Rw7G031960

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr7
OG0000154
Physical Location & Seq
Forward (+)
46059437 .. 46061913
2477 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw7G031960.1

Sequence Viewer

Length: 999 bp
ATGGCAACAGAGAACAATTACGTGCAGCCTTCAATACCACGCTTTGATGGTCACTATGACCATTGGAGCATACTAATGGAGAACTTTCTGAGGTCGAAGGAGTATTGGAGCCTCATTGAGACAGGCTTTACTGAGCCTGCCACTGGAGAGGGGATGACGGCAGCACAGAGAAGGGCATTGGATGAGTTGAAGTTGAAAGATCTCAAGAAGTATGAAGGCAATGCAAGAGTGAAACGCTCTCAGCTCCAAGCACTACGTCGAGAGTTTGAGACCCTTGAGATGAAGGTTGGTGAGTCTGTTTTAGATTATTTCTCAAGAGTTATGTCAGTGGCAAATAGGATGCGAACCCATGGTGAACAGATGCAAGATGTTACTGTGGTGGAGAAGATACTTCGCTCCTTGACTGACAAGTTCAACTACATAGTCTGCTCCATTGAAGAATCCAAAGACATTGATCAGTTATCAGTGGATGAGCTGCAGAGTTCGTTGCTCGTACATGAGCAAAAACTCAATCGAAATAATGGAGAGGAGCAAGCAGCCTTGAAAGTTGAATGCTTCAGATGTCATGGGCTTGGTCACTTTCATTCGGAGTGTTTTGCGAAGCTTCACAAAGACAAGCAAAAGAATGGGGAGCAGTCCAATTTTGCAGAGAAAAAGGAAGAGGAAGAAGAGACACTTCTGATGGCATTGCATGTGAAGGAGAAGCCTGAAGCAAACACATGGTACTTAGACTCCGGGTGTAATAATCACATGTGCGGTACCTACAAATTGTATAATCCCACCACGAAGAAGATTGTGATCAGCCGAGATGTTGTTTTTGATGAGGAGAGCACATGGAATTGGGCAGACAAGATCACCCAACGAAAGCACATACCTGTGAGCTTTGATGAAGAACAATTAGGAGTGCAGCAACAAATCCATCCTACAGTAGGAGTGCAGGAACAAATCCCTCCTACAGTAGGAGCGCGGCAACAAATCCCTCCTACAGTAGAAGTGTAG
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

332

Amino Acids

38.42

Weight (kDa)

5.63

Isoelectric Point (pI)

