Rw1G014600

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr1
OG0018346
Physical Location & Seq
Reverse (-)
32638707 .. 32639060
354 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw1G014600.1

Sequence Viewer

Length: 354 bp
ATGGAATCATCGGAATCACCTTATTGGAAAGAGGCTATTCAAAGTGAAGTGGAATCCATTATACAAAATAATACTTGGACATTGGTTGATTTGCCTCCTGGACATAAACCAATAGGCCATAAATGGATTTTTAAAAGAAAGATGAGACCTGATGGTACCATAGAAAAATACAAAGCTCGTATAGTAGCTAAAAGGTATCATCAAAAAGAAGGTGTAGATTTTTTTGACACTTATTCGCCGGTGACAAGAATTACATCAATACGAACTTTAATTGCTATAGCTGCTGTACACATGCAATTTGGAAATACATCAAATGGATGTGAAAACCGCATTTCTAAATGGCGAACTAGATGA
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
Retrotran_gag_2

Protein Analysis

117

Amino Acids

13.65

Weight (kDa)

9.76

Isoelectric Point (pI)

37.17

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RVT_2 PF07727 23 - 97 1.8e-21 Reverse transcriptase (RNA-dependent DNA polymerase)
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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Orthologous Genes (Group: OG0018346)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g09832
malus_domestica MD17G1125600.v1.1
pyrus_communis pycom07g08290 pycom08g03650 pycom10g05700 pycom13g21050 pycom17g16760
rosa_wichuraiana Rw1G014600 Rw4G005310 Rw4G016610

