Rw7G028240

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr7
OG0000562
Physical Location & Seq
Reverse (-)
38057541 .. 38059029
1489 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw7G028240.1

Sequence Viewer

Length: 1101 bp
ATGACAGAAGGAGAAGGTTCTCTCGTTGCAAAGCTAGGAGAAGGTTCTCTCGTTGCAAAGACAGAAAGCCTAGATGGGAATCCAAATCAACGTCTATGCTCAATGCTTCTAAATGAGTTCAACTACCTTACTTGGTCAAGAGCCATCACTCTAGCCCTTGGTGGAAGATCAAAGCTTAGCTTCATCAATGACAAAAACAACATCCCAGATGCCTCATCACGTGAATATGAAAGTTGGTTATCCAAAGACCAACTTGTTATGTCATGGCTTATTAATTCAATGGAGCCAAAACTTGCTGAAATCTTCAGCTATTCGGAGTCATCTCGACATCTCTGGATGCTGTCAAAGACATTATTCCAACTCAAAAAGGATCTTGCAGGGATTCAACAAGGTAATCTCTCATTTGTTCAAAATCTTGGCAACTTAAAAGCCAAGTGGAATGAACTTGATATATATAGACCTCACACCACTGATACCACCATATTGCTGAAAAGAGATGAAGAAGATAAAGTGTTCCAACTGCTTGCAAGTCTGGGATCTGAATATGAAGATCTAAGAAGTCATCTTTTGATGAGTCCTGAGCTTCCTTCGTTCACAACAGTATGCAACTCCATTCAACATGAAGAAGTGCGCAAAAAGGTGATGAATATAGACAGTAGAGCTGGAGGGTTAGAGGCTAGAGCATTTGCTGCAAACAAAAGTGTCACAAGCGACAGAACATACAAGGGCAAGAGGCCAGACCTGAAATGCACTCATTGTGAACGCATTGGACGAACTGGTATAGGCCACACAAGAGAGAGATGTTGGATATTGCATCCAGAATTGAAACCTAAGCACCATTCAGAGAAGCTCTATTACATCTCTAATCCAAAGGCAAACTTCGGCAACACTTCTGGAGATATGATGAACTTCACAACCAATCCAATAACTCTCATAAATGAGTTTGCTACATATCTTCAAAAGAAGCAAGGCAGTTTAGAAAGCAATGAAAATGGAAGCACAACTGCTATGCTTGGAAAATTTGCAGGTTTTCTAGCAAAATCAAATATGGCTTCTTCAGAGGATATCCCAGGATCGAGTGTCCAAGAAGAAGATTGGTGA
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

366

Amino Acids

41.2

Weight (kDa)

6.77

Isoelectric Point (pI)

