FvH4_3g20503

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0000278
Physical Location & Seq
Reverse (-)
13576583 .. 13577314
732 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_3g20503.t1

Sequence Viewer

Length: 732 bp
ATGGCGGAGCCATCGTCATCGTCAGCAACAATGGTGAAGTTGACATCGTCAAATTACTCCATTTGGAAGCCCAGAATGGAAGACATCCTTTACTGCAAGGATATGTACAAGCCTCTTCAAAATGGTGGAGAGAAGCCAGCAGGCAAGTCCGACATGGAATGGAGCATCCTGAACAGAAAAGCTGTTGCAGGAATTCGTCAATGGGTTGATGAAAGTGTTTTTCATCATGTTGCACAAGAAACCAATGCCTACTTGATGTGGACCAAGTTGGAGTCCATGTACGAGCGCAAGACCGCACAAAACAAAGCCTCGTTCATTCGGCGGTTGGTGAACACGAAGTACAGGGATGGTCGAAGTGTTTCAGAACACTTGAGTGACTTCCAAGGCATGGTGAATCAGTTGACGAATATGAAGATGGTGCTTGATGATGAGTTGCAAGCATTGTTGTTACTAAGCTCGTTGCCAGACAGCTGGGACACGTTGGTGGTGTCATTAAGCAACTCAGCTCCTCAAGGCATTCTCACACTGAACACTGTAAAAGATAGCATGTTTAATGAAGAAGAAAGGATGAAGGAGCAAGGAATATCGACCGAGTCGGAAGCCCTCGTCACCGATAATCGTGAAAGCAATCGAAAGTTCCACAACCGAGGCAAAGCAAAGGACCGGTCAAGGGGCAATCCAGCCCAAAGAAGAACATCAGATGTTATCATTGTGGCAATAAAGGTCACATGA
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 zf-CCHC

Protein Analysis

244

Amino Acids

27.67

Weight (kDa)

8.85

Isoelectric Point (pI)

37.81

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 27 - 193 5.5e-36 gag-polypeptide of LTR copia-type
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: OG0000278)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G29785
fragaria_vesca FvH4_1g10046 FvH4_1g17351 FvH4_1g18441 FvH4_1g24222 FvH4_2g00141 FvH4_2g05931 FvH4_2g06671 FvH4_2g14030 FvH4_2g15291 FvH4_2g22611 FvH4_2g22612 FvH4_2g26380 FvH4_2g39202 FvH4_2g39202 FvH4_3g06691 FvH4_3g08580 FvH4_3g20502 FvH4_3g20503 FvH4_3g22421 FvH4_3g42580 FvH4_4g02061 FvH4_4g06794 FvH4_4g08661 FvH4_4g11771 FvH4_4g14601 FvH4_4g14721 FvH4_4g20921 FvH4_4g33601 FvH4_4g33602 FvH4_5g07492 FvH4_5g20321 FvH4_5g21591 FvH4_5g30343 FvH4_5g37875 FvH4_6g04372 FvH4_6g04373 FvH4_6g04373 FvH4_6g21377 FvH4_6g23760 FvH4_6g29471 FvH4_6g43142 FvH4_7g14351 FvH4_7g14352 FvH4_7g22582 FvH4_7g22583 FvH4_7g22584
malus_domestica MD00G1179400.v1.1 MD01G1170500.v1.1 MD03G1286700.v1.1 MD04G1054600.v1.1 MD04G1071700.v1.1 MD04G1193900.v1.1 MD08G1054300.v1.1 MD08G1217500.v1.1 MD09G1034600.v1.1 MD09G1098100.v1.1 MD10G1018300.v1.1 MD10G1220000.v1.1 MD10G1250300.v1.1 MD12G1014400.v1.1 MD15G1021000.v1.1 MD16G1112200.v1.1
prunus_persica Prupe.1G188900_v2.0.a1 Prupe.1G258000_v2.0.a1 Prupe.4G233400_v2.0.a1
pyrus_communis pycom01g10100 pycom02g01340 pycom03g19700 pycom05g01320 pycom07g16000 pycom07g16520 pycom11g26500 pycom13g09380 pycom13g13960 pycom14g08180 pycom14g16810 pycom16g09590
rosa_chinensis RchiOBHm_Chr1g0319891 RchiOBHm_Chr1g0333711 RchiOBHm_Chr2g0115331 RchiOBHm_Chr2g0143411 RchiOBHm_Chr2g0167631 RchiOBHm_Chr3g0448581 RchiOBHm_Chr3g0494991 RchiOBHm_Chr4g0442471 RchiOBHm_Chr6g0262311 RchiOBHm_Chr6g0301831 RchiOBHm_Chr6g0301841 RchiOBHm_Chr7g0183451
rosa_roxburghii Rroxscaffold_1G00039280 Rroxscaffold_1G00047670 Rroxscaffold_1G00066330 Rroxscaffold_2G00107510 Rroxscaffold_3G00255410 Rroxscaffold_4G00301460 Rroxscaffold_5G00352730 Rroxscaffold_7G00166350 Rroxscaffold_7G00166360 Rroxscaffold_7G00203820
rosa_rugosa Rorug03G0240500 Rorug05G0191700 Rorug06G0310200
rosa_samantha Rh2BG287000 Rh4CG073500 Rh4CG176200 Rh4CG191400 Rh5BG356100 Rh5BG434100 Rh6AG110600 Rh6AG421900 Rh6AG422000 Rh6AG422100 Rh6BG428600 Rh6BG428700 Rh6BG428800 Rh6CG435200 Rh6CG435300 Rh6CG435400 Rh6DG422000 Rh6DG422100 Rh6DG422200 Rh7BG190500 Rh7CG172800 Rh7CG225200
rosa_wichuraiana Rw2G044060 Rw6G036540

