Rw6G015860

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr6
OG0000258
Physical Location & Seq
Forward (+)
30686671 .. 30688816
2146 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw6G015860.1

Sequence Viewer

Length: 828 bp
ATGGATCAATCGGTATCTACTATGAAGAATCATGTGGAGAAACCTGAGAAATTCAAGGGTTCAGATTTCAAACGTTGGCAACAGAAGATGTTGTTCTATTTGACAACTCTTCATGTGGCAGATGTTCTCACAACCGAGGCTCCAAAGGATCTTCCCGAAGGAGATGGAGAGAATGTTCCAACTGATGCTCAAAAGGCCGAAAATCAGAAGGCCATTGTTGCCTGGGCGAGCAATGTGTTTCTGTGCAAGAATTATATCCTCAATGCCTTAGACGATTCCTTGTATGATATTTACTCATCATTCAAAACAGCAAAGGAATTATGGGAGTCGTTGGACAACAAATATAAGACTGAAGTTGCTTGTTCAAAGAAATTTGTCATTGGCAAGTTTCTGAATTACAAGATGGTCGATGCCAAGTCTGTTGTCAAGCAAGTGGAGGAACTTCAAGTCATTGTTCATGAGTTAGATGAAGAAGGTATGGGATTGAACTCGAATTTTCTTGTTGGTTCTGTTATTGAAAAGTTACCTCCTTCATGGAAAGATTTCAAAGTATATCTGAAACATCTAACTGAGGATATGAATTTTGAGCAATTGGTTCTAAAACTTCGTGTTGAAGAGGATCACCGGAAGAATGAAAGGGCTGATGCTACTTCTATGGAGCCAAACGCAAACATGATTGGAGGAAGTCCATCAAAGGCCAAGTTTCAGAAAAACAAAGGCAAGAATGTTGCTGCCAAACCAAGTCTTGCTGCTGTCAAGAAGTCACTCGCCCCACAAAAGACCAAATTCCCTTTCCAAAGAGAACTAAACTTGGACCAAAAACAATAG
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

Protein Analysis

275

Amino Acids

31.34

Weight (kDa)

8.55

Isoelectric Point (pI)

