RchiOBHm_Chr1g0366991

GAG-pre-integrase domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
1
OG0018861
Physical Location & Seq
Reverse (-)
57411623 .. 57420203
8581 bp
Loading structure...
UTR
Exon/CDS
Intron
N/A

Sequence Viewer

Length: 996 bp
ATGGAACTCATCCATGTCCTCCAGAATTCATTGCTGGTACTGATGGTTCTCTCACAGCAAATACCAAAGCTTATGAAAAATGGTTGCAACAAGATAGTTTTGTTATCTAAGATTACCAACACTCTCTCTGCTGAGGCTCTTAAATTGGTAATTGGCTGTGAAACTTCAATGGAGGTATGGACCACTCTCAAACAGCAATTTGCACCAAATTCTGAATTTCACATTATGCGATTGAAGTCTATTTTGCAAAATATCCGAAAAGGATCAGATTCTATTGACAAATATTTGTTGCGATTTATAAATGTCAGAAATAATTTAGCTGTTGTTGGTGTTAGTATGTCAGATCAGGATATCAAAATGCTGATTTTAGCTGGCCTTCCTAATGAATATGCTCACACTAGGCAAATTATCAGAGGGAAAGATCATATTACTATGGAAGAAGTGAGGTCATTGCTTTTATCTGCTGAGTTTGAATTGGAATTAGAGCAAAAAGGTCCTCCTTTCTCACCAATGAATGCAATGGTAGCAAATAATGTCGGCTATGTTGGAACTTCCCCTAGATTTAGTTCAAATGAAGTTGCATGTTCTGTACCTAATGCACCTTCTGGGTTCATTGTTGCCACTCCTGGACCAATTATTGCCTCATCTACATCATACATGCCTACTGGTGTCACTCCACAAGTTGGTGTGTTTTCAAACAATGCTTATGTTCAATCACAAGCCAATACAGTTCCGAACAATTACCCTCAGTTTCCAAACAACAACAATTCAAGGAATGGAGGCAATAACAATATAAACAGCAACTCAGGGAGCTACTTCAAACCAAGGTTTAACTCAAATCAAGATCCACTGAAATGCCAAATTTGTGAGAAGCCTGGACATAGTGCTTATAAATGCTTTCAGAGAAACCCACAGAAACAAGGTGAAGCCTCTAGCTCTACTGTTGAATGTCATATTTGCAAGAAATCAGGCCATACTACAAAAACTTGCAGGTAG
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
RVT_2 gag_pre-integrs rve

Protein Analysis

331

Amino Acids

36.5

Weight (kDa)

9.17

Isoelectric Point (pI)

