Rh1CG270400

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr1C
OG0000258
Physical Location & Seq
Forward (+)
53634698 .. 53637067
2370 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh1CG270400.1

Sequence Viewer

Length: 1074 bp
ATGTGTTTTGGGTGTGTAGTCTTCCTACAAGAGAAGAGAAACGTAGATTTTATGGAGGGCATTGGTAGAATTAAGAATTTCAAGAATTTCTGTTCTGCTTATGGGTTGCTATTCTATTTTTTTGTGTGCATAGGTCGAATTAAGAACTTCAAGAATTTCTGTTCTGCTTATGGATTGTATTCTAAATTGGTTTGTGGATTAATTCAGAATATAGTTGACAAAACAGACCAGTTGAACCTTCAAGAAGATGAAAAATTGCAGGCAAAACAAGAGCTCCTAAACAAGAGACACCGAAGTTTGTTGTCTCATTATTTCAAACCGACAGCTGAACAAGACAATGAAAAGCAAGTTCCTACCACTGAAGAACCAGAAGTTAGTTTGGGAACCAGAGAAAAGGAGAATGAGAACAAGAGTTCTGTATCAAAGTTAAGATCCCGACTAGCTCAGATTGAGCCTATTCGTTTTTATGGGAAGAACTACCATATCTGGGCGCAACAGATGAAACTTTACCTAAAGAAATTGAAGGTTGCATATGTACTCTGTGAGCCCTGCCCAACCATTATGCTTGGATTAGAAGCAAGTCCAGAGGAAATTGTTCAATCCATGGCTGCTAAACAGAAATGGATGAATGATGACACCAGGTGTGGTCGTACGATCTTGCATCATCTATCTGTTTGTCTATTTCATGCTTACTCACAGAAACAGAAGACTATGACTGCGAAAGATCTGTGGAAAGATCTAGAATTAAAATTTGGAACAGAAGCATCTATGATTACAACAGAGACATCTCTGGTTGAAAAGTACATCAAATTTCGGATCCTTAGGACAAAACCAATTGTGGAGCAAGTTAAAGAATTCAATAGTATCTTTGATTCTCTTTTCGCTTCTGGACTGGTGGTCGATGAGAAATTCCATGTCAATGTCCTCATCTCTAAGCTCAACCCTTCTTGGAAAAATGTTTTCAACCGGTTGATAGGCAAGGAATATCTGAGTAGTCTTGCAATGGTGATGGATATTTTGAGGGTTGAAGAAGGGCGGCGCTTCATGAGGAAGAATTTGAAGTTACATTCATGA
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

357

Amino Acids

41.62

Weight (kDa)

9.26

Isoelectric Point (pI)

