Rh4DG113100

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr4D
OG0000370
Physical Location & Seq
Reverse (-)
17862221 .. 17879890
17670 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh4DG113100.1

Sequence Viewer

Length: 666 bp
ATGGCAGAAGAACAACATAAGGGTGAGGCTAGTGGCAATATGGAAGTCATAGCTGCTATTCAAGATATGGCAATTGCAATGAGGGAAAATCACAATGGTAATCATCAAGAAGGTAATGAAGAACGAGTTATGAGAATACAAGGTGAATTTCGTAAGGCCCGACCTCCTATATTCAAGGGTACCTTAGATCCCATGATAGCTGAAGAATGGTTGAGACAAATGAAGAGAACCCTGAATAATCAAAAAGTGCCGGAAGATTTGAAAGTAATTATTTCATGTACTTACTTGGAAGGTGCAGCTTATTATCACTGGTGGGAATCAGTTCTTGCTACTCCAAACACTGAAATTACAACCTGGGATGCATTTGAAGTTATTTTTCTTGAGAAATATTTCCCAGACACAGTAAAGCAAGCTAAGGCAAAAGAGTTTATGTTTCTATCTAAAGGGGAAATGACAATAGCTGAATACCAAGGTAGATTTGAGGAATTGATGCGGTTTGCTCCAGGTATTATTCCCAATGAGGCTGCTAAAGCAAAGAAATTTGAGGAAGGACTTAATCCTGAGATTAGGGAGAAAGTTGAAGATAAAATAACCGTCTTTCTTCCGAAGCAACAACAGACACTGGATTCCTCTCTCACATCTGAATCCTCCAACATTTTCTCATAG
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
RVP_2 Retrotrans_gag

Protein Analysis

221

Amino Acids

25.47

Weight (kDa)

5.14

Isoelectric Point (pI)

40.04

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 52 - 194 4.1e-08 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 95 - 187 2.2e-15 Retrotransposon gag protein
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: OG0000370)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g29481 FvH4_2g11454 FvH4_3g19661 FvH4_3g28463 FvH4_3g31691 FvH4_3g34551 FvH4_3g35241 FvH4_4g06575 FvH4_4g09082 FvH4_4g15804 FvH4_4g15805 FvH4_4g16178 FvH4_4g16282 FvH4_5g25163 FvH4_6g27413 FvH4_7g02962 FvH4_7g04361
malus_domestica MD01G1095000.v1.1 MD02G1270200.v1.1 MD02G1270300.v1.1 MD02G1270400.v1.1 MD06G1059100.v1.1 MD08G1226500.v1.1
prunus_persica Prupe.1G169500_v2.0.a1 Prupe.5G195800_v2.0.a1
pyrus_communis pycom01g00010 pycom01g00770 pycom02g23140 pycom03g11760 pycom04g06090 pycom05g06900 pycom05g08070 pycom05g14500 pycom06g03050 pycom07g06250 pycom07g07540 pycom07g10580 pycom08g04990 pycom1146g00060 pycom11g01080 pycom11g15270 pycom11g15460 pycom11g24900 pycom12419g00150 pycom12424g00120 pycom13g08740 pycom13g24950 pycom13g25960 pycom13g26030 pycom13g27820 pycom16g23270 pycom16g25020 pycom16g25960 pycom17g07780 pycom17g08210 pycom17g13100
rosa_chinensis RchiOBHm_Chr1g0329421 RchiOBHm_Chr4g0397711 RchiOBHm_Chr4g0403481 RchiOBHm_Chr5g0019091 RchiOBHm_Chr5g0049101
rosa_laevigata RLG00000029892
rosa_multiflora Rmu_sc0001866.1_g000007
rosa_roxburghii Rroxscaffold_2G00094160 Rroxscaffold_3G00229110 Rroxscaffold_4G00321100 Rroxscaffold_7G00196040 Rroxscaffold_7G00196280
rosa_rugosa Rorug05G0160500 Rorug06G0096500
rosa_samantha Rh1AG098600 Rh1AG098800 Rh1BG078200 Rh1BG078700 Rh1BG178500 Rh1CG094600 Rh1CG094900 Rh1DG101700 Rh1DG109600 Rh2AG175800 Rh2AG175900 Rh2AG511400 Rh2BG114700 Rh2CG042200 Rh2CG116600 Rh2CG317500 Rh2DG327700 Rh2DG337800 Rh4CG142700 Rh4DG113100 Rh5BG335800 Rh5CG360600 Rh5DG352000 Rh6BG071400 Rh6BG417100 Rh6CG463300 Rh6CG463400 Rh7BG186600 Rh7CG196500 Rh7CG196600 Rh7CG448900 Rh7DG228300
rosa_wichuraiana Rw4G006560 Rw4G017340 Rw5G030450

