RLG00000027845

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_laevigata
Chr6
OG0000258
Physical Location & Seq
Reverse (-)
15998277 .. 15999395
1119 bp
Loading structure...
UTR
Exon/CDS
Intron
RLM00000027845

Sequence Viewer

Length: 636 bp
ATGAAAGGCACGGAGTGCCCATCAATCAAAAAGAATGCACCTGCTGTAGTGGAAACCACAAAAAAAGTCATTAAGAAGATGAAGACTGAATCGAAGTTAAGATCTAGACGTGCCAGCAAGGTTTACCCTGTCCGTTTCTATGGGAAGAACTACCCTCTATGGGCGCAACAGAAGGAGCTTTTCCTACGGCAACTATGTGTTGCATATGTACCCTACAAGCCATGCCCTAGCCTTATGGTTGGACCTGAAGCAACTACTGAAGACATTGCTCAATCAAAGGTTGCCGTTCAGAAATGGATGGCCAATGACTCCCTATGTCGCCGCACGATCTTGAATGATCACCTGTCTTTTTCTCTGTCTTATACTTGCTTAAAGCAAAAGAAAACTACTACTGCTAAAAAACTGTGGGAAGATCTAAAATTTTTATCTGCAACACATGCAACAAAGAGATCTCTGGTTAGACAGTACATGGAATTTCTGATGCTGGAGAAGAAACCAATTGTAGAGCAAGTTCAAGAATTTAATTGCATTTTCGATTGCATGGTTGCTTCTGGAGTTTTGGTTGATGAGAAATTCACGTTGATGTCATCATCTCTAAGCTCCCCGAGTCATGGAGGGATGCACACATCAAGTTGA
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

212

Amino Acids

24.03

Weight (kDa)

9.61

Isoelectric Point (pI)

