Rroxscaffold_4G00296760

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000004
OG0000258
Physical Location & Seq
Reverse (-)
16810121 .. 16813165
3045 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_4G00296760.1

Sequence Viewer

Length: 984 bp
ATGGCAAGGCGGCAATGGACTAGGCTTGGGCCCGAGCAAGAGCGGCGGTTGGACAGCTTGGAAGCGGTGGATCCCCACATGTTTTGGGCAATGATGGTGTCTCCTAAAGCAGAATGGTGGCACGCGGCGGCGGTACAGTGCGGTAGGGCTACAGTGGGTTGTGGCGGTAGGGCTACGGCGAGTCATGGTGGCTCGTGGGTATGCAGATTGCAGCCTAATATAGTCGACAAAACAGACCAGTTGAACCTTCAAGAAGATGAAAAATTGCAGGCAGAACAAGAGCTACTAAACAAGAGAAACCGAAGTTTGTTGCCTCATTATTTCAAACCGACAGCTGAACAAGACAATGAAAAGCAAGTTCCTACCACTAAAGAACCAGAAGTTAGTTTGGGAACCAGAGAAAAGGAGAAAGAGAATTACAAGAGTTGTGTATCAAAGTTAAGATCCCGACTAGATCAGATTGAGCCTATTCGTTTTTATGGGAAGAACTACCATATCTGGGCGCAACAGATGAAACTTTACCTAAAGAAATTGAAGGTTGCATATGTACTCTGTGAGCCCTGCCCAACCATTATGCTTGGATTAGAAGCAAGTCCAGTGGAAATTGCTCAATCCATGGCTGCTAAACAGAAATGGATGAATGATGACACCAGGTGTGGTCGTACGATCTTGCATCATCTATCTGTTTGTTTATTTCATGCTTACTCACAGAAACAGAAGACTATGACTGCGAAAGAACTGTGGAAAGATCTAGAATTAAAATTTGGAACAGAAGCATCTATGATTACAACAAAGACATCTCTGGTTGAAAAGTACATCAAATTTCGGATCCTTAGTACAAAACCAATTGTGGAGCAAGTTAAAGAATTCAATAGTATCTTTGATTCTCTTTTCGCTTCTGGACTGGTGGTCGATGAAAAATTCCATGTCAATGTCCTCATCTCTAAGCTCCCCCTTCTTGGAAAAATGTTTTCAACCGGTTGA
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
DEK_C PC4 Retrotran_gag_2

Protein Analysis

327

Amino Acids

37.58

Weight (kDa)

9.11

Isoelectric Point (pI)

