Rw6G019100

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr6
OG0000106
Physical Location & Seq
Forward (+)
38078924 .. 38080333
1410 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw6G019100.1

Sequence Viewer

Length: 1206 bp
ATGGCAAGTTCAAGCTCAAGTGGTGATCTTCAAACTCCAATATTTGTTGGAGAAAATTTCAACTTCTGGAGAATCAAGATGAGGATAATCCTCAAATCCTATGATATTTGGTATCTAAAGATGGAGCTGAAATCAAACATGAAGAAGGATGCTAAAACTCTTGCAATAATCCATGGAGCAGTCTCAGATGAAATCTTCCCCAGAATCTCAAATGAGGAGACTTCAGAATCTGCGTGGGATGTTCAGACGAAGAGTACAGAGGTACTACTGAGAGATTTTGAATATATTAGAATGAAAGATGGTGAATCTCTTGAAGATTATCTCACTAGGCCTTATGGAGAAACTCTAGATGATAAAAGAGTAGTTCAGAAAATACGTATTAGCTTATCAGAGAAGTTTGATTCCATAGTTTATGTTATTGATATGGCAAAAGATATTGAAACCTTAGGGGTTCAAAAAGTCATTGGTTCTCTAAAAGCCTATGATCAAAGGTTGAATAAGTGTGCTGAAAGTGCAATGGAGAGTGCCTTTCAAACACTTAGCCTTAGTGTAAAGAATTCTGATCAACCTAGTTCTTCTCAAGGCAAAAGCAATAAGAGAAACAATGAAGAAAAGGGTAGTTCAAGTTATAGTGTTATGGTGAAATGCAAAACTTGTGGAAAGTTTCACATTGGTGTTTGTTGGTTTAAAGGAAAGCCAAAATATCAAAACTGTAACAGGTTTGGACATGTGCAAAAGGATTGCAATCTGAATAAGCATCAAGCACACTTCACCGAAGAGCAAGACAATGATGGTAACATGTTCTTTGCTTGTCAAGCAGCAACTACACTGAAAAATGAAAATGTTTGGTTTGTTGATAGTGGTTGCAGCAATCATATGACAACAAATCAATCCATTCTTGTGGATATTGATAAATCTGTGAACACAAGAGTAAAGATGGGCAATGGTGATCTAGTACAAAAGATTATAAGAGAAGTGTTGTTGGTTCCAGAATTGGATCAAAACCTTCAAAGTATTAGGCAGCTACAAGAGACTGGTTACCCAGTACTTTTTAATGATAATTTGTGCATAATCTATGAAAATAAAAAGAAAATGCAGGTTGGGGAAACCATCAAAATGGAGAAGAACATATGTTTTCCTATCTCTTTCAAATATCCAAGTAACATGGCTTTGAAGGTTAATGTTCTAGATGACTCTTGGCTTTGA
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
DUF4219 Retrotran_gag_2 gag_pre-integrs zf-CCHC

Protein Analysis

401

Amino Acids

45.86

Weight (kDa)

7.49

Isoelectric Point (pI)

