Rw2G044060

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr2
OG0000278
Physical Location & Seq
Forward (+)
70746773 .. 70747378
606 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw2G044060.1

Sequence Viewer

Length: 606 bp
ATGGCTGGTGTAGCACAGGTTTCAAATGATTTTGGAGAATTTCTCACAGTCTCCAAAGGTAATTACACTTGTTCCCAATGTGATTGGATATTGGATACTGGTTCTTCTCATCATCTTTGCTCCAGGAGAGAATATTTTGATACGTTCCAAGAAGTCCAAGGATTTGTGACTTGGGGTAATGGCACAAGGCGTCATGTCATGGGTGTTGGAACGGTGAAGATCAAGATGTTTGATGGAGTAGTTCGCACTTTGGGTGATGTTGTATATGTCGCAAGGTTCCGGAGAAATTTAATATCCTTAAGCCAGTTAGACTCTAAAGGCTGCAGGGTTTCTTCAGCAAGGGGAGTTATGAAAATATCACGTGGCTACATGGTCCTAATGAAGGGAGAAAAGTGTGGAAGTATGTTCCGCTTGATAGGAAAAACTCAGACCTCGAAGGTTGAAGGGAAACGTTGTGCACAAGGATGCAGGTACCTGAAGCGGGTCTCGTTTGCGAGCATAGCAAAGACTCCAGTTACAAGTTTCCATGTTTCAGACGATGGTGAGAAAGTAAATCCTGCTAGGAAAAGGGTCAAGTCAATGTCCCTCTTCAGAGTCAACAAGTGA
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

201

Amino Acids

22.46

Weight (kDa)

10.07

Isoelectric Point (pI)

29.04

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pol_BBD PF22936 29 - 108 1.6e-25 Pol polyprotein, beta-barrel domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