41.53

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 195 - 349 4.1e-14 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) 1036
AclWI GGATC 3 cut(s) 426, 811, 824
AcsI RAATTY 8 cut(s) 76, 85, 154, 749, 809, 854, 908, 1054
AcuI CTGAAG 1 cut(s) 381
AdeI CACNNNGTG 1 cut(s) 642
AfaI GTAC 3 cut(s) 537, 652, 803
AfiI CCNNNNNNNGG 1 cut(s) 487
AgeI ACCGGT 1 cut(s) 966
AhdI GACNNNNNGTC 1 cut(s) 896
AjnI CCWGG 1 cut(s) 638
AjuI GAANNNNNNNTTGG 2 cut(s) 735, 767
AluBI AGCT 4 cut(s) 274, 326, 443, 937
AluI AGCT 4 cut(s) 274, 326, 443, 937
Alw21I GWGCWC 1 cut(s) 276
Alw26I GTCTC 3 cut(s) 280, 309, 776
AlwI GGATC 3 cut(s) 426, 811, 824
ApeKI GCWGC 1 cut(s) 608
ApoI RAATTY 8 cut(s) 76, 85, 154, 749, 809, 854, 908, 1054
AseI ATTAAT 1 cut(s) 200
AsiGI ACCGGT 1 cut(s) 966
Asp700I GAANNNNTTC 1 cut(s) 594
AspLEI GCGC 2 cut(s) 493, 1041
AsuHPI GGTGA 1 cut(s) 1018
AxyI CCTNAGG 1 cut(s) 821
BamHI GGATCC 1 cut(s) 816
BanII GRGCYC 2 cut(s) 276, 549
BbsI GAAGAC 2 cut(s) 13, 713
Bbv12I GWGCWC 1 cut(s) 276
BbvI GCAGC 1 cut(s) 595
BccI CCATC 1 cut(s) 1003
BciT130I CCWGG 1 cut(s) 640
BcoDI GTCTC 3 cut(s) 280, 309, 776
BfaI CTAG 2 cut(s) 440, 740
BfoI RGCGCY 1 cut(s) 1042
BglII AGATCT 2 cut(s) 724, 736
BisI GCNGC 2 cut(s) 609, 1037
BlsI GCNGC 2 cut(s) 610, 1038
Bme1390I CCNGG 1 cut(s) 640
BmeRI GACNNNNNGTC 1 cut(s) 896
BmiI GGNNCC 2 cut(s) 385, 818
BmrFI CCNGG 1 cut(s) 640
BmsI GCATC 2 cut(s) 670, 773
BpiI GAAGAC 2 cut(s) 13, 713
BsaJI CCNNGG 1 cut(s) 603
BsaWI WCCGGW 1 cut(s) 966
BsaXI ACNNNNNCTCC 2 cut(s) 258, 288
Bsc4I CCNNNNNNNGG 1 cut(s) 487
Bse118I RCCGGY 1 cut(s) 966
Bse1I ACTGG 2 cut(s) 229, 897
Bse21I CCTNAGG 1 cut(s) 821
Bse3DI GCAATG 1 cut(s) 1008
BseBI CCWGG 1 cut(s) 640
BseDI CCNNGG 1 cut(s) 603
BseGI GGATG 1 cut(s) 630
BseLI CCNNNNNNNGG 1 cut(s) 487
BseMI GCAATG 1 cut(s) 1008
BseMII CTCAG 2 cut(s) 458, 980
BseNI ACTGG 2 cut(s) 229, 897
BseXI GCAGC 1 cut(s) 595
BshTI ACCGGT 1 cut(s) 966
BsiHKAI GWGCWC 1 cut(s) 276
BsiSI CCGG 1 cut(s) 967
BsiWI CGTACG 1 cut(s) 650
BslI CCNNNNNNNGG 1 cut(s) 487
BsmAI GTCTC 3 cut(s) 280, 309, 776
Bsp1286I GDGCHC 2 cut(s) 276, 549
Bsp143I GATC 5 cut(s) 431, 654, 724, 736, 816
Bsp19I CCATGG 1 cut(s) 603
BspACI CCGC 1 cut(s) 1036
BspCNI CTCAG 2 cut(s) 457, 981
BspHI TCATGA 2 cut(s) 1044, 1070
BspLI GGNNCC 2 cut(s) 385, 818
BspPI GGATC 3 cut(s) 426, 811, 824
BsrDI GCAATG 1 cut(s) 1008
BsrFI RCCGGY 1 cut(s) 966
BsrI ACTGG 2 cut(s) 229, 897
BssAI RCCGGY 1 cut(s) 966
BssECI CCNNGG 1 cut(s) 603
BssMI GATC 5 cut(s) 431, 654, 724, 736, 816
BssT1I CCWWGG 1 cut(s) 603
Bst2UI CCWGG 1 cut(s) 640