51.06

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 69 - 174 3.3e-18 gag-polypeptide of LTR copia-type
SH3_retrovirus PF25597 255 - 284 4.3e-10 Retroviral polymerase SH3-like domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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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)
Acc65I GGTACC 1 cut(s) 758
AccB1I GGYRCC 1 cut(s) 758
AccII CGCG 1 cut(s) 967
AciI CCGC 2 cut(s) 756, 967
AcuI CTGAAG 2 cut(s) 541, 729
AfaI GTAC 3 cut(s) 495, 725, 760
AfiI CCNNNNNNNGG 3 cut(s) 143, 929, 959
AflIII ACRYGT 1 cut(s) 750
AgsI TTSAA 7 cut(s) 33, 190, 196, 415, 437, 544, 551
AluBI AGCT 4 cut(s) 244, 475, 604, 882
AluI AGCT 4 cut(s) 244, 475, 604, 882
Alw21I GWGCWC 1 cut(s) 833
Alw26I GTCTC 3 cut(s) 113, 263, 665
ApeKI GCWGC 5 cut(s) 25, 161, 475, 536, 907
Asp718I GGTACC 1 cut(s) 758
AspLEI GCGC 1 cut(s) 967
AsuC2I CCSGG 1 cut(s) 736
AsuHPI GGTGA 3 cut(s) 302, 365, 847
BanI GGYRCC 1 cut(s) 758
Bbv12I GWGCWC 1 cut(s) 833
BbvI GCAGC 5 cut(s) 37, 173, 462, 548, 919
BccI CCATC 3 cut(s) 41, 676, 927
BceAI ACGGC 1 cut(s) 174
BclI TGATCA 2 cut(s) 454, 798
BcnI CCSGG 1 cut(s) 736
BcoDI GTCTC 3 cut(s) 113, 263, 665
BfmI CTRYAG 4 cut(s) 476, 924, 954, 984
BglII AGATCT 1 cut(s) 199
BisI GCNGC 6 cut(s) 26, 162, 476, 537, 908, 968
BlsI GCNGC 6 cut(s) 27, 163, 477, 538, 909, 969
Bme1390I CCNGG 1 cut(s) 736
BmiI GGNNCC 2 cut(s) 110, 760
BmrFI CCNGG 1 cut(s) 736
BmsI GCATC 2 cut(s) 330, 351
BpmI CTGGAG 1 cut(s) 165
BpuEI CTTGAG 3 cut(s) 188, 296, 298
BpuMI CCSGG 1 cut(s) 736
BsaAI YACGTR 1 cut(s) 22
BsaBI GATNNNNATC 1 cut(s) 797
BsaI GGTCTC 1 cut(s) 263
BsaJI CCNNGG 1 cut(s) 349
BsaXI ACNNNNNCTCC 2 cut(s) 716, 746
Bsc4I CCNNNNNNNGG 3 cut(s) 143, 929, 959
Bse1I ACTGG 1 cut(s) 148
Bse3DI GCAATG 2 cut(s) 226, 686
Bse8I GATNNNNATC 1 cut(s) 797
BseDI CCNNGG 1 cut(s) 349
BseGI GGATG 5 cut(s) 159, 187, 345, 475, 919
BseJI GATNNNNATC 1 cut(s) 797
BseLI CCNNNNNNNGG 3 cut(s) 143, 929, 959
BseMI GCAATG 2 cut(s) 226, 686
BseMII CTCAG 3 cut(s) 80, 123, 254
BseNI ACTGG 1 cut(s) 148
BseRI GAGGAG 2 cut(s) 542, 839
BseXI GCAGC 5 cut(s) 37, 173, 462, 548, 919
BsgI GTGCAG 3 cut(s) 44, 926, 956
Bsh1236I CGCG 1 cut(s) 967
BshNI GGYRCC 1 cut(s) 758
BsiHKAI GWGCWC 1 cut(s) 833
BsiSI CCGG 1 cut(s) 735
BslI CCNNNNNNNGG 3 cut(s) 143, 929, 959
BsmAI GTCTC 3 cut(s) 113, 263, 665
BsmI GAATGC 1 cut(s) 557
Bso31I GGTCTC 1 cut(s) 263
Bsp1286I GDGCHC 1 cut(s) 833
Bsp143I GATC 4 cut(s) 199, 454, 798, 852
Bsp19I CCATGG 1 cut(s) 349
BspACI CCGC 2 cut(s) 756, 967
BspCNI CTCAG 3 cut(s) 81, 124, 253
BspFNI CGCG 1 cut(s) 967
BspLI GGNNCC 2 cut(s) 110, 760
