Rw2G020790

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr2
OG0000154
Physical Location & Seq
Forward (+)
28467168 .. 28467596
429 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw2G020790.1

Sequence Viewer

Length: 429 bp
ATGGAGACAATTCTCATCAAAGAGATAGCCAAAAACATTTGGGACTCAATGAGACAGAAATACCAAGGTTCTACAAAGGTGAAGAGAGCTCAGCTGCAGGCACTTCGAAGAGAGTTTGAGGTGCTCCAAATGAAAGATGGAGAGACGATAGATGAATACTTTGCTCGGACATTAACCATTGTCAACAAGATGAAAGCTCATGGTGAAAGAATGGAGCAGCTTGTGATTGTAGAGAAAATTCTAAGGTCGATGCCTGTCAAATTTAATTACGTGGTGTGCTCCATAGAAGAATCCAACAATCTCACCACAATGTCTATTGATGAACTACAAAGCAGTCTGCTTGTTCATGAGCAAAGAATGCGTATCCATACCGGAGAGGAGCAAGCTTTGAAGGTGTCCTATGAAGACGGAGTTGGAGCAAGAGGATGA
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

142

Amino Acids

16.48

Weight (kDa)

6.85

Isoelectric Point (pI)

58.1

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 9 - 121 5.6e-23 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
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000154)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g02351 FvH4_1g18383 FvH4_1g18442 FvH4_1g19622 FvH4_2g08148 FvH4_2g16312 FvH4_3g06912 FvH4_3g10761 FvH4_3g12332 FvH4_3g12332 FvH4_3g14182 FvH4_3g21021 FvH4_3g35231 FvH4_3g45132 FvH4_4g08663 FvH4_4g30271 FvH4_4g30272 FvH4_4g30901 FvH4_4g30902 FvH4_5g12471 FvH4_5g22951 FvH4_6g07331 FvH4_6g07332 FvH4_6g41872 FvH4_6g43841 FvH4_6g43842 FvH4_6g48811 FvH4_7g03911 FvH4_7g13272 FvH4_7g21181 FvH4_7g29024 FvH4_7g33702
malus_domestica MD00G1037700.v1.1 MD01G1037300.v1.1 MD01G1096700.v1.1 MD01G1101100.v1.1 MD01G1129400.v1.1 MD02G1295200.v1.1 MD03G1131300.v1.1 MD04G1072100.v1.1 MD05G1104800.v1.1 MD07G1028600.v1.1 MD07G1274600.v1.1 MD08G1027200.v1.1 MD09G1044400.v1.1 MD09G1044700.v1.1 MD09G1129500.v1.1 MD09G1238700.v1.1 MD10G1011700.v1.1 MD10G1071400.v1.1 MD10G1108600.v1.1 MD10G1162100.v1.1 MD10G1162300.v1.1 MD11G1016700.v1.1 MD11G1074500.v1.1 MD15G1058600.v1.1 MD15G1383000.v1.1 MD16G1192200.v1.1 MD17G1077400.v1.1 MD17G1077500.v1.1