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)
Acc36I ACCTGC 1 cut(s) 459
Acc65I GGTACC 1 cut(s) 471
AccB1I GGYRCC 1 cut(s) 471
AccIII TCCGGA 1 cut(s) 279
AciI CCGC 2 cut(s) 409, 481
AclI AACGTT 1 cut(s) 451
AcsI RAATTY 2 cut(s) 38, 286
AcuI CTGAAG 3 cut(s) 318, 497, 574
AcvI CACGTG 1 cut(s) 362
AcyI GRCGYC 1 cut(s) 190
AfaI GTAC 1 cut(s) 473
AfiI CCNNNNNNNGG 2 cut(s) 382, 481
AflII CTTAAG 1 cut(s) 298
AgsI TTSAA 2 cut(s) 24, 443
AjnI CCWGG 1 cut(s) 122
Alw21I GWGCWC 1 cut(s) 460
Alw26I GTCTC 2 cut(s) 55, 490
Alw44I GTGCAC 1 cut(s) 456
Aor13HI TCCGGA 1 cut(s) 279
ApaLI GTGCAC 1 cut(s) 456
ApeKI GCWGC 1 cut(s) 321
ApoI RAATTY 2 cut(s) 38, 286
Asp718I GGTACC 1 cut(s) 471
AspS9I GGNCC 1 cut(s) 373
AsuHPI GGTGA 3 cut(s) 226, 266, 554
AvaII GGWCC 1 cut(s) 373
BaeGI GKGCMC 1 cut(s) 460
BanI GGYRCC 1 cut(s) 471
BbrPI CACGTG 1 cut(s) 362
Bbv12I GWGCWC 1 cut(s) 460
BbvI GCAGC 1 cut(s) 308
BccI CCATC 2 cut(s) 227, 533
BciT130I CCWGG 1 cut(s) 124
BciVI GTATCC 1 cut(s) 88
BcoDI GTCTC 2 cut(s) 55, 490
BfaI CTAG 1 cut(s) 561
BfmI CTRYAG 1 cut(s) 322
BfrI CTTAAG 1 cut(s) 298
BfuAI ACCTGC 1 cut(s) 459
BfuI GTATCC 1 cut(s) 88
BisI GCNGC 1 cut(s) 322
BlsI GCNGC 1 cut(s) 323
Bme1390I CCNGG 1 cut(s) 124
Bme18I GGWCC 1 cut(s) 373
BmgT120I GGNCC 1 cut(s) 373
BmiI GGNNCC 2 cut(s) 278, 473
BmrFI CCNGG 1 cut(s) 124
BmsI GCATC 1 cut(s) 455
BplI GAGNNNNNCTC 2 cut(s) 27, 59
BpmI CTGGAG 2 cut(s) 106, 495
BsaAI YACGTR 1 cut(s) 362
BsaHI GRCGYC 1 cut(s) 190
BsaI GGTCTC 1 cut(s) 490
BsaJI CCNNGG 1 cut(s) 157
BsaWI WCCGGW 1 cut(s) 279
Bsc4I CCNNNNNNNGG 2 cut(s) 382, 481
Bse1I ACTGG 3 cut(s) 103, 304, 512
BseAI TCCGGA 1 cut(s) 279
BseBI CCWGG 1 cut(s) 124
BseDI CCNNGG 1 cut(s) 157
BseGI GGATG 1 cut(s) 470
BseLI CCNNNNNNNGG 2 cut(s) 382, 481
BseMII CTCAG 1 cut(s) 440
BseNI ACTGG 3 cut(s) 103, 304, 512
BseSI GKGCMC 1 cut(s) 460
BseXI GCAGC 1 cut(s) 308
BshNI GGYRCC 1 cut(s) 471
BsiHKAI GWGCWC 1 cut(s) 460
BsiSI CCGG 1 cut(s) 280
BslFI GGGAC 1 cut(s) 568
BslI CCNNNNNNNGG 2 cut(s) 382, 481
BsmAI GTCTC 2 cut(s) 55, 490
BsmFI GGGAC 1 cut(s) 568
Bso31I GGTCTC 1 cut(s) 490
Bsp1286I GDGCHC 1 cut(s) 460
Bsp13I TCCGGA 1 cut(s) 279
Bsp143I GATC 1 cut(s) 219
BspACI CCGC 2 cut(s) 409, 481
BspCNI CTCAG 1 cut(s) 439
BspEI TCCGGA 1 cut(s) 279
BspLI GGNNCC 2 cut(s) 278, 473
BspMAI CTGCAG 1 cut(s) 326
BspMI ACCTGC 1 cut(s) 459
BspT107I GGYRCC 1 cut(s) 471
