FvH4_1g29481

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb1
OG0000370
Physical Location & Seq
Forward (+)
22612839 .. 22621304
8466 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_1g29481.t1

Sequence Viewer

Length: 477 bp
ATGAAGGCGCTTATGGGAGCAATTTGGGTGATTCGTAGCGAGACCGGTGGAGACGCTGGTTGTCGTGGACGGTGGCACTTCACTGTTGCAGTTCAGGCGCGGTGGCTGAGGAGTGGTGGAGATGGCATTGAGCAGGAGGAGGCCATGCATGAGGCTGAGGGACTAAGAGATGTGCATGGGAAGGGGAAGGCCGTTGCAGGAGGCAGTGGCGCTGAGGGTCTTGATGGTGCGTCTGGGAAGAGGCAGCAGACCGATCAGCAGGCTCTAGCTACTGTGCCAGCTGCACCTATCCGACAGGTAGAGCCCTTGAGATGCTACCGTTGCGATGGGTTAGGACATATTGCTAGGGAGTGCCACAAGCGAAAGACTCAGGCTTGCTATAGATGTGGGCAGGTGGGGCACCTGGCTAGGGAGTGTACTCGACCTCAGGAGGACAGACAGGGGTACCAGCAGAGGCAGTTGCCTCCAACCCAGTAG
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
RVP_2 Retrotrans_gag zf-CCHC

Protein Analysis

159

Amino Acids

17.27

Weight (kDa)

8.94

Isoelectric Point (pI)

73.15

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
zf-CCHC PF00098 125 - 140 8.3e-08 Zinc knuckle
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000370)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g29481 FvH4_2g11454 FvH4_3g19661 FvH4_3g28463 FvH4_3g31691 FvH4_3g34551 FvH4_3g35241 FvH4_4g06575 FvH4_4g09082 FvH4_4g15804 FvH4_4g15805 FvH4_4g16178 FvH4_4g16282 FvH4_5g25163 FvH4_6g27413 FvH4_7g02962 FvH4_7g04361
malus_domestica MD01G1095000.v1.1 MD02G1270200.v1.1 MD02G1270300.v1.1 MD02G1270400.v1.1 MD06G1059100.v1.1 MD08G1226500.v1.1
prunus_persica Prupe.1G169500_v2.0.a1 Prupe.5G195800_v2.0.a1
pyrus_communis pycom01g00010 pycom01g00770 pycom02g23140 pycom03g11760 pycom04g06090 pycom05g06900 pycom05g08070 pycom05g14500 pycom06g03050 pycom07g06250 pycom07g07540 pycom07g10580 pycom08g04990 pycom1146g00060 pycom11g01080 pycom11g15270 pycom11g15460 pycom11g24900 pycom12419g00150 pycom12424g00120 pycom13g08740 pycom13g24950 pycom13g25960 pycom13g26030 pycom13g27820 pycom16g23270 pycom16g25020 pycom16g25960 pycom17g07780 pycom17g08210 pycom17g13100
rosa_chinensis RchiOBHm_Chr1g0329421 RchiOBHm_Chr4g0397711 RchiOBHm_Chr4g0403481 RchiOBHm_Chr5g0019091 RchiOBHm_Chr5g0049101
rosa_laevigata RLG00000029892
rosa_multiflora Rmu_sc0001866.1_g000007
rosa_roxburghii Rroxscaffold_2G00094160 Rroxscaffold_3G00229110 Rroxscaffold_4G00321100 Rroxscaffold_7G00196040 Rroxscaffold_7G00196280
rosa_rugosa Rorug05G0160500 Rorug06G0096500
rosa_samantha Rh1AG098600 Rh1AG098800 Rh1BG078200 Rh1BG078700 Rh1BG178500 Rh1CG094600 Rh1CG094900 Rh1DG101700 Rh1DG109600 Rh2AG175800 Rh2AG175900 Rh2AG511400 Rh2BG114700 Rh2CG042200 Rh2CG116600 Rh2CG317500 Rh2DG327700 Rh2DG337800 Rh4CG142700 Rh4DG113100 Rh5BG335800 Rh5CG360600 Rh5DG352000 Rh6BG071400 Rh6BG417100 Rh6CG463300 Rh6CG463400 Rh7BG186600 Rh7CG196500 Rh7CG196600 Rh7CG448900 Rh7DG228300
rosa_wichuraiana Rw4G006560 Rw4G017340 Rw5G030450