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB7I CCANNNNNTGG 1 cut(s) 388
AciI CCGC 3 cut(s) 5, 294, 322
AcsI RAATTY 1 cut(s) 192
AfaI GTAC 3 cut(s) 107, 281, 341
AfiI CCNNNNNNNGG 2 cut(s) 388, 670
AflIII ACRYGT 1 cut(s) 477
AgeI ACCGGT 1 cut(s) 663
AgsI TTSAA 1 cut(s) 119
AleI CACNNNNGTG 2 cut(s) 372, 482
AluBI AGCT 4 cut(s) 182, 456, 471, 506
AluI AGCT 4 cut(s) 182, 456, 471, 506
ApoI RAATTY 1 cut(s) 192
ArsI GACNNNNNNTTYG 2 cut(s) 650, 682
AsiGI ACCGGT 1 cut(s) 663
Asp700I GAANNNNTTC 1 cut(s) 358
AspLEI GCGC 1 cut(s) 288
AspS9I GGNCC 2 cut(s) 261, 661
AsuHPI GGTGA 4 cut(s) 46, 340, 403, 601
AvaII GGWCC 2 cut(s) 261, 661
BbsI GAAGAC 1 cut(s) 87
BccI CCATC 3 cut(s) 19, 341, 409
Bme18I GGWCC 2 cut(s) 261, 661
BmgT120I GGNCC 2 cut(s) 261, 661
BmiI GGNNCC 1 cut(s) 9
BmsI GCATC 1 cut(s) 174
BpiI GAAGAC 1 cut(s) 87
BpuEI CTTGAG 2 cut(s) 391, 495
BsaJI CCNNGG 2 cut(s) 382, 646
BsaWI WCCGGW 1 cut(s) 663
BsaXI ACNNNNNCTCC 3 cut(s) 29, 263, 293
Bsc4I CCNNNNNNNGG 2 cut(s) 388, 670
Bse118I RCCGGY 1 cut(s) 663
BseDI CCNNGG 2 cut(s) 382, 646
BseGI GGATG 4 cut(s) 84, 165, 352, 573
BseLI CCNNNNNNNGG 2 cut(s) 388, 670
BseMII CTCAG 1 cut(s) 516
BseRI GAGGAG 1 cut(s) 498
BseYI CCCAGC 1 cut(s) 471
Bsh1285I CGRYCG 1 cut(s) 591
BshTI ACCGGT 1 cut(s) 663
BsiEI CGRYCG 1 cut(s) 591
BsiSI CCGG 1 cut(s) 664
BslFI GGGAC 1 cut(s) 488
BslI CCNNNNNNNGG 2 cut(s) 388, 670
BsmFI GGGAC 1 cut(s) 488
BsmI GAATGC 1 cut(s) 516
Bsp1407I TGTACA 1 cut(s) 105
BspACI CCGC 3 cut(s) 5, 294, 322
BspCNI CTCAG 1 cut(s) 515
BspLI GGNNCC 1 cut(s) 9
BsrFI RCCGGY 1 cut(s) 663
BsrGI TGTACA 1 cut(s) 105
BssAI RCCGGY 1 cut(s) 663
BssECI CCNNGG 2 cut(s) 382, 646
BssT1I CCWWGG 1 cut(s) 382
Bst4CI ACNGT 1 cut(s) 535
Bst6I CTCTTC 1 cut(s) 120
BstAUI TGTACA 1 cut(s) 105
BstC8I GCNNGC 3 cut(s) 138, 142, 438
BstDEI CTNAG 2 cut(s) 452, 502
BstF5I GGATG 4 cut(s) 84, 165, 352, 573
BstHHI GCGC 1 cut(s) 288
BstMCI CGRYCG 1 cut(s) 591
BstNSI RCATGY 1 cut(s) 550
