RchiOBHm_Chr6g0301841

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
6
OG0000278
Physical Location & Seq
Reverse (-)
62118292 .. 62119606
1315 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ27111

Sequence Viewer

Length: 741 bp
ATGCCTGAACCAGTTTCCTCCGACGATATTTGCATTATTTGGCATCCGCAACTAGGATGCGACCAAGACTATAATCTAAACGCTCCATCATGGGAAGTCGAGAAGTTCAATGGAAAGAACAATTTCAAGATGTGGCAAGTTGAGGTATGTGATGTCCTAGCCGTTGAGGGTTTAGTTGAAGCTCTGGATGGGAAACCCAGTTACATGAAGCAAGCCGAGTGGAAGGTGCTTGATCAGAAAGCTTGTTCGATACTTCGGTTCTATATGTCCAAAAAGGTCAAGCAGAAAGTCATGGCAGCGAAATCCGCGAAAGAGATTTTGGAAAAGCTTGGGAAAATTTATTTGAATAACTCATTTAATGAGCGAATTCTCAAGATGCAGCTTTACAAGTTGAGGATGGATGAGAGGACTACTAGTATGCAGGAGCATGTAGATGAGTTTAACAGGAGGGTCTGGGAGCTTTCAGGGTATGATGTGGAGTTTAGCGACGAAGACAAGGTTGCGATTCTTCTGGCCTCGCTTCCTGAAAAGTATAATGATCTAGTGATGGGTATGATGTATGGGAAGGACAGTGTAGTTTTTGATCATGTCGTATCTTTGCTTCTATATAAGGAGAGTAAGAATGCTGAAGCTAAAGCTCGAGTGACAAAAGATCAGAGTTGTGGTGGTTCGAAGAGTTCCAGGTCTTCTAACTCGAGAAATTATGAAGGCAAAGAGTGTTATTACTGTCATGAAATTTGA
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 zf-CCHC

Protein Analysis

246

Amino Acids

28.44

Weight (kDa)

5.92

Isoelectric Point (pI)

51.96

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 67 - 209 4.7e-24 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
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Orthologous Genes (Group: OG0000278)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G29785
fragaria_vesca FvH4_1g10046 FvH4_1g17351 FvH4_1g18441 FvH4_1g24222 FvH4_2g00141 FvH4_2g05931 FvH4_2g06671 FvH4_2g14030 FvH4_2g15291 FvH4_2g22611 FvH4_2g22612 FvH4_2g26380 FvH4_2g39202 FvH4_2g39202 FvH4_3g06691 FvH4_3g08580 FvH4_3g20502 FvH4_3g20503 FvH4_3g22421 FvH4_3g42580 FvH4_4g02061 FvH4_4g06794 FvH4_4g08661 FvH4_4g11771 FvH4_4g14601 FvH4_4g14721 FvH4_4g20921 FvH4_4g33601 FvH4_4g33602 FvH4_5g07492 FvH4_5g20321 FvH4_5g21591 FvH4_5g30343 FvH4_5g37875 FvH4_6g04372 FvH4_6g04373 FvH4_6g04373 FvH4_6g21377 FvH4_6g23760 FvH4_6g29471 FvH4_6g43142 FvH4_7g14351 FvH4_7g14352 FvH4_7g22582 FvH4_7g22583 FvH4_7g22584
malus_domestica MD00G1179400.v1.1 MD01G1170500.v1.1 MD03G1286700.v1.1 MD04G1054600.v1.1 MD04G1071700.v1.1 MD04G1193900.v1.1 MD08G1054300.v1.1 MD08G1217500.v1.1 MD09G1034600.v1.1 MD09G1098100.v1.1 MD10G1018300.v1.1 MD10G1220000.v1.1 MD10G1250300.v1.1 MD12G1014400.v1.1 MD15G1021000.v1.1 MD16G1112200.v1.1
prunus_persica Prupe.1G188900_v2.0.a1 Prupe.1G258000_v2.0.a1 Prupe.4G233400_v2.0.a1
pyrus_communis pycom01g10100 pycom02g01340 pycom03g19700 pycom05g01320 pycom07g16000 pycom07g16520 pycom11g26500 pycom13g09380 pycom13g13960 pycom14g08180 pycom14g16810 pycom16g09590
rosa_chinensis RchiOBHm_Chr1g0319891 RchiOBHm_Chr1g0333711 RchiOBHm_Chr2g0115331 RchiOBHm_Chr2g0143411 RchiOBHm_Chr2g0167631 RchiOBHm_Chr3g0448581 RchiOBHm_Chr3g0494991 RchiOBHm_Chr4g0442471 RchiOBHm_Chr6g0262311 RchiOBHm_Chr6g0301831 RchiOBHm_Chr6g0301841 RchiOBHm_Chr7g0183451
rosa_roxburghii Rroxscaffold_1G00039280 Rroxscaffold_1G00047670 Rroxscaffold_1G00066330 Rroxscaffold_2G00107510 Rroxscaffold_3G00255410 Rroxscaffold_4G00301460 Rroxscaffold_5G00352730 Rroxscaffold_7G00166350 Rroxscaffold_7G00166360 Rroxscaffold_7G00203820
rosa_rugosa Rorug03G0240500 Rorug05G0191700 Rorug06G0310200
rosa_samantha Rh2BG287000 Rh4CG073500 Rh4CG176200 Rh4CG191400 Rh5BG356100 Rh5BG434100 Rh6AG110600 Rh6AG421900 Rh6AG422000 Rh6AG422100 Rh6BG428600 Rh6BG428700 Rh6BG428800 Rh6CG435200 Rh6CG435300 Rh6CG435400 Rh6DG422000 Rh6DG422100 Rh6DG422200 Rh7BG190500 Rh7CG172800 Rh7CG225200
rosa_wichuraiana Rw2G044060 Rw6G036540

