Rh2DG327700

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr2D
OG0000370
Physical Location & Seq
Forward (+)
41428373 .. 41435534
7162 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh2DG327700.1

Sequence Viewer

Length: 1161 bp
ATGGCAACTTTGTATGTTAATGAAGGAATTAATCTATACATGGAAGCTAGATGGATTTTAAGTAATCCCGAAAACATGAGGATTCTGCATGATGAGGCTATTGCAAATGGGATGCTTAGGACGAAGGATTGGGGGCCACCCAATTACCAACAAGTAACTCAATCTGAAGGGACCATGGCCGATAGAAGAAATCCACCTGTTGACTCAGATGAGTTCGTCGAAGCCTTCACAAGAAGGATGGAGGAAAATCAAGTCGGTGGGAGGCTAGGACGACTAGTAACACACATAAGGAGTCTAGGAGCAAGGAAATTTACTGGAGGGAAACCTCACGAGGCTGAAGAATGGATTTACAATCTGGAAATCCACTTTGAAATGATGGACTGTACCCAAGTAGAGTTACGAAGAGTGGCTACTTGTCTTTTAGAAGGAGATGCTCGTTTCTGGTGGGACACTATCAAACGTGTCACACTCCCTGCAGCAATGGAACTCATGGAATGGGCTGTCTTCAAAGAGAAATTTCTGGAAAAATATTTTCCACAAGTTGAGAGAGACAAGAAAGAATTAGAGTTTTTTCAACTTACCCAACGAAAGATGACTGTGATTGAATATGAGACCAAGTTCACTAAACTTTCTCGTTTTGCTCTACACATGGTAGATACCGATGATAAAAAGGCAAGACGATTCATTGGAGGACTGAATTCCAATATTCGAAGAATGGTCACTCAACGTGGAATCACGTACGGGGAAGCTGTGGACAAAGCCCTAACTCAAGAGGAAGAAAATCAAAAATACCACATGGAGAAGGAGCGAGAGAATGGCTTCCGAGGAAAGAGAAGTCATCCAATGTCAAACCAGAAAAGCGGACAACCATGGAAGCAGCAAACAAGGAGAGACGCATTTCAAAAGCCGACAACATTAACTCAAAAAGGAAAGGAGGTAGCAAGAGGCCCAATTCGGTGTTTCAACTGTGGAGAAACGGGGCACATGTCTAATGCTTGTCCAAAGCCACGTCGCCTTCCAGGATCTTGTTACAATTGTGGCAAGATGGGACATTTCTCAAATCAGTGCGATGCACCGAGGCAAAAAAATAACCCACCACCTCGTCCTGTCCAGCTAAATGCCATAGCTTGTGAGAACATCGTGATGGAAGGTAACGAGTAG
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

386

Amino Acids

44.88

Weight (kDa)

8.94

Isoelectric Point (pI)

44.85

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotrans_gag PF03732 136 - 233 4.6e-19 Retrotransposon gag protein
zf-CCHC PF00098 319 - 335 9.3e-07 Zinc knuckle
zf-CCHC PF00098 342 - 357 4.6e-06 Zinc knuckle
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

