FvH4_3g06912

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0000154
Physical Location & Seq
Forward (+)
4001339 .. 4002807
1469 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_3g06912.t1

Sequence Viewer

Length: 867 bp
ATGGAACTCTTCTTCAAAATCATGGAGTACACGGTGGTGATCAATGGATTTACAGATCCAGGAGACCAAGCAAATCTCACACGAGATGAAAGAGAAGAATTGATTCGAAATAGGAAGAAGGATTGCAGAGCTTTGATGTATATATTTGGAGCAATTGATTCTGAAGTTTATGAGAAGATTGCACATGTTACAACATCAAAGGAGGCATGGGATTGTCTGATCAATACTTATGTGGGGCGAGATAAAGTGAAGAAGGTGAGATTGCAAACTCTATGGCGACAGTTCGAGCTTCTTCAGATGGAGAAGAAGGAAAGCATCTCTGAATACTTTGCAAGAACATTGGCTATTGTCAATCAAATGAAAGCCAATGGGGAGGATATCAAAGAGCTGCAGATTGTGGAGAAGATTCTTCGAACCTTGACAGAGCGGTTTGAAGGAAAAGTCATAGCCATTGAGGAGTCACAAGATCTCAATGCTATGACGAATGAGTGCAGCTTGAGAAGGTCAGAGAACAAGCAGTTTCATGCCAAGTTTGCAGAAGACAATGATATCAATGAGGAGACTTTGTTGATGGCTTTTAGTGCAATGAGTAATGGTGAACATATCACATGGTACTTGGACACAGGTTGCAACAATCATATGTCCGGCCACAAGGAGCTGTTTGTTGAGCTGAATGAGTCAATACGAGCTGAGATTACATTTGGGAATGCTGCAAGGATGTCGGTTAAAGGAAAAGGCAAGATCTTTATACAGTTGAAGAATGGGATGTACAACACTATATCAGGTGTATATTATGTGCCTGGCCTTAATCACAACTTGCTTAGTGTGAGGCAATTATCAGAGAGGGGGAAAGGCCTTGAGAGCTAA
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

289

Amino Acids

33.25

Weight (kDa)

5.97

Isoelectric Point (pI)

36.23

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 32 - 157 2.7e-24 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 204 - 283 2.8e-26 Pol polyprotein, beta-barrel domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