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccII CGCG 1 cut(s) 308
AciI CCGC 2 cut(s) 47, 306
AcsI RAATTY 3 cut(s) 336, 366, 735
AcuI CTGAAG 1 cut(s) 648
AfiI CCNNNNNNNGG 1 cut(s) 53
AgsI TTSAA 4 cut(s) 109, 127, 179, 346
AhlI ACTAGT 1 cut(s) 413
AjnI CCWGG 1 cut(s) 680
AjuI GAANNNNNNNTTGG 2 cut(s) 302, 334
AluBI AGCT 7 cut(s) 182, 242, 328, 382, 460, 632, 638
AluI AGCT 7 cut(s) 182, 242, 328, 382, 460, 632, 638
Ama87I CYCGRG 2 cut(s) 639, 694
AoxI GGCC 1 cut(s) 513
ApeKI GCWGC 2 cut(s) 296, 379
ApoI RAATTY 3 cut(s) 336, 366, 735
Asp700I GAANNNNTTC 1 cut(s) 122
AsuII TTCGAA 1 cut(s) 671
AvaI CYCGRG 2 cut(s) 639, 694
BaeI ACNNNNGTAYC 2 cut(s) 242, 275
BarI GAAGNNNNNNTAC 2 cut(s) 585, 617
BbsI GAAGAC 2 cut(s) 498, 678
BbvI GCAGC 2 cut(s) 308, 391
BccI CCATC 4 cut(s) 94, 182, 391, 541
BceAI ACGGC 1 cut(s) 146
BciT130I CCWGG 1 cut(s) 682
BclI TGATCA 2 cut(s) 232, 583
BcuI ACTAGT 1 cut(s) 413
BfaI CTAG 4 cut(s) 53, 158, 414, 542
BisI GCNGC 2 cut(s) 297, 380
BlsI GCNGC 2 cut(s) 298, 381
Bme1390I CCNGG 1 cut(s) 682
BmeT110I CYCGRG 2 cut(s) 639, 694
BmrFI CCNGG 1 cut(s) 682
BmrI ACTGGG 1 cut(s) 192
BmsI GCATC 3 cut(s) 47, 52, 366
BmuI ACTGGG 1 cut(s) 192
BpiI GAAGAC 2 cut(s) 498, 678
Bpu14I TTCGAA 1 cut(s) 671
BpuEI CTTGAG 1 cut(s) 356
Bsc4I CCNNNNNNNGG 1 cut(s) 53
Bse1I ACTGG 2 cut(s) 11, 198
BseBI CCWGG 1 cut(s) 682
BseGI GGATG 5 cut(s) 43, 62, 193, 402, 406
BseLI CCNNNNNNNGG 1 cut(s) 53
BseNI ACTGG 2 cut(s) 11, 198
BseXI GCAGC 2 cut(s) 308, 391
Bsh1236I CGCG 1 cut(s) 308
BshFI GGCC 1 cut(s) 515
BsiHKCI CYCGRG 2 cut(s) 639, 694
BslI CCNNNNNNNGG 1 cut(s) 53
BsmI GAATGC 1 cut(s) 628
BsnI GGCC 1 cut(s) 515
BsoBI CYCGRG 2 cut(s) 639, 694
Bsp119I TTCGAA 1 cut(s) 671
Bsp143I GATC 4 cut(s) 232, 538, 583, 652
BspACI CCGC 2 cut(s) 47, 306
BspANI GGCC 1 cut(s) 515
BspFNI CGCG 1 cut(s) 308
BspHI TCATGA 1 cut(s) 730
BspT104I TTCGAA 1 cut(s) 671
BsrI ACTGG 2 cut(s) 11, 198
BssMI GATC 4 cut(s) 232, 538, 583, 652
Bst2UI CCWGG 1 cut(s) 682
