Rw5G032610

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr5
OG0000333
Physical Location & Seq
Reverse (-)
55319615 .. 55321961
2347 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw5G032610.1

Sequence Viewer

Length: 621 bp
ATGGCCAGTAAATGCAAAGCAGAAAATACAAAGATAGAGAGGCTCAATAATATCAATCATTGCATATGGAAAAGAAGAATCACCTATCTGCCTACCCATGAGAAAACGTTATATACGTTAAAAACTGAGAGGCCTCCTGTTGCATCTCGGAATTATATTAAATGGGAAGAAGATAATGCATTAGCTATTGCTACGATTGTCAATCATATGGAAGATGATTTGATTCCTCTTTATGAAGGATATGAGACCGCCAAAGAAATCATGAATGTGTTGGATGAAAAATATGGGCCTAAATCTCAAACATACATTCAATTGTTGCTTGAGAAATATAACAACACTCGTATGAACGAAAATGAAGATATGGTGGATCATATTACCAAAATAGAGGTATTAGCAAAGGACTTGTCTAATGCTGGTCATCCTATTCCTGATCAAATGCAAGTTTCTACAGTTCTCAACAGTCTTCCCAAATCATGGGATCATGTGGTGACTTCTTTGACCTATGGTCAAAAAGAGTTGTCCAAGAATAATTTGCCTGCTATGTTAGCAGTTGAAGAAAAAATGTTCTTCATGGAAGTTGTAGAGGACGTTAAACCGAGCGCGTGCATATGTAGTACGTAA
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 zf-CCHC

Protein Analysis

206

Amino Acids

23.75

Weight (kDa)

5.57

Isoelectric Point (pI)

37.45

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 39 - 186 9.5e-26 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: OG0000333)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G11910 AT3G11910 AT3G11910 AT3G11910 AT5G06600 AT5G06600 AT5G06600
fragaria_vesca FvH4_3g26930 FvH4_3g39132 FvH4_6g21220 FvH4_6g21220 FvH4_6g21220 FvH4_6g21220 FvH4_6g21220 FvH4_6g21220
malus_domestica MD02G1261100.v1.1 MD03G1161100.v1.1 MD07G1059900.v1.1 MD11G1177100.v1.1 MD12G1047900.v1.1 MD12G1048000.v1.1 MD12G1048400.v1.1 MD12G1048500.v1.1 MD12G1048700.v1.1 MD12G1048800.v1.1 MD12G1056200.v1.1 MD14G1046300.v1.1 MD14G1046500.v1.1 MD15G1166900.v1.1
prunus_persica Prupe.2G066200_v2.0.a1 Prupe.2G066200_v2.0.a1 Prupe.6G149500_v2.0.a1 Prupe.6G149500_v2.0.a1 Prupe.6G149500_v2.0.a1 Prupe.6G149500_v2.0.a1 Prupe.7G087600_v2.0.a1 Prupe.7G087600_v2.0.a1 Prupe.7G087600_v2.0.a1 Prupe.7G087600_v2.0.a1 Prupe.7G087600_v2.0.a1
pyrus_communis pycom02g22320 pycom03g11340 pycom07g04580 pycom11g14290 pycom11g15110 pycom12g04110 pycom12g04140 pycom12g04160 pycom12g04210 pycom12g04220 pycom12g04230 pycom12g04290 pycom12g04320 pycom12g04330 pycom12g04350 pycom12g04360 pycom14g03880 pycom14g03900 pycom16g18750
rosa_chinensis RchiOBHm_Chr1g0324111 RchiOBHm_Chr1g0324241 RchiOBHm_Chr3g0477691 RchiOBHm_Chr5g0049371 RchiOBHm_Chr5g0070531
rosa_laevigata RLG00000008612 RLG00000023698 RLG00000034613 RLG00000036139
rosa_multiflora Rmu_co8271779.1_g000001 Rmu_sc0006187.1_g000014
rosa_roxburghii Rroxscaffold_1G00010670 Rroxscaffold_1G00030450 Rroxscaffold_1G00031950 Rroxscaffold_1G00031970 Rroxscaffold_1G00032320 Rroxscaffold_1G00055490 Rroxscaffold_2G00083610 Rroxscaffold_2G00084480 Rroxscaffold_2G00115610 Rroxscaffold_3G00261320 Rroxscaffold_4G00312220 Rroxscaffold_4G00325820 Rroxscaffold_5G00339170 Rroxscaffold_5G00364030 Rroxscaffold_6G00403750
rosa_rugosa Rorug03G0162700 Rorug03G0162800 Rorug03G0162900 Rorug05G0247700 Rorug05G0406600 Rorug05G0406800
rosa_samantha Rh1AG060300 Rh3AG213000 Rh3BG246600 Rh3CG240400 Rh3DG239700 Rh5AG324400 Rh5AG462100 Rh5BG335500 Rh5BG480200 Rh5BG480300 Rh5CG360200 Rh5CG504500 Rh5CG504600 Rh5DG347800 Rh5DG492200 Rh5DG492300
rosa_wichuraiana Rw3G019270 Rw3G026910 Rw5G030650 Rw5G032610 Rw5G043040

