Rroxscaffold_1G00014610

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000001
OG0000154
Physical Location & Seq
Forward (+)
18157690 .. 18158301
612 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_1G00014610.1

Sequence Viewer

Length: 612 bp
ATGAGTGAGGATAAGAGTTTGGCAAAGATCCCTCACTTCGATGGCGTCCACTATGACCATTGGGGTGAACTGTTGGAAAATTTCCTCGGATCAAAGGGTTTATGGAGCCTTATAGAGAATGGTTTCGAGGAACCAAGAAGGGGAACGGGGTTGACCGATGCGCAGTTAGCGTTGTTGGATGATGCAAGGACCAAAGATCACAAGGTGAAGCACTACCTGTACCAGGCCATCGACGAGTCACTTTCGAGCAAATTACGGGACGGACACAACTCAAAAGTTGTCCGGGACTCGCCGAAGAGGAAATTTGGTGGGAATGCTCGAGTTAAGAGGTCTCTTCTTCAAGCTTTGAGAAGAGACTTTGAGATGTTGGAGATGAAGAAAAGTGAGACAATCATTGAGTATTTCGCTAGGGTCACGGTTGTGGCAAACAAAATGAGGAGCAATGGTGAAACCATGCCGGATTCCAAAGTAGTAGAGAAGATCTTGAGGACGTTGACCGAGAGATTCACCTATGTGGTGGTGTCTATCGAGGAGTCAAAGGACACGTACACCCTCTCAATTGATGAGTTGCGAGTTCACTTGTGGTTCATGAGCGAAGTTCCACAAAGTTGA
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

203

Amino Acids

23.45

Weight (kDa)

7.08

Isoelectric Point (pI)