43.22

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 36 - 156 9.9e-19 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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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 2 cut(s) 299, 891
Acc36I ACCTGC 1 cut(s) 981
AccB7I CCANNNNNTGG 1 cut(s) 683
AclWI GGATC 2 cut(s) 271, 839
AcsI RAATTY 4 cut(s) 25, 208, 215, 861
AfaI GTAC 2 cut(s) 39, 591
AfiI CCNNNNNNNGG 1 cut(s) 683
AgsI TTSAA 9 cut(s) 168, 235, 473, 570, 696, 713, 771, 820, 947
AjnI CCWGG 2 cut(s) 625, 874
AluBI AGCT 5 cut(s) 70, 320, 371, 813, 936
AluI AGCT 5 cut(s) 70, 320, 371, 813, 936
AlwI GGATC 2 cut(s) 271, 839
AoxI GGCC 2 cut(s) 373, 970
ApoI RAATTY 4 cut(s) 25, 208, 215, 861
AspS9I GGNCC 3 cut(s) 180, 494, 629
AsuHPI GGTGA 2 cut(s) 498, 935
AvaII GGWCC 3 cut(s) 180, 494, 629
BbvCI CCTCAGC 1 cut(s) 132
BccI CCATC 1 cut(s) 37
BciT130I CCWGG 2 cut(s) 627, 876
BfaI CTAG 3 cut(s) 399, 558, 933
BfuAI ACCTGC 1 cut(s) 981
Bme1390I CCNGG 2 cut(s) 627, 876
Bme18I GGWCC 3 cut(s) 180, 494, 629
BmgT120I GGNCC 3 cut(s) 180, 494, 629
BmrFI CCNGG 2 cut(s) 627, 876
BpmI CTGGAG 1 cut(s) 5
Bpu10I CCTNAGC 1 cut(s) 132
BsaJI CCNNGG 1 cut(s) 824
Bsc4I CCNNNNNNNGG 1 cut(s) 683
Bse1I ACTGG 1 cut(s) 670
Bse3DI GCAATG 3 cut(s) 29, 449, 525
BseBI CCWGG 2 cut(s) 627, 876
BseDI CCNNGG 1 cut(s) 824
BseGI GGATG 1 cut(s) 9
BseLI CCNNNNNNNGG 1 cut(s) 683
BseMI GCAATG 3 cut(s) 29, 449, 525
BseMII CTCAG 4 cut(s) 123, 456, 761, 819
BseNI ACTGG 1 cut(s) 670
BshFI GGCC 2 cut(s) 375, 972
BslI CCNNNNNNNGG 1 cut(s) 683
BsmI GAATGC 1 cut(s) 520
BsnI GGCC 2 cut(s) 375, 972
Bsp143I GATC 4 cut(s) 263, 343, 421, 844
BspANI GGCC 2 cut(s) 375, 972
BspCNI CTCAG 4 cut(s) 124, 457, 760, 818
BspMI ACCTGC 1 cut(s) 981
BspPI GGATC 2 cut(s) 271, 839
BsrDI GCAATG 3 cut(s) 29, 449, 525
BsrI ACTGG 1 cut(s) 670
BssECI CCNNGG 1 cut(s) 824
BssMI GATC 4 cut(s) 263, 343, 421, 844
BssT1I CCWWGG 1 cut(s) 824
Bst2UI CCWGG 2 cut(s) 627, 876
Bst4CI ACNGT 2 cut(s) 730, 943
BstC8I GCNNGC 1 cut(s) 373
BstDEI CTNAG 5 cut(s) 108, 132, 465, 747, 805
BstF5I GGATG 1 cut(s) 9
BstKTI GATC 4 cut(s) 266, 346, 424, 847
BstMBI GATC 4 cut(s) 263, 343, 421, 844
BstMWI GCNNNNNNNGC 1 cut(s) 524
BstNI CCWGG 2 cut(s) 627, 876
BstNSI RCATGY 2 cut(s) 585, 661
BstSCI CCNGG 2 cut(s) 625, 874
BstX2I RGATCY 1 cut(s) 844
BstYI RGATCY 1 cut(s) 844
BsuRI GGCC 2 cut(s) 375, 972
BtsCI GGATG 1 cut(s) 9
BtsIMutI CAGTG 1 cut(s) 848
BveI ACCTGC 1 cut(s) 981
Cac8I GCNNGC 1 cut(s) 373
Cfr13I GGNCC 3 cut(s) 180, 494, 629
Csp6I GTAC 2 cut(s) 38, 590
CviAII CATG 3 cut(s) 14, 582, 658
CviQI GTAC 2 cut(s) 38, 590
DdeI CTNAG 5 cut(s) 108, 132, 465, 747, 805
DpnI GATC 4 cut(s) 265, 345, 423, 846
DpnII GATC 4 cut(s) 263, 343, 421, 844