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB7I CCANNNNNTGG 1 cut(s) 474
AccII CGCG 1 cut(s) 602
AciI CCGC 1 cut(s) 249
AclI AACGTT 1 cut(s) 107
AclWI GGATC 2 cut(s) 375, 486
AcoI YGGCCR 1 cut(s) 3
AfaI GTAC 1 cut(s) 616
AfiI CCNNNNNNNGG 1 cut(s) 474
AgsI TTSAA 2 cut(s) 311, 554
AhdI GACNNNNNGTC 1 cut(s) 504
AluBI AGCT 1 cut(s) 185
AluI AGCT 1 cut(s) 185
Alw26I GTCTC 1 cut(s) 239
AlwI GGATC 2 cut(s) 375, 486
AoxI GGCC 3 cut(s) 3, 131, 287
ArsI GACNNNNNNTTYG 2 cut(s) 389, 421
AspLEI GCGC 1 cut(s) 602
AspS9I GGNCC 1 cut(s) 287
AsuHPI GGTGA 2 cut(s) 73, 499
BalI TGGCCA 1 cut(s) 5
BbsI GAAGAC 1 cut(s) 455
BclI TGATCA 1 cut(s) 430
BcoDI GTCTC 1 cut(s) 239
BfmI CTRYAG 1 cut(s) 447
BmeRI GACNNNNNGTC 1 cut(s) 504
BmgT120I GGNCC 1 cut(s) 287
BmsI GCATC 1 cut(s) 152
BpiI GAAGAC 1 cut(s) 455
BpuEI CTTGAG 1 cut(s) 341
BsaAI YACGTR 1 cut(s) 618
BsaI GGTCTC 1 cut(s) 239
Bsc4I CCNNNNNNNGG 1 cut(s) 474
Bse1I ACTGG 1 cut(s) 6
Bse3DI GCAATG 1 cut(s) 58
BseGI GGATG 2 cut(s) 280, 418
BseLI CCNNNNNNNGG 1 cut(s) 474
BseMI GCAATG 1 cut(s) 58
BseMII CTCAG 1 cut(s) 117
BseNI ACTGG 1 cut(s) 6
Bsh1236I CGCG 1 cut(s) 602
BshFI GGCC 3 cut(s) 5, 133, 289
BslI CCNNNNNNNGG 1 cut(s) 474
BsmAI GTCTC 1 cut(s) 239
BsnI GGCC 3 cut(s) 5, 133, 289
Bso31I GGTCTC 1 cut(s) 239
Bsp143I GATC 3 cut(s) 367, 430, 478
BspACI CCGC 1 cut(s) 249
BspANI GGCC 3 cut(s) 5, 133, 289
BspCNI CTCAG 1 cut(s) 118
BspFNI CGCG 1 cut(s) 602
BspHI TCATGA 1 cut(s) 261
BspPI GGATC 2 cut(s) 375, 486
BspTNI GGTCTC 1 cut(s) 239
BsrDI GCAATG 1 cut(s) 58
BsrI ACTGG 1 cut(s) 6
BssMI GATC 3 cut(s) 367, 430, 478
Bst4CI ACNGT 2 cut(s) 451, 461
BstBAI YACGTR 1 cut(s) 618
BstC8I GCNNGC 2 cut(s) 537, 604
BstDEI CTNAG 1 cut(s) 126
BstF5I GGATG 2 cut(s) 280, 418
BstFNI CGCG 1 cut(s) 602
BstHHI GCGC 1 cut(s) 602
BstKTI GATC 3 cut(s) 370, 433, 481
BstMAI GTCTC 1 cut(s) 239
