Rorug05G0406800

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000005
OG0000333
Physical Location & Seq
Forward (+)
56066077 .. 56068037
1961 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug05G0406800.1

Sequence Viewer

Length: 636 bp
ATGGTCCAAGTGAGGGATAGAAGAGAGGGGAAGATCTCGGCGAGAATAGACCGGGTCGAAGGTATTTTTGCTTCTTTGGTGGCTTTGATGTTCAATTGCGTGAAGAGAGATGACATTGATTACTCTCCTTACGAAGAGGGCGAGTGGAGGACTCAGTACACTCCTTATGAACATTTAGATGATTCTATGCTTCAGGAATTGAATATGTGTATATTCTGTTTTCCTACTTCCTCAGTCATTCCACTTCATGATCACCCTGGCCTGACTGTTTTTAGCAAAGTTCTGTATGGTTCTTTGCATGTGAGAGCTTACGATTGGGTGGAGCCTTCCCACGAAAGCAAGGGATCAAATTACTTTCCAGGAGATGAGATGACTCGAATTTTCTGGAAATCAATCAAGGATAAGCTTATTCTCCCCTTTTTGGATTTGGACATTAAGTACTTTGACCTTGGTCTTCCTCACCGTGATACCACTGATGATAAAGTTACCGTTGAAAGTGCAGAGGCTACTCTTAAGCAGCAGCTGTGGTTGATAGTCTGGCCATCTTTTAGAAGTGAAGGTGCTGCAGTGCTGTTGTTTTGGCTTACTCTTGATTGCTGCTTGGTTATAAATGATGGGTTTCATATTGTAATTTGA
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

211

Amino Acids

24.5

Weight (kDa)

5.01

Isoelectric Point (pI)

30.86

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCO_ADO PF07847 65 - 116 1.9e-21 PCO_ADO
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: OG0000333)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G11910 AT3G11910 AT3G11910 AT3G11910 AT5G06600 AT5G06600 AT5G06600
fragaria_vesca FvH4_3g26930 FvH4_3g39132 FvH4_6g21220 FvH4_6g21220 FvH4_6g21220 FvH4_6g21220 FvH4_6g21220 FvH4_6g21220
malus_domestica MD02G1261100.v1.1 MD03G1161100.v1.1 MD07G1059900.v1.1 MD11G1177100.v1.1 MD12G1047900.v1.1 MD12G1048000.v1.1 MD12G1048400.v1.1 MD12G1048500.v1.1 MD12G1048700.v1.1 MD12G1048800.v1.1 MD12G1056200.v1.1 MD14G1046300.v1.1 MD14G1046500.v1.1 MD15G1166900.v1.1
prunus_persica Prupe.2G066200_v2.0.a1 Prupe.2G066200_v2.0.a1 Prupe.6G149500_v2.0.a1 Prupe.6G149500_v2.0.a1 Prupe.6G149500_v2.0.a1 Prupe.6G149500_v2.0.a1 Prupe.7G087600_v2.0.a1 Prupe.7G087600_v2.0.a1 Prupe.7G087600_v2.0.a1 Prupe.7G087600_v2.0.a1 Prupe.7G087600_v2.0.a1
pyrus_communis pycom02g22320 pycom03g11340 pycom07g04580 pycom11g14290 pycom11g15110 pycom12g04110 pycom12g04140 pycom12g04160 pycom12g04210 pycom12g04220 pycom12g04230 pycom12g04290 pycom12g04320 pycom12g04330 pycom12g04350 pycom12g04360 pycom14g03880 pycom14g03900 pycom16g18750
rosa_chinensis RchiOBHm_Chr1g0324111 RchiOBHm_Chr1g0324241 RchiOBHm_Chr3g0477691 RchiOBHm_Chr5g0049371 RchiOBHm_Chr5g0070531
rosa_laevigata RLG00000008612 RLG00000023698 RLG00000034613 RLG00000036139
rosa_multiflora Rmu_co8271779.1_g000001 Rmu_sc0006187.1_g000014
rosa_roxburghii Rroxscaffold_1G00010670 Rroxscaffold_1G00030450 Rroxscaffold_1G00031950 Rroxscaffold_1G00031970 Rroxscaffold_1G00032320 Rroxscaffold_1G00055490 Rroxscaffold_2G00083610 Rroxscaffold_2G00084480 Rroxscaffold_2G00115610 Rroxscaffold_3G00261320 Rroxscaffold_4G00312220 Rroxscaffold_4G00325820 Rroxscaffold_5G00339170 Rroxscaffold_5G00364030 Rroxscaffold_6G00403750
rosa_rugosa Rorug03G0162700 Rorug03G0162800 Rorug03G0162900 Rorug05G0247700 Rorug05G0406600 Rorug05G0406800
rosa_samantha Rh1AG060300 Rh3AG213000 Rh3BG246600 Rh3CG240400 Rh3DG239700 Rh5AG324400 Rh5AG462100 Rh5BG335500 Rh5BG480200 Rh5BG480300 Rh5CG360200 Rh5CG504500 Rh5CG504600 Rh5DG347800 Rh5DG492200 Rh5DG492300
rosa_wichuraiana Rw3G019270 Rw3G026910 Rw5G030650 Rw5G032610 Rw5G043040