Bst4CI ACNGT 2 cut(s) 572, 728
Bst6I CTCTTC 1 cut(s) 668
BstBI TTCGAA 1 cut(s) 671
BstC8I GCNNGC 1 cut(s) 213
BstF5I GGATG 5 cut(s) 43, 62, 193, 402, 406
BstFNI CGCG 1 cut(s) 308
BstKTI GATC 4 cut(s) 235, 541, 586, 655
BstMBI GATC 4 cut(s) 232, 538, 583, 652
BstMWI GCNNNNNNNGC 1 cut(s) 305
BstNI CCWGG 1 cut(s) 682
BstNSI RCATGY 1 cut(s) 431
BstSCI CCNGG 1 cut(s) 680
BstUI CGCG 1 cut(s) 308
BstV1I GCAGC 2 cut(s) 308, 391
BstV2I GAAGAC 2 cut(s) 498, 678
BsuRI GGCC 1 cut(s) 515
BtsCI GGATG 5 cut(s) 43, 62, 193, 402, 406
BtsIMutI CAGTG 1 cut(s) 577
Cac8I GCNNGC 1 cut(s) 213
CciI TCATGA 1 cut(s) 730
CspCI CAANNNNNGTGG 2 cut(s) 200, 235
CviAII CATG 6 cut(s) 90, 205, 292, 428, 587, 731
DpnI GATC 4 cut(s) 234, 540, 585, 654
DpnII GATC 4 cut(s) 232, 538, 583, 652
Eam1104I CTCTTC 1 cut(s) 668
EarI CTCTTC 1 cut(s) 668
Eco57I CTGAAG 1 cut(s) 648
Eco88I CYCGRG 2 cut(s) 639, 694
EcoRI GAATTC 1 cut(s) 366
EcoRII CCWGG 1 cut(s) 680
FaeI CATG 6 cut(s) 93, 208, 295, 431, 590, 734
FatI CATG 6 cut(s) 89, 204, 291, 427, 586, 730
FbaI TGATCA 2 cut(s) 232, 583
Fnu4HI GCNGC 2 cut(s) 297, 380
FokI GGATG 5 cut(s) 30, 69, 200, 409, 413
Fsp4HI GCNGC 2 cut(s) 297, 380
FspBI CTAG 4 cut(s) 53, 158, 414, 542
GluI GCNGC 2 cut(s) 297, 380
HaeIII GGCC 1 cut(s) 515
Hin1II CATG 6 cut(s) 93, 208, 295, 431, 590, 734
HindIII AAGCTT 2 cut(s) 240, 326
HinfI GANTC 1 cut(s) 505
Hpy188I TCNGA 3 cut(s) 22, 237, 657
Hpy188III TCNNGA 7 cut(s) 100, 127, 185, 373, 524, 696, 731
Hpy99I CGWCG 2 cut(s) 26, 491
HpyAV CCTTC 3 cut(s) 217, 559, 701
HpyCH4III ACNGT 2 cut(s) 572, 728
HpyCH4V TGCA 3 cut(s) 33, 379, 421
HpyF10VI GCNNNNNNNGC 1 cut(s) 305
Hsp92II CATG 6 cut(s) 93, 208, 295, 431, 590, 734
Ksp22I TGATCA 2 cut(s) 232, 583
Kzo9I GATC 4 cut(s) 232, 538, 583, 652
LmnI GCTCC 3 cut(s) 88, 424, 457
Lsp1109I GCAGC 2 cut(s) 308, 391
LweI GCATC 3 cut(s) 47, 52, 366
MaeI CTAG 4 cut(s) 53, 158, 414, 542
MaeIII GTNAC 2 cut(s) 200, 643
MalI GATC 4 cut(s) 234, 540, 585, 654
