Rmu_sc0016952.1_g000003

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_multiflora
Rmu_sc0016952.1
OG0000128
Physical Location & Seq
Forward (+)
11668 .. 12093
426 bp
Loading structure...
UTR
Exon/CDS
Intron
Rmu_sc0016952.1_g000003.1.cds

Sequence Viewer

Length: 426 bp
atgttagagctcaccaacaccaaacaatggaatgacgagccagccatagaattcatcaaccgttggcgtgcattaagcctcgattgcaaggaccgactcttagagttgtcagcagtagaaatgtgtattcaaggcatgcattgggacttactgtacatccttcaagggataaagcctcgtacctttgtagaacttgccactcgagctcatgacatggaacttagcatcgctagtcatggtcgaagaaaaggtgaaatcattgaaccacataatcaaaaaagtgtcatggagtctttggcgatcacaactcttgtcaagatcacagcacgaatcaagtcaaataaccaaaacaagttggagccgactcatgatcaaacaaggcggcacactcttagagagctagaagctaaaagttaccctttttaa
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

141

Amino Acids

16.46

Weight (kDa)

7.85

Isoelectric Point (pI)

45.27

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)
AccB7I CCANNNNNTGG 1 cut(s) 27
AciI CCGC 1 cut(s) 382
AcsI RAATTY 1 cut(s) 50
AfaI GTAC 2 cut(s) 155, 181
AfiI CCNNNNNNNGG 1 cut(s) 27
AgsI TTSAA 3 cut(s) 131, 164, 263
AluBI AGCT 4 cut(s) 10, 206, 400, 407
AluI AGCT 4 cut(s) 10, 206, 400, 407
Alw21I GWGCWC 2 cut(s) 12, 208
Ama87I CYCGRG 1 cut(s) 201
ApoI RAATTY 1 cut(s) 50
AspS9I GGNCC 1 cut(s) 91
AsuHPI GGTGA 2 cut(s) 4, 263
AvaI CYCGRG 1 cut(s) 201
AvaII GGWCC 1 cut(s) 91
BanII GRGCYC 2 cut(s) 12, 208
Bbv12I GWGCWC 2 cut(s) 12, 208
BclI TGATCA 1 cut(s) 370
BfaI CTAG 2 cut(s) 231, 401
BisI GCNGC 1 cut(s) 383
BlsI GCNGC 1 cut(s) 384
Bme18I GGWCC 1 cut(s) 91
BmeT110I CYCGRG 1 cut(s) 201
BmgT120I GGNCC 1 cut(s) 91
BmiI GGNNCC 1 cut(s) 360
BmsI GCATC 1 cut(s) 234
Bsc4I CCNNNNNNNGG 1 cut(s) 27
BseGI GGATG 1 cut(s) 156
BseLI CCNNNNNNNGG 1 cut(s) 27
BsiHKAI GWGCWC 2 cut(s) 12, 208
BsiHKCI CYCGRG 1 cut(s) 201
BslFI GGGAC 1 cut(s) 158
BslI CCNNNNNNNGG 1 cut(s) 27
BsmFI GGGAC 1 cut(s) 158
BsoBI CYCGRG 1 cut(s) 201
Bsp1286I GDGCHC 2 cut(s) 12, 208
Bsp1407I TGTACA 1 cut(s) 153
Bsp143I GATC 3 cut(s) 300, 318, 370
BspACI CCGC 1 cut(s) 382
BspHI TCATGA 2 cut(s) 208, 367
BspLI GGNNCC 1 cut(s) 360
BsrGI TGTACA 1 cut(s) 153
BssMI GATC 3 cut(s) 300, 318, 370
Bst4CI ACNGT 2 cut(s) 62, 153
BstAUI TGTACA 1 cut(s) 153
BstC8I GCNNGC 3 cut(s) 42, 69, 137
BstDEI CTNAG 3 cut(s) 100, 221, 392
BstF5I GGATG 1 cut(s) 156
BstKTI GATC 3 cut(s) 303, 321, 373
BstMBI GATC 3 cut(s) 300, 318, 370
BstMWI GCNNNNNNNGC 2 cut(s) 84, 203
BstNSI RCATGY 1 cut(s) 139
BtgZI GCGATG 1 cut(s) 211
BtsCI GGATG 1 cut(s) 156
Cac8I GCNNGC 3 cut(s) 42, 69, 137
CciI TCATGA 2 cut(s) 208, 367
Cfr13I GGNCC 1 cut(s) 91
Csp6I GTAC 2 cut(s) 154, 180
CviAII CATG 6 cut(s) 136, 209, 214, 236, 286, 368
CviJI RGCY 9 cut(s) 10, 40, 44, 78, 175, 206, 361, 400, 407
CviKI_1 RGCY 9 cut(s) 10, 40, 44, 78, 175, 206, 361, 400, 407
CviQI GTAC 2 cut(s) 154, 180
DdeI CTNAG 3 cut(s) 100, 221, 392
DpnI GATC 3 cut(s) 302, 320, 372
DpnII GATC 3 cut(s) 300, 318, 370
Ecl136II GAGCTC 2 cut(s) 10, 206
Eco24I GRGCYC 2 cut(s) 12, 208
Eco47I GGWCC 1 cut(s) 91
Eco53kI GAGCTC 2 cut(s) 10, 206