47.2

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 205 - 318 3.5e-11 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
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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)
AccBSI CCGCTC 1 cut(s) 43
AccI GTMKAC 1 cut(s) 225
AccII CGCG 1 cut(s) 125
AciI CCGC 9 cut(s) 10, 43, 46, 65, 125, 128, 131, 141, 165
AclWI GGATC 5 cut(s) 65, 78, 438, 823, 836
AcsI RAATTY 4 cut(s) 761, 821, 866, 920
AdeI CACNNNGTG 1 cut(s) 654
AfaI GTAC 5 cut(s) 135, 549, 664, 815, 838
AfiI CCNNNNNNNGG 2 cut(s) 499, 959
AflIII ACRYGT 1 cut(s) 78
AgeI ACCGGT 1 cut(s) 977
AgsI TTSAA 7 cut(s) 244, 251, 325, 535, 809, 871, 975
AhdI GACNNNNNGTC 1 cut(s) 908
AjnI CCWGG 1 cut(s) 650
AjuI GAANNNNNNNTTGG 2 cut(s) 747, 779
AluBI AGCT 4 cut(s) 57, 283, 335, 949
AluI AGCT 4 cut(s) 57, 283, 335, 949
Alw26I GTCTC 1 cut(s) 105
AlwI GGATC 5 cut(s) 65, 78, 438, 823, 836
Ama87I CYCGRG 1 cut(s) 32
AoxI GGCC 1 cut(s) 29
ApaI GGGCCC 1 cut(s) 33
ApeKI GCWGC 2 cut(s) 211, 620
ApoI RAATTY 4 cut(s) 761, 821, 866, 920
AsiGI ACCGGT 1 cut(s) 977
AspLEI GCGC 1 cut(s) 505
AspS9I GGNCC 2 cut(s) 29, 30
AvaI CYCGRG 1 cut(s) 32
BaeGI GKGCMC 1 cut(s) 33
BamHI GGATCC 2 cut(s) 70, 828
BanII GRGCYC 2 cut(s) 33, 561
BauI CACGAG 1 cut(s) 193
BbsI GAAGAC 1 cut(s) 725
BbvI GCAGC 2 cut(s) 223, 607
BccI CCATC 1 cut(s) 88
BceAI ACGGC 1 cut(s) 192
BciT130I CCWGG 1 cut(s) 652
BcoDI GTCTC 1 cut(s) 105
BfaI CTAG 3 cut(s) 21, 452, 752
BfmI CTRYAG 1 cut(s) 150
BglII AGATCT 1 cut(s) 748
BisI GCNGC 6 cut(s) 11, 44, 126, 129, 212, 621
BlsI GCNGC 6 cut(s) 12, 45, 127, 130, 213, 622
Bme1390I CCNGG 1 cut(s) 652
BmeRI GACNNNNNGTC 1 cut(s) 908
BmeT110I CYCGRG 1 cut(s) 32
BmgT120I GGNCC 2 cut(s) 29, 30
BmiI GGNNCC 4 cut(s) 31, 72, 394, 830
BmrFI CCNGG 1 cut(s) 652
BmsI GCATC 2 cut(s) 682, 785
BpiI GAAGAC 1 cut(s) 725
BsaJI CCNNGG 1 cut(s) 615
BsaWI WCCGGW 1 cut(s) 977
Bsc4I CCNNNNNNNGG 2 cut(s) 499, 959
Bse118I RCCGGY 1 cut(s) 977
Bse1I ACTGG 3 cut(s) 238, 596, 909
Bse3DI GCAATG 2 cut(s) 20, 96
BseBI CCWGG 1 cut(s) 652
BseDI CCNNGG 1 cut(s) 615
BseGI GGATG 1 cut(s) 642
BseLI CCNNNNNNNGG 2 cut(s) 499, 959
BseMI GCAATG 2 cut(s) 20, 96
BseNI ACTGG 3 cut(s) 238, 596, 909
BseSI GKGCMC 1 cut(s) 33
BseXI GCAGC 2 cut(s) 223, 607
Bsh1236I CGCG 1 cut(s) 125
BshFI GGCC 1 cut(s) 31
BshTI ACCGGT 1 cut(s) 977
BsiHKCI CYCGRG 1 cut(s) 32
BsiSI CCGG 1 cut(s) 978
BsiWI CGTACG 1 cut(s) 662
BslI CCNNNNNNNGG 2 cut(s) 499, 959
BsmAI GTCTC 1 cut(s) 105
BsnI GGCC 1 cut(s) 31
BsoBI CYCGRG 1 cut(s) 32
Bsp120I GGGCCC 1 cut(s) 29
Bsp1286I GDGCHC 2 cut(s) 33, 561
Bsp143I GATC 6 cut(s) 70, 443, 454, 666, 748, 828
Bsp19I CCATGG 1 cut(s) 615
BspACI CCGC 9 cut(s) 10, 43, 46, 65, 125, 128, 131, 141, 165
BspANI GGCC 1 cut(s) 31
BspFNI CGCG 1 cut(s) 125
BspLI GGNNCC 4 cut(s) 31, 72, 394, 830
BspPI GGATC 5 cut(s) 65, 78, 438, 823, 836
