FvH4_6g43841

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb6
OG0000154
Physical Location & Seq
Forward (+)
33879760 .. 33880576
817 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_6g43841.t1

Sequence Viewer

Length: 777 bp
ATGGCAGCAGAGTCGAGTAATTTTGCACAACCCTGCATCCCTAAGTTTGATGGGGATTATGAGCATTGGAGTATGCTTATGGAGAATCTCCTGCGTTCAAAAGAGTACTGGAGTGTTGTTGAGACAGGGTATGAAGAGCCTGCATCTGAAGAAGTTTTGAATGCAGGACAGAGAAAAATCTTGGAGGACATGAAGCTGAAGGATCTGAAAGCCAAAAATTACTTGTTTCAACCAATTGACAAGTCCATACTGAAAACAATTGTTCAAAAGGAGACTGCCAAACAGCTATGGGACTCCATGAAAGTCAAGTATCAGGGAAACGCTACGGTAAAGCGTGCTCAGCTTCAAGTACTCCGCAGGAACTTTGAAGTGTTGGAGATGAAATCTGGAGAGTCTGTCACAGACTACTTTGGTAGGGTGATGATGGTCGCAAACGATATGAGGAATTATGGAGAGGACATGCCTGATGTGAAGATTGTTGAGAAGATTCTGCGTACACTCTCAGAGAAGTTCAATTACATTGTCTGTTCGATTGAAGAATCCAAAGACATTAATCATCTCTCAGTAGATGAGTTACAAAGCTCACTGCTTGTGCATGAACAGAAGTTTCGGAAGAGTGAAGGAGATGATCAAGCACTGAGAGTTTATGATGAGCGAATTGGAGGCAGAGGCCGAGGAAGGAGCAATTCTAGAGGAAGAGGTCGTGGGAGAGGAACTCAAGCATTCAACAAAGCCATAGTGGAATGTTTCAAATGTCACAAGCTCGGACATTACTAG
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

259

Amino Acids

29.82

Weight (kDa)

8.51

Isoelectric Point (pI)