Eco88I CYCGRG 1 cut(s) 201
EcoICRI GAGCTC 2 cut(s) 10, 206
EcoRI GAATTC 1 cut(s) 50
EcoT22I ATGCAT 1 cut(s) 141
EcoT38I GRGCYC 2 cut(s) 12, 208
FaeI CATG 6 cut(s) 139, 212, 217, 239, 289, 371
FaiI YATR 8 cut(s) 47, 137, 210, 215, 237, 270, 287, 369
FalI AAGNNNNNCTT 1 cut(s) 403
FaqI GGGAC 1 cut(s) 158
FatI CATG 6 cut(s) 135, 208, 213, 235, 285, 367
FbaI TGATCA 1 cut(s) 370
Fnu4HI GCNGC 1 cut(s) 383
FokI GGATG 1 cut(s) 143
FriOI GRGCYC 2 cut(s) 12, 208
Fsp4HI GCNGC 1 cut(s) 383
FspBI CTAG 2 cut(s) 231, 401
GluI GCNGC 1 cut(s) 383
Hin1II CATG 6 cut(s) 139, 212, 217, 239, 289, 371
HinfI GANTC 4 cut(s) 96, 290, 330, 364
HphI GGTGA 2 cut(s) 4, 263
Hpy188III TCNNGA 3 cut(s) 209, 316, 368
HpyAV CCTTC 1 cut(s) 170
HpyCH4III ACNGT 2 cut(s) 62, 153
HpyCH4V TGCA 3 cut(s) 71, 87, 139
HpyF10VI GCNNNNNNNGC 2 cut(s) 84, 203
HpyF3I CTNAG 3 cut(s) 100, 221, 392
Hsp92II CATG 6 cut(s) 139, 212, 217, 239, 289, 371
Ksp22I TGATCA 1 cut(s) 370
Kzo9I GATC 3 cut(s) 300, 318, 370
LmnI GCTCC 1 cut(s) 358
LpnPI CCDG 1 cut(s) 54
LweI GCATC 1 cut(s) 234
MaeI CTAG 2 cut(s) 231, 401
MaeIII GTNAC 1 cut(s) 413
MalI GATC 3 cut(s) 302, 320, 372
MboI GATC 3 cut(s) 300, 318, 370
MboII GAAGA 1 cut(s) 255
MhlI GDGCHC 2 cut(s) 12, 208
MluCI AATT 1 cut(s) 50
MlyI GAGTC 3 cut(s) 90, 299, 358
MmeI TCCRAC 1 cut(s) 336
MnlI CCTC 2 cut(s) 89, 186
Mph1103I ATGCAT 1 cut(s) 141
MseI TTAA 2 cut(s) 74, 424
MwoI GCNNNNNNNGC 2 cut(s) 84, 203
NdeII GATC 3 cut(s) 300, 318, 370
NlaIII CATG 6 cut(s) 139, 212, 217, 239, 289, 371
NlaIV GGNNCC 1 cut(s) 360
NsiI ATGCAT 1 cut(s) 141
NspI RCATGY 1 cut(s) 139
PaeI GCATGC 1 cut(s) 139
PaeR7I CTCGAG 1 cut(s) 201
PagI TCATGA 2 cut(s) 208, 367
PfeI GAWTC 1 cut(s) 330
PflMI CCANNNNNTGG 1 cut(s) 27
PkrI GCNGC 1 cut(s) 384
PleI GAGTC 3 cut(s) 90, 298, 358
PpsI GAGTC 3 cut(s) 90, 298, 358
Psp124BI GAGCTC 2 cut(s) 12, 208
PspN4I GGNNCC 1 cut(s) 360
PspPI GGNCC 1 cut(s) 91
PspXI VCTCGAGB 1 cut(s) 201
RsaI GTAC 2 cut(s) 155, 181
RsaNI GTAC 2 cut(s) 154, 180
SacI GAGCTC 2 cut(s) 12, 208
SaqAI TTAA 2 cut(s) 74, 424
SatI GCNGC 1 cut(s) 383
Sau3AI GATC 3 cut(s) 300, 318, 370
Sau96I GGNCC 1 cut(s) 91
SchI GAGTC 3 cut(s) 90, 299, 358
SduI GDGCHC 2 cut(s) 12, 208
SetI ASST 6 cut(s) 12, 185, 208, 253, 402, 409
SfaNI GCATC 1 cut(s) 234
Sfr274I CTCGAG 1 cut(s) 201
SinI GGWCC 1 cut(s) 91
SlaI CTCGAG 1 cut(s) 201
SmlI CTYRAG 1 cut(s) 201
SmoI CTYRAG 1 cut(s) 201
SphI GCATGC 1 cut(s) 139
Sse9I AATT 1 cut(s) 50
SsiI CCGC 1 cut(s) 382
SspMI CTAG 2 cut(s) 231, 401
SstI GAGCTC 2 cut(s) 12, 208
TaaI ACNGT 2 cut(s) 62, 153
TaqI TCGA 3 cut(s) 81, 202, 241
TaqII GACCGA 1 cut(s) 108
TasI AATT 1 cut(s) 50
TatI WGTACW 1 cut(s) 153
TauI GCSGC 1 cut(s) 385
TfiI GAWTC 1 cut(s) 330
Tru1I TTAA 2 cut(s) 74, 424
Tru9I TTAA 2 cut(s) 74, 424
TspDTI ATGAA 1 cut(s) 43
Van91I CCANNNNNTGG 1 cut(s) 27
VpaK11BI GGWCC 1 cut(s) 91
XapI RAATTY 1 cut(s) 50
XceI RCATGY 1 cut(s) 139
XhoI CTCGAG 1 cut(s) 201
XspI CTAG 2 cut(s) 231, 401
Zsp2I ATGCAT 1 cut(s) 141
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.