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)
AccBSI CCGCTC 1 cut(s) 427
AciI CCGC 1 cut(s) 427
AclWI GGATC 1 cut(s) 50
AcoI YGGCCR 1 cut(s) 646
AcuI CTGAAG 2 cut(s) 183, 278
AfaI GTAC 3 cut(s) 29, 614, 770
AflIII ACRYGT 1 cut(s) 184
AgsI TTSAA 3 cut(s) 16, 434, 757
AjnI CCWGG 2 cut(s) 58, 799
AleI CACNNNNGTG 1 cut(s) 35
AluBI AGCT 8 cut(s) 131, 289, 388, 495, 658, 670, 689, 864
AluI AGCT 8 cut(s) 131, 289, 388, 495, 658, 670, 689, 864
Alw26I GTCTC 2 cut(s) 57, 554
AlwI GGATC 1 cut(s) 50
AoxI GGCC 3 cut(s) 646, 802, 853
ApeKI GCWGC 3 cut(s) 388, 492, 710
Asp700I GAANNNNTTC 1 cut(s) 102
AsuHPI GGTGA 3 cut(s) 49, 268, 608
AsuII TTCGAA 2 cut(s) 106, 412
BauI CACGAG 1 cut(s) 81
BbsI GAAGAC 1 cut(s) 546
BbvI GCAGC 3 cut(s) 375, 504, 697
BccI CCATC 2 cut(s) 292, 565
BcgI CGANNNNNNTGC 2 cut(s) 702, 736
BciT130I CCWGG 2 cut(s) 60, 801
BclI TGATCA 2 cut(s) 39, 219
BcoDI GTCTC 2 cut(s) 57, 554
BfmI CTRYAG 1 cut(s) 389
BglII AGATCT 2 cut(s) 466, 741
BisI GCNGC 3 cut(s) 389, 493, 711
BlsI GCNGC 3 cut(s) 390, 494, 712
Bme1390I CCNGG 2 cut(s) 60, 801
BmrFI CCNGG 2 cut(s) 60, 801
BmsI GCATC 1 cut(s) 324
BpiI GAAGAC 1 cut(s) 546
Bpu14I TTCGAA 2 cut(s) 106, 412
BpuEI CTTGAG 1 cut(s) 517
BsaI GGTCTC 1 cut(s) 57
BsaXI ACNNNNNCTCC 2 cut(s) 551, 581
Bse3DI GCAATG 1 cut(s) 591
BseBI CCWGG 2 cut(s) 60, 801
BseGI GGATG 2 cut(s) 723, 771
BseMI GCAATG 1 cut(s) 591
BseMII CTCAG 1 cut(s) 681
BseRI GAGGAG 2 cut(s) 470, 572
BseXI GCAGC 3 cut(s) 375, 504, 697
BsgI GTGCAG 1 cut(s) 511
BshFI GGCC 3 cut(s) 648, 804, 855
BsiSI CCGG 1 cut(s) 645
BsmAI GTCTC 2 cut(s) 57, 554
BsmI GAATGC 1 cut(s) 712
BsnI GGCC 3 cut(s) 648, 804, 855
Bso31I GGTCTC 1 cut(s) 57
Bsp119I TTCGAA 2 cut(s) 106, 412
Bsp1407I TGTACA 1 cut(s) 768
Bsp143I GATC 5 cut(s) 39, 55, 219, 466, 741
BspACI CCGC 1 cut(s) 427
BspANI GGCC 3 cut(s) 648, 804, 855
BspCNI CTCAG 1 cut(s) 682
BspMAI CTGCAG 1 cut(s) 393
BspPI GGATC 1 cut(s) 50
BspT104I TTCGAA 2 cut(s) 106, 412
BspTNI GGTCTC 1 cut(s) 57
BsrBI CCGCTC 1 cut(s) 427
BsrDI GCAATG 1 cut(s) 591
BsrGI TGTACA 1 cut(s) 768
BssMI GATC 5 cut(s) 39, 55, 219, 466, 741
BssSI CACGAG 1 cut(s) 81
Bst2BI CACGAG 1 cut(s) 81
Bst2UI CCWGG 2 cut(s) 60, 801
Bst4CI ACNGT 3 cut(s) 34, 282, 753
Bst6I CTCTTC 1 cut(s) 14
BstAUI TGTACA 1 cut(s) 768
BstBI TTCGAA 2 cut(s) 106, 412
BstDEI CTNAG 2 cut(s) 690, 821
BstF5I GGATG 2 cut(s) 723, 771
BstKTI GATC 5 cut(s) 42, 58, 222, 469, 744
BstMAI GTCTC 2 cut(s) 57, 554
BstMBI GATC 5 cut(s) 39, 55, 219, 466, 741
BstMWI GCNNNNNNNGC 3 cut(s) 533, 581, 861
BstNI CCWGG 2 cut(s) 60, 801
BstNSI RCATGY 1 cut(s) 188
BstSCI CCNGG 2 cut(s) 58, 799
BstSFI CTRYAG 1 cut(s) 389
BstV1I GCAGC 3 cut(s) 375, 504, 697
BstV2I GAAGAC 1 cut(s) 546
BstX2I RGATCY 3 cut(s) 55, 466, 741
BstYI RGATCY 3 cut(s) 55, 466, 741
BsuRI GGCC 3 cut(s) 648, 804, 855
BtsCI GGATG 2 cut(s) 723, 771
Csp6I GTAC 3 cut(s) 28, 613, 769
CviAII CATG 5 cut(s) 22, 185, 207, 524, 609
CviQI GTAC 3 cut(s) 28, 613, 769
DdeI CTNAG 2 cut(s) 690, 821
DpnI GATC 5 cut(s) 41, 57, 221, 468, 743
DpnII GATC 5 cut(s) 39, 55, 219, 466, 741
EaeI YGGCCR 1 cut(s) 646
Eam1104I CTCTTC 1 cut(s) 14
EarI CTCTTC 1 cut(s) 14
Eco147I AGGCCT 1 cut(s) 855
Eco31I GGTCTC 1 cut(s) 57
Eco32I GATATC 2 cut(s) 379, 550
Eco57I CTGAAG 2 cut(s) 183, 278
EcoRII CCWGG 2 cut(s) 58, 799
