Rh1DG282000

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr1D
OG0000258
Physical Location & Seq
Forward (+)
50350204 .. 50352632
2429 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1DG282000.1

Sequence Viewer

Length: 720 bp
ATGTCTTCAGAACCAGAAGTTAGTTTGGGAACCAGAGAAAAGGAGAATGAGAACAAGAGTTCTGTATCAAAGTTAAGATCCCGACTAGCTCAGATTGAGCCTATTCGTTTTTATGGGAAGAACTACCATATCTGGGAGCAACAGATGAAACTTTACCTAAAGAAATTGAAGGTTGCATATGTACTCTGTGAGCCCTGCCCAACCATTATGCTTGGATTAGAAGCAAGTCCAGAGGAAATTGTTCAATCCATGGCTGCTAAACAGAAATGGATGAATGATGACACCAGGTGTGGTCGTACGATCTTGCATCATCTATCTGTTTGTTTATTTCATGCTTACTCACAGAAACAGAAGACTATGACTGCGAAAGAACTGTGGAAAGATCTAGAATTAAAATTTGGAACAGAAGCATCTATGATTACAACAGAGACATCTCTGGTTGAAAAGTACATCAAATTTCGGATCCTTGGGACAAAACCAATTGTGGAGCAAGTTAAAGAATTCAATAGTATCTTTGATTCTCTTTTCGCTTCTGGACTGGTGGTCGATGAGAAATTCCATGTCAATGTCCTCATCTCTAAGCTCCCCCCTTCTTGGAAAAATGTTTTCAACCGGTTGATAGGCAAGGAGTATCTGAGTAGTCTTGCAATGGTGATGGATATTTTGAGGGTTGAAGAAGGGCGGCGCTTCATGAGGAAGAATTTGAAGTTACATTCATGA
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
DEK_C PC4 Retrotran_gag_2

Protein Analysis

239

Amino Acids

27.75

Weight (kDa)

9.3

Isoelectric Point (pI)

46.87

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 77 - 231 6.3e-16 gag-polypeptide of LTR copia-type
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000258)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G00980
fragaria_vesca FvH4_1g25682 FvH4_2g13961 FvH4_2g20162 FvH4_2g24753 FvH4_3g12191 FvH4_3g12632 FvH4_3g16171 FvH4_4g05871 FvH4_4g05873 FvH4_4g10121 FvH4_4g15488 FvH4_4g23911 FvH4_4g27782 FvH4_5g08912 FvH4_5g23001 FvH4_5g24552 FvH4_5g32801 FvH4_5g32802 FvH4_6g05093 FvH4_6g19722 FvH4_6g20391 FvH4_6g33792 FvH4_7g01381 FvH4_7g16761 FvH4_7g16761 FvH4_7g16761
malus_domestica MD01G1082500.v1.1 MD15G1436400.v1.1
prunus_persica Prupe.2G021400_v2.0.a1 Prupe.2G052400_v2.0.a1 Prupe.2G065000_v2.0.a1 Prupe.2G187700_v2.0.a1 Prupe.2G187800_v2.0.a1 Prupe.2G189900_v2.0.a1 Prupe.2G191300_v2.0.a1 Prupe.2G191700_v2.0.a1 Prupe.4G265600_v2.0.a1 Prupe.7G014200_v2.0.a1 Prupe.7G039000_v2.0.a1
pyrus_communis pycom01g05590 pycom01g05910 pycom02g12230 pycom02g25840 pycom03g15580 pycom04g04480 pycom05g09230 pycom05g23350 pycom05g23360 pycom07g08380 pycom09g01980 pycom09g01990 pycom11g18190 pycom11g18200 pycom11g21580 pycom13g04160 pycom15g25800 pycom16g16210 pycom16g17230 pycom16g24560 pycom16g25700 pycom17g11020
rosa_chinensis RchiOBHm_Chr1g0359981 RchiOBHm_Chr2g0151961 RchiOBHm_Chr2g0171331 RchiOBHm_Chr5g0081471 RchiOBHm_Chr6g0283031 RchiOBHm_Chr7g0197111 RchiOBHm_Chr7g0222601
rosa_laevigata RLG00000027843 RLG00000027845 RLG00000030065
rosa_multiflora Rmu_sc0000381.1_g000031 Rmu_sc0001179.1_g000035 Rmu_sc0001616.1_g000046 Rmu_sc0001851.1_g000032 Rmu_sc0002152.1_g000013 Rmu_sc0004031.1_g000015 Rmu_sc0004645.1_g000003 Rmu_sc0007393.1_g000001 Rmu_sc0008949.1_g000003 Rmu_sc0009799.1_g000011 Rmu_sc0011614.1_g000001 Rmu_sc0011699.1_g000009 Rmu_sc0019280.1_g000001 Rmu_sc0023984.1_g000001 Rmu_ssc0000050.1_g000036
rosa_roxburghii Rroxscaffold_1G00022650 Rroxscaffold_1G00033480 Rroxscaffold_3G00270250 Rroxscaffold_4G00296600 Rroxscaffold_4G00296760 Rroxscaffold_6G00409840
rosa_rugosa Rorug01G0273800 Rorug01G0273900 Rorug01G0274000
rosa_samantha Rh1AG287300 Rh1AG288100 Rh1BG253000 Rh1BG253500 Rh1BG399800 Rh1CG270400 Rh1CG271000 Rh1DG282000 Rh1DG282500 Rh4DG126500 Rh5DG194600 Rh5DG461100
rosa_wichuraiana Rw0G009130 Rw1G002590 Rw1G008490 Rw1G012210 Rw1G014290 Rw1G014490 Rw1G025510 Rw2G025840 Rw2G026170 Rw2G036510 Rw3G003050 Rw4G009270 Rw5G002350 Rw5G013930 Rw5G019500 Rw5G025890 Rw5G029960 Rw5G032360 Rw6G009890 Rw6G015670 Rw6G015860 Rw7G010030 Rw7G032600 Rw7G032770