Eco130I CCWWGG 1 cut(s) 824
Eco32I GATATC 1 cut(s) 352
Eco47I GGWCC 3 cut(s) 180, 494, 629
EcoO109I RGGNCCY 1 cut(s) 494
EcoRI GAATTC 1 cut(s) 25
EcoRII CCWGG 2 cut(s) 625, 874
EcoRV GATATC 1 cut(s) 352
EcoT14I CCWWGG 1 cut(s) 824
ErhI CCWWGG 1 cut(s) 824
FaeI CATG 3 cut(s) 17, 585, 661
FatI CATG 3 cut(s) 13, 581, 657
FspBI CTAG 3 cut(s) 399, 558, 933
GsuI CTGGAG 1 cut(s) 5
HaeIII GGCC 2 cut(s) 375, 972
Hin1II CATG 3 cut(s) 17, 585, 661
HindIII AAGCTT 1 cut(s) 68
HinfI GANTC 1 cut(s) 269
HphI GGTGA 2 cut(s) 498, 935
Hpy188I TCNGA 8 cut(s) 214, 257, 268, 308, 343, 413, 735, 903
Hpy188III TCNNGA 3 cut(s) 22, 347, 842
HpyAV CCTTC 2 cut(s) 386, 612
HpyCH4III ACNGT 2 cut(s) 730, 943
HpyCH4V TGCA 8 cut(s) 87, 203, 247, 518, 581, 599, 960, 990
HpyF10VI GCNNNNNNNGC 1 cut(s) 524
HpyF3I CTNAG 5 cut(s) 108, 132, 465, 747, 805
Hsp92II CATG 3 cut(s) 17, 585, 661
Kzo9I GATC 4 cut(s) 263, 343, 421, 844
LmnI GCTCC 1 cut(s) 810
MaeI CTAG 3 cut(s) 399, 558, 933
MaeIII GTNAC 1 cut(s) 670
MalI GATC 4 cut(s) 265, 345, 423, 846
MboI GATC 4 cut(s) 263, 343, 421, 844
MboII GAAGA 1 cut(s) 449
MflI RGATCY 1 cut(s) 844
MmeI TCCRAC 1 cut(s) 526
MseI TTAA 2 cut(s) 141, 831
MslI CAYNNNNRTG 1 cut(s) 853
MspR9I CCNGG 2 cut(s) 627, 876
Mva1269I GAATGC 1 cut(s) 520
MvaI CCWGG 2 cut(s) 627, 876
MwoI GCNNNNNNNGC 1 cut(s) 524
NdeII GATC 4 cut(s) 263, 343, 421, 844
NlaIII CATG 3 cut(s) 17, 585, 661
NmuCI GTSAC 1 cut(s) 670
NspI RCATGY 2 cut(s) 585, 661
PctI GAATGC 1 cut(s) 520
PfeI GAWTC 1 cut(s) 269
PflMI CCANNNNNTGG 1 cut(s) 683
PfoI TCCNGGA 1 cut(s) 625
PpuMI RGGWCCY 1 cut(s) 494
PsiI TTATAA 2 cut(s) 299, 891
Psp5II RGGWCCY 1 cut(s) 494
Psp6I CCWGG 2 cut(s) 625, 874
PspGI CCWGG 2 cut(s) 625, 874
PspPI GGNCC 3 cut(s) 180, 494, 629
PspPPI RGGWCCY 1 cut(s) 494
PsrI GAACNNNNNNTAC 2 cut(s) 30, 62
PsuI RGATCY 1 cut(s) 844
RsaI GTAC 2 cut(s) 39, 591
RsaNI GTAC 2 cut(s) 38, 590
RseI CAYNNNNRTG 1 cut(s) 853
SaqAI TTAA 2 cut(s) 141, 831
Sau3AI GATC 4 cut(s) 263, 343, 421, 844
Sau96I GGNCC 3 cut(s) 180, 494, 629
ScrFI CCNGG 2 cut(s) 627, 876
SinI GGWCC 3 cut(s) 180, 494, 629
SmiMI CAYNNNNRTG 1 cut(s) 853
SspI AATATT 1 cut(s) 284
SspMI CTAG 3 cut(s) 399, 558, 933
StyD4I CCNGG 2 cut(s) 625, 874
StyI CCWWGG 1 cut(s) 824
TaaI ACNGT 2 cut(s) 730, 943
TfiI GAWTC 1 cut(s) 269
Tru1I TTAA 2 cut(s) 141, 831
Tru9I TTAA 2 cut(s) 141, 831
TscAI CASTG 1 cut(s) 855
TseFI GTSAC 1 cut(s) 670
Tsp45I GTSAC 1 cut(s) 670
TspDTI ATGAA 6 cut(s) 18, 89, 399, 527, 588, 601
TspRI CASTG 1 cut(s) 855
Van91I CCANNNNNTGG 1 cut(s) 683
VpaK11BI GGWCC 3 cut(s) 180, 494, 629
XapI RAATTY 4 cut(s) 25, 208, 215, 861
XceI RCATGY 2 cut(s) 585, 661
XspI CTAG 3 cut(s) 399, 558, 933
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.