Rroxscaffold_2G00138900

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000002
OG0000154
Physical Location & Seq
Forward (+)
77094788 .. 77097160
2373 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_2G00138900.1

Sequence Viewer

Length: 1053 bp
ATGGCGAACCGAGGGAATGATTTTCCTCAATGCCCAGTTGGTAAATTTGATGGGAAAGGGAACTTCCAGCATTGGAGATCACAGATGGAGCTCTTCTTCAAAATAATGGAGTACACAAAGGTGGTGATAAATGGATTTGCAGATCCAGGAGACCAAGCAAATCTCACACAAAATCAGAGGGAGGAACTGATTCGAAACAGAAAGAAAGATAGCAGAGCCCTGATGTATATTTATGGAGTAATTGATTCTGAAGTCTATGAGAAGATTGCACATGTTACCACATCGAAAGAGGCCTGGGATTGTCTAATCAATACCTTTATTGGAAGAGATAAAGTGAAAAAGTTGAGGTTGCAGACTCTACGACGACAGTTCGAGCTTCTTCAAATGGAGAAAAGGGAAAGTATCTCCGATTACTTTGCAAGAACATTGGCCATTGTCAACCAAATGAAGGCCAATGGGGAGGTCATCAAAGAACTCCAGATTGTGGAGAAAATCCTTCGAACCTTGACGGAGCGGTTTGAAGGAAAGGTCACAGCCATTGAGGAGTCTCAAGACCTTAATGCTATGACGGTGGATGACTTATTGAGTTCCTTGCAGGCCTATGAACAAAGGCTGAATGAGAAGTCGGAAATGGTGATTGAAGAAGCATTACAGACTCAGTTAAGCTTCAAAAAGGAGAAAAATTGGTCGTCCCGTGGTGAGTCAAGCTCAACTCAGAAGAACCAAAACTCAAGTTACAAGAGAGGTTCACAGGGCAGATTTGGAACAAGAAGAGGAAGAGGAAGGGGCTTTCATTGGAGTCAAGGAAGAGATAGAGCAAATGTCCAGTGCTTTAATTGTCATGGATATGGTCATTACAAAAATGAATGCAGCTTGAGAAGGTCGGAGAACAAGCAGTTTCATGCCAAGTTTGCAGAGGACAACAATGACAGTGAAGAGACTTTGTTGATGGCTTTCAGTGCTATGAGTAATGGTGAACAGATCACATGGTACCTGGACACAGGCTGTAGCAATCATATGCTAACCAAGTTCCAGAAACAGAGACTCCACTAG
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
DUF4219 Retrotran_gag_2 zf-CCHC

Protein Analysis

350

Amino Acids

40.77

Weight (kDa)

9.06

Isoelectric Point (pI)

