Rw2G026170

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr2
OG0000258
Physical Location & Seq
Forward (+)
40339093 .. 40341108
2016 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw2G026170.1

Sequence Viewer

Length: 843 bp
ATGGATCCTGCTGGTGTTAAGTCCCACATTGAGAAGCCTGAGAAATTCAAAGGTGTGGATTTCAAACGATGGCAGCAAAAGATGTTGTTCTACTTAACAACGTTGAACCTGGCGCAAGTCATAACTTCTGAGGCTCCTCAAGTACCAAACGAGGGAGACATCCCTGCTGCAACTCGTAAGGCTGTTGAAGCATGGAATCAAAGCGAGTTCCTGTGTAAAAACTACATTTTGAATGCCTTAGACGATTCATTATATGATGTCTATTTGTCATTCAAAACTGCTAAGGAGTTGTGGGAATCCCTCGAGAAGAAGTACAAATCCGAGGTTGCAAGTGCCAAAAAGTTCGTCATTGGAAGGTTCCTGAACTTCAAGATGAACGACATCAACTCTGTTGTGAAACAAGTGGAGGAACTCCAGATTATTGTTCACGAGTTAGATGATGAAGGTATGGGACTAAAAGAGACTTTTCTTGTTGGTTCAATCATTGAAAAATTACCCCCTTCTTGGAAAGATTTCAAAATCTATCTCAAACACCTAACTGAAGATATGACCCTTGATGAACTAATTCTCAAACTTCGTGTGGAAGAGGATCACCGAAAGAATGAGAAATCTGATGTGACTTCTATGGAGGCAAAAGCCAACATAATTGAAGGCAGTACATTGAAGCCTAAGTTTTCCCTCAATCAAAAGAAGAAAGGAAAAGTTGCTGTCAAGAAAGCATTCACTGCCCCAAAGGCTAATACTTTCAAGAAGAAAATTCAAGTTGAGAAGTTGAATCAGTGTGTTGAGAAGGTGCTACTGCCAAATTTTGGTGGCCATCGGAGATGGTGGCGGCGGCGGTAG
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

32.44

Weight (kDa)

9.36

Isoelectric Point (pI)

