FvH4_3g21021

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0000154
Physical Location & Seq
Forward (+)
14040902 .. 14041848
947 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_3g21021.t1

Sequence Viewer

Length: 762 bp
ATGGCCAATAGGGTCGAGTTCTCGCAGTGCCCAGTCGGAAAATTTGACGGGAAGGGCAACTTTCAACATTGGAGAGCCCAGATGGAGCTTTTCTTCAAGGTGATGGAATACACGGAAGTTGTGATGAACGGCTTCACAGATCCGGGAGATCAAACTAATCTCACACAGAACCAGAGAGAGGAGTTAATCAAAAATAGAAAGAAGGATAGCAGAGCCCTGATGTACATCTATGGAGCCATTGATTCAGAGATATATGAGAAGATTGCACATGCTGCTACTGCGAAGGAGGCTTGGGATTGTCTCATCAATTGCTATGTGGGACAAGATAAGGTGAAAAAGGTTCGGCTCCAGACTTTACGGCGGCAATTTGAGCTTCTTCAGATGGAGAAAAGGGAGAGCATCTCTGATTACTTCTCACGCACCTTGGCAATTGTCAATCAGATGAAAGCCAATGGTGAGGTTTTATCAAATCTACAAGTTGTGGAGAAAATTCTTTGGACTTTGACAGATCGGTTCGAAGGCAAAGTCACAGCGATAGAGGAGTCAAGAGATCTGGCTGCAGTGACGGTTGATGAGCTTATGGGTTCTCTACAAGCCTATGAGCAGAGGCTAAATGAGAAGTCAGAGGTTGCAATTGAAGAAGCGTTGGAGACTCAGTTGAGTTTAAAGAAAGAGAGAAACTTGGCGCACCGAAGTGAAGGAAGTTCCCGCAAGAAGGAGGTTAGAGGGTCAGGAGTTCCATGCCAAGATTGCAGAGAATGA
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

254

Amino Acids

29.16

Weight (kDa)

6.08

Isoelectric Point (pI)

