RchiOBHm_Chr6g0283031

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
6
OG0000258
Physical Location & Seq
Reverse (-)
46272308 .. 46273426
1119 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ25376

Sequence Viewer

Length: 597 bp
ATGGTTGAAAACAAATCTGTAGATAGCCAAATCCATGAGTATCAAGAGCTTTTAAGGGGAATAGAAAAGAAAGGAACCAAGTTTAGTGAAGACTTCAAAGTGTCTTGCCTTATAGATAAATTGCCTCCTTCATGGGATGAACATGGCAAGACTCTTAGGCATAAACAAGGAGAGTTTACCCTTCGTCAAGCCATGAATAACCTTAGAGTTGAAGAAAAACAAAGGGTAGACCAAAAGGAAAAACCTGAGAAAACATCCATTGTGAACTTAGTTGTGGGAAACAAAAACCATAATCACAACAAGACTAAATTCCACAACAGAAATCGAAGAAGCAACTTTCAGCCTAGGGGAATAAACTTTAAGAACAATAGAGCCAACCATAACAACCAGTTCCAGAAATTTAAGGATCAAGGGAGAGAAAAGATATCTTGCTTTGTTTGTGGGAGGACCAACCATGTAGCAAGGAATTGCTTCTACAAAAGGACTGAGGAGAACAAGTCTCAAGCAAATAGGAATGGTCCAAAAGCTCAAGTGAATATGCTAATGGAGCAAGAGTCCTCTCAACCATTATTCAAAAATCAAGTGGAGGACGTGTAA
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
Retrotran_gag_2

Protein Analysis

198

Amino Acids

23.35

Weight (kDa)

9.79

Isoelectric Point (pI)

