FvH4_4g10121

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb4
OG0000258
Physical Location & Seq
Reverse (-)
12996936 .. 12997987
1052 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_4g10121.t1

Sequence Viewer

Length: 831 bp
ATGACAAACTTAGATCAAGAAGCTCTTAGTGTCAAACTTGGAAAATTTAGTGGACACCATTTTCGTAGATGGCAAAAACAGTTGAAATATTGGCTGTCTGTTCTTGGATTTATGTCTGCCATTGAAGGGCATGATCCAAACACATCATCTTCTTGGTTTAGCCAAGAGGATATGGAGTATTATTGCTATAATAGAATATTATGTGCCTTGTCTGACCATCTTTATGATGTGTATCATTCTACAACATCCACAGCCAAAGAACTTTGGGATGCATTAGAGGCTAAATATGGAATTGTAGATGCTGGAGTTGATAGGCTTACTGTCTCTAACTTTAATAGTTATAAGATGGTTGAAACCAAATATGTAGGAGACCAAATCCATGAGTACCAAGAACTTTTAAGAGGAGAGTTCACCCTCCGTCAAGCTATGAATTCCCTTAGAATAGAAGAGAAACAAAGGGTAGATCAGAAGGGAAAAGCTGAGAGTACTCCTGTTGTGAATTTAGTTGTGGGAAATAGAAACCATAATCAAAACAAGACTAGATTCCACAATAAAAATGGGAGAAATAACTTTCAGCCTAGGGGAATGAAATTTAAGAACAATAGAGCCAACCATAACAAACAGTTCCAGAACTCTAAGGATCAAGGGAGAGAGAAGATGTCTTGCTTTGTTTGTGGGAGGACCAATCATATGGCAAAGAATTGCTTCTACAAAAAGACTGAGGAGATCAAGTCTCAAGCAAATCAGAATGGTCCAAAGGCTCAAGTAAATATGATAGTGGAGCAAGAGTCCTCTCAACCATTGTTCAAAAATCGAGTGGAGGACGTGTAA
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

277

Amino Acids

32.18

Weight (kDa)

9.21

Isoelectric Point (pI)