33.35

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 53 - 208 9.4e-29 gag-polypeptide of LTR copia-type
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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Orthologous Genes (Group: OG0000154)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g02351 FvH4_1g18383 FvH4_1g18442 FvH4_1g19622 FvH4_2g08148 FvH4_2g16312 FvH4_3g06912 FvH4_3g10761 FvH4_3g12332 FvH4_3g12332 FvH4_3g14182 FvH4_3g21021 FvH4_3g35231 FvH4_3g45132 FvH4_4g08663 FvH4_4g30271 FvH4_4g30272 FvH4_4g30901 FvH4_4g30902 FvH4_5g12471 FvH4_5g22951 FvH4_6g07331 FvH4_6g07332 FvH4_6g41872 FvH4_6g43841 FvH4_6g43842 FvH4_6g48811 FvH4_7g03911 FvH4_7g13272 FvH4_7g21181 FvH4_7g29024 FvH4_7g33702
malus_domestica MD00G1037700.v1.1 MD01G1037300.v1.1 MD01G1096700.v1.1 MD01G1101100.v1.1 MD01G1129400.v1.1 MD02G1295200.v1.1 MD03G1131300.v1.1 MD04G1072100.v1.1 MD05G1104800.v1.1 MD07G1028600.v1.1 MD07G1274600.v1.1 MD08G1027200.v1.1 MD09G1044400.v1.1 MD09G1044700.v1.1 MD09G1129500.v1.1 MD09G1238700.v1.1 MD10G1011700.v1.1 MD10G1071400.v1.1 MD10G1108600.v1.1 MD10G1162100.v1.1 MD10G1162300.v1.1 MD11G1016700.v1.1 MD11G1074500.v1.1 MD15G1058600.v1.1 MD15G1383000.v1.1 MD16G1192200.v1.1 MD17G1077400.v1.1 MD17G1077500.v1.1
pyrus_communis pycom01g03520 pycom02g00350 pycom03g09910 pycom03g13960 pycom03g13970 pycom03g19180 pycom04g08410 pycom04g10140 pycom06g03750 pycom07g09240 pycom07g09260 pycom08g20130 pycom09g11020 pycom10g12690 pycom14g04140 pycom14g05710 pycom16g06380 pycom17g05500 pycom808g00140
rosa_chinensis RchiOBHm_Chr1g0316211 RchiOBHm_Chr1g0319901 RchiOBHm_Chr1g0321811 RchiOBHm_Chr1g0329831 RchiOBHm_Chr1g0330721 RchiOBHm_Chr1g0330731 RchiOBHm_Chr1g0368461 RchiOBHm_Chr1g0381111 RchiOBHm_Chr2g0154461 RchiOBHm_Chr2g0164521 RchiOBHm_Chr2g0175301 RchiOBHm_Chr3g0451301 RchiOBHm_Chr3g0453691 RchiOBHm_Chr3g0470191 RchiOBHm_Chr3g0486561 RchiOBHm_Chr4g0409141 RchiOBHm_Chr4g0409151 RchiOBHm_Chr4g0421231 RchiOBHm_Chr4g0440701 RchiOBHm_Chr5g0018211 RchiOBHm_Chr5g0023611 RchiOBHm_Chr5g0045971 RchiOBHm_Chr5g0056061 RchiOBHm_Chr5g0063381 RchiOBHm_Chr5g0064011 RchiOBHm_Chr5g0064021 RchiOBHm_Chr5g0064041 RchiOBHm_Chr6g0259681 RchiOBHm_Chr6g0259691 RchiOBHm_Chr6g0296531 RchiOBHm_Chr7g0186421 RchiOBHm_Chr7g0192321 RchiOBHm_Chr7g0198271 RchiOBHm_Chr7g0198951 RchiOBHm_Chr7g0237911
rosa_laevigata RLG00000026946
rosa_roxburghii Rroxscaffold_1G00014460 Rroxscaffold_1G00014610 Rroxscaffold_1G00028950 Rroxscaffold_1G00052630 Rroxscaffold_2G00104760 Rroxscaffold_2G00138900 Rroxscaffold_2G00145210 Rroxscaffold_3G00220110 Rroxscaffold_4G00297860 Rroxscaffold_4G00321570 Rroxscaffold_5G00332990 Rroxscaffold_5G00360870
rosa_samantha Rh1AG319600 Rh1CG299100 Rh4DG385900 Rh5BG032200
rosa_wichuraiana Rw0G002380 Rw0G003050 Rw0G003940 Rw1G002730 Rw1G003260 Rw1G005490 Rw1G016140 Rw1G016150 Rw1G017930 Rw1G017940 Rw1G022540 Rw1G022630 Rw1G031080 Rw1G039680 Rw2G003340 Rw2G003720 Rw2G006640 Rw2G020790 Rw2G025650 Rw2G028430 Rw2G029550 Rw2G034920 Rw2G040820 Rw2G048420 Rw2G048570 Rw3G010040 Rw3G022790 Rw3G023350 Rw3G025140 Rw3G028810 Rw4G000680 Rw4G003350 Rw4G004640 Rw4G026650 Rw4G034500 Rw5G008490 Rw5G020650 Rw5G023000 Rw5G033610 Rw5G037280 Rw5G046620 Rw5G050250 Rw6G001410 Rw6G005690 Rw6G005820 Rw6G010920 Rw6G022790 Rw6G023940 Rw6G026290 Rw6G028610 Rw6G031260 Rw6G036550 Rw6G036560 Rw7G015300 Rw7G017250 Rw7G018150 Rw7G031960 Rw7G036490