40.94

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 63 - 213 1.1e-25 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: OG0000258)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G00980
fragaria_vesca FvH4_1g25682 FvH4_2g13961 FvH4_2g20162 FvH4_2g24753 FvH4_3g12191 FvH4_3g12632 FvH4_3g16171 FvH4_4g05871 FvH4_4g05873 FvH4_4g10121 FvH4_4g15488 FvH4_4g23911 FvH4_4g27782 FvH4_5g08912 FvH4_5g23001 FvH4_5g24552 FvH4_5g32801 FvH4_5g32802 FvH4_6g05093 FvH4_6g19722 FvH4_6g20391 FvH4_6g33792 FvH4_7g01381 FvH4_7g16761 FvH4_7g16761 FvH4_7g16761
malus_domestica MD01G1082500.v1.1 MD15G1436400.v1.1
prunus_persica Prupe.2G021400_v2.0.a1 Prupe.2G052400_v2.0.a1 Prupe.2G065000_v2.0.a1 Prupe.2G187700_v2.0.a1 Prupe.2G187800_v2.0.a1 Prupe.2G189900_v2.0.a1 Prupe.2G191300_v2.0.a1 Prupe.2G191700_v2.0.a1 Prupe.4G265600_v2.0.a1 Prupe.7G014200_v2.0.a1 Prupe.7G039000_v2.0.a1
pyrus_communis pycom01g05590 pycom01g05910 pycom02g12230 pycom02g25840 pycom03g15580 pycom04g04480 pycom05g09230 pycom05g23350 pycom05g23360 pycom07g08380 pycom09g01980 pycom09g01990 pycom11g18190 pycom11g18200 pycom11g21580 pycom13g04160 pycom15g25800 pycom16g16210 pycom16g17230 pycom16g24560 pycom16g25700 pycom17g11020
rosa_chinensis RchiOBHm_Chr1g0359981 RchiOBHm_Chr2g0151961 RchiOBHm_Chr2g0171331 RchiOBHm_Chr5g0081471 RchiOBHm_Chr6g0283031 RchiOBHm_Chr7g0197111 RchiOBHm_Chr7g0222601
rosa_laevigata RLG00000027843 RLG00000027845 RLG00000030065
rosa_multiflora Rmu_sc0000381.1_g000031 Rmu_sc0001179.1_g000035 Rmu_sc0001616.1_g000046 Rmu_sc0001851.1_g000032 Rmu_sc0002152.1_g000013 Rmu_sc0004031.1_g000015 Rmu_sc0004645.1_g000003 Rmu_sc0007393.1_g000001 Rmu_sc0008949.1_g000003 Rmu_sc0009799.1_g000011 Rmu_sc0011614.1_g000001 Rmu_sc0011699.1_g000009 Rmu_sc0019280.1_g000001 Rmu_sc0023984.1_g000001 Rmu_ssc0000050.1_g000036
rosa_roxburghii Rroxscaffold_1G00022650 Rroxscaffold_1G00033480 Rroxscaffold_3G00270250 Rroxscaffold_4G00296600 Rroxscaffold_4G00296760 Rroxscaffold_6G00409840
rosa_rugosa Rorug01G0273800 Rorug01G0273900 Rorug01G0274000
rosa_samantha Rh1AG287300 Rh1AG288100 Rh1BG253000 Rh1BG253500 Rh1BG399800 Rh1CG270400 Rh1CG271000 Rh1DG282000 Rh1DG282500 Rh4DG126500 Rh5DG194600 Rh5DG461100
rosa_wichuraiana Rw0G009130 Rw1G002590 Rw1G008490 Rw1G012210 Rw1G014290 Rw1G014490 Rw1G025510 Rw2G025840 Rw2G026170 Rw2G036510 Rw3G003050 Rw4G009270 Rw5G002350 Rw5G013930 Rw5G019500 Rw5G025890 Rw5G029960 Rw5G032360 Rw6G009890 Rw6G015670 Rw6G015860 Rw7G010030 Rw7G032600 Rw7G032770

