RchiOBHm_Chr5g0019091

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
5
OG0000370
Physical Location & Seq
Forward (+)
13563613 .. 13566626
3014 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ29923

Sequence Viewer

Length: 762 bp
ATGCCAGATACAGAGATTACAACTTGGGATGCTTTTGAGAATATTTTCCTAGAGAAATATTTTCCAAGTACGGTGAAAGGGATGAAGGCTAGGGAATTTGTTAATCTTGTTCAAGGTGAGCTGTCCATAGCTGATTATCAAGCAAAATTTGAAGAACTGATGCGTTTTGCACCGAATATGATTCTTGATGAATATACTAAAGCAAAGAGATTTGAAGATGGTCTTAAGCCAATGATTCGGGAAAAGGTGGCAATTCTGAAATTGAATAGGTATGCTGATGTGGTGGAACGAGCTCTTATAGCAGAACAGAGTGTTTTAGAATCTTTGAAGACATTAGATTTCAAAAACCCAAGTCCACCCACAAGCGAGTCTCAAAGGGAAGGACAAAATGGTAGACAGCCTAAACCTGATTTTCCCTCTTATAGGCAAACACAGAGGTTAGAGAGGACCGCTCAAGATCCCCGAGTTTGTTTCCAATGTGGAAAATTTGGACATATCCAAAAGAACTGCCCACTGTTACAAATCCGTGCCCCACAACGTCATACATATGCTCCTTACCCACCTCAACAGAATTACCAGAGGCCACAGTATGGTCAACATCCTAGACATCAAGGAGGAGTACCTACTCAAGCTAGGCCAAATGGACCAACAAGTGGAAGACAACCTGCACAACTCGCACAGGGTCGAGTGTATTGTTTGGGTCAAGTTAATAATCAGACTGATCTCGAAAGGGTGGAAGGTATACTTTTAGATAAAATGTGA
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 zf-CCHC

Protein Analysis

253

Amino Acids

29.11

Weight (kDa)

9.1

Isoelectric Point (pI)