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 2 cut(s) 361, 709
AclWI GGATC 1 cut(s) 134
AcoI YGGCCR 1 cut(s) 3
AcsI RAATTY 2 cut(s) 41, 489
AcuI CTGAAG 1 cut(s) 362
AfaI GTAC 1 cut(s) 224
AfiI CCNNNNNNNGG 2 cut(s) 178, 715
AgsI TTSAA 3 cut(s) 65, 97, 638
AleI CACNNNNGTG 1 cut(s) 693
AluBI AGCT 3 cut(s) 88, 373, 577
AluI AGCT 3 cut(s) 88, 373, 577
Alw26I GTCTC 2 cut(s) 305, 644
AlwI GGATC 1 cut(s) 134
AoxI GGCC 1 cut(s) 3
ApeKI GCWGC 2 cut(s) 272, 557
ApoI RAATTY 2 cut(s) 41, 489
ArsI GACNNNNNNTTYG 2 cut(s) 510, 542
Asp700I GAANNNNTTC 1 cut(s) 131
AspLEI GCGC 1 cut(s) 688
AsuC2I CCSGG 1 cut(s) 144
AsuHPI GGTGA 3 cut(s) 112, 343, 467
AsuII TTCGAA 1 cut(s) 516
BaeGI GKGCMC 1 cut(s) 32
BalI TGGCCA 1 cut(s) 5
BanII GRGCYC 2 cut(s) 79, 217
BbvI GCAGC 2 cut(s) 259, 544
BccI CCATC 3 cut(s) 76, 97, 376
BceAI ACGGC 2 cut(s) 145, 374
BcnI CCSGG 1 cut(s) 144
BcoDI GTCTC 2 cut(s) 305, 644
BfmI CTRYAG 1 cut(s) 558
BglII AGATCT 1 cut(s) 550
BisI GCNGC 3 cut(s) 273, 362, 558
BlsI GCNGC 3 cut(s) 274, 363, 559
Bme1390I CCNGG 1 cut(s) 144
BmiI GGNNCC 2 cut(s) 235, 347
BmrFI CCNGG 1 cut(s) 144
BmrI ACTGGG 1 cut(s) 26
BmsI GCATC 1 cut(s) 408
BmuI ACTGGG 1 cut(s) 26
BplI GAGNNNNNCTC 2 cut(s) 386, 418
BpmI CTGGAG 1 cut(s) 332
Bpu14I TTCGAA 1 cut(s) 516
BpuMI CCSGG 1 cut(s) 144
BsaBI GATNNNNATC 1 cut(s) 224
BsaJI CCNNGG 1 cut(s) 423
BsaXI ACNNNNNCTCC 2 cut(s) 641, 671
Bsc4I CCNNNNNNNGG 2 cut(s) 178, 715
Bse1I ACTGG 1 cut(s) 32
Bse8I GATNNNNATC 1 cut(s) 224
BseDI CCNNGG 1 cut(s) 423
BseJI GATNNNNATC 1 cut(s) 224
BseLI CCNNNNNNNGG 2 cut(s) 178, 715
BseMII CTCAG 1 cut(s) 668
BseNI ACTGG 1 cut(s) 32
BseRI GAGGAG 2 cut(s) 194, 554
BseSI GKGCMC 1 cut(s) 32
BseXI GCAGC 2 cut(s) 259, 544
BshFI GGCC 1 cut(s) 5
BsiSI CCGG 1 cut(s) 143
BslFI GGGAC 1 cut(s) 333
BslI CCNNNNNNNGG 2 cut(s) 178, 715
BsmAI GTCTC 2 cut(s) 305, 644
BsmFI GGGAC 1 cut(s) 333
BsnI GGCC 1 cut(s) 5
Bsp119I TTCGAA 1 cut(s) 516
Bsp1286I GDGCHC 3 cut(s) 32, 79, 217
Bsp1407I TGTACA 1 cut(s) 222
Bsp143I GATC 4 cut(s) 139, 148, 508, 550
BspACI CCGC 2 cut(s) 361, 709
BspANI GGCC 1 cut(s) 5
BspCNI CTCAG 1 cut(s) 667
BspLI GGNNCC 2 cut(s) 235, 347
BspMAI CTGCAG 1 cut(s) 562
BspPI GGATC 1 cut(s) 134
BspT104I TTCGAA 1 cut(s) 516
BsrGI TGTACA 1 cut(s) 222
BsrI ACTGG 1 cut(s) 32
BssECI CCNNGG 1 cut(s) 423
