Rmu_sc0023989.1_g000003

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_multiflora
Rmu_sc0023989.1
OG0000128
Physical Location & Seq
Forward (+)
12154 .. 12666
513 bp
Loading structure...
UTR
Exon/CDS
Intron
Rmu_sc0023989.1_g000003.1.cds

Sequence Viewer

Length: 513 bp
atggaagttagcatcgctagtcatggtcgaagaaaaggtgaaatcgttaaaccacataatcagaaacttgtcatggagtctttggcgatcacagctcctgtcaaaatcacagtacaaaacaagttggagccaactcatggtcaaacaaggcaacacactcttagagagctagaagctaaaagttaccctttttcagattccgatgttgctgacatgttggaagattttcttcaaaagaaaataatcaaactgccaaactgcaaacgtctggaagagatgcatcgcatcaatgacccaaagtactgcaaataccattgtgtcatcggtcacccggcggagaagtgctttgtgttgaaagacctcaacatgaagctcgcacaacaaggaaaaatttgtttagacattgaagctgacgtggctcaatcaaatcatgctgccatcatctttgaacaactcaaagtagtgtcgtcgtcacctttgctgggggcatgctacttgcgtaaattgccttag
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

170

Amino Acids

19.27

Weight (kDa)

8.86

Isoelectric Point (pI)