49.93

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 1 - 79 1.5e-07 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)
AccI GTMKAC 1 cut(s) 228
AclWI GGATC 1 cut(s) 414
AcsI RAATTY 2 cut(s) 308, 398
AflIII ACRYGT 1 cut(s) 591
AgsI TTSAA 4 cut(s) 8, 97, 212, 574
AjiI CACGTC 1 cut(s) 592
AluBI AGCT 2 cut(s) 49, 527
AluI AGCT 2 cut(s) 49, 527
Alw26I GTCTC 1 cut(s) 504
AlwI GGATC 1 cut(s) 414
ApoI RAATTY 2 cut(s) 308, 398
Asp700I GAANNNNTTC 1 cut(s) 470
AspA2I CCTAGG 1 cut(s) 344
AspS9I GGNCC 2 cut(s) 447, 518
AvaII GGWCC 2 cut(s) 447, 518
AvrII CCTAGG 1 cut(s) 344
BbsI GAAGAC 1 cut(s) 96
BcoDI GTCTC 1 cut(s) 504
BfaI CTAG 1 cut(s) 345
BfmI CTRYAG 1 cut(s) 18
BlnI CCTAGG 1 cut(s) 344
Bme18I GGWCC 2 cut(s) 447, 518
BmgBI CACGTC 1 cut(s) 592
BmgT120I GGNCC 2 cut(s) 447, 518
BmiI GGNNCC 1 cut(s) 76
BpiI GAAGAC 1 cut(s) 96
BpuEI CTTGAG 2 cut(s) 486, 513
BsaJI CCNNGG 1 cut(s) 344
BsaXI ACNNNNNCTCC 5 cut(s) 482, 512, 539, 569, 578
Bse1I ACTGG 1 cut(s) 388
BseDI CCNNGG 1 cut(s) 344
BseGI GGATG 2 cut(s) 142, 254
BseMII CTCAG 2 cut(s) 237, 477
BseNI ACTGG 1 cut(s) 388
BseRI GAGGAG 1 cut(s) 503
BsmAI GTCTC 1 cut(s) 504
Bsp143I GATC 1 cut(s) 406
BspCNI CTCAG 2 cut(s) 238, 478
BspLI GGNNCC 1 cut(s) 76
BspPI GGATC 1 cut(s) 414
BsrI ACTGG 1 cut(s) 388
BssECI CCNNGG 1 cut(s) 344
BssMI GATC 1 cut(s) 406
BssT1I CCWWGG 1 cut(s) 344
BstDEI CTNAG 5 cut(s) 155, 203, 246, 268, 486
BstF5I GGATG 2 cut(s) 142, 254
BstKTI GATC 1 cut(s) 409
BstMAI GTCTC 1 cut(s) 504
BstMBI GATC 1 cut(s) 406
BstMWI GCNNNNNNNGC 1 cut(s) 547
BstSFI CTRYAG 1 cut(s) 18
BstV2I GAAGAC 1 cut(s) 96
BtrI CACGTC 1 cut(s) 592
BtsCI GGATG 2 cut(s) 142, 254
Cfr13I GGNCC 2 cut(s) 447, 518
CviAII CATG 5 cut(s) 35, 132, 143, 193, 455
CviJI RGCY 6 cut(s) 27, 49, 191, 343, 374, 527
CviKI_1 RGCY 6 cut(s) 27, 49, 191, 343, 374, 527
DdeI CTNAG 5 cut(s) 155, 203, 246, 268, 486
DpnI GATC 1 cut(s) 408
DpnII GATC 1 cut(s) 406
Eco130I CCWWGG 1 cut(s) 344
Eco32I GATATC 1 cut(s) 426
Eco47I GGWCC 2 cut(s) 447, 518
EcoRV GATATC 1 cut(s) 426
EcoT14I CCWWGG 1 cut(s) 344
ErhI CCWWGG 1 cut(s) 344
FaeI CATG 5 cut(s) 38, 135, 146, 196, 458
FatI CATG 5 cut(s) 34, 131, 142, 192, 454
FblI GTMKAC 1 cut(s) 228
FokI GGATG 2 cut(s) 149, 241
FspBI CTAG 1 cut(s) 345
Hin1II CATG 5 cut(s) 38, 135, 146, 196, 458
HinfI GANTC 2 cut(s) 151, 554
Hpy166II GTNNAC 3 cut(s) 177, 229, 265
Hpy188III TCNNGA 2 cut(s) 44, 394
Hpy8I GTNNAC 3 cut(s) 177, 229, 265
HpyAV CCTTC 2 cut(s) 138, 191
HpyCH4IV ACGT 1 cut(s) 591
HpyF10VI GCNNNNNNNGC 1 cut(s) 547
HpyF3I CTNAG 5 cut(s) 155, 203, 246, 268, 486
HpySE526I ACGT 1 cut(s) 591
Hsp92II CATG 5 cut(s) 38, 135, 146, 196, 458
Kzo9I GATC 1 cut(s) 406
LmnI GCTCC 1 cut(s) 547
LpnPI CCDG 3 cut(s) 258, 401, 407
MaeI CTAG 1 cut(s) 345
MaeII ACGT 1 cut(s) 591
MalI GATC 1 cut(s) 408
MboI GATC 1 cut(s) 406
MboII GAAGA 3 cut(s) 101, 224, 339
MluCI AATT 4 cut(s) 119, 308, 398, 466
MlyI GAGTC 2 cut(s) 145, 563
MnlI CCTC 5 cut(s) 135, 438, 481, 568, 580
MroXI GAANNNNTTC 1 cut(s) 470
MseI TTAA 3 cut(s) 53, 360, 402
MwoI GCNNNNNNNGC 1 cut(s) 547
NdeII GATC 1 cut(s) 406
NlaIII CATG 5 cut(s) 38, 135, 146, 196, 458
NlaIV GGNNCC 1 cut(s) 76
PdmI GAANNNNTTC 1 cut(s) 470
PleI GAGTC 2 cut(s) 145, 562
PpsI GAGTC 2 cut(s) 145, 562
PspN4I GGNNCC 1 cut(s) 76
PspPI GGNCC 2 cut(s) 447, 518
SaqAI TTAA 3 cut(s) 53, 360, 402
Sau3AI GATC 1 cut(s) 406
Sau96I GGNCC 2 cut(s) 447, 518
SchI GAGTC 2 cut(s) 145, 563
SetI ASST 5 cut(s) 51, 204, 247, 529, 594
SfcI CTRYAG 1 cut(s) 18
SinI GGWCC 2 cut(s) 447, 518
SmlI CTYRAG 2 cut(s) 501, 528
SmoI CTYRAG 2 cut(s) 501, 528
Sse9I AATT 4 cut(s) 119, 308, 398, 466
SspMI CTAG 1 cut(s) 345
StyI CCWWGG 1 cut(s) 344
TaiI ACGT 1 cut(s) 594
TaqI TCGA 1 cut(s) 325
TasI AATT 4 cut(s) 119, 308, 398, 466
Tru1I TTAA 3 cut(s) 53, 360, 402
Tru9I TTAA 3 cut(s) 53, 360, 402
TspDTI ATGAA 3 cut(s) 120, 153, 209
VpaK11BI GGWCC 2 cut(s) 447, 518
XapI RAATTY 2 cut(s) 308, 398
XmaJI CCTAGG 1 cut(s) 344
XmiI GTMKAC 1 cut(s) 228
XmnI GAANNNNTTC 1 cut(s) 470
XspI CTAG 1 cut(s) 345
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.