Rw4G009760

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr4
OG0000562
Physical Location & Seq
Reverse (-)
22106311 .. 22109149
2839 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw4G009760.1

Sequence Viewer

Length: 1083 bp
ATGAGTTCAACGTACCTTCCTTGGTTAAGAGACATCACTCTAGCTCTTGGTGGAAGATCAAAGCTCAGTTTCATCAGTGACAAAAACAACATCCCAGATGCCTCATCATCTGAATACGAAAATTGGTTATCCAAAGACCAACTGGTTATGTCATGGCTTCTTAATTCAATGGAGCCAAAAATTGCTGAAATCTTCAGCTATTCAGAGTCATCTCGACATCTTTGGGTTGTTGTCAAAGACATGTATGGCAACCGAAACAATGCAGCAAGAGTGATCCAACTCATAAAGGATCTTGCAGGGATTCAACAAGGTAATCTCTCATTTGTTCAACATCTTGGCAACTTAAAAGCCAAGTGGAATGAACTTTATATGTATAGACCTCACACCACTGATGCCACCATATTGTTGAAAAGAGTTGAAGAAGATAAAGTGTTCAAACTGCTTGCAAGTCTGGGATCTGAATATAAAGATCTCAAAAGCCATCTTTTGATGAGCCCTGAGCTTCCTTCTTTCACAACAGTATGCAACTCTATTCAACGTGAAGAAGTGCGTAAAAAGGTGATGAATGTAGACACCAGTGATGGAGGGTCAAAAGCTAGAGCATTTGCTACAAACAAAAGTGTCACAAGCGACAGAACATACAAGGGCAAGAGGCTAGATCTGAAGTGCACACATTGTGAATGCATTGGACAAATTGGTATAGGCCACACAAGAGAGAGATGTTGGATATTGCATCCAGAACTGAAACCTAAGTTCAATAAGGAACATAAGCATCAAAGAGGCAACATTCAGAGAAGCTCTTACATCTCTAATTCAAAGGCAAACTTCAGCAACACTTTTGAAGATATGATGAACTTCACGTTCAATCCAATAACTCTCATAAATGAGTTTGCTACATATCTTCAAAAGAAGCAAGGCAGTTTAAAGAACAATGAAAATGGAAGCACAACTGCCATGCTTGGAAAGTTTGCTGGTTTTCTGGTAAAATCAGATATGGCTTCTTCAGAGGATATACCAGGTATTATTTGTGCCATTTCCACAGCTTTAGATGTCAAATCTGAAGGAAAAGGAAAAGAAAGTTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00940 ko01110 map00940 map01110
Pfam Domains
Protein Families
Retrotran_gag_2

Protein Analysis

360

Amino Acids

40.67

Weight (kDa)

9.16

Isoelectric Point (pI)

38.83

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 30 - 187 1.2e-10 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
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Orthologous Genes (Group: OG0000562)

Species Orthologous Gene IDs
fragaria_vesca FvH4_2g17331 FvH4_3g36541
malus_domestica MD07G1078600.v1.1 MD10G1237700.v1.1 MD10G1333400.v1.1 MD11G1102200.v1.1 MD13G1138400.v1.1 MD14G1033400.v1.1 MD15G1053300.v1.1
prunus_persica Prupe.1G465400_v2.0.a1 Prupe.3G136000_v2.0.a1 Prupe.7G119900_v2.0.a1
pyrus_communis pycom01g04630 pycom03g13050 pycom04g21190 pycom05g04910 pycom05g05510 pycom08g15850 pycom09g15040 pycom1094g00010 pycom11g02000 pycom12g06150 pycom13g24110 pycom13g24910 pycom14g00050 pycom15g21970 pycom15g35170 pycom15g35180 pycom16g14620 pycom16g14630 pycom808g00110
rosa_chinensis RchiOBHm_Chr1g0322851 RchiOBHm_Chr1g0365941 RchiOBHm_Chr3g0453341 RchiOBHm_Chr4g0388371 RchiOBHm_Chr4g0394021 RchiOBHm_Chr5g0013181 RchiOBHm_Chr6g0261721 RchiOBHm_Chr6g0261731 RchiOBHm_Chr7g0188861 RchiOBHm_Chr7g0192331 RchiOBHm_Chr7g0231721
rosa_multiflora Rmu_sc0002521.1_g000006 Rmu_sc0003255.1_g000026 Rmu_sc0004191.1_g000036 Rmu_sc0004414.1_g000014 Rmu_sc0005670.1_g000006 Rmu_sc0006081.1_g000001 Rmu_sc0007215.1_g000004 Rmu_sc0010088.1_g000010 Rmu_sc0020285.1_g000003 Rmu_sc0026896.1_g000002 Rmu_ssc0000019.1_g000029
rosa_roxburghii Rroxscaffold_3G00224890 Rroxscaffold_6G00400640 Rroxscaffold_7G00176590 Rroxscaffold_7G00189230
rosa_samantha Rh4BG046700
rosa_wichuraiana Rw1G012690 Rw1G031370 Rw2G042180 Rw2G043670 Rw2G046240 Rw2G049890 Rw2G050760 Rw2G051280 Rw2G053590 Rw3G007590 Rw3G026850 Rw4G001540 Rw4G009760 Rw4G019270 Rw5G000720 Rw5G005620 Rw5G041560 Rw6G007370 Rw6G009830 Rw6G015360 Rw6G031160 Rw7G004930 Rw7G011010 Rw7G024230 Rw7G028240

