RchiOBHm_Chr3g0488601

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
3
OG0000703
Physical Location & Seq
Reverse (-)
36249087 .. 36252990
3904 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ45293

Sequence Viewer

Length: 312 bp
ATGGAACACTCTCGAGATAGAGCTGCTGGTGGATCGGTCAATAGCCCTCCATGGTTTGATGGAGGCTGTGAGAAGTATACTCAACAGAAGATTTACATAAAATCATATCTTTATGCACAAGACGAACATGTGTGGAATATTGTTGAAAATGGCTGGAGGATACCTGTTGTTCAAGCTAAAGGTGAGAGTTCATCCACTACCACTCCTAAACCTAGGAAGGATTGGACTGATGAGGAAGTACGTGATCTTCAAGTTGACTTCAAGGCAAAGAATAGCATATTCACTGCTCTCTCTCTGAACGTGAAAAACTGA
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

103

Amino Acids

11.79

Weight (kDa)

6.72

Isoelectric Point (pI)

30.63

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this protein.
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)
AccI GTMKAC 1 cut(s) 77
AclWI GGATC 1 cut(s) 40
AfaI GTAC 1 cut(s) 240
AflIII ACRYGT 1 cut(s) 127
AgsI TTSAA 4 cut(s) 146, 173, 251, 262
AluBI AGCT 2 cut(s) 23, 176
AluI AGCT 2 cut(s) 23, 176
AlwI GGATC 1 cut(s) 40
Ama87I CYCGRG 1 cut(s) 12
ApeKI GCWGC 1 cut(s) 23
AspA2I CCTAGG 1 cut(s) 212
AsuHPI GGTGA 1 cut(s) 194
AvaI CYCGRG 1 cut(s) 12
AvrII CCTAGG 1 cut(s) 212
BarI GAAGNNNNNNTAC 2 cut(s) 231, 263
BbvI GCAGC 1 cut(s) 10
BccI CCATC 1 cut(s) 53
BciVI GTATCC 1 cut(s) 153
BfaI CTAG 1 cut(s) 213
BfuI GTATCC 1 cut(s) 153
BisI GCNGC 1 cut(s) 24
BlnI CCTAGG 1 cut(s) 212
BlsI GCNGC 1 cut(s) 25
BmeT110I CYCGRG 1 cut(s) 12
BpmI CTGGAG 1 cut(s) 175
BsaAI YACGTR 1 cut(s) 242
BsaJI CCNNGG 2 cut(s) 50, 212
BsaXI ACNNNNNCTCC 2 cut(s) 187, 217
BseDI CCNNGG 2 cut(s) 50, 212
BseGI GGATG 1 cut(s) 191
BseXI GCAGC 1 cut(s) 10
BsiHKCI CYCGRG 1 cut(s) 12
BsoBI CYCGRG 1 cut(s) 12
Bsp143I GATC 2 cut(s) 32, 244
Bsp19I CCATGG 1 cut(s) 50
BspPI GGATC 1 cut(s) 40
BssECI CCNNGG 2 cut(s) 50, 212
BssMI GATC 2 cut(s) 32, 244
BssNAI GTATAC 1 cut(s) 78
BssT1I CCWWGG 2 cut(s) 50, 212
Bst1107I GTATAC 1 cut(s) 78
BstBAI YACGTR 1 cut(s) 242
BstDSI CCRYGG 1 cut(s) 50
BstF5I GGATG 1 cut(s) 191
BstKTI GATC 2 cut(s) 35, 247
BstMBI GATC 2 cut(s) 32, 244
BstNSI RCATGY 1 cut(s) 131
BstV1I GCAGC 1 cut(s) 10
BstZ17I GTATAC 1 cut(s) 78
BsuI GTATCC 1 cut(s) 153
BtgI CCRYGG 1 cut(s) 50
BtsCI GGATG 1 cut(s) 191
