Rh2CG116600

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr2C
OG0000370
Physical Location & Seq
Reverse (-)
10255552 .. 10256469
918 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh2CG116600.1

Sequence Viewer

Length: 918 bp
ATGGTGGCCTTGCTTGAGTTTAAGCACCAAAAACCACCAGCTTTTAAGGGTGAACCAGACCCAGTTGTAGCTGAACAATGGTTAGATGAAATCAACAAGATACTAGATGCCCTTAGAATTCGGGAAAGCGACTCTAGAATTACTCTTGCTGCTTACCAGTTTACCGGAGAAGCTGCCCAATGGTGGAAGATGATTAAGAGATCTTGTAATGTGGAGACTATGTCTTGGGATCAGTTCTGCAAAATATTTCTTGATAAGTTCTTTCCCCCTGTGCTGCAAGAAGCTAAAGTAGAAGAATTCAATAAGTTGTATCAAGGGAAGATGTCGGCAATGGAATATGATTCTCGGTTCATAGAATTGTCTAGGTATGCTCCTGAACTTGTGTCAACAGAAGCTAATAAAGCTCGTAAATTTGAACGTGGGCTTCGACCAAACATTAGATCAAAAGTGTCAGTTTTAAGGTTGCCAACTTATGCTAAAGTACTTGAAAGAGCTTCGATAGCTGAAGCAGATTGTGAGGAGTTTAAGAAAGTACGTGAGAAGACTCGACAAAGAATGGGTCAGCATTCAGGAAATCCCAATAAGAAGCAAAAGACATCGTCGTCATCATCTCAAAGTTTCATTGTACCACGGCTTCAGCAGCAAACTCGTTCAGGATTGGGGGTTTGTTTCAAGTGCGGACAACCTGGACACTTTAAAAGAGACTGCCCCCAAGGGGAGGGATCCCAGAGTTTCATGGGACCACCAAAGTTCACTCGTTCTGCACAGGTACAGCCACACATTCAACCTCAACAATCATCAGGTTCGAAAGGAAGTTTCCAACGAACTCAACCATCGTCTCAAGCTTCAGTTGGGTCACAACAACGACAAATTCAAACTAAAGGACTGGAACAAAGGCTCCAAGAGCAGAAAACTTAG
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

305

Amino Acids

34.86

Weight (kDa)

9.71

Isoelectric Point (pI)

