Rroxscaffold_1G00014460

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000001
OG0000154
Physical Location & Seq
Forward (+)
17872137 .. 17877359
5223 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_1G00014460.1

Sequence Viewer

Length: 531 bp
ATGGTTTCGAGGAACCAAGAAGGGGAACAGGGGTTGACCGATGCGCAGTTAGCGTTGTTGGATGATGCAAGGACCAAAGATCACAAGGTGAAGCACTACCGTACCAGGCCATCGACGAGTCACTTTCGAGCAAATTACGGGATGTACACAACTCAAAAGTTGTCCGGGGACTCGCCGAAGAGGAAATTTGGTGGGAATGCTCGAGTTAAGAGGTCTCTTCTTCAAGCTTTGAGAAGAGACTTTGAGATGTTGGAGATGAAGAAAAGTGAGACAATCATTGAGTATTTCGCTAGGGTCACGGTTGTGGCAAACAAAATGAGGAGCAATGGTGAAACCATGCCGGATTCCAAAGTAGTAGAGAAGATCTTGAGGACGTTGACCGAGAGATTCACCTATGTGGTGGTGTCTATCGAGGAGTCAAAGGACACGTACACCCTCTCAATTGATGAGTTGCGAGTTCACTTTGTGGTTCATGAGCGAGAGTTCCACAAAGTTGAATCGAGAAGAAGAAGATCAGGCCTTAAAGATTGA
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

176

Amino Acids

20.57

Weight (kDa)

9.86

Isoelectric Point (pI)