43.42

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 59 - 133 4.4e-07 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: OG0000258)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G00980
fragaria_vesca FvH4_1g25682 FvH4_2g13961 FvH4_2g20162 FvH4_2g24753 FvH4_3g12191 FvH4_3g12632 FvH4_3g16171 FvH4_4g05871 FvH4_4g05873 FvH4_4g10121 FvH4_4g15488 FvH4_4g23911 FvH4_4g27782 FvH4_5g08912 FvH4_5g23001 FvH4_5g24552 FvH4_5g32801 FvH4_5g32802 FvH4_6g05093 FvH4_6g19722 FvH4_6g20391 FvH4_6g33792 FvH4_7g01381 FvH4_7g16761 FvH4_7g16761 FvH4_7g16761
malus_domestica MD01G1082500.v1.1 MD15G1436400.v1.1
prunus_persica Prupe.2G021400_v2.0.a1 Prupe.2G052400_v2.0.a1 Prupe.2G065000_v2.0.a1 Prupe.2G187700_v2.0.a1 Prupe.2G187800_v2.0.a1 Prupe.2G189900_v2.0.a1 Prupe.2G191300_v2.0.a1 Prupe.2G191700_v2.0.a1 Prupe.4G265600_v2.0.a1 Prupe.7G014200_v2.0.a1 Prupe.7G039000_v2.0.a1
pyrus_communis pycom01g05590 pycom01g05910 pycom02g12230 pycom02g25840 pycom03g15580 pycom04g04480 pycom05g09230 pycom05g23350 pycom05g23360 pycom07g08380 pycom09g01980 pycom09g01990 pycom11g18190 pycom11g18200 pycom11g21580 pycom13g04160 pycom15g25800 pycom16g16210 pycom16g17230 pycom16g24560 pycom16g25700 pycom17g11020
rosa_chinensis RchiOBHm_Chr1g0359981 RchiOBHm_Chr2g0151961 RchiOBHm_Chr2g0171331 RchiOBHm_Chr5g0081471 RchiOBHm_Chr6g0283031 RchiOBHm_Chr7g0197111 RchiOBHm_Chr7g0222601
rosa_laevigata RLG00000027843 RLG00000027845 RLG00000030065
rosa_multiflora Rmu_sc0000381.1_g000031 Rmu_sc0001179.1_g000035 Rmu_sc0001616.1_g000046 Rmu_sc0001851.1_g000032 Rmu_sc0002152.1_g000013 Rmu_sc0004031.1_g000015 Rmu_sc0004645.1_g000003 Rmu_sc0007393.1_g000001 Rmu_sc0008949.1_g000003 Rmu_sc0009799.1_g000011 Rmu_sc0011614.1_g000001 Rmu_sc0011699.1_g000009 Rmu_sc0019280.1_g000001 Rmu_sc0023984.1_g000001 Rmu_ssc0000050.1_g000036
rosa_roxburghii Rroxscaffold_1G00022650 Rroxscaffold_1G00033480 Rroxscaffold_3G00270250 Rroxscaffold_4G00296600 Rroxscaffold_4G00296760 Rroxscaffold_6G00409840
rosa_rugosa Rorug01G0273800 Rorug01G0273900 Rorug01G0274000
rosa_samantha Rh1AG287300 Rh1AG288100 Rh1BG253000 Rh1BG253500 Rh1BG399800 Rh1CG270400 Rh1CG271000 Rh1DG282000 Rh1DG282500 Rh4DG126500 Rh5DG194600 Rh5DG461100
rosa_wichuraiana Rw0G009130 Rw1G002590 Rw1G008490 Rw1G012210 Rw1G014290 Rw1G014490 Rw1G025510 Rw2G025840 Rw2G026170 Rw2G036510 Rw3G003050 Rw4G009270 Rw5G002350 Rw5G013930 Rw5G019500 Rw5G025890 Rw5G029960 Rw5G032360 Rw6G009890 Rw6G015670 Rw6G015860 Rw7G010030 Rw7G032600 Rw7G032770