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AclI AACGTT 1 cut(s) 73
AclWI GGATC 3 cut(s) 12, 156, 627
AcsI RAATTY 5 cut(s) 50, 371, 493, 580, 785
AcuI CTGAAG 1 cut(s) 372
AgsI TTSAA 9 cut(s) 55, 70, 304, 366, 446, 487, 518, 547, 614
AjnI CCWGG 1 cut(s) 221
AjuI GAANNNNNNNTTGG 2 cut(s) 776, 808
AloI GAACNNNNNNTCC 2 cut(s) 159, 191
AlwI GGATC 3 cut(s) 12, 156, 627
AoxI GGCC 3 cut(s) 195, 210, 696
ApeKI GCWGC 2 cut(s) 731, 749
ApoI RAATTY 5 cut(s) 50, 371, 493, 580, 785
Asp700I GAANNNNTTC 1 cut(s) 542
AspS9I GGNCC 1 cut(s) 814
AsuHPI GGTGA 1 cut(s) 614
AvaII GGWCC 1 cut(s) 814
BbvI GCAGC 2 cut(s) 718, 736
BccI CCATC 3 cut(s) 158, 397, 697
BciT130I CCWGG 1 cut(s) 223
BisI GCNGC 2 cut(s) 732, 750
BlsI GCNGC 2 cut(s) 733, 751
Bme1390I CCNGG 1 cut(s) 223
Bme18I GGWCC 1 cut(s) 814
BmgT120I GGNCC 1 cut(s) 814
BmiI GGNNCC 2 cut(s) 141, 660
BmrFI CCNGG 1 cut(s) 223
BmsI GCATC 3 cut(s) 175, 400, 634
BsaJI CCNNGG 2 cut(s) 135, 222
BsaWI WCCGGW 1 cut(s) 624
BsaXI ACNNNNNCTCC 4 cut(s) 124, 154, 159, 189
Bse3DI GCAATG 1 cut(s) 238
BseBI CCWGG 1 cut(s) 223
BseDI CCNNGG 2 cut(s) 135, 222
BseMI GCAATG 1 cut(s) 238
BseMII CTCAG 2 cut(s) 36, 561
BseXI GCAGC 2 cut(s) 718, 736
BshFI GGCC 3 cut(s) 197, 212, 698
BsiSI CCGG 1 cut(s) 625
BsnI GGCC 3 cut(s) 197, 212, 698
Bsp143I GATC 3 cut(s) 4, 148, 619
BspANI GGCC 3 cut(s) 197, 212, 698
BspCNI CTCAG 2 cut(s) 37, 562
BspHI TCATGA 1 cut(s) 457
BspLI GGNNCC 2 cut(s) 141, 660
BspPI GGATC 3 cut(s) 12, 156, 627
BsrDI GCAATG 1 cut(s) 238
BssECI CCNNGG 2 cut(s) 135, 222
BssMI GATC 3 cut(s) 4, 148, 619
Bst2UI CCWGG 1 cut(s) 223
Bst6I CTCTTC 2 cut(s) 114, 609
BstC8I GCNNGC 1 cut(s) 229
BstDEI CTNAG 3 cut(s) 45, 268, 570
BstKTI GATC 3 cut(s) 7, 151, 622
BstMBI GATC 3 cut(s) 4, 148, 619
BstMWI GCNNNNNNNGC 2 cut(s) 194, 218
BstNI CCWGG 1 cut(s) 223
BstSCI CCNGG 1 cut(s) 221
BstV1I GCAGC 2 cut(s) 718, 736
BstX2I RGATCY 1 cut(s) 148
BstYI RGATCY 1 cut(s) 148
BsuRI GGCC 3 cut(s) 197, 212, 698
Cac8I GCNNGC 1 cut(s) 229
CciI TCATGA 1 cut(s) 457
Cfr13I GGNCC 1 cut(s) 814
CviAII CATG 5 cut(s) 32, 113, 458, 534, 673
CviJI RGCY 6 cut(s) 140, 197, 212, 641, 661, 698
CviKI_1 RGCY 6 cut(s) 140, 197, 212, 641, 661, 698
DdeI CTNAG 3 cut(s) 45, 268, 570
DpnI GATC 3 cut(s) 6, 150, 621
DpnII GATC 3 cut(s) 4, 148, 619
Eam1104I CTCTTC 2 cut(s) 114, 609
EarI CTCTTC 2 cut(s) 114, 609
Eco47I GGWCC 1 cut(s) 814
Eco57I CTGAAG 1 cut(s) 372
EcoRII CCWGG 1 cut(s) 221
FaeI CATG 5 cut(s) 35, 116, 461, 537, 676
FatI CATG 5 cut(s) 31, 112, 457, 533, 672
Fnu4HI GCNGC 2 cut(s) 732, 750
