Rw1G014290

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr1
OG0000258
Physical Location & Seq
Reverse (-)
31908879 .. 31910185
1307 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw1G014290.1

Sequence Viewer

Length: 927 bp
ATGGATCCTGCTAGTGTTAAATCCCACATTGAGAAGCCTGAGAAATTCAAAGGTGTGGATTTCAAACGATGGAAGCAAAAGATGTTGTTCTACTTGACAATGTTGAACCTGGCCCAAGTCATTACTTTTGAGGTTCCTCAAGCTGTTGAAGCATGGAATCAAAGCGAGTTCCTGTGCAAGAATTACATTCTAAATGCCTTAGATGATTCATTGTATGATGCCTATTCATCATTCAAGACGGCTAAGGAGTTATGGGAATCCCTCGAGAAGAAGTACAAATCCGAGGTTGCAAGTGCGAAGAAGTTCGTCATTGGAAGTTATGGGACTGAACAAGACTTTCTTATTGGTTCAATCATTGAAAAATTAACCCCTTCTAGGAGGGATTTCAAAATTTATCTCAAGCACCTAACTGAAGATATGAATCTTGATGAGCTTATTCTCAAACTTCGTGTGCAAGAGGATCACCGAAAGAATGAGAAATCTGATGTGACTTCTATGGAAGCAAAAGCCAACATAATTGAAGGCAGCAACCCTACGCCTAAGTTTTCTCACAATCAAAAGAAGAAGGGAAAAGCTGCTGCCAAGAAAGCATTCACTGCCCCAAAGTGCAACAAGGCATATAATCTGTACATGGGGAATGCTAGTACTGCTGCTGTTGAAGGAAAGGGAAAAGTGGTTCTCAAACTCATTTCCGGAAAAGAACTCACAATCACTAATGTGCTGAATGTTCCTGAGATTCGAAAGAATCTGATTTCTGGCTCCCTTCTTAGCAACAAAGGCTTCAAGTTAGTGTTTGAATCTGATAAGTTTGTACTCACAAAGGGTGTGATGTATGTAGGAAAGGGTTGCCTTATGGAGGGGCTCTTCAAGCTTAATGTACTACCTATTATTAATAATAACAATGCAGGCCCATTCTCCTCGACGTAA
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
No domains found.

Protein Analysis

308

Amino Acids

34.67

Weight (kDa)

9.42

Isoelectric Point (pI)