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 342
AclWI GGATC 2 cut(s) 128, 648
AcsI RAATTY 4 cut(s) 44, 430, 499, 590
AfaI GTAC 2 cut(s) 386, 487
AfiI CCNNNNNNNGG 1 cut(s) 126
AflIII ACRYGT 1 cut(s) 825
AgsI TTSAA 4 cut(s) 85, 125, 353, 808
AjiI CACGTC 1 cut(s) 826
AluBI AGCT 3 cut(s) 23, 425, 479
AluI AGCT 3 cut(s) 23, 425, 479
Alw26I GTCTC 3 cut(s) 328, 363, 738
AlwI GGATC 2 cut(s) 128, 648
ApoI RAATTY 4 cut(s) 44, 430, 499, 590
ArsI GACNNNNNNTTYG 2 cut(s) 45, 77
Asp700I GAANNNNTTC 1 cut(s) 704
AspA2I CCTAGG 1 cut(s) 578
AspS9I GGNCC 2 cut(s) 681, 752
AsuHPI GGTGA 1 cut(s) 403
AvaII GGWCC 2 cut(s) 681, 752
AvrII CCTAGG 1 cut(s) 578
BccI CCATC 3 cut(s) 63, 225, 340
BcoDI GTCTC 3 cut(s) 328, 363, 738
BfaI CTAG 2 cut(s) 540, 579
BlnI CCTAGG 1 cut(s) 578
BmcAI AGTACT 1 cut(s) 487
Bme18I GGWCC 2 cut(s) 681, 752
BmgBI CACGTC 1 cut(s) 826
BmgT120I GGNCC 2 cut(s) 681, 752
BmsI GCATC 2 cut(s) 259, 289
BpmI CTGGAG 1 cut(s) 324
BpuEI CTTGAG 2 cut(s) 720, 747
BsaBI GATNNNNATC 1 cut(s) 231
BsaI GGTCTC 1 cut(s) 363
BsaJI CCNNGG 1 cut(s) 578
BsaXI ACNNNNNCTCC 5 cut(s) 716, 746, 773, 803, 812
Bsc4I CCNNNNNNNGG 1 cut(s) 126
Bse8I GATNNNNATC 1 cut(s) 231
BseDI CCNNGG 1 cut(s) 578
BseGI GGATG 2 cut(s) 245, 274
BseJI GATNNNNATC 1 cut(s) 231
BseLI CCNNNNNNNGG 1 cut(s) 126
BseMII CTCAG 2 cut(s) 471, 711
BseRI GAGGAG 2 cut(s) 417, 737
BslI CCNNNNNNNGG 1 cut(s) 126
BsmAI GTCTC 3 cut(s) 328, 363, 738
Bso31I GGTCTC 1 cut(s) 363
Bsp143I GATC 5 cut(s) 13, 133, 463, 640, 726
BspCNI CTCAG 2 cut(s) 472, 712
BspPI GGATC 2 cut(s) 128, 648
BspTNI GGTCTC 1 cut(s) 363
BssECI CCNNGG 1 cut(s) 578
BssMI GATC 5 cut(s) 13, 133, 463, 640, 726
BssT1I CCWWGG 1 cut(s) 578
Bst4CI ACNGT 3 cut(s) 81, 322, 624
Bst6I CTCTTC 1 cut(s) 441
BstDEI CTNAG 6 cut(s) 10, 26, 437, 480, 636, 720
BstF5I GGATG 2 cut(s) 245, 274
BstKTI GATC 5 cut(s) 16, 136, 466, 643, 729
BstMAI GTCTC 3 cut(s) 328, 363, 738
BstMBI GATC 5 cut(s) 13, 133, 463, 640, 726
BstMWI GCNNNNNNNGC 1 cut(s) 278
BstXI CCANNNNNNTGG 1 cut(s) 691
BtrI CACGTC 1 cut(s) 826
BtsCI GGATG 2 cut(s) 245, 274
Cfr13I GGNCC 2 cut(s) 681, 752
Csp6I GTAC 2 cut(s) 385, 486
CviAII CATG 2 cut(s) 131, 380
CviQI GTAC 2 cut(s) 385, 486
DdeI CTNAG 6 cut(s) 10, 26, 437, 480, 636, 720
DpnI GATC 5 cut(s) 15, 135, 465, 642, 728
DpnII GATC 5 cut(s) 13, 133, 463, 640, 726
Eam1104I CTCTTC 1 cut(s) 441
EarI CTCTTC 1 cut(s) 441
Eco130I CCWWGG 1 cut(s) 578
Eco31I GGTCTC 1 cut(s) 363
Eco47I GGWCC 2 cut(s) 681, 752
EcoRI GAATTC 1 cut(s) 430
EcoT14I CCWWGG 1 cut(s) 578
EcoT22I ATGCAT 1 cut(s) 274
ErhI CCWWGG 1 cut(s) 578
FaeI CATG 2 cut(s) 134, 383
FalI AAGNNNNNCTT 4 cut(s) 9, 41, 689, 721