39.37

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 42 - 167 1.8e-09 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 283 - 319 4.9e-09 Pol polyprotein, beta-barrel 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: OG0000106)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G20980 AT3G21000
fragaria_vesca FvH4_1g15931 FvH4_1g15931 FvH4_1g18381 FvH4_1g18382 FvH4_1g22571 FvH4_1g24950 FvH4_1g29372 FvH4_2g03582 FvH4_2g09851 FvH4_2g13112 FvH4_2g20843 FvH4_2g22701 FvH4_2g22702 FvH4_2g23403 FvH4_2g40201 FvH4_3g03542 FvH4_3g03543 FvH4_3g04761 FvH4_3g10464 FvH4_3g12741 FvH4_3g15781 FvH4_3g30981 FvH4_4g00985 FvH4_4g07035 FvH4_4g08192 FvH4_4g08211 FvH4_4g08553 FvH4_4g14242 FvH4_4g14243 FvH4_4g14641 FvH4_4g14843 FvH4_4g14844 FvH4_4g15061 FvH4_4g16281 FvH4_4g19152 FvH4_4g26451 FvH4_5g06442 FvH4_5g22521 FvH4_5g24301 FvH4_5g38641 FvH4_6g02393 FvH4_6g12782 FvH4_6g13871 FvH4_6g19391 FvH4_6g20105 FvH4_6g21292 FvH4_6g23581 FvH4_6g29153 FvH4_6g29691 FvH4_6g30871 FvH4_6g33351 FvH4_6g37042 FvH4_6g38781 FvH4_6g40340 FvH4_7g11221 FvH4_7g23352 FvH4_7g23352 FvH4_7g31212 FvH4_7g32172 FvH4_7g32173 FvH4_7g33701
malus_domestica MD03G1006900.v1.1 MD04G1039100.v1.1 MD04G1239100.v1.1 MD05G1048700.v1.1 MD08G1001800.v1.1 MD09G1165800.v1.1 MD11G1065200.v1.1 MD11G1138200.v1.1 MD14G1033300.v1.1 MD14G1173900.v1.1 MD15G1218200.v1.1 MD16G1034000.v1.1
prunus_persica Prupe.1G219500_v2.0.a1 Prupe.2G169400_v2.0.a1 Prupe.4G109700_v2.0.a1 Prupe.7G022000_v2.0.a1
pyrus_communis pycom01g02000 pycom02g13350 pycom03g01010 pycom04g05000 pycom04g06100 pycom05g05580 pycom05g09950 pycom05g13280 pycom05g26610 pycom06g05940 pycom06g07760 pycom07g06120 pycom07g24780 pycom08g08820 pycom09g03600 pycom09g07200 pycom10g01280 pycom10g06730 pycom10g08410 pycom10g25520 pycom11g00470 pycom11g05250 pycom11g25180 pycom12g08050 pycom13g14760 pycom13g28170 pycom15g14310 pycom15g19880 pycom15g24230 pycom15g33640 pycom16g02150 pycom16g16240 pycom16g20050 pycom16g21090 pycom17g06100
rosa_chinensis RchiOBHm_Chr1g0322161 RchiOBHm_Chr1g0326341 RchiOBHm_Chr1g0357701 RchiOBHm_Chr1g0379861 RchiOBHm_Chr1g0383421 RchiOBHm_Chr2g0093981 RchiOBHm_Chr2g0139051 RchiOBHm_Chr2g0145501 RchiOBHm_Chr3g0450971 RchiOBHm_Chr3g0451441 RchiOBHm_Chr3g0457411 RchiOBHm_Chr4g0436261 RchiOBHm_Chr5g0051431 RchiOBHm_Chr5g0064031 RchiOBHm_Chr5g0073141 RchiOBHm_Chr5g0080061 RchiOBHm_Chr7g0200561 RchiOBHm_Chr7g0235911