pyrus_communis pycom01g03520 pycom02g00350 pycom03g09910 pycom03g13960 pycom03g13970 pycom03g19180 pycom04g08410 pycom04g10140 pycom06g03750 pycom07g09240 pycom07g09260 pycom08g20130 pycom09g11020 pycom10g12690 pycom14g04140 pycom14g05710 pycom16g06380 pycom17g05500 pycom808g00140
rosa_chinensis RchiOBHm_Chr1g0316211 RchiOBHm_Chr1g0319901 RchiOBHm_Chr1g0321811 RchiOBHm_Chr1g0329831 RchiOBHm_Chr1g0330721 RchiOBHm_Chr1g0330731 RchiOBHm_Chr1g0368461 RchiOBHm_Chr1g0381111 RchiOBHm_Chr2g0154461 RchiOBHm_Chr2g0164521 RchiOBHm_Chr2g0175301 RchiOBHm_Chr3g0451301 RchiOBHm_Chr3g0453691 RchiOBHm_Chr3g0470191 RchiOBHm_Chr3g0486561 RchiOBHm_Chr4g0409141 RchiOBHm_Chr4g0409151 RchiOBHm_Chr4g0421231 RchiOBHm_Chr4g0440701 RchiOBHm_Chr5g0018211 RchiOBHm_Chr5g0023611 RchiOBHm_Chr5g0045971 RchiOBHm_Chr5g0056061 RchiOBHm_Chr5g0063381 RchiOBHm_Chr5g0064011 RchiOBHm_Chr5g0064021 RchiOBHm_Chr5g0064041 RchiOBHm_Chr6g0259681 RchiOBHm_Chr6g0259691 RchiOBHm_Chr6g0296531 RchiOBHm_Chr7g0186421 RchiOBHm_Chr7g0192321 RchiOBHm_Chr7g0198271 RchiOBHm_Chr7g0198951 RchiOBHm_Chr7g0237911
rosa_laevigata RLG00000026946
rosa_roxburghii Rroxscaffold_1G00014460 Rroxscaffold_1G00014610 Rroxscaffold_1G00028950 Rroxscaffold_1G00052630 Rroxscaffold_2G00104760 Rroxscaffold_2G00138900 Rroxscaffold_2G00145210 Rroxscaffold_3G00220110 Rroxscaffold_4G00297860 Rroxscaffold_4G00321570 Rroxscaffold_5G00332990 Rroxscaffold_5G00360870
rosa_samantha Rh1AG319600 Rh1CG299100 Rh4DG385900 Rh5BG032200
rosa_wichuraiana Rw0G002380 Rw0G003050 Rw0G003940 Rw1G002730 Rw1G003260 Rw1G005490 Rw1G016140 Rw1G016150 Rw1G017930 Rw1G017940 Rw1G022540 Rw1G022630 Rw1G031080 Rw1G039680 Rw2G003340 Rw2G003720 Rw2G006640 Rw2G020790 Rw2G025650 Rw2G028430 Rw2G029550 Rw2G034920 Rw2G040820 Rw2G048420 Rw2G048570 Rw3G010040 Rw3G022790 Rw3G023350 Rw3G025140 Rw3G028810 Rw4G000680 Rw4G003350 Rw4G004640 Rw4G026650 Rw4G034500 Rw5G008490 Rw5G020650 Rw5G023000 Rw5G033610 Rw5G037280 Rw5G046620 Rw5G050250 Rw6G001410 Rw6G005690 Rw6G005820 Rw6G010920 Rw6G022790 Rw6G023940 Rw6G026290 Rw6G028610 Rw6G031260 Rw6G036550 Rw6G036560 Rw7G015300 Rw7G017250 Rw7G018150 Rw7G031960 Rw7G036490