FatI CATG 2 cut(s) 130, 379
FauNDI CATATG 1 cut(s) 690
FokI GGATG 2 cut(s) 232, 281
FspBI CTAG 2 cut(s) 540, 579
GsuI CTGGAG 1 cut(s) 324
Hin1II CATG 2 cut(s) 134, 383
HinfI GANTC 2 cut(s) 543, 788
HphI GGTGA 1 cut(s) 403
Hpy166II GTNNAC 2 cut(s) 53, 411
Hpy188I TCNGA 3 cut(s) 214, 468, 747
Hpy188III TCNNGA 2 cut(s) 17, 628
Hpy8I GTNNAC 2 cut(s) 53, 411
HpyAV CCTTC 2 cut(s) 119, 463
HpyCH4III ACNGT 3 cut(s) 81, 322, 624
HpyCH4IV ACGT 1 cut(s) 825
HpyCH4V TGCA 1 cut(s) 272
HpyF10VI GCNNNNNNNGC 1 cut(s) 278
HpyF3I CTNAG 6 cut(s) 10, 26, 437, 480, 636, 720
HpySE526I ACGT 1 cut(s) 825
Hsp92II CATG 2 cut(s) 134, 383
Kzo9I GATC 5 cut(s) 13, 133, 463, 640, 726
LmnI GCTCC 1 cut(s) 781
LpnPI CCDG 3 cut(s) 288, 504, 641
LweI GCATC 2 cut(s) 259, 289
MaeI CTAG 2 cut(s) 540, 579
MaeII ACGT 1 cut(s) 825
MalI GATC 5 cut(s) 15, 135, 465, 642, 728
MboI GATC 5 cut(s) 13, 133, 463, 640, 726
MboII GAAGA 3 cut(s) 141, 458, 667
MluCI AATT 6 cut(s) 44, 291, 430, 499, 590, 700
MlyI GAGTC 1 cut(s) 797
MnlI CCTC 8 cut(s) 160, 271, 395, 425, 672, 715, 802, 814
Mph1103I ATGCAT 1 cut(s) 274
MroXI GAANNNNTTC 1 cut(s) 704
MseI TTAA 3 cut(s) 333, 398, 594
MslI CAYNNNNRTG 1 cut(s) 222
MwoI GCNNNNNNNGC 1 cut(s) 278
NdeI CATATG 1 cut(s) 690
NdeII GATC 5 cut(s) 13, 133, 463, 640, 726
NlaIII CATG 2 cut(s) 134, 383
NsiI ATGCAT 1 cut(s) 274
PdmI GAANNNNTTC 1 cut(s) 704
PfeI GAWTC 1 cut(s) 543
PleI GAGTC 1 cut(s) 796
PpsI GAGTC 1 cut(s) 796
PsiI TTATAA 1 cut(s) 342
PspPI GGNCC 2 cut(s) 681, 752
RsaI GTAC 2 cut(s) 386, 487
RsaNI GTAC 2 cut(s) 385, 486
RseI CAYNNNNRTG 1 cut(s) 222
SaqAI TTAA 3 cut(s) 333, 398, 594
Sau3AI GATC 5 cut(s) 13, 133, 463, 640, 726
Sau96I GGNCC 2 cut(s) 681, 752
ScaI AGTACT 1 cut(s) 487
SchI GAGTC 1 cut(s) 797
SetI ASST 4 cut(s) 25, 427, 481, 828
SfaNI GCATC 2 cut(s) 259, 289
SinI GGWCC 2 cut(s) 681, 752
SmiMI CAYNNNNRTG 1 cut(s) 222
SmlI CTYRAG 2 cut(s) 735, 762
SmoI CTYRAG 2 cut(s) 735, 762
Sse9I AATT 6 cut(s) 44, 291, 430, 499, 590, 700
SspI AATATT 2 cut(s) 89, 198
SspMI CTAG 2 cut(s) 540, 579
StyI CCWWGG 1 cut(s) 578
TaaI ACNGT 3 cut(s) 81, 322, 624
TaiI ACGT 1 cut(s) 828
TaqI TCGA 1 cut(s) 814
TasI AATT 6 cut(s) 44, 291, 430, 499, 590, 700
TatI WGTACW 1 cut(s) 485
TfiI GAWTC 1 cut(s) 543
Tru1I TTAA 3 cut(s) 333, 398, 594
Tru9I TTAA 3 cut(s) 333, 398, 594
TspDTI ATGAA 2 cut(s) 443, 602
TspGWI ACGGA 1 cut(s) 407
VpaK11BI GGWCC 2 cut(s) 681, 752
XapI RAATTY 4 cut(s) 44, 430, 499, 590
XcmI CCANNNNNNNNNTGG 1 cut(s) 554
XmaJI CCTAGG 1 cut(s) 578
XmnI GAANNNNTTC 1 cut(s) 704
XspI CTAG 2 cut(s) 540, 579
ZrmI AGTACT 1 cut(s) 487
Zsp2I ATGCAT 1 cut(s) 274
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.