37.95

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 30 - 63 7.8e-10 gag-polypeptide of LTR copia-type
Retrotran_gag_2 PF14223 166 - 213 6.7e-06 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)
Acc16I TGCGCA 1 cut(s) 632
Acc36I ACCTGC 1 cut(s) 1016
AclWI GGATC 3 cut(s) 378, 544, 1081
AcsI RAATTY 1 cut(s) 1019
AcuI CTGAAG 2 cut(s) 289, 1041
AcvI CACGTG 1 cut(s) 221
AgsI TTSAA 7 cut(s) 121, 279, 386, 410, 617, 826, 959
AjnI CCWGG 1 cut(s) 1069
AluBI AGCT 7 cut(s) 34, 175, 180, 309, 583, 662, 850
AluI AGCT 7 cut(s) 34, 175, 180, 309, 583, 662, 850
AlwI GGATC 3 cut(s) 378, 544, 1081
AoxI GGCC 2 cut(s) 734, 784
ApeKI GCWGC 1 cut(s) 689
ApoI RAATTY 1 cut(s) 1019
AseI ATTAAT 1 cut(s) 273
AspLEI GCGC 1 cut(s) 633
AsuHPI GGTGA 1 cut(s) 652
BarI GAAGNNNNNNTAC 2 cut(s) 839, 871
BbrPI CACGTG 1 cut(s) 221
BbvI GCAGC 1 cut(s) 676
BccI CCATC 2 cut(s) 68, 152
BciT130I CCWGG 1 cut(s) 1071
BfaI CTAG 5 cut(s) 35, 71, 152, 678, 1034
BfuAI ACCTGC 1 cut(s) 1016
BglII AGATCT 1 cut(s) 550
BisI GCNGC 1 cut(s) 690
BlpI GCTNAGC 1 cut(s) 176
BlsI GCNGC 1 cut(s) 691
Bme1390I CCNGG 1 cut(s) 1071
BmiI GGNNCC 1 cut(s) 285
BmrFI CCNGG 1 cut(s) 1071
BmsI GCATC 3 cut(s) 199, 327, 823
BpmI CTGGAG 2 cut(s) 684, 915
Bpu10I CCTNAGC 2 cut(s) 579, 831
Bpu1102I GCTNAGC 1 cut(s) 176
BsaAI YACGTR 1 cut(s) 221
BsaBI GATNNNNATC 1 cut(s) 78
BsaJI CCNNGG 2 cut(s) 157, 1069
Bse1I ACTGG 1 cut(s) 781
Bse3DI GCAATG 1 cut(s) 991
Bse8I GATNNNNATC 1 cut(s) 78
BseBI CCWGG 1 cut(s) 1071
BseDI CCNNGG 2 cut(s) 157, 1069
BseGI GGATG 3 cut(s) 201, 342, 814
BseJI GATNNNNATC 1 cut(s) 78
BseMI GCAATG 1 cut(s) 991
BseMII CTCAG 1 cut(s) 570
BseNI ACTGG 1 cut(s) 781
BseXI GCAGC 1 cut(s) 676
BshFI GGCC 2 cut(s) 736, 786
BsnI GGCC 2 cut(s) 736, 786
Bsp143I GATC 5 cut(s) 167, 370, 536, 550, 1073
Bsp1720I GCTNAGC 1 cut(s) 176
BspANI GGCC 2 cut(s) 736, 786
BspCNI CTCAG 1 cut(s) 571
BspLI GGNNCC 1 cut(s) 285
BspMI ACCTGC 1 cut(s) 1016
BspPI GGATC 3 cut(s) 378, 544, 1081
BsrDI GCAATG 1 cut(s) 991
BsrI ACTGG 1 cut(s) 781
BssECI CCNNGG 2 cut(s) 157, 1069
BssMI GATC 5 cut(s) 167, 370, 536, 550, 1073
BssT1I CCWWGG 1 cut(s) 157
Bst2UI CCWGG 1 cut(s) 1071
Bst4CI ACNGT 2 cut(s) 601, 656
BstAPI GCANNNNNTGC 1 cut(s) 689
BstBAI YACGTR 1 cut(s) 221
BstC8I GCNNGC 1 cut(s) 525
BstDEI CTNAG 4 cut(s) 176, 554, 579, 831
BstF5I GGATG 3 cut(s) 201, 342, 814
BstHHI GCGC 1 cut(s) 633
BstKTI GATC 5 cut(s) 170, 373, 539, 553, 1076
BstMBI GATC 5 cut(s) 167, 370, 536, 550, 1073
BstMWI GCNNNNNNNGC 1 cut(s) 689
BstNI CCWGG 1 cut(s) 1071
BstSCI CCNGG 1 cut(s) 1069
BstV1I GCAGC 1 cut(s) 676
BstX2I RGATCY 3 cut(s) 370, 536, 550
BstYI RGATCY 3 cut(s) 370, 536, 550
BsuRI GGCC 2 cut(s) 736, 786
BtsCI GGATG 3 cut(s) 201, 342, 814
BtsIMutI CAGTG 1 cut(s) 468
BveI ACCTGC 1 cut(s) 1016
Cac8I GCNNGC 1 cut(s) 525
CfoI GCGC 1 cut(s) 633
CviAII CATG 2 cut(s) 264, 620
DdeI CTNAG 4 cut(s) 176, 554, 579, 831
DpnI GATC 5 cut(s) 169, 372, 538, 552, 1075
DpnII GATC 5 cut(s) 167, 370, 536, 550, 1073
Eco130I CCWWGG 1 cut(s) 157
Eco32I GATATC 1 cut(s) 1066
Eco57I CTGAAG 2 cut(s) 289, 1041
Eco72I CACGTG 1 cut(s) 221
EcoRII CCWGG 1 cut(s) 1069
EcoRV GATATC 1 cut(s) 1066
EcoT14I CCWWGG 1 cut(s) 157
