FvH4_c2g00053

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
contig_2
OG0000118
Physical Location & Seq
Forward (+)
47821 .. 48748
928 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_c2g00053.t1

Sequence Viewer

Length: 741 bp
ATGGATCTTGCAGCTTTGGCTAAAACAATTGAAGGCTTAGCCGCTCAAATTGGTCATCTTGAGACCAGAATACAGGATCAAGCAGTTGCTTCTGAGCAACGTTTGGCTGCAATTGAAGCTTCTATCCAGAACGAAGAAGAGAGTGTTGGTGGAGGATCAAGGATGCAGTCTAGGAGGAATGGTCGCAGGCAGGCTGTTCGAAACAACAATGGGCAAGATGGACATGATCCTGAGGAAAAAGCACTGAAGTCTATCAAAGTTGAAGCTCCAAACTTTGATGGCCAGCTGAATGCGAAGGTGTGTCTAGATTGGATATCAGACATGGACCACTATTTTGACTGGTACGAGTTGTCTGAAACTCGAAGGGTGCGGTTTGCAAAGATGAAGTTGGTGGGCAAAGCTAGAGAATGGTGGAGTGGTGTGGAAAGGCGAGCTGCAAGAGCCGGTGATGAACCTATCACTCATTGGGAGGAGATGAAAGAAAGGCTGAAGGAGAAGTACGTTCCTTTGGCTTACAAAGAGCGCTTGCTGGACCAGTGGCAATCTCTTCGTCAAGGGAACATGACAGCTGCTGAGTATATTGATAAGTTTGAAGAATTTATGGTGAGATGCAACATAAATGAAGATCCTTCTGTGACACTCGCTCGTTTCAGAACCGGCCTTCGTCCAGAACTTCAGAGGGAGCTGATTCCTCATGAAGAAAGGGAGTACAATCTGGTGTTCGAGGAGGGGCATCTGTAA
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
Retrotrans_gag zf-CCHC

Protein Analysis

247

Amino Acids

28.57

Weight (kDa)

5.55

Isoelectric Point (pI)