67.69

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 3 - 166 3.6e-17 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 49 - 144 4.6e-20 Retrotransposon gag protein
zf-CCHC PF00098 222 - 238 2.2e-08 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)
AasI GACNNNNNNGTC 1 cut(s) 601
AciI CCGC 1 cut(s) 678
AclWI GGATC 3 cut(s) 237, 717, 730
AcsI RAATTY 4 cut(s) 117, 296, 410, 870
AcuI CTGAAG 3 cut(s) 525, 620, 831
AfaI GTAC 4 cut(s) 483, 534, 627, 771
AfiI CCNNNNNNNGG 3 cut(s) 183, 715, 718
AgsI TTSAA 6 cut(s) 301, 416, 488, 673, 785, 875
AjnI CCWGG 1 cut(s) 685
AloI GAACNNNNNNTCC 2 cut(s) 882, 914
AluBI AGCT 9 cut(s) 41, 71, 173, 284, 395, 404, 494, 503, 845
AluI AGCT 9 cut(s) 41, 71, 173, 284, 395, 404, 494, 503, 845
Alw26I GTCTC 3 cut(s) 209, 696, 843
AlwI GGATC 3 cut(s) 237, 717, 730
AoxI GGCC 1 cut(s) 6
ApeKI GCWGC 4 cut(s) 149, 173, 274, 640
ApoI RAATTY 4 cut(s) 117, 296, 410, 870
ArsI GACNNNNNNTTYG 2 cut(s) 544, 576
AspS9I GGNCC 1 cut(s) 740
AsuHPI GGTGA 1 cut(s) 62
AsuII TTCGAA 1 cut(s) 806
AvaII GGWCC 1 cut(s) 740
BamHI GGATCC 1 cut(s) 722
BarI GAAGNNNNNNTAC 2 cut(s) 618, 650
BbsI GAAGAC 1 cut(s) 548
BbvI GCAGC 4 cut(s) 136, 160, 261, 652
BccI CCATC 1 cut(s) 841
BceAI ACGGC 1 cut(s) 647
BcgI CGANNNNNNTGC 2 cut(s) 629, 663
BciT130I CCWGG 1 cut(s) 687
BcoDI GTCTC 3 cut(s) 209, 696, 843
BfaI CTAG 3 cut(s) 104, 135, 363
BglII AGATCT 1 cut(s) 200
BisI GCNGC 4 cut(s) 150, 174, 275, 641
BlsI GCNGC 4 cut(s) 151, 175, 276, 642
BmcAI AGTACT 1 cut(s) 483
Bme1390I CCNGG 1 cut(s) 687
Bme18I GGWCC 1 cut(s) 740
BmgT120I GGNCC 1 cut(s) 740
BmiI GGNNCC 3 cut(s) 724, 741, 899
BmrFI CCNGG 1 cut(s) 687
BmrI ACTGGG 1 cut(s) 56
BmsI GCATC 1 cut(s) 97
BmuI ACTGGG 1 cut(s) 56
BpiI GAAGAC 1 cut(s) 548
Bpu14I TTCGAA 1 cut(s) 806
BpuEI CTTGAG 2 cut(s) 35, 825
BsaAI YACGTR 1 cut(s) 536
BsaJI CCNNGG 2 cut(s) 629, 712
BsaWI WCCGGW 1 cut(s) 164
BsaXI ACNNNNNCTCC 4 cut(s) 206, 236, 882, 912
Bsc4I CCNNNNNNNGG 3 cut(s) 183, 715, 718
Bse1I ACTGG 3 cut(s) 62, 157, 891
Bse3DI GCAATG 1 cut(s) 336
BseBI CCWGG 1 cut(s) 687
BseDI CCNNGG 2 cut(s) 629, 712
BseLI CCNNNNNNNGG 3 cut(s) 183, 715, 718
BseMI GCAATG 1 cut(s) 336
BseNI ACTGG 3 cut(s) 62, 157, 891
BseRI GAGGAG 1 cut(s) 533
BseXI GCAGC 4 cut(s) 136, 160, 261, 652
BsgI GTGCAG 1 cut(s) 747
BshFI GGCC 1 cut(s) 8
BsiSI CCGG 1 cut(s) 165
BslFI GGGAC 1 cut(s) 753
BslI CCNNNNNNNGG 3 cut(s) 183, 715, 718
BsmAI GTCTC 3 cut(s) 209, 696, 843
BsmBI CGTCTC 1 cut(s) 843
BsmFI GGGAC 1 cut(s) 753