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)
AciI CCGC 1 cut(s) 861
AclWI GGATC 1 cut(s) 1030
AcoI YGGCCR 1 cut(s) 177
AcsI RAATTY 3 cut(s) 308, 515, 697
AcuI CTGAAG 2 cut(s) 186, 357
AfaI GTAC 2 cut(s) 385, 740
AflIII ACRYGT 2 cut(s) 460, 984
AgsI TTSAA 6 cut(s) 371, 508, 575, 605, 902, 964
AhlI ACTAGT 1 cut(s) 274
AjiI CACGTC 1 cut(s) 1010
AjnI CCWGG 1 cut(s) 1018
AluBI AGCT 4 cut(s) 47, 749, 1114, 1127
AluI AGCT 4 cut(s) 47, 749, 1114, 1127
Alw26I GTCTC 3 cut(s) 543, 605, 885
AlwI GGATC 1 cut(s) 1030
AoxI GGCC 3 cut(s) 134, 177, 946
ApeKI GCWGC 2 cut(s) 476, 877
ApoI RAATTY 3 cut(s) 308, 515, 697
AseI ATTAAT 1 cut(s) 30
Asp700I GAANNNNTTC 1 cut(s) 818
AspS9I GGNCC 3 cut(s) 134, 171, 947
AsuII TTCGAA 1 cut(s) 709
AvaII GGWCC 1 cut(s) 171
BaeGI GKGCMC 1 cut(s) 984
BarI GAAGNNNNNNTAC 2 cut(s) 394, 426
BauI CACGAG 1 cut(s) 329
BbsI GAAGAC 1 cut(s) 496
BbvI GCAGC 2 cut(s) 488, 889
BccI CCATC 5 cut(s) 45, 232, 370, 1039, 1138
BciT130I CCWGG 1 cut(s) 1020
BcoDI GTCTC 3 cut(s) 543, 605, 885
BcuI ACTAGT 1 cut(s) 274
BfaI CTAG 4 cut(s) 48, 266, 275, 296
BfmI CTRYAG 1 cut(s) 474
BisI GCNGC 2 cut(s) 477, 878
BlsI GCNGC 2 cut(s) 478, 879
Bme1390I CCNGG 1 cut(s) 1020
Bme18I GGWCC 1 cut(s) 171
BmgBI CACGTC 1 cut(s) 1010
BmgT120I GGNCC 3 cut(s) 134, 171, 947
BmiI GGNNCC 2 cut(s) 135, 172
BmrFI CCNGG 1 cut(s) 1020
BmsI GCATC 3 cut(s) 102, 421, 1060
BpiI GAAGAC 1 cut(s) 496
BpmI CTGGAG 1 cut(s) 336
Bpu10I CCTNAGC 1 cut(s) 116
Bpu14I TTCGAA 1 cut(s) 709
BpuEI CTTGAG 1 cut(s) 753
BsaAI YACGTR 1 cut(s) 738
BsaI GGTCTC 1 cut(s) 605
BsaJI CCNNGG 4 cut(s) 174, 823, 869, 1076
Bse1I ACTGG 1 cut(s) 319
Bse3DI GCAATG 1 cut(s) 486
BseBI CCWGG 1 cut(s) 1020
BseDI CCNNGG 4 cut(s) 174, 823, 869, 1076
BseGI GGATG 3 cut(s) 117, 243, 838
BseMI GCAATG 1 cut(s) 486
BseMII CTCAG 1 cut(s) 219
BseNI ACTGG 1 cut(s) 319
BseSI GKGCMC 1 cut(s) 984
BseXI GCAGC 2 cut(s) 488, 889
BshFI GGCC 3 cut(s) 136, 179, 948
BsiWI CGTACG 1 cut(s) 738
BslFI GGGAC 3 cut(s) 184, 461, 1062
BsmAI GTCTC 3 cut(s) 543, 605, 885
BsmBI CGTCTC 1 cut(s) 885
BsmFI GGGAC 3 cut(s) 184, 461, 1062
BsnI GGCC 3 cut(s) 136, 179, 948
Bso31I GGTCTC 1 cut(s) 605
Bsp119I TTCGAA 1 cut(s) 709
Bsp1286I GDGCHC 1 cut(s) 984
Bsp143I GATC 1 cut(s) 1022
Bsp19I CCATGG 2 cut(s) 174, 869
BspACI CCGC 1 cut(s) 861
BspANI GGCC 3 cut(s) 136, 179, 948
BspCNI CTCAG 1 cut(s) 218
BspLI GGNNCC 2 cut(s) 135, 172
BspMAI CTGCAG 1 cut(s) 478
BspPI GGATC 1 cut(s) 1030
BspT104I TTCGAA 1 cut(s) 709
BspTNI GGTCTC 1 cut(s) 605
BsrDI GCAATG 1 cut(s) 486
BsrI ACTGG 1 cut(s) 319
BssECI CCNNGG 4 cut(s) 174, 823, 869, 1076
BssMI GATC 1 cut(s) 1022
BssSI CACGAG 1 cut(s) 329
BssT1I CCWWGG 2 cut(s) 174, 869