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 1 cut(s) 682
AclWI GGATC 3 cut(s) 72, 457, 470
AcsI RAATTY 5 cut(s) 395, 455, 500, 554, 700
AdeI CACNNNGTG 1 cut(s) 288
AfaI GTAC 3 cut(s) 183, 298, 449
AfiI CCNNNNNNNGG 2 cut(s) 133, 594
AgeI ACCGGT 1 cut(s) 612
AgsI TTSAA 7 cut(s) 169, 245, 443, 505, 610, 674, 706
AhdI GACNNNNNGTC 1 cut(s) 542
AjnI CCWGG 1 cut(s) 284
AjuI GAANNNNNNNTTGG 2 cut(s) 381, 413
AluBI AGCT 2 cut(s) 89, 583
AluI AGCT 2 cut(s) 89, 583
Alw26I GTCTC 1 cut(s) 422
AlwI GGATC 3 cut(s) 72, 457, 470
ApeKI GCWGC 1 cut(s) 254
ApoI RAATTY 5 cut(s) 395, 455, 500, 554, 700
AsiGI ACCGGT 1 cut(s) 612
Asp700I GAANNNNTTC 1 cut(s) 240
AspLEI GCGC 1 cut(s) 687
AsuHPI GGTGA 1 cut(s) 664
BamHI GGATCC 1 cut(s) 462
BanII GRGCYC 1 cut(s) 195
BbsI GAAGAC 1 cut(s) 359
BbvI GCAGC 1 cut(s) 241
BccI CCATC 1 cut(s) 649
BciT130I CCWGG 1 cut(s) 286
BcoDI GTCTC 1 cut(s) 422
BfaI CTAG 2 cut(s) 86, 386
BfoI RGCGCY 1 cut(s) 688
BglII AGATCT 1 cut(s) 382
BisI GCNGC 2 cut(s) 255, 683
BlsI GCNGC 2 cut(s) 256, 684
Bme1390I CCNGG 1 cut(s) 286
BmeRI GACNNNNNGTC 1 cut(s) 542
BmiI GGNNCC 2 cut(s) 31, 464
BmrFI CCNGG 1 cut(s) 286
BmsI GCATC 2 cut(s) 316, 419
BpiI GAAGAC 1 cut(s) 359
BsaJI CCNNGG 2 cut(s) 249, 466
BsaWI WCCGGW 1 cut(s) 612
Bsc4I CCNNNNNNNGG 2 cut(s) 133, 594
Bse118I RCCGGY 1 cut(s) 612
Bse1I ACTGG 1 cut(s) 543
Bse3DI GCAATG 1 cut(s) 654
BseBI CCWGG 1 cut(s) 286
BseDI CCNNGG 2 cut(s) 249, 466
BseGI GGATG 1 cut(s) 276
BseLI CCNNNNNNNGG 2 cut(s) 133, 594
BseMI GCAATG 1 cut(s) 654
BseMII CTCAG 2 cut(s) 104, 626
BseNI ACTGG 1 cut(s) 543
BseXI GCAGC 1 cut(s) 241
BshTI ACCGGT 1 cut(s) 612
BsiSI CCGG 1 cut(s) 613
BsiWI CGTACG 1 cut(s) 296
BslFI GGGAC 1 cut(s) 484
BslI CCNNNNNNNGG 2 cut(s) 133, 594
BsmAI GTCTC 1 cut(s) 422
BsmFI GGGAC 1 cut(s) 484
Bsp1286I GDGCHC 1 cut(s) 195
Bsp143I GATC 4 cut(s) 77, 300, 382, 462
Bsp19I CCATGG 1 cut(s) 249
BspACI CCGC 1 cut(s) 682
BspCNI CTCAG 2 cut(s) 103, 627
BspHI TCATGA 2 cut(s) 690, 716
BspLI GGNNCC 2 cut(s) 31, 464
BspPI GGATC 3 cut(s) 72, 457, 470
BsrDI GCAATG 1 cut(s) 654
BsrFI RCCGGY 1 cut(s) 612
BsrI ACTGG 1 cut(s) 543
BssAI RCCGGY 1 cut(s) 612
BssECI CCNNGG 2 cut(s) 249, 466
BssMI GATC 4 cut(s) 77, 300, 382, 462
