RchiOBHm_Chr3g0462591

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
3
OG0000703
Physical Location & Seq
Forward (+)
10240405 .. 10241405
1001 bp
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UTR
Exon/CDS
Intron
PRQ42894

Sequence Viewer

Length: 915 bp
ATGGATAGAGATAGAGAACGTTCTGGCTCTATAAACTGTCCACCTTTTTTTGATGGGAATGATTATTCTCAGTGGAAAATTATGATGCAAGCCTTCTTACATTCACAGGATGAACATATCTGGAATATTGTTGAATTTGGGTGGGAGGTTCCCACAAAGGAAACTAAGTCTAAAGAGAGTGAGAGTTCTGCTTCCGTAAAAGAACCTAAGTCTAGGCAAGATTGGTCTATAGCTGAAGTACGTGATTTTAACAATGATGTTAAAGCACGGCACAGCTTGTATACGGCTCTTTCTATGAAAGAAAAGAAGCGTATTGGAACTTGTAAGACTGCGAAGAAGGCATGGGATCTTCTTCAAATGACTTATGAAGGAAACAAGAAAGTTAGGACTCAGAAACTTCAGAAATTAATTTCTGAGTTTGAGACAATGACTATGGGAGATGATGAGTCCATTGATGATTTTCATTCTAGGCTTATAAATGTGACGAATGAGTGTGATAGTCTTAGTGATCCTATTGCTGAGAATAGGATTGTAAAGAAATTCCTTAGGTCCTTACCCTTGAGTTTTCAAAATAAACAAACTGCCATTGAAGAAGTTCAGGATTTAGATACCTATACCTTAGATGAACTTCTTGGGAATCTTCAAACTTTTGAAATGAAAATCAGGCCAGATAAGAAAGTAAAAACCATTGCCTTGAATGCTGTTAGGAAAGTGGATGAAAAGCCAAAAGAGTTAGTAAAGGAAAAGGATAGTGACTCCGATTTTACTGCTGAAGACTTTGCTCTCTTAACCAAACATTACAAAAAGTTTTTAAGGTCTGGTAATTCGTTTCAAAATTCCAAGAACTTCTCTGGGTCTAGTTCTAGGAGAAATATGAGCGGGTTTCGGACATCTTGCGGCAGATTGTGGAAATAA
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
DUF4219 Retrotran_gag_2

Protein Analysis

304

Amino Acids

35.3

Weight (kDa)

8.67

Isoelectric Point (pI)