BstMBI GATC 3 cut(s) 367, 430, 478
BstMWI GCNNNNNNNGC 1 cut(s) 545
BstSFI CTRYAG 1 cut(s) 447
BstSNI TACGTA 1 cut(s) 618
BstUI CGCG 1 cut(s) 602
BstV2I GAAGAC 1 cut(s) 455
BsuRI GGCC 3 cut(s) 5, 133, 289
BtsCI GGATG 2 cut(s) 280, 418
Cac8I GCNNGC 2 cut(s) 537, 604
CciI TCATGA 1 cut(s) 261
CfoI GCGC 1 cut(s) 602
Cfr13I GGNCC 1 cut(s) 287
Csp6I GTAC 1 cut(s) 615
CviAII CATG 5 cut(s) 98, 262, 474, 482, 571
CviJI RGCY 5 cut(s) 5, 43, 133, 185, 289
CviKI_1 RGCY 5 cut(s) 5, 43, 133, 185, 289
CviQI GTAC 1 cut(s) 615
DdeI CTNAG 1 cut(s) 126
DpnI GATC 3 cut(s) 369, 432, 480
DpnII GATC 3 cut(s) 367, 430, 478
DriI GACNNNNNGTC 1 cut(s) 504
EaeI YGGCCR 1 cut(s) 3
Eam1105I GACNNNNNGTC 1 cut(s) 504
Eco105I TACGTA 1 cut(s) 618
Eco147I AGGCCT 1 cut(s) 133
Eco31I GGTCTC 1 cut(s) 239
EcoT22I ATGCAT 1 cut(s) 181
FaeI CATG 5 cut(s) 101, 265, 477, 485, 574
FatI CATG 5 cut(s) 97, 261, 473, 481, 570
FauNDI CATATG 3 cut(s) 65, 207, 608
FbaI TGATCA 1 cut(s) 430
FokI GGATG 2 cut(s) 287, 405
GlaI GCGC 1 cut(s) 601
HaeIII GGCC 3 cut(s) 5, 133, 289
HhaI GCGC 1 cut(s) 602
Hin1II CATG 5 cut(s) 101, 265, 477, 485, 574
Hin6I GCGC 1 cut(s) 600
HinP1I GCGC 1 cut(s) 600
HinfI GANTC 2 cut(s) 78, 223
HphI GGTGA 2 cut(s) 73, 499
Hpy188I TCNGA 1 cut(s) 150
Hpy188III TCNNGA 2 cut(s) 262, 428
HpyAV CCTTC 1 cut(s) 230
HpyCH4III ACNGT 2 cut(s) 451, 461
HpyCH4IV ACGT 4 cut(s) 107, 116, 588, 617
HpyCH4V TGCA 6 cut(s) 15, 63, 143, 179, 439, 606
HpyF10VI GCNNNNNNNGC 1 cut(s) 545
HpyF3I CTNAG 1 cut(s) 126
HpySE526I ACGT 4 cut(s) 107, 116, 588, 617
Hsp92II CATG 5 cut(s) 101, 265, 477, 485, 574
HspAI GCGC 1 cut(s) 600
Ksp22I TGATCA 1 cut(s) 430
Kzo9I GATC 3 cut(s) 367, 430, 478
LpnPI CCDG 5 cut(s) 19, 150, 399, 441, 549
LweI GCATC 1 cut(s) 152
MaeII ACGT 4 cut(s) 107, 116, 588, 617
MaeIII GTNAC 1 cut(s) 487
MalI GATC 3 cut(s) 369, 432, 480