38.42

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 47 - 107 2.5e-08 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 198 - 261 1.3e-12 Pol polyprotein, beta-barrel domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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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)
AccIII TCCGGA 1 cut(s) 692
AclWI GGATC 2 cut(s) 12, 468
AcsI RAATTY 2 cut(s) 44, 390
AcuI CTGAAG 1 cut(s) 432
AfaI GTAC 5 cut(s) 275, 629, 646, 813, 879
AfiI CCNNNNNNNGG 2 cut(s) 375, 856
AjnI CCWGG 1 cut(s) 108
AjuI GAANNNNNNNTTGG 2 cut(s) 575, 607
AleI CACNNNNGTG 1 cut(s) 716
AloI GAACNNNNNNTCC 2 cut(s) 660, 692
AluBI AGCT 4 cut(s) 143, 433, 575, 871
AluI AGCT 4 cut(s) 143, 433, 575, 871
AlwI GGATC 2 cut(s) 12, 468
Ama87I CYCGRG 1 cut(s) 263
Aor13HI TCCGGA 1 cut(s) 692
AoxI GGCC 2 cut(s) 111, 907
ApeKI GCWGC 4 cut(s) 525, 575, 578, 650
ApoI RAATTY 2 cut(s) 44, 390
AseI ATTAAT 1 cut(s) 891
Asp700I GAANNNNTTC 2 cut(s) 302, 590
AspS9I GGNCC 2 cut(s) 112, 908
AsuHPI GGTGA 1 cut(s) 455
AsuII TTCGAA 1 cut(s) 739
AvaI CYCGRG 1 cut(s) 263
BamHI GGATCC 1 cut(s) 4
BanII GRGCYC 1 cut(s) 864
BbvI GCAGC 4 cut(s) 537, 562, 565, 637
BccI CCATC 1 cut(s) 63
BceAI ACGGC 1 cut(s) 255
BciT130I CCWGG 1 cut(s) 110
BfaI CTAG 3 cut(s) 12, 375, 642
BisI GCNGC 4 cut(s) 526, 576, 579, 651
BlsI GCNGC 4 cut(s) 527, 577, 580, 652
BmcAI AGTACT 1 cut(s) 646
Bme1390I CCNGG 1 cut(s) 110
BmeT110I CYCGRG 1 cut(s) 263
BmgT120I GGNCC 2 cut(s) 112, 908
BmiI GGNNCC 3 cut(s) 6, 135, 760
BmrFI CCNGG 1 cut(s) 110
BmsI GCATC 1 cut(s) 208
Bpu10I CCTNAGC 1 cut(s) 243
Bpu14I TTCGAA 1 cut(s) 739
BpuEI CTTGAG 2 cut(s) 123, 383
BsaBI GATNNNNATC 1 cut(s) 420
BsaJI CCNNGG 1 cut(s) 282
BsaWI WCCGGW 1 cut(s) 692
Bsc4I CCNNNNNNNGG 2 cut(s) 375, 856
Bse8I GATNNNNATC 1 cut(s) 420
BseAI TCCGGA 1 cut(s) 692
BseBI CCWGG 1 cut(s) 110
BseDI CCNNGG 1 cut(s) 282
BseJI GATNNNNATC 1 cut(s) 420
BseLI CCNNNNNNNGG 2 cut(s) 375, 856
BseMII CTCAG 2 cut(s) 30, 723
BseRI GAGGAG 1 cut(s) 907
BseXI GCAGC 4 cut(s) 537, 562, 565, 637
BshFI GGCC 2 cut(s) 113, 909
BsiHKCI CYCGRG 1 cut(s) 263
BsiSI CCGG 1 cut(s) 693
BslFI GGGAC 1 cut(s) 337
BslI CCNNNNNNNGG 2 cut(s) 375, 856
BsmFI GGGAC 1 cut(s) 337
BsmI GAATGC 2 cut(s) 590, 643
BsnI GGCC 2 cut(s) 113, 909
BsoBI CYCGRG 1 cut(s) 263
Bsp119I TTCGAA 1 cut(s) 739
Bsp1286I GDGCHC 1 cut(s) 864
Bsp13I TCCGGA 1 cut(s) 692
Bsp1407I TGTACA 1 cut(s) 627
Bsp143I GATC 2 cut(s) 4, 460
BspANI GGCC 2 cut(s) 113, 909
BspCNI CTCAG 2 cut(s) 31, 724