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc65I GGTACC 1 cut(s) 155
AccB1I GGYRCC 1 cut(s) 155
AciI CCGC 1 cut(s) 328
AfaI GTAC 2 cut(s) 157, 288
AgsI TTSAA 1 cut(s) 41
AjnI CCWGG 1 cut(s) 97
AluBI AGCT 3 cut(s) 176, 188, 281
AluI AGCT 3 cut(s) 176, 188, 281
Alw26I GTCTC 1 cut(s) 139
AoxI GGCC 1 cut(s) 115
ApeKI GCWGC 1 cut(s) 281
Asp718I GGTACC 1 cut(s) 155
AsuHPI GGTGA 2 cut(s) 9, 253
BanI GGYRCC 1 cut(s) 155
BbvI GCAGC 1 cut(s) 268
BccI CCATC 1 cut(s) 146
BciT130I CCWGG 1 cut(s) 99
BcoDI GTCTC 1 cut(s) 139
BfaI CTAG 1 cut(s) 348
BfmI CTRYAG 1 cut(s) 276
BisI GCNGC 1 cut(s) 282
BlsI GCNGC 1 cut(s) 283
Bme1390I CCNGG 1 cut(s) 99
BmiI GGNNCC 1 cut(s) 157
BmrFI CCNGG 1 cut(s) 99
BsaI GGTCTC 1 cut(s) 139
Bse118I RCCGGY 1 cut(s) 238
BseBI CCWGG 1 cut(s) 99
BseGI GGATG 1 cut(s) 323
BseXI GCAGC 1 cut(s) 268
BshFI GGCC 1 cut(s) 117
BshNI GGYRCC 1 cut(s) 155
BsiSI CCGG 1 cut(s) 239
BsmAI GTCTC 1 cut(s) 139
BsnI GGCC 1 cut(s) 117
Bso31I GGTCTC 1 cut(s) 139
Bsp1407I TGTACA 1 cut(s) 286
BspACI CCGC 1 cut(s) 328
BspANI GGCC 1 cut(s) 117
BspLI GGNNCC 1 cut(s) 157
BspT107I GGYRCC 1 cut(s) 155
BspTNI GGTCTC 1 cut(s) 139
BsrFI RCCGGY 1 cut(s) 238
BsrGI TGTACA 1 cut(s) 286
BssAI RCCGGY 1 cut(s) 238
Bst2UI CCWGG 1 cut(s) 99
BstAUI TGTACA 1 cut(s) 286
BstF5I GGATG 1 cut(s) 323
BstMAI GTCTC 1 cut(s) 139
BstMWI GCNNNNNNNGC 1 cut(s) 281
BstNI CCWGG 1 cut(s) 99
BstNSI RCATGY 1 cut(s) 295
BstSCI CCNGG 1 cut(s) 97
BstSFI CTRYAG 1 cut(s) 276
BstV1I GCAGC 1 cut(s) 268
BsuRI GGCC 1 cut(s) 117
BtsCI GGATG 1 cut(s) 323
Cfr10I RCCGGY 1 cut(s) 238
Csp6I GTAC 2 cut(s) 156, 287
CviAII CATG 1 cut(s) 292
CviJI RGCY 5 cut(s) 35, 117, 176, 188, 281
CviKI_1 RGCY 5 cut(s) 35, 117, 176, 188, 281
CviQI GTAC 2 cut(s) 156, 287
DraI TTTAAA 1 cut(s) 133
Eco31I GGTCTC 1 cut(s) 139
EcoRII CCWGG 1 cut(s) 97
FaeI CATG 1 cut(s) 295
FaiI YATR 7 cut(s) 62, 105, 120, 161, 182, 278, 293
FatI CATG 1 cut(s) 291
Fnu4HI GCNGC 1 cut(s) 282
FokI GGATG 1 cut(s) 330
Fsp4HI GCNGC 1 cut(s) 282
FspBI CTAG 1 cut(s) 348
GluI GCNGC 1 cut(s) 282
HaeIII GGCC 1 cut(s) 117
HapII CCGG 1 cut(s) 239
Hin1II CATG 1 cut(s) 295
HinfI GANTC 3 cut(s) 5, 14, 53
HpaII CCGG 1 cut(s) 239
HphI GGTGA 2 cut(s) 9, 253
Hpy166II GTNNAC 1 cut(s) 289
Hpy188I TCNGA 1 cut(s) 13
Hpy8I GTNNAC 1 cut(s) 289
HpyAV CCTTC 1 cut(s) 203
HpyCH4V TGCA 1 cut(s) 295
HpyF10VI GCNNNNNNNGC 1 cut(s) 281
Hsp92II CATG 1 cut(s) 295
KpnI GGTACC 1 cut(s) 159
LpnPI CCDG 4 cut(s) 84, 111, 162, 252
Lsp1109I GCAGC 1 cut(s) 268
MaeI CTAG 1 cut(s) 348
MaeIII GTNAC 1 cut(s) 241
MluCI AATT 3 cut(s) 249, 270, 296
MnlI CCTC 2 cut(s) 25, 105
MseI TTAA 2 cut(s) 132, 269
MspI CCGG 1 cut(s) 239
MspR9I CCNGG 1 cut(s) 99
MvaI CCWGG 1 cut(s) 99
MwoI GCNNNNNNNGC 1 cut(s) 281
NlaIII CATG 1 cut(s) 295
NlaIV GGNNCC 1 cut(s) 157
NmuCI GTSAC 1 cut(s) 241
NspI RCATGY 1 cut(s) 295
PfeI GAWTC 3 cut(s) 5, 14, 53
PfoI TCCNGGA 1 cut(s) 97
PkrI GCNGC 1 cut(s) 283
Psp6I CCWGG 1 cut(s) 97
PspGI CCWGG 1 cut(s) 97
PspN4I GGNNCC 1 cut(s) 157
RsaI GTAC 2 cut(s) 157, 288
RsaNI GTAC 2 cut(s) 156, 287
SaqAI TTAA 2 cut(s) 132, 269
SatI GCNGC 1 cut(s) 282
ScrFI CCNGG 1 cut(s) 99
SetI ASST 7 cut(s) 22, 151, 178, 190, 197, 214, 283
SfcI CTRYAG 1 cut(s) 276
SgeI CNNG 8 cut(s) 87, 110, 111, 161, 189, 251, 258, 304
SgrAI CRCCGGYG 1 cut(s) 238
Sse9I AATT 3 cut(s) 249, 270, 296
SsiI CCGC 1 cut(s) 328
SspMI CTAG 1 cut(s) 348
StyD4I CCNGG 1 cut(s) 97
TasI AATT 3 cut(s) 249, 270, 296
TatI WGTACW 1 cut(s) 286
TfiI GAWTC 3 cut(s) 5, 14, 53
Tru1I TTAA 2 cut(s) 132, 269
Tru9I TTAA 2 cut(s) 132, 269
TseFI GTSAC 1 cut(s) 241
TseI GCWGC 1 cut(s) 281
Tsp45I GTSAC 1 cut(s) 241
XceI RCATGY 1 cut(s) 295
XspI CTAG 1 cut(s) 348
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.