Rh1BG253000

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr1B
OG0000258
Physical Location & Seq
Forward (+)
38186093 .. 38188521
2429 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1BG253000.1

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
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Publication-ready
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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.