Rh5CG504600

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5C
OG0000333
Physical Location & Seq
Forward (+)
70115873 .. 70117699
1827 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5CG504600.1

Sequence Viewer

Length: 750 bp
ATGGATTCTGATTCTGAAACCTCCCTCTCAGCGATGGTATACCCAGAACTCAAGACCACCCACAGACTCGACTTTGGCGTCAACTTTCATATCTGGAGACAAAAAATAGGCTTCGTCCTCGTCGACAACAAGGTCAACTACGTCCTCACCGAGCCAAAACCCCCGGAAAAAGACGTCGCTGGCCACCAGAAGTGGATCCACGACGACTTCATCGCCCGGCACCTCATCATGGGAACCCTAAACGACCACGTGTACATGAGCTACGAGACACACGAGACTGCCAAGTCCCTCATGGACGCTCTCACCGCCACTTACACCCAACCCTCGATGACGAAGCGGATGTACAAGCTCCGCAACTACGTGGGGCACAAGATGGCCGAGGGCAAATCCATCCATGAGCATATTATGGAGATGACCTCGATGGCTTATGATCTCCAATGCGAGGGGTTGAAGATTCCGGAGGAAGTTCAGGCTGTGATGCTGATGAATAGCGTGCCGGAGAGTTGGGACGAGATGATGACCGTGGTGAGGTTGAACATGGATTTCGATAAGTCTAAGTCGGGTGAGCCAGATTTCGGTTTGCACAAGGTGAGCAGCAGGCTCAGGGAGATCGGGGCTTTGGAAAAGTTGTATCGGAGGCAGGAGGAGGAGGAGGAGGCCAAGCAGAGGAGGCCGCATTTCAATGGCCATTGCCATACTTGTGGAGAATATGGGCATCACCGTAATCACTGCACCATCGCCATGAAATAG
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

249

Amino Acids

29.0

Weight (kDa)

6.27

Isoelectric Point (pI)

