Rroxscaffold_4G00325290

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000004
OG0000128
Physical Location & Seq
Reverse (-)
57013883 .. 57019690
5808 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_4G00325290.1

Sequence Viewer

Length: 522 bp
ATGTGTATTCAAGGCATGCATTGGGACTTACTTGTACATCCTTCGAGGATAAAGCCTCGCACCTGCGAGGAACTTGCCACTCCATCTCATGACATGGAACTTAGCATCGCTAGTCATAGTCGAAGAAGAGATGAAATCATTGAACCACAAAATCATAAACGTGTCATGGAGTCCTTGGCAATCACAACTCCCGTCAAGATCATAACACGAGTCAAGTCAAATAATCAAAACAAGTTGGAGCCGACTCATGATCAAACAAGGCGGTGCACTCTTAGAGAGCTAGAAGCTAAAAGTTACCCTTTTCCGCATTCCGATGTTGTTGACATGTTGGAAGACTTGCTTCAAAAGAAAATAATCAAATTGCCATACCGCAAGCGTCGGAAGAGATGCATCGTATCAATGAACCAAAGTATTGCAAATACCACCGTCAATCAGCGGGAAGTTGGGAGAAGCACGGGTTTGCTAAAGCGTGACTCTAGCTTCGGCCGGGTTGCGGCGTTACCCTTGCTTCGCCGGAAGTAA
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
Retrotrans_gag

Protein Analysis

173

Amino Acids

20.11

Weight (kDa)

10.17

Isoelectric Point (pI)