BssT1I CCWWGG 2 cut(s) 249, 466
Bst2UI CCWGG 1 cut(s) 286
Bst4CI ACNGT 1 cut(s) 375
BstDEI CTNAG 3 cut(s) 90, 579, 635
BstDSI CCRYGG 1 cut(s) 249
BstF5I GGATG 1 cut(s) 276
BstH2I RGCGCY 1 cut(s) 688
BstHHI GCGC 1 cut(s) 687
BstKTI GATC 4 cut(s) 80, 303, 385, 465
BstMAI GTCTC 1 cut(s) 422
BstMBI GATC 4 cut(s) 77, 300, 382, 462
BstNI CCWGG 1 cut(s) 286
BstSCI CCNGG 1 cut(s) 284
BstV1I GCAGC 1 cut(s) 241
BstV2I GAAGAC 1 cut(s) 359
BstX2I RGATCY 3 cut(s) 77, 382, 462
BstYI RGATCY 3 cut(s) 77, 382, 462
BtgI CCRYGG 1 cut(s) 249
BtsCI GGATG 1 cut(s) 276
CciI TCATGA 2 cut(s) 690, 716
CfoI GCGC 1 cut(s) 687
Cfr10I RCCGGY 1 cut(s) 612
CsiI ACCWGGT 1 cut(s) 284
Csp6I GTAC 3 cut(s) 182, 297, 448
CspAI ACCGGT 1 cut(s) 612
CviAII CATG 5 cut(s) 250, 332, 560, 691, 717
CviJI RGCY 5 cut(s) 89, 100, 193, 254, 583
CviKI_1 RGCY 5 cut(s) 89, 100, 193, 254, 583
CviQI GTAC 3 cut(s) 182, 297, 448
DdeI CTNAG 3 cut(s) 90, 579, 635
DpnI GATC 4 cut(s) 79, 302, 384, 464
DpnII GATC 4 cut(s) 77, 300, 382, 462
DraIII CACNNNGTG 1 cut(s) 288
DriI GACNNNNNGTC 1 cut(s) 542
Eam1105I GACNNNNNGTC 1 cut(s) 542
Eco130I CCWWGG 2 cut(s) 249, 466
Eco24I GRGCYC 1 cut(s) 195
EcoRI GAATTC 1 cut(s) 500
EcoRII CCWGG 1 cut(s) 284
EcoT14I CCWWGG 2 cut(s) 249, 466
EcoT38I GRGCYC 1 cut(s) 195
ErhI CCWWGG 2 cut(s) 249, 466
FaeI CATG 5 cut(s) 253, 335, 563, 694, 720
FaqI GGGAC 1 cut(s) 484
FatI CATG 5 cut(s) 249, 331, 559, 690, 716
FauNDI CATATG 1 cut(s) 178
Fnu4HI GCNGC 2 cut(s) 255, 683
FokI GGATG 1 cut(s) 283
FriOI GRGCYC 1 cut(s) 195
Fsp4HI GCNGC 2 cut(s) 255, 683
FspBI CTAG 2 cut(s) 86, 386
GlaI GCGC 1 cut(s) 686
GluI GCNGC 2 cut(s) 255, 683
HaeII RGCGCY 1 cut(s) 688
HapII CCGG 1 cut(s) 613
HhaI GCGC 1 cut(s) 687
Hin1II CATG 5 cut(s) 253, 335, 563, 694, 720
Hin6I GCGC 1 cut(s) 685
HinP1I GCGC 1 cut(s) 685
HinfI GANTC 1 cut(s) 518
HpaII CCGG 1 cut(s) 613
HphI GGTGA 1 cut(s) 664
Hpy188I TCNGA 4 cut(s) 10, 93, 462, 636
Hpy188III TCNNGA 6 cut(s) 81, 230, 386, 534, 691, 717
HpyAV CCTTC 3 cut(s) 163, 600, 671
HpyCH4III ACNGT 1 cut(s) 375
HpyCH4V TGCA 3 cut(s) 176, 307, 647
HpyF3I CTNAG 3 cut(s) 90, 579, 635
Hsp92II CATG 5 cut(s) 253, 335, 563, 694, 720
HspAI GCGC 1 cut(s) 685
Kzo9I GATC 4 cut(s) 77, 300, 382, 462
