FvH4_1g18141

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb1
OG0017966
Physical Location & Seq
Forward (+)
10552387 .. 10557654
5268 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_1g18141.t1

Sequence Viewer

Length: 546 bp
ATGTCCAATGATGATATCCCTCCACCGAAATCAAGCGGTGATAATCCTCCTCCACCGAAATCAGGCGGTGATCCTCCTCCACCAAAACCAAACAGTTCCGGTTCAGATGCCGATCCCTTCAAGGCAGAACCTTCCAATCCTTACTTCATCCACCACTCGGATCATCCTGGCTTAGTCCTAGTCTCCAAACTCCTAAATGGGGATAATTTTTCTGGTTGGAAAAGGGCTATGTCTCTGGATTCAAGGAGTTGCCCCAGTCTCTGCTATTGCGGAGGCTTACCGGCTGCGGTTGAGGTTGAGCAGCCTAAGGCCACTAGGAGTAGTGCTGCTTCACAAAACATCACTACAAGCTGTGGGAATACTGTTCCGATGTGCAAAAAGCTCGACGATTTAGGTGGCTGGCTCGTCGACAACGTGATGTCAGCCTTCTTTGGTTCTCTGCAACGCTGCTCTTGCATGCACATCGACACCAAAGACGACCCTGATCACGATCCTATTTGCATGCCTCTTGCTACTGCCAACAACAAAGATATTGATATTAATTGA
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_3

Protein Analysis

182

Amino Acids

19.24

Weight (kDa)

5.02

Isoelectric Point (pI)

68.37

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 51 - 79 4.7e-11 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: OG0017966)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g18110 FvH4_1g18141
prunus_persica Prupe.6G217400_v2.0.a1
rosa_chinensis RchiOBHm_Chr2g0108601
rosa_laevigata RLG00000017680
rosa_roxburghii Rroxscaffold_2G00134990
rosa_samantha Rh2AG203600 Rh2BG216400 Rh2CG207500 Rh2DG210600
rosa_wichuraiana Rw2G016270