65.13

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this protein.
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: OG0000128)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g28082 FvH4_2g15191 FvH4_2g31621 FvH4_3g07261 FvH4_3g22806 FvH4_3g26703 FvH4_3g26704 FvH4_3g31360 FvH4_4g01161 FvH4_4g22271 FvH4_4g25732 FvH4_5g00242 FvH4_5g28911 FvH4_5g32461 FvH4_6g13112 FvH4_6g53790 FvH4_6g53791 FvH4_7g03661 FvH4_7g04125 FvH4_7g04126
pyrus_communis pycom01g01950 pycom01g01960 pycom01g03260 pycom01g07760 pycom01g11430 pycom01g23980 pycom02g15030 pycom02g18630 pycom03g12320 pycom03g18810 pycom03g19250 pycom04g05010 pycom04g06520 pycom04g06680 pycom04g09630 pycom04g09640 pycom05g06850 pycom05g07540 pycom05g08940 pycom06g04300 pycom06g05750 pycom06g06960 pycom06g19690 pycom07g08750 pycom07g10700 pycom07g10910 pycom07g27480 pycom07g27790 pycom07g27800 pycom08g13620 pycom09g03540 pycom09g03550 pycom09g09870 pycom09g13480 pycom09g14360 pycom09g14890 pycom09g14930 pycom09g15760 pycom10g02190 pycom10g05270 pycom10g06810 pycom10g06830 pycom10g08060 pycom10g08520 pycom11g02350 pycom11g14170 pycom11g15050 pycom11g19270 pycom11g20160 pycom11g22420 pycom12g08620 pycom12g08630 pycom12g10440 pycom12g16590 pycom133g00190 pycom13g20730 pycom13g22230 pycom13g22670 pycom13g23230 pycom13g23250 pycom13g24880 pycom13g25300 pycom13g28040 pycom13g29010 pycom14g07570 pycom14g18650 pycom15g04500 pycom15g09310 pycom15g27210 pycom15g30810 pycom15g34920 pycom16g16040 pycom16g17260 pycom16g17940 pycom16g20990 pycom16g23470 pycom16g24160 pycom16g24720 pycom16g25910 pycom16g25920 pycom16g26370 pycom17g03310 pycom17g12670 pycom17g17530 pycom17g25090 pycom17g27300 pycom17g27310 pycom420g00140 pycom420g00160 pycom420g00320 pycom505g00220 pycom520g00740 pycom520g01010 pycom520g01020 pycom576g00060 pycom675g00040
rosa_laevigata RLG00000022630
rosa_multiflora Rmu_co7993280.1_g000001 Rmu_co8054704.1_g000001 Rmu_co8148394.1_g000001 Rmu_co8243015.1_g000001 Rmu_co8272095.1_g000001 Rmu_co8282359.1_g000001 Rmu_co8334783.1_g000001 Rmu_co8404405.1_g000001 Rmu_sc0000161.1_g000030 Rmu_sc0000418.1_g000026 Rmu_sc0000488.1_g000015 Rmu_sc0000706.1_g000041 Rmu_sc0000720.1_g000013 Rmu_sc0000776.1_g000022 Rmu_sc0000948.1_g000017 Rmu_sc0001167.1_g000045 Rmu_sc0001167.1_g000047 Rmu_sc0001211.1_g000054 Rmu_sc0001241.1_g000019 Rmu_sc0001307.1_g000021 Rmu_sc0001438.1_g000043 Rmu_sc0001468.1_g000032 Rmu_sc0001851.1_g000020 Rmu_sc0002026.1_g000023 Rmu_sc0002811.1_g000016 Rmu_sc0002958.1_g000002 Rmu_sc0002958.1_g000003 Rmu_sc0003745.1_g000010 Rmu_sc0004234.1_g000006 Rmu_sc0004234.1_g000008 Rmu_sc0005035.1_g000001 Rmu_sc0005320.1_g000010 Rmu_sc0005866.1_g000006 Rmu_sc0006139.1_g000009 Rmu_sc0006504.1_g000008 Rmu_sc0006695.1_g000049 Rmu_sc0006695.1_g000050 Rmu_sc0006981.1_g000001 Rmu_sc0007108.1_g000012 Rmu_sc0007355.1_g000001 Rmu_sc0007873.1_g000015 Rmu_sc0007961.1_g000003 Rmu_sc0008991.1_g000005 Rmu_sc0009528.1_g000009 Rmu_sc0013299.1_g000003 Rmu_sc0013532.1_g000015 Rmu_sc0015524.1_g000001 Rmu_sc0015793.1_g000001 Rmu_sc0015817.1_g000006 Rmu_sc0015930.1_g000003 Rmu_sc0015930.1_g000006 Rmu_sc0016952.1_g000002 Rmu_sc0016952.1_g000003 Rmu_sc0018715.1_g000003 Rmu_sc0018715.1_g000005 Rmu_sc0023934.1_g000003 Rmu_sc0023989.1_g000002 Rmu_sc0023989.1_g000003 Rmu_sc0028612.1_g000001 Rmu_sc0029049.1_g000001 Rmu_sc0029639.1_g000001 Rmu_sc0035263.1_g000001 Rmu_sc0037892.1_g000001 Rmu_ssc0000170.1_g000024 Rmu_ssc0000233.1_g000057 Rmu_ssc0000259.1_g000055 Rmu_ssc0000259.1_g000057
rosa_roxburghii Rroxscaffold_4G00287780 Rroxscaffold_4G00325290 Rroxscaffold_5G00333910 Rroxscaffold_7G00211350
rosa_rugosa Rorug01G0056300 Rorug04G0149000 Rorug07G0222000
rosa_samantha Rh1AG072900 Rh1CG072000
rosa_wichuraiana Rw0G003630 Rw0G005250 Rw0G020770 Rw0G023770 Rw1G005460 Rw1G005980 Rw1G007190 Rw1G011350 Rw1G022520 Rw1G028660 Rw2G018620 Rw2G019490 Rw4G006910 Rw4G013020 Rw4G023970 Rw5G044650 Rw6G006590 Rw6G012210 Rw6G023750 Rw7G027370 Rw7G027460 Rw7G035570