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 608
AclWI GGATC 1 cut(s) 352
AcoI YGGCCR 1 cut(s) 539
AcsI RAATTY 1 cut(s) 378
AcuI CTGAAG 1 cut(s) 176
AfaI GTAC 2 cut(s) 158, 440
AfiI CCNNNNNNNGG 2 cut(s) 13, 421
AflII CTTAAG 1 cut(s) 512
AgsI TTSAA 3 cut(s) 94, 202, 494
AjnI CCWGG 2 cut(s) 256, 358
AluBI AGCT 3 cut(s) 308, 406, 523
AluI AGCT 3 cut(s) 308, 406, 523
AlwI GGATC 1 cut(s) 352
AlwNI CAGNNNCTG 1 cut(s) 523
AoxI GGCC 2 cut(s) 259, 539
ApeKI GCWGC 4 cut(s) 517, 520, 563, 597
ApoI RAATTY 1 cut(s) 378
AspS9I GGNCC 1 cut(s) 4
AsuC2I CCSGG 1 cut(s) 53
AsuHPI GGTGA 2 cut(s) 245, 452
AvaII GGWCC 1 cut(s) 4
BalI TGGCCA 1 cut(s) 541
BarI GAAGNNNNNNTAC 2 cut(s) 55, 87
BbsI GAAGAC 1 cut(s) 446
BbvI GCAGC 4 cut(s) 529, 532, 550, 584
BccI CCATC 2 cut(s) 550, 608
BciT130I CCWGG 2 cut(s) 258, 360
BclI TGATCA 1 cut(s) 250
BcnI CCSGG 1 cut(s) 53
BfmI CTRYAG 1 cut(s) 564
BfrI CTTAAG 1 cut(s) 512
BglII AGATCT 1 cut(s) 33
BisI GCNGC 4 cut(s) 518, 521, 564, 598
BlsI GCNGC 4 cut(s) 519, 522, 565, 599
BmcAI AGTACT 1 cut(s) 440
Bme1390I CCNGG 3 cut(s) 53, 258, 360
Bme18I GGWCC 1 cut(s) 4
BmgT120I GGNCC 1 cut(s) 4
BmiI GGNNCC 1 cut(s) 324
BmrFI CCNGG 3 cut(s) 53, 258, 360
BoxI GACNNNNGTC 1 cut(s) 450
BpiI GAAGAC 1 cut(s) 446
BpuMI CCSGG 1 cut(s) 53
BsaJI CCNNGG 2 cut(s) 256, 448
Bsc4I CCNNNNNNNGG 2 cut(s) 13, 421
BseBI CCWGG 2 cut(s) 258, 360
BseDI CCNNGG 2 cut(s) 256, 448
BseLI CCNNNNNNNGG 2 cut(s) 13, 421
BseMII CTCAG 2 cut(s) 167, 246
BseXI GCAGC 4 cut(s) 529, 532, 550, 584
BsgI GTGCAG 1 cut(s) 519
BshFI GGCC 2 cut(s) 261, 541
BsiSI CCGG 1 cut(s) 52
BslI CCNNNNNNNGG 2 cut(s) 13, 421
BsnI GGCC 2 cut(s) 261, 541
Bsp143I GATC 3 cut(s) 33, 250, 344
BspANI GGCC 2 cut(s) 261, 541
BspCNI CTCAG 2 cut(s) 166, 245
BspHI TCATGA 1 cut(s) 247
BspLI GGNNCC 1 cut(s) 324
BspMAI CTGCAG 1 cut(s) 568
BspPI GGATC 1 cut(s) 352
BspTI CTTAAG 1 cut(s) 512
BssECI CCNNGG 2 cut(s) 256, 448
BssMI GATC 3 cut(s) 33, 250, 344
BssT1I CCWWGG 1 cut(s) 448
Bst2UI CCWGG 2 cut(s) 258, 360
Bst4CI ACNGT 3 cut(s) 268, 464, 490
Bst6I CTCTTC 3 cut(s) 16, 98, 129
BstAFI CTTAAG 1 cut(s) 512
BstDEI CTNAG 2 cut(s) 153, 232
BstKTI GATC 3 cut(s) 36, 253, 347
BstMBI GATC 3 cut(s) 33, 250, 344
BstNI CCWGG 2 cut(s) 258, 360