ErhI CCWWGG 1 cut(s) 157
FaeI CATG 2 cut(s) 267, 623
FalI AAGNNNNNCTT 6 cut(s) 164, 196, 237, 269, 863, 895
FatI CATG 2 cut(s) 263, 619
Fnu4HI GCNGC 1 cut(s) 690
FokI GGATG 3 cut(s) 188, 349, 801
Fsp4HI GCNGC 1 cut(s) 690
FspBI CTAG 5 cut(s) 35, 71, 152, 678, 1034
FspI TGCGCA 1 cut(s) 632
GlaI GCGC 1 cut(s) 632
GluI GCNGC 1 cut(s) 690
GsuI CTGGAG 2 cut(s) 684, 915
HaeIII GGCC 2 cut(s) 736, 786
HhaI GCGC 1 cut(s) 633
Hin1II CATG 2 cut(s) 267, 623
Hin6I GCGC 1 cut(s) 631
HinP1I GCGC 1 cut(s) 631
HindIII AAGCTT 1 cut(s) 173
HinfI GANTC 4 cut(s) 79, 317, 382, 574
HphI GGTGA 1 cut(s) 652
Hpy166II GTNNAC 2 cut(s) 594, 761
Hpy188I TCNGA 4 cut(s) 316, 541, 844, 1060
Hpy188III TCNNGA 6 cut(s) 138, 324, 334, 578, 818, 894
Hpy8I GTNNAC 2 cut(s) 594, 761
HpyAV CCTTC 3 cut(s) 8, 35, 597
HpyCH4III ACNGT 2 cut(s) 601, 656
HpyCH4IV ACGT 2 cut(s) 91, 220
HpyCH4V TGCA 9 cut(s) 29, 56, 377, 527, 606, 692, 750, 814, 1025
HpyF10VI GCNNNNNNNGC 1 cut(s) 689
HpyF3I CTNAG 4 cut(s) 176, 554, 579, 831
HpySE526I ACGT 2 cut(s) 91, 220
Hsp92II CATG 2 cut(s) 267, 623
HspAI GCGC 1 cut(s) 631
Kzo9I GATC 5 cut(s) 167, 370, 536, 550, 1073
LmnI GCTCC 1 cut(s) 283
Lsp1109I GCAGC 1 cut(s) 676
LweI GCATC 3 cut(s) 199, 327, 823
MaeI CTAG 5 cut(s) 35, 71, 152, 678, 1034
MaeII ACGT 2 cut(s) 91, 220
MaeIII GTNAC 1 cut(s) 703
MalI GATC 5 cut(s) 169, 372, 538, 552, 1075
MboI GATC 5 cut(s) 167, 370, 536, 550, 1073
MboII GAAGA 9 cut(s) 177, 295, 512, 515, 560, 635, 947, 1047, 1100
MflI RGATCY 3 cut(s) 370, 536, 550
MluCI AATT 3 cut(s) 274, 821, 1019
MlyI GAGTC 2 cut(s) 326, 583
MmeI TCCRAC 3 cut(s) 382, 541, 785
MnlI CCTC 6 cut(s) 223, 471, 659, 667, 726, 1054
MseI TTAA 2 cut(s) 273, 425
MspR9I CCNGG 1 cut(s) 1071
MvaI CCWGG 1 cut(s) 1071
MwoI GCNNNNNNNGC 1 cut(s) 689
NdeII GATC 5 cut(s) 167, 370, 536, 550, 1073
NlaIII CATG 2 cut(s) 267, 623
NlaIV GGNNCC 1 cut(s) 285
NmuCI GTSAC 1 cut(s) 703
NsbI TGCGCA 1 cut(s) 632
PcsI WCGNNNNNNNCGW 1 cut(s) 769
PfeI GAWTC 2 cut(s) 79, 382
PkrI GCNGC 1 cut(s) 691
PleI GAGTC 2 cut(s) 325, 582
PmaCI CACGTG 1 cut(s) 221
PmlI CACGTG 1 cut(s) 221
PpsI GAGTC 2 cut(s) 325, 582
Ppu21I YACGTR 1 cut(s) 221
PshBI ATTAAT 1 cut(s) 273
Psp6I CCWGG 1 cut(s) 1069
PspCI CACGTG 1 cut(s) 221
PspGI CCWGG 1 cut(s) 1069
PspN4I GGNNCC 1 cut(s) 285
PsuI RGATCY 3 cut(s) 370, 536, 550
SaqAI TTAA 2 cut(s) 273, 425
SatI GCNGC 1 cut(s) 690
Sau3AI GATC 5 cut(s) 167, 370, 536, 550, 1073
SchI GAGTC 2 cut(s) 326, 583
ScrFI CCNGG 1 cut(s) 1071
SfaNI GCATC 3 cut(s) 199, 327, 823
Sse9I AATT 3 cut(s) 274, 821, 1019
SspMI CTAG 5 cut(s) 35, 71, 152, 678, 1034
StyD4I CCNGG 1 cut(s) 1069
StyI CCWWGG 1 cut(s) 157
TaaI ACNGT 2 cut(s) 601, 656
TaiI ACGT 2 cut(s) 94, 223
TaqI TCGA 2 cut(s) 325, 1076
TasI AATT 3 cut(s) 274, 821, 1019
TfiI GAWTC 2 cut(s) 79, 382
Tru1I TTAA 2 cut(s) 273, 425
Tru9I TTAA 2 cut(s) 273, 425
TscAI CASTG 1 cut(s) 475
TseFI GTSAC 1 cut(s) 703
TseI GCWGC 1 cut(s) 689
Tsp45I GTSAC 1 cut(s) 703
TspDTI ATGAA 9 cut(s) 172, 243, 456, 513, 561, 636, 659, 920, 1002
TspRI CASTG 1 cut(s) 475
VspI ATTAAT 1 cut(s) 273
XapI RAATTY 1 cut(s) 1019
XspI CTAG 5 cut(s) 35, 71, 152, 678, 1034
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.