Bst6I CTCTTC 1 cut(s) 29
BstC8I GCNNGC 1 cut(s) 261
BstDEI CTNAG 4 cut(s) 444, 821, 933, 989
BstDSI CCRYGG 1 cut(s) 603
BstF5I GGATG 1 cut(s) 630
BstH2I RGCGCY 1 cut(s) 1042
BstHHI GCGC 2 cut(s) 493, 1041
BstKTI GATC 5 cut(s) 434, 657, 727, 739, 819
BstMAI GTCTC 3 cut(s) 280, 309, 776
BstMBI GATC 5 cut(s) 431, 654, 724, 736, 816
BstNI CCWGG 1 cut(s) 640
BstSCI CCNGG 1 cut(s) 638
BstV1I GCAGC 1 cut(s) 595
BstV2I GAAGAC 2 cut(s) 13, 713
BstX2I RGATCY 4 cut(s) 431, 724, 736, 816
BstYI RGATCY 4 cut(s) 431, 724, 736, 816
Bsu36I CCTNAGG 1 cut(s) 821
BtgI CCRYGG 1 cut(s) 603
BtsCI GGATG 1 cut(s) 630
BtsIMutI CAGTG 1 cut(s) 357
Cac8I GCNNGC 1 cut(s) 261
CciI TCATGA 2 cut(s) 1044, 1070
CfoI GCGC 2 cut(s) 493, 1041
Cfr10I RCCGGY 1 cut(s) 966
CsiI ACCWGGT 1 cut(s) 638
Csp6I GTAC 3 cut(s) 536, 651, 802
CspAI ACCGGT 1 cut(s) 966
CviAII CATG 5 cut(s) 604, 686, 914, 1045, 1071
CviJI RGCY 7 cut(s) 274, 326, 443, 454, 547, 608, 937
CviKI_1 RGCY 7 cut(s) 274, 326, 443, 454, 547, 608, 937
CviQI GTAC 3 cut(s) 536, 651, 802
DdeI CTNAG 4 cut(s) 444, 821, 933, 989
DpnI GATC 5 cut(s) 433, 656, 726, 738, 818
DpnII GATC 5 cut(s) 431, 654, 724, 736, 816
DraIII CACNNNGTG 1 cut(s) 642
DriI GACNNNNNGTC 1 cut(s) 896
Eam1104I CTCTTC 1 cut(s) 29
Eam1105I GACNNNNNGTC 1 cut(s) 896
EarI CTCTTC 1 cut(s) 29
Ecl136II GAGCTC 1 cut(s) 274
Eco130I CCWWGG 1 cut(s) 603
Eco24I GRGCYC 2 cut(s) 276, 549
Eco53kI GAGCTC 1 cut(s) 274
Eco57I CTGAAG 1 cut(s) 381
Eco81I CCTNAGG 1 cut(s) 821
EcoICRI GAGCTC 1 cut(s) 274
EcoRI GAATTC 1 cut(s) 854
EcoRII CCWGG 1 cut(s) 638
EcoT14I CCWWGG 1 cut(s) 603
EcoT38I GRGCYC 2 cut(s) 276, 549
ErhI CCWWGG 1 cut(s) 603
FaeI CATG 5 cut(s) 607, 689, 917, 1048, 1074
FatI CATG 5 cut(s) 603, 685, 913, 1044, 1070
FauNDI CATATG 1 cut(s) 532
Fnu4HI GCNGC 2 cut(s) 609, 1037
FokI GGATG 1 cut(s) 637
FriOI GRGCYC 2 cut(s) 276, 549
Fsp4HI GCNGC 2 cut(s) 609, 1037
FspBI CTAG 2 cut(s) 440, 740
GlaI GCGC 2 cut(s) 492, 1040
GluI GCNGC 2 cut(s) 609, 1037
HaeII RGCGCY 1 cut(s) 1042
HapII CCGG 1 cut(s) 967
HhaI GCGC 2 cut(s) 493, 1041
Hin1II CATG 5 cut(s) 607, 689, 917, 1048, 1074
Hin6I GCGC 2 cut(s) 491, 1039
HinP1I GCGC 2 cut(s) 491, 1039
HincII GTYRAC 1 cut(s) 217
HindII GTYRAC 1 cut(s) 217
HinfI GANTC 1 cut(s) 872
HpaII CCGG 1 cut(s) 967
HphI GGTGA 1 cut(s) 1018
Hpy166II GTNNAC 1 cut(s) 217
Hpy188I TCNGA 4 cut(s) 207, 447, 816, 990
Hpy188III TCNNGA 9 cut(s) 82, 151, 242, 435, 584, 740, 888, 1045, 1071
Hpy8I GTNNAC 1 cut(s) 217
HpyAV CCTTC 4 cut(s) 248, 517, 954, 1025
HpyCH4IV ACGT 1 cut(s) 42
HpyCH4V TGCA 5 cut(s) 129, 259, 530, 661, 1001
