Rw3G022790

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr3
OG0000154
Physical Location & Seq
Forward (+)
28128402 .. 28129503
1102 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw3G022790.1

Sequence Viewer

Length: 627 bp
ATGGTCATTATGACCATTGGGCCATGCTCATGGAGAACTTCCTTCATTCGAAGGAGTATTGGCACATGGTGGAGATTGGCTCAACGAAAGTTAAGAGAAGATGCAAAACTGAAGGACTTGAAGGTAAAAAACTACTTGTTCCAGGCCATTGACAGAACCATTATGGAGACCATCTTGAATAAGGAGACAGCAAAAGGAATTTGGGACTCGATGAGACAGAAATATCAAGGCTCAACGAAGGTTAAGAGAGCTCAATTGCAAGCGCTTAGAAGGGAGTTTGAATGCCCTAGTTGGGGAAAAATAGCAAACTATGCTGAACTTGAAGAGGAGGAGGAGCTCTTGCTGATGGCCTATGTGGAGTTCCTGGACAGTGGATGCAGTAACCATATGTGTGGCAACAGAAAATGGTTCTTCAACCTCGATGAAACCTTCAAGAATTCTGTGAAGCTTGGCAACAACACTAGAATGGCAGTAACAGGGAAGGGAAACATTAAGCTAGAAGTTCATGGCATGACTCAGGTAATAAGTGACATGTATTATATTCCTGAGTTGAAAAACAATTTGTTGAGTATAGGACAATTGCAAGAAAAAGGCTTGGCAATTCTTATACAGCATGGAAGTGTCTAG
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

208

Amino Acids

24.12

Weight (kDa)

9.33

Isoelectric Point (pI)