BsmI GAATGC 1 cut(s) 565
BsnI GGCC 1 cut(s) 8
Bsp119I TTCGAA 1 cut(s) 806
Bsp143I GATC 4 cut(s) 200, 229, 440, 722
BspACI CCGC 1 cut(s) 678
BspANI GGCC 1 cut(s) 8
BspLI GGNNCC 3 cut(s) 724, 741, 899
BspPI GGATC 3 cut(s) 237, 717, 730
BspT104I TTCGAA 1 cut(s) 806
BsrDI GCAATG 1 cut(s) 336
BsrI ACTGG 3 cut(s) 62, 157, 891
BssECI CCNNGG 2 cut(s) 629, 712
BssMI GATC 4 cut(s) 200, 229, 440, 722
BssT1I CCWWGG 1 cut(s) 712
Bst2UI CCWGG 1 cut(s) 687
BstBAI YACGTR 1 cut(s) 536
BstBI TTCGAA 1 cut(s) 806
BstDEI CTNAG 2 cut(s) 113, 915
BstDSI CCRYGG 1 cut(s) 629
BstKTI GATC 4 cut(s) 203, 232, 443, 725
BstMAI GTCTC 3 cut(s) 209, 696, 843
BstMBI GATC 4 cut(s) 200, 229, 440, 722
BstMWI GCNNNNNNNGC 4 cut(s) 401, 500, 640, 904
BstNI CCWGG 1 cut(s) 687
BstSCI CCNGG 1 cut(s) 685
BstV1I GCAGC 4 cut(s) 136, 160, 261, 652
BstV2I GAAGAC 1 cut(s) 548
BstX2I RGATCY 2 cut(s) 200, 722
BstYI RGATCY 2 cut(s) 200, 722
BsuRI GGCC 1 cut(s) 8
BtgI CCRYGG 1 cut(s) 629
Cfr13I GGNCC 1 cut(s) 740
Csp6I GTAC 4 cut(s) 482, 533, 626, 770
CviAII CATG 1 cut(s) 736
CviQI GTAC 4 cut(s) 482, 533, 626, 770
DdeI CTNAG 2 cut(s) 113, 915
DpnI GATC 4 cut(s) 202, 231, 442, 724
DpnII GATC 4 cut(s) 200, 229, 440, 722
DraI TTTAAA 1 cut(s) 697
DrdI GACNNNNNNGTC 1 cut(s) 601
DseDI GACNNNNNNGTC 1 cut(s) 601
Eco130I CCWWGG 1 cut(s) 712
Eco47I GGWCC 1 cut(s) 740
Eco57I CTGAAG 3 cut(s) 525, 620, 831
EcoRI GAATTC 2 cut(s) 117, 296
EcoRII CCWGG 1 cut(s) 685
EcoT14I CCWWGG 1 cut(s) 712
ErhI CCWWGG 1 cut(s) 712
Esp3I CGTCTC 1 cut(s) 843
FaeI CATG 1 cut(s) 739
FaiI YATR 6 cut(s) 221, 339, 353, 369, 474, 737
FaqI GGGAC 1 cut(s) 753
FatI CATG 1 cut(s) 735
Fnu4HI GCNGC 4 cut(s) 150, 174, 275, 641
Fsp4HI GCNGC 4 cut(s) 150, 174, 275, 641
FspBI CTAG 3 cut(s) 104, 135, 363
GluI GCNGC 4 cut(s) 150, 174, 275, 641
HaeIII GGCC 1 cut(s) 8
HapII CCGG 1 cut(s) 165
Hin1II CATG 1 cut(s) 739
HincII GTYRAC 1 cut(s) 387
HindII GTYRAC 1 cut(s) 387
HindIII AAGCTT 1 cut(s) 843
HinfI GANTC 3 cut(s) 131, 341, 544
HpaII CCGG 1 cut(s) 165
HphI GGTGA 1 cut(s) 62
Hpy166II GTNNAC 4 cut(s) 53, 162, 387, 753
Hpy188III TCNNGA 6 cut(s) 122, 135, 251, 374, 570, 654
Hpy8I GTNNAC 4 cut(s) 53, 162, 387, 753
Hpy99I CGWCG 1 cut(s) 604
HpyCH4IV ACGT 2 cut(s) 418, 535
HpyCH4V TGCA 3 cut(s) 240, 277, 764
HpyF10VI GCNNNNNNNGC 4 cut(s) 401, 500, 640, 904
HpyF3I CTNAG 2 cut(s) 113, 915
HpySE526I ACGT 2 cut(s) 418, 535
Hsp92II CATG 1 cut(s) 739
Kzo9I GATC 4 cut(s) 200, 229, 440, 722
LmnI GCTCC 2 cut(s) 376, 903