53.32

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotrans_gag PF03732 125 - 223 4.9e-20 Retrotransposon gag protein
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: OG0000118)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g01361 FvH4_1g07161 FvH4_1g07431 FvH4_1g07821 FvH4_1g08223 FvH4_1g10041 FvH4_1g12132 FvH4_1g15053 FvH4_1g18161 FvH4_1g18400 FvH4_1g18931 FvH4_1g19242 FvH4_1g19461 FvH4_1g20550 FvH4_1g21381 FvH4_1g21542 FvH4_1g22102 FvH4_1g23991 FvH4_1g24542 FvH4_1g24951 FvH4_1g24960 FvH4_1g25272 FvH4_1g25552 FvH4_1g25771 FvH4_1g28771 FvH4_1g29201 FvH4_1g29611 FvH4_2g01181 FvH4_2g02491 FvH4_2g04621 FvH4_2g04631 FvH4_2g07460 FvH4_2g08540 FvH4_2g08550 FvH4_2g09292 FvH4_2g10501 FvH4_2g12101 FvH4_2g12220 FvH4_2g12551 FvH4_2g14071 FvH4_2g14241 FvH4_2g15041 FvH4_2g15311 FvH4_2g18971 FvH4_2g19220 FvH4_2g19260 FvH4_2g19611 FvH4_2g19652 FvH4_2g20211 FvH4_2g20231 FvH4_2g21541 FvH4_2g22380 FvH4_2g27712 FvH4_2g28171 FvH4_2g29879 FvH4_2g32391 FvH4_3g02171 FvH4_3g05531 FvH4_3g09750 FvH4_3g10310 FvH4_3g10460 FvH4_3g13172 FvH4_3g15232 FvH4_3g18481 FvH4_3g18621 FvH4_3g20504 FvH4_3g20812 FvH4_3g22320 FvH4_3g22930 FvH4_3g22940 FvH4_3g23752 FvH4_3g24791 FvH4_3g26411 FvH4_3g26432 FvH4_3g27201 FvH4_3g27862 FvH4_3g28871 FvH4_3g28954 FvH4_3g29131 FvH4_3g29832 FvH4_3g29922 FvH4_3g30190 FvH4_3g32231 FvH4_3g32250 FvH4_3g33460 FvH4_3g34670 FvH4_3g36982 FvH4_3g37001 FvH4_3g38252 FvH4_3g38772 FvH4_3g40141 FvH4_3g40181 FvH4_3g42521 FvH4_4g00090 FvH4_4g00290 FvH4_4g00301 FvH4_4g00530 FvH4_4g00823 FvH4_4g02300 FvH4_4g02450 FvH4_4g03360 FvH4_4g04481 FvH4_4g04761 FvH4_4g06301 FvH4_4g06630 FvH4_4g08312 FvH4_4g08552 FvH4_4g10053 FvH4_4g11971 FvH4_4g13211 FvH4_4g13511 FvH4_4g15351 FvH4_4g16360 FvH4_4g16601 FvH4_4g18462 FvH4_4g22911 FvH4_4g23221 FvH4_4g24301 FvH4_4g24721 FvH4_4g27905 FvH4_4g28971 FvH4_4g29540 FvH4_4g30720 FvH4_4g31521 FvH4_4g33371 FvH4_4g34111 FvH4_4g35740 FvH4_5g00131 FvH4_5g02530 FvH4_5g02550 FvH4_5g02560 FvH4_5g02580 FvH4_5g03783 FvH4_5g05681 FvH4_5g05681 FvH4_5g09371 FvH4_5g09381 FvH4_5g14611 FvH4_5g15341 FvH4_5g19801 FvH4_5g20110 FvH4_5g20911 FvH4_5g22230 FvH4_5g25751 FvH4_5g26070 FvH4_5g26471 FvH4_5g27072 FvH4_5g27471 FvH4_5g27471 FvH4_5g27998 FvH4_5g28291 FvH4_5g30951 FvH4_5g31082 FvH4_5g31890 FvH4_5g32251 FvH4_5g34112 FvH4_5g37184 FvH4_5g37993 FvH4_5g38271 FvH4_6g00153 FvH4_6g00640 FvH4_6g05921 FvH4_6g08591 FvH4_6g09511 FvH4_6g10331 FvH4_6g10401 FvH4_6g14161 FvH4_6g14171 FvH4_6g18481 FvH4_6g19721 FvH4_6g19980 FvH4_6g20104 FvH4_6g20112 FvH4_6g21261 FvH4_6g21651 FvH4_6g22051 FvH4_6g23141 FvH4_6g24822 FvH4_6g25082 FvH4_6g25391 FvH4_6g25560 FvH4_6g26350 FvH4_6g27031 FvH4_6g27810 FvH4_6g27971 FvH4_6g28331 FvH4_6g29391 FvH4_6g30781 FvH4_6g32221 FvH4_6g34680 FvH4_6g36181 FvH4_6g36551 FvH4_6g37491 FvH4_6g37663 FvH4_6g39590 FvH4_6g40582 FvH4_6g43843 FvH4_6g50551 FvH4_7g00240 FvH4_7g00731 FvH4_7g01031 FvH4_7g03301 FvH4_7g08180 FvH4_7g08180 FvH4_7g10631 FvH4_7g19710 FvH4_7g23892 FvH4_7g25280 FvH4_7g25551 FvH4_7g30121 FvH4_7g31931 FvH4_7g32672 FvH4_c21g00040 FvH4_c2g00053
prunus_persica Prupe.1G448800_v2.0.a1
rosa_chinensis RchiOBHm_Chr1g0322451 RchiOBHm_Chr5g0015171
rosa_laevigata RLG00000003077 RLG00000018186 RLG00000030343
rosa_multiflora Rmu_co8096726.1_g000001
rosa_roxburghii Rroxscaffold_157G00438380 Rroxscaffold_1G00001730 Rroxscaffold_3G00236310
rosa_rugosa Rorug02G0236500
rosa_samantha Rh4BG247300 Rh6BG286200 Rh6CG287300 Rh7DG257500