44.99

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) 137
AciI CCGC 1 cut(s) 335
AcsI RAATTY 1 cut(s) 390
AfaI GTAC 2 cut(s) 114, 302
AfiI CCNNNNNNNGG 2 cut(s) 137, 482
AflIII ACRYGT 1 cut(s) 213
AgsI TTSAA 4 cut(s) 233, 355, 407, 449
AjiI CACGTC 1 cut(s) 415
AluBI AGCT 5 cut(s) 95, 169, 176, 373, 410
AluI AGCT 5 cut(s) 95, 169, 176, 373, 410
AlwNI CAGNNNCTG 1 cut(s) 98
ApeKI GCWGC 1 cut(s) 434
ApoI RAATTY 1 cut(s) 390
Asp700I GAANNNNTTC 1 cut(s) 225
AsuC2I CCSGG 1 cut(s) 332
AsuHPI GGTGA 3 cut(s) 50, 320, 465
BbvI GCAGC 1 cut(s) 421
BccI CCATC 1 cut(s) 446
BcnI CCSGG 1 cut(s) 332
BfaI CTAG 2 cut(s) 18, 170
BisI GCNGC 1 cut(s) 435
BlsI GCNGC 1 cut(s) 436
BmcAI AGTACT 1 cut(s) 302
Bme1390I CCNGG 1 cut(s) 332
BmgBI CACGTC 1 cut(s) 415
BmiI GGNNCC 1 cut(s) 129
BmrFI CCNGG 1 cut(s) 332
BmsI GCATC 4 cut(s) 21, 267, 289, 294
BpuMI CCSGG 1 cut(s) 332
Bsc4I CCNNNNNNNGG 2 cut(s) 137, 482
BseLI CCNNNNNNNGG 2 cut(s) 137, 482
BseXI GCAGC 1 cut(s) 421
BseYI CCCAGC 1 cut(s) 481
BsiSI CCGG 1 cut(s) 332
BslI CCNNNNNNNGG 2 cut(s) 137, 482
Bsp143I GATC 1 cut(s) 87
BspACI CCGC 1 cut(s) 335
BspLI GGNNCC 1 cut(s) 129
BssMI GATC 1 cut(s) 87
Bst4CI ACNGT 1 cut(s) 112
Bst6I CTCTTC 1 cut(s) 267
BstC8I GCNNGC 2 cut(s) 375, 490
BstDEI CTNAG 2 cut(s) 161, 510
BstEII GGTNACC 1 cut(s) 326
BstKTI GATC 1 cut(s) 90
BstMBI GATC 1 cut(s) 87
BstMWI GCNNNNNNNGC 3 cut(s) 92, 416, 505
BstNSI RCATGY 2 cut(s) 217, 492
BstPI GGTNACC 1 cut(s) 326
BstSCI CCNGG 1 cut(s) 330
BstV1I GCAGC 1 cut(s) 421
BtgZI GCGATG 1 cut(s) 266
BtrI CACGTC 1 cut(s) 415
Cac8I GCNNGC 2 cut(s) 375, 490
CaiI CAGNNNCTG 1 cut(s) 98
Csp6I GTAC 2 cut(s) 113, 301
CviAII CATG 7 cut(s) 23, 73, 137, 214, 367, 431, 489
CviJI RGCY 7 cut(s) 95, 130, 169, 176, 373, 410, 419
CviKI_1 RGCY 7 cut(s) 95, 130, 169, 176, 373, 410, 419
CviQI GTAC 2 cut(s) 113, 301
DdeI CTNAG 2 cut(s) 161, 510
DpnI GATC 1 cut(s) 89
DpnII GATC 1 cut(s) 87
Eam1104I CTCTTC 1 cut(s) 267
EarI CTCTTC 1 cut(s) 267
EciI GGCGGA 1 cut(s) 350
Eco91I GGTNACC 1 cut(s) 326
EcoO65I GGTNACC 1 cut(s) 326
EcoT22I ATGCAT 1 cut(s) 282
FaeI CATG 7 cut(s) 26, 76, 140, 217, 370, 434, 492
FaiI YATR 8 cut(s) 24, 57, 74, 138, 215, 368, 432, 490
FalI AAGNNNNNCTT 4 cut(s) 172, 204, 213, 245
FatI CATG 7 cut(s) 22, 72, 136, 213, 366, 430, 488
Fnu4HI GCNGC 1 cut(s) 435
Fsp4HI GCNGC 1 cut(s) 435
FspBI CTAG 2 cut(s) 18, 170
GluI GCNGC 1 cut(s) 435
GsaI CCCAGC 1 cut(s) 485
HapII CCGG 1 cut(s) 332
Hin1II CATG 7 cut(s) 26, 76, 140, 217, 370, 434, 492
HinfI GANTC 2 cut(s) 77, 197
HpaII CCGG 1 cut(s) 332
HphI GGTGA 3 cut(s) 50, 320, 465
Hpy188I TCNGA 3 cut(s) 63, 196, 202
Hpy188III TCNNGA 1 cut(s) 269
Hpy99I CGWCG 1 cut(s) 472
HpyCH4III ACNGT 1 cut(s) 112
HpyCH4IV ACGT 2 cut(s) 265, 414
HpyCH4V TGCA 3 cut(s) 261, 280, 306
HpyF10VI GCNNNNNNNGC 3 cut(s) 92, 416, 505
HpyF3I CTNAG 2 cut(s) 161, 510
HpySE526I ACGT 2 cut(s) 265, 414
Hsp92II CATG 7 cut(s) 26, 76, 140, 217, 370, 434, 492
Kzo9I GATC 1 cut(s) 87
LmnI GCTCC 2 cut(s) 100, 127
LpnPI CCDG 4 cut(s) 111, 254, 345, 467
Lsp1109I GCAGC 1 cut(s) 421
LweI GCATC 4 cut(s) 21, 267, 289, 294
MaeI CTAG 2 cut(s) 18, 170
MaeII ACGT 2 cut(s) 265, 414
MaeIII GTNAC 3 cut(s) 182, 326, 471
MalI GATC 1 cut(s) 89
MboI GATC 1 cut(s) 87
MboII GAAGA 4 cut(s) 42, 221, 233, 284
MluCI AATT 2 cut(s) 390, 503
MlyI GAGTC 1 cut(s) 86
MmeI TCCRAC 2 cut(s) 105, 198
MnlI CCTC 1 cut(s) 371
Mph1103I ATGCAT 1 cut(s) 282
MroXI GAANNNNTTC 1 cut(s) 225
MseI TTAA 1 cut(s) 48
MspI CCGG 1 cut(s) 332
MspR9I CCNGG 1 cut(s) 332
MwoI GCNNNNNNNGC 3 cut(s) 92, 416, 505
NciI CCSGG 1 cut(s) 332
NdeII GATC 1 cut(s) 87
NlaIII CATG 7 cut(s) 26, 76, 140, 217, 370, 434, 492
NlaIV GGNNCC 1 cut(s) 129
NmuCI GTSAC 2 cut(s) 326, 471
NsiI ATGCAT 1 cut(s) 282
NspI RCATGY 2 cut(s) 217, 492
PaeI GCATGC 1 cut(s) 492
PciI ACATGT 1 cut(s) 213
PdmI GAANNNNTTC 1 cut(s) 225
PfeI GAWTC 1 cut(s) 197
PflMI CCANNNNNTGG 1 cut(s) 137
PkrI GCNGC 1 cut(s) 436
PleI GAGTC 1 cut(s) 85
PpsI GAGTC 1 cut(s) 85
PscI ACATGT 1 cut(s) 213
PspEI GGTNACC 1 cut(s) 326
PspFI CCCAGC 1 cut(s) 481
PspN4I GGNNCC 1 cut(s) 129
PstNI CAGNNNCTG 1 cut(s) 98
RsaI GTAC 2 cut(s) 114, 302
RsaNI GTAC 2 cut(s) 113, 301
SaqAI TTAA 1 cut(s) 48
SatI GCNGC 1 cut(s) 435
Sau3AI GATC 1 cut(s) 87
ScaI AGTACT 1 cut(s) 302
SchI GAGTC 1 cut(s) 86
ScrFI CCNGG 1 cut(s) 332
SfaNI GCATC 4 cut(s) 21, 267, 289, 294
SphI GCATGC 1 cut(s) 492
Sse9I AATT 2 cut(s) 390, 503
SsiI CCGC 1 cut(s) 335
SspMI CTAG 2 cut(s) 18, 170
StyD4I CCNGG 1 cut(s) 330
TaaI ACNGT 1 cut(s) 112
TaiI ACGT 2 cut(s) 268, 417
TaqI TCGA 1 cut(s) 28
TaqII GACCGA 1 cut(s) 314
TasI AATT 2 cut(s) 390, 503
TatI WGTACW 2 cut(s) 112, 300
TfiI GAWTC 1 cut(s) 197
Tru1I TTAA 1 cut(s) 48
Tru9I TTAA 1 cut(s) 48
TseFI GTSAC 2 cut(s) 326, 471
TseI GCWGC 1 cut(s) 434
Tsp45I GTSAC 2 cut(s) 326, 471
TspDTI ATGAA 1 cut(s) 383
Van91I CCANNNNNTGG 1 cut(s) 137
XapI RAATTY 1 cut(s) 390
XceI RCATGY 2 cut(s) 217, 492
XmnI GAANNNNTTC 1 cut(s) 225
XspI CTAG 2 cut(s) 18, 170
ZrmI AGTACT 1 cut(s) 302
Zsp2I ATGCAT 1 cut(s) 282
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.