Lsp1109I GCAGC 4 cut(s) 136, 160, 261, 652
LweI GCATC 1 cut(s) 97
MaeI CTAG 3 cut(s) 104, 135, 363
MaeII ACGT 2 cut(s) 418, 535
MaeIII GTNAC 1 cut(s) 855
MalI GATC 4 cut(s) 202, 231, 442, 724
MboI GATC 4 cut(s) 200, 229, 440, 722
MboII GAAGA 4 cut(s) 199, 305, 331, 553
MflI RGATCY 2 cut(s) 200, 722
MluCI AATT 6 cut(s) 117, 138, 296, 356, 410, 870
MlyI GAGTC 2 cut(s) 125, 538
MmeI TCCRAC 1 cut(s) 844
MnlI CCTC 3 cut(s) 511, 712, 798
MseI TTAA 6 cut(s) 21, 45, 195, 458, 525, 696
MspI CCGG 1 cut(s) 165
MspR9I CCNGG 1 cut(s) 687
Mva1269I GAATGC 1 cut(s) 565
MvaI CCWGG 1 cut(s) 687
MwoI GCNNNNNNNGC 4 cut(s) 401, 500, 640, 904
NdeII GATC 4 cut(s) 200, 229, 440, 722
NlaIII CATG 1 cut(s) 739
NlaIV GGNNCC 3 cut(s) 724, 741, 899
NmuCI GTSAC 1 cut(s) 855
NspV TTCGAA 1 cut(s) 806
PcsI WCGNNNNNNNCGW 1 cut(s) 424
PctI GAATGC 1 cut(s) 565
PfeI GAWTC 1 cut(s) 341
PflFI GACNNNGTC 2 cut(s) 220, 598
PkrI GCNGC 4 cut(s) 151, 175, 276, 642
PleI GAGTC 2 cut(s) 125, 538
PpsI GAGTC 2 cut(s) 125, 538
Ppu21I YACGTR 1 cut(s) 536
Psp6I CCWGG 1 cut(s) 685
PspGI CCWGG 1 cut(s) 685
PspN4I GGNNCC 3 cut(s) 724, 741, 899
PspPI GGNCC 1 cut(s) 740
PsuI RGATCY 2 cut(s) 200, 722
PsyI GACNNNGTC 2 cut(s) 220, 598
RsaI GTAC 4 cut(s) 483, 534, 627, 771
RsaNI GTAC 4 cut(s) 482, 533, 626, 770
SaqAI TTAA 6 cut(s) 21, 45, 195, 458, 525, 696
SatI GCNGC 4 cut(s) 150, 174, 275, 641
Sau3AI GATC 4 cut(s) 200, 229, 440, 722
Sau96I GGNCC 1 cut(s) 740
ScaI AGTACT 1 cut(s) 483
SchI GAGTC 2 cut(s) 125, 538
ScrFI CCNGG 1 cut(s) 687
SfaNI GCATC 1 cut(s) 97
SfuI TTCGAA 1 cut(s) 806
SinI GGWCC 1 cut(s) 740
SmlI CTYRAG 2 cut(s) 14, 840
SmoI CTYRAG 2 cut(s) 14, 840
Sse9I AATT 6 cut(s) 117, 138, 296, 356, 410, 870
SsiI CCGC 1 cut(s) 678
SspI AATATT 1 cut(s) 246
SspMI CTAG 3 cut(s) 104, 135, 363
StyD4I CCNGG 1 cut(s) 685
StyI CCWWGG 1 cut(s) 712
TaiI ACGT 2 cut(s) 421, 538
TaqI TCGA 4 cut(s) 427, 497, 547, 806
TasI AATT 6 cut(s) 117, 138, 296, 356, 410, 870
TatI WGTACW 1 cut(s) 481
TfiI GAWTC 1 cut(s) 341
Tru1I TTAA 6 cut(s) 21, 45, 195, 458, 525, 696
Tru9I TTAA 6 cut(s) 21, 45, 195, 458, 525, 696
TseFI GTSAC 1 cut(s) 855
TseI GCWGC 4 cut(s) 149, 173, 274, 640
Tsp45I GTSAC 1 cut(s) 855
TspDTI ATGAA 4 cut(s) 102, 340, 610, 724
Tth111I GACNNNGTC 2 cut(s) 220, 598
VpaK11BI GGWCC 1 cut(s) 740
XapI RAATTY 4 cut(s) 117, 296, 410, 870
XbaI TCTAGA 1 cut(s) 134
XspI CTAG 3 cut(s) 104, 135, 363
ZrmI AGTACT 1 cut(s) 483
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.