Rh6BG428800

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr6B
OG0000278
Physical Location & Seq
Reverse (-)
64926154 .. 64927850
1697 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh6BG428800.1

Sequence Viewer

Length: 792 bp
ATGCCTGAACCAGTTTCCCCCGACGATATTTGGCATCCACAACTAGGATGCGACCAAGACTATAATCTAAACGCTCCATCATGGGAAATCGAGAAGTTCAATGGAAAGAACAATTTCAAGATGTGGCAAGTTGAGGTATGTGATGTCCTAGCCGTTGAGGGTTTAGTTGAAGCTCTGGATGGGAAACCCAGTTACATGAAGCAAGCTGAGTGGAAGGTGCTTGATCAGAAAGCTTGTTCGATACTTCGGTTCTATATGTCCAAAAAGGTCAAGCAGAAAGTCATGGCAGCGAAATCCGCGAAAGAGATTTTGGAAAAGCTTGGGAAAATTTATTTGAATAACTCATTTAATGAGCGAATTCTCAAGATGCAGCTTTACAAGTTGAGGATGGATGAGAGGATTACTAGTATGCAGGAGCATGTAGATGAGTTTAACAGGAGGGTCTGGGAGCTTTCAGGGTATGATGTGGAGTTTAGCGACGAAGACAAGGTTGCAATTCTTCTGGCCTCGCTTCCTGAAAAGTATAATGATCTAGTGATGGGTATGATGTATGGGAAGGACAGTGTAGTTTTTGATGATGTCGTATCTTTGCTTCTATTTAAGGAGAGTAAGAATGCTGAAGCTAGAGCTCGAGTGACAAAAGATCAGAGTTGTGGTGGTTCGAAGAGTTCCAGGTCTTCTAGCTCGAGAAATTATGAAGGGAAAGAGTGTTATTACTGTCATGAAATTGGACACATTCTGAATCACTGTCCCAAGCTGCAGCTGAAGAAGAGAAATAAGAATTTGTTCTAA
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

263

Amino Acids

30.49

Weight (kDa)

7.55

Isoelectric Point (pI)