42.44

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 56 - 209 8.3e-28 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)
Acc65I GGTACC 1 cut(s) 990
AccB1I GGYRCC 1 cut(s) 990
AccB7I CCANNNNNTGG 1 cut(s) 484
AccBSI CCGCTC 1 cut(s) 514
AciI CCGC 1 cut(s) 514
AclWI GGATC 1 cut(s) 137
AcoI YGGCCR 1 cut(s) 429
AcsI RAATTY 1 cut(s) 44
AcuI CTGAAG 1 cut(s) 270
AfaI GTAC 2 cut(s) 113, 992
AfiI CCNNNNNNNGG 2 cut(s) 448, 484
AflIII ACRYGT 1 cut(s) 271
AgsI TTSAA 5 cut(s) 100, 383, 521, 641, 670
AjnI CCWGG 3 cut(s) 145, 293, 993
AleI CACNNNNGTG 1 cut(s) 119
AluBI AGCT 5 cut(s) 91, 376, 666, 708, 873
AluI AGCT 5 cut(s) 91, 376, 666, 708, 873
Alw21I GWGCWC 1 cut(s) 93
Alw26I GTCTC 4 cut(s) 144, 552, 932, 1036
AlwI GGATC 1 cut(s) 137
AoxI GGCC 4 cut(s) 291, 429, 450, 597
ApeKI GCWGC 1 cut(s) 870
ApoI RAATTY 1 cut(s) 44
Asp700I GAANNNNTTC 1 cut(s) 189
Asp718I GGTACC 1 cut(s) 990
AsuHPI GGTGA 4 cut(s) 136, 646, 710, 986
AsuII TTCGAA 2 cut(s) 193, 499
BalI TGGCCA 1 cut(s) 431
BanI GGYRCC 1 cut(s) 990
BanII GRGCYC 2 cut(s) 93, 220
BarI GAAGNNNNNNTAC 2 cut(s) 633, 665
Bbv12I GWGCWC 1 cut(s) 93
BbvI GCAGC 1 cut(s) 882
BccI CCATC 3 cut(s) 44, 79, 943
BcgI CGANNNNNNTGC 2 cut(s) 398, 432
BciT130I CCWGG 3 cut(s) 147, 295, 995
BcoDI GTCTC 4 cut(s) 144, 552, 932, 1036
BfaI CTAG 1 cut(s) 1051
BfmI CTRYAG 1 cut(s) 1006
BisI GCNGC 1 cut(s) 871
BlsI GCNGC 1 cut(s) 872
Bme1390I CCNGG 3 cut(s) 147, 295, 995
BmiI GGNNCC 1 cut(s) 992
BmrFI CCNGG 3 cut(s) 147, 295, 995
BmrI ACTGGG 1 cut(s) 29
BmuI ACTGGG 1 cut(s) 29
BplI GAGNNNNNCTC 2 cut(s) 692, 724
BpmI CTGGAG 1 cut(s) 461
Bpu14I TTCGAA 2 cut(s) 193, 499
BpuEI CTTGAG 3 cut(s) 534, 715, 895
BsaI GGTCTC 1 cut(s) 144
BsaJI CCNNGG 3 cut(s) 10, 294, 694
BsaXI ACNNNNNCTCC 1 cut(s) 1029
Bsc4I CCNNNNNNNGG 2 cut(s) 448, 484
Bse1I ACTGG 2 cut(s) 35, 826
BseBI CCWGG 3 cut(s) 147, 295, 995
BseDI CCNNGG 3 cut(s) 10, 294, 694
BseGI GGATG 1 cut(s) 580
BseLI CCNNNNNNNGG 2 cut(s) 448, 484
BseMII CTCAG 2 cut(s) 671, 728
BseNI ACTGG 2 cut(s) 35, 826
BseRI GAGGAG 1 cut(s) 557
BseXI GCAGC 1 cut(s) 882
BshFI GGCC 4 cut(s) 293, 431, 452, 599
BshNI GGYRCC 1 cut(s) 990
BsiHKAI GWGCWC 1 cut(s) 93
BslFI GGGAC 1 cut(s) 676
BslI CCNNNNNNNGG 2 cut(s) 448, 484
BsmAI GTCTC 4 cut(s) 144, 552, 932, 1036
BsmFI GGGAC 1 cut(s) 676
BsmI GAATGC 1 cut(s) 872
BsnI GGCC 4 cut(s) 293, 431, 452, 599
Bso31I GGTCTC 1 cut(s) 144
Bsp119I TTCGAA 2 cut(s) 193, 499
Bsp1286I GDGCHC 2 cut(s) 93, 220