LmnI GCTCC 3 cut(s) 136, 487, 588
Lsp1109I GCAGC 1 cut(s) 241
LweI GCATC 2 cut(s) 316, 419
MabI ACCWGGT 1 cut(s) 284
MaeI CTAG 2 cut(s) 86, 386
MaeIII GTNAC 1 cut(s) 708
MalI GATC 4 cut(s) 79, 302, 384, 464
MboI GATC 4 cut(s) 77, 300, 382, 462
MboII GAAGA 4 cut(s) 130, 364, 686, 709
MfeI CAATTG 1 cut(s) 480
MflI RGATCY 3 cut(s) 77, 382, 462
MhlI GDGCHC 1 cut(s) 195
MluCI AATT 9 cut(s) 164, 237, 389, 395, 455, 480, 500, 554, 700
MnlI CCTC 4 cut(s) 226, 581, 660, 687
MroXI GAANNNNTTC 1 cut(s) 240
MseI TTAA 3 cut(s) 74, 392, 495
MslI CAYNNNNRTG 1 cut(s) 564
MspI CCGG 1 cut(s) 613
MspR9I CCNGG 1 cut(s) 286
MunI CAATTG 1 cut(s) 480
MvaI CCWGG 1 cut(s) 286
NcoI CCATGG 1 cut(s) 249
NdeI CATATG 1 cut(s) 178
NdeII GATC 4 cut(s) 77, 300, 382, 462
NlaIII CATG 5 cut(s) 253, 335, 563, 694, 720
NlaIV GGNNCC 2 cut(s) 31, 464
PagI TCATGA 2 cut(s) 690, 716
PdmI GAANNNNTTC 1 cut(s) 240
PfeI GAWTC 1 cut(s) 518
Pfl23II CGTACG 1 cut(s) 296
PinAI ACCGGT 1 cut(s) 612
PkrI GCNGC 2 cut(s) 256, 684
Psp6I CCWGG 1 cut(s) 284
PspGI CCWGG 1 cut(s) 284
PspLI CGTACG 1 cut(s) 296
PspN4I GGNNCC 2 cut(s) 31, 464
PsuI RGATCY 3 cut(s) 77, 382, 462
RsaI GTAC 3 cut(s) 183, 298, 449
RsaNI GTAC 3 cut(s) 182, 297, 448
RseI CAYNNNNRTG 1 cut(s) 564
SaqAI TTAA 3 cut(s) 74, 392, 495
SatI GCNGC 2 cut(s) 255, 683
Sau3AI GATC 4 cut(s) 77, 300, 382, 462
ScrFI CCNGG 1 cut(s) 286
SduI GDGCHC 1 cut(s) 195
SetI ASST 5 cut(s) 91, 159, 174, 290, 585
SexAI ACCWGGT 1 cut(s) 284
SfaNI GCATC 2 cut(s) 316, 419
SmiMI CAYNNNNRTG 1 cut(s) 564
Sse9I AATT 9 cut(s) 164, 237, 389, 395, 455, 480, 500, 554, 700
SsiI CCGC 1 cut(s) 682
SspMI CTAG 2 cut(s) 86, 386
StyD4I CCNGG 1 cut(s) 284
StyI CCWWGG 2 cut(s) 249, 466
TaaI ACNGT 1 cut(s) 375
TaqI TCGA 1 cut(s) 546
TasI AATT 9 cut(s) 164, 237, 389, 395, 455, 480, 500, 554, 700
TatI WGTACW 2 cut(s) 181, 447
TauI GCSGC 1 cut(s) 685
TfiI GAWTC 1 cut(s) 518
Tru1I TTAA 3 cut(s) 74, 392, 495
Tru9I TTAA 3 cut(s) 74, 392, 495
TseI GCWGC 1 cut(s) 254
TspDTI ATGAA 5 cut(s) 161, 287, 320, 679, 705
XapI RAATTY 5 cut(s) 395, 455, 500, 554, 700
XbaI TCTAGA 1 cut(s) 385
XmnI GAANNNNTTC 1 cut(s) 240
XspI CTAG 2 cut(s) 86, 386
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.