BstNSI RCATGY 1 cut(s) 302
BstPAI GACNNNNGTC 1 cut(s) 450
BstSCI CCNGG 3 cut(s) 51, 256, 358
BstSFI CTRYAG 1 cut(s) 564
BstV1I GCAGC 4 cut(s) 529, 532, 550, 584
BstV2I GAAGAC 1 cut(s) 446
BstX2I RGATCY 1 cut(s) 33
BstYI RGATCY 1 cut(s) 33
BsuRI GGCC 2 cut(s) 261, 541
BtsI GCAGTG 1 cut(s) 573
BtsIMutI CAGTG 2 cut(s) 471, 573
CaiI CAGNNNCTG 1 cut(s) 523
CciI TCATGA 1 cut(s) 247
Cfr13I GGNCC 1 cut(s) 4
Csp6I GTAC 2 cut(s) 157, 439
CviAII CATG 2 cut(s) 248, 299
CviJI RGCY 9 cut(s) 83, 261, 308, 325, 406, 506, 523, 541, 583
CviKI_1 RGCY 9 cut(s) 83, 261, 308, 325, 406, 506, 523, 541, 583
CviQI GTAC 2 cut(s) 157, 439
DdeI CTNAG 2 cut(s) 153, 232
DpnI GATC 3 cut(s) 35, 252, 346
DpnII GATC 3 cut(s) 33, 250, 344
EaeI YGGCCR 1 cut(s) 539
Eam1104I CTCTTC 3 cut(s) 16, 98, 129
EarI CTCTTC 3 cut(s) 16, 98, 129
Eco130I CCWWGG 1 cut(s) 448
Eco47I GGWCC 1 cut(s) 4
Eco57I CTGAAG 1 cut(s) 176
EcoRII CCWGG 2 cut(s) 256, 358
EcoT14I CCWWGG 1 cut(s) 448
ErhI CCWWGG 1 cut(s) 448
FaeI CATG 2 cut(s) 251, 302
FaiI YATR 9 cut(s) 168, 188, 206, 212, 249, 288, 300, 608, 624
FatI CATG 2 cut(s) 247, 298
FbaI TGATCA 1 cut(s) 250
Fnu4HI GCNGC 4 cut(s) 518, 521, 564, 598
Fsp4HI GCNGC 4 cut(s) 518, 521, 564, 598
GluI GCNGC 4 cut(s) 518, 521, 564, 598
HaeIII GGCC 2 cut(s) 261, 541
HapII CCGG 1 cut(s) 52
Hin1II CATG 2 cut(s) 251, 302
HindIII AAGCTT 1 cut(s) 404
HinfI GANTC 3 cut(s) 151, 182, 373
HpaII CCGG 1 cut(s) 52
HphI GGTGA 2 cut(s) 245, 452
Hpy166II GTNNAC 1 cut(s) 159
Hpy188III TCNNGA 4 cut(s) 194, 248, 385, 590
Hpy8I GTNNAC 1 cut(s) 159
HpyAV CCTTC 3 cut(s) 53, 336, 551
HpyCH4III ACNGT 3 cut(s) 268, 464, 490
HpyCH4V TGCA 3 cut(s) 298, 500, 566
HpyF3I CTNAG 2 cut(s) 153, 232
Hsp92II CATG 2 cut(s) 251, 302
Ksp22I TGATCA 1 cut(s) 250
Kzo9I GATC 3 cut(s) 33, 250, 344
LmnI GCTCC 1 cut(s) 322
LpnPI CCDG 9 cut(s) 65, 179, 243, 270, 275, 345, 370, 372, 523
Lsp1109I GCAGC 4 cut(s) 529, 532, 550, 584
MaeIII GTNAC 1 cut(s) 484
MalI GATC 3 cut(s) 35, 252, 346
MboI GATC 3 cut(s) 33, 250, 344
MboII GAAGA 5 cut(s) 33, 43, 115, 146, 446
MfeI CAATTG 1 cut(s) 94
MflI RGATCY 1 cut(s) 33
MlsI TGGCCA 1 cut(s) 541
MluCI AATT 5 cut(s) 94, 197, 349, 378, 630
MluNI TGGCCA 1 cut(s) 541