BspEI TCCGGA 1 cut(s) 692
BspLI GGNNCC 3 cut(s) 6, 135, 760
BspPI GGATC 2 cut(s) 12, 468
BspQI GCTCTTC 1 cut(s) 869
BspT104I TTCGAA 1 cut(s) 739
BsrGI TGTACA 1 cut(s) 627
BssECI CCNNGG 1 cut(s) 282
BssMI GATC 2 cut(s) 4, 460
Bst2UI CCWGG 1 cut(s) 110
Bst6I CTCTTC 1 cut(s) 869
BstAPI GCANNNNNTGC 1 cut(s) 596
BstAUI TGTACA 1 cut(s) 627
BstBI TTCGAA 1 cut(s) 739
BstC8I GCNNGC 1 cut(s) 907
BstDEI CTNAG 6 cut(s) 39, 199, 243, 540, 732, 767
BstENI CCTNNNNNAGG 1 cut(s) 854
BstKTI GATC 2 cut(s) 7, 463
BstMBI GATC 2 cut(s) 4, 460
BstMWI GCNNNNNNNGC 6 cut(s) 149, 587, 596, 647, 777, 868
BstNI CCWGG 1 cut(s) 110
BstSCI CCNGG 1 cut(s) 108
BstV1I GCAGC 4 cut(s) 537, 562, 565, 637
BstX2I RGATCY 1 cut(s) 4
BstYI RGATCY 1 cut(s) 4
BsuRI GGCC 2 cut(s) 113, 909
BtsI GCAGTG 1 cut(s) 594
BtsIMutI CAGTG 1 cut(s) 594
Cac8I GCNNGC 1 cut(s) 907
Cfr13I GGNCC 2 cut(s) 112, 908
Csp6I GTAC 5 cut(s) 274, 628, 645, 812, 878
CviAII CATG 2 cut(s) 153, 631
CviQI GTAC 5 cut(s) 274, 628, 645, 812, 878
DdeI CTNAG 6 cut(s) 39, 199, 243, 540, 732, 767
DpnI GATC 2 cut(s) 6, 462
DpnII GATC 2 cut(s) 4, 460
Eam1104I CTCTTC 1 cut(s) 869
EarI CTCTTC 1 cut(s) 869
Eco24I GRGCYC 1 cut(s) 864
Eco57I CTGAAG 1 cut(s) 432
Eco88I CYCGRG 1 cut(s) 263
EcoNI CCTNNNNNAGG 1 cut(s) 854
EcoRII CCWGG 1 cut(s) 108
EcoT38I GRGCYC 1 cut(s) 864
FaeI CATG 2 cut(s) 156, 634
FalI AAGNNNNNCTT 2 cut(s) 324, 356
FaqI GGGAC 1 cut(s) 337
FatI CATG 2 cut(s) 152, 630
Fnu4HI GCNGC 4 cut(s) 526, 576, 579, 651
FriOI GRGCYC 1 cut(s) 864
Fsp4HI GCNGC 4 cut(s) 526, 576, 579, 651
FspBI CTAG 3 cut(s) 12, 375, 642
GluI GCNGC 4 cut(s) 526, 576, 579, 651
HaeIII GGCC 2 cut(s) 113, 909
HapII CCGG 1 cut(s) 693
Hin1II CATG 2 cut(s) 156, 634
HindIII AAGCTT 1 cut(s) 869
HinfI GANTC 7 cut(s) 157, 206, 257, 421, 736, 745, 797
HpaII CCGG 1 cut(s) 693
HphI GGTGA 1 cut(s) 455
Hpy188I TCNGA 4 cut(s) 283, 484, 750, 802
Hpy188III TCNNGA 5 cut(s) 235, 265, 425, 693, 731
Hpy99I CGWCG 1 cut(s) 925
HpyAV CCTTC 5 cut(s) 381, 515, 559, 653, 773
HpyCH4IV ACGT 1 cut(s) 923
HpyCH4V TGCA 5 cut(s) 177, 290, 454, 609, 905
HpyF10VI GCNNNNNNNGC 6 cut(s) 149, 587, 596, 647, 777, 868
HpyF3I CTNAG 6 cut(s) 39, 199, 243, 540, 732, 767
HpySE526I ACGT 1 cut(s) 923
Hsp92II CATG 2 cut(s) 156, 634
Kpn2I TCCGGA 1 cut(s) 692
Kzo9I GATC 2 cut(s) 4, 460
LguI GCTCTTC 1 cut(s) 869
LmnI GCTCC 1 cut(s) 764
LpnPI CCDG 9 cut(s) 21, 51, 95, 122, 185, 706, 741, 744, 891
Lsp1109I GCAGC 4 cut(s) 537, 562, 565, 637
LweI GCATC 1 cut(s) 208
MaeI CTAG 3 cut(s) 12, 375, 642
