Rh6AG110600

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr6A
OG0000278
Physical Location & Seq
Reverse (-)
16153723 .. 16158232
4510 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh6AG110600.1

Sequence Viewer

Length: 804 bp
ATGGCGACGAAGTACGAAATAGAGCAGTTCAATGGGAACAATTTCTCATTGTGGAAAATGAGGATAAAAGCAGTCTTGAGAAAAGATAACTGCTTGGCGGCAATTGGAGATAGGCCTGAGGAGATCACTGACGATGGTAAGTGGAACGAGATGGATGGCAATGCGATTGCTAATCTGCATCTAGCACTAGCCGATGAAGTATTGTCGAGTGTGGCGGAGAAGAAGACGGCAAAAGAGATATGGGATACACTCACAAAATTGTACGAGGCCAAATCACTACACAACAAAATCTTCTTGAAGAGAAAGCTTTACACCATTCGGATGATGGAGTCGACGACAATGACTGACCACATCAACACACTCAACACCTTGTTCTCACATCTCACAGCAATGGGGCATAACATAGAGACGGGTGAACGTGCTGAAATTCTACTTCAAAGTCTACCTGATTCGTATGATCAACTCATCATCAACGTAACCAACAATCTAGAAATACTAGTCTTCGATGATATTGCAGCTGCGGTTCTTGAAGAAGAAAGTCGGCGCAAGAGCAAAGAAGATAGATTGGGTGGCTCACAGCAGGCCAAAGCTTTGATGATAACGAGAGGGAGATCAACGGAACATGGCCCCAGTGGGAGTCAAAGTCAGAGTAGATCAAAATCTAAAAATGCTAAGGAGGCAGCAATGGTATCAAATGGACGCCAAGCATCTCCAAGTGCTGTAGCACATGCCGGATGTGTCTTGAAGGCTATGATGGCTGATTTCAACCGATCTTTATACTCCCCATGGAACTATACATCATGA
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

267

Amino Acids

29.86

Weight (kDa)

7.07

Isoelectric Point (pI)