64.01

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 63 - 160 9.9e-14 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: 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)
Acc16I TGCGCA 1 cut(s) 45
AcsI RAATTY 1 cut(s) 185
AdeI CACNNNGTG 2 cut(s) 88, 466
AfaI GTAC 3 cut(s) 103, 146, 431
AfiI CCNNNNNNNGG 1 cut(s) 22
AflIII ACRYGT 1 cut(s) 426
AgsI TTSAA 2 cut(s) 224, 497
AjnI CCWGG 1 cut(s) 104
AleI CACNNNNGTG 2 cut(s) 302, 395
AluBI AGCT 1 cut(s) 227
AluI AGCT 1 cut(s) 227
Alw26I GTCTC 3 cut(s) 219, 231, 263
Ama87I CYCGRG 1 cut(s) 201
AoxI GGCC 2 cut(s) 107, 517
ApoI RAATTY 1 cut(s) 185
AspLEI GCGC 1 cut(s) 46
AspS9I GGNCC 1 cut(s) 72
AsuC2I CCSGG 1 cut(s) 166
AsuHPI GGTGA 3 cut(s) 100, 341, 382
AvaI CYCGRG 1 cut(s) 201
AvaII GGWCC 1 cut(s) 72
BaeI ACNNNNGTAYC 2 cut(s) 85, 118
BccI CCATC 1 cut(s) 118
BciT130I CCWGG 1 cut(s) 106
BcnI CCSGG 1 cut(s) 166
BcoDI GTCTC 3 cut(s) 219, 231, 263
BfaI CTAG 1 cut(s) 291
BglII AGATCT 1 cut(s) 363
Bme1390I CCNGG 2 cut(s) 106, 166
Bme18I GGWCC 1 cut(s) 72
BmeT110I CYCGRG 1 cut(s) 201
BmgT120I GGNCC 1 cut(s) 72
BmiI GGNNCC 1 cut(s) 14
BmrFI CCNGG 2 cut(s) 106, 166
BmsI GCATC 2 cut(s) 31, 55
BpuEI CTTGAG 1 cut(s) 388
BpuMI CCSGG 1 cut(s) 166
BsaAI YACGTR 1 cut(s) 429
BsaI GGTCTC 1 cut(s) 219
BsaJI CCNNGG 1 cut(s) 165
BsaXI ACNNNNNCTCC 2 cut(s) 313, 343
Bsc4I CCNNNNNNNGG 1 cut(s) 22
Bse3DI GCAATG 1 cut(s) 331
BseBI CCWGG 1 cut(s) 106
BseDI CCNNGG 1 cut(s) 165
BseGI GGATG 2 cut(s) 67, 147
BseLI CCNNNNNNNGG 1 cut(s) 22
BseMI GCAATG 1 cut(s) 331
BseRI GAGGAG 2 cut(s) 334, 428
BshFI GGCC 2 cut(s) 109, 519
BsiHKCI CYCGRG 1 cut(s) 201
BsiSI CCGG 2 cut(s) 165, 341
BslFI GGGAC 1 cut(s) 182
BslI CCNNNNNNNGG 1 cut(s) 22
BsmAI GTCTC 3 cut(s) 219, 231, 263
BsmFI GGGAC 1 cut(s) 182
BsmI GAATGC 1 cut(s) 202
BsnI GGCC 2 cut(s) 109, 519
Bso31I GGTCTC 1 cut(s) 219
BsoBI CYCGRG 1 cut(s) 201
Bsp1407I TGTACA 1 cut(s) 144
Bsp143I GATC 3 cut(s) 79, 363, 512
BspANI GGCC 2 cut(s) 109, 519
BspHI TCATGA 1 cut(s) 472
BspLI GGNNCC 1 cut(s) 14
BspTNI GGTCTC 1 cut(s) 219
BsrDI GCAATG 1 cut(s) 331
BsrGI TGTACA 1 cut(s) 144
BssECI CCNNGG 1 cut(s) 165
BssMI GATC 3 cut(s) 79, 363, 512
Bst2UI CCWGG 1 cut(s) 106
Bst4CI ACNGT 2 cut(s) 101, 301
Bst6I CTCTTC 3 cut(s) 173, 222, 229
BstAUI TGTACA 1 cut(s) 144
BstBAI YACGTR 1 cut(s) 429
BstF5I GGATG 2 cut(s) 67, 147
BstHHI GCGC 1 cut(s) 46
BstKTI GATC 3 cut(s) 82, 366, 515
BstMAI GTCTC 3 cut(s) 219, 231, 263
BstMBI GATC 3 cut(s) 79, 363, 512
BstMWI GCNNNNNNNGC 1 cut(s) 50
BstNI CCWGG 1 cut(s) 106
BstSCI CCNGG 2 cut(s) 104, 164
BstX2I RGATCY 1 cut(s) 363
BstYI RGATCY 1 cut(s) 363
BsuRI GGCC 2 cut(s) 109, 519
BtsCI GGATG 2 cut(s) 67, 147
CciI TCATGA 1 cut(s) 472
CfoI GCGC 1 cut(s) 46
Cfr13I GGNCC 1 cut(s) 72
Csp6I GTAC 3 cut(s) 102, 145, 430
CviAII CATG 2 cut(s) 337, 473
CviJI RGCY 3 cut(s) 109, 227, 519
CviKI_1 RGCY 3 cut(s) 109, 227, 519
CviQI GTAC 3 cut(s) 102, 145, 430
DpnI GATC 3 cut(s) 81, 365, 514
DpnII GATC 3 cut(s) 79, 363, 512
DraIII CACNNNGTG 2 cut(s) 88, 466
Eam1104I CTCTTC 3 cut(s) 173, 222, 229
EarI CTCTTC 3 cut(s) 173, 222, 229
Eco147I AGGCCT 1 cut(s) 519
Eco31I GGTCTC 1 cut(s) 219
Eco47I GGWCC 1 cut(s) 72
Eco88I CYCGRG 1 cut(s) 201
EcoRII CCWGG 1 cut(s) 104
FaeI CATG 2 cut(s) 340, 476
FaiI YATR 3 cut(s) 338, 396, 474
FaqI GGGAC 1 cut(s) 182
FatI CATG 2 cut(s) 336, 472
FokI GGATG 2 cut(s) 74, 154