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccI GTMKAC 1 cut(s) 570
AclWI GGATC 3 cut(s) 268, 297, 463
AcuI CTGAAG 5 cut(s) 178, 683, 811, 987, 1080
AdeI CACNNNGTG 1 cut(s) 677
AfaI GTAC 1 cut(s) 14
AflIII ACRYGT 1 cut(s) 240
AjnI CCWGG 1 cut(s) 1015
AluBI AGCT 7 cut(s) 44, 64, 198, 502, 596, 798, 1043
AluI AGCT 7 cut(s) 44, 64, 198, 502, 596, 798, 1043
Alw21I GWGCWC 1 cut(s) 671
Alw26I GTCTC 1 cut(s) 24
Alw44I GTGCAC 1 cut(s) 667
AlwI GGATC 3 cut(s) 268, 297, 463
AoxI GGCC 1 cut(s) 703
ApaLI GTGCAC 1 cut(s) 667
ApeKI GCWGC 1 cut(s) 263
AsuHPI GGTGA 1 cut(s) 571
BaeGI GKGCMC 1 cut(s) 671
BanII GRGCYC 1 cut(s) 497
Bbv12I GWGCWC 1 cut(s) 671
BbvI GCAGC 1 cut(s) 275
BccI CCATC 2 cut(s) 489, 575
BciT130I CCWGG 1 cut(s) 1017
BcoDI GTCTC 1 cut(s) 24
BfaI CTAG 3 cut(s) 41, 597, 656
BglII AGATCT 2 cut(s) 469, 658
BisI GCNGC 1 cut(s) 264
BlsI GCNGC 1 cut(s) 265
Bme1390I CCNGG 1 cut(s) 1017
BmiI GGNNCC 1 cut(s) 174
BmrFI CCNGG 1 cut(s) 1017
BmsI GCATC 4 cut(s) 88, 382, 742, 781
Bpu10I CCTNAGC 1 cut(s) 498
BsaJI CCNNGG 1 cut(s) 20
Bse1I ACTGG 2 cut(s) 147, 576
BseBI CCWGG 1 cut(s) 1017
BseDI CCNNGG 1 cut(s) 20
BseGI GGATG 2 cut(s) 90, 733
BseMII CTCAG 2 cut(s) 79, 489
BseNI ACTGG 2 cut(s) 147, 576
BseSI GKGCMC 1 cut(s) 671
BseXI GCAGC 1 cut(s) 275
BshFI GGCC 1 cut(s) 705
BsiHKAI GWGCWC 1 cut(s) 671
BsmAI GTCTC 1 cut(s) 24
BsmI GAATGC 1 cut(s) 686
BsnI GGCC 1 cut(s) 705
Bsp1286I GDGCHC 2 cut(s) 497, 671
Bsp143I GATC 6 cut(s) 56, 273, 289, 455, 469, 658
BspANI GGCC 1 cut(s) 705
BspCNI CTCAG 2 cut(s) 78, 490
BspLI GGNNCC 1 cut(s) 174
BspPI GGATC 3 cut(s) 268, 297, 463
BsrI ACTGG 2 cut(s) 147, 576
BssECI CCNNGG 1 cut(s) 20
BssMI GATC 6 cut(s) 56, 273, 289, 455, 469, 658
BssT1I CCWWGG 1 cut(s) 20
Bst2UI CCWGG 1 cut(s) 1017
Bst4CI ACNGT 1 cut(s) 520
BstC8I GCNNGC 1 cut(s) 444
BstDEI CTNAG 3 cut(s) 65, 498, 750
BstF5I GGATG 2 cut(s) 90, 733
BstKTI GATC 6 cut(s) 59, 276, 292, 458, 472, 661
BstMAI GTCTC 1 cut(s) 24
BstMBI GATC 6 cut(s) 56, 273, 289, 455, 469, 658
BstNI CCWGG 1 cut(s) 1017