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AarI CACCTGC 1 cut(s) 382
Acc36I ACCTGC 1 cut(s) 382
Acc65I GGTACC 1 cut(s) 444
AccB1I GGYRCC 2 cut(s) 399, 444
AccII CGCG 1 cut(s) 100
AciI CCGC 1 cut(s) 100
AfaI GTAC 2 cut(s) 418, 446
AfiI CCNNNNNNNGG 1 cut(s) 409
AgeI ACCGGT 1 cut(s) 44
AjnI CCWGG 1 cut(s) 402
AluBI AGCT 2 cut(s) 269, 281
AluI AGCT 2 cut(s) 269, 281
Alw26I GTCTC 2 cut(s) 35, 45
AoxI GGCC 2 cut(s) 141, 189
ApeKI GCWGC 2 cut(s) 244, 281
AsiGI ACCGGT 1 cut(s) 44
Asp718I GGTACC 1 cut(s) 444
AspLEI GCGC 3 cut(s) 10, 100, 212
AsuHPI GGTGA 1 cut(s) 40
AxyI CCTNAGG 1 cut(s) 426
BaeGI GKGCMC 1 cut(s) 402
BaeI ACNNNNGTAYC 2 cut(s) 428, 461
BanI GGYRCC 2 cut(s) 399, 444
BanII GRGCYC 1 cut(s) 306
BbvCI CCTCAGC 3 cut(s) 107, 156, 213
BbvI GCAGC 2 cut(s) 256, 268
BccI CCATC 3 cut(s) 116, 218, 320
BceAI ACGGC 1 cut(s) 176
BciT130I CCWGG 1 cut(s) 404
BcoDI GTCTC 2 cut(s) 35, 45
BfaI CTAG 3 cut(s) 266, 345, 408
BfmI CTRYAG 1 cut(s) 379
BfoI RGCGCY 2 cut(s) 11, 213
BfuAI ACCTGC 1 cut(s) 382
BisI GCNGC 2 cut(s) 245, 282
BlsI GCNGC 2 cut(s) 246, 283
Bme1390I CCNGG 1 cut(s) 404
BmiI GGNNCC 2 cut(s) 401, 446
BmrFI CCNGG 1 cut(s) 404
BmrI ACTGGG 1 cut(s) 466
BmsI GCATC 1 cut(s) 302
BmuI ACTGGG 1 cut(s) 466
Bpu10I CCTNAGC 3 cut(s) 107, 156, 213
BpuEI CTTGAG 1 cut(s) 328
BsaI GGTCTC 1 cut(s) 35
BsaWI WCCGGW 1 cut(s) 44
Bsc4I CCNNNNNNNGG 1 cut(s) 409
Bse118I RCCGGY 1 cut(s) 44
Bse1I ACTGG 1 cut(s) 472
Bse21I CCTNAGG 1 cut(s) 426
BseBI CCWGG 1 cut(s) 404
BseLI CCNNNNNNNGG 1 cut(s) 409
BseMII CTCAG 5 cut(s) 98, 147, 204, 383, 440
BseNI ACTGG 1 cut(s) 472
BseRI GAGGAG 2 cut(s) 124, 152
BseSI GKGCMC 1 cut(s) 402
BseXI GCAGC 2 cut(s) 256, 268
BsgI GTGCAG 1 cut(s) 267
Bsh1236I CGCG 1 cut(s) 100
BshFI GGCC 2 cut(s) 143, 191
BshNI GGYRCC 2 cut(s) 399, 444
BshTI ACCGGT 1 cut(s) 44
BsiSI CCGG 1 cut(s) 45
BslFI GGGAC 1 cut(s) 174
BslI CCNNNNNNNGG 1 cut(s) 409
BsmAI GTCTC 2 cut(s) 35, 45
BsmBI CGTCTC 1 cut(s) 45
BsmFI GGGAC 1 cut(s) 174
BsnI GGCC 2 cut(s) 143, 191
Bso31I GGTCTC 1 cut(s) 35
Bsp1286I GDGCHC 2 cut(s) 306, 402
Bsp143I GATC 1 cut(s) 253
BspACI CCGC 1 cut(s) 100
BspANI GGCC 2 cut(s) 143, 191
BspCNI CTCAG 5 cut(s) 99, 148, 205, 382, 439