BspTI CTTAAG 1 cut(s) 298
BspTNI GGTCTC 1 cut(s) 490
BsrI ACTGG 3 cut(s) 103, 304, 512
BssECI CCNNGG 1 cut(s) 157
BssMI GATC 1 cut(s) 219
BssNI GRCGYC 1 cut(s) 190
BssT1I CCWWGG 1 cut(s) 157
Bst2UI CCWGG 1 cut(s) 124
Bst4CI ACNGT 2 cut(s) 49, 214
Bst6I CTCTTC 1 cut(s) 593
BstACI GRCGYC 1 cut(s) 190
BstAFI CTTAAG 1 cut(s) 298
BstBAI YACGTR 1 cut(s) 362
BstC8I GCNNGC 1 cut(s) 496
BstDEI CTNAG 1 cut(s) 426
BstENI CCTNNNNNAGG 1 cut(s) 380
BstF5I GGATG 1 cut(s) 470
BstKTI GATC 1 cut(s) 222
BstMAI GTCTC 2 cut(s) 55, 490
BstMBI GATC 1 cut(s) 219
BstMWI GCNNNNNNNGC 2 cut(s) 11, 500
BstNI CCWGG 1 cut(s) 124
BstSCI CCNGG 1 cut(s) 122
BstSFI CTRYAG 1 cut(s) 322
BstSLI GKGCMC 1 cut(s) 460
BstV1I GCAGC 1 cut(s) 308
BsuI GTATCC 1 cut(s) 88
BtsCI GGATG 1 cut(s) 470
BveI ACCTGC 1 cut(s) 459
Cac8I GCNNGC 1 cut(s) 496
Cfr13I GGNCC 1 cut(s) 373
CseI GACGC 1 cut(s) 179
Csp6I GTAC 1 cut(s) 472
CviAII CATG 4 cut(s) 194, 199, 370, 527
CviJI RGCY 4 cut(s) 5, 303, 321, 366
CviKI_1 RGCY 4 cut(s) 5, 303, 321, 366
CviQI GTAC 1 cut(s) 472
DdeI CTNAG 1 cut(s) 426
DpnI GATC 1 cut(s) 221
DpnII GATC 1 cut(s) 219
Eam1104I CTCTTC 1 cut(s) 593
EarI CTCTTC 1 cut(s) 593
Eco130I CCWWGG 1 cut(s) 157
Eco31I GGTCTC 1 cut(s) 490
Eco47I GGWCC 1 cut(s) 373
Eco57I CTGAAG 3 cut(s) 318, 497, 574
Eco72I CACGTG 1 cut(s) 362
EcoNI CCTNNNNNAGG 1 cut(s) 380
EcoRII CCWGG 1 cut(s) 122
EcoT14I CCWWGG 1 cut(s) 157
ErhI CCWWGG 1 cut(s) 157
FaeI CATG 4 cut(s) 197, 202, 373, 530
FaiI YATR 9 cut(s) 195, 200, 265, 267, 350, 371, 404, 500, 528
FaqI GGGAC 1 cut(s) 568
FatI CATG 4 cut(s) 193, 198, 369, 526
FauI CCCGC 1 cut(s) 474
Fnu4HI GCNGC 1 cut(s) 322
FokI GGATG 1 cut(s) 477
Fsp4HI GCNGC 1 cut(s) 322
FspBI CTAG 1 cut(s) 561
GluI GCNGC 1 cut(s) 322
GsuI CTGGAG 2 cut(s) 106, 495
HapII CCGG 1 cut(s) 280
HgaI GACGC 1 cut(s) 179
Hin1I GRCGYC 1 cut(s) 190
Hin1II CATG 4 cut(s) 197, 202, 373, 530
HincII GTYRAC 1 cut(s) 598
HindII GTYRAC 1 cut(s) 598
HinfI GANTC 3 cut(s) 311, 508, 594
HpaII CCGG 1 cut(s) 280
HphI GGTGA 3 cut(s) 226, 266, 554
Hpy166II GTNNAC 2 cut(s) 458, 598
Hpy188I TCNGA 3 cut(s) 429, 535, 593
Hpy188III TCNNGA 2 cut(s) 223, 280
Hpy8I GTNNAC 2 cut(s) 458, 598
HpyAV CCTTC 3 cut(s) 376, 430, 437
HpyCH4III ACNGT 2 cut(s) 49, 214
HpyCH4IV ACGT 3 cut(s) 143, 361, 451
HpyCH4V TGCA 3 cut(s) 324, 458, 468
HpyF10VI GCNNNNNNNGC 2 cut(s) 11, 500
HpyF3I CTNAG 1 cut(s) 426