50.27

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 38 - 177 1.3e-23 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: 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)
AasI GACNNNNNNGTC 3 cut(s) 77, 131, 283
AatII GACGTC 1 cut(s) 177
AccB1I GGYRCC 1 cut(s) 219
AccI GTMKAC 2 cut(s) 39, 123
AccIII TCCGGA 1 cut(s) 457
AciI CCGC 4 cut(s) 306, 337, 352, 674
AclWI GGATC 2 cut(s) 190, 203
AcoI YGGCCR 3 cut(s) 181, 375, 685
AcvI CACGTG 1 cut(s) 250
AcyI GRCGYC 2 cut(s) 78, 174
AdeI CACNNNGTG 1 cut(s) 589
AfaI GTAC 2 cut(s) 254, 344
AfiI CCNNNNNNNGG 5 cut(s) 229, 442, 528, 575, 666
AflIII ACRYGT 1 cut(s) 249
AgsI TTSAA 3 cut(s) 451, 535, 682
AluBI AGCT 2 cut(s) 261, 349
AluI AGCT 2 cut(s) 261, 349
Alw26I GTCTC 3 cut(s) 91, 260, 269
AlwI GGATC 2 cut(s) 190, 203
Aor13HI TCCGGA 1 cut(s) 457
AoxI GGCC 5 cut(s) 181, 375, 657, 671, 685
ApeKI GCWGC 1 cut(s) 594
AsuC2I CCSGG 2 cut(s) 164, 217
AsuHPI GGTGA 6 cut(s) 139, 295, 538, 575, 601, 710
BaeGI GKGCMC 1 cut(s) 369
BalI TGGCCA 2 cut(s) 183, 687
BamHI GGATCC 1 cut(s) 195
BanI GGYRCC 1 cut(s) 219
BarI GAAGNNNNNNTAC 2 cut(s) 326, 358
BauI CACGAG 1 cut(s) 272
BbrPI CACGTG 1 cut(s) 250
BbvI GCAGC 1 cut(s) 606
BccI CCATC 5 cut(s) 28, 367, 398, 415, 743
BcnI CCSGG 2 cut(s) 164, 217
BcoDI GTCTC 3 cut(s) 91, 260, 269
BisI GCNGC 2 cut(s) 595, 674
BlsI GCNGC 2 cut(s) 596, 675
Bme1390I CCNGG 2 cut(s) 164, 217
BmiI GGNNCC 3 cut(s) 197, 221, 235
BmrFI CCNGG 2 cut(s) 164, 217
BmsI GCATC 2 cut(s) 468, 724
BplI GAGNNNNNCTC 2 cut(s) 401, 433
BpmI CTGGAG 1 cut(s) 115
Bpu10I CCTNAGC 1 cut(s) 602
BpuEI CTTGAG 1 cut(s) 35
BpuMI CCSGG 2 cut(s) 164, 217
BsaAI YACGTR 2 cut(s) 250, 361
BsaHI GRCGYC 2 cut(s) 78, 174
BsaJI CCNNGG 3 cut(s) 162, 378, 522
BsaWI WCCGGW 1 cut(s) 457
Bsc4I CCNNNNNNNGG 5 cut(s) 229, 442, 528, 575, 666
Bse3DI GCAATG 1 cut(s) 688
BseAI TCCGGA 1 cut(s) 457
BseDI CCNNGG 3 cut(s) 162, 378, 522
BseGI GGATG 2 cut(s) 345, 390
BseLI CCNNNNNNNGG 5 cut(s) 229, 442, 528, 575, 666
BseMI GCAATG 1 cut(s) 688
BseMII CTCAG 2 cut(s) 42, 616
BseRI GAGGAG 5 cut(s) 659, 662, 665, 668, 682
BseSI GKGCMC 1 cut(s) 369
BseXI GCAGC 1 cut(s) 606
BsgI GTGCAG 1 cut(s) 715
BshFI GGCC 5 cut(s) 183, 377, 659, 673, 687
BshNI GGYRCC 1 cut(s) 219
BsiSI CCGG 4 cut(s) 164, 217, 458, 497
BslFI GGGAC 2 cut(s) 271, 521
BslI CCNNNNNNNGG 5 cut(s) 229, 442, 528, 575, 666
BsmAI GTCTC 3 cut(s) 91, 260, 269
BsmFI GGGAC 2 cut(s) 271, 521
BsnI GGCC 5 cut(s) 183, 377, 659, 673, 687
Bsp1286I GDGCHC 1 cut(s) 369
Bsp13I TCCGGA 1 cut(s) 457
Bsp1407I TGTACA 2 cut(s) 252, 342
