Rroxscaffold_4G00300220

GAG-pre-integrase domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000004
OG0000703
Physical Location & Seq
Forward (+)
20404192 .. 20410323
6132 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_4G00300220.1

Sequence Viewer

Length: 609 bp
ATGGGTGGTTTGCGTTCTAAAGATAACTGTTATCATGAACGTGCTAATAAATCTGTTGAAGTGAAGACATGTACGAAAGCCAAGACATCGGATGATGTTCCTAAACTTTGGCATAGGCGACCGGGGCATGTAAATTTTCAAGACTTGCTGAAACTTTCACACAAGGAAAGTGTAAGAGGTATGCCTTCTCCGAGCGGTAAGCCGGACAAGATGTGTGACGGTTGCAAGGTAGGTATACAAACTCGTGCCTCACATGGAGCAGTTAATTCATCCACTACAACTCATCCTTTGGAACATATGCATATGGACCTCGTTGGACCTTCACAAACCGAAAGCATGGGTGGTAAGAAATACATTTTGGTTGTAGTTGATGACTTTCCACGTTTTACTTGGGTGAATTTTCTTAGAGAAAAGAGTGATACATTTGAAAGCTTTAAGGGATTGTGCAAAAGAATAACAAATGAAAAACATTCATCAAACTTGTGCATTGTCAAAGTTAGGACCGATAATGGGACTGAATTTAAGAATGCATTGTTTGCTGAATTTTTCTTGAGCAAGGAATTTCACATGAGTTTTCAGCTCCAATTACCCCACAACAGAATGGTGTAG
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
gag_pre-integrs

Protein Analysis

202

Amino Acids

22.97

Weight (kDa)

9.33

Isoelectric Point (pI)