HpySE526I ACGT 3 cut(s) 143, 361, 451
Hsp92I GRCGYC 1 cut(s) 190
Hsp92II CATG 4 cut(s) 197, 202, 373, 530
Kpn2I TCCGGA 1 cut(s) 279
KpnI GGTACC 1 cut(s) 475
Kzo9I GATC 1 cut(s) 219
LmnI GCTCC 1 cut(s) 125
Lsp1109I GCAGC 1 cut(s) 308
LweI GCATC 1 cut(s) 455
MaeI CTAG 1 cut(s) 561
MaeII ACGT 3 cut(s) 143, 361, 451
MaeIII GTNAC 2 cut(s) 166, 514
MalI GATC 1 cut(s) 221
MboI GATC 1 cut(s) 219
MboII GAAGA 4 cut(s) 96, 229, 324, 580
MhlI GDGCHC 1 cut(s) 460
MluCI AATT 3 cut(s) 38, 61, 286
MlyI GAGTC 3 cut(s) 305, 502, 603
MmeI TCCRAC 1 cut(s) 187
MnlI CCTC 2 cut(s) 442, 596
MroI TCCGGA 1 cut(s) 279
MseI TTAA 2 cut(s) 290, 299
MslI CAYNNNNRTG 1 cut(s) 463
MspCI CTTAAG 1 cut(s) 298
MspI CCGG 1 cut(s) 280
MspR9I CCNGG 1 cut(s) 124
MvaI CCWGG 1 cut(s) 124
MwoI GCNNNNNNNGC 2 cut(s) 11, 500
NdeII GATC 1 cut(s) 219
NlaIII CATG 4 cut(s) 197, 202, 373, 530
NlaIV GGNNCC 2 cut(s) 278, 473
NmuCI GTSAC 1 cut(s) 166
PfoI TCCNGGA 1 cut(s) 122
PkrI GCNGC 1 cut(s) 323
PleI GAGTC 3 cut(s) 305, 502, 602
PmaCI CACGTG 1 cut(s) 362
PmlI CACGTG 1 cut(s) 362
PpsI GAGTC 3 cut(s) 305, 502, 602
Ppu21I YACGTR 1 cut(s) 362
Psp1406I AACGTT 1 cut(s) 451
Psp6I CCWGG 1 cut(s) 122
PspCI CACGTG 1 cut(s) 362
PspGI CCWGG 1 cut(s) 122
PspN4I GGNNCC 2 cut(s) 278, 473
PspPI GGNCC 1 cut(s) 373
PstI CTGCAG 1 cut(s) 326
RsaI GTAC 1 cut(s) 473
RsaNI GTAC 1 cut(s) 472
RseI CAYNNNNRTG 1 cut(s) 463
SaqAI TTAA 2 cut(s) 290, 299
SatI GCNGC 1 cut(s) 322
Sau3AI GATC 1 cut(s) 219
Sau96I GGNCC 1 cut(s) 373
SchI GAGTC 3 cut(s) 305, 502, 603
ScrFI CCNGG 1 cut(s) 124
SduI GDGCHC 1 cut(s) 460
SfaNI GCATC 1 cut(s) 455
SfcI CTRYAG 1 cut(s) 322
SinI GGWCC 1 cut(s) 373
SmiMI CAYNNNNRTG 1 cut(s) 463
SmlI CTYRAG 1 cut(s) 298
SmoI CTYRAG 1 cut(s) 298
Sse9I AATT 3 cut(s) 38, 61, 286
SsiI CCGC 2 cut(s) 409, 481
SspI AATATT 1 cut(s) 134
SspMI CTAG 1 cut(s) 561
StyD4I CCNGG 1 cut(s) 122
StyI CCWWGG 1 cut(s) 157
TaaI ACNGT 2 cut(s) 49, 214
TaiI ACGT 3 cut(s) 146, 364, 454
TaqI TCGA 1 cut(s) 434
TasI AATT 3 cut(s) 38, 61, 286
Tru1I TTAA 2 cut(s) 290, 299
Tru9I TTAA 2 cut(s) 290, 299
TseFI GTSAC 1 cut(s) 166
TseI GCWGC 1 cut(s) 321
Tsp45I GTSAC 1 cut(s) 166
TspDTI ATGAA 2 cut(s) 365, 395
Vha464I CTTAAG 1 cut(s) 298
VneI GTGCAC 1 cut(s) 456
VpaK11BI GGWCC 1 cut(s) 373
XagI CCTNNNNNAGG 1 cut(s) 380
XapI RAATTY 2 cut(s) 38, 286
XspI CTAG 1 cut(s) 561
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.