BstV2I GAAGAC 1 cut(s) 87
BstXI CCANNNNNNTGG 1 cut(s) 471
BtsCI GGATG 4 cut(s) 84, 165, 352, 573
BtsIMutI CAGTG 2 cut(s) 524, 531
Cac8I GCNNGC 3 cut(s) 138, 142, 438
CfoI GCGC 1 cut(s) 288
Cfr10I RCCGGY 1 cut(s) 663
Cfr13I GGNCC 2 cut(s) 261, 661
Csp6I GTAC 3 cut(s) 106, 280, 340
CspAI ACCGGT 1 cut(s) 663
CviAII CATG 6 cut(s) 154, 227, 277, 388, 547, 729
CviQI GTAC 3 cut(s) 106, 280, 340
DdeI CTNAG 2 cut(s) 452, 502
Eam1104I CTCTTC 1 cut(s) 120
EarI CTCTTC 1 cut(s) 120
EciI GGCGGA 1 cut(s) 20
Eco130I CCWWGG 1 cut(s) 382
Eco47I GGWCC 2 cut(s) 261, 661
EcoRI GAATTC 1 cut(s) 192
EcoT14I CCWWGG 1 cut(s) 382
ErhI CCWWGG 1 cut(s) 382
FaeI CATG 6 cut(s) 157, 230, 280, 391, 550, 732
FaiI YATR 8 cut(s) 104, 155, 228, 278, 389, 410, 548, 730
FalI AAGNNNNNCTT 2 cut(s) 72, 104
FaqI GGGAC 1 cut(s) 488
FatI CATG 6 cut(s) 153, 226, 276, 387, 546, 728
FokI GGATG 4 cut(s) 71, 152, 359, 580
GlaI GCGC 1 cut(s) 287
GsaI CCCAGC 1 cut(s) 475
HapII CCGG 1 cut(s) 664
HhaI GCGC 1 cut(s) 288
Hin1II CATG 6 cut(s) 157, 230, 280, 391, 550, 732
Hin6I GCGC 1 cut(s) 286
HinP1I GCGC 1 cut(s) 286
HincII GTYRAC 2 cut(s) 42, 402
HindII GTYRAC 2 cut(s) 42, 402
HinfI GANTC 3 cut(s) 272, 394, 593
HpaII CCGG 1 cut(s) 664
HphI GGTGA 4 cut(s) 46, 340, 403, 601
Hpy166II GTNNAC 4 cut(s) 42, 261, 331, 402
Hpy188I TCNGA 4 cut(s) 151, 364, 598, 700
Hpy188III TCNNGA 2 cut(s) 169, 620
Hpy8I GTNNAC 4 cut(s) 42, 261, 331, 402
HpyAV CCTTC 1 cut(s) 565
HpyCH4III ACNGT 1 cut(s) 535
HpyCH4IV ACGT 1 cut(s) 479
HpyCH4V TGCA 4 cut(s) 96, 188, 233, 436
HpyF3I CTNAG 2 cut(s) 452, 502
HpySE526I ACGT 1 cut(s) 479
Hsp92II CATG 6 cut(s) 157, 230, 280, 391, 550, 732
HspAI GCGC 1 cut(s) 286
LmnI GCTCC 4 cut(s) 7, 162, 511, 574
LweI GCATC 1 cut(s) 174
MaeII ACGT 1 cut(s) 479
MaeIII GTNAC 4 cut(s) 374, 447, 607, 724
MboII GAAGA 6 cut(s) 92, 107, 424, 569, 572, 702
MluCI AATT 2 cut(s) 52, 192
MlyI GAGTC 2 cut(s) 281, 602
MmeI TCCRAC 3 cut(s) 174, 249, 576