43.24

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 30 - 203 1.7e-28 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) 809
AciI CCGC 3 cut(s) 832, 835, 838
AclI AACGTT 1 cut(s) 101
AclWI GGATC 2 cut(s) 12, 597
AcoI YGGCCR 1 cut(s) 814
AcsI RAATTY 3 cut(s) 44, 756, 805
AcuI CTGAAG 1 cut(s) 561
AfaI GTAC 3 cut(s) 144, 314, 658
AfiI CCNNNNNNNGG 3 cut(s) 152, 504, 809
AjnI CCWGG 1 cut(s) 108
Alw26I GTCTC 2 cut(s) 150, 455
AlwI GGATC 2 cut(s) 12, 597
Ama87I CYCGRG 1 cut(s) 302
AoxI GGCC 1 cut(s) 814
ApeKI GCWGC 2 cut(s) 73, 167
ApoI RAATTY 3 cut(s) 44, 756, 805
ArsI GACNNNNNNTTYG 2 cut(s) 330, 362
Asp700I GAANNNNTTC 3 cut(s) 512, 564, 719
AspLEI GCGC 1 cut(s) 115
AsuHPI GGTGA 1 cut(s) 584
AvaI CYCGRG 1 cut(s) 302
BalI TGGCCA 1 cut(s) 816
BamHI GGATCC 1 cut(s) 4
BauI CACGAG 1 cut(s) 428
BbvI GCAGC 2 cut(s) 85, 154
BccI CCATC 3 cut(s) 63, 819, 825
BciT130I CCWGG 1 cut(s) 110
BcoDI GTCTC 2 cut(s) 150, 455
BglI GCCNNNNNGGC 1 cut(s) 734
BisI GCNGC 4 cut(s) 74, 168, 833, 836
BlsI GCNGC 4 cut(s) 75, 169, 834, 837
Bme1390I CCNGG 1 cut(s) 110
BmeT110I CYCGRG 1 cut(s) 302
BmiI GGNNCC 3 cut(s) 6, 135, 359
BmrFI CCNGG 1 cut(s) 110
BpmI CTGGAG 1 cut(s) 398
Bpu10I CCTNAGC 1 cut(s) 282
BpuEI CTTGAG 1 cut(s) 123
BsaJI CCNNGG 1 cut(s) 321
Bsc4I CCNNNNNNNGG 3 cut(s) 152, 504, 809
BseBI CCWGG 1 cut(s) 110
BseDI CCNNGG 1 cut(s) 321
BseGI GGATG 1 cut(s) 159
BseLI CCNNNNNNNGG 3 cut(s) 152, 504, 809
BseMII CTCAG 2 cut(s) 30, 120
BseRI GAGGAG 1 cut(s) 126
BseXI GCAGC 2 cut(s) 85, 154
BshFI GGCC 1 cut(s) 816
BsiHKCI CYCGRG 1 cut(s) 302
BslFI GGGAC 2 cut(s) 7, 465
BslI CCNNNNNNNGG 3 cut(s) 152, 504, 809
BsmAI GTCTC 2 cut(s) 150, 455
BsmFI GGGAC 2 cut(s) 7, 465
BsmI GAATGC 2 cut(s) 238, 719
BsnI GGCC 1 cut(s) 816
BsoBI CYCGRG 1 cut(s) 302
Bsp143I GATC 2 cut(s) 4, 589
BspACI CCGC 3 cut(s) 832, 835, 838
BspANI GGCC 1 cut(s) 816
BspCNI CTCAG 2 cut(s) 31, 121
BspLI GGNNCC 3 cut(s) 6, 135, 359
BspPI GGATC 2 cut(s) 12, 597
BssECI CCNNGG 1 cut(s) 321
BssMI GATC 2 cut(s) 4, 589
BssSI CACGAG 1 cut(s) 428
Bst2BI CACGAG 1 cut(s) 428
Bst2UI CCWGG 1 cut(s) 110
Bst6I CTCTTC 1 cut(s) 579
BstAPI GCANNNNNTGC 1 cut(s) 725
BstDEI CTNAG 5 cut(s) 39, 129, 238, 282, 669
BstF5I GGATG 1 cut(s) 159
BstHHI GCGC 1 cut(s) 115
BstKTI GATC 2 cut(s) 7, 592
BstMAI GTCTC 2 cut(s) 150, 455
BstMBI GATC 2 cut(s) 4, 589
BstMWI GCNNNNNNNGC 3 cut(s) 188, 725, 734
BstNI CCWGG 1 cut(s) 110
BstSCI CCNGG 1 cut(s) 108
BstV1I GCAGC 2 cut(s) 85, 154
BstX2I RGATCY 1 cut(s) 4
BstYI RGATCY 1 cut(s) 4
BsuRI GGCC 1 cut(s) 816
BtsCI GGATG 1 cut(s) 159
BtsI GCAGTG 1 cut(s) 723
BtsIMutI CAGTG 2 cut(s) 723, 785
CfoI GCGC 1 cut(s) 115
Csp6I GTAC 3 cut(s) 143, 313, 657
CviAII CATG 1 cut(s) 192
CviJI RGCY 7 cut(s) 37, 134, 182, 638, 667, 737, 816
CviKI_1 RGCY 7 cut(s) 37, 134, 182, 638, 667, 737, 816
CviQI GTAC 3 cut(s) 143, 313, 657
DdeI CTNAG 5 cut(s) 39, 129, 238, 282, 669
DpnI GATC 2 cut(s) 6, 591
DpnII GATC 2 cut(s) 4, 589
EaeI YGGCCR 1 cut(s) 814
Eam1104I CTCTTC 1 cut(s) 579
EarI CTCTTC 1 cut(s) 579
Eco57I CTGAAG 1 cut(s) 561
Eco88I CYCGRG 1 cut(s) 302
EcoRII CCWGG 1 cut(s) 108
FaeI CATG 1 cut(s) 195
FaiI YATR 8 cut(s) 122, 193, 253, 255, 449, 548, 626, 644