Bsp143I GATC 3 cut(s) 195, 430, 609
BspACI CCGC 4 cut(s) 306, 337, 352, 674
BspANI GGCC 5 cut(s) 183, 377, 659, 673, 687
BspCNI CTCAG 2 cut(s) 41, 615
BspEI TCCGGA 1 cut(s) 457
BspLI GGNNCC 3 cut(s) 197, 221, 235
BspPI GGATC 2 cut(s) 190, 203
BspT107I GGYRCC 1 cut(s) 219
BsrDI GCAATG 1 cut(s) 688
BsrGI TGTACA 2 cut(s) 252, 342
BssECI CCNNGG 3 cut(s) 162, 378, 522
BssMI GATC 3 cut(s) 195, 430, 609
BssNAI GTATAC 1 cut(s) 40
BssNI GRCGYC 2 cut(s) 78, 174
BssSI CACGAG 1 cut(s) 272
Bst1107I GTATAC 1 cut(s) 40
Bst2BI CACGAG 1 cut(s) 272
Bst4CI ACNGT 2 cut(s) 523, 722
BstACI GRCGYC 2 cut(s) 78, 174
BstAUI TGTACA 2 cut(s) 252, 342
BstBAI YACGTR 2 cut(s) 250, 361
BstC8I GCNNGC 3 cut(s) 181, 494, 599
BstDEI CTNAG 3 cut(s) 28, 555, 602
BstDSI CCRYGG 1 cut(s) 522
BstF5I GGATG 2 cut(s) 345, 390
BstKTI GATC 3 cut(s) 198, 433, 612
BstMAI GTCTC 3 cut(s) 91, 260, 269
BstMBI GATC 3 cut(s) 195, 430, 609
BstMWI GCNNNNNNNGC 2 cut(s) 305, 670
BstSCI CCNGG 2 cut(s) 162, 215
BstSLI GKGCMC 1 cut(s) 369
BstV1I GCAGC 1 cut(s) 606
BstX2I RGATCY 1 cut(s) 195
BstXI CCANNNNNNTGG 1 cut(s) 701
BstYI RGATCY 1 cut(s) 195
BstZ17I GTATAC 1 cut(s) 40
BsuRI GGCC 5 cut(s) 183, 377, 659, 673, 687
BtgI CCRYGG 1 cut(s) 522
BtgZI GCGATG 3 cut(s) 47, 196, 721
BtsCI GGATG 2 cut(s) 345, 390
BtsI GCAGTG 1 cut(s) 727
BtsIMutI CAGTG 1 cut(s) 727
Cac8I GCNNGC 3 cut(s) 181, 494, 599
CseI GACGC 2 cut(s) 67, 305
Csp6I GTAC 2 cut(s) 253, 343
CviAII CATG 6 cut(s) 229, 256, 292, 395, 538, 742
CviQI GTAC 2 cut(s) 253, 343
DdeI CTNAG 3 cut(s) 28, 555, 602
DpnI GATC 3 cut(s) 197, 432, 611
DpnII GATC 3 cut(s) 195, 430, 609
DraIII CACNNNGTG 1 cut(s) 589
DrdI GACNNNNNNGTC 3 cut(s) 77, 131, 283
DseDI GACNNNNNNGTC 3 cut(s) 77, 131, 283
EaeI YGGCCR 3 cut(s) 181, 375, 685
Eco72I CACGTG 1 cut(s) 250
FaeI CATG 6 cut(s) 232, 259, 295, 398, 541, 745
FaqI GGGAC 2 cut(s) 271, 521
FatI CATG 6 cut(s) 228, 255, 291, 394, 537, 741
FblI GTMKAC 2 cut(s) 39, 123
Fnu4HI GCNGC 2 cut(s) 595, 674
FokI GGATG 2 cut(s) 352, 377
Fsp4HI GCNGC 2 cut(s) 595, 674
GluI GCNGC 2 cut(s) 595, 674
GsuI CTGGAG 1 cut(s) 115
HaeIII GGCC 5 cut(s) 183, 377, 659, 673, 687
HapII CCGG 4 cut(s) 164, 217, 458, 497
HgaI GACGC 2 cut(s) 67, 305
Hin1I GRCGYC 2 cut(s) 78, 174
Hin1II CATG 6 cut(s) 232, 259, 295, 398, 541, 745
HincII GTYRAC 3 cut(s) 82, 124, 136
HindII GTYRAC 3 cut(s) 82, 124, 136
HinfI GANTC 4 cut(s) 5, 11, 66, 454
HpaII CCGG 4 cut(s) 164, 217, 458, 497
HphI GGTGA 6 cut(s) 139, 295, 538, 575, 601, 710
Hpy166II GTNNAC 5 cut(s) 40, 82, 124, 136, 253
