Rh5DG492300

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5D
OG0000333
Physical Location & Seq
Forward (+)
77370721 .. 77373412
2692 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5DG492300.1

Sequence Viewer

Length: 456 bp
ATGGACGCTCTCACCGCCACTTACACCCAACCCTCGATGACGAAGCGGATGTACAAGCTCCGCAACTACGTGGGGCACAAGATGGCCGAGGGCAAATCCGTCCATGAGCATATTATGGAGATGGGCTCGATGGCTTATGATATCCAATGCGAGGGGTTGAAGATTCCGGAGGAAGTTCAGGCTGTGATGCTGATGAATAGCGTGCCGGAGAGTTGGGACGAGATGATGACCGTGGTGAGGTTGAACATGGATTTCGATAAGTCTAAGTCGGGTGAGCCAGATTTCGGTTTGCACAAGGTGAGCAGCAGGCTCAGGGAGATCGGGGCTTTGAAAAAGTTGTATCGGAGGCAGGAGGAGGAGGAGGCCAAGCAGAGGAGGCCGCATTTCAATGGCCATTGCCATACTTGTGGAGAATATGGGCATCACCGTAATCACTGCACCATTGCCATGAAATAG
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

151

Amino Acids

17.55

Weight (kDa)

7.76

Isoelectric Point (pI)