59.54

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 64 - 205 4.5e-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 1 cut(s) 297
AcsI RAATTY 3 cut(s) 327, 357, 781
AcuI CTGAAG 2 cut(s) 639, 785
AfiI CCNNNNNNNGG 1 cut(s) 44
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
Alw21I GWGCWC 1 cut(s) 631
Ama87I CYCGRG 2 cut(s) 630, 685
AoxI GGCC 1 cut(s) 504
ApeKI GCWGC 4 cut(s) 287, 370, 757, 760
ApoI RAATTY 3 cut(s) 327, 357, 781
Asp700I GAANNNNTTC 2 cut(s) 113, 785
AsuII TTCGAA 1 cut(s) 662
AvaI CYCGRG 2 cut(s) 630, 685
BaeI ACNNNNGTAYC 2 cut(s) 233, 266
BanII GRGCYC 1 cut(s) 631
BarI GAAGNNNNNNTAC 2 cut(s) 576, 608
BbsI GAAGAC 2 cut(s) 489, 669
Bbv12I GWGCWC 1 cut(s) 631
BbvI GCAGC 4 cut(s) 299, 382, 744, 772
BccI CCATC 4 cut(s) 85, 173, 382, 532
BceAI ACGGC 1 cut(s) 137
BciT130I CCWGG 1 cut(s) 673
BclI TGATCA 1 cut(s) 223
BcuI ACTAGT 1 cut(s) 404
BfaI CTAG 6 cut(s) 44, 149, 405, 533, 624, 681
BfmI CTRYAG 1 cut(s) 758
BisI GCNGC 4 cut(s) 288, 371, 758, 761
BlsI GCNGC 4 cut(s) 289, 372, 759, 762
Bme1390I CCNGG 1 cut(s) 673
BmeT110I CYCGRG 2 cut(s) 630, 685
BmrFI CCNGG 1 cut(s) 673
BmrI ACTGGG 1 cut(s) 183
BmsI GCATC 3 cut(s) 38, 43, 357
BmuI ACTGGG 1 cut(s) 183
BpiI GAAGAC 2 cut(s) 489, 669
Bpu14I TTCGAA 1 cut(s) 662
BpuEI CTTGAG 1 cut(s) 347
Bsc4I CCNNNNNNNGG 1 cut(s) 44
Bse1I ACTGG 2 cut(s) 11, 189
BseBI CCWGG 1 cut(s) 673
BseGI GGATG 5 cut(s) 34, 53, 184, 393, 397
BseLI CCNNNNNNNGG 1 cut(s) 44
BseMII CTCAG 1 cut(s) 198
BseNI ACTGG 2 cut(s) 11, 189
BseXI GCAGC 4 cut(s) 299, 382, 744, 772
Bsh1236I CGCG 1 cut(s) 299
BshFI GGCC 1 cut(s) 506
BsiHKAI GWGCWC 1 cut(s) 631
BsiHKCI CYCGRG 2 cut(s) 630, 685
BslFI GGGAC 1 cut(s) 735
BslI CCNNNNNNNGG 1 cut(s) 44
BsmFI GGGAC 1 cut(s) 735
BsmI GAATGC 1 cut(s) 619
BsnI GGCC 1 cut(s) 506
BsoBI CYCGRG 2 cut(s) 630, 685
Bsp119I TTCGAA 1 cut(s) 662
Bsp1286I GDGCHC 1 cut(s) 631
Bsp143I GATC 3 cut(s) 223, 529, 643
BspACI CCGC 1 cut(s) 297
BspANI GGCC 1 cut(s) 506
BspCNI CTCAG 1 cut(s) 199
BspFNI CGCG 1 cut(s) 299
BspHI TCATGA 1 cut(s) 721
BspMAI CTGCAG 1 cut(s) 762
BspT104I TTCGAA 1 cut(s) 662
BsrI ACTGG 2 cut(s) 11, 189
BssMI GATC 3 cut(s) 223, 529, 643
Bst2UI CCWGG 1 cut(s) 673
Bst4CI ACNGT 3 cut(s) 563, 719, 749
Bst6I CTCTTC 2 cut(s) 659, 764
BstBI TTCGAA 1 cut(s) 662
BstC8I GCNNGC 1 cut(s) 204
BstDEI CTNAG 1 cut(s) 207
BstF5I GGATG 5 cut(s) 34, 53, 184, 393, 397
BstFNI CGCG 1 cut(s) 299
BstKTI GATC 3 cut(s) 226, 532, 646
BstMBI GATC 3 cut(s) 223, 529, 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) 758
BstUI CGCG 1 cut(s) 299
BstV1I GCAGC 4 cut(s) 299, 382, 744, 772
BstV2I GAAGAC 2 cut(s) 489, 669
BsuRI GGCC 1 cut(s) 506
BtsCI GGATG 5 cut(s) 34, 53, 184, 393, 397
BtsIMutI CAGTG 2 cut(s) 568, 745
Cac8I GCNNGC 1 cut(s) 204
CciI TCATGA 1 cut(s) 721
CspCI CAANNNNNGTGG 2 cut(s) 191, 226
CviAII CATG 5 cut(s) 81, 196, 283, 419, 722
DdeI CTNAG 1 cut(s) 207
DpnI GATC 3 cut(s) 225, 531, 645
DpnII GATC 3 cut(s) 223, 529, 643
Eam1104I CTCTTC 2 cut(s) 659, 764
EarI CTCTTC 2 cut(s) 659, 764
Ecl136II GAGCTC 1 cut(s) 629
Eco24I GRGCYC 1 cut(s) 631
Eco53kI GAGCTC 1 cut(s) 629
Eco57I CTGAAG 2 cut(s) 639, 785
Eco88I CYCGRG 2 cut(s) 630, 685
EcoICRI GAGCTC 1 cut(s) 629
EcoRI GAATTC 1 cut(s) 357
EcoRII CCWGG 1 cut(s) 671
