RchiOBHm_Chr5g0015171

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
5
OG0000118
Physical Location & Seq
Reverse (-)
10476483 .. 10478859
2377 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ29560

Sequence Viewer

Length: 945 bp
ATGCGAGGAGGGGGATCTATAAGGTGCTATAGATGTCAAGGTTATGGTCACTATGCTGGTCAATGCCCAACTAAAGAGCAAACTCGAAGTTTGTTTGCAGCAAGCACAGAAGAAGAGGCTGATGCTCAAGGAGAATTGGAGGAAGAATTTTATGAGCCTGAAATTCCAGCTACTGATGATGATTTGGAGGGTGAACCTATAGACATTGTTCAACCAAGAATGGCTGTGGTTAGATGCACTTTGACTCAACCTAAGAGTACTGAATATTGGTGGAGAACAAACATTTTTCACACTTATGTCAAGTGTGGAGACAAAAGTTATAAGGTCATCATTGACAACGGAAGCTGCATCAATGTTGTCTCCCCTCAAACTATCTCTAAACTGGGTTTGACCGCTGCTGATCATCCTCAACCCTATCGTGTGGCATGGATTGACAAGTCTTCCATTCCCGTGACACAGCGATGTCAAGTTCCCATTCAGTTTTCATCTTACAAGGATACTGTTTGGTGTGATGTGGTACCGATGGACGTGGGACACATTCTTTTGGGCAGACCATGGTTGTATGATCTGAATGTAACCATTTCGGGCCGTGCCAACTCATGCTCCTTTATTCATGAAGGAAAGCACATCAAGTTGAACCCAATCCAGCCCAGACCAATACCTCAACCAACACATAGCAAGGGAGGACAACAACCAAAATCCCTTAATATCATCAGTCCAAGACACTTTGCAAGGGAGACAACAGGTGATTCTGTTATTTTTATATTGATTGCAAAGGAATCTCACCCTTTGACTAGTTTGGAGTTGCCCTCGGATGTGAAATCAATCCTTGAACAGTTTACTGATGTATTTGCTGAGGACCTTCCAAATGAACTTCCTCCTCTCCGGGATATTCAACATGCGAATTTACCACAGTATCGGATGAATCCAACCGAGCAACATTAA
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
Chromo RVT_1 Retrotrans_gag rve zf-H2C2

Protein Analysis

314

Amino Acids

35.41

Weight (kDa)

5.67

Isoelectric Point (pI)

