Rw5G037280

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr5
OG0000154
Physical Location & Seq
Reverse (-)
65671976 .. 65672941
966 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw5G037280.1

Sequence Viewer

Length: 966 bp
ATGAGTGAAGAGAAGAATTTCCTGCAACCTGCCATACCACGCTTTGATGGTCATTACGACCATTGGAGCATGATTATGGAAAACTTTTTGAGATCTAAAGGTTATTGGAGTCTAGTTGAGACTGGTTATGAAGAATCACAGGCAGGAGCAGCGTTGAGTGAGATGCAGCAAAAGCAATTGGAGGAGTTGAGGGCTAAAGACCTCAAAGTGAAGAATTACCTGTTCCAGGCGATTGACAGGACAATTCTTGAGCAAATTCTGGAGAAACACACCTGGAAGCAGATATGGGATTCTATGAAGAAAAAGTTCAAGGGAAATGCTAGGGTGAAGCGTTCGGCTCTAAAAGCGTTGAGAAGAGATTTCGAGATTCTGGAGATGAAAGTAGGTGAGACTATCACTGATTATTTTGCTCATGTTATGGCTATTGCTGACAAGATGAGGAGTAATGGTGAGCAAATGAGACAAGTTACCATTGTGGAGAAGATCCTTAGGATTTTGACCGAGAAATTTAACTATATAGTTGTCTCGATCGAAGAATCTAAGGATATTGATTCACTCACAATTGATAAACTGCAAAGTTCACTCATTGTGCATGAACAGAAGTTTCATGAAAGTCGTGGAGAAGAGCAAGCACTCAAAGTAACACATGAAGAGAGATATAGTGGAAGAGGACGTGGGAGAGCTGTGTTCAGAGGAGGAAGAGGCAGAGGAGGGGGTCGTCAACCCTACAACAAAGCCATCGTTGAGTGTTTCAAATGTCATCAACTTGGACACTATCAATATGAGTGTCCAAAATGGGATAGACAGGCCAATTATGGGGAGTTGGATGATACAGAAGAAATGCTTCTCATGGCTTACGTAGAGATGCATGGAGCAAGTCAAAATGACGCATGGTTTCTTAACTCAGGTTGTAGTAACCATATGTGTGGTGATAGATCATTGTTTTGTGAGTTGGATGAAGGGTAA
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

321

Amino Acids

37.43

Weight (kDa)

6.44

Isoelectric Point (pI)