34.2

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 33 - 94 1.4e-06 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 121 - 198 3.1e-29 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
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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) 198, 436
AcuI CTGAAG 1 cut(s) 131
AdeI CACNNNGTG 1 cut(s) 69
AfeI AGCGCT 1 cut(s) 264
AfiI CCNNNNNNNGG 2 cut(s) 292, 293
AflIII ACRYGT 1 cut(s) 531
AgsI TTSAA 7 cut(s) 121, 178, 281, 323, 415, 433, 553
AjnI CCWGG 2 cut(s) 141, 363
AluBI AGCT 4 cut(s) 251, 337, 448, 496
AluI AGCT 4 cut(s) 251, 337, 448, 496
Alw21I GWGCWC 2 cut(s) 253, 339
Alw26I GTCTC 3 cut(s) 161, 179, 208
Aor51HI AGCGCT 1 cut(s) 264
AoxI GGCC 3 cut(s) 20, 144, 348
ApoI RAATTY 2 cut(s) 198, 436
AspLEI GCGC 1 cut(s) 265
AspS9I GGNCC 1 cut(s) 20
AsuII TTCGAA 1 cut(s) 49
BanII GRGCYC 2 cut(s) 253, 339
Bbv12I GWGCWC 2 cut(s) 253, 339
BccI CCATC 2 cut(s) 179, 340
BciT130I CCWGG 2 cut(s) 143, 365
BcoDI GTCTC 3 cut(s) 161, 179, 208
BfaI CTAG 4 cut(s) 288, 462, 497, 625
BfoI RGCGCY 1 cut(s) 266
Bme1390I CCNGG 2 cut(s) 143, 365
BmgT120I GGNCC 1 cut(s) 20
BmrFI CCNGG 2 cut(s) 143, 365
BmsI GCATC 2 cut(s) 91, 365
BplI GAGNNNNNCTC 2 cut(s) 64, 96
Bpu14I TTCGAA 1 cut(s) 49
BsaI GGTCTC 1 cut(s) 161
Bsc4I CCNNNNNNNGG 2 cut(s) 292, 293
BseBI CCWGG 2 cut(s) 143, 365
BseGI GGATG 1 cut(s) 380
BseLI CCNNNNNNNGG 2 cut(s) 292, 293
BseMII CTCAG 2 cut(s) 530, 537
BseRI GAGGAG 3 cut(s) 341, 344, 347
BshFI GGCC 3 cut(s) 22, 146, 350
BsiHKAI GWGCWC 2 cut(s) 253, 339
BslFI GGGAC 1 cut(s) 218
BslI CCNNNNNNNGG 2 cut(s) 292, 293
BsmAI GTCTC 3 cut(s) 161, 179, 208
BsmFI GGGAC 1 cut(s) 218
BsmI GAATGC 1 cut(s) 287
BsnI GGCC 3 cut(s) 22, 146, 350
Bso31I GGTCTC 1 cut(s) 161
Bsp119I TTCGAA 1 cut(s) 49
Bsp1286I GDGCHC 2 cut(s) 253, 339
BspANI GGCC 3 cut(s) 22, 146, 350
BspCNI CTCAG 2 cut(s) 529, 538
BspT104I TTCGAA 1 cut(s) 49
BspTNI GGTCTC 1 cut(s) 161
Bst2UI CCWGG 2 cut(s) 143, 365
Bst4CI ACNGT 1 cut(s) 371
Bst6I CTCTTC 1 cut(s) 318
BstAPI GCANNNNNTGC 1 cut(s) 311
BstBI TTCGAA 1 cut(s) 49
BstC8I GCNNGC 1 cut(s) 261
BstDEI CTNAG 3 cut(s) 266, 516, 546
BstF5I GGATG 1 cut(s) 380
BstH2I RGCGCY 1 cut(s) 266
BstHHI GCGC 1 cut(s) 265
BstMAI GTCTC 3 cut(s) 161, 179, 208
BstMWI GCNNNNNNNGC 1 cut(s) 311
BstNI CCWGG 2 cut(s) 143, 365
BstNSI RCATGY 1 cut(s) 535
BstSCI CCNGG 2 cut(s) 141, 363
BstXI CCANNNNNNTGG 2 cut(s) 30, 392
BsuRI GGCC 3 cut(s) 22, 146, 350
BtsCI GGATG 1 cut(s) 380
BtsIMutI CAGTG 1 cut(s) 376
Cac8I GCNNGC 1 cut(s) 261
CfoI GCGC 1 cut(s) 265
Cfr13I GGNCC 1 cut(s) 20
CviAII CATG 7 cut(s) 24, 30, 66, 506, 511, 532, 614
DdeI CTNAG 3 cut(s) 266, 516, 546
DraIII CACNNNGTG 1 cut(s) 69
Eam1104I CTCTTC 1 cut(s) 318
EarI CTCTTC 1 cut(s) 318
Ecl136II GAGCTC 2 cut(s) 251, 337
Eco24I GRGCYC 2 cut(s) 253, 339
Eco31I GGTCTC 1 cut(s) 161
Eco47III AGCGCT 1 cut(s) 264
Eco53kI GAGCTC 2 cut(s) 251, 337
Eco57I CTGAAG 1 cut(s) 131
EcoICRI GAGCTC 2 cut(s) 251, 337