41.92

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotrans_gag PF03732 5 - 77 5.8e-13 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)
Acc36I ACCTGC 1 cut(s) 673
AccB7I CCANNNNNTGG 2 cut(s) 590, 653
AccBSI CCGCTC 1 cut(s) 452
AccI GTMKAC 2 cut(s) 394, 742
AciI CCGC 1 cut(s) 450
AclWI GGATC 1 cut(s) 452
AcsI RAATTY 3 cut(s) 95, 146, 485
AfaI GTAC 2 cut(s) 70, 621
AfiI CCNNNNNNNGG 3 cut(s) 423, 590, 653
AflII CTTAAG 1 cut(s) 224
AgsI TTSAA 6 cut(s) 113, 152, 215, 265, 328, 343
AluBI AGCT 4 cut(s) 121, 131, 293, 632
AluI AGCT 4 cut(s) 121, 131, 293, 632
Alw21I GWGCWC 1 cut(s) 295
Alw26I GTCTC 1 cut(s) 375
AlwI GGATC 1 cut(s) 452
Ama87I CYCGRG 1 cut(s) 462
AoxI GGCC 2 cut(s) 581, 635
ApoI RAATTY 3 cut(s) 95, 146, 485
Asp700I GAANNNNTTC 1 cut(s) 44
AspS9I GGNCC 2 cut(s) 447, 644
AsuHPI GGTGA 2 cut(s) 85, 128
AvaI CYCGRG 1 cut(s) 462
AvaII GGWCC 2 cut(s) 447, 644
BaeGI GKGCMC 1 cut(s) 532
BanII GRGCYC 1 cut(s) 295
BbsI GAAGAC 2 cut(s) 335, 664
Bbv12I GWGCWC 1 cut(s) 295
BccI CCATC 1 cut(s) 212
BcoDI GTCTC 1 cut(s) 375
BfaI CTAG 4 cut(s) 50, 90, 603, 633
BfrI CTTAAG 1 cut(s) 224
BfuAI ACCTGC 1 cut(s) 673
Bme18I GGWCC 2 cut(s) 447, 644
BmeT110I CYCGRG 1 cut(s) 462
BmgT120I GGNCC 2 cut(s) 447, 644
BmsI GCATC 2 cut(s) 19, 150
BpiI GAAGAC 2 cut(s) 335, 664
BplI GAGNNNNNCTC 2 cut(s) 436, 468
BpuEI CTTGAG 2 cut(s) 438, 612
BsaXI ACNNNNNCTCC 2 cut(s) 535, 565
Bsc4I CCNNNNNNNGG 3 cut(s) 423, 590, 653
BseGI GGATG 3 cut(s) 34, 87, 598
BseLI CCNNNNNNNGG 3 cut(s) 423, 590, 653
BseRI GAGGAG 1 cut(s) 630
BseSI GKGCMC 1 cut(s) 532
BsgI GTGCAG 1 cut(s) 651
BshFI GGCC 2 cut(s) 583, 637
BsiHKAI GWGCWC 1 cut(s) 295
BsiHKCI CYCGRG 1 cut(s) 462
BslI CCNNNNNNNGG 3 cut(s) 423, 590, 653
BsmAI GTCTC 1 cut(s) 375
BsnI GGCC 2 cut(s) 583, 637
BsoBI CYCGRG 1 cut(s) 462
Bsp1286I GDGCHC 2 cut(s) 295, 532
Bsp143I GATC 2 cut(s) 457, 721
BspACI CCGC 1 cut(s) 450
BspANI GGCC 2 cut(s) 583, 637
BspMI ACCTGC 1 cut(s) 673
BspPI GGATC 1 cut(s) 452
BspTI CTTAAG 1 cut(s) 224
BsrBI CCGCTC 1 cut(s) 452
BssMI GATC 2 cut(s) 457, 721
BssNAI GTATAC 1 cut(s) 743
Bst1107I GTATAC 1 cut(s) 743
Bst4CI ACNGT 3 cut(s) 73, 516, 588
BstAFI CTTAAG 1 cut(s) 224
BstENI CCTNNNNNAGG 1 cut(s) 421
BstF5I GGATG 3 cut(s) 34, 87, 598
BstKTI GATC 2 cut(s) 460, 724
BstMAI GTCTC 1 cut(s) 375
BstMBI GATC 2 cut(s) 457, 721
BstMWI GCNNNNNNNGC 2 cut(s) 299, 674
BstSLI GKGCMC 1 cut(s) 532
BstV2I GAAGAC 2 cut(s) 335, 664
BstX2I RGATCY 1 cut(s) 457
BstYI RGATCY 1 cut(s) 457
BstZ17I GTATAC 1 cut(s) 743
BsuRI GGCC 2 cut(s) 583, 637
BtsCI GGATG 3 cut(s) 34, 87, 598
BtsIMutI CAGTG 1 cut(s) 512
BveI ACCTGC 1 cut(s) 673
Cfr13I GGNCC 2 cut(s) 447, 644
Csp6I GTAC 2 cut(s) 69, 620
CviJI RGCY 9 cut(s) 89, 121, 131, 229, 293, 400, 583, 632, 637
CviKI_1 RGCY 9 cut(s) 89, 121, 131, 229, 293, 400, 583, 632, 637
CviQI GTAC 2 cut(s) 69, 620
DpnI GATC 2 cut(s) 459, 723
DpnII GATC 2 cut(s) 457, 721
Ecl136II GAGCTC 1 cut(s) 293
Eco24I GRGCYC 1 cut(s) 295
Eco47I GGWCC 2 cut(s) 447, 644
Eco53kI GAGCTC 1 cut(s) 293