63.86

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 28 - 194 3.6e-19 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)
Acc16I TGCGCA 1 cut(s) 162
AclWI GGATC 2 cut(s) 22, 97
AcsI RAATTY 2 cut(s) 79, 302
AcyI GRCGYC 1 cut(s) 45
AdeI CACNNNGTG 1 cut(s) 205
AfaI GTAC 2 cut(s) 221, 548
AfiI CCNNNNNNNGG 2 cut(s) 140, 223
AflIII ACRYGT 1 cut(s) 543
AgsI TTSAA 1 cut(s) 341
AjnI CCWGG 1 cut(s) 222
AleI CACNNNNGTG 2 cut(s) 419, 512
AluBI AGCT 1 cut(s) 344
AluI AGCT 1 cut(s) 344
Alw26I GTCTC 3 cut(s) 336, 348, 380
AlwI GGATC 2 cut(s) 22, 97
Ama87I CYCGRG 1 cut(s) 318
AoxI GGCC 1 cut(s) 225
ApoI RAATTY 2 cut(s) 79, 302
Asp700I GAANNNNTTC 1 cut(s) 122
AspLEI GCGC 1 cut(s) 163
AspS9I GGNCC 1 cut(s) 189
AsuC2I CCSGG 1 cut(s) 284
AsuHPI GGTGA 4 cut(s) 77, 217, 458, 499
AvaI CYCGRG 1 cut(s) 318
AvaII GGWCC 1 cut(s) 189
BccI CCATC 2 cut(s) 35, 236
BciT130I CCWGG 1 cut(s) 224
BcnI CCSGG 1 cut(s) 284
BcoDI GTCTC 3 cut(s) 336, 348, 380
BfaI CTAG 1 cut(s) 408
BglII AGATCT 1 cut(s) 480
Bme1390I CCNGG 2 cut(s) 224, 284
Bme18I GGWCC 1 cut(s) 189
BmeT110I CYCGRG 1 cut(s) 318
BmgT120I GGNCC 1 cut(s) 189
BmiI GGNNCC 2 cut(s) 107, 132
BmrFI CCNGG 2 cut(s) 224, 284
BmsI GCATC 2 cut(s) 148, 172
BpuEI CTTGAG 1 cut(s) 505
BpuMI CCSGG 1 cut(s) 284
BsaAI YACGTR 1 cut(s) 546
BsaHI GRCGYC 1 cut(s) 45
BsaI GGTCTC 1 cut(s) 336
BsaJI CCNNGG 1 cut(s) 85
BsaXI ACNNNNNCTCC 2 cut(s) 430, 460
Bsc4I CCNNNNNNNGG 2 cut(s) 140, 223
Bse3DI GCAATG 1 cut(s) 448
BseBI CCWGG 1 cut(s) 224
BseDI CCNNGG 1 cut(s) 85
BseGI GGATG 1 cut(s) 184
BseLI CCNNNNNNNGG 2 cut(s) 140, 223
BseMI GCAATG 1 cut(s) 448
BseRI GAGGAG 2 cut(s) 451, 545
BshFI GGCC 1 cut(s) 227
BsiHKCI CYCGRG 1 cut(s) 318
BsiSI CCGG 2 cut(s) 283, 458
BslFI GGGAC 2 cut(s) 272, 299
BslI CCNNNNNNNGG 2 cut(s) 140, 223
BsmAI GTCTC 3 cut(s) 336, 348, 380
BsmFI GGGAC 2 cut(s) 272, 299
BsmI GAATGC 1 cut(s) 319
BsnI GGCC 1 cut(s) 227
Bso31I GGTCTC 1 cut(s) 336
BsoBI CYCGRG 1 cut(s) 318
Bsp143I GATC 4 cut(s) 27, 89, 196, 480
BspANI GGCC 1 cut(s) 227
BspHI TCATGA 1 cut(s) 588
BspLI GGNNCC 2 cut(s) 107, 132
BspPI GGATC 2 cut(s) 22, 97
BspTNI GGTCTC 1 cut(s) 336
BsrDI GCAATG 1 cut(s) 448
BssECI CCNNGG 1 cut(s) 85
BssMI GATC 4 cut(s) 27, 89, 196, 480
BssNI GRCGYC 1 cut(s) 45
Bst2UI CCWGG 1 cut(s) 224
Bst4CI ACNGT 2 cut(s) 72, 418
Bst6I CTCTTC 3 cut(s) 290, 339, 346
BstACI GRCGYC 1 cut(s) 45
BstBAI YACGTR 1 cut(s) 546
BstENI CCTNNNNNAGG 1 cut(s) 221
BstF5I GGATG 1 cut(s) 184
BstHHI GCGC 1 cut(s) 163
BstKTI GATC 4 cut(s) 30, 92, 199, 483
BstMAI GTCTC 3 cut(s) 336, 348, 380
BstMBI GATC 4 cut(s) 27, 89, 196, 480
BstMWI GCNNNNNNNGC 1 cut(s) 167
BstNI CCWGG 1 cut(s) 224
BstSCI CCNGG 2 cut(s) 222, 282
BstX2I RGATCY 2 cut(s) 27, 480
BstYI RGATCY 2 cut(s) 27, 480
BsuRI GGCC 1 cut(s) 227
BtsCI GGATG 1 cut(s) 184
CciI TCATGA 1 cut(s) 588
CfoI GCGC 1 cut(s) 163
Cfr13I GGNCC 1 cut(s) 189
CseI GACGC 1 cut(s) 34
Csp6I GTAC 2 cut(s) 220, 547
CviAII CATG 2 cut(s) 454, 589
CviJI RGCY 3 cut(s) 108, 227, 344
CviKI_1 RGCY 3 cut(s) 108, 227, 344
CviQI GTAC 2 cut(s) 220, 547
DpnI GATC 4 cut(s) 29, 91, 198, 482
DpnII GATC 4 cut(s) 27, 89, 196, 480
DraIII CACNNNGTG 1 cut(s) 205
Eam1104I CTCTTC 3 cut(s) 290, 339, 346
EarI CTCTTC 3 cut(s) 290, 339, 346
Eco31I GGTCTC 1 cut(s) 336
Eco47I GGWCC 1 cut(s) 189
Eco88I CYCGRG 1 cut(s) 318
EcoNI CCTNNNNNAGG 1 cut(s) 221
EcoRII CCWGG 1 cut(s) 222
FaeI CATG 2 cut(s) 457, 592
FaiI YATR 6 cut(s) 54, 103, 113, 455, 513, 590
FaqI GGGAC 2 cut(s) 272, 299
FatI CATG 2 cut(s) 453, 588
FokI GGATG 1 cut(s) 191
FspBI CTAG 1 cut(s) 408
FspI TGCGCA 1 cut(s) 162