47.06

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this protein.
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: OG0000118)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g01361 FvH4_1g07161 FvH4_1g07431 FvH4_1g07821 FvH4_1g08223 FvH4_1g10041 FvH4_1g12132 FvH4_1g15053 FvH4_1g18161 FvH4_1g18400 FvH4_1g18931 FvH4_1g19242 FvH4_1g19461 FvH4_1g20550 FvH4_1g21381 FvH4_1g21542 FvH4_1g22102 FvH4_1g23991 FvH4_1g24542 FvH4_1g24951 FvH4_1g24960 FvH4_1g25272 FvH4_1g25552 FvH4_1g25771 FvH4_1g28771 FvH4_1g29201 FvH4_1g29611 FvH4_2g01181 FvH4_2g02491 FvH4_2g04621 FvH4_2g04631 FvH4_2g07460 FvH4_2g08540 FvH4_2g08550 FvH4_2g09292 FvH4_2g10501 FvH4_2g12101 FvH4_2g12220 FvH4_2g12551 FvH4_2g14071 FvH4_2g14241 FvH4_2g15041 FvH4_2g15311 FvH4_2g18971 FvH4_2g19220 FvH4_2g19260 FvH4_2g19611 FvH4_2g19652 FvH4_2g20211 FvH4_2g20231 FvH4_2g21541 FvH4_2g22380 FvH4_2g27712 FvH4_2g28171 FvH4_2g29879 FvH4_2g32391 FvH4_3g02171 FvH4_3g05531 FvH4_3g09750 FvH4_3g10310 FvH4_3g10460 FvH4_3g13172 FvH4_3g15232 FvH4_3g18481 FvH4_3g18621 FvH4_3g20504 FvH4_3g20812 FvH4_3g22320 FvH4_3g22930 FvH4_3g22940 FvH4_3g23752 FvH4_3g24791 FvH4_3g26411 FvH4_3g26432 FvH4_3g27201 FvH4_3g27862 FvH4_3g28871 FvH4_3g28954 FvH4_3g29131 FvH4_3g29832 FvH4_3g29922 FvH4_3g30190 FvH4_3g32231 FvH4_3g32250 FvH4_3g33460 FvH4_3g34670 FvH4_3g36982 FvH4_3g37001 FvH4_3g38252 FvH4_3g38772 FvH4_3g40141 FvH4_3g40181 FvH4_3g42521 FvH4_4g00090 FvH4_4g00290 FvH4_4g00301 FvH4_4g00530 FvH4_4g00823 FvH4_4g02300 FvH4_4g02450 FvH4_4g03360 FvH4_4g04481 FvH4_4g04761 FvH4_4g06301 FvH4_4g06630 FvH4_4g08312 FvH4_4g08552 FvH4_4g10053 FvH4_4g11971 FvH4_4g13211 FvH4_4g13511 FvH4_4g15351 FvH4_4g16360 FvH4_4g16601 FvH4_4g18462 FvH4_4g22911 FvH4_4g23221 FvH4_4g24301 FvH4_4g24721 FvH4_4g27905 FvH4_4g28971 FvH4_4g29540 FvH4_4g30720 FvH4_4g31521 FvH4_4g33371 FvH4_4g34111 FvH4_4g35740 FvH4_5g00131 FvH4_5g02530 FvH4_5g02550 FvH4_5g02560 FvH4_5g02580 FvH4_5g03783 FvH4_5g05681 FvH4_5g05681 FvH4_5g09371 FvH4_5g09381 FvH4_5g14611 FvH4_5g15341 FvH4_5g19801 FvH4_5g20110 FvH4_5g20911 FvH4_5g22230 FvH4_5g25751 FvH4_5g26070 FvH4_5g26471 FvH4_5g27072 FvH4_5g27471 FvH4_5g27471 FvH4_5g27998 FvH4_5g28291 FvH4_5g30951 FvH4_5g31082 FvH4_5g31890 FvH4_5g32251 FvH4_5g34112 FvH4_5g37184 FvH4_5g37993 FvH4_5g38271 FvH4_6g00153 FvH4_6g00640 FvH4_6g05921 FvH4_6g08591 FvH4_6g09511 FvH4_6g10331 FvH4_6g10401 FvH4_6g14161 FvH4_6g14171 FvH4_6g18481 FvH4_6g19721 FvH4_6g19980 FvH4_6g20104 FvH4_6g20112 FvH4_6g21261 FvH4_6g21651 FvH4_6g22051 FvH4_6g23141 FvH4_6g24822 FvH4_6g25082 FvH4_6g25391 FvH4_6g25560 FvH4_6g26350 FvH4_6g27031 FvH4_6g27810 FvH4_6g27971 FvH4_6g28331 FvH4_6g29391 FvH4_6g30781 FvH4_6g32221 FvH4_6g34680 FvH4_6g36181 FvH4_6g36551 FvH4_6g37491 FvH4_6g37663 FvH4_6g39590 FvH4_6g40582 FvH4_6g43843 FvH4_6g50551 FvH4_7g00240 FvH4_7g00731 FvH4_7g01031 FvH4_7g03301 FvH4_7g08180 FvH4_7g08180 FvH4_7g10631 FvH4_7g19710 FvH4_7g23892 FvH4_7g25280 FvH4_7g25551 FvH4_7g30121 FvH4_7g31931 FvH4_7g32672 FvH4_c21g00040 FvH4_c2g00053
prunus_persica Prupe.1G448800_v2.0.a1
rosa_chinensis RchiOBHm_Chr1g0322451 RchiOBHm_Chr5g0015171
rosa_laevigata RLG00000003077 RLG00000018186 RLG00000030343
rosa_multiflora Rmu_co8096726.1_g000001
rosa_roxburghii Rroxscaffold_157G00438380 Rroxscaffold_1G00001730 Rroxscaffold_3G00236310
rosa_rugosa Rorug02G0236500
rosa_samantha Rh4BG247300 Rh6BG286200 Rh6CG287300 Rh7DG257500