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc65I GGTACC 1 cut(s) 179
AccB1I GGYRCC 1 cut(s) 179
AciI CCGC 1 cut(s) 493
AclWI GGATC 1 cut(s) 182
AcsI RAATTY 2 cut(s) 146, 539
AcuI CTGAAG 1 cut(s) 222
AfaI GTAC 2 cut(s) 181, 280
AgsI TTSAA 5 cut(s) 62, 175, 262, 368, 581
AjnI CCWGG 2 cut(s) 353, 502
AluBI AGCT 5 cut(s) 53, 200, 299, 413, 461
AluI AGCT 5 cut(s) 53, 200, 299, 413, 461
Alw26I GTCTC 1 cut(s) 208
AlwI GGATC 1 cut(s) 182
AlwNI CAGNNNCTG 1 cut(s) 622
AoxI GGCC 1 cut(s) 156
ApeKI GCWGC 3 cut(s) 53, 296, 524
ApoI RAATTY 2 cut(s) 146, 539
Asp700I GAANNNNTTC 2 cut(s) 321, 389
Asp718I GGTACC 1 cut(s) 179
AspS9I GGNCC 1 cut(s) 157
AsuHPI GGTGA 2 cut(s) 35, 155
BanI GGYRCC 1 cut(s) 179
BbvI GCAGC 3 cut(s) 40, 308, 511
BciT130I CCWGG 2 cut(s) 355, 504
BcoDI GTCTC 1 cut(s) 208
BfaI CTAG 1 cut(s) 30
BisI GCNGC 3 cut(s) 54, 297, 525
BlsI GCNGC 3 cut(s) 55, 298, 526
Bme1390I CCNGG 2 cut(s) 355, 504
BmgT120I GGNCC 1 cut(s) 157
BmiI GGNNCC 1 cut(s) 181
BmrFI CCNGG 2 cut(s) 355, 504
BmsI GCATC 2 cut(s) 349, 480
BpmI CTGGAG 1 cut(s) 486
Bpu10I CCTNAGC 1 cut(s) 414
BpuEI CTTGAG 1 cut(s) 401
BsaJI CCNNGG 2 cut(s) 354, 469
Bse1I ACTGG 2 cut(s) 314, 627
Bse3DI GCAATG 1 cut(s) 84
BseBI CCWGG 2 cut(s) 355, 504
BseDI CCNNGG 2 cut(s) 354, 469
BseGI GGATG 1 cut(s) 364
BseMI GCAATG 1 cut(s) 84
BseMII CTCAG 1 cut(s) 552
BseNI ACTGG 2 cut(s) 314, 627
BseXI GCAGC 3 cut(s) 40, 308, 511
BsgI GTGCAG 1 cut(s) 315
BshFI GGCC 1 cut(s) 158
BshNI GGYRCC 1 cut(s) 179
BsiSI CCGG 1 cut(s) 251
BsmAI GTCTC 1 cut(s) 208
BsnI GGCC 1 cut(s) 158
Bsp143I GATC 1 cut(s) 187
BspACI CCGC 1 cut(s) 493
BspANI GGCC 1 cut(s) 158
BspCNI CTCAG 1 cut(s) 553
BspLI GGNNCC 1 cut(s) 181
BspPI GGATC 1 cut(s) 182
BspT107I GGYRCC 1 cut(s) 179
BsrDI GCAATG 1 cut(s) 84
BsrI ACTGG 2 cut(s) 314, 627
BssECI CCNNGG 2 cut(s) 354, 469
BssMI GATC 1 cut(s) 187
BssT1I CCWWGG 1 cut(s) 469
Bst2UI CCWGG 2 cut(s) 355, 504
Bst4CI ACNGT 2 cut(s) 403, 595