BspFNI CGCG 1 cut(s) 100
BspLI GGNNCC 2 cut(s) 401, 446
BspMI ACCTGC 1 cut(s) 382
BspT107I GGYRCC 2 cut(s) 399, 444
BspTNI GGTCTC 1 cut(s) 35
BsrFI RCCGGY 1 cut(s) 44
BsrI ACTGG 1 cut(s) 472
BssAI RCCGGY 1 cut(s) 44
BssMI GATC 1 cut(s) 253
Bst2UI CCWGG 1 cut(s) 404
Bst4CI ACNGT 4 cut(s) 72, 85, 274, 320
Bst6I CTCTTC 1 cut(s) 233
BstC8I GCNNGC 3 cut(s) 261, 279, 376
BstDEI CTNAG 6 cut(s) 107, 156, 164, 213, 369, 426
BstFNI CGCG 1 cut(s) 100
BstH2I RGCGCY 2 cut(s) 11, 213
BstHHI GCGC 3 cut(s) 10, 100, 212
BstKTI GATC 1 cut(s) 256
BstMAI GTCTC 2 cut(s) 35, 45
BstMBI GATC 1 cut(s) 253
BstMWI GCNNNNNNNGC 3 cut(s) 95, 321, 397
BstNI CCWGG 1 cut(s) 404
BstSCI CCNGG 1 cut(s) 402
BstSFI CTRYAG 1 cut(s) 379
BstSLI GKGCMC 1 cut(s) 402
BstUI CGCG 1 cut(s) 100
BstV1I GCAGC 2 cut(s) 256, 268
Bsu36I CCTNAGG 1 cut(s) 426
BsuRI GGCC 2 cut(s) 143, 191
BtgZI GCGATG 1 cut(s) 339
BtsI GCAGTG 1 cut(s) 211
BtsIMutI CAGTG 2 cut(s) 81, 211
BveI ACCTGC 1 cut(s) 382
Cac8I GCNNGC 3 cut(s) 261, 279, 376
CfoI GCGC 3 cut(s) 10, 100, 212
Cfr10I RCCGGY 1 cut(s) 44
CseI GACGC 2 cut(s) 62, 219
Csp6I GTAC 2 cut(s) 417, 445
CspAI ACCGGT 1 cut(s) 44
CviAII CATG 3 cut(s) 145, 149, 176
CviQI GTAC 2 cut(s) 417, 445
DdeI CTNAG 6 cut(s) 107, 156, 164, 213, 369, 426
DpnI GATC 1 cut(s) 255
DpnII GATC 1 cut(s) 253
Eam1104I CTCTTC 1 cut(s) 233
EarI CTCTTC 1 cut(s) 233
Eco24I GRGCYC 1 cut(s) 306
Eco31I GGTCTC 1 cut(s) 35
Eco81I CCTNAGG 1 cut(s) 426
EcoRII CCWGG 1 cut(s) 402
EcoT22I ATGCAT 1 cut(s) 150
EcoT38I GRGCYC 1 cut(s) 306
Esp3I CGTCTC 1 cut(s) 45
FaeI CATG 3 cut(s) 148, 152, 179
FaiI YATR 6 cut(s) 14, 146, 150, 177, 339, 381
FaqI GGGAC 1 cut(s) 174
FatI CATG 3 cut(s) 144, 148, 175
Fnu4HI GCNGC 2 cut(s) 245, 282
FriOI GRGCYC 1 cut(s) 306
Fsp4HI GCNGC 2 cut(s) 245, 282
FspBI CTAG 3 cut(s) 266, 345, 408
GlaI GCGC 3 cut(s) 9, 99, 211
GluI GCNGC 2 cut(s) 245, 282
HaeII RGCGCY 2 cut(s) 11, 213
HaeIII GGCC 2 cut(s) 143, 191
HapII CCGG 1 cut(s) 45
HgaI GACGC 2 cut(s) 62, 219
HhaI GCGC 3 cut(s) 10, 100, 212
Hin1II CATG 3 cut(s) 148, 152, 179
Hin6I GCGC 3 cut(s) 8, 98, 210
HinP1I GCGC 3 cut(s) 8, 98, 210
HinfI GANTC 2 cut(s) 31, 367
HpaII CCGG 1 cut(s) 45