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AarI CACCTGC 1 cut(s) 71
Acc36I ACCTGC 1 cut(s) 71
AciI CCGC 5 cut(s) 262, 305, 370, 436, 494
AcoI YGGCCR 1 cut(s) 484
AfaI GTAC 1 cut(s) 36
AfiI CCNNNNNNNGG 1 cut(s) 493
AflIII ACRYGT 2 cut(s) 160, 324
AgsI TTSAA 3 cut(s) 11, 143, 344
AluBI AGCT 3 cut(s) 280, 287, 480
AluI AGCT 3 cut(s) 280, 287, 480
Alw21I GWGCWC 1 cut(s) 269
Alw44I GTGCAC 1 cut(s) 265
AoxI GGCC 1 cut(s) 484
ApaLI GTGCAC 1 cut(s) 265
ArsI GACNNNNNNTTYG 2 cut(s) 464, 496
AsuC2I CCSGG 1 cut(s) 488
BaeGI GKGCMC 1 cut(s) 269
BauI CACGAG 1 cut(s) 207
BbsI GAAGAC 1 cut(s) 339
Bbv12I GWGCWC 1 cut(s) 269
BccI CCATC 1 cut(s) 91
BcgI CGANNNNNNTGC 2 cut(s) 56, 90
BclI TGATCA 1 cut(s) 250
BcnI CCSGG 1 cut(s) 488
BfaI CTAG 3 cut(s) 111, 281, 477
BfuAI ACCTGC 1 cut(s) 71
BisI GCNGC 1 cut(s) 495
BlsI GCNGC 1 cut(s) 496
Bme1390I CCNGG 1 cut(s) 488
BmiI GGNNCC 1 cut(s) 240
BmrFI CCNGG 1 cut(s) 488
BmsI GCATC 3 cut(s) 114, 377, 399
BpiI GAAGAC 1 cut(s) 339
BpuMI CCSGG 1 cut(s) 488
BsaJI CCNNGG 1 cut(s) 174
Bsc4I CCNNNNNNNGG 1 cut(s) 493
BseDI CCNNGG 1 cut(s) 174
BseGI GGATG 1 cut(s) 37
BseLI CCNNNNNNNGG 1 cut(s) 493
BseSI GKGCMC 1 cut(s) 269
BseX3I CGGCCG 1 cut(s) 484
Bsh1285I CGRYCG 1 cut(s) 487
BshFI GGCC 1 cut(s) 486
BsiEI CGRYCG 1 cut(s) 487
BsiHKAI GWGCWC 1 cut(s) 269
BsiSI CCGG 2 cut(s) 487, 514
BslFI GGGAC 1 cut(s) 38
BslI CCNNNNNNNGG 1 cut(s) 493
BsmFI GGGAC 1 cut(s) 38
BsmI GAATGC 1 cut(s) 307
BsnI GGCC 1 cut(s) 486
Bsp1286I GDGCHC 1 cut(s) 269
Bsp1407I TGTACA 1 cut(s) 34
Bsp143I GATC 2 cut(s) 198, 250
BspACI CCGC 5 cut(s) 262, 305, 370, 436, 494
BspANI GGCC 1 cut(s) 486
BspHI TCATGA 2 cut(s) 88, 247
BspLI GGNNCC 1 cut(s) 240
BspMI ACCTGC 1 cut(s) 71
BsrGI TGTACA 1 cut(s) 34
BssECI CCNNGG 1 cut(s) 174
BssMI GATC 2 cut(s) 198, 250
BssSI CACGAG 1 cut(s) 207
BssT1I CCWWGG 1 cut(s) 174
Bst2BI CACGAG 1 cut(s) 207
Bst4CI ACNGT 1 cut(s) 427
Bst6I CTCTTC 2 cut(s) 121, 377
BstAUI TGTACA 1 cut(s) 34
BstC8I GCNNGC 2 cut(s) 17, 374
BstDEI CTNAG 2 cut(s) 101, 272
