 1 cut(s) 590
Mva1269I GAATGC 1 cut(s) 724
MvaI CCWGG 1 cut(s) 223
MwoI GCNNNNNNNGC 2 cut(s) 146, 194
NdeII GATC 2 cut(s) 4, 619
NlaIII CATG 7 cut(s) 25, 35, 116, 461, 537, 580, 670
NlaIV GGNNCC 2 cut(s) 141, 654
PagI TCATGA 1 cut(s) 457
PctI GAATGC 1 cut(s) 724
PdmI GAANNNNTTC 1 cut(s) 542
PfeI GAWTC 2 cut(s) 28, 275
PflMI CCANNNNNTGG 1 cut(s) 800
PkrI GCNGC 3 cut(s) 724, 745, 748
PleI GAGTC 2 cut(s) 226, 334
PpsI GAGTC 2 cut(s) 226, 334
Psp6I CCWGG 1 cut(s) 221
PspGI CCWGG 1 cut(s) 221
PspN4I GGNNCC 2 cut(s) 141, 654
PspPI GGNCC 1 cut(s) 829
SatI GCNGC 3 cut(s) 723, 744, 747
Sau3AI GATC 2 cut(s) 4, 619
Sau96I GGNCC 1 cut(s) 829
SchI GAGTC 2 cut(s) 227, 335
ScrFI CCNGG 1 cut(s) 223
SduI GDGCHC 1 cut(s) 62
SetI ASST 4 cut(s) 46, 478, 529, 552
SfaNI GCATC 3 cut(s) 175, 400, 634
SfcI CTRYAG 1 cut(s) 213
SinI GGWCC 1 cut(s) 829
Sse9I AATT 8 cut(s) 50, 250, 317, 394, 493, 521, 590, 823
StyD4I CCNGG 1 cut(s) 221
StyI CCWWGG 1 cut(s) 144
TaqI TCGA 1 cut(s) 491
TasI AATT 8 cut(s) 50, 250, 317, 394, 493, 521, 590, 823
TfiI GAWTC 2 cut(s) 28, 275
TseI GCWGC 3 cut(s) 722, 743, 746
TspDTI ATGAA 6 cut(s) 38, 101, 446, 483, 522, 648
Van91I CCANNNNNTGG 1 cut(s) 800
VpaK11BI GGWCC 1 cut(s) 829
XapI RAATTY 3 cut(s) 50, 493, 823
XmnI GAANNNNTTC 1 cut(s) 542
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.