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AcsI RAATTY 2 cut(s) 237, 260
AgsI TTSAA 1 cut(s) 391
AjuI GAANNNNNNNTTGG 2 cut(s) 396, 428
AluBI AGCT 5 cut(s) 89, 94, 197, 220, 386
AluI AGCT 5 cut(s) 89, 94, 197, 220, 386
Alw21I GWGCWC 3 cut(s) 91, 126, 281
Alw26I GTCTC 2 cut(s) 46, 137
ApeKI GCWGC 2 cut(s) 94, 217
ApoI RAATTY 2 cut(s) 237, 260
AsuHPI GGTGA 3 cut(s) 91, 215, 295
AsuII TTCGAA 1 cut(s) 106
BanII GRGCYC 1 cut(s) 91
BbsI GAAGAC 1 cut(s) 411
Bbv12I GWGCWC 3 cut(s) 91, 126, 281
BbvI GCAGC 2 cut(s) 81, 229
BccI CCATC 1 cut(s) 131
BcgI CGANNNNNNTGC 2 cut(s) 86, 120
BciVI GTATCC 1 cut(s) 374
BcoDI GTCTC 2 cut(s) 46, 137
BfmI CTRYAG 1 cut(s) 95
BfuI GTATCC 1 cut(s) 374
BisI GCNGC 2 cut(s) 95, 218
BlpI GCTNAGC 1 cut(s) 90
BlsI GCNGC 2 cut(s) 96, 219
BmsI GCATC 1 cut(s) 240
BpiI GAAGAC 1 cut(s) 411
Bpu1102I GCTNAGC 1 cut(s) 90
Bpu14I TTCGAA 1 cut(s) 106
BsaAI YACGTR 1 cut(s) 271
BsaJI CCNNGG 1 cut(s) 64
BsaWI WCCGGW 1 cut(s) 371
BseDI CCNNGG 1 cut(s) 64
BseMII CTCAG 1 cut(s) 104
BseRI GAGGAG 1 cut(s) 392
BseXI GCAGC 2 cut(s) 81, 229
BsiHKAI GWGCWC 3 cut(s) 91, 126, 281
BsiSI CCGG 1 cut(s) 372
BslFI GGGAC 1 cut(s) 56
BsmAI GTCTC 2 cut(s) 46, 137
BsmBI CGTCTC 1 cut(s) 137
BsmFI GGGAC 1 cut(s) 56
BsmI GAATGC 1 cut(s) 363
Bsp119I TTCGAA 1 cut(s) 106
Bsp1286I GDGCHC 3 cut(s) 91, 126, 281
Bsp1720I GCTNAGC 1 cut(s) 90
BspCNI CTCAG 1 cut(s) 103
BspHI TCATGA 1 cut(s) 346
BspMAI CTGCAG 1 cut(s) 99
BspT104I TTCGAA 1 cut(s) 106
BssECI CCNNGG 1 cut(s) 64
BssT1I CCWWGG 1 cut(s) 64
Bst6I CTCTTC 2 cut(s) 77, 103
BstAPI GCANNNNNTGC 1 cut(s) 358
BstBAI YACGTR 1 cut(s) 271
BstBI TTCGAA 1 cut(s) 106
BstC8I GCNNGC 2 cut(s) 99, 384
BstDEI CTNAG 2 cut(s) 90, 242
BstMAI GTCTC 2 cut(s) 46, 137
BstMWI GCNNNNNNNGC 1 cut(s) 358
BstSFI CTRYAG 1 cut(s) 95
BstV1I GCAGC 2 cut(s) 81, 229
BstV2I GAAGAC 1 cut(s) 411
BsuI GTATCC 1 cut(s) 374
Cac8I GCNNGC 2 cut(s) 99, 384
CciI TCATGA 1 cut(s) 346
CviAII CATG 2 cut(s) 200, 347
CviJI RGCY 6 cut(s) 29, 89, 94, 197, 220, 386
CviKI_1 RGCY 6 cut(s) 29, 89, 94, 197, 220, 386
DdeI CTNAG 2 cut(s) 90, 242
Eam1104I CTCTTC 2 cut(s) 77, 103
EarI CTCTTC 2 cut(s) 77, 103
Ecl136II GAGCTC 1 cut(s) 89
Eco130I CCWWGG 1 cut(s) 64
Eco24I GRGCYC 1 cut(s) 91
Eco53kI GAGCTC 1 cut(s) 89
EcoICRI GAGCTC 1 cut(s) 89
EcoT14I CCWWGG 1 cut(s) 64
EcoT38I GRGCYC 1 cut(s) 91
ErhI CCWWGG 1 cut(s) 64
Esp3I CGTCTC 1 cut(s) 137