Bsp143I GATC 3 cut(s) 77, 142, 981
BspACI CCGC 1 cut(s) 514
BspANI GGCC 4 cut(s) 293, 431, 452, 599
BspCNI CTCAG 2 cut(s) 670, 727
BspLI GGNNCC 1 cut(s) 992
BspPI GGATC 1 cut(s) 137
BspQI GCTCTTC 1 cut(s) 98
BspT104I TTCGAA 2 cut(s) 193, 499
BspT107I GGYRCC 1 cut(s) 990
BspTNI GGTCTC 1 cut(s) 144
BsrBI CCGCTC 1 cut(s) 514
BsrI ACTGG 2 cut(s) 35, 826
BssECI CCNNGG 3 cut(s) 10, 294, 694
BssMI GATC 3 cut(s) 77, 142, 981
Bst2UI CCWGG 3 cut(s) 147, 295, 995
Bst4CI ACNGT 3 cut(s) 369, 571, 932
Bst6I CTCTTC 6 cut(s) 98, 319, 766, 772, 802, 930
BstBI TTCGAA 2 cut(s) 193, 499
BstC8I GCNNGC 1 cut(s) 597
BstDEI CTNAG 2 cut(s) 657, 714
BstDSI CCRYGG 1 cut(s) 694
BstF5I GGATG 1 cut(s) 580
BstKTI GATC 3 cut(s) 80, 145, 984
BstMAI GTCTC 4 cut(s) 144, 552, 932, 1036
BstMBI GATC 3 cut(s) 77, 142, 981
BstMWI GCNNNNNNNGC 2 cut(s) 911, 959
BstNI CCWGG 3 cut(s) 147, 295, 995
BstNSI RCATGY 1 cut(s) 275
BstSCI CCNGG 3 cut(s) 145, 293, 993
BstSFI CTRYAG 1 cut(s) 1006
BstV1I GCAGC 1 cut(s) 882
BstX2I RGATCY 1 cut(s) 142
BstYI RGATCY 1 cut(s) 142
BsuRI GGCC 4 cut(s) 293, 431, 452, 599
BtgI CCRYGG 1 cut(s) 694
BtsCI GGATG 1 cut(s) 580
BtsIMutI CAGTG 3 cut(s) 833, 937, 964
Cac8I GCNNGC 1 cut(s) 597
Csp6I GTAC 2 cut(s) 112, 991
CviAII CATG 4 cut(s) 272, 842, 902, 987
CviQI GTAC 2 cut(s) 112, 991
DdeI CTNAG 2 cut(s) 657, 714
DpnI GATC 3 cut(s) 79, 144, 983
DpnII GATC 3 cut(s) 77, 142, 981
EaeI YGGCCR 1 cut(s) 429
Eam1104I CTCTTC 6 cut(s) 98, 319, 766, 772, 802, 930
EarI CTCTTC 6 cut(s) 98, 319, 766, 772, 802, 930
Ecl136II GAGCTC 1 cut(s) 91
Eco147I AGGCCT 2 cut(s) 293, 599
Eco24I GRGCYC 2 cut(s) 93, 220
Eco31I GGTCTC 1 cut(s) 144
Eco53kI GAGCTC 1 cut(s) 91
Eco57I CTGAAG 1 cut(s) 270
EcoICRI GAGCTC 1 cut(s) 91
EcoRII CCWGG 3 cut(s) 145, 293, 993
EcoT38I GRGCYC 2 cut(s) 93, 220
FaeI CATG 4 cut(s) 275, 845, 905, 990
FaqI GGGAC 1 cut(s) 676
FatI CATG 4 cut(s) 271, 841, 901, 986
FauNDI CATATG 1 cut(s) 1017
Fnu4HI GCNGC 1 cut(s) 871
FokI GGATG 1 cut(s) 587
FriOI GRGCYC 2 cut(s) 93, 220
Fsp4HI GCNGC 1 cut(s) 871
FspBI CTAG 1 cut(s) 1051
GluI GCNGC 1 cut(s) 871
GsuI CTGGAG 1 cut(s) 461
HaeIII GGCC 4 cut(s) 293, 431, 452, 599
Hin1II CATG 4 cut(s) 275, 845, 905, 990
HincII GTYRAC 1 cut(s) 439
HindII GTYRAC 1 cut(s) 439
HindIII AAGCTT 1 cut(s) 664
HinfI GANTC 8 cut(s) 190, 245, 355, 545, 655, 701, 799, 1044
HphI GGTGA 4 cut(s) 136, 646, 710, 986
Hpy166II GTNNAC 4 cut(s) 114, 439, 749, 977