Bst2BI CACGAG 1 cut(s) 329
Bst2UI CCWGG 1 cut(s) 1020
Bst4CI ACNGT 3 cut(s) 383, 598, 968
Bst6I CTCTTC 1 cut(s) 397
BstBAI YACGTR 1 cut(s) 738
BstBI TTCGAA 1 cut(s) 709
BstDEI CTNAG 2 cut(s) 116, 205
BstDSI CCRYGG 2 cut(s) 174, 869
BstF5I GGATG 3 cut(s) 117, 243, 838
BstKTI GATC 1 cut(s) 1025
BstMAI GTCTC 3 cut(s) 543, 605, 885
BstMBI GATC 1 cut(s) 1022
BstNI CCWGG 1 cut(s) 1020
BstNSI RCATGY 1 cut(s) 988
BstSCI CCNGG 1 cut(s) 1018
BstSFI CTRYAG 1 cut(s) 474
BstSLI GKGCMC 1 cut(s) 984
BstV1I GCAGC 2 cut(s) 488, 889
BstV2I GAAGAC 1 cut(s) 496
BstX2I RGATCY 1 cut(s) 1022
BstYI RGATCY 1 cut(s) 1022
BsuRI GGCC 3 cut(s) 136, 179, 948
BtgI CCRYGG 2 cut(s) 174, 869
BtgZI GCGATG 1 cut(s) 1083
BtrI CACGTC 1 cut(s) 1010
BtsCI GGATG 3 cut(s) 117, 243, 838
BtsIMutI CAGTG 1 cut(s) 1070
Cfr13I GGNCC 3 cut(s) 134, 171, 947
CseI GACGC 1 cut(s) 902
Csp6I GTAC 2 cut(s) 384, 739
CviAII CATG 9 cut(s) 40, 76, 89, 175, 490, 649, 796, 870, 985
CviQI GTAC 2 cut(s) 384, 739
DdeI CTNAG 2 cut(s) 116, 205
DpnI GATC 1 cut(s) 1024
DpnII GATC 1 cut(s) 1022
EaeI YGGCCR 1 cut(s) 177
Eam1104I CTCTTC 1 cut(s) 397
EarI CTCTTC 1 cut(s) 397
Eco130I CCWWGG 2 cut(s) 174, 869
Eco31I GGTCTC 1 cut(s) 605
Eco47I GGWCC 1 cut(s) 171
Eco57I CTGAAG 2 cut(s) 186, 357
EcoRI GAATTC 1 cut(s) 697
EcoRII CCWGG 1 cut(s) 1018
EcoT14I CCWWGG 2 cut(s) 174, 869
ErhI CCWWGG 2 cut(s) 174, 869
Esp3I CGTCTC 1 cut(s) 885
FaeI CATG 9 cut(s) 43, 79, 92, 178, 493, 652, 799, 873, 988
FaqI GGGAC 3 cut(s) 184, 461, 1062
FatI CATG 9 cut(s) 39, 75, 88, 174, 489, 648, 795, 869, 984
Fnu4HI GCNGC 2 cut(s) 477, 878
FokI GGATG 3 cut(s) 124, 250, 825
Fsp4HI GCNGC 2 cut(s) 477, 878
FspBI CTAG 4 cut(s) 48, 266, 275, 296
GluI GCNGC 2 cut(s) 477, 878
GsuI CTGGAG 1 cut(s) 336
HaeIII GGCC 3 cut(s) 136, 179, 948
HgaI GACGC 1 cut(s) 902
Hin1II CATG 9 cut(s) 43, 79, 92, 178, 493, 652, 799, 873, 988
HincII GTYRAC 1 cut(s) 202
HindII GTYRAC 1 cut(s) 202
HinfI GANTC 5 cut(s) 82, 203, 292, 681, 732
Hpy166II GTNNAC 3 cut(s) 202, 621, 754
Hpy188I TCNGA 3 cut(s) 166, 208, 824
Hpy188III TCNNGA 6 cut(s) 68, 329, 356, 521, 770, 1141
Hpy8I GTNNAC 3 cut(s) 202, 621, 754
Hpy99I CGWCG 2 cut(s) 221, 1014
HpyAV CCTTC 9 cut(s) 17, 118, 161, 228, 235, 419, 796, 1025, 1142
HpyCH4III ACNGT 3 cut(s) 383, 598, 968
HpyCH4IV ACGT 4 cut(s) 460, 727, 737, 1009
HpyCH4V TGCA 4 cut(s) 88, 104, 476, 1073
HpyF3I CTNAG 2 cut(s) 116, 205
HpySE526I ACGT 4 cut(s) 460, 727, 737, 1009
Hsp92II CATG 9 cut(s) 43, 79, 92, 178, 493, 652, 799, 873, 988
Kzo9I GATC 1 cut(s) 1022
LmnI GCTCC 2 cut(s) 299, 805
Lsp1109I GCAGC 2 cut(s) 488, 889
LweI GCATC 3 cut(s) 102, 421, 1060
MaeI CTAG 4 cut(s) 48, 266, 275, 296