FaqI GGGAC 2 cut(s) 7, 465
FatI CATG 1 cut(s) 191
Fnu4HI GCNGC 4 cut(s) 74, 168, 833, 836
FokI GGATG 1 cut(s) 146
Fsp4HI GCNGC 4 cut(s) 74, 168, 833, 836
GlaI GCGC 1 cut(s) 114
GluI GCNGC 4 cut(s) 74, 168, 833, 836
GsuI CTGGAG 1 cut(s) 398
HaeIII GGCC 1 cut(s) 816
HhaI GCGC 1 cut(s) 115
Hin1II CATG 1 cut(s) 195
Hin6I GCGC 1 cut(s) 113
HinP1I GCGC 1 cut(s) 113
HinfI GANTC 4 cut(s) 196, 245, 296, 775
HphI GGTGA 1 cut(s) 584
Hpy166II GTNNAC 1 cut(s) 427
Hpy188I TCNGA 4 cut(s) 130, 322, 613, 822
Hpy188III TCNNGA 7 cut(s) 304, 361, 370, 415, 428, 712, 748
Hpy8I GTNNAC 1 cut(s) 427
HpyAV CCTTC 5 cut(s) 348, 437, 510, 644, 784
HpyCH4IV ACGT 1 cut(s) 101
HpyCH4V TGCA 2 cut(s) 170, 329
HpyF10VI GCNNNNNNNGC 3 cut(s) 188, 725, 734
HpyF3I CTNAG 5 cut(s) 39, 129, 238, 282, 669
HpySE526I ACGT 1 cut(s) 101
Hsp92II CATG 1 cut(s) 195
HspAI GCGC 1 cut(s) 113
Kzo9I GATC 2 cut(s) 4, 589
LmnI GCTCC 1 cut(s) 139
LpnPI CCDG 8 cut(s) 21, 51, 95, 122, 177, 224, 374, 428
Lsp1109I GCAGC 2 cut(s) 85, 154
MaeII ACGT 1 cut(s) 101
MaeIII GTNAC 1 cut(s) 616
MalI GATC 2 cut(s) 6, 591
MboI GATC 2 cut(s) 4, 589
MboII GAAGA 5 cut(s) 319, 554, 596, 703, 763
MflI RGATCY 1 cut(s) 4
MlsI TGGCCA 1 cut(s) 816
MluCI AATT 6 cut(s) 44, 491, 564, 645, 756, 805
MluNI TGGCCA 1 cut(s) 816
MnlI CCTC 9 cut(s) 124, 145, 147, 311, 316, 400, 580, 622, 689
Mox20I TGGCCA 1 cut(s) 816
MroXI GAANNNNTTC 3 cut(s) 512, 564, 719
MscI TGGCCA 1 cut(s) 816
MseI TTAA 2 cut(s) 18, 95
Msp20I TGGCCA 1 cut(s) 816
MspR9I CCNGG 1 cut(s) 110
Mva1269I GAATGC 2 cut(s) 238, 719
MvaI CCWGG 1 cut(s) 110
MwoI GCNNNNNNNGC 3 cut(s) 188, 725, 734
NdeII GATC 2 cut(s) 4, 589
NlaIII CATG 1 cut(s) 195
NlaIV GGNNCC 3 cut(s) 6, 135, 359
NmuCI GTSAC 1 cut(s) 616
PaeR7I CTCGAG 1 cut(s) 302
PctI GAATGC 2 cut(s) 238, 719
PdmI GAANNNNTTC 3 cut(s) 512, 564, 719
PfeI GAWTC 4 cut(s) 196, 245, 296, 775
PflMI CCANNNNNTGG 1 cut(s) 809
PkrI GCNGC 4 cut(s) 75, 169, 834, 837
Psp1406I AACGTT 1 cut(s) 101
Psp6I CCWGG 1 cut(s) 108
PspGI CCWGG 1 cut(s) 108
PspN4I GGNNCC 3 cut(s) 6, 135, 359
PsuI RGATCY 1 cut(s) 4
RsaI GTAC 3 cut(s) 144, 314, 658
RsaNI GTAC 3 cut(s) 143, 313, 657
SaqAI TTAA 2 cut(s) 18, 95
SatI GCNGC 4 cut(s) 74, 168, 833, 836
Sau3AI GATC 2 cut(s) 4, 589
ScrFI CCNGG 1 cut(s) 110
SetI ASST 8 cut(s) 55, 104, 111, 327, 359, 448, 537, 795
Sfr274I CTCGAG 1 cut(s) 302
SlaI CTCGAG 1 cut(s) 302
SmlI CTYRAG 2 cut(s) 138, 302
SmoI CTYRAG 2 cut(s) 138, 302
Sse9I AATT 6 cut(s) 44, 491, 564, 645, 756, 805
SsiI CCGC 3 cut(s) 832, 835, 838
StyD4I CCNGG 1 cut(s) 108
TaiI ACGT 1 cut(s) 104
TaqI TCGA 1 cut(s) 303
TasI AATT 6 cut(s) 44, 491, 564, 645, 756, 805
TatI WGTACW 2 cut(s) 312, 656
TauI GCSGC 2 cut(s) 835, 838
TfiI GAWTC 4 cut(s) 196, 245, 296, 775
Tru1I TTAA 2 cut(s) 18, 95
Tru9I TTAA 2 cut(s) 18, 95
TscAI CASTG 2 cut(s) 730, 785
TseFI GTSAC 1 cut(s) 616
TseI GCWGC 2 cut(s) 73, 167
Tsp45I GTSAC 1 cut(s) 616
TspDTI ATGAA 4 cut(s) 237, 389, 456, 573
TspRI CASTG 2 cut(s) 730, 785
Van91I CCANNNNNTGG 1 cut(s) 809
XapI RAATTY 3 cut(s) 44, 756, 805
XhoI CTCGAG 1 cut(s) 302
XmnI GAANNNNTTC 3 cut(s) 512, 564, 719
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.