Rw5G030450

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr5
OG0000370
Physical Location & Seq
Forward (+)
48296895 .. 48299283
2389 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw5G030450.1

Sequence Viewer

Length: 939 bp
ATGGATCCTCAGAGAGGCAGGGCCAGGGGTAGCGGCATGGTTACCTCTAAAGAGGAGTTCTATCTTGAGAAGGAGGTGGTGCAACCTGTTCCATCTACTGTTGGGACGGTTGATGCTACTCACCTAACTAGGCTGACTAGGGAAGTTATTAGATTGGGGGCAGTGGCATTTCAGGGTGGTACAGATTACTTGTTGGCCGATCAGTGGATTGAGAACATGGAGACCTACTATGATATGGTTGTCTGTACCGACATGGAGAAGAAGATTACAGCTACATTCCTTCTCCAGGGTGAGGCAGGACGGTGGTGGGATTCTATGCTAAAGACAAGGAACATATCAACCATTACTTGGGAGGGTTTTGTGGAACTCTTTCGGGACATGTACCTTCCCGCTTCTGGGAGGGAGAAATTGGAGGTTGACTTCATTTCTCTAGTCCAGGGGACTATGAGTGTCAAGGACTATGAGGCCCGGTTCTCACAATTGTACTGGTTTGTTAGGCCAATGGATCCAGTGTCTTTGGCTCGGAAGTTCCAACGGGGACTGAATCTGGTGATTAGAGAAAGGGTGACTCCTTTTCAGTTGCCTACTATGGCACTTATCTTTGCTAGTGCTCTTAGATTTGAGCAAGAACTTCTAACGTCTCAAGGGGAGATGACTACTATGGGAGATTCCCAGGGAAAGGGAAAGGCAGTTGCCGAGAGCAGTGAGAAGATGGACAGTCATGGTGGGTCCTGGAAGAGACAACGGACTTATCATCAGGCGCCAGCTAGGGTAGCAACTGCACTTGCTGGGCAGGTAGCACACCTGAGATGTTTCAACTGCGGTGAGTTAGACCATGTTTCCAAAGCGTGCAAGAAGCCAAGGAGCAAGGTATGCTTTAGATGTGGCCAGACTGGGCATATAGCCAGAGAGTGTACTCGACCTCAGGATGGCAGGTAG
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
RVP_2 Retrotrans_gag zf-CCHC

Protein Analysis

312

Amino Acids

35.35

Weight (kDa)

8.78

Isoelectric Point (pI)

41.78

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 55 - 189 5.9e-06 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 91 - 182 1.6e-17 Retrotransposon gag protein
zf-CCHC PF00098 291 - 306 1.8e-07 Zinc knuckle
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: OG0000370)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g29481 FvH4_2g11454 FvH4_3g19661 FvH4_3g28463 FvH4_3g31691 FvH4_3g34551 FvH4_3g35241 FvH4_4g06575 FvH4_4g09082 FvH4_4g15804 FvH4_4g15805 FvH4_4g16178 FvH4_4g16282 FvH4_5g25163 FvH4_6g27413 FvH4_7g02962 FvH4_7g04361
malus_domestica MD01G1095000.v1.1 MD02G1270200.v1.1 MD02G1270300.v1.1 MD02G1270400.v1.1 MD06G1059100.v1.1 MD08G1226500.v1.1
prunus_persica Prupe.1G169500_v2.0.a1 Prupe.5G195800_v2.0.a1
pyrus_communis pycom01g00010 pycom01g00770 pycom02g23140 pycom03g11760 pycom04g06090 pycom05g06900 pycom05g08070 pycom05g14500 pycom06g03050 pycom07g06250 pycom07g07540 pycom07g10580 pycom08g04990 pycom1146g00060 pycom11g01080 pycom11g15270 pycom11g15460 pycom11g24900 pycom12419g00150 pycom12424g00120 pycom13g08740 pycom13g24950 pycom13g25960 pycom13g26030 pycom13g27820 pycom16g23270 pycom16g25020 pycom16g25960 pycom17g07780 pycom17g08210 pycom17g13100
rosa_chinensis RchiOBHm_Chr1g0329421 RchiOBHm_Chr4g0397711 RchiOBHm_Chr4g0403481 RchiOBHm_Chr5g0019091 RchiOBHm_Chr5g0049101
rosa_laevigata RLG00000029892
rosa_multiflora Rmu_sc0001866.1_g000007
rosa_roxburghii Rroxscaffold_2G00094160 Rroxscaffold_3G00229110 Rroxscaffold_4G00321100 Rroxscaffold_7G00196040 Rroxscaffold_7G00196280
rosa_rugosa Rorug05G0160500 Rorug06G0096500
rosa_samantha Rh1AG098600 Rh1AG098800 Rh1BG078200 Rh1BG078700 Rh1BG178500 Rh1CG094600 Rh1CG094900 Rh1DG101700 Rh1DG109600 Rh2AG175800 Rh2AG175900 Rh2AG511400 Rh2BG114700 Rh2CG042200 Rh2CG116600 Rh2CG317500 Rh2DG327700 Rh2DG337800 Rh4CG142700 Rh4DG113100 Rh5BG335800 Rh5CG360600 Rh5DG352000 Rh6BG071400 Rh6BG417100 Rh6CG463300 Rh6CG463400 Rh7BG186600 Rh7CG196500 Rh7CG196600 Rh7CG448900 Rh7DG228300
rosa_wichuraiana Rw4G006560 Rw4G017340 Rw5G030450