Hpy188I TCNGA 3 cut(s) 10, 16, 636
Hpy188III TCNNGA 3 cut(s) 52, 94, 458
Hpy8I GTNNAC 5 cut(s) 40, 82, 124, 136, 253
Hpy99I CGWCG 3 cut(s) 125, 179, 206
HpyCH4III ACNGT 2 cut(s) 523, 722
HpyCH4IV ACGT 4 cut(s) 141, 174, 249, 360
HpyCH4V TGCA 2 cut(s) 583, 732
HpyF10VI GCNNNNNNNGC 2 cut(s) 305, 670
HpyF3I CTNAG 3 cut(s) 28, 555, 602
HpySE526I ACGT 4 cut(s) 141, 174, 249, 360
Hsp92I GRCGYC 2 cut(s) 78, 174
Hsp92II CATG 6 cut(s) 232, 259, 295, 398, 541, 745
Kpn2I TCCGGA 1 cut(s) 457
Kzo9I GATC 3 cut(s) 195, 430, 609
LmnI GCTCC 1 cut(s) 354
Lsp1109I GCAGC 1 cut(s) 606
LweI GCATC 2 cut(s) 468, 724
MaeII ACGT 4 cut(s) 141, 174, 249, 360
MalI GATC 3 cut(s) 197, 432, 611
MboI GATC 3 cut(s) 195, 430, 609
MboII GAAGA 1 cut(s) 463
MflI RGATCY 1 cut(s) 195
MhlI GDGCHC 1 cut(s) 369
MlsI TGGCCA 2 cut(s) 183, 687
MluNI TGGCCA 2 cut(s) 183, 687
MlyI GAGTC 1 cut(s) 60
Mox20I TGGCCA 2 cut(s) 183, 687
MroI TCCGGA 1 cut(s) 457
MscI TGGCCA 2 cut(s) 183, 687
MslI CAYNNNNRTG 3 cut(s) 681, 699, 740
Msp20I TGGCCA 2 cut(s) 183, 687
MspI CCGG 4 cut(s) 164, 217, 458, 497
MspR9I CCNGG 2 cut(s) 164, 217
MwoI GCNNNNNNNGC 2 cut(s) 305, 670
NciI CCSGG 2 cut(s) 164, 217
NdeII GATC 3 cut(s) 195, 430, 609
NlaIII CATG 6 cut(s) 232, 259, 295, 398, 541, 745
NlaIV GGNNCC 3 cut(s) 197, 221, 235
NmeAIII GCCGAG 1 cut(s) 403
PcsI WCGNNNNNNNCGW 4 cut(s) 75, 120, 147, 270
PfeI GAWTC 3 cut(s) 5, 11, 454
PkrI GCNGC 2 cut(s) 596, 675
PleI GAGTC 1 cut(s) 60
PmaCI CACGTG 1 cut(s) 250
PmlI CACGTG 1 cut(s) 250
PpsI GAGTC 1 cut(s) 60
Ppu21I YACGTR 2 cut(s) 250, 361
PspCI CACGTG 1 cut(s) 250
PspN4I GGNNCC 3 cut(s) 197, 221, 235
PsuI RGATCY 1 cut(s) 195
RsaI GTAC 2 cut(s) 254, 344
RsaNI GTAC 2 cut(s) 253, 343
RseI CAYNNNNRTG 3 cut(s) 681, 699, 740
SalI GTCGAC 1 cut(s) 122
SatI GCNGC 2 cut(s) 595, 674
Sau3AI GATC 3 cut(s) 195, 430, 609
SchI GAGTC 1 cut(s) 60
ScrFI CCNGG 2 cut(s) 164, 217
SduI GDGCHC 1 cut(s) 369
SfaNI GCATC 2 cut(s) 468, 724
SmiMI CAYNNNNRTG 3 cut(s) 681, 699, 740
SmlI CTYRAG 1 cut(s) 50
SmoI CTYRAG 1 cut(s) 50
SsiI CCGC 4 cut(s) 306, 337, 352, 674
StyD4I CCNGG 2 cut(s) 162, 215
TaaI ACNGT 2 cut(s) 523, 722
TaiI ACGT 4 cut(s) 144, 177, 252, 363
TaqI TCGA 5 cut(s) 69, 123, 326, 419, 546
TatI WGTACW 2 cut(s) 252, 342
TauI GCSGC 1 cut(s) 676
TfiI GAWTC 3 cut(s) 5, 11, 454
TscAI CASTG 1 cut(s) 734
TseI GCWGC 1 cut(s) 594
TspDTI ATGAA 3 cut(s) 77, 199, 500
TspRI CASTG 1 cut(s) 734
XcmI CCANNNNNNNNNTGG 1 cut(s) 289
XmiI GTMKAC 2 cut(s) 39, 123
ZraI GACGTC 1 cut(s) 175
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.