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccI GTMKAC 1 cut(s) 408
AciI CCGC 4 cut(s) 36, 66, 270, 287
AclWI GGATC 4 cut(s) 65, 107, 168, 485
AfiI CCNNNNNNNGG 3 cut(s) 62, 157, 199
AgsI TTSAA 2 cut(s) 121, 243
AjnI CCWGG 1 cut(s) 166
AjuI GAANNNNNNNTTGG 2 cut(s) 128, 160
AluBI AGCT 2 cut(s) 351, 382
AluI AGCT 2 cut(s) 351, 382
Alw26I GTCTC 3 cut(s) 187, 237, 263
AlwI GGATC 4 cut(s) 65, 107, 168, 485
AlwNI CAGNNNCTG 1 cut(s) 261
AoxI GGCC 1 cut(s) 309
ApeKI GCWGC 4 cut(s) 284, 301, 326, 447
AseI ATTAAT 1 cut(s) 540
AsuHPI GGTGA 2 cut(s) 50, 80
AxyI CCTNAGG 1 cut(s) 306
BarI GAAGNNNNNNTAC 2 cut(s) 313, 345
BbvI GCAGC 4 cut(s) 271, 313, 313, 434
BcgI CGANNNNNNTGC 4 cut(s) 364, 398, 445, 479
BciT130I CCWGG 1 cut(s) 168
BclI TGATCA 1 cut(s) 484
BcoDI GTCTC 3 cut(s) 187, 237, 263
BfaI CTAG 2 cut(s) 179, 315
BisI GCNGC 4 cut(s) 285, 302, 327, 448
BlsI GCNGC 4 cut(s) 286, 303, 328, 449
Bme1390I CCNGG 1 cut(s) 168
BmrFI CCNGG 1 cut(s) 168
BmrI ACTGGG 1 cut(s) 249
BmsI GCATC 1 cut(s) 97
BmuI ACTGGG 1 cut(s) 249
BsaBI GATNNNNATC 2 cut(s) 111, 489
BsaWI WCCGGW 1 cut(s) 98
Bsc4I CCNNNNNNNGG 3 cut(s) 62, 157, 199
Bse118I RCCGGY 1 cut(s) 280
Bse1I ACTGG 1 cut(s) 255
Bse21I CCTNAGG 1 cut(s) 306
Bse8I GATNNNNATC 2 cut(s) 111, 489
BseBI CCWGG 1 cut(s) 168
BseGI GGATG 2 cut(s) 147, 163
BseJI GATNNNNATC 2 cut(s) 111, 489
BseLI CCNNNNNNNGG 3 cut(s) 62, 157, 199
BseNI ACTGG 1 cut(s) 255
BseRI GAGGAG 2 cut(s) 39, 66
BseXI GCAGC 4 cut(s) 271, 313, 313, 434
BshFI GGCC 1 cut(s) 311
BsiSI CCGG 2 cut(s) 99, 281
BslI CCNNNNNNNGG 3 cut(s) 62, 157, 199
BsmAI GTCTC 3 cut(s) 187, 237, 263
BsnI GGCC 1 cut(s) 311
Bsp143I GATC 5 cut(s) 70, 112, 160, 484, 490
BspACI CCGC 4 cut(s) 36, 66, 270, 287
BspANI GGCC 1 cut(s) 311
BspPI GGATC 4 cut(s) 65, 107, 168, 485
BsrFI RCCGGY 1 cut(s) 280
BsrI ACTGG 1 cut(s) 255
BssAI RCCGGY 1 cut(s) 280
BssMI GATC 5 cut(s) 70, 112, 160, 484, 490
Bst2UI CCWGG 1 cut(s) 168
Bst4CI ACNGT 2 cut(s) 95, 364
BstC8I GCNNGC 3 cut(s) 401, 458, 503
BstDEI CTNAG 2 cut(s) 172, 306
BstF5I GGATG 2 cut(s) 147, 163
BstKTI GATC 5 cut(s) 73, 115, 163, 487, 493
BstMAI GTCTC 3 cut(s) 187, 237, 263
BstMBI GATC 5 cut(s) 70, 112, 160, 484, 490
BstMWI GCNNNNNNNGC 1 cut(s) 453
BstNI CCWGG 1 cut(s) 168
BstNSI RCATGY 2 cut(s) 460, 505
BstSCI CCNGG 1 cut(s) 166
BstV1I GCAGC 4 cut(s) 271, 313, 313, 434
Bsu36I CCTNAGG 1 cut(s) 306
BsuRI GGCC 1 cut(s) 311
BtsCI GGATG 2 cut(s) 147, 163
Cac8I GCNNGC 3 cut(s) 401, 458, 503
CaiI CAGNNNCTG 1 cut(s) 261
Cfr10I RCCGGY 1 cut(s) 280
CviAII CATG 2 cut(s) 457, 502
DdeI CTNAG 2 cut(s) 172, 306
DpnI GATC 5 cut(s) 72, 114, 162, 486, 492
DpnII GATC 5 cut(s) 70, 112, 160, 484, 490
Eco32I GATATC 1 cut(s) 16