GlaI GCGC 1 cut(s) 162
HaeIII GGCC 1 cut(s) 227
HapII CCGG 2 cut(s) 283, 458
HgaI GACGC 1 cut(s) 34
HhaI GCGC 1 cut(s) 163
Hin1I GRCGYC 1 cut(s) 45
Hin1II CATG 2 cut(s) 457, 592
Hin6I GCGC 1 cut(s) 161
HinP1I GCGC 1 cut(s) 161
HincII GTYRAC 2 cut(s) 153, 495
HindII GTYRAC 2 cut(s) 153, 495
HindIII AAGCTT 1 cut(s) 342
HinfI GANTC 5 cut(s) 236, 287, 461, 504, 533
HpaII CCGG 2 cut(s) 283, 458
HphI GGTGA 4 cut(s) 77, 217, 458, 499
Hpy166II GTNNAC 6 cut(s) 49, 68, 153, 495, 549, 577
Hpy188I TCNGA 1 cut(s) 89
Hpy188III TCNNGA 2 cut(s) 484, 589
Hpy8I GTNNAC 6 cut(s) 49, 68, 153, 495, 549, 577
Hpy99I CGWCG 1 cut(s) 236
HpyAV CCTTC 1 cut(s) 132
HpyCH4III ACNGT 2 cut(s) 72, 418
HpyCH4IV ACGT 2 cut(s) 491, 545
HpyCH4V TGCA 1 cut(s) 185
HpyF10VI GCNNNNNNNGC 1 cut(s) 167
HpySE526I ACGT 2 cut(s) 491, 545
Hsp92I GRCGYC 1 cut(s) 45
Hsp92II CATG 2 cut(s) 457, 592
HspAI GCGC 1 cut(s) 161
Kzo9I GATC 4 cut(s) 27, 89, 196, 480
LmnI GCTCC 2 cut(s) 105, 438
LpnPI CCDG 5 cut(s) 209, 230, 236, 296, 471
LweI GCATC 2 cut(s) 148, 172
MaeI CTAG 1 cut(s) 408
MaeII ACGT 2 cut(s) 491, 545
MaeIII GTNAC 2 cut(s) 237, 412
MalI GATC 4 cut(s) 29, 91, 198, 482
MboI GATC 4 cut(s) 27, 89, 196, 480
MboII GAAGA 6 cut(s) 307, 326, 329, 363, 388, 490
MfeI CAATTG 1 cut(s) 558
MflI RGATCY 2 cut(s) 27, 480
MluCI AATT 4 cut(s) 79, 251, 302, 558
MlyI GAGTC 3 cut(s) 245, 281, 542
MmeI TCCRAC 3 cut(s) 54, 156, 348
MnlI CCTC 9 cut(s) 42, 95, 121, 291, 321, 429, 480, 523, 563
MroXI GAANNNNTTC 1 cut(s) 122
MseI TTAA 1 cut(s) 324
MslI CAYNNNNRTG 4 cut(s) 39, 63, 419, 512
MspI CCGG 2 cut(s) 283, 458
MspR9I CCNGG 2 cut(s) 224, 284
MunI CAATTG 1 cut(s) 558
Mva1269I GAATGC 1 cut(s) 319
MvaI CCWGG 1 cut(s) 224
MwoI GCNNNNNNNGC 1 cut(s) 167
NciI CCSGG 1 cut(s) 284
NdeII GATC 4 cut(s) 27, 89, 196, 480
NlaIII CATG 2 cut(s) 457, 592
NlaIV GGNNCC 2 cut(s) 107, 132
NmuCI GTSAC 2 cut(s) 237, 412
NsbI TGCGCA 1 cut(s) 162
OliI CACNNNNGTG 2 cut(s) 419, 512
PaeR7I CTCGAG 1 cut(s) 318
PagI TCATGA 1 cut(s) 588
PctI GAATGC 1 cut(s) 319
PdmI GAANNNNTTC 1 cut(s) 122
PfeI GAWTC 2 cut(s) 461, 504
PfoI TCCNGGA 1 cut(s) 282
PleI GAGTC 3 cut(s) 244, 281, 541
PpsI GAGTC 3 cut(s) 244, 281, 541
Ppu21I YACGTR 1 cut(s) 546
Psp6I CCWGG 1 cut(s) 222
PspGI CCWGG 1 cut(s) 222
PspN4I GGNNCC 2 cut(s) 107, 132
PspPI GGNCC 1 cut(s) 189
PspXI VCTCGAGB 1 cut(s) 318
PsuI RGATCY 2 cut(s) 27, 480
RsaI GTAC 2 cut(s) 221, 548
RsaNI GTAC 2 cut(s) 220, 547
RseI CAYNNNNRTG 4 cut(s) 39, 63, 419, 512
SaqAI TTAA 1 cut(s) 324
Sau3AI GATC 4 cut(s) 27, 89, 196, 480
Sau96I GGNCC 1 cut(s) 189
SchI GAGTC 3 cut(s) 245, 281, 542
ScrFI CCNGG 2 cut(s) 224, 284
SetI ASST 7 cut(s) 207, 219, 332, 346, 494, 512, 548
SfaNI GCATC 2 cut(s) 148, 172
Sfr274I CTCGAG 1 cut(s) 318
SinI GGWCC 1 cut(s) 189
SlaI CTCGAG 1 cut(s) 318
SmiMI CAYNNNNRTG 4 cut(s) 39, 63, 419, 512
SmlI CTYRAG 2 cut(s) 318, 484
SmoI CTYRAG 2 cut(s) 318, 484
Sse9I AATT 4 cut(s) 79, 251, 302, 558
SspMI CTAG 1 cut(s) 408
StyD4I CCNGG 2 cut(s) 222, 282
TaaI ACNGT 2 cut(s) 72, 418
TaiI ACGT 2 cut(s) 494, 548
TaqI TCGA 6 cut(s) 39, 126, 231, 245, 319, 528
TaqII GACCGA 2 cut(s) 170, 512
TasI AATT 4 cut(s) 79, 251, 302, 558
TfiI GAWTC 2 cut(s) 461, 504
Tru1I TTAA 1 cut(s) 324
Tru9I TTAA 1 cut(s) 324
TseFI GTSAC 2 cut(s) 237, 412
Tsp45I GTSAC 2 cut(s) 237, 412
TspDTI ATGAA 2 cut(s) 389, 577
TspGWI ACGGA 1 cut(s) 276
VpaK11BI GGWCC 1 cut(s) 189
XagI CCTNNNNNAGG 1 cut(s) 221
XapI RAATTY 2 cut(s) 79, 302
XhoI CTCGAG 1 cut(s) 318
XmnI GAANNNNTTC 1 cut(s) 122
XspI CTAG 1 cut(s) 408
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.