RLG00000035900

Integrase core domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_laevigata
Chr7
OG0019676
Physical Location & Seq
Forward (+)
73190444 .. 73190960
517 bp
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UTR
Exon/CDS
Intron
RLM00000035900

Sequence Viewer

Length: 381 bp
ATGTTTGAGAAGTTTAAGCAATCTATGATGCATGAGTTTGAGATGACTGACCTAGGGAGGATGAGGTTTTTCCTTGGGGTTGAAGTTTTGCAAAATGAGGAGGGTATATATATTTGCCAGAACAAGTATGCTCGAGACATCTTAGAAAGGTTTGGAATGGCGAGTAGCAATCCTATTAAAAATCCCATTGTACCGGGGTTTAAATTGGTTAAAGATGAGAAGGGGGCCAAGGTTGATGCCACTGCCTTCAACCAGATAGTTGGGAGTCTGATATATTTAACGACAACTGGGCTGGATTTGATGTATGTTGTTAGCCTAATTAGCAAGTATATGGGAAATCCCACTGTGATGCATCTTGTAGCTGCAAAAATGGTACTTTGA
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

127

Amino Acids

14.29

Weight (kDa)

7.83

Isoelectric Point (pI)

32.67

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RVT_2 PF07727 1 - 64 1.7e-13 Reverse transcriptase (RNA-dependent DNA polymerase)
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Orthologous Genes (Group: OG0019676)

Species Orthologous Gene IDs
fragaria_vesca FvH4_2g40202
rosa_chinensis RchiOBHm_Chr1g0369901 RchiOBHm_Chr2g0121901
rosa_laevigata RLG00000035900
rosa_roxburghii Rroxscaffold_3G00244770 Rroxscaffold_5G00337010
rosa_wichuraiana Rw2G023390