MnlI CCTC 5 cut(s) 123, 319, 519, 614, 641
MroXI GAANNNNTTC 1 cut(s) 358
MseI TTAA 2 cut(s) 494, 552
MslI CAYNNNNRTG 2 cut(s) 372, 482
MspA1I CMGCKG 1 cut(s) 471
MspI CCGG 1 cut(s) 664
Mva1269I GAATGC 1 cut(s) 516
NlaIII CATG 6 cut(s) 157, 230, 280, 391, 550, 732
NlaIV GGNNCC 1 cut(s) 9
NmuCI GTSAC 3 cut(s) 374, 607, 724
NspI RCATGY 1 cut(s) 550
OliI CACNNNNGTG 2 cut(s) 372, 482
PctI GAATGC 1 cut(s) 516
PdmI GAANNNNTTC 1 cut(s) 358
PfeI GAWTC 1 cut(s) 394
PflFI GACNNNGTC 2 cut(s) 46, 592
PflMI CCANNNNNTGG 1 cut(s) 388
PinAI ACCGGT 1 cut(s) 663
PleI GAGTC 2 cut(s) 280, 601
PpsI GAGTC 2 cut(s) 280, 601
PspFI CCCAGC 1 cut(s) 471
PspN4I GGNNCC 1 cut(s) 9
PspPI GGNCC 2 cut(s) 261, 661
PsrI GAACNNNNNNTAC 2 cut(s) 323, 355
PsyI GACNNNGTC 2 cut(s) 46, 592
PvuII CAGCTG 1 cut(s) 471
RsaI GTAC 3 cut(s) 107, 281, 341
RsaNI GTAC 3 cut(s) 106, 280, 340
RseI CAYNNNNRTG 2 cut(s) 372, 482
SaqAI TTAA 2 cut(s) 494, 552
Sau96I GGNCC 2 cut(s) 261, 661
SchI GAGTC 2 cut(s) 281, 602
SetI ASST 6 cut(s) 184, 458, 473, 482, 508, 726
SfaNI GCATC 1 cut(s) 174
SinI GGWCC 2 cut(s) 261, 661
SmiMI CAYNNNNRTG 2 cut(s) 372, 482
SmlI CTYRAG 2 cut(s) 370, 510
SmoI CTYRAG 2 cut(s) 370, 510
Sse9I AATT 2 cut(s) 52, 192
SsiI CCGC 3 cut(s) 5, 294, 322
StyI CCWWGG 1 cut(s) 382
TaaI ACNGT 1 cut(s) 535
TaiI ACGT 1 cut(s) 482
TaqI TCGA 3 cut(s) 352, 587, 631
TaqII GACCGA 1 cut(s) 605
TasI AATT 2 cut(s) 52, 192
TatI WGTACW 2 cut(s) 105, 339
TfiI GAWTC 1 cut(s) 394
Tru1I TTAA 2 cut(s) 494, 552
Tru9I TTAA 2 cut(s) 494, 552
TscAI CASTG 2 cut(s) 531, 538
TseFI GTSAC 3 cut(s) 374, 607, 724
Tsp45I GTSAC 3 cut(s) 374, 607, 724
TspDTI ATGAA 6 cut(s) 212, 225, 304, 425, 570, 584
TspRI CASTG 2 cut(s) 531, 538
Tth111I GACNNNGTC 2 cut(s) 46, 592
Van91I CCANNNNNTGG 1 cut(s) 388
VpaK11BI GGWCC 2 cut(s) 261, 661
XapI RAATTY 1 cut(s) 192
XceI RCATGY 1 cut(s) 550
XmnI GAANNNNTTC 1 cut(s) 358
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.