BstNSI RCATGY 1 cut(s) 244
BstSCI CCNGG 1 cut(s) 1015
BstSLI GKGCMC 1 cut(s) 671
BstV1I GCAGC 1 cut(s) 275
BstX2I RGATCY 4 cut(s) 289, 455, 469, 658
BstYI RGATCY 4 cut(s) 289, 455, 469, 658
BsuRI GGCC 1 cut(s) 705
BtsCI GGATG 2 cut(s) 90, 733
BtsIMutI CAGTG 3 cut(s) 82, 387, 583
Cac8I GCNNGC 1 cut(s) 444
CsiI ACCWGGT 1 cut(s) 1015
Csp6I GTAC 1 cut(s) 13
CviAII CATG 3 cut(s) 153, 241, 955
CviQI GTAC 1 cut(s) 13
DdeI CTNAG 3 cut(s) 65, 498, 750
DpnI GATC 6 cut(s) 58, 275, 291, 457, 471, 660
DpnII GATC 6 cut(s) 56, 273, 289, 455, 469, 658
DraI TTTAAA 1 cut(s) 924
DraIII CACNNNGTG 1 cut(s) 677
Eco130I CCWWGG 1 cut(s) 20
Eco24I GRGCYC 1 cut(s) 497
Eco57I CTGAAG 5 cut(s) 178, 683, 811, 987, 1080
EcoRII CCWGG 1 cut(s) 1015
EcoT14I CCWWGG 1 cut(s) 20
EcoT22I ATGCAT 1 cut(s) 686
EcoT38I GRGCYC 1 cut(s) 497
ErhI CCWWGG 1 cut(s) 20
FaeI CATG 3 cut(s) 156, 244, 958
FalI AAGNNNNNCTT 2 cut(s) 809, 841
FatI CATG 3 cut(s) 152, 240, 954
FblI GTMKAC 1 cut(s) 570
Fnu4HI GCNGC 1 cut(s) 264
FokI GGATG 2 cut(s) 77, 720
FriOI GRGCYC 1 cut(s) 497
Fsp4HI GCNGC 1 cut(s) 264
FspBI CTAG 3 cut(s) 41, 597, 656
GluI GCNGC 1 cut(s) 264
HaeIII GGCC 1 cut(s) 705
Hin1II CATG 3 cut(s) 156, 244, 958
HinfI GANTC 2 cut(s) 206, 301
HphI GGTGA 1 cut(s) 571
Hpy166II GTNNAC 2 cut(s) 571, 669
Hpy188I TCNGA 8 cut(s) 112, 205, 460, 663, 792, 991, 1006, 1060
Hpy188III TCNNGA 2 cut(s) 213, 737
Hpy8I GTNNAC 2 cut(s) 571, 669
HpyAV CCTTC 3 cut(s) 26, 516, 1055
HpyCH4III ACNGT 1 cut(s) 520
HpyCH4IV ACGT 3 cut(s) 11, 538, 860
HpyCH4V TGCA 7 cut(s) 263, 296, 446, 525, 669, 684, 733
HpyF3I CTNAG 3 cut(s) 65, 498, 750
HpySE526I ACGT 3 cut(s) 11, 538, 860
Hsp92II CATG 3 cut(s) 156, 244, 958
Kzo9I GATC 6 cut(s) 56, 273, 289, 455, 469, 658
LmnI GCTCC 1 cut(s) 172
Lsp1109I GCAGC 1 cut(s) 275
LweI GCATC 4 cut(s) 88, 382, 742, 781
MabI ACCWGGT 1 cut(s) 1015
MaeI CTAG 3 cut(s) 41, 597, 656
MaeII ACGT 3 cut(s) 11, 538, 860
MaeIII GTNAC 2 cut(s) 77, 622
MalI GATC 6 cut(s) 58, 275, 291, 457, 471, 660