63.12

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 90 - 193 3.2e-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)
AarI CACCTGC 1 cut(s) 49
Acc36I ACCTGC 1 cut(s) 49
AciI CCGC 1 cut(s) 322
AcoI YGGCCR 1 cut(s) 300
AcsI RAATTY 4 cut(s) 419, 473, 518, 572
AcuI CTGAAG 2 cut(s) 267, 279
AdeI CACNNNGTG 1 cut(s) 15
AfaI GTAC 2 cut(s) 210, 467
AfiI CCNNNNNNNGG 2 cut(s) 160, 611
AgsI TTSAA 2 cut(s) 334, 515
AjiI CACGTC 1 cut(s) 110
AluBI AGCT 2 cut(s) 178, 600
AluI AGCT 2 cut(s) 178, 600
Ama87I CYCGRG 1 cut(s) 604
AoxI GGCC 1 cut(s) 300
ApoI RAATTY 4 cut(s) 419, 473, 518, 572
AspLEI GCGC 1 cut(s) 166
AspS9I GGNCC 1 cut(s) 242
AsuHPI GGTGA 1 cut(s) 332
AvaI CYCGRG 1 cut(s) 604
AvaII GGWCC 1 cut(s) 242
BaeGI GKGCMC 1 cut(s) 20
BalI TGGCCA 1 cut(s) 302
BbsI GAAGAC 2 cut(s) 89, 267
BccI CCATC 2 cut(s) 28, 292
BceAI ACGGC 2 cut(s) 203, 269
BclI TGATCA 1 cut(s) 337
BfaI CTAG 2 cut(s) 105, 228
BfmI CTRYAG 1 cut(s) 45
BfuAI ACCTGC 1 cut(s) 49
BglII AGATCT 3 cut(s) 101, 412, 449
BisI GCNGC 1 cut(s) 322
BlsI GCNGC 1 cut(s) 323
Bme18I GGWCC 1 cut(s) 242
BmeT110I CYCGRG 1 cut(s) 604
BmgBI CACGTC 1 cut(s) 110
BmgT120I GGNCC 1 cut(s) 242
BmsI GCATC 2 cut(s) 471, 609
BpiI GAAGAC 2 cut(s) 89, 267
BpmI CTGGAG 2 cut(s) 506, 573
BsaXI ACNNNNNCTCC 2 cut(s) 546, 576
Bsc4I CCNNNNNNNGG 2 cut(s) 160, 611
Bse3DI GCAATG 1 cut(s) 264
BseGI GGATG 2 cut(s) 303, 624
BseLI CCNNNNNNNGG 2 cut(s) 160, 611
BseMI GCAATG 1 cut(s) 264
BseSI GKGCMC 1 cut(s) 20
BshFI GGCC 1 cut(s) 302
BsiHKCI CYCGRG 1 cut(s) 604
BslI CCNNNNNNNGG 2 cut(s) 160, 611
BsmI GAATGC 1 cut(s) 40
BsnI GGCC 1 cut(s) 302
BsoBI CYCGRG 1 cut(s) 604
Bsp1286I GDGCHC 1 cut(s) 20
Bsp143I GATC 5 cut(s) 101, 327, 337, 412, 449
BspACI CCGC 1 cut(s) 322
BspANI GGCC 1 cut(s) 302
BspMI ACCTGC 1 cut(s) 49
BsrDI GCAATG 1 cut(s) 264
BssMI GATC 5 cut(s) 101, 327, 337, 412, 449
Bst4CI ACNGT 2 cut(s) 405, 465
BstAPI GCANNNNNTGC 2 cut(s) 15, 437
BstC8I GCNNGC 1 cut(s) 115
BstDEI CTNAG 1 cut(s) 596
BstF5I GGATG 2 cut(s) 303, 624
BstHHI GCGC 1 cut(s) 166
BstKTI GATC 5 cut(s) 104, 330, 340, 415, 452
BstMBI GATC 5 cut(s) 101, 327, 337, 412, 449
BstMWI GCNNNNNNNGC 2 cut(s) 15, 437
BstNSI RCATGY 1 cut(s) 440
BstSFI CTRYAG 1 cut(s) 45
BstSLI GKGCMC 1 cut(s) 20
BstV2I GAAGAC 2 cut(s) 89, 267
BstX2I RGATCY 3 cut(s) 101, 412, 449
BstYI RGATCY 3 cut(s) 101, 412, 449
BsuRI GGCC 1 cut(s) 302
BtrI CACGTC 1 cut(s) 110
BtsCI GGATG 2 cut(s) 303, 624
BveI ACCTGC 1 cut(s) 49
Cac8I GCNNGC 1 cut(s) 115
CfoI GCGC 1 cut(s) 166
Cfr13I GGNCC 1 cut(s) 242
Csp6I GTAC 2 cut(s) 209, 466
CviAII CATG 5 cut(s) 222, 437, 469, 541, 611
CviJI RGCY 5 cut(s) 178, 220, 231, 302, 600
CviKI_1 RGCY 5 cut(s) 178, 220, 231, 302, 600
CviQI GTAC 2 cut(s) 209, 466
DdeI CTNAG 1 cut(s) 596
DpnI GATC 5 cut(s) 103, 329, 339, 414, 451
DpnII GATC 5 cut(s) 101, 327, 337, 412, 449
DraIII CACNNNGTG 1 cut(s) 15
EaeI YGGCCR 1 cut(s) 300
Eco47I GGWCC 1 cut(s) 242
Eco57I CTGAAG 2 cut(s) 267, 279
Eco88I CYCGRG 1 cut(s) 604
FaeI CATG 5 cut(s) 225, 440, 472, 544, 614
FatI CATG 5 cut(s) 221, 436, 468, 540, 610
FauNDI CATATG 1 cut(s) 205
FbaI TGATCA 1 cut(s) 337
Fnu4HI GCNGC 1 cut(s) 322
FokI GGATG 2 cut(s) 310, 631