MaeII ACGT 4 cut(s) 460, 727, 737, 1009
MaeIII GTNAC 7 cut(s) 154, 277, 396, 463, 718, 1028, 1151
MalI GATC 1 cut(s) 1024
MboI GATC 1 cut(s) 1022
MboII GAAGA 6 cut(s) 198, 350, 414, 496, 723, 788
MfeI CAATTG 1 cut(s) 1033
MflI RGATCY 1 cut(s) 1022
MhlI GDGCHC 1 cut(s) 984
MluCI AATT 8 cut(s) 27, 142, 308, 515, 560, 697, 951, 1033
MlyI GAGTC 2 cut(s) 197, 301
MroXI GAANNNNTTC 1 cut(s) 818
MseI TTAA 4 cut(s) 18, 30, 59, 917
MslI CAYNNNNRTG 1 cut(s) 1142
MspR9I CCNGG 1 cut(s) 1020
MunI CAATTG 1 cut(s) 1033
MvaI CCWGG 1 cut(s) 1020
NcoI CCATGG 2 cut(s) 174, 869
NdeII GATC 1 cut(s) 1022
NlaIII CATG 9 cut(s) 43, 79, 92, 178, 493, 652, 799, 873, 988
NlaIV GGNNCC 2 cut(s) 135, 172
NmuCI GTSAC 2 cut(s) 463, 718
NspI RCATGY 1 cut(s) 988
NspV TTCGAA 1 cut(s) 709
PciI ACATGT 1 cut(s) 984
PdmI GAANNNNTTC 1 cut(s) 818
PfeI GAWTC 3 cut(s) 82, 681, 732
Pfl23II CGTACG 1 cut(s) 738
PfoI TCCNGGA 1 cut(s) 1018
PkrI GCNGC 2 cut(s) 478, 879
PleI GAGTC 2 cut(s) 197, 300
PpsI GAGTC 2 cut(s) 197, 300
Ppu21I YACGTR 1 cut(s) 738
PscI ACATGT 1 cut(s) 984
PshBI ATTAAT 1 cut(s) 30
Psp6I CCWGG 1 cut(s) 1018
PspGI CCWGG 1 cut(s) 1018
PspLI CGTACG 1 cut(s) 738
PspN4I GGNNCC 2 cut(s) 135, 172
PspPI GGNCC 3 cut(s) 134, 171, 947
PstI CTGCAG 1 cut(s) 478
PsuI RGATCY 1 cut(s) 1022
RsaI GTAC 2 cut(s) 385, 740
RsaNI GTAC 2 cut(s) 384, 739
RseI CAYNNNNRTG 1 cut(s) 1142
SaqAI TTAA 4 cut(s) 18, 30, 59, 917
SatI GCNGC 2 cut(s) 477, 878
Sau3AI GATC 1 cut(s) 1022
Sau96I GGNCC 3 cut(s) 134, 171, 947
SchI GAGTC 2 cut(s) 197, 301
ScrFI CCNGG 1 cut(s) 1020
SduI GDGCHC 1 cut(s) 984
SfaNI GCATC 3 cut(s) 102, 421, 1060
SfcI CTRYAG 1 cut(s) 474
SfuI TTCGAA 1 cut(s) 709
SinI GGWCC 1 cut(s) 171
SmiMI CAYNNNNRTG 1 cut(s) 1142
SmlI CTYRAG 1 cut(s) 768
SmoI CTYRAG 1 cut(s) 768
SpeI ACTAGT 1 cut(s) 274
Sse9I AATT 8 cut(s) 27, 142, 308, 515, 560, 697, 951, 1033
SsiI CCGC 1 cut(s) 861
SspI AATATT 2 cut(s) 530, 706
SspMI CTAG 4 cut(s) 48, 266, 275, 296
StyD4I CCNGG 1 cut(s) 1018
StyI CCWWGG 2 cut(s) 174, 869
TaaI ACNGT 3 cut(s) 383, 598, 968
TaiI ACGT 4 cut(s) 463, 730, 740, 1012
TaqI TCGA 2 cut(s) 219, 709
TasI AATT 8 cut(s) 27, 142, 308, 515, 560, 697, 951, 1033
TfiI GAWTC 3 cut(s) 82, 681, 732
Tru1I TTAA 4 cut(s) 18, 30, 59, 917
Tru9I TTAA 4 cut(s) 18, 30, 59, 917
TscAI CASTG 1 cut(s) 1070
TseFI GTSAC 2 cut(s) 463, 718
TseI GCWGC 2 cut(s) 476, 877
Tsp45I GTSAC 2 cut(s) 463, 718
TspDTI ATGAA 2 cut(s) 36, 673
TspRI CASTG 1 cut(s) 1070
VpaK11BI GGWCC 1 cut(s) 171
VspI ATTAAT 1 cut(s) 30
XapI RAATTY 3 cut(s) 308, 515, 697
XceI RCATGY 1 cut(s) 988
XmnI GAANNNNTTC 1 cut(s) 818
XspI CTAG 4 cut(s) 48, 266, 275, 296
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.