EcoRV GATATC 2 cut(s) 379, 550
FaeI CATG 5 cut(s) 25, 188, 210, 527, 612
FatI CATG 5 cut(s) 21, 184, 206, 523, 608
FauNDI CATATG 1 cut(s) 639
FbaI TGATCA 2 cut(s) 39, 219
Fnu4HI GCNGC 3 cut(s) 389, 493, 711
FokI GGATG 2 cut(s) 730, 778
Fsp4HI GCNGC 3 cut(s) 389, 493, 711
GluI GCNGC 3 cut(s) 389, 493, 711
HaeIII GGCC 3 cut(s) 648, 804, 855
HapII CCGG 1 cut(s) 645
Hin1II CATG 5 cut(s) 25, 188, 210, 527, 612
HinfI GANTC 5 cut(s) 103, 158, 406, 458, 677
HpaII CCGG 1 cut(s) 645
HphI GGTGA 3 cut(s) 49, 268, 608
Hpy166II GTNNAC 2 cut(s) 30, 599
Hpy188I TCNGA 6 cut(s) 163, 219, 297, 322, 508, 841
Hpy8I GTNNAC 2 cut(s) 30, 599
HpyAV CCTTC 5 cut(s) 112, 247, 301, 428, 495
HpyCH4III ACNGT 3 cut(s) 34, 282, 753
HpyF10VI GCNNNNNNNGC 3 cut(s) 533, 581, 861
HpyF3I CTNAG 2 cut(s) 690, 821
Hsp92II CATG 5 cut(s) 25, 188, 210, 527, 612
Ksp22I TGATCA 2 cut(s) 39, 219
Kzo9I GATC 5 cut(s) 39, 55, 219, 466, 741
LmnI GCTCC 2 cut(s) 149, 655
LpnPI CCDG 7 cut(s) 45, 72, 609, 658, 768, 786, 813
Lsp1109I GCAGC 3 cut(s) 375, 504, 697
LweI GCATC 1 cut(s) 324
MaeIII GTNAC 2 cut(s) 187, 459
MalI GATC 5 cut(s) 41, 57, 221, 468, 743
MbiI CCGCTC 1 cut(s) 427
MboI GATC 5 cut(s) 39, 55, 219, 466, 741
MfeI CAATTG 1 cut(s) 153
MflI RGATCY 3 cut(s) 55, 466, 741
MluCI AATT 3 cut(s) 98, 153, 833
MlyI GAGTC 2 cut(s) 467, 686
MnlI CCTC 6 cut(s) 196, 367, 448, 550, 822, 837
MroXI GAANNNNTTC 1 cut(s) 102
MseI TTAA 2 cut(s) 726, 807
MslI CAYNNNNRTG 1 cut(s) 35
MspI CCGG 1 cut(s) 645
MspR9I CCNGG 2 cut(s) 60, 801
MunI CAATTG 1 cut(s) 153
Mva1269I GAATGC 1 cut(s) 712
MvaI CCWGG 2 cut(s) 60, 801
MwoI GCNNNNNNNGC 3 cut(s) 533, 581, 861
NdeI CATATG 1 cut(s) 639
NdeII GATC 5 cut(s) 39, 55, 219, 466, 741
NlaIII CATG 5 cut(s) 25, 188, 210, 527, 612
NmuCI GTSAC 1 cut(s) 459
NspI RCATGY 1 cut(s) 188
NspV TTCGAA 2 cut(s) 106, 412
OliI CACNNNNGTG 1 cut(s) 35
PceI AGGCCT 1 cut(s) 855
PciI ACATGT 1 cut(s) 184
PctI GAATGC 1 cut(s) 712
PdmI GAANNNNTTC 1 cut(s) 102
PfeI GAWTC 3 cut(s) 103, 158, 406
PfoI TCCNGGA 1 cut(s) 58
PkrI GCNGC 3 cut(s) 390, 494, 712
PleI GAGTC 2 cut(s) 466, 685
PpsI GAGTC 2 cut(s) 466, 685
PscI ACATGT 1 cut(s) 184
Psp6I CCWGG 2 cut(s) 58, 799
PspGI CCWGG 2 cut(s) 58, 799
PstI CTGCAG 1 cut(s) 393
PsuI RGATCY 3 cut(s) 55, 466, 741
RsaI GTAC 3 cut(s) 29, 614, 770
RsaNI GTAC 3 cut(s) 28, 613, 769
RseI CAYNNNNRTG 1 cut(s) 35
SaqAI TTAA 2 cut(s) 726, 807
SatI GCNGC 3 cut(s) 389, 493, 711
Sau3AI GATC 5 cut(s) 39, 55, 219, 466, 741
SchI GAGTC 2 cut(s) 467, 686
ScrFI CCNGG 2 cut(s) 60, 801
SfaNI GCATC 1 cut(s) 324
SfcI CTRYAG 1 cut(s) 389
SfuI TTCGAA 2 cut(s) 106, 412
SmiMI CAYNNNNRTG 1 cut(s) 35
SmlI CTYRAG 2 cut(s) 496, 857
SmoI CTYRAG 2 cut(s) 496, 857
Sse9I AATT 3 cut(s) 98, 153, 833
SseBI AGGCCT 1 cut(s) 855
SsiI CCGC 1 cut(s) 427
StuI AGGCCT 1 cut(s) 855
StyD4I CCNGG 2 cut(s) 58, 799
TaaI ACNGT 3 cut(s) 34, 282, 753
TaqI TCGA 3 cut(s) 106, 285, 412
TasI AATT 3 cut(s) 98, 153, 833
TatI WGTACW 2 cut(s) 27, 768
TfiI GAWTC 3 cut(s) 103, 158, 406
Tru1I TTAA 2 cut(s) 726, 807
Tru9I TTAA 2 cut(s) 726, 807
TseFI GTSAC 1 cut(s) 459
TseI GCWGC 3 cut(s) 388, 492, 710
Tsp45I GTSAC 1 cut(s) 459
TspDTI ATGAA 3 cut(s) 102, 374, 512
XceI RCATGY 1 cut(s) 188
XmnI GAANNNNTTC 1 cut(s) 102
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.