EcoRI GAATTC 1 cut(s) 436
EcoRII CCWGG 2 cut(s) 141, 363
EcoT38I GRGCYC 2 cut(s) 253, 339
FaeI CATG 7 cut(s) 27, 33, 69, 509, 514, 535, 617
FaqI GGGAC 1 cut(s) 218
FatI CATG 7 cut(s) 23, 29, 65, 505, 510, 531, 613
FauNDI CATATG 1 cut(s) 387
FokI GGATG 1 cut(s) 387
FriOI GRGCYC 2 cut(s) 253, 339
FspBI CTAG 4 cut(s) 288, 462, 497, 625
GlaI GCGC 1 cut(s) 264
HaeII RGCGCY 1 cut(s) 266
HaeIII GGCC 3 cut(s) 22, 146, 350
HhaI GCGC 1 cut(s) 265
Hin1II CATG 7 cut(s) 27, 33, 69, 509, 514, 535, 617
Hin6I GCGC 1 cut(s) 263
HinP1I GCGC 1 cut(s) 263
HindIII AAGCTT 1 cut(s) 446
HinfI GANTC 2 cut(s) 206, 514
Hpy188III TCNNGA 3 cut(s) 175, 433, 545
HpyAV CCTTC 8 cut(s) 45, 52, 106, 115, 232, 264, 439, 475
HpyCH4III ACNGT 1 cut(s) 371
HpyCH4V TGCA 4 cut(s) 104, 259, 378, 583
HpyF10VI GCNNNNNNNGC 1 cut(s) 311
HpyF3I CTNAG 3 cut(s) 266, 516, 546
Hsp92II CATG 7 cut(s) 27, 33, 69, 509, 514, 535, 617
HspAI GCGC 1 cut(s) 263
LmnI GCTCC 1 cut(s) 334
LpnPI CCDG 7 cut(s) 128, 155, 350, 377, 462, 503, 558
LweI GCATC 2 cut(s) 91, 365
MaeI CTAG 4 cut(s) 288, 462, 497, 625
MaeIII GTNAC 3 cut(s) 380, 472, 527
MboII GAAGA 3 cut(s) 110, 335, 403
MfeI CAATTG 2 cut(s) 254, 578
MhlI GDGCHC 2 cut(s) 253, 339
MluCI AATT 6 cut(s) 198, 254, 436, 559, 578, 600
MlyI GAGTC 2 cut(s) 200, 508
MnlI CCTC 4 cut(s) 319, 322, 325, 428
MseI TTAA 3 cut(s) 92, 243, 492
MslI CAYNNNNRTG 4 cut(s) 28, 390, 464, 618
MspR9I CCNGG 2 cut(s) 143, 365
MunI CAATTG 2 cut(s) 254, 578
Mva1269I GAATGC 1 cut(s) 287
MvaI CCWGG 2 cut(s) 143, 365
MwoI GCNNNNNNNGC 1 cut(s) 311
NdeI CATATG 1 cut(s) 387
NlaIII CATG 7 cut(s) 27, 33, 69, 509, 514, 535, 617
NmuCI GTSAC 1 cut(s) 527
NspI RCATGY 1 cut(s) 535
NspV TTCGAA 1 cut(s) 49
PciI ACATGT 1 cut(s) 531
PctI GAATGC 1 cut(s) 287
PfoI TCCNGGA 1 cut(s) 363
PleI GAGTC 2 cut(s) 200, 508
PpsI GAGTC 2 cut(s) 200, 508
PscI ACATGT 1 cut(s) 531
Psp124BI GAGCTC 2 cut(s) 253, 339
Psp6I CCWGG 2 cut(s) 141, 363
PspGI CCWGG 2 cut(s) 141, 363
PspPI GGNCC 1 cut(s) 20
RseI CAYNNNNRTG 4 cut(s) 28, 390, 464, 618
SacI GAGCTC 2 cut(s) 253, 339
SaqAI TTAA 3 cut(s) 92, 243, 492
Sau96I GGNCC 1 cut(s) 20
SchI GAGTC 2 cut(s) 200, 508
ScrFI CCNGG 2 cut(s) 143, 365
SduI GDGCHC 2 cut(s) 253, 339
SetI ASST 9 cut(s) 126, 243, 253, 339, 420, 431, 450, 498, 522
SfaNI GCATC 2 cut(s) 91, 365
SfuI TTCGAA 1 cut(s) 49
SmiMI CAYNNNNRTG 4 cut(s) 28, 390, 464, 618
Sse9I AATT 6 cut(s) 198, 254, 436, 559, 578, 600
SspMI CTAG 4 cut(s) 288, 462, 497, 625
SstI GAGCTC 2 cut(s) 253, 339
StyD4I CCNGG 2 cut(s) 141, 363
TaaI ACNGT 1 cut(s) 371
TaqI TCGA 3 cut(s) 49, 209, 420
TasI AATT 6 cut(s) 198, 254, 436, 559, 578, 600
Tru1I TTAA 3 cut(s) 92, 243, 492
Tru9I TTAA 3 cut(s) 92, 243, 492
TscAI CASTG 1 cut(s) 376
TseFI GTSAC 1 cut(s) 527
Tsp45I GTSAC 1 cut(s) 527
TspDTI ATGAA 3 cut(s) 34, 438, 494
TspRI CASTG 1 cut(s) 376
XapI RAATTY 2 cut(s) 198, 436
XceI RCATGY 1 cut(s) 535
XspI CTAG 4 cut(s) 288, 462, 497, 625
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.