BstF5I GGATG 1 cut(s) 37
BstKTI GATC 2 cut(s) 201, 253
BstMBI GATC 2 cut(s) 198, 250
BstMCI CGRYCG 1 cut(s) 487
BstNSI RCATGY 2 cut(s) 19, 328
BstSCI CCNGG 1 cut(s) 486
BstSLI GKGCMC 1 cut(s) 269
BstV2I GAAGAC 1 cut(s) 339
BstZI CGGCCG 1 cut(s) 484
BsuRI GGCC 1 cut(s) 486
BtgZI GCGATG 1 cut(s) 91
BtsCI GGATG 1 cut(s) 37
BveI ACCTGC 1 cut(s) 71
Cac8I GCNNGC 2 cut(s) 17, 374
CciI TCATGA 2 cut(s) 88, 247
CseI GACGC 1 cut(s) 365
Csp6I GTAC 1 cut(s) 35
CviAII CATG 6 cut(s) 16, 89, 94, 166, 248, 325
CviJI RGCY 6 cut(s) 55, 241, 280, 287, 480, 486
CviKI_1 RGCY 6 cut(s) 55, 241, 280, 287, 480, 486
CviQI GTAC 1 cut(s) 35
DdeI CTNAG 2 cut(s) 101, 272
DpnI GATC 2 cut(s) 200, 252
DpnII GATC 2 cut(s) 198, 250
EaeI YGGCCR 1 cut(s) 484
EagI CGGCCG 1 cut(s) 484
Eam1104I CTCTTC 2 cut(s) 121, 377
EarI CTCTTC 2 cut(s) 121, 377
EclXI CGGCCG 1 cut(s) 484
Eco130I CCWWGG 1 cut(s) 174
Eco52I CGGCCG 1 cut(s) 484
EcoT14I CCWWGG 1 cut(s) 174
EcoT22I ATGCAT 2 cut(s) 21, 392
ErhI CCWWGG 1 cut(s) 174
FaeI CATG 6 cut(s) 19, 92, 97, 169, 251, 328
FalI AAGNNNNNCTT 4 cut(s) 283, 315, 324, 356
FaqI GGGAC 1 cut(s) 38
FatI CATG 6 cut(s) 15, 88, 93, 165, 247, 324
FauI CCCGC 1 cut(s) 429
FbaI TGATCA 1 cut(s) 250
Fnu4HI GCNGC 1 cut(s) 495
FokI GGATG 1 cut(s) 24
Fsp4HI GCNGC 1 cut(s) 495
FspBI CTAG 3 cut(s) 111, 281, 477
GluI GCNGC 1 cut(s) 495
HaeIII GGCC 1 cut(s) 486
HapII CCGG 2 cut(s) 487, 514
HgaI GACGC 1 cut(s) 365
Hin1II CATG 6 cut(s) 19, 92, 97, 169, 251, 328
HincII GTYRAC 1 cut(s) 322
HindII GTYRAC 1 cut(s) 322
HinfI GANTC 4 cut(s) 170, 210, 244, 473
HpaII CCGG 2 cut(s) 487, 514
Hpy166II GTNNAC 2 cut(s) 267, 322
Hpy188I TCNGA 2 cut(s) 313, 381
Hpy188III TCNNGA 3 cut(s) 89, 196, 248
Hpy8I GTNNAC 2 cut(s) 267, 322
Hpy99I CGWCG 1 cut(s) 381
HpyAV CCTTC 1 cut(s) 51
HpyCH4III ACNGT 1 cut(s) 427
HpyCH4IV ACGT 1 cut(s) 160
HpyCH4V TGCA 4 cut(s) 19, 267, 390, 416
HpyF3I CTNAG 2 cut(s) 101, 272
HpySE526I ACGT 1 cut(s) 160
Hsp92II CATG 6 cut(s) 19, 92, 97, 169, 251, 328
Ksp22I TGATCA 1 cut(s) 250
Kzo9I GATC 2 cut(s) 198, 250