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 2 cut(s) 784, 924
AccB1I GGYRCC 1 cut(s) 760
AccB7I CCANNNNNTGG 1 cut(s) 348
AciI CCGC 3 cut(s) 33, 390, 822
AclWI GGATC 3 cut(s) 12, 500, 513
AcoI YGGCCR 2 cut(s) 195, 886
AcyI GRCGYC 1 cut(s) 761
AfaI GTAC 5 cut(s) 181, 247, 383, 485, 916
AfiI CCNNNNNNNGG 9 cut(s) 14, 204, 286, 292, 348, 395, 396, 679, 929
AflIII ACRYGT 1 cut(s) 378
AgsI TTSAA 1 cut(s) 817
AjnI CCWGG 5 cut(s) 23, 285, 435, 672, 731
AluBI AGCT 2 cut(s) 272, 767
AluI AGCT 2 cut(s) 272, 767
Alw21I GWGCWC 1 cut(s) 613
Alw26I GTCTC 3 cut(s) 215, 645, 733
AlwI GGATC 3 cut(s) 12, 500, 513
AoxI GGCC 5 cut(s) 21, 195, 465, 497, 886
Asp700I GAANNNNTTC 1 cut(s) 369
AspLEI GCGC 1 cut(s) 763
AspS9I GGNCC 3 cut(s) 21, 466, 729
AsuC2I CCSGG 1 cut(s) 469
AsuHPI GGTGA 5 cut(s) 113, 302, 562, 577, 836
AvaII GGWCC 1 cut(s) 729
AxyI CCTNAGG 1 cut(s) 924
BalI TGGCCA 1 cut(s) 888
BamHI GGATCC 2 cut(s) 4, 505
BanI GGYRCC 1 cut(s) 760
Bbv12I GWGCWC 1 cut(s) 613
BccI CCATC 3 cut(s) 100, 706, 923
BciT130I CCWGG 5 cut(s) 25, 287, 437, 674, 733
BcnI CCSGG 1 cut(s) 469
BcoDI GTCTC 3 cut(s) 215, 645, 733
BfaI CTAG 5 cut(s) 129, 138, 431, 606, 768
BfoI RGCGCY 1 cut(s) 764
BfuAI ACCTGC 2 cut(s) 784, 924
BisI GCNGC 1 cut(s) 34
BlsI GCNGC 1 cut(s) 35
Bme1390I CCNGG 6 cut(s) 25, 287, 437, 469, 674, 733
Bme18I GGWCC 1 cut(s) 729
BmgT120I GGNCC 3 cut(s) 21, 466, 729
BmiI GGNNCC 4 cut(s) 6, 507, 730, 762
BmrFI CCNGG 6 cut(s) 25, 287, 437, 469, 674, 733
BmrI ACTGGG 1 cut(s) 903
BmsI GCATC 1 cut(s) 103
BmuI ACTGGG 1 cut(s) 903
BpmI CTGGAG 1 cut(s) 269
BpuEI CTTGAG 2 cut(s) 86, 627
BpuMI CCSGG 1 cut(s) 469
BsaHI GRCGYC 1 cut(s) 761
BsaI GGTCTC 1 cut(s) 215
BsaJI CCNNGG 6 cut(s) 24, 286, 436, 672, 673, 860
Bsc4I CCNNNNNNNGG 9 cut(s) 14, 204, 286, 292, 348, 395, 396, 679, 929
Bse1I ACTGG 3 cut(s) 491, 509, 898
Bse21I CCTNAGG 1 cut(s) 924
BseBI CCWGG 5 cut(s) 25, 287, 437, 674, 733
BseDI CCNNGG 6 cut(s) 24, 286, 436, 672, 673, 860
BseGI GGATG 1 cut(s) 934
BseLI CCNNNNNNNGG 9 cut(s) 14, 204, 286, 292, 348, 395, 396, 679, 929
BseMII CTCAG 3 cut(s) 23, 797, 938
BseNI ACTGG 3 cut(s) 491, 509, 898
BseRI GAGGAG 1 cut(s) 68
BseYI CCCAGC 1 cut(s) 788
BsgI GTGCAG 1 cut(s) 765
BshFI GGCC 5 cut(s) 23, 197, 467, 499, 888
BshNI GGYRCC 1 cut(s) 760