Eco88I CYCGRG 1 cut(s) 462
EcoICRI GAGCTC 1 cut(s) 293
EcoNI CCTNNNNNAGG 1 cut(s) 421
EcoT38I GRGCYC 1 cut(s) 295
FalI AAGNNNNNCTT 4 cut(s) 207, 239, 729, 761
FauNDI CATATG 1 cut(s) 547
FblI GTMKAC 2 cut(s) 394, 742
FokI GGATG 3 cut(s) 41, 94, 585
FriOI GRGCYC 1 cut(s) 295
FspBI CTAG 4 cut(s) 50, 90, 603, 633
HaeIII GGCC 2 cut(s) 583, 637
HincII GTYRAC 1 cut(s) 596
HindII GTYRAC 1 cut(s) 596
HinfI GANTC 4 cut(s) 181, 235, 320, 368
HphI GGTGA 2 cut(s) 85, 128
Hpy166II GTNNAC 4 cut(s) 356, 395, 596, 743
Hpy188I TCNGA 2 cut(s) 258, 717
Hpy188III TCNNGA 4 cut(s) 185, 239, 455, 725
Hpy8I GTNNAC 4 cut(s) 356, 395, 596, 743
HpyAV CCTTC 3 cut(s) 79, 374, 731
HpyCH4III ACNGT 3 cut(s) 73, 516, 588
HpyCH4IV ACGT 1 cut(s) 538
HpyCH4V TGCA 2 cut(s) 170, 668
HpyF10VI GCNNNNNNNGC 2 cut(s) 299, 674
HpySE526I ACGT 1 cut(s) 538
Kzo9I GATC 2 cut(s) 457, 721
LmnI GCTCC 1 cut(s) 556
LpnPI CCDG 5 cut(s) 18, 420, 590, 665, 678
LweI GCATC 2 cut(s) 19, 150
MaeI CTAG 4 cut(s) 50, 90, 603, 633
MaeII ACGT 1 cut(s) 538
MaeIII GTNAC 1 cut(s) 516
MalI GATC 2 cut(s) 459, 723
MbiI CCGCTC 1 cut(s) 452
MboI GATC 2 cut(s) 457, 721
MboII GAAGA 4 cut(s) 164, 227, 340, 669
MflI RGATCY 1 cut(s) 457
MhlI GDGCHC 2 cut(s) 295, 532
MluCI AATT 6 cut(s) 95, 146, 252, 260, 485, 571
MlyI GAGTC 1 cut(s) 377
MnlI CCTC 6 cut(s) 427, 429, 438, 573, 573, 608
MroXI GAANNNNTTC 1 cut(s) 44
MseI TTAA 3 cut(s) 102, 225, 708
MslI CAYNNNNRTG 1 cut(s) 546
MspCI CTTAAG 1 cut(s) 224
MwoI GCNNNNNNNGC 2 cut(s) 299, 674
NdeI CATATG 1 cut(s) 547
NdeII GATC 2 cut(s) 457, 721
PdmI GAANNNNTTC 1 cut(s) 44
PfeI GAWTC 3 cut(s) 181, 235, 320
PflMI CCANNNNNTGG 2 cut(s) 590, 653
PleI GAGTC 1 cut(s) 376
PpsI GAGTC 1 cut(s) 376
Psp124BI GAGCTC 1 cut(s) 295
PspPI GGNCC 2 cut(s) 447, 644
PsuI RGATCY 1 cut(s) 457
RsaI GTAC 2 cut(s) 70, 621
RsaNI GTAC 2 cut(s) 69, 620
RseI CAYNNNNRTG 1 cut(s) 546
SacI GAGCTC 1 cut(s) 295
SaqAI TTAA 3 cut(s) 102, 225, 708
Sau3AI GATC 2 cut(s) 457, 721
Sau96I GGNCC 2 cut(s) 447, 644
SchI GAGTC 1 cut(s) 377
SduI GDGCHC 2 cut(s) 295, 532
SfaNI GCATC 2 cut(s) 19, 150
SinI GGWCC 2 cut(s) 447, 644
SmiMI CAYNNNNRTG 1 cut(s) 546
SmlI CTYRAG 3 cut(s) 224, 453, 627
SmoI CTYRAG 3 cut(s) 224, 453, 627
Sse9I AATT 6 cut(s) 95, 146, 252, 260, 485, 571
SsiI CCGC 1 cut(s) 450
SspI AATATT 2 cut(s) 43, 59
SspMI CTAG 4 cut(s) 50, 90, 603, 633
SstI GAGCTC 1 cut(s) 295
TaaI ACNGT 3 cut(s) 73, 516, 588
TaiI ACGT 1 cut(s) 541
TaqI TCGA 2 cut(s) 685, 726
TasI AATT 6 cut(s) 95, 146, 252, 260, 485, 571
TfiI GAWTC 3 cut(s) 181, 235, 320
Tru1I TTAA 3 cut(s) 102, 225, 708
Tru9I TTAA 3 cut(s) 102, 225, 708
TscAI CASTG 1 cut(s) 519
TspDTI ATGAA 2 cut(s) 98, 204
TspGWI ACGGA 1 cut(s) 515
TspRI CASTG 1 cut(s) 519
Van91I CCANNNNNTGG 2 cut(s) 590, 653
Vha464I CTTAAG 1 cut(s) 224
VpaK11BI GGWCC 2 cut(s) 447, 644
XagI CCTNNNNNAGG 1 cut(s) 421
XapI RAATTY 3 cut(s) 95, 146, 485
XmiI GTMKAC 2 cut(s) 394, 742
XmnI GAANNNNTTC 1 cut(s) 44
XspI CTAG 4 cut(s) 50, 90, 603, 633
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.