MboI GATC 6 cut(s) 56, 273, 289, 455, 469, 658
MboII GAAGA 8 cut(s) 66, 184, 431, 434, 554, 854, 893, 993
MflI RGATCY 4 cut(s) 289, 455, 469, 658
MhlI GDGCHC 2 cut(s) 497, 671
MluCI AATT 5 cut(s) 121, 163, 180, 693, 811
MlyI GAGTC 1 cut(s) 215
MmeI TCCRAC 2 cut(s) 301, 704
MnlI CCTC 6 cut(s) 112, 390, 578, 645, 773, 1000
Mph1103I ATGCAT 1 cut(s) 686
MseI TTAA 4 cut(s) 26, 162, 344, 923
MspR9I CCNGG 1 cut(s) 1017
Mva1269I GAATGC 1 cut(s) 686
MvaI CCWGG 1 cut(s) 1017
NdeII GATC 6 cut(s) 56, 273, 289, 455, 469, 658
NlaIII CATG 3 cut(s) 156, 244, 958
NlaIV GGNNCC 1 cut(s) 174
NmuCI GTSAC 2 cut(s) 77, 622
NsiI ATGCAT 1 cut(s) 686
NspI RCATGY 1 cut(s) 244
PciI ACATGT 1 cut(s) 240
PctI GAATGC 1 cut(s) 686
PfeI GAWTC 1 cut(s) 301
PkrI GCNGC 1 cut(s) 265
PleI GAGTC 1 cut(s) 214
PpsI GAGTC 1 cut(s) 214
PscI ACATGT 1 cut(s) 240
Psp6I CCWGG 1 cut(s) 1015
PspGI CCWGG 1 cut(s) 1015
PspN4I GGNNCC 1 cut(s) 174
PsuI RGATCY 4 cut(s) 289, 455, 469, 658
RsaI GTAC 1 cut(s) 14
RsaNI GTAC 1 cut(s) 13
SaqAI TTAA 4 cut(s) 26, 162, 344, 923
SatI GCNGC 1 cut(s) 264
Sau3AI GATC 6 cut(s) 56, 273, 289, 455, 469, 658
SchI GAGTC 1 cut(s) 215
ScrFI CCNGG 1 cut(s) 1017
SduI GDGCHC 2 cut(s) 497, 671
SexAI ACCWGGT 1 cut(s) 1015
SfaNI GCATC 4 cut(s) 88, 382, 742, 781
Sse9I AATT 5 cut(s) 121, 163, 180, 693, 811
SspMI CTAG 3 cut(s) 41, 597, 656
StyD4I CCNGG 1 cut(s) 1015
StyI CCWWGG 1 cut(s) 20
TaaI ACNGT 1 cut(s) 520
TaiI ACGT 3 cut(s) 14, 541, 863
TaqI TCGA 1 cut(s) 214
TasI AATT 5 cut(s) 121, 163, 180, 693, 811
TfiI GAWTC 1 cut(s) 301
Tru1I TTAA 4 cut(s) 26, 162, 344, 923
Tru9I TTAA 4 cut(s) 26, 162, 344, 923
TscAI CASTG 3 cut(s) 82, 394, 583
TseFI GTSAC 2 cut(s) 77, 622
TseI GCWGC 1 cut(s) 263
Tsp45I GTSAC 2 cut(s) 77, 622
TspDTI ATGAA 5 cut(s) 61, 375, 578, 866, 948
TspRI CASTG 3 cut(s) 82, 394, 583
VneI GTGCAC 1 cut(s) 667
XceI RCATGY 1 cut(s) 244
XcmI CCANNNNNNNNNTGG 1 cut(s) 139
XmiI GTMKAC 1 cut(s) 570
XspI CTAG 3 cut(s) 41, 597, 656
Zsp2I ATGCAT 1 cut(s) 686
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.