BspMAI CTGCAG 1 cut(s) 480
BspT107I GGYRCC 1 cut(s) 758
BspTNI GGTCTC 1 cut(s) 263
BsrDI GCAATG 2 cut(s) 226, 686
BsrI ACTGG 1 cut(s) 148
BssECI CCNNGG 1 cut(s) 349
BssMI GATC 4 cut(s) 199, 454, 798, 852
BssT1I CCWWGG 1 cut(s) 349
Bst4CI ACNGT 4 cut(s) 376, 928, 958, 988
Bst6I CTCTTC 2 cut(s) 654, 663
BstBAI YACGTR 1 cut(s) 22
BstC8I GCNNGC 2 cut(s) 138, 534
BstDEI CTNAG 4 cut(s) 89, 132, 240, 727
BstDSI CCRYGG 1 cut(s) 349
BstENI CCTNNNNNAGG 2 cut(s) 927, 957
BstF5I GGATG 5 cut(s) 159, 187, 345, 475, 919
BstFNI CGCG 1 cut(s) 967
BstHHI GCGC 1 cut(s) 967
BstKTI GATC 4 cut(s) 202, 457, 801, 855
BstMAI GTCTC 3 cut(s) 113, 263, 665
BstMBI GATC 4 cut(s) 199, 454, 798, 852
BstNSI RCATGY 2 cut(s) 695, 754
BstSCI CCNGG 1 cut(s) 734
BstSFI CTRYAG 4 cut(s) 476, 924, 954, 984
BstUI CGCG 1 cut(s) 967
BstV1I GCAGC 5 cut(s) 37, 173, 462, 548, 919
BstX2I RGATCY 1 cut(s) 199
BstYI RGATCY 1 cut(s) 199
BtgI CCRYGG 1 cut(s) 349
BtsCI GGATG 5 cut(s) 159, 187, 345, 475, 919
BtsIMutI CAGTG 3 cut(s) 141, 333, 471
Cac8I GCNNGC 2 cut(s) 138, 534
CfoI GCGC 1 cut(s) 967
Csp6I GTAC 3 cut(s) 494, 724, 759
CviAII CATG 7 cut(s) 350, 497, 566, 692, 720, 751, 834
CviQI GTAC 3 cut(s) 494, 724, 759
DdeI CTNAG 4 cut(s) 89, 132, 240, 727
DpnI GATC 4 cut(s) 201, 456, 800, 854
DpnII GATC 4 cut(s) 199, 454, 798, 852
Eam1104I CTCTTC 2 cut(s) 654, 663
EarI CTCTTC 2 cut(s) 654, 663
Eco130I CCWWGG 1 cut(s) 349
Eco31I GGTCTC 1 cut(s) 263
Eco57I CTGAAG 2 cut(s) 541, 729
EcoNI CCTNNNNNAGG 2 cut(s) 927, 957
EcoT14I CCWWGG 1 cut(s) 349
ErhI CCWWGG 1 cut(s) 349
FaeI CATG 7 cut(s) 353, 500, 569, 695, 723, 754, 837
FalI AAGNNNNNCTT 2 cut(s) 660, 692
FatI CATG 7 cut(s) 349, 496, 565, 691, 719, 750, 833
FbaI TGATCA 2 cut(s) 454, 798
Fnu4HI GCNGC 6 cut(s) 26, 162, 476, 537, 908, 968
FokI GGATG 5 cut(s) 166, 194, 352, 482, 906
Fsp4HI GCNGC 6 cut(s) 26, 162, 476, 537, 908, 968
GlaI GCGC 1 cut(s) 966
GluI GCNGC 6 cut(s) 26, 162, 476, 537, 908, 968
GsuI CTGGAG 1 cut(s) 165
HapII CCGG 1 cut(s) 735
HhaI GCGC 1 cut(s) 967
Hin1II CATG 7 cut(s) 353, 500, 569, 695, 723, 754, 837
Hin6I GCGC 1 cut(s) 965
HinP1I GCGC 1 cut(s) 965
HindIII AAGCTT 1 cut(s) 602
HinfI GANTC 3 cut(s) 293, 440, 731
HpaII CCGG 1 cut(s) 735
HphI GGTGA 3 cut(s) 302, 365, 847
Hpy166II GTNNAC 1 cut(s) 356
Hpy188I TCNGA 4 cut(s) 90, 560, 589, 681
Hpy188III TCNNGA 3 cut(s) 205, 260, 315
Hpy8I GTNNAC 1 cut(s) 356
Hpy99I CGWCG 1 cut(s) 261
HpyAV CCTTC 6 cut(s) 39, 91, 165, 209, 277, 691
HpyCH4III ACNGT 4 cut(s) 376, 928, 958, 988
HpyCH4IV ACGT 2 cut(s) 21, 256
HpyCH4V TGCA 8 cut(s) 25, 224, 364, 478, 647, 691, 907, 937