HphI GGTGA 1 cut(s) 40
Hpy166II GTNNAC 2 cut(s) 68, 417
Hpy188I TCNGA 1 cut(s) 293
Hpy188III TCNNGA 2 cut(s) 221, 428
Hpy8I GTNNAC 2 cut(s) 68, 417
HpyAV CCTTC 2 cut(s) 175, 181
HpyCH4III ACNGT 4 cut(s) 72, 85, 274, 320
HpyCH4V TGCA 5 cut(s) 89, 148, 175, 197, 284
HpyF10VI GCNNNNNNNGC 3 cut(s) 95, 321, 397
HpyF3I CTNAG 6 cut(s) 107, 156, 164, 213, 369, 426
Hsp92II CATG 3 cut(s) 148, 152, 179
HspAI GCGC 3 cut(s) 8, 98, 210
KpnI GGTACC 1 cut(s) 448
Kzo9I GATC 1 cut(s) 253
LmnI GCTCC 1 cut(s) 17
Lsp1109I GCAGC 2 cut(s) 256, 268
LweI GCATC 1 cut(s) 302
MaeI CTAG 3 cut(s) 266, 345, 408
MalI GATC 1 cut(s) 255
MboI GATC 1 cut(s) 253
MboII GAAGA 1 cut(s) 250
MhlI GDGCHC 2 cut(s) 306, 402
MluCI AATT 1 cut(s) 21
MlyI GAGTC 1 cut(s) 361
MmeI TCCRAC 1 cut(s) 316
Mph1103I ATGCAT 1 cut(s) 150
MspA1I CMGCKG 1 cut(s) 281
MspI CCGG 1 cut(s) 45
MspR9I CCNGG 1 cut(s) 404
MvaI CCWGG 1 cut(s) 404
MvnI CGCG 1 cut(s) 100
MwoI GCNNNNNNNGC 3 cut(s) 95, 321, 397
NdeII GATC 1 cut(s) 253
NlaIII CATG 3 cut(s) 148, 152, 179
NlaIV GGNNCC 2 cut(s) 401, 446
NsiI ATGCAT 1 cut(s) 150
PaqCI CACCTGC 1 cut(s) 382
PfeI GAWTC 1 cut(s) 31
PinAI ACCGGT 1 cut(s) 44
PkrI GCNGC 2 cut(s) 246, 283
PleI GAGTC 1 cut(s) 361
PpsI GAGTC 1 cut(s) 361
Psp6I CCWGG 1 cut(s) 402
PspGI CCWGG 1 cut(s) 402
PspN4I GGNNCC 2 cut(s) 401, 446
PvuII CAGCTG 1 cut(s) 281
RsaI GTAC 2 cut(s) 418, 446
RsaNI GTAC 2 cut(s) 417, 445
SatI GCNGC 2 cut(s) 245, 282
Sau3AI GATC 1 cut(s) 253
SchI GAGTC 1 cut(s) 361
ScrFI CCNGG 1 cut(s) 404
SduI GDGCHC 2 cut(s) 306, 402
SetI ASST 7 cut(s) 271, 283, 289, 300, 396, 405, 427
SfaNI GCATC 1 cut(s) 302
SfcI CTRYAG 1 cut(s) 379
SmlI CTYRAG 1 cut(s) 307
SmoI CTYRAG 1 cut(s) 307
Sse9I AATT 1 cut(s) 21
SsiI CCGC 1 cut(s) 100
SspMI CTAG 3 cut(s) 266, 345, 408
StyD4I CCNGG 1 cut(s) 402
TaaI ACNGT 4 cut(s) 72, 85, 274, 320
TaqI TCGA 1 cut(s) 421
TaqII GACCGA 1 cut(s) 266
TasI AATT 1 cut(s) 21
TatI WGTACW 1 cut(s) 416
TfiI GAWTC 1 cut(s) 31
TscAI CASTG 2 cut(s) 88, 211
TseI GCWGC 2 cut(s) 244, 281
TspDTI ATGAA 1 cut(s) 17
TspRI CASTG 2 cut(s) 88, 211
XspI CTAG 3 cut(s) 266, 345, 408
Zsp2I ATGCAT 1 cut(s) 150
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.