41.36

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
gag_pre-integrs PF13976 10 - 78 2.5e-13 GAG-pre-integrase domain
rve PF00665 94 - 192 5e-09 Integrase core domain
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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccBSI CCGCTC 1 cut(s) 195
AccI GTMKAC 1 cut(s) 235
AciI CCGC 1 cut(s) 195
AcsI RAATTY 5 cut(s) 133, 397, 518, 542, 560
AfaI GTAC 1 cut(s) 73
AfiI CCNNNNNNNGG 1 cut(s) 510
AflIII ACRYGT 1 cut(s) 68
AgsI TTSAA 3 cut(s) 59, 140, 428
AjuI GAANNNNNNNTTGG 2 cut(s) 341, 373
AluBI AGCT 2 cut(s) 432, 580
AluI AGCT 2 cut(s) 432, 580
ApoI RAATTY 5 cut(s) 133, 397, 518, 542, 560
AspS9I GGNCC 3 cut(s) 307, 317, 501
AsuC2I CCSGG 1 cut(s) 123
AsuHPI GGTGA 1 cut(s) 406
AvaII GGWCC 3 cut(s) 307, 317, 501
BauI CACGAG 1 cut(s) 243
BbsI GAAGAC 1 cut(s) 71
BcnI CCSGG 1 cut(s) 123
Bme1390I CCNGG 1 cut(s) 123
Bme18I GGWCC 3 cut(s) 307, 317, 501
BmgT120I GGNCC 3 cut(s) 307, 317, 501
BmrFI CCNGG 1 cut(s) 123
BpiI GAAGAC 1 cut(s) 71
BpuEI CTTGAG 1 cut(s) 571
BpuMI CCSGG 1 cut(s) 123
BsaJI CCNNGG 1 cut(s) 122
Bsc4I CCNNNNNNNGG 1 cut(s) 510
BseDI CCNNGG 1 cut(s) 122
BseGI GGATG 3 cut(s) 97, 269, 283
BseLI CCNNNNNNNGG 1 cut(s) 510
Bsh1285I CGRYCG 1 cut(s) 122
BsiEI CGRYCG 1 cut(s) 122
BsiSI CCGG 2 cut(s) 122, 203
BslFI GGGAC 1 cut(s) 526
BslI CCNNNNNNNGG 1 cut(s) 510
BsmFI GGGAC 1 cut(s) 526
BsmI GAATGC 1 cut(s) 532
BspACI CCGC 1 cut(s) 195
BspHI TCATGA 1 cut(s) 34
BsrBI CCGCTC 1 cut(s) 195
BssECI CCNNGG 1 cut(s) 122
BssNAI GTATAC 1 cut(s) 236
BssSI CACGAG 1 cut(s) 243
Bst1107I GTATAC 1 cut(s) 236
Bst2BI CACGAG 1 cut(s) 243
Bst4CI ACNGT 2 cut(s) 29, 221
BstAPI GCANNNNNTGC 1 cut(s) 536
BstDEI CTNAG 1 cut(s) 404
BstF5I GGATG 3 cut(s) 97, 269, 283
BstMCI CGRYCG 1 cut(s) 122
BstMWI GCNNNNNNNGC 2 cut(s) 124, 536
BstNSI RCATGY 2 cut(s) 72, 131
BstSCI CCNGG 1 cut(s) 121
BstV2I GAAGAC 1 cut(s) 71
BstZ17I GTATAC 1 cut(s) 236
BtsCI GGATG 3 cut(s) 97, 269, 283
CciI TCATGA 1 cut(s) 34
Cfr13I GGNCC 3 cut(s) 307, 317, 501
Csp6I GTAC 1 cut(s) 72
CviAII CATG 6 cut(s) 35, 69, 128, 254, 337, 568
CviJI RGCY 4 cut(s) 80, 202, 432, 580
CviKI_1 RGCY 4 cut(s) 80, 202, 432, 580
CviQI GTAC 1 cut(s) 72
DdeI CTNAG 1 cut(s) 404
Eco47I GGWCC 3 cut(s) 307, 317, 501
EcoT22I ATGCAT 2 cut(s) 303, 532
FaeI CATG 6 cut(s) 38, 72, 131, 257, 340, 571
FaqI GGGAC 1 cut(s) 526
FatI CATG 6 cut(s) 34, 68, 127, 253, 336, 567
FauNDI CATATG 2 cut(s) 297, 303
FblI GTMKAC 1 cut(s) 235
FokI GGATG 3 cut(s) 104, 256, 270
HapII CCGG 2 cut(s) 122, 203
Hin1II CATG 6 cut(s) 38, 72, 131, 257, 340, 571
HindIII AAGCTT 1 cut(s) 430
HpaII CCGG 2 cut(s) 122, 203
HphI GGTGA 1 cut(s) 406
Hpy166II GTNNAC 1 cut(s) 236
Hpy188I TCNGA 2 cut(s) 91, 192
Hpy188III TCNNGA 3 cut(s) 35, 140, 550
Hpy8I GTNNAC 1 cut(s) 236
HpyAV CCTTC 2 cut(s) 195, 330
HpyCH4III ACNGT 2 cut(s) 29, 221
HpyCH4IV ACGT 2 cut(s) 40, 382
HpyCH4V TGCA 5 cut(s) 225, 301, 447, 486, 530
HpyF10VI GCNNNNNNNGC 2 cut(s) 124, 536
HpyF3I CTNAG 1 cut(s) 404
HpySE526I ACGT 2 cut(s) 40, 382
Hsp92II CATG 6 cut(s) 38, 72, 131, 257, 340, 571
LmnI GCTCC 2 cut(s) 257, 585
LpnPI CCDG 2 cut(s) 135, 216
MaeII ACGT 2 cut(s) 40, 382
MaeIII GTNAC 1 cut(s) 215
MbiI CCGCTC 1 cut(s) 195
MboII GAAGA 1 cut(s) 76
MluCI AATT 7 cut(s) 133, 265, 397, 518, 542, 560, 584
MmeI TCCRAC 1 cut(s) 295
MnlI CCTC 3 cut(s) 170, 259, 320
Mph1103I ATGCAT 2 cut(s) 303, 532
MseI TTAA 3 cut(s) 264, 435, 522
MslI CAYNNNNRTG 1 cut(s) 39
MspI CCGG 2 cut(s) 122, 203
MspR9I CCNGG 1 cut(s) 123
Mva1269I GAATGC 1 cut(s) 532
MwoI GCNNNNNNNGC 2 cut(s) 124, 536
NciI CCSGG 1 cut(s) 123
NdeI CATATG 2 cut(s) 297, 303
NlaIII CATG 6 cut(s) 38, 72, 131, 257, 340, 571
NmuCI GTSAC 1 cut(s) 215
NsiI ATGCAT 2 cut(s) 303, 532
NspI RCATGY 2 cut(s) 72, 131
PagI TCATGA 1 cut(s) 34
PciI ACATGT 1 cut(s) 68
PctI GAATGC 1 cut(s) 532
PscI ACATGT 1 cut(s) 68
PspPI GGNCC 3 cut(s) 307, 317, 501
RsaI GTAC 1 cut(s) 73
RsaNI GTAC 1 cut(s) 72
RseI CAYNNNNRTG 1 cut(s) 39
SaqAI TTAA 3 cut(s) 264, 435, 522
Sau96I GGNCC 3 cut(s) 307, 317, 501
ScrFI CCNGG 1 cut(s) 123
SetI ASST 9 cut(s) 43, 181, 231, 235, 312, 322, 385, 434, 582
SinI GGWCC 3 cut(s) 307, 317, 501
SmiMI CAYNNNNRTG 1 cut(s) 39
SmlI CTYRAG 1 cut(s) 550
SmoI CTYRAG 1 cut(s) 550
Sse9I AATT 7 cut(s) 133, 265, 397, 518, 542, 560, 584
SsiI CCGC 1 cut(s) 195
StyD4I CCNGG 1 cut(s) 121
TaaI ACNGT 2 cut(s) 29, 221
TaiI ACGT 2 cut(s) 43, 385
TaqII GACCGA 1 cut(s) 518
TasI AATT 7 cut(s) 133, 265, 397, 518, 542, 560, 584
Tru1I TTAA 3 cut(s) 264, 435, 522
Tru9I TTAA 3 cut(s) 264, 435, 522
TseFI GTSAC 1 cut(s) 215
Tsp45I GTSAC 1 cut(s) 215
TspDTI ATGAA 4 cut(s) 51, 258, 462, 477
VpaK11BI GGWCC 3 cut(s) 307, 317, 501
XapI RAATTY 5 cut(s) 133, 397, 518, 542, 560
XceI RCATGY 2 cut(s) 72, 131
XcmI CCANNNNNNNNNTGG 1 cut(s) 387
XmiI GTMKAC 1 cut(s) 235
Zsp2I ATGCAT 2 cut(s) 303, 532
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.