Bst6I CTCTTC 1 cut(s) 218
BstC8I GCNNGC 1 cut(s) 411
BstDEI CTNAG 3 cut(s) 184, 414, 561
BstF5I GGATG 1 cut(s) 364
BstKTI GATC 1 cut(s) 190
BstMAI GTCTC 1 cut(s) 208
BstMBI GATC 1 cut(s) 187
BstMWI GCNNNNNNNGC 1 cut(s) 530
BstNI CCWGG 2 cut(s) 355, 504
BstSCI CCNGG 2 cut(s) 353, 502
BstV1I GCAGC 3 cut(s) 40, 308, 511
BstX2I RGATCY 1 cut(s) 187
BstYI RGATCY 1 cut(s) 187
BsuRI GGCC 1 cut(s) 158
BtsCI GGATG 1 cut(s) 364
BtsIMutI CAGTG 3 cut(s) 307, 339, 620
Cac8I GCNNGC 1 cut(s) 411
CaiI CAGNNNCTG 1 cut(s) 622
Cfr13I GGNCC 1 cut(s) 157
Csp6I GTAC 2 cut(s) 180, 279
CviAII CATG 2 cut(s) 193, 276
CviJI RGCY 8 cut(s) 29, 53, 158, 200, 299, 413, 461, 524
CviKI_1 RGCY 8 cut(s) 29, 53, 158, 200, 299, 413, 461, 524
CviQI GTAC 2 cut(s) 180, 279
DdeI CTNAG 3 cut(s) 184, 414, 561
DpnI GATC 1 cut(s) 189
DpnII GATC 1 cut(s) 187
Eam1104I CTCTTC 1 cut(s) 218
EarI CTCTTC 1 cut(s) 218
Eco130I CCWWGG 1 cut(s) 469
Eco57I CTGAAG 1 cut(s) 222
EcoRII CCWGG 2 cut(s) 353, 502
EcoT14I CCWWGG 1 cut(s) 469
EcoT22I ATGCAT 1 cut(s) 364
ErhI CCWWGG 1 cut(s) 469
FaeI CATG 2 cut(s) 196, 279
FalI AAGNNNNNCTT 2 cut(s) 167, 199
FatI CATG 2 cut(s) 192, 275
Fnu4HI GCNGC 3 cut(s) 54, 297, 525
FokI GGATG 1 cut(s) 371
Fsp4HI GCNGC 3 cut(s) 54, 297, 525
FspBI CTAG 1 cut(s) 30
GluI GCNGC 3 cut(s) 54, 297, 525
GsuI CTGGAG 1 cut(s) 486
HaeIII GGCC 1 cut(s) 158
HapII CCGG 1 cut(s) 251
Hin1II CATG 2 cut(s) 196, 279
HinfI GANTC 3 cut(s) 317, 626, 644
HpaII CCGG 1 cut(s) 251
HphI GGTGA 2 cut(s) 35, 155
Hpy188I TCNGA 2 cut(s) 606, 643
Hpy188III TCNNGA 4 cut(s) 62, 107, 380, 560
HpyAV CCTTC 3 cut(s) 104, 284, 542
HpyCH4III ACNGT 2 cut(s) 403, 595
HpyCH4V TGCA 3 cut(s) 77, 296, 362
HpyF10VI GCNNNNNNNGC 1 cut(s) 530
HpyF3I CTNAG 3 cut(s) 184, 414, 561
Hsp92II CATG 2 cut(s) 196, 279
KpnI GGTACC 1 cut(s) 183
Kzo9I GATC 1 cut(s) 187
LmnI GCTCC 1 cut(s) 505
Lsp1109I GCAGC 3 cut(s) 40, 308, 511
LweI GCATC 2 cut(s) 349, 480