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AfaI GTAC 2 cut(s) 192, 375
AgsI TTSAA 2 cut(s) 83, 250
AluBI AGCT 1 cut(s) 362
AluI AGCT 1 cut(s) 362
Alw26I GTCTC 1 cut(s) 129
Ama87I CYCGRG 1 cut(s) 132
AoxI GGCC 1 cut(s) 225
ApeKI GCWGC 1 cut(s) 362
AspA2I CCTAGG 1 cut(s) 52
AspS9I GGNCC 1 cut(s) 225
AsuC2I CCSGG 1 cut(s) 195
AvaI CYCGRG 1 cut(s) 132
AvrII CCTAGG 1 cut(s) 52
BbvI GCAGC 1 cut(s) 349
BcnI CCSGG 1 cut(s) 195
BcoDI GTCTC 1 cut(s) 129
BfaI CTAG 1 cut(s) 53
BisI GCNGC 1 cut(s) 363
BlnI CCTAGG 1 cut(s) 52
BlsI GCNGC 1 cut(s) 364
Bme1390I CCNGG 1 cut(s) 195
BmeT110I CYCGRG 1 cut(s) 132
BmgT120I GGNCC 1 cut(s) 225
BmiI GGNNCC 1 cut(s) 226
BmrFI CCNGG 1 cut(s) 195
BmrI ACTGGG 1 cut(s) 297
BmsI GCATC 4 cut(s) 18, 226, 339, 361
BmuI ACTGGG 1 cut(s) 297
BpuMI CCSGG 1 cut(s) 195
BsaJI CCNNGG 4 cut(s) 52, 73, 194, 228
Bse1I ACTGG 1 cut(s) 292
BseDI CCNNGG 4 cut(s) 52, 73, 194, 228
BseGI GGATG 1 cut(s) 66
BseNI ACTGG 1 cut(s) 292
BseRI GAGGAG 1 cut(s) 113
BseXI GCAGC 1 cut(s) 349
BshFI GGCC 1 cut(s) 227
BsiHKCI CYCGRG 1 cut(s) 132
BsiSI CCGG 1 cut(s) 194
BsmAI GTCTC 1 cut(s) 129
BsnI GGCC 1 cut(s) 227
BsoBI CYCGRG 1 cut(s) 132
BspANI GGCC 1 cut(s) 227
BspLI GGNNCC 1 cut(s) 226
BsrI ACTGG 1 cut(s) 292
BssECI CCNNGG 4 cut(s) 52, 73, 194, 228
BssT1I CCWWGG 3 cut(s) 52, 73, 228
Bst4CI ACNGT 1 cut(s) 346
BstDEI CTNAG 1 cut(s) 142
BstF5I GGATG 1 cut(s) 66
BstMAI GTCTC 1 cut(s) 129
BstMWI GCNNNNNNNGC 1 cut(s) 321
BstSCI CCNGG 1 cut(s) 193
BstV1I GCAGC 1 cut(s) 349
BstXI CCANNNNNNTGG 1 cut(s) 260
BsuRI GGCC 1 cut(s) 227
BtsCI GGATG 1 cut(s) 66
BtsI GCAGTG 1 cut(s) 240
BtsIMutI CAGTG 2 cut(s) 240, 342
Cfr13I GGNCC 1 cut(s) 225
Csp6I GTAC 2 cut(s) 191, 374
CviAII CATG 1 cut(s) 32
CviJI RGCY 4 cut(s) 227, 292, 315, 362
CviKI_1 RGCY 4 cut(s) 227, 292, 315, 362
CviQI GTAC 2 cut(s) 191, 374
DdeI CTNAG 1 cut(s) 142
DraI TTTAAA 1 cut(s) 202
Eco130I CCWWGG 3 cut(s) 52, 73, 228
Eco88I CYCGRG 1 cut(s) 132
EcoT14I CCWWGG 3 cut(s) 52, 73, 228
EcoT22I ATGCAT 2 cut(s) 33, 354
ErhI CCWWGG 3 cut(s) 52, 73, 228
FaeI CATG 1 cut(s) 35
FatI CATG 1 cut(s) 31
Fnu4HI GCNGC 1 cut(s) 363
FokI GGATG 1 cut(s) 73
Fsp4HI GCNGC 1 cut(s) 363
FspBI CTAG 1 cut(s) 53
GluI GCNGC 1 cut(s) 363
HaeIII GGCC 1 cut(s) 227
HapII CCGG 1 cut(s) 194
Hin1II CATG 1 cut(s) 35
HinfI GANTC 1 cut(s) 265
HpaII CCGG 1 cut(s) 194
Hpy188I TCNGA 1 cut(s) 270
Hpy188III TCNNGA 1 cut(s) 134
HpyAV CCTTC 2 cut(s) 214, 256
HpyCH4III ACNGT 1 cut(s) 346
HpyCH4V TGCA 4 cut(s) 31, 91, 352, 365
HpyF10VI GCNNNNNNNGC 1 cut(s) 321
HpyF3I CTNAG 1 cut(s) 142
Hsp92II CATG 1 cut(s) 35
LpnPI CCDG 5 cut(s) 131, 207, 266, 273, 278
Lsp1109I GCAGC 1 cut(s) 349
LweI GCATC 4 cut(s) 18, 226, 339, 361
MaeI CTAG 1 cut(s) 53
MluCI AATT 2 cut(s) 203, 318
MlyI GAGTC 1 cut(s) 274
MnlI CCTC 4 cut(s) 51, 57, 91, 94
Mph1103I ATGCAT 2 cut(s) 33, 354
MseI TTAA 5 cut(s) 15, 177, 201, 210, 278
MslI CAYNNNNRTG 1 cut(s) 347
MspI CCGG 1 cut(s) 194
MspR9I CCNGG 1 cut(s) 195
MwoI GCNNNNNNNGC 1 cut(s) 321
NciI CCSGG 1 cut(s) 195
NlaIII CATG 1 cut(s) 35
NlaIV GGNNCC 1 cut(s) 226
NsiI ATGCAT 2 cut(s) 33, 354
PaeR7I CTCGAG 1 cut(s) 132
PkrI GCNGC 1 cut(s) 364
PleI GAGTC 1 cut(s) 273
PpsI GAGTC 1 cut(s) 273
PspN4I GGNNCC 1 cut(s) 226
PspPI GGNCC 1 cut(s) 225
RsaI GTAC 2 cut(s) 192, 375
RsaNI GTAC 2 cut(s) 191, 374
RseI CAYNNNNRTG 1 cut(s) 347
SaqAI TTAA 5 cut(s) 15, 177, 201, 210, 278
SatI GCNGC 1 cut(s) 363
Sau96I GGNCC 1 cut(s) 225
SchI GAGTC 1 cut(s) 274
ScrFI CCNGG 1 cut(s) 195
SetI ASST 5 cut(s) 54, 68, 152, 234, 364
SfaNI GCATC 4 cut(s) 18, 226, 339, 361
Sfr274I CTCGAG 1 cut(s) 132
SlaI CTCGAG 1 cut(s) 132
SmiMI CAYNNNNRTG 1 cut(s) 347
SmlI CTYRAG 1 cut(s) 132
SmoI CTYRAG 1 cut(s) 132
Sse9I AATT 2 cut(s) 203, 318
SspMI CTAG 1 cut(s) 53
StyD4I CCNGG 1 cut(s) 193
StyI CCWWGG 3 cut(s) 52, 73, 228
TaaI ACNGT 1 cut(s) 346
TaqI TCGA 1 cut(s) 133
TasI AATT 2 cut(s) 203, 318
Tru1I TTAA 5 cut(s) 15, 177, 201, 210, 278
Tru9I TTAA 5 cut(s) 15, 177, 201, 210, 278
TscAI CASTG 2 cut(s) 247, 349
TseI GCWGC 1 cut(s) 362
TspRI CASTG 2 cut(s) 247, 349
XhoI CTCGAG 1 cut(s) 132
XmaJI CCTAGG 1 cut(s) 52
XspI CTAG 1 cut(s) 53
Zsp2I ATGCAT 2 cut(s) 33, 354
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.