BsrBI CCGCTC 1 cut(s) 43
BsrDI GCAATG 2 cut(s) 20, 96
BsrFI RCCGGY 1 cut(s) 977
BsrI ACTGG 3 cut(s) 238, 596, 909
BssAI RCCGGY 1 cut(s) 977
BssECI CCNNGG 1 cut(s) 615
BssMI GATC 6 cut(s) 70, 443, 454, 666, 748, 828
BssSI CACGAG 1 cut(s) 193
BssT1I CCWWGG 1 cut(s) 615
Bst2BI CACGAG 1 cut(s) 193
Bst2UI CCWGG 1 cut(s) 652
Bst4CI ACNGT 3 cut(s) 138, 154, 741
BstC8I GCNNGC 2 cut(s) 123, 270
BstDEI CTNAG 2 cut(s) 833, 945
BstDSI CCRYGG 1 cut(s) 615
BstF5I GGATG 1 cut(s) 642
BstFNI CGCG 1 cut(s) 125
BstHHI GCGC 1 cut(s) 505
BstKTI GATC 6 cut(s) 73, 446, 457, 669, 751, 831
BstMAI GTCTC 1 cut(s) 105
BstMBI GATC 6 cut(s) 70, 443, 454, 666, 748, 828
BstMWI GCNNNNNNNGC 1 cut(s) 43
BstNI CCWGG 1 cut(s) 652
BstNSI RCATGY 1 cut(s) 82
BstSCI CCNGG 1 cut(s) 650
BstSFI CTRYAG 1 cut(s) 150
BstSLI GKGCMC 1 cut(s) 33
BstUI CGCG 1 cut(s) 125
BstV1I GCAGC 2 cut(s) 223, 607
BstV2I GAAGAC 1 cut(s) 725
BstX2I RGATCY 4 cut(s) 70, 443, 748, 828
BstYI RGATCY 4 cut(s) 70, 443, 748, 828
BsuRI GGCC 1 cut(s) 31
BtgI CCRYGG 1 cut(s) 615
BtsCI GGATG 1 cut(s) 642
BtsIMutI CAGTG 3 cut(s) 143, 159, 603
Cac8I GCNNGC 2 cut(s) 123, 270
CfoI GCGC 1 cut(s) 505
Cfr10I RCCGGY 1 cut(s) 977
Cfr13I GGNCC 2 cut(s) 29, 30
CsiI ACCWGGT 1 cut(s) 650
Csp6I GTAC 5 cut(s) 134, 548, 663, 814, 837
CspAI ACCGGT 1 cut(s) 977
CspCI CAANNNNNGTGG 4 cut(s) 65, 100, 579, 614
CviAII CATG 5 cut(s) 79, 185, 616, 698, 926
CviQI GTAC 5 cut(s) 134, 548, 663, 814, 837
DdeI CTNAG 2 cut(s) 833, 945
DpnI GATC 6 cut(s) 72, 445, 456, 668, 750, 830
DpnII GATC 6 cut(s) 70, 443, 454, 666, 748, 828
DraIII CACNNNGTG 1 cut(s) 654
DriI GACNNNNNGTC 1 cut(s) 908
Eam1105I GACNNNNNGTC 1 cut(s) 908
Eco130I CCWWGG 1 cut(s) 615
Eco24I GRGCYC 2 cut(s) 33, 561
Eco88I CYCGRG 1 cut(s) 32
EcoRI GAATTC 1 cut(s) 866
EcoRII CCWGG 1 cut(s) 650
EcoT14I CCWWGG 1 cut(s) 615
EcoT38I GRGCYC 2 cut(s) 33, 561
ErhI CCWWGG 1 cut(s) 615
FaeI CATG 5 cut(s) 82, 188, 619, 701, 929
FatI CATG 5 cut(s) 78, 184, 615, 697, 925
FauNDI CATATG 1 cut(s) 544
FblI GTMKAC 1 cut(s) 225
Fnu4HI GCNGC 6 cut(s) 11, 44, 126, 129, 212, 621
FokI GGATG 1 cut(s) 649
FriOI GRGCYC 2 cut(s) 33, 561
Fsp4HI GCNGC 6 cut(s) 11, 44, 126, 129, 212, 621
FspBI CTAG 3 cut(s) 21, 452, 752
GlaI GCGC 1 cut(s) 504
GluI GCNGC 6 cut(s) 11, 44, 126, 129, 212, 621
HaeIII GGCC 1 cut(s) 31
HapII CCGG 1 cut(s) 978
HhaI GCGC 1 cut(s) 505
Hin1II CATG 5 cut(s) 82, 188, 619, 701, 929
Hin6I GCGC 1 cut(s) 503
HinP1I GCGC 1 cut(s) 503
HincII GTYRAC 1 cut(s) 226
HindII GTYRAC 1 cut(s) 226
HinfI GANTC 2 cut(s) 181, 884
HpaII CCGG 1 cut(s) 978
Hpy166II GTNNAC 1 cut(s) 226
Hpy188I TCNGA 2 cut(s) 459, 828
Hpy188III TCNNGA 4 cut(s) 251, 447, 752, 900
Hpy8I GTNNAC 1 cut(s) 226
HpyAV CCTTC 3 cut(s) 257, 529, 965
HpyCH4III ACNGT 3 cut(s) 138, 154, 741
HpyCH4V TGCA 5 cut(s) 204, 211, 268, 542, 673
HpyF10VI GCNNNNNNNGC 1 cut(s) 43