BssMI GATC 4 cut(s) 139, 148, 508, 550
BssT1I CCWWGG 1 cut(s) 423
Bst4CI ACNGT 1 cut(s) 568
BstAPI GCANNNNNTGC 1 cut(s) 272
BstAUI TGTACA 1 cut(s) 222
BstBI TTCGAA 1 cut(s) 516
BstDEI CTNAG 1 cut(s) 654
BstHHI GCGC 1 cut(s) 688
BstKTI GATC 4 cut(s) 142, 151, 511, 553
BstMAI GTCTC 2 cut(s) 305, 644
BstMBI GATC 4 cut(s) 139, 148, 508, 550
BstMWI GCNNNNNNNGC 5 cut(s) 272, 278, 287, 370, 750
BstNSI RCATGY 1 cut(s) 272
BstSCI CCNGG 1 cut(s) 142
BstSFI CTRYAG 1 cut(s) 558
BstSLI GKGCMC 1 cut(s) 32
BstV1I GCAGC 2 cut(s) 259, 544
BstX2I RGATCY 2 cut(s) 139, 550
BstYI RGATCY 2 cut(s) 139, 550
BsuRI GGCC 1 cut(s) 5
BtsI GCAGTG 2 cut(s) 32, 567
BtsIMutI CAGTG 2 cut(s) 32, 567
CfoI GCGC 1 cut(s) 688
Csp6I GTAC 1 cut(s) 223
CviAII CATG 2 cut(s) 269, 741
CviQI GTAC 1 cut(s) 223
DdeI CTNAG 1 cut(s) 654
DpnI GATC 4 cut(s) 141, 150, 510, 552
DpnII GATC 4 cut(s) 139, 148, 508, 550
DraI TTTAAA 1 cut(s) 666
EaeI YGGCCR 1 cut(s) 3
Eco130I CCWWGG 1 cut(s) 423
Eco24I GRGCYC 2 cut(s) 79, 217
Eco57I CTGAAG 1 cut(s) 362
EcoT14I CCWWGG 1 cut(s) 423
EcoT38I GRGCYC 2 cut(s) 79, 217
ErhI CCWWGG 1 cut(s) 423
FaeI CATG 2 cut(s) 272, 744
FaiI YATR 8 cut(s) 231, 253, 255, 270, 315, 581, 600, 742
FalI AAGNNNNNCTT 2 cut(s) 44, 76
FaqI GGGAC 1 cut(s) 333
FatI CATG 2 cut(s) 268, 740
FauI CCCGC 1 cut(s) 716
Fnu4HI GCNGC 3 cut(s) 273, 362, 558
FriOI GRGCYC 2 cut(s) 79, 217
Fsp4HI GCNGC 3 cut(s) 273, 362, 558
GlaI GCGC 1 cut(s) 687
GluI GCNGC 3 cut(s) 273, 362, 558
GsuI CTGGAG 1 cut(s) 332
HaeIII GGCC 1 cut(s) 5
HapII CCGG 1 cut(s) 143
HhaI GCGC 1 cut(s) 688
Hin1II CATG 2 cut(s) 272, 744
Hin6I GCGC 1 cut(s) 686
HinP1I GCGC 1 cut(s) 686
HinfI GANTC 3 cut(s) 242, 542, 652
HpaII CCGG 1 cut(s) 143
HphI GGTGA 3 cut(s) 112, 343, 467
Hpy188I TCNGA 6 cut(s) 38, 247, 381, 406, 441, 625
Hpy188III TCNNGA 3 cut(s) 349, 546, 732
HpyAV CCTTC 6 cut(s) 46, 196, 277, 512, 692, 709
HpyCH4III ACNGT 1 cut(s) 568
HpyCH4V TGCA 4 cut(s) 266, 560, 632, 753
HpyF10VI GCNNNNNNNGC 5 cut(s) 272, 278, 287, 370, 750
HpyF3I CTNAG 1 cut(s) 654
Hsp92II CATG 2 cut(s) 272, 744
HspAI GCGC 1 cut(s) 686
Kzo9I GATC 4 cut(s) 139, 148, 508, 550
LmnI GCTCC 3 cut(s) 85, 233, 351
LpnPI CCDG 8 cut(s) 45, 92, 156, 185, 230, 362, 539, 717
Lsp1109I GCAGC 2 cut(s) 259, 544
LweI GCATC 1 cut(s) 408
MaeIII GTNAC 2 cut(s) 526, 562