49.53

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 26 - 205 1.4e-25 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)
Acc36I ACCTGC 1 cut(s) 37
AclWI GGATC 1 cut(s) 478
AcsI RAATTY 3 cut(s) 16, 255, 506
AfiI CCNNNNNNNGG 2 cut(s) 226, 816
AgsI TTSAA 2 cut(s) 310, 754
AjiI CACGTC 1 cut(s) 674
AjnI CCWGG 2 cut(s) 225, 272
AluBI AGCT 1 cut(s) 683
AluI AGCT 1 cut(s) 683
Alw26I GTCTC 4 cut(s) 113, 383, 454, 529
AlwI GGATC 1 cut(s) 478
AoxI GGCC 1 cut(s) 807
ApeKI GCWGC 2 cut(s) 149, 166
ApoI RAATTY 3 cut(s) 16, 255, 506
Asp700I GAANNNNTTC 3 cut(s) 17, 305, 843
AsuHPI GGTGA 4 cut(s) 337, 398, 461, 941
AxyI CCTNAGG 1 cut(s) 488
BbvI GCAGC 2 cut(s) 161, 178
BccI CCATC 2 cut(s) 41, 746
BciT130I CCWGG 2 cut(s) 227, 274
BcoDI GTCTC 4 cut(s) 113, 383, 454, 529
BfaI CTAG 2 cut(s) 113, 321
BfuAI ACCTGC 1 cut(s) 37
BglII AGATCT 1 cut(s) 92
BisI GCNGC 2 cut(s) 150, 167
BlsI GCNGC 2 cut(s) 151, 168
Bme1390I CCNGG 2 cut(s) 227, 274
BmgBI CACGTC 1 cut(s) 674
BmrFI CCNGG 2 cut(s) 227, 274
BmsI GCATC 2 cut(s) 153, 855
BpmI CTGGAG 2 cut(s) 281, 392
BpuEI CTTGAG 1 cut(s) 269
BsaAI YACGTR 1 cut(s) 859
BsaXI ACNNNNNCTCC 2 cut(s) 433, 463
Bsc4I CCNNNNNNNGG 2 cut(s) 226, 816
Bse1I ACTGG 1 cut(s) 127
Bse21I CCTNAGG 1 cut(s) 488
BseBI CCWGG 2 cut(s) 227, 274
BseGI GGATG 2 cut(s) 832, 961
BseLI CCNNNNNNNGG 2 cut(s) 226, 816
BseMII CTCAG 1 cut(s) 918
BseNI ACTGG 1 cut(s) 127
BseRI GAGGAG 4 cut(s) 197, 454, 708, 723
BseXI GCAGC 2 cut(s) 161, 178
Bsh1285I CGRYCG 1 cut(s) 531
BshFI GGCC 1 cut(s) 809
BsiEI CGRYCG 1 cut(s) 531
BslI CCNNNNNNNGG 2 cut(s) 226, 816
BsmAI GTCTC 4 cut(s) 113, 383, 454, 529
BsnI GGCC 1 cut(s) 809
Bsp143I GATC 4 cut(s) 92, 483, 528, 935
BspANI GGCC 1 cut(s) 809
BspCNI CTCAG 1 cut(s) 917
BspHI TCATGA 1 cut(s) 607
BspMI ACCTGC 1 cut(s) 37
BspPI GGATC 1 cut(s) 478
BspQI GCTCTTC 1 cut(s) 618
BsrI ACTGG 1 cut(s) 127
BssMI GATC 4 cut(s) 92, 483, 528, 935
Bst2UI CCWGG 2 cut(s) 227, 274
Bst6I CTCTTC 6 cut(s) 3, 349, 618, 645, 661, 694
BstBAI YACGTR 1 cut(s) 859
BstC8I GCNNGC 1 cut(s) 630
BstDEI CTNAG 3 cut(s) 488, 540, 904
BstENI CCTNNNNNAGG 1 cut(s) 224
BstF5I GGATG 2 cut(s) 832, 961
BstKTI GATC 4 cut(s) 95, 486, 531, 938
BstMAI GTCTC 4 cut(s) 113, 383, 454, 529
BstMBI GATC 4 cut(s) 92, 483, 528, 935
BstMCI CGRYCG 1 cut(s) 531
BstMWI GCNNNNNNNGC 3 cut(s) 149, 172, 344
BstNI CCWGG 2 cut(s) 227, 274
BstSCI CCNGG 2 cut(s) 225, 272
BstSNI TACGTA 1 cut(s) 859
BstV1I GCAGC 2 cut(s) 161, 178
BstX2I RGATCY 2 cut(s) 92, 483
BstXI CCANNNNNNTGG 1 cut(s) 926
BstYI RGATCY 2 cut(s) 92, 483
Bsu36I CCTNAGG 1 cut(s) 488
BsuRI GGCC 1 cut(s) 809
BtrI CACGTC 1 cut(s) 674
BtsCI GGATG 2 cut(s) 832, 961
BtsIMutI CAGTG 1 cut(s) 396
BveI ACCTGC 1 cut(s) 37
Cac8I GCNNGC 1 cut(s) 630
CciI TCATGA 1 cut(s) 607
CseI GACGC 1 cut(s) 896
CviAII CATG 8 cut(s) 70, 413, 593, 608, 647, 850, 869, 891
CviJI RGCY 7 cut(s) 194, 338, 422, 683, 737, 809, 854
CviKI_1 RGCY 7 cut(s) 194, 338, 422, 683, 737, 809, 854
DdeI CTNAG 3 cut(s) 488, 540, 904
DpnI GATC 4 cut(s) 94, 485, 530, 937
DpnII GATC 4 cut(s) 92, 483, 528, 935
Eam1104I CTCTTC 6 cut(s) 3, 349, 618, 645, 661, 694
EarI CTCTTC 6 cut(s) 3, 349, 618, 645, 661, 694
Eco105I TACGTA 1 cut(s) 859
Eco81I CCTNAGG 1 cut(s) 488
EcoNI CCTNNNNNAGG 1 cut(s) 224
EcoRII CCWGG 2 cut(s) 225, 272
EcoT22I ATGCAT 1 cut(s) 870
FaeI CATG 8 cut(s) 73, 416, 596, 611, 650, 853, 872, 894