MlyI GAGTC 2 cut(s) 145, 367
MnlI CCTC 7 cut(s) 6, 19, 130, 141, 241, 468, 496
Mox20I TGGCCA 1 cut(s) 541
MscI TGGCCA 1 cut(s) 541
MseI TTAA 2 cut(s) 435, 513
MslI CAYNNNNRTG 1 cut(s) 177
Msp20I TGGCCA 1 cut(s) 541
MspA1I CMGCKG 1 cut(s) 523
MspCI CTTAAG 1 cut(s) 512
MspI CCGG 1 cut(s) 52
MspR9I CCNGG 3 cut(s) 53, 258, 360
MunI CAATTG 1 cut(s) 94
MvaI CCWGG 2 cut(s) 258, 360
NciI CCSGG 1 cut(s) 53
NdeII GATC 3 cut(s) 33, 250, 344
NlaIII CATG 2 cut(s) 251, 302
NlaIV GGNNCC 1 cut(s) 324
NmeAIII GCCGAG 1 cut(s) 17
NspI RCATGY 1 cut(s) 302
PagI TCATGA 1 cut(s) 247
PcsI WCGNNNNNNNCGW 1 cut(s) 138
PfeI GAWTC 1 cut(s) 182
PflFI GACNNNGTC 1 cut(s) 53
PfoI TCCNGGA 1 cut(s) 358
PkrI GCNGC 4 cut(s) 519, 522, 565, 599
PleI GAGTC 2 cut(s) 145, 367
PpsI GAGTC 2 cut(s) 145, 367
PshAI GACNNNNGTC 1 cut(s) 450
PsiI TTATAA 1 cut(s) 608
Psp6I CCWGG 2 cut(s) 256, 358
PspGI CCWGG 2 cut(s) 256, 358
PspN4I GGNNCC 1 cut(s) 324
PspPI GGNCC 1 cut(s) 4
PstI CTGCAG 1 cut(s) 568
PstNI CAGNNNCTG 1 cut(s) 523
PsuI RGATCY 1 cut(s) 33
PsyI GACNNNGTC 1 cut(s) 53
PvuII CAGCTG 1 cut(s) 523
RsaI GTAC 2 cut(s) 158, 440
RsaNI GTAC 2 cut(s) 157, 439
RseI CAYNNNNRTG 1 cut(s) 177
SaqAI TTAA 2 cut(s) 435, 513
SatI GCNGC 4 cut(s) 518, 521, 564, 598
Sau3AI GATC 3 cut(s) 33, 250, 344
Sau96I GGNCC 1 cut(s) 4
ScaI AGTACT 1 cut(s) 440
SchI GAGTC 2 cut(s) 145, 367
ScrFI CCNGG 3 cut(s) 53, 258, 360
SetI ASST 6 cut(s) 64, 310, 408, 450, 525, 562
SfcI CTRYAG 1 cut(s) 564
SinI GGWCC 1 cut(s) 4
SmiMI CAYNNNNRTG 1 cut(s) 177
SmlI CTYRAG 1 cut(s) 512
SmoI CTYRAG 1 cut(s) 512
Sse9I AATT 5 cut(s) 94, 197, 349, 378, 630
StyD4I CCNGG 3 cut(s) 51, 256, 358
StyI CCWWGG 1 cut(s) 448
TaaI ACNGT 3 cut(s) 268, 464, 490
TaqI TCGA 2 cut(s) 57, 376
TasI AATT 5 cut(s) 94, 197, 349, 378, 630
TatI WGTACW 2 cut(s) 156, 438
TfiI GAWTC 1 cut(s) 182
Tru1I TTAA 2 cut(s) 435, 513
Tru9I TTAA 2 cut(s) 435, 513
TscAI CASTG 2 cut(s) 478, 573
TseI GCWGC 4 cut(s) 517, 520, 563, 597
TspDTI ATGAA 3 cut(s) 183, 236, 611
TspRI CASTG 2 cut(s) 478, 573
Tth111I GACNNNGTC 1 cut(s) 53
Vha464I CTTAAG 1 cut(s) 512
VpaK11BI GGWCC 1 cut(s) 4
XapI RAATTY 1 cut(s) 378
XceI RCATGY 1 cut(s) 302
ZrmI AGTACT 1 cut(s) 440
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.