Rroxscaffold_7G00166350

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000007
OG0000278
Physical Location & Seq
Forward (+)
7841992 .. 7843172
1181 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_7G00166350.1

Sequence Viewer

Length: 774 bp
ATGCCTGATCCAGTTTCCCCCGACGATATTTGGCATCCGCAACTAGGATGCGACCAAGACTATAATCTAAACGCTCCATCATGGGAAATCGAGAAGTTCAATGGAAAGAACAATTTCAAGATGTGGCAAGTTGAGGTTTGTGATGTCCTAGCCGTTGAGGGTTTAGTTGAAGCTCTGGATGGGAAACCCAGTTACATGAAGCAAGCCCAGTGGAAGGTGCTTGATCAGAAAGCTTGTTCGATACTTCGGTTCTATATGTCCAAAAAGGTCGAGCAGAAAGTCATGGCAGCGAAATCCGCGAAAGAGATTTTGGAAAAGCTTGGGAAAATTTATTTGAATAACTCATTTAATGAGCGAATTCTCAAGATGCAGCTTTACAAGTTGAGGATGGATGAGAGGACTACTAGTATGCAGGAGCATGTAGATGAATTTAACAGGAGGGTCTGGGAGCTTTCAGGGTATGATGTGGAGTTTAGCGACGAAGACAAGGTTGCGATTCTTCTGGCCTCGCTTCCTGAAAAGTATAATGATCTAGTGATGGGTATGATGTATGGGAAGGACAGTGTAGTTTTTGATCATGTTGTATCTTTGCTTCTATATAAGGAGAGTAAGAATGCTGAAGCTAAAGCTCGAGTGACAAAAGATCAGAGTTGTGGTGGTTCTAAGAGTTCCAGGTCTTCTAACTCAAGAAATTATGAAGGCAAAGAAATTGGACACATTCTGAATCACTGTCCCAAGCTGCAGCTGAAGAAGACAAATAAGAATTTGTTCTAA
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

257

Amino Acids

29.65

Weight (kDa)

7.59

Isoelectric Point (pI)