42.67

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 27 - 207 2.1e-33 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 1 cut(s) 355
AclWI GGATC 1 cut(s) 210
AcuI CTGAAG 2 cut(s) 168, 218
AfaI GTAC 3 cut(s) 107, 351, 496
AluBI AGCT 5 cut(s) 196, 286, 343, 582, 763
AluI AGCT 5 cut(s) 196, 286, 343, 582, 763
Alw21I GWGCWC 1 cut(s) 340
Alw26I GTCTC 2 cut(s) 116, 266
AlwI GGATC 1 cut(s) 210
AoxI GGCC 1 cut(s) 670
ApeKI GCWGC 1 cut(s) 5
AseI ATTAAT 1 cut(s) 552
AsuHPI GGTGA 1 cut(s) 430
BarI GAAGNNNNNNTAC 2 cut(s) 500, 532
Bbv12I GWGCWC 1 cut(s) 340
BbvI GCAGC 1 cut(s) 17
BccI CCATC 2 cut(s) 44, 418
BcgI CGANNNNNNTGC 1 cut(s) 28
BclI TGATCA 1 cut(s) 628
BcoDI GTCTC 2 cut(s) 116, 266
BfaI CTAG 2 cut(s) 690, 775
BisI GCNGC 1 cut(s) 6
BlpI GCTNAGC 1 cut(s) 339
BlsI GCNGC 1 cut(s) 7
BmcAI AGTACT 2 cut(s) 107, 351
BmsI GCATC 2 cut(s) 45, 152
BplI GAGNNNNNCTC 2 cut(s) 700, 732
BpmI CTGGAG 2 cut(s) 130, 408
Bpu1102I GCTNAGC 1 cut(s) 339
BpuEI CTTGAG 1 cut(s) 702
BsaJI CCNNGG 1 cut(s) 673
BsaXI ACNNNNNCTCC 2 cut(s) 381, 411
Bse1I ACTGG 1 cut(s) 113
BseDI CCNNGG 1 cut(s) 673
BseGI GGATG 1 cut(s) 36
BseMII CTCAG 4 cut(s) 353, 516, 576, 629
BseNI ACTGG 1 cut(s) 113
BseXI GCAGC 1 cut(s) 17
BshFI GGCC 1 cut(s) 672
BsiHKAI GWGCWC 1 cut(s) 340
BslFI GGGAC 1 cut(s) 305
BsmAI GTCTC 2 cut(s) 116, 266
BsmFI GGGAC 1 cut(s) 305
BsmI GAATGC 2 cut(s) 166, 722
BsnI GGCC 1 cut(s) 672
Bsp1286I GDGCHC 1 cut(s) 340
Bsp143I GATC 2 cut(s) 202, 628
Bsp1720I GCTNAGC 1 cut(s) 339
BspACI CCGC 1 cut(s) 355
BspANI GGCC 1 cut(s) 672
BspCNI CTCAG 4 cut(s) 352, 515, 575, 630
BspPI GGATC 1 cut(s) 210
BspQI GCTCTTC 1 cut(s) 129
BsrI ACTGG 1 cut(s) 113
BssECI CCNNGG 1 cut(s) 673
BssMI GATC 2 cut(s) 202, 628
Bst4CI ACNGT 1 cut(s) 328
Bst6I CTCTTC 3 cut(s) 129, 608, 691
BstC8I GCNNGC 2 cut(s) 141, 336
BstDEI CTNAG 5 cut(s) 42, 339, 502, 562, 638
BstF5I GGATG 1 cut(s) 36
BstKTI GATC 2 cut(s) 205, 631
BstMAI GTCTC 2 cut(s) 116, 266
BstMBI GATC 2 cut(s) 202, 628
BstMWI GCNNNNNNNGC 1 cut(s) 340
BstNSI RCATGY 1 cut(s) 463
BstV1I GCAGC 1 cut(s) 17
BstX2I RGATCY 1 cut(s) 202
BstYI RGATCY 1 cut(s) 202
BsuRI GGCC 1 cut(s) 672
BtsCI GGATG 1 cut(s) 36
BtsI GCAGTG 1 cut(s) 584
BtsIMutI CAGTG 2 cut(s) 584, 635
Cac8I GCNNGC 2 cut(s) 141, 336
Csp6I GTAC 3 cut(s) 106, 350, 495
CviAII CATG 4 cut(s) 190, 298, 460, 596
CviJI RGCY 9 cut(s) 139, 196, 212, 286, 343, 582, 672, 734, 763
CviKI_1 RGCY 9 cut(s) 139, 196, 212, 286, 343, 582, 672, 734, 763
CviQI GTAC 3 cut(s) 106, 350, 495
DdeI CTNAG 5 cut(s) 42, 339, 502, 562, 638
DpnI GATC 2 cut(s) 204, 630
DpnII GATC 2 cut(s) 202, 628
Eam1104I CTCTTC 3 cut(s) 129, 608, 691
EarI CTCTTC 3 cut(s) 129, 608, 691
Eco57I CTGAAG 2 cut(s) 168, 218
FaeI CATG 4 cut(s) 193, 301, 463, 599
FaqI GGGAC 1 cut(s) 305
FatI CATG 4 cut(s) 189, 297, 459, 595
FbaI TGATCA 1 cut(s) 628
Fnu4HI GCNGC 1 cut(s) 6