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 321
Acc65I GGTACC 1 cut(s) 517
AccB1I GGYRCC 1 cut(s) 517
AciI CCGC 1 cut(s) 393
AclWI GGATC 1 cut(s) 22
AcsI RAATTY 3 cut(s) 146, 162, 904
AfaI GTAC 2 cut(s) 259, 519
AgsI TTSAA 4 cut(s) 212, 637, 833, 896
AhlI ACTAGT 1 cut(s) 794
AjiI CACGTC 1 cut(s) 529
AluBI AGCT 2 cut(s) 170, 345
AluI AGCT 2 cut(s) 170, 345
Alw26I GTCTC 3 cut(s) 303, 364, 731
AlwI GGATC 1 cut(s) 22
AlwNI CAGNNNCTG 1 cut(s) 173
AoxI GGCC 1 cut(s) 586
ApeKI GCWGC 3 cut(s) 98, 345, 395
ApoI RAATTY 3 cut(s) 146, 162, 904
Asp718I GGTACC 1 cut(s) 517
AspS9I GGNCC 2 cut(s) 586, 859
AsuC2I CCSGG 1 cut(s) 887
AsuHPI GGTGA 3 cut(s) 203, 758, 776
AvaII GGWCC 1 cut(s) 859
BaeI ACNNNNGTAYC 2 cut(s) 899, 932
BanI GGYRCC 1 cut(s) 517
BbsI GAAGAC 1 cut(s) 432
BbvCI CCTCAGC 1 cut(s) 855
BbvI GCAGC 3 cut(s) 110, 332, 382
BccI CCATC 1 cut(s) 517
BceAI ACGGC 1 cut(s) 573
BciVI GTATCC 1 cut(s) 490
BclI TGATCA 1 cut(s) 400
BcnI CCSGG 1 cut(s) 887
BcoDI GTCTC 3 cut(s) 303, 364, 731
BcuI ACTAGT 1 cut(s) 794
BfaI CTAG 1 cut(s) 795
BfmI CTRYAG 2 cut(s) 28, 198
BfuI GTATCC 1 cut(s) 490
BisI GCNGC 3 cut(s) 99, 346, 396
BlsI GCNGC 3 cut(s) 100, 347, 397
BmcAI AGTACT 1 cut(s) 259
Bme1390I CCNGG 1 cut(s) 887
Bme18I GGWCC 1 cut(s) 859
BmgBI CACGTC 1 cut(s) 529
BmgT120I GGNCC 2 cut(s) 586, 859
BmiI GGNNCC 1 cut(s) 519
BmrFI CCNGG 1 cut(s) 887
BmrI ACTGGG 1 cut(s) 392
BmsI GCATC 3 cut(s) 112, 224, 357
BmuI ACTGGG 1 cut(s) 392
BpiI GAAGAC 1 cut(s) 432
BplI GAGNNNNNCTC 2 cut(s) 794, 826
Bpu10I CCTNAGC 1 cut(s) 855
BpuEI CTTGAG 1 cut(s) 111
BpuMI CCSGG 1 cut(s) 887
BsaJI CCNNGG 2 cut(s) 554, 810
BsaXI ACNNNNNCTCC 2 cut(s) 587, 617
Bse1I ACTGG 1 cut(s) 387
BseDI CCNNGG 2 cut(s) 554, 810
BseGI GGATG 3 cut(s) 403, 820, 927
BseMII CTCAG 1 cut(s) 846
BseNI ACTGG 1 cut(s) 387
BseRI GAGGAG 2 cut(s) 21, 870
BseXI GCAGC 3 cut(s) 110, 332, 382
BshFI GGCC 1 cut(s) 588
BshNI GGYRCC 1 cut(s) 517
BsiSI CCGG 1 cut(s) 886
BslFI GGGAC 1 cut(s) 546
BsmAI GTCTC 3 cut(s) 303, 364, 731
BsmFI GGGAC 1 cut(s) 546
BsnI GGCC 1 cut(s) 588
Bsp143I GATC 3 cut(s) 14, 400, 565
Bsp19I CCATGG 1 cut(s) 554
BspACI CCGC 1 cut(s) 393
BspANI GGCC 1 cut(s) 588
BspCNI CTCAG 1 cut(s) 847
BspHI TCATGA 1 cut(s) 613
BspLI GGNNCC 1 cut(s) 519
BspPI GGATC 1 cut(s) 22
BspT107I GGYRCC 1 cut(s) 517
BsrI ACTGG 1 cut(s) 387
BssECI CCNNGG 2 cut(s) 554, 810