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccBSI CCGCTC 1 cut(s) 44
AciI CCGC 2 cut(s) 42, 370
AclI AACGTT 1 cut(s) 100
AclWI GGATC 5 cut(s) 12, 84, 163, 221, 620
AcoI YGGCCR 1 cut(s) 280
AcsI RAATTY 1 cut(s) 596
AcuI CTGAAG 3 cut(s) 266, 509, 659
AfaI GTAC 3 cut(s) 344, 500, 710
AfeI AGCGCT 1 cut(s) 524
AgsI TTSAA 4 cut(s) 32, 116, 263, 593
AjuI GAANNNNNNNTTGG 2 cut(s) 129, 161
AluBI AGCT 8 cut(s) 14, 119, 266, 286, 401, 434, 569, 685
AluI AGCT 8 cut(s) 14, 119, 266, 286, 401, 434, 569, 685
Alw26I GTCTC 1 cut(s) 56
AlwI GGATC 5 cut(s) 12, 84, 163, 221, 620
AlwNI CAGNNNCTG 1 cut(s) 572
Aor51HI AGCGCT 1 cut(s) 524
AoxI GGCC 2 cut(s) 280, 658
ApeKI GCWGC 4 cut(s) 11, 107, 434, 569
ApoI RAATTY 1 cut(s) 596
ArsI GACNNNNNNTTYG 2 cut(s) 317, 349
AspLEI GCGC 1 cut(s) 525
AspS9I GGNCC 2 cut(s) 325, 532
AsuHPI GGTGA 2 cut(s) 458, 616
AsuII TTCGAA 1 cut(s) 199
AvaII GGWCC 2 cut(s) 325, 532
AxyI CCTNAGG 1 cut(s) 231
BalI TGGCCA 1 cut(s) 282
BarI GAAGNNNNNNTAC 2 cut(s) 482, 514
BbvI GCAGC 4 cut(s) 23, 94, 421, 556
BccI CCATC 2 cut(s) 212, 272
BcgI CGANNNNNNTGC 4 cut(s) 179, 213, 530, 564
BcoDI GTCTC 1 cut(s) 56
BfaI CTAG 3 cut(s) 171, 305, 402
BfoI RGCGCY 1 cut(s) 526
BisI GCNGC 5 cut(s) 12, 42, 108, 435, 570
BlpI GCTNAGC 1 cut(s) 37
BlsI GCNGC 5 cut(s) 13, 43, 109, 436, 571
Bme18I GGWCC 2 cut(s) 325, 532
BmgT120I GGNCC 2 cut(s) 325, 532
BmsI GCATC 2 cut(s) 153, 599
Bpu1102I GCTNAGC 1 cut(s) 37
Bpu14I TTCGAA 1 cut(s) 199
BpuEI CTTGAG 1 cut(s) 80
BsaI GGTCTC 1 cut(s) 56
BsaXI ACNNNNNCTCC 2 cut(s) 166, 196
Bse118I RCCGGY 2 cut(s) 443, 656
Bse1I ACTGG 2 cut(s) 344, 535
Bse21I CCTNAGG 1 cut(s) 231
BseGI GGATG 1 cut(s) 168
BseMII CTCAG 3 cut(s) 84, 222, 564
BseNI ACTGG 2 cut(s) 344, 535
BseRI GAGGAG 2 cut(s) 485, 740
BseXI GCAGC 4 cut(s) 23, 94, 421, 556
BshFI GGCC 2 cut(s) 282, 660
BsiSI CCGG 2 cut(s) 444, 657
BsmAI GTCTC 1 cut(s) 56
BsmI GAATGC 1 cut(s) 295
BsnI GGCC 2 cut(s) 282, 660
Bso31I GGTCTC 1 cut(s) 56
Bsp119I TTCGAA 1 cut(s) 199
Bsp143I GATC 5 cut(s) 4, 76, 155, 226, 625
Bsp1720I GCTNAGC 1 cut(s) 37
BspACI CCGC 2 cut(s) 42, 370
BspANI GGCC 2 cut(s) 282, 660
BspCNI CTCAG 3 cut(s) 85, 223, 565
BspHI TCATGA 1 cut(s) 694
BspPI GGATC 5 cut(s) 12, 84, 163, 221, 620
BspT104I TTCGAA 1 cut(s) 199
BspTNI GGTCTC 1 cut(s) 56
BsrBI CCGCTC 1 cut(s) 44
BsrFI RCCGGY 2 cut(s) 443, 656