45.88

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 48 - 220 1.2e-23 gag-polypeptide of LTR copia-type
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 476
AccBSI CCGCTC 1 cut(s) 879
AccI GTMKAC 1 cut(s) 281
AciI CCGC 2 cut(s) 879, 897
AclI AACGTT 1 cut(s) 19
AclWI GGATC 2 cut(s) 354, 503
AcsI RAATTY 3 cut(s) 134, 539, 835
AcuI CTGAAG 3 cut(s) 255, 383, 792
AfaI GTAC 1 cut(s) 240
AgsI TTSAA 8 cut(s) 134, 356, 569, 590, 644, 653, 697, 833
AluBI AGCT 2 cut(s) 233, 276
AluI AGCT 2 cut(s) 233, 276
Alw26I GTCTC 1 cut(s) 416
AlwI GGATC 2 cut(s) 354, 503
AoxI GGCC 1 cut(s) 665
ApoI RAATTY 3 cut(s) 134, 539, 835
AseI ATTAAT 1 cut(s) 407
Asp700I GAANNNNTTC 1 cut(s) 594
AspS9I GGNCC 1 cut(s) 549
AvaII GGWCC 1 cut(s) 549
AxyI CCTNAGG 1 cut(s) 545
BbsI GAAGAC 1 cut(s) 780
BccI CCATC 1 cut(s) 47
BceAI ACGGC 2 cut(s) 284, 300
BcgI CGANNNNNNTGC 2 cut(s) 749, 783
BcoDI GTCTC 1 cut(s) 416
BfaI CTAG 4 cut(s) 213, 468, 858, 864
BfmI CTRYAG 1 cut(s) 228
BisI GCNGC 1 cut(s) 898
BlsI GCNGC 1 cut(s) 899
Bme18I GGWCC 1 cut(s) 549
BmgT120I GGNCC 1 cut(s) 549
BmiI GGNNCC 1 cut(s) 150
BmsI GCATC 1 cut(s) 75
BpiI GAAGAC 1 cut(s) 780
BpuEI CTTGAG 1 cut(s) 580
BsaAI YACGTR 1 cut(s) 242
Bse21I CCTNAGG 1 cut(s) 545
Bse3DI GCAATG 1 cut(s) 687
BseGI GGATG 2 cut(s) 115, 721
BseMI GCAATG 1 cut(s) 687
BseMII CTCAG 4 cut(s) 83, 404, 405, 510
BshFI GGCC 1 cut(s) 667
BsmAI GTCTC 1 cut(s) 416
BsmI GAATGC 1 cut(s) 703
BsnI GGCC 1 cut(s) 667
Bsp143I GATC 2 cut(s) 346, 508
BspACI CCGC 2 cut(s) 879, 897
BspANI GGCC 1 cut(s) 667
BspCNI CTCAG 4 cut(s) 82, 403, 406, 511
BspLI GGNNCC 1 cut(s) 150
BspPI GGATC 2 cut(s) 354, 503
BsrBI CCGCTC 1 cut(s) 879
BsrDI GCAATG 1 cut(s) 687
BssMI GATC 2 cut(s) 346, 508
BssNAI GTATAC 1 cut(s) 282
Bst1107I GTATAC 1 cut(s) 282
Bst4CI ACNGT 1 cut(s) 38
BstBAI YACGTR 1 cut(s) 242
BstC8I GCNNGC 1 cut(s) 90
BstDEI CTNAG 9 cut(s) 69, 165, 207, 390, 414, 503, 519, 545, 619
BstF5I GGATG 2 cut(s) 115, 721
BstKTI GATC 2 cut(s) 349, 511
BstMAI GTCTC 1 cut(s) 416
BstMBI GATC 2 cut(s) 346, 508
BstMWI GCNNNNNNNGC 2 cut(s) 338, 698
BstSFI CTRYAG 1 cut(s) 228
BstV2I GAAGAC 1 cut(s) 780
BstX2I RGATCY 1 cut(s) 346
BstYI RGATCY 1 cut(s) 346
BstZ17I GTATAC 1 cut(s) 282
Bsu36I CCTNAGG 1 cut(s) 545
BsuRI GGCC 1 cut(s) 667
BtsCI GGATG 2 cut(s) 115, 721
BtsIMutI CAGTG 1 cut(s) 77
Cac8I GCNNGC 1 cut(s) 90
Cfr13I GGNCC 1 cut(s) 549
Csp6I GTAC 1 cut(s) 239
CviAII CATG 1 cut(s) 342
CviJI RGCY 8 cut(s) 27, 92, 233, 276, 287, 472, 667, 724
CviKI_1 RGCY 8 cut(s) 27, 92, 233, 276, 287, 472, 667, 724
CviQI GTAC 1 cut(s) 239
DdeI CTNAG 9 cut(s) 69, 165, 207, 390, 414, 503, 519, 545, 619
DpnI GATC 2 cut(s) 348, 510
DpnII GATC 2 cut(s) 346, 508
Eco47I GGWCC 1 cut(s) 549
Eco57I CTGAAG 3 cut(s) 255, 383, 792
Eco81I CCTNAGG 1 cut(s) 545
EcoO109I RGGNCCY 1 cut(s) 549
FaeI CATG 1 cut(s) 345
FatI CATG 1 cut(s) 341
FauI CCCGC 1 cut(s) 872
FblI GTMKAC 1 cut(s) 281
Fnu4HI GCNGC 1 cut(s) 898