MboI GATC 3 cut(s) 367, 430, 478
MboII GAAGA 8 cut(s) 87, 179, 182, 224, 368, 455, 559, 566
MfeI CAATTG 1 cut(s) 311
MlsI TGGCCA 1 cut(s) 5
MluCI AATT 3 cut(s) 151, 311, 529
MluNI TGGCCA 1 cut(s) 5
MmeI TCCRAC 1 cut(s) 252
MnlI CCTC 6 cut(s) 33, 123, 144, 237, 379, 577
Mox20I TGGCCA 1 cut(s) 5
Mph1103I ATGCAT 1 cut(s) 181
MscI TGGCCA 1 cut(s) 5
MseI TTAA 3 cut(s) 119, 159, 591
MslI CAYNNNNRTG 2 cut(s) 266, 341
Msp20I TGGCCA 1 cut(s) 5
MunI CAATTG 1 cut(s) 311
MvnI CGCG 1 cut(s) 602
MwoI GCNNNNNNNGC 1 cut(s) 545
NdeI CATATG 3 cut(s) 65, 207, 608
NdeII GATC 3 cut(s) 367, 430, 478
NlaIII CATG 5 cut(s) 101, 265, 477, 485, 574
NmuCI GTSAC 1 cut(s) 487
NsiI ATGCAT 1 cut(s) 181
PagI TCATGA 1 cut(s) 261
PceI AGGCCT 1 cut(s) 133
PcsI WCGNNNNNNNCGW 1 cut(s) 113
PfeI GAWTC 2 cut(s) 78, 223
PflMI CCANNNNNTGG 1 cut(s) 474
Ppu21I YACGTR 1 cut(s) 618
Psp1406I AACGTT 1 cut(s) 107
PspPI GGNCC 1 cut(s) 287
RsaI GTAC 1 cut(s) 616
RsaNI GTAC 1 cut(s) 615
RseI CAYNNNNRTG 2 cut(s) 266, 341
SaqAI TTAA 3 cut(s) 119, 159, 591
Sau3AI GATC 3 cut(s) 367, 430, 478
Sau96I GGNCC 1 cut(s) 287
SetI ASST 8 cut(s) 86, 110, 119, 187, 390, 503, 591, 620
SfaNI GCATC 1 cut(s) 152
SfcI CTRYAG 1 cut(s) 447
SmiMI CAYNNNNRTG 2 cut(s) 266, 341
SmlI CTYRAG 1 cut(s) 320
SmoI CTYRAG 1 cut(s) 320
SnaBI TACGTA 1 cut(s) 618
Sse9I AATT 3 cut(s) 151, 311, 529
SseBI AGGCCT 1 cut(s) 133
SsiI CCGC 1 cut(s) 249
StuI AGGCCT 1 cut(s) 133
TaaI ACNGT 2 cut(s) 451, 461
TaiI ACGT 4 cut(s) 110, 119, 591, 620
TasI AATT 3 cut(s) 151, 311, 529
TfiI GAWTC 2 cut(s) 78, 223
Tru1I TTAA 3 cut(s) 119, 159, 591
Tru9I TTAA 3 cut(s) 119, 159, 591
TseFI GTSAC 1 cut(s) 487
Tsp45I GTSAC 1 cut(s) 487
TspDTI ATGAA 6 cut(s) 249, 278, 291, 359, 369, 559
Van91I CCANNNNNTGG 1 cut(s) 474
Zsp2I ATGCAT 1 cut(s) 181
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.