HpyF3I CTNAG 4 cut(s) 444, 821, 933, 989
HpySE526I ACGT 1 cut(s) 42
Hsp92II CATG 5 cut(s) 607, 689, 917, 1048, 1074
HspAI GCGC 2 cut(s) 491, 1039
Kzo9I GATC 5 cut(s) 431, 654, 724, 736, 816
LmnI GCTCC 2 cut(s) 279, 841
Lsp1109I GCAGC 1 cut(s) 595
LweI GCATC 2 cut(s) 670, 773
MabI ACCWGGT 1 cut(s) 638
MaeI CTAG 2 cut(s) 440, 740
MaeII ACGT 1 cut(s) 42
MaeIII GTNAC 1 cut(s) 1062
MalI GATC 5 cut(s) 433, 656, 726, 738, 818
MboI GATC 5 cut(s) 431, 654, 724, 736, 816
MboII GAAGA 8 cut(s) 13, 46, 257, 374, 484, 718, 1040, 1063
MfeI CAATTG 1 cut(s) 834
MflI RGATCY 4 cut(s) 431, 724, 736, 816
MhlI GDGCHC 2 cut(s) 276, 549
MnlI CCTC 5 cut(s) 49, 580, 935, 1014, 1041
MroXI GAANNNNTTC 1 cut(s) 594
MseI TTAA 6 cut(s) 72, 141, 200, 428, 746, 849
MslI CAYNNNNRTG 1 cut(s) 918
MspA1I CMGCKG 1 cut(s) 326
MspI CCGG 1 cut(s) 967
MspR9I CCNGG 1 cut(s) 640
MunI CAATTG 1 cut(s) 834
MvaI CCWGG 1 cut(s) 640
NcoI CCATGG 1 cut(s) 603
NdeI CATATG 1 cut(s) 532
NdeII GATC 5 cut(s) 431, 654, 724, 736, 816
NlaIII CATG 5 cut(s) 607, 689, 917, 1048, 1074
NlaIV GGNNCC 2 cut(s) 385, 818
PagI TCATGA 2 cut(s) 1044, 1070
PdmI GAANNNNTTC 1 cut(s) 594
PfeI GAWTC 1 cut(s) 872
Pfl23II CGTACG 1 cut(s) 650
PinAI ACCGGT 1 cut(s) 966
PkrI GCNGC 2 cut(s) 610, 1038
PshBI ATTAAT 1 cut(s) 200
Psp124BI GAGCTC 1 cut(s) 276
Psp6I CCWGG 1 cut(s) 638
PspGI CCWGG 1 cut(s) 638
PspLI CGTACG 1 cut(s) 650
PspN4I GGNNCC 2 cut(s) 385, 818
PsuI RGATCY 4 cut(s) 431, 724, 736, 816
PvuII CAGCTG 1 cut(s) 326
RsaI GTAC 3 cut(s) 537, 652, 803
RsaNI GTAC 3 cut(s) 536, 651, 802
RseI CAYNNNNRTG 1 cut(s) 918
SacI GAGCTC 1 cut(s) 276
SaqAI TTAA 6 cut(s) 72, 141, 200, 428, 746, 849
SatI GCNGC 2 cut(s) 609, 1037
Sau3AI GATC 5 cut(s) 431, 654, 724, 736, 816
ScrFI CCNGG 1 cut(s) 640
SduI GDGCHC 2 cut(s) 276, 549
SexAI ACCWGGT 1 cut(s) 638
SfaNI GCATC 2 cut(s) 670, 773
SmiMI CAYNNNNRTG 1 cut(s) 918
SsiI CCGC 1 cut(s) 1036
SspMI CTAG 2 cut(s) 440, 740
SstI GAGCTC 1 cut(s) 276
StyD4I CCNGG 1 cut(s) 638
StyI CCWWGG 1 cut(s) 603
TaiI ACGT 1 cut(s) 45
TaqI TCGA 2 cut(s) 136, 900
TatI WGTACW 2 cut(s) 535, 801
TauI GCSGC 1 cut(s) 1039
TfiI GAWTC 1 cut(s) 872
Tru1I TTAA 6 cut(s) 72, 141, 200, 428, 746, 849
Tru9I TTAA 6 cut(s) 72, 141, 200, 428, 746, 849
TscAI CASTG 1 cut(s) 364
TseI GCWGC 1 cut(s) 608
TspDTI ATGAA 7 cut(s) 264, 354, 515, 641, 674, 1033, 1059
TspRI CASTG 1 cut(s) 364
VspI ATTAAT 1 cut(s) 200
XapI RAATTY 8 cut(s) 76, 85, 154, 749, 809, 854, 908, 1054
XbaI TCTAGA 1 cut(s) 739
XmnI GAANNNNTTC 1 cut(s) 594
XspI CTAG 2 cut(s) 440, 740
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.