53.7

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 2 - 80 1.2e-13 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)
AccIII TCCGGA 1 cut(s) 166
AciI CCGC 4 cut(s) 15, 46, 61, 380
AcoI YGGCCR 2 cut(s) 84, 391
AdeI CACNNNGTG 1 cut(s) 298
AfaI GTAC 1 cut(s) 53
AfiI CCNNNNNNNGG 4 cut(s) 151, 237, 284, 372
AgsI TTSAA 4 cut(s) 160, 244, 331, 388
AluBI AGCT 1 cut(s) 58
AluI AGCT 1 cut(s) 58
Aor13HI TCCGGA 1 cut(s) 166
AoxI GGCC 4 cut(s) 84, 363, 377, 391
ApeKI GCWGC 1 cut(s) 303
AsuHPI GGTGA 5 cut(s) 4, 247, 284, 310, 416
BaeGI GKGCMC 1 cut(s) 78
BalI TGGCCA 1 cut(s) 393
BanII GRGCYC 1 cut(s) 128
BarI GAAGNNNNNNTAC 2 cut(s) 35, 67
BbvI GCAGC 1 cut(s) 315
BccI CCATC 3 cut(s) 76, 115, 124
BisI GCNGC 2 cut(s) 304, 380
BlsI GCNGC 2 cut(s) 305, 381
BmsI GCATC 2 cut(s) 177, 430
BplI GAGNNNNNCTC 2 cut(s) 110, 142
Bpu10I CCTNAGC 1 cut(s) 311
BsaAI YACGTR 1 cut(s) 70
BsaJI CCNNGG 2 cut(s) 87, 231
BsaWI WCCGGW 1 cut(s) 166
Bsc4I CCNNNNNNNGG 4 cut(s) 151, 237, 284, 372
Bse3DI GCAATG 2 cut(s) 394, 441
BseAI TCCGGA 1 cut(s) 166
BseDI CCNNGG 2 cut(s) 87, 231
BseGI GGATG 1 cut(s) 54
BseLI CCNNNNNNNGG 4 cut(s) 151, 237, 284, 372
BseMI GCAATG 2 cut(s) 394, 441
BseMII CTCAG 1 cut(s) 325
BseRI GAGGAG 4 cut(s) 368, 371, 374, 388
BseSI GKGCMC 1 cut(s) 78
BseXI GCAGC 1 cut(s) 315
BsgI GTGCAG 1 cut(s) 421
BshFI GGCC 4 cut(s) 86, 365, 379, 393
BsiSI CCGG 2 cut(s) 167, 206
BslFI GGGAC 1 cut(s) 230
BslI CCNNNNNNNGG 4 cut(s) 151, 237, 284, 372
BsmFI GGGAC 1 cut(s) 230
BsnI GGCC 4 cut(s) 86, 365, 379, 393
Bsp1286I GDGCHC 2 cut(s) 78, 128
Bsp13I TCCGGA 1 cut(s) 166
Bsp1407I TGTACA 1 cut(s) 51
Bsp143I GATC 1 cut(s) 318
BspACI CCGC 4 cut(s) 15, 46, 61, 380
BspANI GGCC 4 cut(s) 86, 365, 379, 393
BspCNI CTCAG 1 cut(s) 324
BspEI TCCGGA 1 cut(s) 166
BsrDI GCAATG 2 cut(s) 394, 441
BsrGI TGTACA 1 cut(s) 51
BssECI CCNNGG 2 cut(s) 87, 231
BssMI GATC 1 cut(s) 318
Bst4CI ACNGT 2 cut(s) 232, 428
BstAUI TGTACA 1 cut(s) 51
BstBAI YACGTR 1 cut(s) 70
BstC8I GCNNGC 2 cut(s) 203, 308
BstDEI CTNAG 2 cut(s) 264, 311
BstDSI CCRYGG 1 cut(s) 231
BstF5I GGATG 1 cut(s) 54
BstKTI GATC 1 cut(s) 321
BstMBI GATC 1 cut(s) 318
BstMWI GCNNNNNNNGC 2 cut(s) 14, 376
BstSLI GKGCMC 1 cut(s) 78
BstV1I GCAGC 1 cut(s) 315
BstXI CCANNNNNNTGG 1 cut(s) 407
BsuRI GGCC 4 cut(s) 86, 365, 379, 393
BtgI CCRYGG 1 cut(s) 231
BtsCI GGATG 1 cut(s) 54
BtsI GCAGTG 1 cut(s) 433
BtsIMutI CAGTG 1 cut(s) 433
Cac8I GCNNGC 2 cut(s) 203, 308
CseI GACGC 1 cut(s) 14
Csp6I GTAC 1 cut(s) 52
CviAII CATG 3 cut(s) 104, 247, 448
CviQI GTAC 1 cut(s) 52
DdeI CTNAG 2 cut(s) 264, 311
DpnI GATC 1 cut(s) 320
DpnII GATC 1 cut(s) 318
DraIII CACNNNGTG 1 cut(s) 298
EaeI YGGCCR 2 cut(s) 84, 391
Eco24I GRGCYC 1 cut(s) 128
Eco32I GATATC 1 cut(s) 142
EcoRV GATATC 1 cut(s) 142
EcoT38I GRGCYC 1 cut(s) 128
FaeI CATG 3 cut(s) 107, 250, 451
FaiI YATR 8 cut(s) 105, 111, 116, 138, 248, 402, 417, 449
FaqI GGGAC 1 cut(s) 230
FatI CATG 3 cut(s) 103, 246, 447
Fnu4HI GCNGC 2 cut(s) 304, 380
FokI GGATG 1 cut(s) 61
FriOI GRGCYC 1 cut(s) 128
Fsp4HI GCNGC 2 cut(s) 304, 380
GluI GCNGC 2 cut(s) 304, 380
HaeIII GGCC 4 cut(s) 86, 365, 379, 393
HapII CCGG 2 cut(s) 167, 206
HgaI GACGC 1 cut(s) 14
Hin1II CATG 3 cut(s) 107, 250, 451
HinfI GANTC 1 cut(s) 163
HpaII CCGG 2 cut(s) 167, 206
HphI GGTGA 5 cut(s) 4, 247, 284, 310, 416
Hpy188I TCNGA 1 cut(s) 345
Hpy188III TCNNGA 1 cut(s) 167
HpyCH4III ACNGT 2 cut(s) 232, 428
HpyCH4IV ACGT 1 cut(s) 69
HpyCH4V TGCA 2 cut(s) 292, 438
HpyF10VI GCNNNNNNNGC 2 cut(s) 14, 376
HpyF3I CTNAG 2 cut(s) 264, 311
HpySE526I ACGT 1 cut(s) 69
Hsp92II CATG 3 cut(s) 107, 250, 451
Kpn2I TCCGGA 1 cut(s) 166
Kzo9I GATC 1 cut(s) 318
LmnI GCTCC 1 cut(s) 63
LpnPI CCDG 7 cut(s) 164, 180, 219, 291, 292, 298, 335
Lsp1109I GCAGC 1 cut(s) 315
LweI GCATC 2 cut(s) 177, 430
MaeII ACGT 1 cut(s) 69
MalI GATC 1 cut(s) 320
MboI GATC 1 cut(s) 318
MboII GAAGA 1 cut(s) 172
MhlI GDGCHC 2 cut(s) 78, 128
MlsI TGGCCA 1 cut(s) 393
MluNI TGGCCA 1 cut(s) 393
Mox20I TGGCCA 1 cut(s) 393
MroI TCCGGA 1 cut(s) 166
MscI TGGCCA 1 cut(s) 393
MslI CAYNNNNRTG 3 cut(s) 387, 405, 446
Msp20I TGGCCA 1 cut(s) 393
MspI CCGG 2 cut(s) 167, 206
MwoI GCNNNNNNNGC 2 cut(s) 14, 376
NdeII GATC 1 cut(s) 318
NlaIII CATG 3 cut(s) 107, 250, 451
NmeAIII GCCGAG 1 cut(s) 112
PfeI GAWTC 1 cut(s) 163
PkrI GCNGC 2 cut(s) 305, 381
Ppu21I YACGTR 1 cut(s) 70
RsaI GTAC 1 cut(s) 53
RsaNI GTAC 1 cut(s) 52
RseI CAYNNNNRTG 3 cut(s) 387, 405, 446
SatI GCNGC 2 cut(s) 304, 380
Sau3AI GATC 1 cut(s) 318
SduI GDGCHC 2 cut(s) 78, 128
SetI ASST 4 cut(s) 60, 72, 242, 300
SfaNI GCATC 2 cut(s) 177, 430
SmiMI CAYNNNNRTG 3 cut(s) 387, 405, 446
SsiI CCGC 4 cut(s) 15, 46, 61, 380
TaaI ACNGT 2 cut(s) 232, 428
TaiI ACGT 1 cut(s) 72
TaqI TCGA 3 cut(s) 35, 128, 255
TatI WGTACW 1 cut(s) 51
TauI GCSGC 1 cut(s) 382
TfiI GAWTC 1 cut(s) 163
TscAI CASTG 1 cut(s) 440
TseI GCWGC 1 cut(s) 303
TspDTI ATGAA 1 cut(s) 209
TspGWI ACGGA 1 cut(s) 88
TspRI CASTG 1 cut(s) 440
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.