MaeI CTAG 1 cut(s) 30
MalI GATC 1 cut(s) 189
MboI GATC 1 cut(s) 187
MboII GAAGA 7 cut(s) 20, 131, 215, 235, 266, 593, 593
MfeI CAATTG 1 cut(s) 72
MflI RGATCY 1 cut(s) 187
MluCI AATT 6 cut(s) 72, 146, 267, 345, 485, 539
MnlI CCTC 8 cut(s) 19, 75, 174, 475, 514, 538, 640, 658
Mph1103I ATGCAT 1 cut(s) 364
MroXI GAANNNNTTC 2 cut(s) 321, 389
MseI TTAA 1 cut(s) 555
MslI CAYNNNNRTG 1 cut(s) 21
MspI CCGG 1 cut(s) 251
MspR9I CCNGG 2 cut(s) 355, 504
MunI CAATTG 1 cut(s) 72
MvaI CCWGG 2 cut(s) 355, 504
MwoI GCNNNNNNNGC 1 cut(s) 530
NdeII GATC 1 cut(s) 187
NlaIII CATG 2 cut(s) 196, 279
NlaIV GGNNCC 1 cut(s) 181
NsiI ATGCAT 1 cut(s) 364
PcsI WCGNNNNNNNCGW 1 cut(s) 157
PdmI GAANNNNTTC 2 cut(s) 321, 389
PfeI GAWTC 3 cut(s) 317, 626, 644
PkrI GCNGC 3 cut(s) 55, 298, 526
Psp6I CCWGG 2 cut(s) 353, 502
PspGI CCWGG 2 cut(s) 353, 502
PspN4I GGNNCC 1 cut(s) 181
PspPI GGNCC 1 cut(s) 157
PstNI CAGNNNCTG 1 cut(s) 622
PsuI RGATCY 1 cut(s) 187
RsaI GTAC 2 cut(s) 181, 280
RsaNI GTAC 2 cut(s) 180, 279
RseI CAYNNNNRTG 1 cut(s) 21
SaqAI TTAA 1 cut(s) 555
SatI GCNGC 3 cut(s) 54, 297, 525
Sau3AI GATC 1 cut(s) 187
Sau96I GGNCC 1 cut(s) 157
ScrFI CCNGG 2 cut(s) 355, 504
SfaNI GCATC 2 cut(s) 349, 480
SmiMI CAYNNNNRTG 1 cut(s) 21
SmlI CTYRAG 1 cut(s) 380
SmoI CTYRAG 1 cut(s) 380
Sse9I AATT 6 cut(s) 72, 146, 267, 345, 485, 539
SsiI CCGC 1 cut(s) 493
SspI AATATT 1 cut(s) 389
SspMI CTAG 1 cut(s) 30
StyD4I CCNGG 2 cut(s) 353, 502
StyI CCWWGG 1 cut(s) 469
TaaI ACNGT 2 cut(s) 403, 595
TasI AATT 6 cut(s) 72, 146, 267, 345, 485, 539
TatI WGTACW 1 cut(s) 278
TfiI GAWTC 3 cut(s) 317, 626, 644
Tru1I TTAA 1 cut(s) 555
Tru9I TTAA 1 cut(s) 555
TscAI CASTG 3 cut(s) 314, 346, 627
TseI GCWGC 3 cut(s) 53, 296, 524
TspDTI ATGAA 3 cut(s) 132, 236, 264
TspRI CASTG 3 cut(s) 314, 346, 627
XapI RAATTY 2 cut(s) 146, 539
XmnI GAANNNNTTC 2 cut(s) 321, 389
XspI CTAG 1 cut(s) 30
Zsp2I ATGCAT 1 cut(s) 364
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.