Fsp4HI GCNGC 2 cut(s) 732, 750
GluI GCNGC 2 cut(s) 732, 750
HaeIII GGCC 3 cut(s) 197, 212, 698
HapII CCGG 1 cut(s) 625
Hin1II CATG 5 cut(s) 35, 116, 461, 537, 676
HinfI GANTC 3 cut(s) 28, 275, 326
HpaII CCGG 1 cut(s) 625
HphI GGTGA 1 cut(s) 614
Hpy188I TCNGA 5 cut(s) 64, 207, 393, 558, 708
Hpy188III TCNNGA 3 cut(s) 155, 458, 757
HpyAV CCTTC 4 cut(s) 152, 202, 467, 540
HpyCH4IV ACGT 1 cut(s) 73
HpyCH4V TGCA 1 cut(s) 246
HpyF10VI GCNNNNNNNGC 2 cut(s) 194, 218
HpyF3I CTNAG 3 cut(s) 45, 268, 570
HpySE526I ACGT 1 cut(s) 73
Hsp92II CATG 5 cut(s) 35, 116, 461, 537, 676
Kzo9I GATC 3 cut(s) 4, 148, 619
LmnI GCTCC 2 cut(s) 145, 658
LpnPI CCDG 4 cut(s) 57, 208, 235, 638
Lsp1109I GCAGC 2 cut(s) 718, 736
LweI GCATC 3 cut(s) 175, 400, 634
MaeII ACGT 1 cut(s) 73
MaeIII GTNAC 2 cut(s) 522, 762
MalI GATC 3 cut(s) 6, 150, 621
MboI GATC 3 cut(s) 4, 148, 619
MboII GAAGA 7 cut(s) 37, 97, 101, 143, 482, 626, 640
MfeI CAATTG 1 cut(s) 590
MflI RGATCY 1 cut(s) 148
MluCI AATT 9 cut(s) 50, 250, 317, 371, 394, 493, 580, 590, 785
MlyI GAGTC 1 cut(s) 335
MmeI TCCRAC 2 cut(s) 203, 312
MnlI CCTC 7 cut(s) 130, 269, 430, 537, 565, 610, 674
MroXI GAANNNNTTC 1 cut(s) 542
MspI CCGG 1 cut(s) 625
MspR9I CCNGG 1 cut(s) 223
MunI CAATTG 1 cut(s) 590
MvaI CCWGG 1 cut(s) 223
MwoI GCNNNNNNNGC 2 cut(s) 194, 218
NdeII GATC 3 cut(s) 4, 148, 619
NlaIII CATG 5 cut(s) 35, 116, 461, 537, 676
NlaIV GGNNCC 2 cut(s) 141, 660
NmuCI GTSAC 1 cut(s) 762
PagI TCATGA 1 cut(s) 457
PdmI GAANNNNTTC 1 cut(s) 542
PfeI GAWTC 2 cut(s) 28, 275
PkrI GCNGC 2 cut(s) 733, 751
PleI GAGTC 1 cut(s) 334
PpsI GAGTC 1 cut(s) 334
Psp1406I AACGTT 1 cut(s) 73
Psp6I CCWGG 1 cut(s) 221
PspGI CCWGG 1 cut(s) 221
PspN4I GGNNCC 2 cut(s) 141, 660
PspPI GGNCC 1 cut(s) 814
PsuI RGATCY 1 cut(s) 148
SatI GCNGC 2 cut(s) 732, 750
Sau3AI GATC 3 cut(s) 4, 148, 619
Sau96I GGNCC 1 cut(s) 814
SchI GAGTC 1 cut(s) 335
ScrFI CCNGG 1 cut(s) 223
SetI ASST 4 cut(s) 46, 76, 478, 529
SfaNI GCATC 3 cut(s) 175, 400, 634
SinI GGWCC 1 cut(s) 814
Sse9I AATT 9 cut(s) 50, 250, 317, 371, 394, 493, 580, 590, 785
StyD4I CCNGG 1 cut(s) 221
TaiI ACGT 1 cut(s) 76
TaqI TCGA 2 cut(s) 408, 491
TasI AATT 9 cut(s) 50, 250, 317, 371, 394, 493, 580, 590, 785
TfiI GAWTC 2 cut(s) 28, 275
TseFI GTSAC 1 cut(s) 762
TseI GCWGC 2 cut(s) 731, 749
Tsp45I GTSAC 1 cut(s) 762
TspDTI ATGAA 7 cut(s) 38, 101, 446, 483, 522, 593, 648
VpaK11BI GGWCC 1 cut(s) 814
XapI RAATTY 5 cut(s) 50, 371, 493, 580, 785
XmnI GAANNNNTTC 1 cut(s) 542
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.