BssMI GATC 3 cut(s) 14, 400, 565
BssT1I CCWWGG 1 cut(s) 554
Bst4CI ACNGT 3 cut(s) 502, 837, 915
Bst6I CTCTTC 1 cut(s) 108
BstC8I GCNNGC 1 cut(s) 103
BstDEI CTNAG 2 cut(s) 252, 855
BstDSI CCRYGG 1 cut(s) 554
BstF5I GGATG 3 cut(s) 403, 820, 927
BstKTI GATC 3 cut(s) 17, 403, 568
BstMAI GTCTC 3 cut(s) 303, 364, 731
BstMBI GATC 3 cut(s) 14, 400, 565
BstNSI RCATGY 1 cut(s) 902
BstSCI CCNGG 1 cut(s) 885
BstSFI CTRYAG 2 cut(s) 28, 198
BstV1I GCAGC 3 cut(s) 110, 332, 382
BstV2I GAAGAC 1 cut(s) 432
BstX2I RGATCY 1 cut(s) 14
BstYI RGATCY 1 cut(s) 14
BsuI GTATCC 1 cut(s) 490
BsuRI GGCC 1 cut(s) 588
BtgI CCRYGG 1 cut(s) 554
BtgZI GCGATG 1 cut(s) 475
BtrI CACGTC 1 cut(s) 529
BtsCI GGATG 3 cut(s) 403, 820, 927
Cac8I GCNNGC 1 cut(s) 103
CaiI CAGNNNCTG 1 cut(s) 173
CciI TCATGA 1 cut(s) 613
Cfr13I GGNCC 2 cut(s) 586, 859
Csp6I GTAC 2 cut(s) 258, 518
CviAII CATG 5 cut(s) 426, 555, 600, 614, 899
CviJI RGCY 7 cut(s) 119, 157, 170, 224, 345, 588, 649
CviKI_1 RGCY 7 cut(s) 119, 157, 170, 224, 345, 588, 649
CviQI GTAC 2 cut(s) 258, 518
DdeI CTNAG 2 cut(s) 252, 855
DpnI GATC 3 cut(s) 16, 402, 567
DpnII GATC 3 cut(s) 14, 400, 565
Eam1104I CTCTTC 1 cut(s) 108
EarI CTCTTC 1 cut(s) 108
Eco130I CCWWGG 1 cut(s) 554
Eco47I GGWCC 1 cut(s) 859
EcoO109I RGGNCCY 1 cut(s) 859
EcoT14I CCWWGG 1 cut(s) 554
ErhI CCWWGG 1 cut(s) 554
FaeI CATG 5 cut(s) 429, 558, 603, 617, 902
FaqI GGGAC 1 cut(s) 546
FatI CATG 5 cut(s) 425, 554, 599, 613, 898
FbaI TGATCA 1 cut(s) 400
Fnu4HI GCNGC 3 cut(s) 99, 346, 396
FokI GGATG 3 cut(s) 390, 827, 934
Fsp4HI GCNGC 3 cut(s) 99, 346, 396
FspBI CTAG 1 cut(s) 795
GluI GCNGC 3 cut(s) 99, 346, 396
HaeIII GGCC 1 cut(s) 588
HapII CCGG 1 cut(s) 886
Hin1II CATG 5 cut(s) 429, 558, 603, 617, 902
HinfI GANTC 4 cut(s) 244, 749, 779, 925
HpaII CCGG 1 cut(s) 886
HphI GGTGA 3 cut(s) 203, 758, 776
Hpy166II GTNNAC 2 cut(s) 194, 840
Hpy188I TCNGA 3 cut(s) 570, 814, 921
Hpy188III TCNNGA 1 cut(s) 614
Hpy8I GTNNAC 2 cut(s) 194, 840
HpyAV CCTTC 2 cut(s) 611, 872
HpyCH4III ACNGT 3 cut(s) 502, 837, 915
HpyCH4IV ACGT 1 cut(s) 528
HpyCH4V TGCA 5 cut(s) 98, 237, 348, 731, 773
HpyF3I CTNAG 2 cut(s) 252, 855
HpySE526I ACGT 1 cut(s) 528
Hsp92II CATG 5 cut(s) 429, 558, 603, 617, 902
KpnI GGTACC 1 cut(s) 521
Ksp22I TGATCA 1 cut(s) 400
Kzo9I GATC 3 cut(s) 14, 400, 565
LmnI GCTCC 1 cut(s) 608
LpnPI CCDG 8 cut(s) 42, 171, 180, 368, 659, 664, 729, 899