52.79

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 64 - 206 6e-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) 299
AciI CCGC 2 cut(s) 38, 297
AclWI GGATC 1 cut(s) 2
AcsI RAATTY 4 cut(s) 327, 357, 428, 763
AcuI CTGAAG 2 cut(s) 639, 767
AfiI CCNNNNNNNGG 2 cut(s) 44, 214
AgsI TTSAA 4 cut(s) 100, 118, 170, 337
AhlI ACTAGT 1 cut(s) 404
AjnI CCWGG 1 cut(s) 671
AjuI GAANNNNNNNTTGG 2 cut(s) 293, 325
AluBI AGCT 9 cut(s) 173, 233, 319, 373, 451, 623, 629, 739, 745
AluI AGCT 9 cut(s) 173, 233, 319, 373, 451, 623, 629, 739, 745
AlwI GGATC 1 cut(s) 2
Ama87I CYCGRG 1 cut(s) 630
AoxI GGCC 1 cut(s) 504
ApeKI GCWGC 4 cut(s) 287, 370, 739, 742
ApoI RAATTY 4 cut(s) 327, 357, 428, 763
Asp700I GAANNNNTTC 2 cut(s) 113, 767
AvaI CYCGRG 1 cut(s) 630
BaeI ACNNNNGTAYC 2 cut(s) 233, 266
BarI GAAGNNNNNNTAC 2 cut(s) 576, 608
BbsI GAAGAC 3 cut(s) 489, 669, 758
BbvI GCAGC 4 cut(s) 299, 382, 726, 754
BccI CCATC 4 cut(s) 85, 173, 382, 532
BceAI ACGGC 1 cut(s) 137
BciT130I CCWGG 1 cut(s) 673
BclI TGATCA 2 cut(s) 223, 574
BcuI ACTAGT 1 cut(s) 404
BfaI CTAG 4 cut(s) 44, 149, 405, 533
BfmI CTRYAG 1 cut(s) 740
BisI GCNGC 4 cut(s) 288, 371, 740, 743
BlsI GCNGC 4 cut(s) 289, 372, 741, 744
Bme1390I CCNGG 1 cut(s) 673
BmeT110I CYCGRG 1 cut(s) 630
BmrFI CCNGG 1 cut(s) 673
BmrI ACTGGG 2 cut(s) 183, 202
BmsI GCATC 3 cut(s) 38, 43, 357
BmuI ACTGGG 2 cut(s) 183, 202
BpiI GAAGAC 3 cut(s) 489, 669, 758
BpuEI CTTGAG 2 cut(s) 347, 670
Bsc4I CCNNNNNNNGG 2 cut(s) 44, 214
Bse1I ACTGG 3 cut(s) 11, 189, 208
BseBI CCWGG 1 cut(s) 673
BseGI GGATG 5 cut(s) 34, 53, 184, 393, 397
BseLI CCNNNNNNNGG 2 cut(s) 44, 214
BseNI ACTGG 3 cut(s) 11, 189, 208
BseXI GCAGC 4 cut(s) 299, 382, 726, 754
Bsh1236I CGCG 1 cut(s) 299
BshFI GGCC 1 cut(s) 506
BsiHKCI CYCGRG 1 cut(s) 630
BslFI GGGAC 1 cut(s) 717
BslI CCNNNNNNNGG 2 cut(s) 44, 214
BsmFI GGGAC 1 cut(s) 717
BsmI GAATGC 1 cut(s) 619
BsnI GGCC 1 cut(s) 506
BsoBI CYCGRG 1 cut(s) 630
Bsp143I GATC 5 cut(s) 7, 223, 529, 574, 643
BspACI CCGC 2 cut(s) 38, 297
BspANI GGCC 1 cut(s) 506
BspFNI CGCG 1 cut(s) 299
BspMAI CTGCAG 1 cut(s) 744
BspPI GGATC 1 cut(s) 2
BsrI ACTGG 3 cut(s) 11, 189, 208
BssMI GATC 5 cut(s) 7, 223, 529, 574, 643
Bst2UI CCWGG 1 cut(s) 673
Bst4CI ACNGT 2 cut(s) 563, 731
BstC8I GCNNGC 1 cut(s) 204
BstDEI CTNAG 1 cut(s) 663
BstF5I GGATG 5 cut(s) 34, 53, 184, 393, 397
BstFNI CGCG 1 cut(s) 299
BstKTI GATC 5 cut(s) 10, 226, 532, 577, 646
BstMBI GATC 5 cut(s) 7, 223, 529, 574, 643
BstMWI GCNNNNNNNGC 1 cut(s) 296
BstNI CCWGG 1 cut(s) 673
BstNSI RCATGY 1 cut(s) 422
BstSCI CCNGG 1 cut(s) 671
BstSFI CTRYAG 1 cut(s) 740
BstUI CGCG 1 cut(s) 299
BstV1I GCAGC 4 cut(s) 299, 382, 726, 754
BstV2I GAAGAC 3 cut(s) 489, 669, 758
BsuRI GGCC 1 cut(s) 506
BtsCI GGATG 5 cut(s) 34, 53, 184, 393, 397
BtsIMutI CAGTG 3 cut(s) 215, 568, 727
Cac8I GCNNGC 1 cut(s) 204
CspCI CAANNNNNGTGG 2 cut(s) 191, 226
CviAII CATG 5 cut(s) 81, 196, 283, 419, 578
DdeI CTNAG 1 cut(s) 663
DpnI GATC 5 cut(s) 9, 225, 531, 576, 645
DpnII GATC 5 cut(s) 7, 223, 529, 574, 643
Eco57I CTGAAG 2 cut(s) 639, 767
Eco88I CYCGRG 1 cut(s) 630
EcoRI GAATTC 1 cut(s) 357
EcoRII CCWGG 1 cut(s) 671