BtsI GCAGTG 1 cut(s) 282
BtsIMutI CAGTG 1 cut(s) 282
Csp6I GTAC 1 cut(s) 239
CviAII CATG 2 cut(s) 51, 128
CviJI RGCY 5 cut(s) 23, 45, 66, 153, 176
CviKI_1 RGCY 5 cut(s) 23, 45, 66, 153, 176
CviQI GTAC 1 cut(s) 239
DpnI GATC 2 cut(s) 34, 246
DpnII GATC 2 cut(s) 32, 244
Eco130I CCWWGG 2 cut(s) 50, 212
Eco88I CYCGRG 1 cut(s) 12
EcoT14I CCWWGG 2 cut(s) 50, 212
ErhI CCWWGG 2 cut(s) 50, 212
FaeI CATG 2 cut(s) 54, 131
FaiI YATR 7 cut(s) 52, 78, 98, 106, 114, 129, 278
FatI CATG 2 cut(s) 50, 127
FblI GTMKAC 1 cut(s) 77
Fnu4HI GCNGC 1 cut(s) 24
FokI GGATG 1 cut(s) 178
Fsp4HI GCNGC 1 cut(s) 24
FspBI CTAG 1 cut(s) 213
GluI GCNGC 1 cut(s) 24
GsuI CTGGAG 1 cut(s) 175
Hin1II CATG 2 cut(s) 54, 131
HincII GTYRAC 1 cut(s) 256
HindII GTYRAC 1 cut(s) 256
HphI GGTGA 1 cut(s) 194
Hpy166II GTNNAC 2 cut(s) 78, 256
Hpy188I TCNGA 1 cut(s) 297
Hpy188III TCNNGA 2 cut(s) 12, 14
Hpy8I GTNNAC 2 cut(s) 78, 256
HpyAV CCTTC 1 cut(s) 211
HpyCH4IV ACGT 2 cut(s) 241, 300
HpyCH4V TGCA 1 cut(s) 116
HpySE526I ACGT 2 cut(s) 241, 300
Hsp92II CATG 2 cut(s) 54, 131
Kzo9I GATC 2 cut(s) 32, 244
LpnPI CCDG 3 cut(s) 12, 139, 177
Lsp1109I GCAGC 1 cut(s) 10
MaeI CTAG 1 cut(s) 213
MaeII ACGT 2 cut(s) 241, 300
MalI GATC 2 cut(s) 34, 246
MboI GATC 2 cut(s) 32, 244
MboII GAAGA 2 cut(s) 100, 239
MnlI CCTC 4 cut(s) 56, 57, 150, 226
NcoI CCATGG 1 cut(s) 50
NdeII GATC 2 cut(s) 32, 244
NlaIII CATG 2 cut(s) 54, 131
NspI RCATGY 1 cut(s) 131
PaeR7I CTCGAG 1 cut(s) 12
PciI ACATGT 1 cut(s) 127
PkrI GCNGC 1 cut(s) 25
Ppu21I YACGTR 1 cut(s) 242
PscI ACATGT 1 cut(s) 127
RsaI GTAC 1 cut(s) 240
RsaNI GTAC 1 cut(s) 239
SatI GCNGC 1 cut(s) 24
Sau3AI GATC 2 cut(s) 32, 244
SetI ASST 7 cut(s) 25, 166, 178, 184, 214, 244, 303
Sfr274I CTCGAG 1 cut(s) 12
SlaI CTCGAG 1 cut(s) 12
SmlI CTYRAG 1 cut(s) 12
SmoI CTYRAG 1 cut(s) 12
SspI AATATT 1 cut(s) 139
SspMI CTAG 1 cut(s) 213
StyI CCWWGG 2 cut(s) 50, 212
TaiI ACGT 2 cut(s) 244, 303
TaqI TCGA 1 cut(s) 13
TaqII GACCGA 1 cut(s) 25
TscAI CASTG 1 cut(s) 289
TseI GCWGC 1 cut(s) 23
TspDTI ATGAA 1 cut(s) 180
TspRI CASTG 1 cut(s) 289
XceI RCATGY 1 cut(s) 131
XhoI CTCGAG 1 cut(s) 12
XmaJI CCTAGG 1 cut(s) 212
XmiI GTMKAC 1 cut(s) 77
XspI CTAG 1 cut(s) 213
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.