rosa_laevigata RLG00000000145 RLG00000000429 RLG00000020339 RLG00000035212
rosa_multiflora Rmu_co7977988.1_g000001 Rmu_co8037866.1_g000001 Rmu_co8243895.1_g000001 Rmu_co8363787.1_g000001 Rmu_co8381003.1_g000001 Rmu_sc0000263.1_g000006 Rmu_sc0000349.1_g000002 Rmu_sc0000455.1_g000031 Rmu_sc0000936.1_g000022 Rmu_sc0001035.1_g000023 Rmu_sc0001169.1_g000019 Rmu_sc0001250.1_g000026 Rmu_sc0002200.1_g000051 Rmu_sc0002230.1_g000027 Rmu_sc0002591.1_g000039 Rmu_sc0003182.1_g000003 Rmu_sc0003441.1_g000068 Rmu_sc0003722.1_g000018 Rmu_sc0003764.1_g000007 Rmu_sc0006014.1_g000016 Rmu_sc0012582.1_g000002 Rmu_sc0013519.1_g000002 Rmu_sc0014550.1_g000005 Rmu_sc0014857.1_g000007 Rmu_sc0019855.1_g000001 Rmu_sc0030839.1_g000001 Rmu_sc0031308.1_g000001
rosa_roxburghii Rroxscaffold_1G00011290 Rroxscaffold_1G00041340 Rroxscaffold_1G00053780 Rroxscaffold_1G00059130 Rroxscaffold_1G00061580 Rroxscaffold_2G00080940 Rroxscaffold_2G00109540 Rroxscaffold_3G00228400 Rroxscaffold_3G00237710 Rroxscaffold_4G00285210 Rroxscaffold_4G00299600 Rroxscaffold_4G00324940 Rroxscaffold_4G00330580 Rroxscaffold_5G00333000 Rroxscaffold_5G00347920 Rroxscaffold_5G00375310 Rroxscaffold_6G00394760 Rroxscaffold_6G00406260 Rroxscaffold_7G00165690 Rroxscaffold_7G00187680
rosa_rugosa Rorug01G0050200 Rorug02G0273800 Rorug06G0490600 Rorug06G0490600 Rorug06G0490700
rosa_samantha Rh1AG348400 Rh5AG222600 Rh6DG000500 Rh6DG194500 Rh7BG452700
rosa_wichuraiana Rw0G003060 Rw0G010530 Rw0G012970 Rw0G022560 Rw0G023390 Rw1G001270 Rw1G001530 Rw1G006070 Rw1G008210 Rw1G022090 Rw1G023320 Rw2G003790 Rw2G004140 Rw2G005280 Rw2G006460 Rw2G019620 Rw2G019840 Rw2G022530 Rw2G023280 Rw2G024990 Rw2G042380 Rw2G051390 Rw3G001640 Rw3G016720 Rw3G017100 Rw3G020890 Rw3G020900 Rw3G021100 Rw4G004820 Rw4G014950 Rw4G030920 Rw4G031400 Rw5G008500 Rw5G017950 Rw5G020170 Rw5G030160 Rw5G033050 Rw5G034640 Rw5G043920 Rw6G005060 Rw6G005540 Rw6G006720 Rw6G008460 Rw6G008670 Rw6G014780 Rw6G019100 Rw6G019350 Rw6G026310 Rw7G016810 Rw7G019180 Rw7G022890 Rw7G025880 Rw7G026390 Rw7G028340 Rw7G034850 Rw7G035170 Rw7G035420 Rw7G037990 Rw7G041560