LmnI GCTCC 1 cut(s) 238
LpnPI CCDG 2 cut(s) 76, 500
LweI GCATC 3 cut(s) 114, 377, 399
MaeI CTAG 3 cut(s) 111, 281, 477
MaeII ACGT 1 cut(s) 160
MaeIII GTNAC 3 cut(s) 293, 470, 498
MalI GATC 2 cut(s) 200, 252
MboI GATC 2 cut(s) 198, 250
MboII GAAGA 4 cut(s) 135, 138, 344, 394
MhlI GDGCHC 1 cut(s) 269
MluCI AATT 1 cut(s) 359
MlyI GAGTC 4 cut(s) 179, 219, 238, 467
MmeI TCCRAC 3 cut(s) 216, 309, 359
MnlI CCTC 3 cut(s) 39, 61, 66
Mph1103I ATGCAT 2 cut(s) 21, 392
MslI CAYNNNNRTG 2 cut(s) 159, 312
MspA1I CMGCKG 1 cut(s) 436
MspI CCGG 2 cut(s) 487, 514
MspR9I CCNGG 1 cut(s) 488
Mva1269I GAATGC 1 cut(s) 307
NciI CCSGG 1 cut(s) 488
NdeII GATC 2 cut(s) 198, 250
NlaIII CATG 6 cut(s) 19, 92, 97, 169, 251, 328
NlaIV GGNNCC 1 cut(s) 240
NmuCI GTSAC 1 cut(s) 470
NsiI ATGCAT 2 cut(s) 21, 392
NspI RCATGY 2 cut(s) 19, 328
PaeI GCATGC 1 cut(s) 19
PagI TCATGA 2 cut(s) 88, 247
PaqCI CACCTGC 1 cut(s) 71
PciI ACATGT 1 cut(s) 324
PctI GAATGC 1 cut(s) 307
PkrI GCNGC 1 cut(s) 496
PleI GAGTC 4 cut(s) 178, 218, 238, 467
PpsI GAGTC 4 cut(s) 178, 218, 238, 467
PscI ACATGT 1 cut(s) 324
PspN4I GGNNCC 1 cut(s) 240
RsaI GTAC 1 cut(s) 36
RsaNI GTAC 1 cut(s) 35
RseI CAYNNNNRTG 2 cut(s) 159, 312
SatI GCNGC 1 cut(s) 495
Sau3AI GATC 2 cut(s) 198, 250
SchI GAGTC 4 cut(s) 179, 219, 238, 467
ScrFI CCNGG 1 cut(s) 488
SduI GDGCHC 1 cut(s) 269
SetI ASST 5 cut(s) 65, 163, 282, 289, 482
SfaNI GCATC 3 cut(s) 114, 377, 399
SmiMI CAYNNNNRTG 2 cut(s) 159, 312
SphI GCATGC 1 cut(s) 19
Sse9I AATT 1 cut(s) 359
SsiI CCGC 5 cut(s) 262, 305, 370, 436, 494
SspMI CTAG 3 cut(s) 111, 281, 477
StyD4I CCNGG 1 cut(s) 486
StyI CCWWGG 1 cut(s) 174
TaaI ACNGT 1 cut(s) 427
TaiI ACGT 1 cut(s) 163
TaqI TCGA 2 cut(s) 44, 121
TasI AATT 1 cut(s) 359
TatI WGTACW 1 cut(s) 34
TauI GCSGC 1 cut(s) 497
TseFI GTSAC 1 cut(s) 470
Tsp45I GTSAC 1 cut(s) 470
TspDTI ATGAA 2 cut(s) 147, 416
VneI GTGCAC 1 cut(s) 265
XceI RCATGY 2 cut(s) 19, 328
XspI CTAG 3 cut(s) 111, 281, 477
Zsp2I ATGCAT 2 cut(s) 21, 392
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.