FalI AAGNNNNNCTT 2 cut(s) 828, 860
FatI CATG 8 cut(s) 69, 412, 592, 607, 646, 849, 868, 890
FauNDI CATATG 1 cut(s) 921
Fnu4HI GCNGC 2 cut(s) 150, 167
FokI GGATG 1 cut(s) 839
Fsp4HI GCNGC 2 cut(s) 150, 167
FspBI CTAG 2 cut(s) 113, 321
GluI GCNGC 2 cut(s) 150, 167
GsuI CTGGAG 2 cut(s) 281, 392
HaeIII GGCC 1 cut(s) 809
HgaI GACGC 1 cut(s) 896
Hin1II CATG 8 cut(s) 73, 416, 596, 611, 650, 853, 872, 894
HincII GTYRAC 1 cut(s) 722
HindII GTYRAC 1 cut(s) 722
HinfI GANTC 6 cut(s) 109, 134, 290, 367, 536, 551
HphI GGTGA 4 cut(s) 337, 398, 461, 941
Hpy166II GTNNAC 2 cut(s) 581, 722
Hpy188I TCNGA 1 cut(s) 692
Hpy188III TCNNGA 6 cut(s) 248, 260, 364, 371, 526, 608
Hpy8I GTNNAC 2 cut(s) 581, 722
HpyAV CCTTC 1 cut(s) 953
HpyCH4IV ACGT 2 cut(s) 673, 858
HpyCH4V TGCA 5 cut(s) 25, 166, 574, 592, 868
HpyF10VI GCNNNNNNNGC 3 cut(s) 149, 172, 344
HpyF3I CTNAG 3 cut(s) 488, 540, 904
HpySE526I ACGT 2 cut(s) 673, 858
Hsp92II CATG 8 cut(s) 73, 416, 596, 611, 650, 853, 872, 894
Kzo9I GATC 4 cut(s) 92, 483, 528, 935
LguI GCTCTTC 1 cut(s) 618
LmnI GCTCC 3 cut(s) 66, 146, 872
Lsp1109I GCAGC 2 cut(s) 161, 178
LweI GCATC 2 cut(s) 153, 855
MaeI CTAG 2 cut(s) 113, 321
MaeII ACGT 2 cut(s) 673, 858
MaeIII GTNAC 3 cut(s) 466, 640, 914
MalI GATC 4 cut(s) 94, 485, 530, 937
MboI GATC 4 cut(s) 92, 483, 528, 935
MfeI CAATTG 2 cut(s) 176, 561
MflI RGATCY 2 cut(s) 92, 483
MluCI AATT 8 cut(s) 16, 176, 214, 243, 255, 506, 561, 811
MlyI GAGTC 1 cut(s) 118
MmeI TCCRAC 2 cut(s) 804, 933
Mph1103I ATGCAT 1 cut(s) 870
MroXI GAANNNNTTC 3 cut(s) 17, 305, 843
MseI TTAA 2 cut(s) 510, 900
MslI CAYNNNNRTG 2 cut(s) 74, 924
MspR9I CCNGG 2 cut(s) 227, 274
MunI CAATTG 2 cut(s) 176, 561
MvaI CCWGG 2 cut(s) 227, 274
MwoI GCNNNNNNNGC 3 cut(s) 149, 172, 344
NdeI CATATG 1 cut(s) 921
NdeII GATC 4 cut(s) 92, 483, 528, 935
NlaIII CATG 8 cut(s) 73, 416, 596, 611, 650, 853, 872, 894
NsiI ATGCAT 1 cut(s) 870
PagI TCATGA 1 cut(s) 607
PciSI GCTCTTC 1 cut(s) 618
PdmI GAANNNNTTC 3 cut(s) 17, 305, 843
PfeI GAWTC 5 cut(s) 134, 290, 367, 536, 551
PkrI GCNGC 2 cut(s) 151, 168
Ple19I CGATCG 1 cut(s) 531
PleI GAGTC 1 cut(s) 117
PpsI GAGTC 1 cut(s) 117
Ppu21I YACGTR 1 cut(s) 859
Psp6I CCWGG 2 cut(s) 225, 272
PspGI CCWGG 2 cut(s) 225, 272
PsuI RGATCY 2 cut(s) 92, 483
PvuI CGATCG 1 cut(s) 531
RseI CAYNNNNRTG 2 cut(s) 74, 924
SapI GCTCTTC 1 cut(s) 618
SaqAI TTAA 2 cut(s) 510, 900
SatI GCNGC 2 cut(s) 150, 167
Sau3AI GATC 4 cut(s) 92, 483, 528, 935
SchI GAGTC 1 cut(s) 118
ScrFI CCNGG 2 cut(s) 227, 274
SfaNI GCATC 2 cut(s) 153, 855
SmiMI CAYNNNNRTG 2 cut(s) 74, 924
SmlI CTYRAG 1 cut(s) 248
SmoI CTYRAG 1 cut(s) 248
SnaBI TACGTA 1 cut(s) 859
Sse9I AATT 8 cut(s) 16, 176, 214, 243, 255, 506, 561, 811
SspMI CTAG 2 cut(s) 113, 321
StyD4I CCNGG 2 cut(s) 225, 272
TaiI ACGT 2 cut(s) 676, 861
TaqI TCGA 3 cut(s) 363, 527, 531
TaqII GACCGA 1 cut(s) 515
TasI AATT 8 cut(s) 16, 176, 214, 243, 255, 506, 561, 811
TfiI GAWTC 5 cut(s) 134, 290, 367, 536, 551
Tru1I TTAA 2 cut(s) 510, 900
Tru9I TTAA 2 cut(s) 510, 900
TscAI CASTG 1 cut(s) 403
TseI GCWGC 2 cut(s) 149, 166
TspDTI ATGAA 7 cut(s) 144, 311, 392, 596, 609, 624, 663
TspRI CASTG 1 cut(s) 403
XagI CCTNNNNNAGG 1 cut(s) 224
XapI RAATTY 3 cut(s) 16, 255, 506
XmnI GAANNNNTTC 3 cut(s) 17, 305, 843
XspI CTAG 2 cut(s) 113, 321
Zsp2I ATGCAT 1 cut(s) 870
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.