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 968
Acc36I ACCTGC 1 cut(s) 1087
AclWI GGATC 1 cut(s) 1005
AcsI RAATTY 2 cut(s) 55, 556
AcuI CTGAAG 1 cut(s) 207
AfaI GTAC 4 cut(s) 256, 264, 957, 1047
AflIII ACRYGT 2 cut(s) 727, 798
AleI CACNNNNGTG 1 cut(s) 672
AluBI AGCT 4 cut(s) 15, 127, 384, 1024
AluI AGCT 4 cut(s) 15, 127, 384, 1024
Alw26I GTCTC 3 cut(s) 187, 212, 1025
AlwI GGATC 1 cut(s) 1005
AlwNI CAGNNNCTG 1 cut(s) 230
AoxI GGCC 1 cut(s) 329
ApeKI GCWGC 3 cut(s) 818, 867, 1021
ApoI RAATTY 2 cut(s) 55, 556
AsuHPI GGTGA 5 cut(s) 35, 314, 652, 763, 959
AxyI CCTNAGG 1 cut(s) 445
BbvI GCAGC 3 cut(s) 830, 879, 1033
BccI CCATC 5 cut(s) 115, 293, 785, 931, 1118
BclI TGATCA 2 cut(s) 484, 562
BcoDI GTCTC 3 cut(s) 187, 212, 1025
BfaI CTAG 5 cut(s) 327, 347, 570, 953, 1187
BfuAI ACCTGC 1 cut(s) 1087
BisI GCNGC 3 cut(s) 819, 868, 1022
BlsI GCNGC 3 cut(s) 820, 869, 1023
BmcAI AGTACT 1 cut(s) 1047
BmiI GGNNCC 1 cut(s) 987
BmrI ACTGGG 1 cut(s) 1037
BmsI GCATC 2 cut(s) 139, 766
BmuI ACTGGG 1 cut(s) 1037
BpmI CTGGAG 1 cut(s) 88
BpuEI CTTGAG 1 cut(s) 564
BsaAI YACGTR 1 cut(s) 377
BsaBI GATNNNNATC 1 cut(s) 744
BsaJI CCNNGG 1 cut(s) 172
Bse1I ACTGG 2 cut(s) 1039, 1043
Bse21I CCTNAGG 1 cut(s) 445
Bse3DI GCAATG 2 cut(s) 522, 949
Bse8I GATNNNNATC 1 cut(s) 744
BseDI CCNNGG 1 cut(s) 172
BseGI GGATG 2 cut(s) 154, 244
BseJI GATNNNNATC 1 cut(s) 744
BseMI GCAATG 2 cut(s) 522, 949
BseMII CTCAG 2 cut(s) 198, 260
BseNI ACTGG 2 cut(s) 1039, 1043
BseRI GAGGAG 1 cut(s) 230
BseXI GCAGC 3 cut(s) 830, 879, 1033
BshFI GGCC 1 cut(s) 331
BsmAI GTCTC 3 cut(s) 187, 212, 1025
BsnI GGCC 1 cut(s) 331
Bsp143I GATC 5 cut(s) 25, 484, 562, 949, 997
Bsp19I CCATGG 1 cut(s) 172
BspANI GGCC 1 cut(s) 331
BspCNI CTCAG 2 cut(s) 197, 261
BspLI GGNNCC 1 cut(s) 987
BspMI ACCTGC 1 cut(s) 1087
BspPI GGATC 1 cut(s) 1005
BspQI GCTCTTC 1 cut(s) 771
BsrDI GCAATG 2 cut(s) 522, 949
BsrI ACTGG 2 cut(s) 1039, 1043
BssECI CCNNGG 1 cut(s) 172
BssMI GATC 5 cut(s) 25, 484, 562, 949, 997
BssT1I CCWWGG 1 cut(s) 172
Bst4CI ACNGT 1 cut(s) 713
Bst6I CTCTTC 2 cut(s) 245, 771
BstBAI YACGTR 1 cut(s) 377
BstDEI CTNAG 5 cut(s) 184, 269, 445, 539, 545
BstDSI CCRYGG 1 cut(s) 172
BstEII GGTNACC 1 cut(s) 1037
BstF5I GGATG 2 cut(s) 154, 244
BstKTI GATC 5 cut(s) 28, 487, 565, 952, 1000
BstMAI GTCTC 3 cut(s) 187, 212, 1025
BstMBI GATC 5 cut(s) 25, 484, 562, 949, 997