53.63

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 40 - 186 6.3e-34 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)
AccI GTMKAC 2 cut(s) 332, 442
AciI CCGC 3 cut(s) 98, 215, 521
AcsI RAATTY 1 cut(s) 426
AcyI GRCGYC 1 cut(s) 700
AfaI GTAC 2 cut(s) 14, 263
AgsI TTSAA 6 cut(s) 31, 298, 437, 530, 745, 766
AhlI ACTAGT 1 cut(s) 496
AluBI AGCT 3 cut(s) 307, 518, 590
AluI AGCT 3 cut(s) 307, 518, 590
Alw26I GTCTC 1 cut(s) 401
AoxI GGCC 4 cut(s) 113, 267, 582, 625
ApeKI GCWGC 3 cut(s) 515, 518, 680
ApoI RAATTY 1 cut(s) 426
Asp700I GAANNNNTTC 1 cut(s) 41
AspLEI GCGC 1 cut(s) 546
AspS9I GGNCC 1 cut(s) 626
AsuHPI GGTGA 1 cut(s) 425
AxyI CCTNAGG 1 cut(s) 117
BbsI GAAGAC 2 cut(s) 230, 493
BbvI GCAGC 3 cut(s) 505, 527, 692
BccI CCATC 5 cut(s) 128, 145, 149, 319, 748
BceAI ACGGC 1 cut(s) 243
BcgI CGANNNNNNTGC 2 cut(s) 494, 528
BciVI GTATCC 1 cut(s) 238
BclI TGATCA 1 cut(s) 457
BcoDI GTCTC 1 cut(s) 401
BcuI ACTAGT 1 cut(s) 496
BfaI CTAG 4 cut(s) 182, 188, 488, 497
BfmI CTRYAG 1 cut(s) 720
BfuI GTATCC 1 cut(s) 238
BisI GCNGC 4 cut(s) 99, 516, 519, 681
BlsI GCNGC 4 cut(s) 100, 517, 520, 682
BmgT120I GGNCC 1 cut(s) 626
BmiI GGNNCC 1 cut(s) 628
BmrI ACTGGG 1 cut(s) 624
BmsI GCATC 2 cut(s) 187, 716
BmuI ACTGGG 1 cut(s) 624
BpiI GAAGAC 2 cut(s) 230, 493
Bpu10I CCTNAGC 1 cut(s) 672
BpuEI CTTGAG 1 cut(s) 97
BsaBI GATNNNNATC 1 cut(s) 658
BsaHI GRCGYC 1 cut(s) 700
BsaJI CCNNGG 1 cut(s) 785
BsaXI ACNNNNNCTCC 2 cut(s) 628, 658
Bse1I ACTGG 1 cut(s) 630
Bse21I CCTNAGG 1 cut(s) 117
Bse3DI GCAATG 3 cut(s) 166, 396, 690
Bse8I GATNNNNATC 1 cut(s) 658
BseDI CCNNGG 1 cut(s) 785
BseGI GGATG 3 cut(s) 160, 327, 740
BseJI GATNNNNATC 1 cut(s) 658
BseMI GCAATG 3 cut(s) 166, 396, 690
BseMII CTCAG 1 cut(s) 108
BseNI ACTGG 1 cut(s) 630
BseRI GAGGAG 1 cut(s) 134
BseXI GCAGC 3 cut(s) 505, 527, 692
BshFI GGCC 4 cut(s) 115, 269, 584, 627
BsiSI CCGG 1 cut(s) 732
BsmAI GTCTC 1 cut(s) 401
BsmBI CGTCTC 1 cut(s) 401
BsnI GGCC 4 cut(s) 115, 269, 584, 627
Bsp143I GATC 5 cut(s) 123, 457, 611, 653, 770
Bsp19I CCATGG 1 cut(s) 785
BspACI CCGC 3 cut(s) 98, 215, 521
BspANI GGCC 4 cut(s) 115, 269, 584, 627
BspCNI CTCAG 1 cut(s) 109
BspHI TCATGA 1 cut(s) 800
BspLI GGNNCC 1 cut(s) 628
BsrDI GCAATG 3 cut(s) 166, 396, 690
BsrI ACTGG 1 cut(s) 630
BssECI CCNNGG 1 cut(s) 785
BssMI GATC 5 cut(s) 123, 457, 611, 653, 770
BssNI GRCGYC 1 cut(s) 700
BssT1I CCWWGG 1 cut(s) 785
Bst6I CTCTTC 1 cut(s) 293