Eco81I CCTNAGG 1 cut(s) 306
EcoRII CCWGG 1 cut(s) 166
EcoRV GATATC 1 cut(s) 16
FaeI CATG 2 cut(s) 460, 505
FaiI YATR 3 cut(s) 230, 458, 503
FatI CATG 2 cut(s) 456, 501
FbaI TGATCA 1 cut(s) 484
FblI GTMKAC 1 cut(s) 408
Fnu4HI GCNGC 4 cut(s) 285, 302, 327, 448
FokI GGATG 2 cut(s) 134, 150
Fsp4HI GCNGC 4 cut(s) 285, 302, 327, 448
FspBI CTAG 2 cut(s) 179, 315
GluI GCNGC 4 cut(s) 285, 302, 327, 448
HaeIII GGCC 1 cut(s) 311
HapII CCGG 2 cut(s) 99, 281
Hin1II CATG 2 cut(s) 460, 505
HincII GTYRAC 1 cut(s) 409
HindII GTYRAC 1 cut(s) 409
HinfI GANTC 1 cut(s) 239
HpaII CCGG 2 cut(s) 99, 281
HphI GGTGA 2 cut(s) 50, 80
Hpy166II GTNNAC 1 cut(s) 409
Hpy188I TCNGA 3 cut(s) 106, 160, 369
Hpy188III TCNNGA 2 cut(s) 236, 488
Hpy8I GTNNAC 1 cut(s) 409
Hpy99I CGWCG 2 cut(s) 389, 410
HpyAV CCTTC 3 cut(s) 127, 141, 436
HpyCH4III ACNGT 2 cut(s) 95, 364
HpyCH4IV ACGT 1 cut(s) 414
HpyCH4V TGCA 5 cut(s) 375, 442, 456, 460, 501
HpyF10VI GCNNNNNNNGC 1 cut(s) 453
HpyF3I CTNAG 2 cut(s) 172, 306
HpySE526I ACGT 1 cut(s) 414
Hsp92II CATG 2 cut(s) 460, 505
Ksp22I TGATCA 1 cut(s) 484
Kzo9I GATC 5 cut(s) 70, 112, 160, 484, 490
Lsp1109I GCAGC 4 cut(s) 271, 313, 313, 434
LweI GCATC 1 cut(s) 97
MaeI CTAG 2 cut(s) 179, 315
MaeII ACGT 1 cut(s) 414
MalI GATC 5 cut(s) 72, 114, 162, 486, 492
MboI GATC 5 cut(s) 70, 112, 160, 484, 490
MluCI AATT 2 cut(s) 205, 541
MmeI TCCRAC 1 cut(s) 197
MnlI CCTC 8 cut(s) 30, 57, 60, 84, 87, 266, 286, 516
MseI TTAA 1 cut(s) 540
MspI CCGG 2 cut(s) 99, 281
MspR9I CCNGG 1 cut(s) 168
MvaI CCWGG 1 cut(s) 168
MwoI GCNNNNNNNGC 1 cut(s) 453
NdeII GATC 5 cut(s) 70, 112, 160, 484, 490
NlaIII CATG 2 cut(s) 460, 505
NspI RCATGY 2 cut(s) 460, 505
PaeI GCATGC 2 cut(s) 460, 505
PcsI WCGNNNNNNNCGW 1 cut(s) 411
PfeI GAWTC 1 cut(s) 239
PkrI GCNGC 4 cut(s) 286, 303, 328, 449
PshBI ATTAAT 1 cut(s) 540
Psp6I CCWGG 1 cut(s) 166
PspGI CCWGG 1 cut(s) 166
PstNI CAGNNNCTG 1 cut(s) 261
SalI GTCGAC 1 cut(s) 407
SaqAI TTAA 1 cut(s) 540
SatI GCNGC 4 cut(s) 285, 302, 327, 448
Sau3AI GATC 5 cut(s) 70, 112, 160, 484, 490
ScrFI CCNGG 1 cut(s) 168
SetI ASST 6 cut(s) 133, 297, 353, 384, 397, 417
SfaNI GCATC 1 cut(s) 97
SphI GCATGC 2 cut(s) 460, 505
Sse9I AATT 2 cut(s) 205, 541
SsiI CCGC 4 cut(s) 36, 66, 270, 287
SspMI CTAG 2 cut(s) 179, 315
StyD4I CCNGG 1 cut(s) 166
TaaI ACNGT 2 cut(s) 95, 364
TaiI ACGT 1 cut(s) 417
TaqI TCGA 3 cut(s) 384, 408, 465
TasI AATT 2 cut(s) 205, 541
TfiI GAWTC 1 cut(s) 239
Tru1I TTAA 1 cut(s) 540
Tru9I TTAA 1 cut(s) 540
TseI GCWGC 4 cut(s) 284, 301, 326, 447
TspDTI ATGAA 1 cut(s) 136
VspI ATTAAT 1 cut(s) 540
XceI RCATGY 2 cut(s) 460, 505
XmiI GTMKAC 1 cut(s) 408
XspI CTAG 2 cut(s) 179, 315
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.