BsrI ACTGG 2 cut(s) 344, 535
BssAI RCCGGY 2 cut(s) 443, 656
BssMI GATC 5 cut(s) 4, 76, 155, 226, 625
Bst6I CTCTTC 2 cut(s) 132, 552
BstBI TTCGAA 1 cut(s) 199
BstC8I GCNNGC 5 cut(s) 188, 192, 284, 432, 527
BstDEI CTNAG 4 cut(s) 37, 93, 231, 573
BstF5I GGATG 1 cut(s) 168
BstH2I RGCGCY 1 cut(s) 526
BstHHI GCGC 1 cut(s) 525
BstKTI GATC 5 cut(s) 7, 79, 158, 229, 628
BstMAI GTCTC 1 cut(s) 56
BstMBI GATC 5 cut(s) 4, 76, 155, 226, 625
BstMWI GCNNNNNNNGC 3 cut(s) 17, 116, 440
BstV1I GCAGC 4 cut(s) 23, 94, 421, 556
BstX2I RGATCY 2 cut(s) 4, 625
BstYI RGATCY 2 cut(s) 4, 625
Bsu36I CCTNAGG 1 cut(s) 231
BsuRI GGCC 2 cut(s) 282, 660
BtsCI GGATG 1 cut(s) 168
BtsIMutI CAGTG 2 cut(s) 242, 542
Cac8I GCNNGC 5 cut(s) 188, 192, 284, 432, 527
CaiI CAGNNNCTG 1 cut(s) 572
CciI TCATGA 1 cut(s) 694
CfoI GCGC 1 cut(s) 525
Cfr10I RCCGGY 2 cut(s) 443, 656
Cfr13I GGNCC 2 cut(s) 325, 532
Csp6I GTAC 3 cut(s) 343, 499, 709
CviAII CATG 4 cut(s) 224, 322, 562, 695
CviQI GTAC 3 cut(s) 343, 499, 709
DdeI CTNAG 4 cut(s) 37, 93, 231, 573
DpnI GATC 5 cut(s) 6, 78, 157, 228, 627
DpnII GATC 5 cut(s) 4, 76, 155, 226, 625
EaeI YGGCCR 1 cut(s) 280
Eam1104I CTCTTC 2 cut(s) 132, 552
EarI CTCTTC 2 cut(s) 132, 552
Eco31I GGTCTC 1 cut(s) 56
Eco32I GATATC 1 cut(s) 315
Eco47I GGWCC 2 cut(s) 325, 532
Eco47III AGCGCT 1 cut(s) 524
Eco57I CTGAAG 3 cut(s) 266, 509, 659
Eco81I CCTNAGG 1 cut(s) 231
EcoRV GATATC 1 cut(s) 315
FaeI CATG 4 cut(s) 227, 325, 565, 698
FaiI YATR 7 cut(s) 225, 323, 563, 579, 602, 617, 696
FatI CATG 4 cut(s) 223, 321, 561, 694
Fnu4HI GCNGC 5 cut(s) 12, 42, 108, 435, 570
FokI GGATG 1 cut(s) 175
Fsp4HI GCNGC 5 cut(s) 12, 42, 108, 435, 570
FspBI CTAG 3 cut(s) 171, 305, 402
GlaI GCGC 1 cut(s) 524
GluI GCNGC 5 cut(s) 12, 42, 108, 435, 570
HaeII RGCGCY 1 cut(s) 526
HaeIII GGCC 2 cut(s) 282, 660
HapII CCGG 2 cut(s) 444, 657
HhaI GCGC 1 cut(s) 525
Hin1II CATG 4 cut(s) 227, 325, 565, 698
Hin6I GCGC 1 cut(s) 523
HinP1I GCGC 1 cut(s) 523
HindIII AAGCTT 1 cut(s) 117
HinfI GANTC 1 cut(s) 688
HpaII CCGG 2 cut(s) 444, 657
HphI GGTGA 2 cut(s) 458, 616
Hpy188I TCNGA 5 cut(s) 94, 319, 355, 653, 678
Hpy188III TCNNGA 6 cut(s) 59, 127, 230, 305, 668, 695
HpyAV CCTTC 6 cut(s) 26, 289, 357, 484, 639, 671
HpyCH4IV ACGT 2 cut(s) 100, 501
HpyCH4V TGCA 6 cut(s) 11, 110, 166, 377, 437, 612
HpyF10VI GCNNNNNNNGC 3 cut(s) 17, 116, 440