BstACI GRCGYC 1 cut(s) 700
BstC8I GCNNGC 1 cut(s) 582
BstDEI CTNAG 2 cut(s) 117, 672
BstDSI CCRYGG 1 cut(s) 785
BstF5I GGATG 3 cut(s) 160, 327, 740
BstHHI GCGC 1 cut(s) 546
BstKTI GATC 5 cut(s) 126, 460, 614, 656, 773
BstMAI GTCTC 1 cut(s) 401
BstMBI GATC 5 cut(s) 123, 457, 611, 653, 770
BstMWI GCNNNNNNNGC 2 cut(s) 677, 755
BstNSI RCATGY 1 cut(s) 731
BstSFI CTRYAG 1 cut(s) 720
BstV1I GCAGC 3 cut(s) 505, 527, 692
BstV2I GAAGAC 2 cut(s) 230, 493
Bsu36I CCTNAGG 1 cut(s) 117
BsuI GTATCC 1 cut(s) 238
BsuRI GGCC 4 cut(s) 115, 269, 584, 627
BtgI CCRYGG 1 cut(s) 785
BtsCI GGATG 3 cut(s) 160, 327, 740
BtsIMutI CAGTG 2 cut(s) 126, 637
Cac8I GCNNGC 1 cut(s) 582
CciI TCATGA 1 cut(s) 800
CfoI GCGC 1 cut(s) 546
Cfr13I GGNCC 1 cut(s) 626
CseI GACGC 1 cut(s) 708
Csp6I GTAC 2 cut(s) 13, 262
CviAII CATG 4 cut(s) 623, 728, 786, 801
CviQI GTAC 2 cut(s) 13, 262
DdeI CTNAG 2 cut(s) 117, 672
DpnI GATC 5 cut(s) 125, 459, 613, 655, 772
DpnII GATC 5 cut(s) 123, 457, 611, 653, 770
Eam1104I CTCTTC 1 cut(s) 293
EarI CTCTTC 1 cut(s) 293
EciI GGCGGA 1 cut(s) 230
Eco130I CCWWGG 1 cut(s) 785
Eco147I AGGCCT 1 cut(s) 115
Eco81I CCTNAGG 1 cut(s) 117
EcoT14I CCWWGG 1 cut(s) 785
ErhI CCWWGG 1 cut(s) 785
Esp3I CGTCTC 1 cut(s) 401
FaeI CATG 4 cut(s) 626, 731, 789, 804
FatI CATG 4 cut(s) 622, 727, 785, 800
FbaI TGATCA 1 cut(s) 457
FblI GTMKAC 2 cut(s) 332, 442
Fnu4HI GCNGC 4 cut(s) 99, 516, 519, 681
FokI GGATG 3 cut(s) 167, 334, 747
Fsp4HI GCNGC 4 cut(s) 99, 516, 519, 681
FspBI CTAG 4 cut(s) 182, 188, 488, 497
GlaI GCGC 1 cut(s) 545
GluI GCNGC 4 cut(s) 99, 516, 519, 681
HaeIII GGCC 4 cut(s) 115, 269, 584, 627
HapII CCGG 1 cut(s) 732
HgaI GACGC 1 cut(s) 708
HhaI GCGC 1 cut(s) 546
Hin1I GRCGYC 1 cut(s) 700
Hin1II CATG 4 cut(s) 626, 731, 789, 804
Hin6I GCGC 1 cut(s) 544
HinP1I GCGC 1 cut(s) 544
HincII GTYRAC 1 cut(s) 333
HindII GTYRAC 1 cut(s) 333
HindIII AAGCTT 2 cut(s) 305, 588
HinfI GANTC 3 cut(s) 329, 449, 637
HpaII CCGG 1 cut(s) 732
HphI GGTGA 1 cut(s) 425
Hpy166II GTNNAC 3 cut(s) 333, 416, 443
Hpy188I TCNGA 2 cut(s) 321, 648
Hpy188III TCNNGA 6 cut(s) 76, 295, 488, 527, 742, 801
Hpy8I GTNNAC 3 cut(s) 333, 416, 443
Hpy99I CGWCG 2 cut(s) 10, 337
HpyAV CCTTC 1 cut(s) 739
HpyCH4IV ACGT 2 cut(s) 418, 474
HpyCH4V TGCA 2 cut(s) 178, 515
HpyF10VI GCNNNNNNNGC 2 cut(s) 677, 755
HpyF3I CTNAG 2 cut(s) 117, 672
HpySE526I ACGT 2 cut(s) 418, 474
Hsp92I GRCGYC 1 cut(s) 700
Hsp92II CATG 4 cut(s) 626, 731, 789, 804