FspBI CTAG 1 cut(s) 291
FspI TGCGCA 1 cut(s) 45
GlaI GCGC 1 cut(s) 45
HaeIII GGCC 2 cut(s) 109, 519
HapII CCGG 2 cut(s) 165, 341
HhaI GCGC 1 cut(s) 46
Hin1II CATG 2 cut(s) 340, 476
Hin6I GCGC 1 cut(s) 44
HinP1I GCGC 1 cut(s) 44
HincII GTYRAC 2 cut(s) 36, 378
HindII GTYRAC 2 cut(s) 36, 378
HindIII AAGCTT 1 cut(s) 225
HinfI GANTC 6 cut(s) 118, 170, 344, 387, 416, 497
HpaII CCGG 2 cut(s) 165, 341
HphI GGTGA 3 cut(s) 100, 341, 382
Hpy166II GTNNAC 5 cut(s) 36, 147, 378, 432, 460
Hpy188III TCNNGA 3 cut(s) 367, 473, 501
Hpy8I GTNNAC 5 cut(s) 36, 147, 378, 432, 460
Hpy99I CGWCG 1 cut(s) 118
HpyAV CCTTC 1 cut(s) 14
HpyCH4III ACNGT 2 cut(s) 101, 301
HpyCH4IV ACGT 2 cut(s) 374, 428
HpyCH4V TGCA 1 cut(s) 68
HpyF10VI GCNNNNNNNGC 1 cut(s) 50
HpySE526I ACGT 2 cut(s) 374, 428
Hsp92II CATG 2 cut(s) 340, 476
HspAI GCGC 1 cut(s) 44
Kzo9I GATC 3 cut(s) 79, 363, 512
LmnI GCTCC 1 cut(s) 321
LpnPI CCDG 6 cut(s) 14, 91, 118, 178, 354, 501
LweI GCATC 2 cut(s) 31, 55
MaeI CTAG 1 cut(s) 291
MaeII ACGT 2 cut(s) 374, 428
MaeIII GTNAC 2 cut(s) 119, 295
MalI GATC 3 cut(s) 81, 365, 514
MboI GATC 3 cut(s) 79, 363, 512
MboII GAAGA 9 cut(s) 190, 209, 212, 246, 271, 373, 516, 519, 522
MfeI CAATTG 1 cut(s) 441
MflI RGATCY 1 cut(s) 363
MluCI AATT 3 cut(s) 133, 185, 441
MlyI GAGTC 3 cut(s) 127, 164, 425
MmeI TCCRAC 2 cut(s) 39, 231
MnlI CCTC 7 cut(s) 3, 174, 204, 312, 363, 406, 446
MseI TTAA 2 cut(s) 207, 522
MslI CAYNNNNRTG 2 cut(s) 302, 395
MspI CCGG 2 cut(s) 165, 341
MspR9I CCNGG 2 cut(s) 106, 166
MunI CAATTG 1 cut(s) 441
Mva1269I GAATGC 1 cut(s) 202
MvaI CCWGG 1 cut(s) 106
MwoI GCNNNNNNNGC 1 cut(s) 50
NciI CCSGG 1 cut(s) 166
NdeII GATC 3 cut(s) 79, 363, 512
NlaIII CATG 2 cut(s) 340, 476
NlaIV GGNNCC 1 cut(s) 14
NmuCI GTSAC 2 cut(s) 119, 295
NsbI TGCGCA 1 cut(s) 45
OliI CACNNNNGTG 2 cut(s) 302, 395
PaeR7I CTCGAG 1 cut(s) 201
PagI TCATGA 1 cut(s) 472
PceI AGGCCT 1 cut(s) 519
PctI GAATGC 1 cut(s) 202
PfeI GAWTC 3 cut(s) 344, 387, 497
PleI GAGTC 3 cut(s) 126, 164, 424
PpsI GAGTC 3 cut(s) 126, 164, 424
Ppu21I YACGTR 1 cut(s) 429
Psp6I CCWGG 1 cut(s) 104
PspGI CCWGG 1 cut(s) 104
PspN4I GGNNCC 1 cut(s) 14
PspPI GGNCC 1 cut(s) 72
PspXI VCTCGAGB 1 cut(s) 201
PsuI RGATCY 1 cut(s) 363
RsaI GTAC 3 cut(s) 103, 146, 431
RsaNI GTAC 3 cut(s) 102, 145, 430
RseI CAYNNNNRTG 2 cut(s) 302, 395
SaqAI TTAA 2 cut(s) 207, 522
Sau3AI GATC 3 cut(s) 79, 363, 512
Sau96I GGNCC 1 cut(s) 72
SchI GAGTC 3 cut(s) 127, 164, 425
ScrFI CCNGG 2 cut(s) 106, 166
SetI ASST 6 cut(s) 90, 215, 229, 377, 395, 431
SfaNI GCATC 2 cut(s) 31, 55
Sfr274I CTCGAG 1 cut(s) 201
SinI GGWCC 1 cut(s) 72
SlaI CTCGAG 1 cut(s) 201
SmiMI CAYNNNNRTG 2 cut(s) 302, 395
SmlI CTYRAG 2 cut(s) 201, 367
SmoI CTYRAG 2 cut(s) 201, 367
Sse9I AATT 3 cut(s) 133, 185, 441
SseBI AGGCCT 1 cut(s) 519
SspMI CTAG 1 cut(s) 291
StuI AGGCCT 1 cut(s) 519
StyD4I CCNGG 2 cut(s) 104, 164
TaaI ACNGT 2 cut(s) 101, 301
TaiI ACGT 2 cut(s) 377, 431
TaqI TCGA 6 cut(s) 8, 113, 127, 202, 411, 500
TaqII GACCGA 2 cut(s) 53, 395
TasI AATT 3 cut(s) 133, 185, 441
TatI WGTACW 1 cut(s) 144
TfiI GAWTC 3 cut(s) 344, 387, 497
Tru1I TTAA 2 cut(s) 207, 522
Tru9I TTAA 2 cut(s) 207, 522
TseFI GTSAC 2 cut(s) 119, 295
Tsp45I GTSAC 2 cut(s) 119, 295
TspDTI ATGAA 2 cut(s) 272, 461
VpaK11BI GGWCC 1 cut(s) 72
XapI RAATTY 1 cut(s) 185
XhoI CTCGAG 1 cut(s) 201
XspI CTAG 1 cut(s) 291
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.