Lsp1109I GCAGC 3 cut(s) 110, 332, 382
LweI GCATC 3 cut(s) 112, 224, 357
MaeI CTAG 1 cut(s) 795
MaeII ACGT 1 cut(s) 528
MaeIII GTNAC 3 cut(s) 47, 451, 574
MalI GATC 3 cut(s) 16, 402, 567
MboI GATC 3 cut(s) 14, 400, 565
MboII GAAGA 4 cut(s) 122, 125, 155, 432
MflI RGATCY 1 cut(s) 14
MluCI AATT 4 cut(s) 134, 146, 162, 904
MlyI GAGTC 1 cut(s) 238
MseI TTAA 2 cut(s) 705, 943
MslI CAYNNNNRTG 3 cut(s) 294, 449, 460
MspA1I CMGCKG 1 cut(s) 395
MspI CCGG 1 cut(s) 886
MspR9I CCNGG 1 cut(s) 887
NciI CCSGG 1 cut(s) 887
NcoI CCATGG 1 cut(s) 554
NdeII GATC 3 cut(s) 14, 400, 565
NlaIII CATG 5 cut(s) 429, 558, 603, 617, 902
NlaIV GGNNCC 1 cut(s) 519
NmuCI GTSAC 2 cut(s) 47, 451
NspI RCATGY 1 cut(s) 902
PagI TCATGA 1 cut(s) 613
PfeI GAWTC 3 cut(s) 749, 779, 925
PfoI TCCNGGA 1 cut(s) 885
PkrI GCNGC 3 cut(s) 100, 347, 397
PleI GAGTC 1 cut(s) 238
PpsI GAGTC 1 cut(s) 238
PpuMI RGGWCCY 1 cut(s) 859
PsiI TTATAA 1 cut(s) 321
Psp5II RGGWCCY 1 cut(s) 859
PspN4I GGNNCC 1 cut(s) 519
PspPI GGNCC 2 cut(s) 586, 859
PspPPI RGGWCCY 1 cut(s) 859
PstNI CAGNNNCTG 1 cut(s) 173
PsuI RGATCY 1 cut(s) 14
RsaI GTAC 2 cut(s) 259, 519
RsaNI GTAC 2 cut(s) 258, 518
RseI CAYNNNNRTG 3 cut(s) 294, 449, 460
SaqAI TTAA 2 cut(s) 705, 943
SatI GCNGC 3 cut(s) 99, 346, 396
Sau3AI GATC 3 cut(s) 14, 400, 565
Sau96I GGNCC 2 cut(s) 586, 859
ScaI AGTACT 1 cut(s) 259
SchI GAGTC 1 cut(s) 238
ScrFI CCNGG 1 cut(s) 887
SfaNI GCATC 3 cut(s) 112, 224, 357
SfcI CTRYAG 2 cut(s) 28, 198
SinI GGWCC 1 cut(s) 859
SmiMI CAYNNNNRTG 3 cut(s) 294, 449, 460
SmlI CTYRAG 1 cut(s) 126
SmoI CTYRAG 1 cut(s) 126
SpeI ACTAGT 1 cut(s) 794
Sse9I AATT 4 cut(s) 134, 146, 162, 904
SsiI CCGC 1 cut(s) 393
SspI AATATT 1 cut(s) 266
SspMI CTAG 1 cut(s) 795
StyD4I CCNGG 1 cut(s) 885
StyI CCWWGG 1 cut(s) 554
TaaI ACNGT 3 cut(s) 502, 837, 915
TaiI ACGT 1 cut(s) 531
TaqI TCGA 1 cut(s) 85
TasI AATT 4 cut(s) 134, 146, 162, 904
TatI WGTACW 1 cut(s) 257
TfiI GAWTC 3 cut(s) 749, 779, 925
Tru1I TTAA 2 cut(s) 705, 943
Tru9I TTAA 2 cut(s) 705, 943
TseFI GTSAC 2 cut(s) 47, 451
TseI GCWGC 3 cut(s) 98, 345, 395
Tsp45I GTSAC 2 cut(s) 47, 451
TspDTI ATGAA 5 cut(s) 474, 602, 630, 885, 938
TspGWI ACGGA 1 cut(s) 354
VpaK11BI GGWCC 1 cut(s) 859
XapI RAATTY 3 cut(s) 146, 162, 904
XceI RCATGY 1 cut(s) 902
XspI CTAG 1 cut(s) 795
ZrmI AGTACT 1 cut(s) 259
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.