BstMWI GCNNNNNNNGC 2 cut(s) 512, 815
BstNSI RCATGY 2 cut(s) 731, 802
BstPI GGTNACC 1 cut(s) 1037
BstSNI TACGTA 1 cut(s) 377
BstV1I GCAGC 3 cut(s) 830, 879, 1033
BstXI CCANNNNNNTGG 2 cut(s) 901, 1117
Bsu36I CCTNAGG 1 cut(s) 445
BsuRI GGCC 1 cut(s) 331
BtgI CCRYGG 1 cut(s) 172
BtsCI GGATG 2 cut(s) 154, 244
BtsIMutI CAGTG 1 cut(s) 827
BveI ACCTGC 1 cut(s) 1087
CaiI CAGNNNCTG 1 cut(s) 230
Csp6I GTAC 4 cut(s) 255, 263, 956, 1046
CspCI CAANNNNNGTGG 2 cut(s) 637, 672
CviAII CATG 5 cut(s) 139, 173, 728, 799, 1165
CviQI GTAC 4 cut(s) 255, 263, 956, 1046
DdeI CTNAG 5 cut(s) 184, 269, 445, 539, 545
DpnI GATC 5 cut(s) 27, 486, 564, 951, 999
DpnII GATC 5 cut(s) 25, 484, 562, 949, 997
DraI TTTAAA 1 cut(s) 688
Eam1104I CTCTTC 2 cut(s) 245, 771
EarI CTCTTC 2 cut(s) 245, 771
Eco105I TACGTA 1 cut(s) 377
Eco130I CCWWGG 1 cut(s) 172
Eco147I AGGCCT 1 cut(s) 331
Eco57I CTGAAG 1 cut(s) 207
Eco81I CCTNAGG 1 cut(s) 445
Eco91I GGTNACC 1 cut(s) 1037
EcoO65I GGTNACC 1 cut(s) 1037
EcoRI GAATTC 1 cut(s) 556
EcoT14I CCWWGG 1 cut(s) 172
ErhI CCWWGG 1 cut(s) 172
FaeI CATG 5 cut(s) 142, 176, 731, 802, 1168
FatI CATG 5 cut(s) 138, 172, 727, 798, 1164
FauNDI CATATG 2 cut(s) 876, 1130
FbaI TGATCA 2 cut(s) 484, 562
Fnu4HI GCNGC 3 cut(s) 819, 868, 1022
FokI GGATG 2 cut(s) 161, 251
Fsp4HI GCNGC 3 cut(s) 819, 868, 1022
FspBI CTAG 5 cut(s) 327, 347, 570, 953, 1187
GluI GCNGC 3 cut(s) 819, 868, 1022
GsuI CTGGAG 1 cut(s) 88
HaeIII GGCC 1 cut(s) 331
Hin1II CATG 5 cut(s) 142, 176, 731, 802, 1168
HinfI GANTC 6 cut(s) 72, 204, 227, 305, 401, 1193
HphI GGTGA 5 cut(s) 35, 314, 652, 763, 959
Hpy166II GTNNAC 1 cut(s) 922
Hpy188I TCNGA 7 cut(s) 187, 226, 246, 369, 391, 562, 750
Hpy188III TCNNGA 6 cut(s) 67, 76, 311, 347, 989, 1187
Hpy8I GTNNAC 1 cut(s) 922
HpyAV CCTTC 3 cut(s) 139, 1016, 1168
HpyCH4III ACNGT 1 cut(s) 713
HpyCH4IV ACGT 1 cut(s) 376
HpyCH4V TGCA 8 cut(s) 164, 515, 648, 733, 744, 867, 1068, 1096
HpyF10VI GCNNNNNNNGC 2 cut(s) 512, 815
HpyF3I CTNAG 5 cut(s) 184, 269, 445, 539, 545
HpySE526I ACGT 1 cut(s) 376
Hsp92II CATG 5 cut(s) 142, 176, 731, 802, 1168
Ksp22I TGATCA 2 cut(s) 484, 562
Kzo9I GATC 5 cut(s) 25, 484, 562, 949, 997
LguI GCTCTTC 1 cut(s) 771
LmnI GCTCC 2 cut(s) 124, 176
LpnPI CCDG 7 cut(s) 52, 214, 703, 1002, 1020, 1056, 1082
Lsp1109I GCAGC 3 cut(s) 830, 879, 1033
LweI GCATC 2 cut(s) 139, 766