BsiHKAI GWGCWC 1 cut(s) 613
BsiSI CCGG 1 cut(s) 469
BslFI GGGAC 4 cut(s) 118, 389, 454, 552
BslI CCNNNNNNNGG 9 cut(s) 14, 204, 286, 292, 348, 395, 396, 679, 929
BsmAI GTCTC 3 cut(s) 215, 645, 733
BsmBI CGTCTC 1 cut(s) 645
BsmFI GGGAC 4 cut(s) 118, 389, 454, 552
BsnI GGCC 5 cut(s) 23, 197, 467, 499, 888
Bso31I GGTCTC 1 cut(s) 215
Bsp1286I GDGCHC 1 cut(s) 613
Bsp143I GATC 3 cut(s) 4, 199, 505
BspACI CCGC 3 cut(s) 33, 390, 822
BspANI GGCC 5 cut(s) 23, 197, 467, 499, 888
BspCNI CTCAG 3 cut(s) 22, 798, 937
BspLI GGNNCC 4 cut(s) 6, 507, 730, 762
BspMI ACCTGC 2 cut(s) 784, 924
BspPI GGATC 3 cut(s) 12, 500, 513
BspT107I GGYRCC 1 cut(s) 760
BspTNI GGTCTC 1 cut(s) 215
BsrI ACTGG 3 cut(s) 491, 509, 898
BssECI CCNNGG 6 cut(s) 24, 286, 436, 672, 673, 860
BssMI GATC 3 cut(s) 4, 199, 505
BssNI GRCGYC 1 cut(s) 761
BssT1I CCWWGG 1 cut(s) 860
Bst2UI CCWGG 5 cut(s) 25, 287, 437, 674, 733
Bst4CI ACNGT 4 cut(s) 100, 109, 303, 719
Bst6I CTCTTC 1 cut(s) 731
BstACI GRCGYC 1 cut(s) 761
BstAPI GCANNNNNTGC 1 cut(s) 873
BstC8I GCNNGC 2 cut(s) 765, 850
BstDEI CTNAG 4 cut(s) 9, 614, 806, 924
BstEII GGTNACC 1 cut(s) 40
BstENI CCTNNNNNAGG 2 cut(s) 12, 284
BstF5I GGATG 1 cut(s) 934
BstH2I RGCGCY 1 cut(s) 764
BstHHI GCGC 1 cut(s) 763
BstKTI GATC 3 cut(s) 7, 202, 508
BstMAI GTCTC 3 cut(s) 215, 645, 733
BstMBI GATC 3 cut(s) 4, 199, 505
BstMWI GCNNNNNNNGC 2 cut(s) 773, 873
BstNI CCWGG 5 cut(s) 25, 287, 437, 674, 733
BstNSI RCATGY 1 cut(s) 382
BstPI GGTNACC 1 cut(s) 40
BstSCI CCNGG 6 cut(s) 23, 285, 435, 467, 672, 731
BstX2I RGATCY 2 cut(s) 4, 505
BstYI RGATCY 2 cut(s) 4, 505
Bsu36I CCTNAGG 1 cut(s) 924
BsuRI GGCC 5 cut(s) 23, 197, 467, 499, 888
BtsCI GGATG 1 cut(s) 934
BtsI GCAGTG 2 cut(s) 168, 709
BtsIMutI CAGTG 4 cut(s) 168, 209, 516, 709
BveI ACCTGC 2 cut(s) 784, 924
Cac8I GCNNGC 2 cut(s) 765, 850
CfoI GCGC 1 cut(s) 763
Cfr13I GGNCC 3 cut(s) 21, 466, 729
Csp6I GTAC 5 cut(s) 180, 246, 382, 484, 915
CviAII CATG 6 cut(s) 37, 217, 253, 379, 722, 836
CviQI GTAC 5 cut(s) 180, 246, 382, 484, 915
DdeI CTNAG 4 cut(s) 9, 614, 806, 924
DinI GGCGCC 1 cut(s) 762
DpnI GATC 3 cut(s) 6, 201, 507
DpnII GATC 3 cut(s) 4, 199, 505
EaeI YGGCCR 2 cut(s) 195, 886
Eam1104I CTCTTC 1 cut(s) 731
EarI CTCTTC 1 cut(s) 731
Eco130I CCWWGG 1 cut(s) 860
Eco31I GGTCTC 1 cut(s) 215
Eco47I GGWCC 1 cut(s) 729