HpyF3I CTNAG 2 cut(s) 833, 945
Hsp92II CATG 5 cut(s) 82, 188, 619, 701, 929
HspAI GCGC 1 cut(s) 503
Kzo9I GATC 6 cut(s) 70, 443, 454, 666, 748, 828
LmnI GCTCC 2 cut(s) 853, 954
Lsp1109I GCAGC 2 cut(s) 223, 607
LweI GCATC 2 cut(s) 682, 785
MabI ACCWGGT 1 cut(s) 650
MaeI CTAG 3 cut(s) 21, 452, 752
MalI GATC 6 cut(s) 72, 445, 456, 668, 750, 830
MbiI CCGCTC 1 cut(s) 43
MboI GATC 6 cut(s) 70, 443, 454, 666, 748, 828
MboII GAAGA 3 cut(s) 266, 496, 730
MfeI CAATTG 1 cut(s) 846
MflI RGATCY 4 cut(s) 70, 443, 748, 828
MhlI GDGCHC 2 cut(s) 33, 561
MlyI GAGTC 1 cut(s) 190
MmeI TCCRAC 1 cut(s) 30
MnlI CCTC 2 cut(s) 324, 947
MseI TTAA 3 cut(s) 440, 758, 861
MslI CAYNNNNRTG 1 cut(s) 930
MspA1I CMGCKG 1 cut(s) 335
MspI CCGG 1 cut(s) 978
MspR9I CCNGG 1 cut(s) 652
MunI CAATTG 1 cut(s) 846
MvaI CCWGG 1 cut(s) 652
MvnI CGCG 1 cut(s) 125
MwoI GCNNNNNNNGC 1 cut(s) 43
NcoI CCATGG 1 cut(s) 615
NdeI CATATG 1 cut(s) 544
NdeII GATC 6 cut(s) 70, 443, 454, 666, 748, 828
NlaIII CATG 5 cut(s) 82, 188, 619, 701, 929
NlaIV GGNNCC 4 cut(s) 31, 72, 394, 830
NspI RCATGY 1 cut(s) 82
PciI ACATGT 1 cut(s) 78
PfeI GAWTC 1 cut(s) 884
Pfl23II CGTACG 1 cut(s) 662
PinAI ACCGGT 1 cut(s) 977
PkrI GCNGC 6 cut(s) 12, 45, 127, 130, 213, 622
PleI GAGTC 1 cut(s) 189
PpsI GAGTC 1 cut(s) 189
PscI ACATGT 1 cut(s) 78
Psp6I CCWGG 1 cut(s) 650
PspGI CCWGG 1 cut(s) 650
PspLI CGTACG 1 cut(s) 662
PspN4I GGNNCC 4 cut(s) 31, 72, 394, 830
PspOMI GGGCCC 1 cut(s) 29
PspPI GGNCC 2 cut(s) 29, 30
PsrI GAACNNNNNNTAC 2 cut(s) 267, 299
PsuI RGATCY 4 cut(s) 70, 443, 748, 828
PvuII CAGCTG 1 cut(s) 335
RsaI GTAC 5 cut(s) 135, 549, 664, 815, 838
RsaNI GTAC 5 cut(s) 134, 548, 663, 814, 837
RseI CAYNNNNRTG 1 cut(s) 930
SalI GTCGAC 1 cut(s) 224
SaqAI TTAA 3 cut(s) 440, 758, 861
SatI GCNGC 6 cut(s) 11, 44, 126, 129, 212, 621
Sau3AI GATC 6 cut(s) 70, 443, 454, 666, 748, 828
Sau96I GGNCC 2 cut(s) 29, 30
SchI GAGTC 1 cut(s) 190
ScrFI CCNGG 1 cut(s) 652
SduI GDGCHC 2 cut(s) 33, 561
SetI ASST 8 cut(s) 59, 249, 285, 337, 525, 540, 656, 951
SexAI ACCWGGT 1 cut(s) 650
SfaNI GCATC 2 cut(s) 682, 785
SfcI CTRYAG 1 cut(s) 150
SmiMI CAYNNNNRTG 1 cut(s) 930
SsiI CCGC 9 cut(s) 10, 43, 46, 65, 125, 128, 131, 141, 165
SspMI CTAG 3 cut(s) 21, 452, 752
StyD4I CCNGG 1 cut(s) 650
StyI CCWWGG 1 cut(s) 615
TaaI ACNGT 3 cut(s) 138, 154, 741
TaqI TCGA 2 cut(s) 225, 912
TatI WGTACW 3 cut(s) 547, 813, 836
TauI GCSGC 4 cut(s) 13, 46, 128, 131
TfiI GAWTC 1 cut(s) 884
Tru1I TTAA 3 cut(s) 440, 758, 861
Tru9I TTAA 3 cut(s) 440, 758, 861
TscAI CASTG 3 cut(s) 143, 159, 603
TseI GCWGC 2 cut(s) 211, 620
TspDTI ATGAA 6 cut(s) 273, 363, 527, 653, 686, 930
TspRI CASTG 3 cut(s) 143, 159, 603
XapI RAATTY 4 cut(s) 761, 821, 866, 920
XbaI TCTAGA 1 cut(s) 751
XceI RCATGY 1 cut(s) 82
XmiI GTMKAC 1 cut(s) 225
XspI CTAG 3 cut(s) 21, 452, 752
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.