FokI GGATG 1 cut(s) 23
Fsp4HI GCNGC 1 cut(s) 6
FspBI CTAG 2 cut(s) 690, 775
GluI GCNGC 1 cut(s) 6
GsuI CTGGAG 2 cut(s) 130, 408
HaeIII GGCC 1 cut(s) 672
Hin1II CATG 4 cut(s) 193, 301, 463, 599
HinfI GANTC 6 cut(s) 11, 85, 293, 392, 487, 539
HphI GGTGA 1 cut(s) 430
Hpy166II GTNNAC 1 cut(s) 497
Hpy188I TCNGA 5 cut(s) 148, 207, 505, 612, 767
Hpy188III TCNNGA 2 cut(s) 387, 690
Hpy8I GTNNAC 1 cut(s) 497
HpyAV CCTTC 3 cut(s) 193, 614, 672
HpyCH4III ACNGT 1 cut(s) 328
HpyCH4V TGCA 5 cut(s) 26, 36, 143, 164, 595
HpyF10VI GCNNNNNNNGC 1 cut(s) 340
HpyF3I CTNAG 5 cut(s) 42, 339, 502, 562, 638
Hsp92II CATG 4 cut(s) 193, 301, 463, 599
Ksp22I TGATCA 1 cut(s) 628
Kzo9I GATC 2 cut(s) 202, 628
LguI GCTCTTC 1 cut(s) 129
LmnI GCTCC 1 cut(s) 681
Lsp1109I GCAGC 1 cut(s) 17
LweI GCATC 2 cut(s) 45, 152
MaeI CTAG 2 cut(s) 690, 775
MaeIII GTNAC 3 cut(s) 397, 573, 755
MalI GATC 2 cut(s) 204, 630
MboI GATC 2 cut(s) 202, 628
MboII GAAGA 7 cut(s) 146, 161, 484, 496, 548, 625, 708
MfeI CAATTG 2 cut(s) 234, 258
MflI RGATCY 1 cut(s) 202
MhlI GDGCHC 1 cut(s) 340
MluCI AATT 8 cut(s) 19, 217, 234, 258, 445, 514, 657, 685
MlyI GAGTC 3 cut(s) 20, 287, 401
MmeI TCCRAC 1 cut(s) 354
MnlI CCTC 9 cut(s) 178, 435, 448, 656, 662, 668, 686, 692, 704
MseI TTAA 1 cut(s) 552
MunI CAATTG 2 cut(s) 234, 258
Mva1269I GAATGC 2 cut(s) 166, 722
MwoI GCNNNNNNNGC 1 cut(s) 340
NdeII GATC 2 cut(s) 202, 628
NlaIII CATG 4 cut(s) 193, 301, 463, 599
NmeAIII GCCGAG 1 cut(s) 698
NmuCI GTSAC 2 cut(s) 397, 755
NspI RCATGY 1 cut(s) 463
PciSI GCTCTTC 1 cut(s) 129
PctI GAATGC 2 cut(s) 166, 722
PfeI GAWTC 3 cut(s) 85, 487, 539
PkrI GCNGC 1 cut(s) 7
PleI GAGTC 3 cut(s) 19, 287, 400
PpsI GAGTC 3 cut(s) 19, 287, 400
PshBI ATTAAT 1 cut(s) 552
PsuI RGATCY 1 cut(s) 202
RsaI GTAC 3 cut(s) 107, 351, 496
RsaNI GTAC 3 cut(s) 106, 350, 495
SapI GCTCTTC 1 cut(s) 129
SaqAI TTAA 1 cut(s) 552
SatI GCNGC 1 cut(s) 6
Sau3AI GATC 2 cut(s) 202, 628
ScaI AGTACT 2 cut(s) 107, 351
SchI GAGTC 3 cut(s) 20, 287, 401
SduI GDGCHC 1 cut(s) 340
SetI ASST 6 cut(s) 198, 288, 345, 584, 703, 765
SfaNI GCATC 2 cut(s) 45, 152
SmlI CTYRAG 1 cut(s) 717
SmoI CTYRAG 1 cut(s) 717
Sse9I AATT 8 cut(s) 19, 217, 234, 258, 445, 514, 657, 685
SsiI CCGC 1 cut(s) 355
SspMI CTAG 2 cut(s) 690, 775
TaaI ACNGT 1 cut(s) 328
TaqI TCGA 2 cut(s) 14, 530
TasI AATT 8 cut(s) 19, 217, 234, 258, 445, 514, 657, 685
TatI WGTACW 2 cut(s) 105, 349
TfiI GAWTC 3 cut(s) 85, 487, 539
Tru1I TTAA 1 cut(s) 552
Tru9I TTAA 1 cut(s) 552
TscAI CASTG 2 cut(s) 591, 642
TseFI GTSAC 2 cut(s) 397, 755
TseI GCWGC 1 cut(s) 5
Tsp45I GTSAC 2 cut(s) 397, 755
TspDTI ATGAA 5 cut(s) 147, 206, 314, 395, 612
TspRI CASTG 2 cut(s) 591, 642
VspI ATTAAT 1 cut(s) 552
XbaI TCTAGA 1 cut(s) 689
XceI RCATGY 1 cut(s) 463
XspI CTAG 2 cut(s) 690, 775
ZrmI AGTACT 2 cut(s) 107, 351
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.