Eco81I CCTNAGG 1 cut(s) 924
Eco91I GGTNACC 1 cut(s) 40
EcoNI CCTNNNNNAGG 2 cut(s) 12, 284
EcoO109I RGGNCCY 1 cut(s) 729
EcoO65I GGTNACC 1 cut(s) 40
EcoRII CCWGG 5 cut(s) 23, 285, 435, 672, 731
EcoT14I CCWWGG 1 cut(s) 860
EgeI GGCGCC 1 cut(s) 762
EheI GGCGCC 1 cut(s) 762
ErhI CCWWGG 1 cut(s) 860
Esp3I CGTCTC 1 cut(s) 645
FaeI CATG 6 cut(s) 40, 220, 256, 382, 725, 839
FalI AAGNNNNNCTT 2 cut(s) 860, 892
FaqI GGGAC 4 cut(s) 118, 389, 454, 552
FatI CATG 6 cut(s) 36, 216, 252, 378, 721, 835
FauI CCCGC 1 cut(s) 397
Fnu4HI GCNGC 1 cut(s) 34
Fsp4HI GCNGC 1 cut(s) 34
FspBI CTAG 5 cut(s) 129, 138, 431, 606, 768
GlaI GCGC 1 cut(s) 762
GluI GCNGC 1 cut(s) 34
GsaI CCCAGC 1 cut(s) 792
GsuI CTGGAG 1 cut(s) 269
HaeII RGCGCY 1 cut(s) 764
HaeIII GGCC 5 cut(s) 23, 197, 467, 499, 888
HapII CCGG 1 cut(s) 469
HhaI GCGC 1 cut(s) 763
Hin1I GRCGYC 1 cut(s) 761
Hin1II CATG 6 cut(s) 40, 220, 256, 382, 725, 839
Hin6I GCGC 1 cut(s) 761
HinP1I GCGC 1 cut(s) 761
HincII GTYRAC 1 cut(s) 418
HindII GTYRAC 1 cut(s) 418
HinfI GANTC 4 cut(s) 311, 544, 568, 668
HpaII CCGG 1 cut(s) 469
HphI GGTGA 5 cut(s) 113, 302, 562, 577, 836
Hpy166II GTNNAC 2 cut(s) 418, 915
Hpy188I TCNGA 2 cut(s) 12, 525
Hpy188III TCNNGA 3 cut(s) 65, 374, 926
Hpy8I GTNNAC 2 cut(s) 418, 915
HpyAV CCTTC 3 cut(s) 64, 290, 395
HpyCH4III ACNGT 4 cut(s) 100, 109, 303, 719
HpyCH4IV ACGT 1 cut(s) 638
HpyCH4V TGCA 3 cut(s) 82, 782, 852
HpyF10VI GCNNNNNNNGC 2 cut(s) 773, 873
HpyF3I CTNAG 4 cut(s) 9, 614, 806, 924
HpySE526I ACGT 1 cut(s) 638
Hsp92I GRCGYC 1 cut(s) 761
Hsp92II CATG 6 cut(s) 40, 220, 256, 382, 725, 839
HspAI GCGC 1 cut(s) 761
KasI GGCGCC 1 cut(s) 760
Kzo9I GATC 3 cut(s) 4, 199, 505
LmnI GCTCC 1 cut(s) 864
LweI GCATC 1 cut(s) 103
MaeI CTAG 5 cut(s) 129, 138, 431, 606, 768
MaeII ACGT 1 cut(s) 638
MaeIII GTNAC 2 cut(s) 40, 565
MalI GATC 3 cut(s) 6, 201, 507
MboI GATC 3 cut(s) 4, 199, 505
MboII GAAGA 4 cut(s) 271, 274, 721, 748
MfeI CAATTG 1 cut(s) 479
MflI RGATCY 2 cut(s) 4, 505
MhlI GDGCHC 1 cut(s) 613
MlsI TGGCCA 1 cut(s) 888
MluCI AATT 2 cut(s) 407, 479
MluNI TGGCCA 1 cut(s) 888
Mly113I GGCGCC 1 cut(s) 761
MlyI GAGTC 1 cut(s) 562
MmeI TCCRAC 1 cut(s) 556
Mox20I TGGCCA 1 cut(s) 888
MroXI GAANNNNTTC 1 cut(s) 369
MscI TGGCCA 1 cut(s) 888
Msp20I TGGCCA 1 cut(s) 888
MspI CCGG 1 cut(s) 469