MaeI CTAG 5 cut(s) 327, 347, 570, 953, 1187
MaeII ACGT 1 cut(s) 376
MaeIII GTNAC 4 cut(s) 713, 794, 1037, 1160
MalI GATC 5 cut(s) 27, 486, 564, 951, 999
MboI GATC 5 cut(s) 25, 484, 562, 949, 997
MboII GAAGA 9 cut(s) 20, 154, 187, 262, 326, 567, 620, 788, 1135
MluCI AATT 4 cut(s) 55, 556, 992, 1060
MlyI GAGTC 1 cut(s) 1187
MmeI TCCRAC 1 cut(s) 28
MnlI CCTC 4 cut(s) 75, 101, 208, 253
MseI TTAA 3 cut(s) 687, 1053, 1179
MslI CAYNNNNRTG 3 cut(s) 672, 899, 1115
MwoI GCNNNNNNNGC 2 cut(s) 512, 815
NcoI CCATGG 1 cut(s) 172
NdeI CATATG 2 cut(s) 876, 1130
NdeII GATC 5 cut(s) 25, 484, 562, 949, 997
NlaIII CATG 5 cut(s) 142, 176, 731, 802, 1168
NlaIV GGNNCC 1 cut(s) 987
NspI RCATGY 2 cut(s) 731, 802
OliI CACNNNNGTG 1 cut(s) 672
PceI AGGCCT 1 cut(s) 331
PciI ACATGT 2 cut(s) 727, 798
PciSI GCTCTTC 1 cut(s) 771
PfeI GAWTC 5 cut(s) 72, 204, 227, 305, 401
PkrI GCNGC 3 cut(s) 820, 869, 1023
PleI GAGTC 1 cut(s) 1187
PpsI GAGTC 1 cut(s) 1187
Ppu21I YACGTR 1 cut(s) 377
PscI ACATGT 2 cut(s) 727, 798
PsiI TTATAA 1 cut(s) 968
PspEI GGTNACC 1 cut(s) 1037
PspN4I GGNNCC 1 cut(s) 987
PstNI CAGNNNCTG 1 cut(s) 230
RsaI GTAC 4 cut(s) 256, 264, 957, 1047
RsaNI GTAC 4 cut(s) 255, 263, 956, 1046
RseI CAYNNNNRTG 3 cut(s) 672, 899, 1115
SapI GCTCTTC 1 cut(s) 771
SaqAI TTAA 3 cut(s) 687, 1053, 1179
SatI GCNGC 3 cut(s) 819, 868, 1022
Sau3AI GATC 5 cut(s) 25, 484, 562, 949, 997
ScaI AGTACT 1 cut(s) 1047
SchI GAGTC 1 cut(s) 1187
SfaNI GCATC 2 cut(s) 139, 766
SmiMI CAYNNNNRTG 3 cut(s) 672, 899, 1115
SmlI CTYRAG 2 cut(s) 16, 579
SmoI CTYRAG 2 cut(s) 16, 579
SnaBI TACGTA 1 cut(s) 377
Sse9I AATT 4 cut(s) 55, 556, 992, 1060
SseBI AGGCCT 1 cut(s) 331
SspI AATATT 1 cut(s) 42
SspMI CTAG 5 cut(s) 327, 347, 570, 953, 1187
StuI AGGCCT 1 cut(s) 331
StyI CCWWGG 1 cut(s) 172
TaaI ACNGT 1 cut(s) 713
TaiI ACGT 1 cut(s) 379
TasI AATT 4 cut(s) 55, 556, 992, 1060
TatI WGTACW 3 cut(s) 254, 955, 1045
TfiI GAWTC 5 cut(s) 72, 204, 227, 305, 401
Tru1I TTAA 3 cut(s) 687, 1053, 1179
Tru9I TTAA 3 cut(s) 687, 1053, 1179
TscAI CASTG 1 cut(s) 834
TseI GCWGC 3 cut(s) 818, 867, 1021
TspDTI ATGAA 6 cut(s) 155, 204, 308, 621, 852, 1092
TspRI CASTG 1 cut(s) 834
XapI RAATTY 2 cut(s) 55, 556
XbaI TCTAGA 2 cut(s) 346, 1186
XceI RCATGY 2 cut(s) 731, 802
XspI CTAG 5 cut(s) 327, 347, 570, 953, 1187
ZrmI AGTACT 1 cut(s) 1047
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.