MalI GATC 4 cut(s) 141, 150, 510, 552
MboI GATC 4 cut(s) 139, 148, 508, 550
MboII GAAGA 4 cut(s) 85, 271, 368, 650
MfeI CAATTG 3 cut(s) 307, 429, 633
MflI RGATCY 2 cut(s) 139, 550
MhlI GDGCHC 3 cut(s) 32, 79, 217
MlsI TGGCCA 1 cut(s) 5
MluCI AATT 6 cut(s) 41, 307, 365, 429, 489, 633
MluNI TGGCCA 1 cut(s) 5
MlyI GAGTC 2 cut(s) 551, 646
MmeI TCCRAC 2 cut(s) 16, 627
MnlI CCTC 8 cut(s) 172, 280, 451, 532, 600, 619, 712, 719
Mox20I TGGCCA 1 cut(s) 5
MroXI GAANNNNTTC 1 cut(s) 131
MscI TGGCCA 1 cut(s) 5
MseI TTAA 2 cut(s) 185, 665
MslI CAYNNNNRTG 1 cut(s) 693
Msp20I TGGCCA 1 cut(s) 5
MspI CCGG 1 cut(s) 143
MspR9I CCNGG 1 cut(s) 144
MunI CAATTG 3 cut(s) 307, 429, 633
MwoI GCNNNNNNNGC 5 cut(s) 272, 278, 287, 370, 750
NciI CCSGG 1 cut(s) 144
NdeII GATC 4 cut(s) 139, 148, 508, 550
NlaIII CATG 2 cut(s) 272, 744
NlaIV GGNNCC 2 cut(s) 235, 347
NmuCI GTSAC 2 cut(s) 526, 562
NspI RCATGY 1 cut(s) 272
NspV TTCGAA 1 cut(s) 516
OliI CACNNNNGTG 1 cut(s) 693
PdmI GAANNNNTTC 1 cut(s) 131
PfeI GAWTC 1 cut(s) 242
PfoI TCCNGGA 1 cut(s) 142
PkrI GCNGC 3 cut(s) 274, 363, 559
PleI GAGTC 2 cut(s) 550, 646
PpsI GAGTC 2 cut(s) 550, 646
PspN4I GGNNCC 2 cut(s) 235, 347
PstI CTGCAG 1 cut(s) 562
PsuI RGATCY 2 cut(s) 139, 550
RsaI GTAC 1 cut(s) 224
RsaNI GTAC 1 cut(s) 223
RseI CAYNNNNRTG 1 cut(s) 693
SaqAI TTAA 2 cut(s) 185, 665
SatI GCNGC 3 cut(s) 273, 362, 558
Sau3AI GATC 4 cut(s) 139, 148, 508, 550
SchI GAGTC 2 cut(s) 551, 646
ScrFI CCNGG 1 cut(s) 144
SduI GDGCHC 3 cut(s) 32, 79, 217
SfaNI GCATC 1 cut(s) 408
SfcI CTRYAG 1 cut(s) 558
SfuI TTCGAA 1 cut(s) 516
SmiMI CAYNNNNRTG 1 cut(s) 693
Sse9I AATT 6 cut(s) 41, 307, 365, 429, 489, 633
SsiI CCGC 2 cut(s) 361, 709
StyD4I CCNGG 1 cut(s) 142
StyI CCWWGG 1 cut(s) 423
TaaI ACNGT 1 cut(s) 568
TaqI TCGA 2 cut(s) 15, 516
TasI AATT 6 cut(s) 41, 307, 365, 429, 489, 633
TatI WGTACW 1 cut(s) 222
TauI GCSGC 1 cut(s) 364
TfiI GAWTC 1 cut(s) 242
Tru1I TTAA 2 cut(s) 185, 665
Tru9I TTAA 2 cut(s) 185, 665
TscAI CASTG 2 cut(s) 32, 567
TseFI GTSAC 2 cut(s) 526, 562
TseI GCWGC 2 cut(s) 272, 557
Tsp45I GTSAC 2 cut(s) 526, 562
TspDTI ATGAA 2 cut(s) 140, 458
TspGWI ACGGA 1 cut(s) 128
TspRI CASTG 2 cut(s) 32, 567
XapI RAATTY 2 cut(s) 41, 489
XceI RCATGY 1 cut(s) 272
XmnI GAANNNNTTC 1 cut(s) 131
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.