MaeII ACGT 1 cut(s) 923
MaeIII GTNAC 1 cut(s) 487
MalI GATC 2 cut(s) 6, 462
MboI GATC 2 cut(s) 4, 460
MboII GAAGA 5 cut(s) 280, 310, 425, 574, 856
MflI RGATCY 1 cut(s) 4
MhlI GDGCHC 1 cut(s) 864
MluCI AATT 5 cut(s) 44, 181, 362, 390, 516
MnlI CCTC 7 cut(s) 124, 147, 272, 277, 372, 451, 850
MroI TCCGGA 1 cut(s) 692
MroXI GAANNNNTTC 2 cut(s) 302, 590
MseI TTAA 4 cut(s) 18, 365, 873, 891
MslI CAYNNNNRTG 1 cut(s) 716
MspI CCGG 1 cut(s) 693
MspR9I CCNGG 1 cut(s) 110
Mva1269I GAATGC 2 cut(s) 590, 643
MvaI CCWGG 1 cut(s) 110
MwoI GCNNNNNNNGC 6 cut(s) 149, 587, 596, 647, 777, 868
NdeII GATC 2 cut(s) 4, 460
NlaIII CATG 2 cut(s) 156, 634
NlaIV GGNNCC 3 cut(s) 6, 135, 760
NmuCI GTSAC 1 cut(s) 487
NspV TTCGAA 1 cut(s) 739
OliI CACNNNNGTG 1 cut(s) 716
PaeR7I CTCGAG 1 cut(s) 263
PciSI GCTCTTC 1 cut(s) 869
PctI GAATGC 2 cut(s) 590, 643
PdmI GAANNNNTTC 2 cut(s) 302, 590
PfeI GAWTC 7 cut(s) 157, 206, 257, 421, 736, 745, 797
PkrI GCNGC 4 cut(s) 527, 577, 580, 652
PshBI ATTAAT 1 cut(s) 891
Psp6I CCWGG 1 cut(s) 108
PspGI CCWGG 1 cut(s) 108
PspN4I GGNNCC 3 cut(s) 6, 135, 760
PspPI GGNCC 2 cut(s) 112, 908
PsuI RGATCY 1 cut(s) 4
RsaI GTAC 5 cut(s) 275, 629, 646, 813, 879
RsaNI GTAC 5 cut(s) 274, 628, 645, 812, 878
RseI CAYNNNNRTG 1 cut(s) 716
SapI GCTCTTC 1 cut(s) 869
SaqAI TTAA 4 cut(s) 18, 365, 873, 891
SatI GCNGC 4 cut(s) 526, 576, 579, 651
Sau3AI GATC 2 cut(s) 4, 460
Sau96I GGNCC 2 cut(s) 112, 908
ScaI AGTACT 1 cut(s) 646
ScrFI CCNGG 1 cut(s) 110
SduI GDGCHC 1 cut(s) 864
SfaNI GCATC 1 cut(s) 208
Sfr274I CTCGAG 1 cut(s) 263
SfuI TTCGAA 1 cut(s) 739
SlaI CTCGAG 1 cut(s) 263
SmiMI CAYNNNNRTG 1 cut(s) 716
SmlI CTYRAG 3 cut(s) 138, 263, 398
SmoI CTYRAG 3 cut(s) 138, 263, 398
Sse9I AATT 5 cut(s) 44, 181, 362, 390, 516
SspMI CTAG 3 cut(s) 12, 375, 642
StyD4I CCNGG 1 cut(s) 108
TaiI ACGT 1 cut(s) 926
TaqI TCGA 3 cut(s) 264, 739, 920
TasI AATT 5 cut(s) 44, 181, 362, 390, 516
TatI WGTACW 5 cut(s) 273, 627, 644, 811, 877
TfiI GAWTC 7 cut(s) 157, 206, 257, 421, 736, 745, 797
Tru1I TTAA 4 cut(s) 18, 365, 873, 891
Tru9I TTAA 4 cut(s) 18, 365, 873, 891
TscAI CASTG 1 cut(s) 601
TseFI GTSAC 1 cut(s) 487
TseI GCWGC 4 cut(s) 525, 575, 578, 650
Tsp45I GTSAC 1 cut(s) 487
TspDTI ATGAA 3 cut(s) 198, 216, 434
TspRI CASTG 1 cut(s) 601
VspI ATTAAT 1 cut(s) 891
XagI CCTNNNNNAGG 1 cut(s) 854
XapI RAATTY 2 cut(s) 44, 390
XhoI CTCGAG 1 cut(s) 263
XmnI GAANNNNTTC 2 cut(s) 302, 590
XspI CTAG 3 cut(s) 12, 375, 642
ZrmI AGTACT 1 cut(s) 646
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.