FaeI CATG 2 cut(s) 203, 350
FaiI YATR 5 cut(s) 201, 284, 348, 369, 402
FaqI GGGAC 1 cut(s) 56
FatI CATG 2 cut(s) 199, 346
Fnu4HI GCNGC 2 cut(s) 95, 218
FriOI GRGCYC 1 cut(s) 91
Fsp4HI GCNGC 2 cut(s) 95, 218
GluI GCNGC 2 cut(s) 95, 218
HapII CCGG 1 cut(s) 372
Hin1II CATG 2 cut(s) 203, 350
HincII GTYRAC 1 cut(s) 184
HindII GTYRAC 1 cut(s) 184
HindIII AAGCTT 1 cut(s) 384
HinfI GANTC 2 cut(s) 44, 290
HpaII CCGG 1 cut(s) 372
HphI GGTGA 3 cut(s) 91, 215, 295
Hpy166II GTNNAC 1 cut(s) 184
Hpy188I TCNGA 1 cut(s) 168
Hpy188III TCNNGA 1 cut(s) 347
Hpy8I GTNNAC 1 cut(s) 184
HpyAV CCTTC 1 cut(s) 385
HpyCH4IV ACGT 1 cut(s) 270
HpyCH4V TGCA 1 cut(s) 97
HpyF10VI GCNNNNNNNGC 1 cut(s) 358
HpyF3I CTNAG 2 cut(s) 90, 242
HpySE526I ACGT 1 cut(s) 270
Hsp92II CATG 2 cut(s) 203, 350
LmnI GCTCC 5 cut(s) 129, 214, 284, 379, 416
LpnPI CCDG 3 cut(s) 83, 267, 385
Lsp1109I GCAGC 2 cut(s) 81, 229
LweI GCATC 1 cut(s) 240
MaeII ACGT 1 cut(s) 270
MboII GAAGA 4 cut(s) 94, 120, 299, 416
MhlI GDGCHC 3 cut(s) 91, 126, 281
MluCI AATT 4 cut(s) 9, 237, 260, 265
MlyI GAGTC 1 cut(s) 38
MmeI TCCRAC 2 cut(s) 318, 394
MnlI CCTC 3 cut(s) 112, 370, 416
MseI TTAA 2 cut(s) 173, 264
MslI CAYNNNNRTG 1 cut(s) 308
MspA1I CMGCKG 1 cut(s) 94
MspI CCGG 1 cut(s) 372
Mva1269I GAATGC 1 cut(s) 363
MwoI GCNNNNNNNGC 1 cut(s) 358
NlaIII CATG 2 cut(s) 203, 350
NspV TTCGAA 1 cut(s) 106
PagI TCATGA 1 cut(s) 346
PctI GAATGC 1 cut(s) 363
PfeI GAWTC 1 cut(s) 290
PkrI GCNGC 2 cut(s) 96, 219
PleI GAGTC 1 cut(s) 38
PpsI GAGTC 1 cut(s) 38
Ppu21I YACGTR 1 cut(s) 271
Psp124BI GAGCTC 1 cut(s) 91
PstI CTGCAG 1 cut(s) 99
PvuII CAGCTG 1 cut(s) 94
RseI CAYNNNNRTG 1 cut(s) 308
SacI GAGCTC 1 cut(s) 91
SaqAI TTAA 2 cut(s) 173, 264
SatI GCNGC 2 cut(s) 95, 218
SchI GAGTC 1 cut(s) 38
SduI GDGCHC 3 cut(s) 91, 126, 281
SfaNI GCATC 1 cut(s) 240
SfcI CTRYAG 1 cut(s) 95
SfuI TTCGAA 1 cut(s) 106
SmiMI CAYNNNNRTG 1 cut(s) 308
Sse9I AATT 4 cut(s) 9, 237, 260, 265
SstI GAGCTC 1 cut(s) 91
StyI CCWWGG 1 cut(s) 64
TaiI ACGT 1 cut(s) 273
TaqI TCGA 2 cut(s) 106, 248
TasI AATT 4 cut(s) 9, 237, 260, 265
TfiI GAWTC 1 cut(s) 290
Tru1I TTAA 2 cut(s) 173, 264
Tru9I TTAA 2 cut(s) 173, 264
TseI GCWGC 2 cut(s) 94, 217
TspDTI ATGAA 6 cut(s) 146, 168, 206, 335, 336, 417
TspGWI ACGGA 1 cut(s) 423
XapI RAATTY 2 cut(s) 237, 260
XcmI CCANNNNNNNNNTGG 1 cut(s) 134
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.