FokI GGATG 2 cut(s) 122, 728
Fsp4HI GCNGC 1 cut(s) 898
FspBI CTAG 4 cut(s) 213, 468, 858, 864
GluI GCNGC 1 cut(s) 898
HaeIII GGCC 1 cut(s) 667
Hin1II CATG 1 cut(s) 345
HinfI GANTC 4 cut(s) 388, 446, 637, 755
Hpy166II GTNNAC 2 cut(s) 41, 282
Hpy188I TCNGA 5 cut(s) 393, 402, 415, 760, 888
Hpy188III TCNNGA 2 cut(s) 121, 599
Hpy8I GTNNAC 2 cut(s) 41, 282
HpyAV CCTTC 3 cut(s) 103, 331, 362
HpyCH4III ACNGT 1 cut(s) 38
HpyCH4IV ACGT 2 cut(s) 19, 241
HpyCH4V TGCA 1 cut(s) 88
HpyF10VI GCNNNNNNNGC 2 cut(s) 338, 698
HpyF3I CTNAG 9 cut(s) 69, 165, 207, 390, 414, 503, 519, 545, 619
HpySE526I ACGT 2 cut(s) 19, 241
Hsp92II CATG 1 cut(s) 345
Kzo9I GATC 2 cut(s) 346, 508
LpnPI CCDG 8 cut(s) 9, 92, 106, 584, 649, 681, 804, 837
LweI GCATC 1 cut(s) 75
MaeI CTAG 4 cut(s) 213, 468, 858, 864
MaeII ACGT 2 cut(s) 19, 241
MaeIII GTNAC 2 cut(s) 481, 752
MalI GATC 2 cut(s) 348, 510
MbiI CCGCTC 1 cut(s) 879
MboI GATC 2 cut(s) 346, 508
MboII GAAGA 6 cut(s) 341, 344, 346, 602, 632, 785
MflI RGATCY 1 cut(s) 346
MluCI AATT 7 cut(s) 78, 134, 404, 408, 539, 823, 835
MlyI GAGTC 3 cut(s) 382, 455, 749
MnlI CCTC 1 cut(s) 139
MroXI GAANNNNTTC 1 cut(s) 594
MseI TTAA 5 cut(s) 249, 261, 407, 788, 812
Mva1269I GAATGC 1 cut(s) 703
MwoI GCNNNNNNNGC 2 cut(s) 338, 698
NdeII GATC 2 cut(s) 346, 508
NlaIII CATG 1 cut(s) 345
NlaIV GGNNCC 1 cut(s) 150
NmuCI GTSAC 2 cut(s) 481, 752
PctI GAATGC 1 cut(s) 703
PdmI GAANNNNTTC 1 cut(s) 594
PfeI GAWTC 1 cut(s) 637
PkrI GCNGC 1 cut(s) 899
PleI GAGTC 3 cut(s) 382, 454, 749
PpsI GAGTC 3 cut(s) 382, 454, 749
Ppu21I YACGTR 1 cut(s) 242
PpuMI RGGWCCY 1 cut(s) 549
PshBI ATTAAT 1 cut(s) 407
PsiI TTATAA 1 cut(s) 476
Psp1406I AACGTT 1 cut(s) 19
Psp5II RGGWCCY 1 cut(s) 549
PspN4I GGNNCC 1 cut(s) 150
PspPI GGNCC 1 cut(s) 549
PspPPI RGGWCCY 1 cut(s) 549
PsuI RGATCY 1 cut(s) 346
RsaI GTAC 1 cut(s) 240
RsaNI GTAC 1 cut(s) 239
SaqAI TTAA 5 cut(s) 249, 261, 407, 788, 812
SatI GCNGC 1 cut(s) 898
Sau3AI GATC 2 cut(s) 346, 508
Sau96I GGNCC 1 cut(s) 549
SchI GAGTC 3 cut(s) 382, 455, 749
SfaNI GCATC 1 cut(s) 75
SfcI CTRYAG 1 cut(s) 228
SinI GGWCC 1 cut(s) 549
SmlI CTYRAG 1 cut(s) 559
SmoI CTYRAG 1 cut(s) 559
Sse9I AATT 7 cut(s) 78, 134, 404, 408, 539, 823, 835
SsiI CCGC 2 cut(s) 879, 897
SspI AATATT 1 cut(s) 127
SspMI CTAG 4 cut(s) 213, 468, 858, 864
TaaI ACNGT 1 cut(s) 38
TaiI ACGT 2 cut(s) 22, 244
TasI AATT 7 cut(s) 78, 134, 404, 408, 539, 823, 835
TauI GCSGC 1 cut(s) 900
TfiI GAWTC 1 cut(s) 637
Tru1I TTAA 5 cut(s) 249, 261, 407, 788, 812
Tru9I TTAA 5 cut(s) 249, 261, 407, 788, 812
TscAI CASTG 1 cut(s) 77
TseFI GTSAC 2 cut(s) 481, 752
Tsp45I GTSAC 2 cut(s) 481, 752
TspDTI ATGAA 7 cut(s) 126, 311, 381, 452, 639, 671, 732
TspGWI ACGGA 1 cut(s) 184
TspRI CASTG 1 cut(s) 77
VpaK11BI GGWCC 1 cut(s) 549
VspI ATTAAT 1 cut(s) 407
XapI RAATTY 3 cut(s) 134, 539, 835
XmiI GTMKAC 1 cut(s) 281
XmnI GAANNNNTTC 1 cut(s) 594
XspI CTAG 4 cut(s) 213, 468, 858, 864
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.