EcoT38I GRGCYC 1 cut(s) 631
FaeI CATG 5 cut(s) 84, 199, 286, 422, 725
FaqI GGGAC 1 cut(s) 735
FatI CATG 5 cut(s) 80, 195, 282, 418, 721
FbaI TGATCA 1 cut(s) 223
Fnu4HI GCNGC 4 cut(s) 288, 371, 758, 761
FokI GGATG 5 cut(s) 21, 60, 191, 400, 404
FriOI GRGCYC 1 cut(s) 631
Fsp4HI GCNGC 4 cut(s) 288, 371, 758, 761
FspBI CTAG 6 cut(s) 44, 149, 405, 533, 624, 681
GluI GCNGC 4 cut(s) 288, 371, 758, 761
HaeIII GGCC 1 cut(s) 506
Hin1II CATG 5 cut(s) 84, 199, 286, 422, 725
HindIII AAGCTT 2 cut(s) 231, 317
HinfI GANTC 1 cut(s) 742
Hpy188I TCNGA 3 cut(s) 228, 648, 741
Hpy188III TCNNGA 7 cut(s) 91, 118, 176, 364, 515, 687, 722
Hpy99I CGWCG 2 cut(s) 26, 482
HpyAV CCTTC 3 cut(s) 208, 550, 692
HpyCH4III ACNGT 3 cut(s) 563, 719, 749
HpyCH4V TGCA 4 cut(s) 370, 412, 494, 760
HpyF10VI GCNNNNNNNGC 1 cut(s) 296
HpyF3I CTNAG 1 cut(s) 207
Hsp92II CATG 5 cut(s) 84, 199, 286, 422, 725
Ksp22I TGATCA 1 cut(s) 223
Kzo9I GATC 3 cut(s) 223, 529, 643
LmnI GCTCC 3 cut(s) 79, 415, 448
Lsp1109I GCAGC 4 cut(s) 299, 382, 744, 772
LweI GCATC 3 cut(s) 38, 43, 357
MaeI CTAG 6 cut(s) 44, 149, 405, 533, 624, 681
MaeIII GTNAC 2 cut(s) 191, 634
MalI GATC 3 cut(s) 225, 531, 645
MboI GATC 3 cut(s) 223, 529, 643
MboII GAAGA 6 cut(s) 491, 494, 669, 676, 778, 781
MhlI GDGCHC 1 cut(s) 631
MluCI AATT 7 cut(s) 112, 327, 357, 495, 691, 726, 781
MnlI CCTC 6 cut(s) 127, 151, 378, 390, 432, 517
MroXI GAANNNNTTC 2 cut(s) 113, 785
MseI TTAA 3 cut(s) 348, 432, 600
MslI CAYNNNNRTG 1 cut(s) 423
MspA1I CMGCKG 1 cut(s) 763
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 3 cut(s) 223, 529, 643
NlaIII CATG 5 cut(s) 84, 199, 286, 422, 725
NmuCI GTSAC 1 cut(s) 634
NspI RCATGY 1 cut(s) 422
NspV TTCGAA 1 cut(s) 662
PaeR7I CTCGAG 2 cut(s) 630, 685
PagI TCATGA 1 cut(s) 721
PctI GAATGC 1 cut(s) 619
PdmI GAANNNNTTC 2 cut(s) 113, 785
PfeI GAWTC 1 cut(s) 742
PkrI GCNGC 4 cut(s) 289, 372, 759, 762
Psp124BI GAGCTC 1 cut(s) 631
Psp6I CCWGG 1 cut(s) 671
PspGI CCWGG 1 cut(s) 671
PspXI VCTCGAGB 1 cut(s) 630
PstI CTGCAG 1 cut(s) 762
PvuII CAGCTG 1 cut(s) 763
RseI CAYNNNNRTG 1 cut(s) 423
SacI GAGCTC 1 cut(s) 631
SaqAI TTAA 3 cut(s) 348, 432, 600
SatI GCNGC 4 cut(s) 288, 371, 758, 761
Sau3AI GATC 3 cut(s) 223, 529, 643
ScrFI CCNGG 1 cut(s) 673
SduI GDGCHC 1 cut(s) 631
SfaNI GCATC 3 cut(s) 38, 43, 357
SfcI CTRYAG 1 cut(s) 758
Sfr274I CTCGAG 2 cut(s) 630, 685
SfuI TTCGAA 1 cut(s) 662
SlaI CTCGAG 2 cut(s) 630, 685
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, 495, 691, 726, 781
SsiI CCGC 1 cut(s) 297
SspMI CTAG 6 cut(s) 44, 149, 405, 533, 624, 681
SstI GAGCTC 1 cut(s) 631
StyD4I CCNGG 1 cut(s) 671
TaaI ACNGT 3 cut(s) 563, 719, 749
TaqI TCGA 5 cut(s) 90, 239, 631, 662, 686
TasI AATT 7 cut(s) 112, 327, 357, 495, 691, 726, 781
TfiI GAWTC 1 cut(s) 742
Tru1I TTAA 3 cut(s) 348, 432, 600
Tru9I TTAA 3 cut(s) 348, 432, 600
TscAI CASTG 2 cut(s) 568, 752
TseFI GTSAC 1 cut(s) 634
TseI GCWGC 4 cut(s) 287, 370, 757, 760
Tsp45I GTSAC 1 cut(s) 634
TspDTI ATGAA 3 cut(s) 212, 711, 738
TspRI CASTG 2 cut(s) 568, 752
XapI RAATTY 3 cut(s) 327, 357, 781
XceI RCATGY 1 cut(s) 422
XhoI CTCGAG 2 cut(s) 630, 685
XmnI GAANNNNTTC 2 cut(s) 113, 785
XspI CTAG 6 cut(s) 44, 149, 405, 533, 624, 681
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.