MboI GATC 4 cut(s) 232, 538, 583, 652
MboII GAAGA 4 cut(s) 500, 503, 678, 685
MluCI AATT 5 cut(s) 121, 336, 366, 700, 735
MmeI TCCRAC 1 cut(s) 45
MnlI CCTC 7 cut(s) 28, 136, 160, 387, 399, 441, 526
MroXI GAANNNNTTC 1 cut(s) 122
MseI TTAA 2 cut(s) 357, 441
MslI CAYNNNNRTG 1 cut(s) 432
MspR9I CCNGG 1 cut(s) 682
Mva1269I GAATGC 1 cut(s) 628
MvaI CCWGG 1 cut(s) 682
MvnI CGCG 1 cut(s) 308
MwoI GCNNNNNNNGC 1 cut(s) 305
NdeII GATC 4 cut(s) 232, 538, 583, 652
NlaIII CATG 6 cut(s) 93, 208, 295, 431, 590, 734
NmeAIII GCCGAG 1 cut(s) 241
NmuCI GTSAC 1 cut(s) 643
NspI RCATGY 1 cut(s) 431
NspV TTCGAA 1 cut(s) 671
PaeR7I CTCGAG 2 cut(s) 639, 694
PagI TCATGA 1 cut(s) 730
PctI GAATGC 1 cut(s) 628
PdmI GAANNNNTTC 1 cut(s) 122
PfeI GAWTC 1 cut(s) 505
PkrI GCNGC 2 cut(s) 298, 381
Psp6I CCWGG 1 cut(s) 680
PspGI CCWGG 1 cut(s) 680
PspXI VCTCGAGB 1 cut(s) 639
RseI CAYNNNNRTG 1 cut(s) 432
SaqAI TTAA 2 cut(s) 357, 441
SatI GCNGC 2 cut(s) 297, 380
Sau3AI GATC 4 cut(s) 232, 538, 583, 652
ScrFI CCNGG 1 cut(s) 682
SfaNI GCATC 3 cut(s) 47, 52, 366
Sfr274I CTCGAG 2 cut(s) 639, 694
SfuI TTCGAA 1 cut(s) 671
SlaI CTCGAG 2 cut(s) 639, 694
SmiMI CAYNNNNRTG 1 cut(s) 432
SmlI CTYRAG 3 cut(s) 371, 639, 694
SmoI CTYRAG 3 cut(s) 371, 639, 694
SpeI ACTAGT 1 cut(s) 413
Sse9I AATT 5 cut(s) 121, 336, 366, 700, 735
SsiI CCGC 2 cut(s) 47, 306
SspMI CTAG 4 cut(s) 53, 158, 414, 542
StyD4I CCNGG 1 cut(s) 680
TaaI ACNGT 2 cut(s) 572, 728
TaqI TCGA 5 cut(s) 99, 248, 640, 671, 695
TasI AATT 5 cut(s) 121, 336, 366, 700, 735
TfiI GAWTC 1 cut(s) 505
Tru1I TTAA 2 cut(s) 357, 441
Tru9I TTAA 2 cut(s) 357, 441
TscAI CASTG 1 cut(s) 577
TseFI GTSAC 1 cut(s) 643
TseI GCWGC 2 cut(s) 296, 379
Tsp45I GTSAC 1 cut(s) 643
TspDTI ATGAA 2 cut(s) 221, 720
TspRI CASTG 1 cut(s) 577
XapI RAATTY 3 cut(s) 336, 366, 735
XceI RCATGY 1 cut(s) 431
XhoI CTCGAG 2 cut(s) 639, 694
XmnI GAANNNNTTC 1 cut(s) 122
XspI CTAG 4 cut(s) 53, 158, 414, 542
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.