HpyF3I CTNAG 4 cut(s) 89, 132, 240, 727
HpySE526I ACGT 2 cut(s) 21, 256
Hsp92II CATG 7 cut(s) 353, 500, 569, 695, 723, 754, 837
HspAI GCGC 1 cut(s) 965
KpnI GGTACC 1 cut(s) 762
Ksp22I TGATCA 2 cut(s) 454, 798
Kzo9I GATC 4 cut(s) 199, 454, 798, 852
LmnI GCTCC 8 cut(s) 66, 108, 249, 401, 434, 529, 631, 962
LpnPI CCDG 7 cut(s) 108, 129, 150, 720, 748, 888, 923
Lsp1109I GCAGC 5 cut(s) 37, 173, 462, 548, 919
LweI GCATC 2 cut(s) 330, 351
MaeII ACGT 2 cut(s) 21, 256
MaeIII GTNAC 3 cut(s) 50, 370, 575
MalI GATC 4 cut(s) 201, 456, 800, 854
MboI GATC 4 cut(s) 199, 454, 798, 852
MboII GAAGA 8 cut(s) 397, 449, 671, 677, 680, 799, 802, 902
MflI RGATCY 1 cut(s) 199
MhlI GDGCHC 1 cut(s) 833
MluCI AATT 5 cut(s) 16, 640, 767, 838, 896
MlyI GAGTC 2 cut(s) 302, 725
MnlI CCTC 8 cut(s) 84, 122, 142, 520, 655, 817, 960, 990
MslI CAYNNNNRTG 2 cut(s) 74, 875
MspI CCGG 1 cut(s) 735
MspR9I CCNGG 1 cut(s) 736
Mva1269I GAATGC 1 cut(s) 557
MvnI CGCG 1 cut(s) 967
NciI CCSGG 1 cut(s) 736
NcoI CCATGG 1 cut(s) 349
NdeII GATC 4 cut(s) 199, 454, 798, 852
NlaIII CATG 7 cut(s) 353, 500, 569, 695, 723, 754, 837
NlaIV GGNNCC 2 cut(s) 110, 760
NmeAIII GCCGAG 1 cut(s) 830
NmuCI GTSAC 2 cut(s) 50, 575
NspI RCATGY 2 cut(s) 695, 754
PciI ACATGT 1 cut(s) 750
PctI GAATGC 1 cut(s) 557
PfeI GAWTC 1 cut(s) 440
PkrI GCNGC 6 cut(s) 27, 163, 477, 538, 909, 969
PleI GAGTC 2 cut(s) 301, 725
PpsI GAGTC 2 cut(s) 301, 725
Ppu21I YACGTR 1 cut(s) 22
PscI ACATGT 1 cut(s) 750
PspN4I GGNNCC 2 cut(s) 110, 760
PstI CTGCAG 1 cut(s) 480
PsuI RGATCY 1 cut(s) 199
RsaI GTAC 3 cut(s) 495, 725, 760
RsaNI GTAC 3 cut(s) 494, 724, 759
RseI CAYNNNNRTG 2 cut(s) 74, 875
SatI GCNGC 6 cut(s) 26, 162, 476, 537, 908, 968
Sau3AI GATC 4 cut(s) 199, 454, 798, 852
SchI GAGTC 2 cut(s) 302, 725
ScrFI CCNGG 1 cut(s) 736
SduI GDGCHC 1 cut(s) 833
SfaNI GCATC 2 cut(s) 330, 351
SfcI CTRYAG 4 cut(s) 476, 924, 954, 984
SmiMI CAYNNNNRTG 2 cut(s) 74, 875
SmlI CTYRAG 3 cut(s) 203, 275, 313
SmoI CTYRAG 3 cut(s) 203, 275, 313
Sse9I AATT 5 cut(s) 16, 640, 767, 838, 896
SsiI CCGC 2 cut(s) 756, 967
StyD4I CCNGG 1 cut(s) 734
StyI CCWWGG 1 cut(s) 349
TaaI ACNGT 4 cut(s) 376, 928, 958, 988
TaiI ACGT 2 cut(s) 24, 259
TaqI TCGA 3 cut(s) 95, 259, 514
TasI AATT 5 cut(s) 16, 640, 767, 838, 896
TauI GCSGC 1 cut(s) 970
TfiI GAWTC 1 cut(s) 440
TscAI CASTG 3 cut(s) 148, 333, 471
TseFI GTSAC 2 cut(s) 50, 575
TseI GCWGC 5 cut(s) 25, 161, 475, 536, 907
Tsp45I GTSAC 2 cut(s) 50, 575
TspDTI ATGAA 4 cut(s) 228, 296, 572, 903
TspRI CASTG 3 cut(s) 148, 333, 471
XagI CCTNNNNNAGG 2 cut(s) 927, 957
XceI RCATGY 2 cut(s) 695, 754
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.