HspAI GCGC 1 cut(s) 544
Ksp22I TGATCA 1 cut(s) 457
Kzo9I GATC 5 cut(s) 123, 457, 611, 653, 770
LpnPI CCDG 5 cut(s) 129, 459, 566, 643, 745
Lsp1109I GCAGC 3 cut(s) 505, 527, 692
LweI GCATC 2 cut(s) 187, 716
MaeI CTAG 4 cut(s) 182, 188, 488, 497
MaeII ACGT 2 cut(s) 418, 474
MaeIII GTNAC 1 cut(s) 475
MalI GATC 5 cut(s) 125, 459, 613, 655, 772
MboI GATC 5 cut(s) 123, 457, 611, 653, 770
MboII GAAGA 8 cut(s) 232, 235, 283, 310, 493, 542, 545, 569
MfeI CAATTG 1 cut(s) 102
MluCI AATT 4 cut(s) 40, 102, 257, 426
MlyI GAGTC 2 cut(s) 338, 646
MnlI CCTC 5 cut(s) 54, 112, 259, 599, 670
MroXI GAANNNNTTC 1 cut(s) 41
MslI CAYNNNNRTG 2 cut(s) 320, 389
MspA1I CMGCKG 1 cut(s) 518
MspI CCGG 1 cut(s) 732
MunI CAATTG 1 cut(s) 102
MwoI GCNNNNNNNGC 2 cut(s) 677, 755
NcoI CCATGG 1 cut(s) 785
NdeII GATC 5 cut(s) 123, 457, 611, 653, 770
NlaIII CATG 4 cut(s) 626, 731, 789, 804
NlaIV GGNNCC 1 cut(s) 628
NspI RCATGY 1 cut(s) 731
PagI TCATGA 1 cut(s) 800
PceI AGGCCT 1 cut(s) 115
PdmI GAANNNNTTC 1 cut(s) 41
PfeI GAWTC 1 cut(s) 449
PkrI GCNGC 4 cut(s) 100, 517, 520, 682
PleI GAGTC 2 cut(s) 337, 645
PpsI GAGTC 2 cut(s) 337, 645
PspN4I GGNNCC 1 cut(s) 628
PspPI GGNCC 1 cut(s) 626
PvuII CAGCTG 1 cut(s) 518
RsaI GTAC 2 cut(s) 14, 263
RsaNI GTAC 2 cut(s) 13, 262
RseI CAYNNNNRTG 2 cut(s) 320, 389
SalI GTCGAC 1 cut(s) 331
SatI GCNGC 4 cut(s) 99, 516, 519, 681
Sau3AI GATC 5 cut(s) 123, 457, 611, 653, 770
Sau96I GGNCC 1 cut(s) 626
SchI GAGTC 2 cut(s) 338, 646
SetI ASST 7 cut(s) 309, 371, 421, 448, 477, 520, 592
SfaNI GCATC 2 cut(s) 187, 716
SfcI CTRYAG 1 cut(s) 720
SmiMI CAYNNNNRTG 2 cut(s) 320, 389
SmlI CTYRAG 1 cut(s) 76
SmoI CTYRAG 1 cut(s) 76
SpeI ACTAGT 1 cut(s) 496
Sse9I AATT 4 cut(s) 40, 102, 257, 426
SseBI AGGCCT 1 cut(s) 115
SsiI CCGC 3 cut(s) 98, 215, 521
SspMI CTAG 4 cut(s) 182, 188, 488, 497
StuI AGGCCT 1 cut(s) 115
StyI CCWWGG 1 cut(s) 785
TaiI ACGT 2 cut(s) 421, 477
TaqI TCGA 3 cut(s) 206, 332, 504
TasI AATT 4 cut(s) 40, 102, 257, 426
TauI GCSGC 1 cut(s) 101
TfiI GAWTC 1 cut(s) 449
TscAI CASTG 2 cut(s) 133, 637
TseI GCWGC 3 cut(s) 515, 518, 680
TspDTI ATGAA 1 cut(s) 210
TspGWI ACGGA 1 cut(s) 632
TspRI CASTG 2 cut(s) 133, 637
XapI RAATTY 1 cut(s) 426
XbaI TCTAGA 1 cut(s) 487
XceI RCATGY 1 cut(s) 731
XcmI CCANNNNNNNNNTGG 1 cut(s) 322
XmiI GTMKAC 2 cut(s) 332, 442
XmnI GAANNNNTTC 1 cut(s) 41
XspI CTAG 4 cut(s) 182, 188, 488, 497
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.