Fsp4HI GCNGC 1 cut(s) 322
FspBI CTAG 2 cut(s) 105, 228
GlaI GCGC 1 cut(s) 165
GluI GCNGC 1 cut(s) 322
GsuI CTGGAG 2 cut(s) 506, 573
HaeIII GGCC 1 cut(s) 302
HhaI GCGC 1 cut(s) 166
Hin1II CATG 5 cut(s) 225, 440, 472, 544, 614
Hin6I GCGC 1 cut(s) 164
HinP1I GCGC 1 cut(s) 164
HinfI GANTC 3 cut(s) 89, 308, 607
HphI GGTGA 1 cut(s) 332
Hpy166II GTNNAC 1 cut(s) 124
Hpy188I TCNGA 2 cut(s) 291, 480
Hpy188III TCNNGA 4 cut(s) 105, 331, 515, 552
Hpy8I GTNNAC 1 cut(s) 124
HpyAV CCTTC 1 cut(s) 166
HpyCH4III ACNGT 2 cut(s) 405, 465
HpyCH4IV ACGT 2 cut(s) 109, 578
HpyCH4V TGCA 7 cut(s) 38, 203, 431, 440, 528, 540, 622
HpyF10VI GCNNNNNNNGC 2 cut(s) 15, 437
HpyF3I CTNAG 1 cut(s) 596
HpySE526I ACGT 2 cut(s) 109, 578
Hsp92II CATG 5 cut(s) 225, 440, 472, 544, 614
HspAI GCGC 1 cut(s) 164
Ksp22I TGATCA 1 cut(s) 337
Kzo9I GATC 5 cut(s) 101, 327, 337, 412, 449
LmnI GCTCC 2 cut(s) 175, 605
LpnPI CCDG 8 cut(s) 54, 127, 141, 258, 356, 440, 470, 537
LweI GCATC 2 cut(s) 471, 609
MaeI CTAG 2 cut(s) 105, 228
MaeII ACGT 2 cut(s) 109, 578
MalI GATC 5 cut(s) 103, 329, 339, 414, 451
MboI GATC 5 cut(s) 101, 327, 337, 412, 449
MboII GAAGA 6 cut(s) 88, 94, 157, 272, 422, 502
MfeI CAATTG 1 cut(s) 498
MflI RGATCY 3 cut(s) 101, 412, 449
MhlI GDGCHC 1 cut(s) 20
MlsI TGGCCA 1 cut(s) 302
MluCI AATT 6 cut(s) 419, 473, 498, 518, 523, 572
MluNI TGGCCA 1 cut(s) 302
MlyI GAGTC 2 cut(s) 302, 616
MmeI TCCRAC 1 cut(s) 220
MnlI CCTC 2 cut(s) 165, 608
Mox20I TGGCCA 1 cut(s) 302
MscI TGGCCA 1 cut(s) 302
MseI TTAA 4 cut(s) 72, 98, 371, 522
MslI CAYNNNNRTG 1 cut(s) 581
Msp20I TGGCCA 1 cut(s) 302
MunI CAATTG 1 cut(s) 498
Mva1269I GAATGC 1 cut(s) 40
MwoI GCNNNNNNNGC 2 cut(s) 15, 437
NdeI CATATG 1 cut(s) 205
NdeII GATC 5 cut(s) 101, 327, 337, 412, 449
NlaIII CATG 5 cut(s) 225, 440, 472, 544, 614
NspI RCATGY 1 cut(s) 440
PaqCI CACCTGC 1 cut(s) 49
PctI GAATGC 1 cut(s) 40
PfeI GAWTC 1 cut(s) 89
PkrI GCNGC 1 cut(s) 323
PleI GAGTC 2 cut(s) 302, 615
PpsI GAGTC 2 cut(s) 302, 615
PspPI GGNCC 1 cut(s) 242
PsrI GAACNNNNNNTAC 2 cut(s) 495, 527
PsuI RGATCY 3 cut(s) 101, 412, 449
RsaI GTAC 2 cut(s) 210, 467
RsaNI GTAC 2 cut(s) 209, 466
RseI CAYNNNNRTG 1 cut(s) 581
SaqAI TTAA 4 cut(s) 72, 98, 371, 522
SatI GCNGC 1 cut(s) 322
Sau3AI GATC 5 cut(s) 101, 327, 337, 412, 449
Sau96I GGNCC 1 cut(s) 242
SchI GAGTC 2 cut(s) 302, 616
SduI GDGCHC 1 cut(s) 20
SetI ASST 9 cut(s) 43, 112, 123, 180, 247, 282, 345, 581, 602
SfaNI GCATC 2 cut(s) 471, 609
SfcI CTRYAG 1 cut(s) 45
SinI GGWCC 1 cut(s) 242
SmiMI CAYNNNNRTG 1 cut(s) 581
Sse9I AATT 6 cut(s) 419, 473, 498, 518, 523, 572
SsiI CCGC 1 cut(s) 322
SspMI CTAG 2 cut(s) 105, 228
TaaI ACNGT 2 cut(s) 405, 465
TaiI ACGT 2 cut(s) 112, 581
TaqI TCGA 2 cut(s) 92, 534
TasI AATT 6 cut(s) 419, 473, 498, 518, 523, 572
TatI WGTACW 1 cut(s) 465
TauI GCSGC 1 cut(s) 324
TfiI GAWTC 1 cut(s) 89
Tru1I TTAA 4 cut(s) 72, 98, 371, 522
Tru9I TTAA 4 cut(s) 72, 98, 371, 522
TspDTI ATGAA 2 cut(s) 17, 95
TspGWI ACGGA 2 cut(s) 26, 122
VpaK11BI GGWCC 1 cut(s) 242
XapI RAATTY 4 cut(s) 419, 473, 518, 572
XbaI TCTAGA 1 cut(s) 104
XceI RCATGY 1 cut(s) 440
XspI CTAG 2 cut(s) 105, 228
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.