HpyF3I CTNAG 4 cut(s) 37, 93, 231, 573
HpySE526I ACGT 2 cut(s) 100, 501
Hsp92II CATG 4 cut(s) 227, 325, 565, 698
HspAI GCGC 1 cut(s) 523
Kzo9I GATC 5 cut(s) 4, 76, 155, 226, 625
LmnI GCTCC 2 cut(s) 271, 682
Lsp1109I GCAGC 4 cut(s) 23, 94, 421, 556
LweI GCATC 2 cut(s) 153, 599
MaeI CTAG 3 cut(s) 171, 305, 402
MaeII ACGT 2 cut(s) 100, 501
MaeIII GTNAC 1 cut(s) 634
MalI GATC 5 cut(s) 6, 78, 157, 228, 627
MbiI CCGCTC 1 cut(s) 44
MboI GATC 5 cut(s) 4, 76, 155, 226, 625
MboII GAAGA 6 cut(s) 146, 149, 539, 605, 635, 710
MfeI CAATTG 2 cut(s) 27, 111
MflI RGATCY 2 cut(s) 4, 625
MlsI TGGCCA 1 cut(s) 282
MluCI AATT 4 cut(s) 27, 48, 111, 596
MluNI TGGCCA 1 cut(s) 282
MnlI CCTC 8 cut(s) 146, 168, 226, 463, 672, 702, 718, 721
Mox20I TGGCCA 1 cut(s) 282
MscI TGGCCA 1 cut(s) 282
Msp20I TGGCCA 1 cut(s) 282
MspA1I CMGCKG 2 cut(s) 286, 569
MspI CCGG 2 cut(s) 444, 657
MunI CAATTG 2 cut(s) 27, 111
Mva1269I GAATGC 1 cut(s) 295
MwoI GCNNNNNNNGC 3 cut(s) 17, 116, 440
NdeII GATC 5 cut(s) 4, 76, 155, 226, 625
NlaIII CATG 4 cut(s) 227, 325, 565, 698
NmuCI GTSAC 1 cut(s) 634
NspV TTCGAA 1 cut(s) 199
PagI TCATGA 1 cut(s) 694
PctI GAATGC 1 cut(s) 295
PfeI GAWTC 1 cut(s) 688
PkrI GCNGC 5 cut(s) 13, 43, 109, 436, 571
Psp1406I AACGTT 1 cut(s) 100
PspPI GGNCC 2 cut(s) 325, 532
PstNI CAGNNNCTG 1 cut(s) 572
PsuI RGATCY 2 cut(s) 4, 625
PvuII CAGCTG 2 cut(s) 286, 569
RsaI GTAC 3 cut(s) 344, 500, 710
RsaNI GTAC 3 cut(s) 343, 499, 709
SatI GCNGC 5 cut(s) 12, 42, 108, 435, 570
Sau3AI GATC 5 cut(s) 4, 76, 155, 226, 625
Sau96I GGNCC 2 cut(s) 325, 532
SfaNI GCATC 2 cut(s) 153, 599
SfuI TTCGAA 1 cut(s) 199
SinI GGWCC 2 cut(s) 325, 532
SmlI CTYRAG 1 cut(s) 59
SmoI CTYRAG 1 cut(s) 59
Sse9I AATT 4 cut(s) 27, 48, 111, 596
SsiI CCGC 2 cut(s) 42, 370
SspMI CTAG 3 cut(s) 171, 305, 402
TaiI ACGT 2 cut(s) 103, 504
TaqI TCGA 3 cut(s) 199, 361, 723
TasI AATT 4 cut(s) 27, 48, 111, 596
TatI WGTACW 1 cut(s) 708
TauI GCSGC 1 cut(s) 44
TfiI GAWTC 1 cut(s) 688
TscAI CASTG 2 cut(s) 249, 542
TseFI GTSAC 1 cut(s) 634
TseI GCWGC 4 cut(s) 11, 107, 434, 569
Tsp45I GTSAC 1 cut(s) 634
TspDTI ATGAA 5 cut(s) 398, 465, 491, 636, 711
TspRI CASTG 2 cut(s) 249, 542
VpaK11BI GGWCC 2 cut(s) 325, 532
XapI RAATTY 1 cut(s) 596
XbaI TCTAGA 1 cut(s) 304
XspI CTAG 3 cut(s) 171, 305, 402
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.