MspR9I CCNGG 6 cut(s) 25, 287, 437, 469, 674, 733
MunI CAATTG 1 cut(s) 479
MvaI CCWGG 5 cut(s) 25, 287, 437, 674, 733
MwoI GCNNNNNNNGC 2 cut(s) 773, 873
NarI GGCGCC 1 cut(s) 761
NciI CCSGG 1 cut(s) 469
NdeII GATC 3 cut(s) 4, 199, 505
NlaIII CATG 6 cut(s) 40, 220, 256, 382, 725, 839
NlaIV GGNNCC 4 cut(s) 6, 507, 730, 762
NmeAIII GCCGAG 1 cut(s) 721
NmuCI GTSAC 1 cut(s) 565
NspI RCATGY 1 cut(s) 382
PasI CCCWGGG 1 cut(s) 673
PciI ACATGT 1 cut(s) 378
PdmI GAANNNNTTC 1 cut(s) 369
PfeI GAWTC 3 cut(s) 311, 544, 668
PflMI CCANNNNNTGG 1 cut(s) 348
PfoI TCCNGGA 1 cut(s) 731
PkrI GCNGC 1 cut(s) 35
PleI GAGTC 1 cut(s) 562
PluTI GGCGCC 1 cut(s) 764
PpsI GAGTC 1 cut(s) 562
PpuMI RGGWCCY 1 cut(s) 729
PscI ACATGT 1 cut(s) 378
Psp5II RGGWCCY 1 cut(s) 729
Psp6I CCWGG 5 cut(s) 23, 285, 435, 672, 731
PspEI GGTNACC 1 cut(s) 40
PspFI CCCAGC 1 cut(s) 788
PspGI CCWGG 5 cut(s) 23, 285, 435, 672, 731
PspN4I GGNNCC 4 cut(s) 6, 507, 730, 762
PspPI GGNCC 3 cut(s) 21, 466, 729
PspPPI RGGWCCY 1 cut(s) 729
PsuI RGATCY 2 cut(s) 4, 505
RsaI GTAC 5 cut(s) 181, 247, 383, 485, 916
RsaNI GTAC 5 cut(s) 180, 246, 382, 484, 915
SatI GCNGC 1 cut(s) 34
Sau3AI GATC 3 cut(s) 4, 199, 505
Sau96I GGNCC 3 cut(s) 21, 466, 729
SchI GAGTC 1 cut(s) 562
ScrFI CCNGG 6 cut(s) 25, 287, 437, 469, 674, 733
SduI GDGCHC 1 cut(s) 613
SfaNI GCATC 1 cut(s) 103
SfoI GGCGCC 1 cut(s) 762
SinI GGWCC 1 cut(s) 729
SmlI CTYRAG 2 cut(s) 65, 642
SmoI CTYRAG 2 cut(s) 65, 642
Sse9I AATT 2 cut(s) 407, 479
SsiI CCGC 3 cut(s) 33, 390, 822
SspDI GGCGCC 1 cut(s) 760
SspMI CTAG 5 cut(s) 129, 138, 431, 606, 768
StyD4I CCNGG 6 cut(s) 23, 285, 435, 467, 672, 731
StyI CCWWGG 1 cut(s) 860
TaaI ACNGT 4 cut(s) 100, 109, 303, 719
TaiI ACGT 1 cut(s) 641
TaqI TCGA 1 cut(s) 919
TasI AATT 2 cut(s) 407, 479
TatI WGTACW 2 cut(s) 483, 914
TauI GCSGC 1 cut(s) 36
TfiI GAWTC 3 cut(s) 311, 544, 668
TscAI CASTG 4 cut(s) 168, 209, 516, 709
TseFI GTSAC 1 cut(s) 565
Tsp45I GTSAC 1 cut(s) 565
TspDTI ATGAA 1 cut(s) 412
TspGWI ACGGA 1 cut(s) 760
TspRI CASTG 4 cut(s) 168, 209, 516, 709
Van91I CCANNNNNTGG 1 cut(s) 348
VpaK11BI GGWCC 1 cut(s) 729
XagI CCTNNNNNAGG 2 cut(s) 12, 284
XceI RCATGY 1 cut(s) 382
XmnI GAANNNNTTC 1 cut(s) 369
XspI CTAG 5 cut(s) 129, 138, 431, 606, 768
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.