FaeI CATG 5 cut(s) 84, 199, 286, 422, 581
FaqI GGGAC 1 cut(s) 717
FatI CATG 5 cut(s) 80, 195, 282, 418, 577
FbaI TGATCA 2 cut(s) 223, 574
Fnu4HI GCNGC 4 cut(s) 288, 371, 740, 743
FokI GGATG 5 cut(s) 21, 60, 191, 400, 404
Fsp4HI GCNGC 4 cut(s) 288, 371, 740, 743
FspBI CTAG 4 cut(s) 44, 149, 405, 533
GluI GCNGC 4 cut(s) 288, 371, 740, 743
HaeIII GGCC 1 cut(s) 506
Hin1II CATG 5 cut(s) 84, 199, 286, 422, 581
HindIII AAGCTT 2 cut(s) 231, 317
HinfI GANTC 2 cut(s) 496, 724
Hpy188I TCNGA 3 cut(s) 228, 648, 723
Hpy188III TCNNGA 6 cut(s) 91, 118, 176, 364, 515, 687
Hpy99I CGWCG 2 cut(s) 26, 482
HpyAV CCTTC 3 cut(s) 208, 550, 692
HpyCH4III ACNGT 2 cut(s) 563, 731
HpyCH4V TGCA 3 cut(s) 370, 412, 742
HpyF10VI GCNNNNNNNGC 1 cut(s) 296
HpyF3I CTNAG 1 cut(s) 663
Hsp92II CATG 5 cut(s) 84, 199, 286, 422, 581
Ksp22I TGATCA 2 cut(s) 223, 574
Kzo9I GATC 5 cut(s) 7, 223, 529, 574, 643
LmnI GCTCC 3 cut(s) 79, 415, 448
Lsp1109I GCAGC 4 cut(s) 299, 382, 726, 754
LweI GCATC 3 cut(s) 38, 43, 357
MaeI CTAG 4 cut(s) 44, 149, 405, 533
MaeIII GTNAC 2 cut(s) 191, 634
MalI GATC 5 cut(s) 9, 225, 531, 576, 645
MboI GATC 5 cut(s) 7, 223, 529, 574, 643
MboII GAAGA 5 cut(s) 491, 494, 669, 760, 763
MluCI AATT 7 cut(s) 112, 327, 357, 428, 691, 708, 763
MnlI CCTC 6 cut(s) 127, 151, 378, 390, 432, 517
MroXI GAANNNNTTC 2 cut(s) 113, 767
MseI TTAA 2 cut(s) 348, 432
MslI CAYNNNNRTG 1 cut(s) 423
MspA1I CMGCKG 1 cut(s) 745
MspR9I CCNGG 1 cut(s) 673
Mva1269I GAATGC 1 cut(s) 619
MvaI CCWGG 1 cut(s) 673
MvnI CGCG 1 cut(s) 299
MwoI GCNNNNNNNGC 1 cut(s) 296
NdeII GATC 5 cut(s) 7, 223, 529, 574, 643
NlaIII CATG 5 cut(s) 84, 199, 286, 422, 581
NmuCI GTSAC 1 cut(s) 634
NspI RCATGY 1 cut(s) 422
PaeR7I CTCGAG 1 cut(s) 630
PctI GAATGC 1 cut(s) 619
PdmI GAANNNNTTC 2 cut(s) 113, 767
PfeI GAWTC 2 cut(s) 496, 724
PkrI GCNGC 4 cut(s) 289, 372, 741, 744
Psp6I CCWGG 1 cut(s) 671
PspGI CCWGG 1 cut(s) 671
PspXI VCTCGAGB 1 cut(s) 630
PstI CTGCAG 1 cut(s) 744
PvuII CAGCTG 1 cut(s) 745
RseI CAYNNNNRTG 1 cut(s) 423
SaqAI TTAA 2 cut(s) 348, 432
SatI GCNGC 4 cut(s) 288, 371, 740, 743
Sau3AI GATC 5 cut(s) 7, 223, 529, 574, 643
ScrFI CCNGG 1 cut(s) 673
SfaNI GCATC 3 cut(s) 38, 43, 357
SfcI CTRYAG 1 cut(s) 740
Sfr274I CTCGAG 1 cut(s) 630
SlaI CTCGAG 1 cut(s) 630
SmiMI CAYNNNNRTG 1 cut(s) 423
SmlI CTYRAG 3 cut(s) 362, 630, 685
SmoI CTYRAG 3 cut(s) 362, 630, 685
SpeI ACTAGT 1 cut(s) 404
Sse9I AATT 7 cut(s) 112, 327, 357, 428, 691, 708, 763
SsiI CCGC 2 cut(s) 38, 297
SspMI CTAG 4 cut(s) 44, 149, 405, 533
StyD4I CCNGG 1 cut(s) 671
TaaI ACNGT 2 cut(s) 563, 731
TaqI TCGA 4 cut(s) 90, 239, 270, 631
TasI AATT 7 cut(s) 112, 327, 357, 428, 691, 708, 763
TfiI GAWTC 2 cut(s) 496, 724
Tru1I TTAA 2 cut(s) 348, 432
Tru9I TTAA 2 cut(s) 348, 432
TscAI CASTG 3 cut(s) 215, 568, 734
TseFI GTSAC 1 cut(s) 634
TseI GCWGC 4 cut(s) 287, 370, 739, 742
Tsp45I GTSAC 1 cut(s) 634
TspDTI ATGAA 3 cut(s) 212, 441, 711
TspRI CASTG 3 cut(s) 215, 568, 734
XapI RAATTY 4 cut(s) 327, 357, 428, 763
XceI RCATGY 1 cut(s) 422
XhoI CTCGAG 1 cut(s) 630
XmnI GAANNNNTTC 2 cut(s) 113, 767
XspI CTAG 4 cut(s) 44, 149, 405, 533
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.