Hpy188I TCNGA 6 cut(s) 177, 250, 409, 628, 717, 886
Hpy188III TCNNGA 3 cut(s) 478, 551, 1033
Hpy8I GTNNAC 4 cut(s) 114, 439, 749, 977
Hpy99I CGWCG 1 cut(s) 366
HpyAV CCTTC 5 cut(s) 442, 506, 515, 777, 873
HpyCH4III ACNGT 3 cut(s) 369, 571, 932
HpyCH4V TGCA 7 cut(s) 140, 269, 352, 419, 595, 870, 914
HpyF10VI GCNNNNNNNGC 2 cut(s) 911, 959
HpyF3I CTNAG 2 cut(s) 657, 714
Hsp92II CATG 4 cut(s) 275, 845, 905, 990
KpnI GGTACC 1 cut(s) 994
Kzo9I GATC 3 cut(s) 77, 142, 981
LguI GCTCTTC 1 cut(s) 98
LmnI GCTCC 2 cut(s) 88, 511
Lsp1109I GCAGC 1 cut(s) 882
MaeI CTAG 1 cut(s) 1051
MaeIII GTNAC 3 cut(s) 274, 529, 734
MalI GATC 3 cut(s) 79, 144, 983
MbiI CCGCTC 1 cut(s) 514
MboI GATC 3 cut(s) 77, 142, 981
MflI RGATCY 1 cut(s) 142
MhlI GDGCHC 2 cut(s) 93, 220
MlsI TGGCCA 1 cut(s) 431
MluCI AATT 4 cut(s) 44, 240, 682, 835
MluNI TGGCCA 1 cut(s) 431
MlyI GAGTC 6 cut(s) 349, 554, 649, 710, 808, 1038
MmeI TCCRAC 2 cut(s) 606, 864
Mox20I TGGCCA 1 cut(s) 431
MroXI GAANNNNTTC 1 cut(s) 189
MscI TGGCCA 1 cut(s) 431
MseI TTAA 3 cut(s) 558, 662, 834
MslI CAYNNNNRTG 2 cut(s) 119, 846
Msp20I TGGCCA 1 cut(s) 431
MspR9I CCNGG 3 cut(s) 147, 295, 995
Mva1269I GAATGC 1 cut(s) 872
MvaI CCWGG 3 cut(s) 147, 295, 995
MwoI GCNNNNNNNGC 2 cut(s) 911, 959
NdeI CATATG 1 cut(s) 1017
NdeII GATC 3 cut(s) 77, 142, 981
NlaIII CATG 4 cut(s) 275, 845, 905, 990
NlaIV GGNNCC 1 cut(s) 992
NmuCI GTSAC 1 cut(s) 529
NspI RCATGY 1 cut(s) 275
NspV TTCGAA 2 cut(s) 193, 499
OliI CACNNNNGTG 1 cut(s) 119
PceI AGGCCT 2 cut(s) 293, 599
PciI ACATGT 1 cut(s) 271
PciSI GCTCTTC 1 cut(s) 98
PctI GAATGC 1 cut(s) 872
PdmI GAANNNNTTC 1 cut(s) 189
PfeI GAWTC 2 cut(s) 190, 245
PflMI CCANNNNNTGG 1 cut(s) 484
PfoI TCCNGGA 1 cut(s) 145
PkrI GCNGC 1 cut(s) 872
PleI GAGTC 6 cut(s) 349, 553, 649, 709, 807, 1038
PpsI GAGTC 6 cut(s) 349, 553, 649, 709, 807, 1038
PscI ACATGT 1 cut(s) 271
Psp124BI GAGCTC 1 cut(s) 93
Psp6I CCWGG 3 cut(s) 145, 293, 993
PspGI CCWGG 3 cut(s) 145, 293, 993
PspN4I GGNNCC 1 cut(s) 992
PsuI RGATCY 1 cut(s) 142
RsaI GTAC 2 cut(s) 113, 992
RsaNI GTAC 2 cut(s) 112, 991
RseI CAYNNNNRTG 2 cut(s) 119, 846
SacI GAGCTC 1 cut(s) 93
SapI GCTCTTC 1 cut(s) 98
SaqAI TTAA 3 cut(s) 558, 662, 834
SatI GCNGC 1 cut(s) 871
Sau3AI GATC 3 cut(s) 77, 142, 981
SchI GAGTC 6 cut(s) 349, 554, 649, 710, 808, 1038
ScrFI CCNGG 3 cut(s) 147, 295, 995
SduI GDGCHC 2 cut(s) 93, 220
SfcI CTRYAG 1 cut(s) 1006
SfuI TTCGAA 2 cut(s) 193, 499
SmiMI CAYNNNNRTG 2 cut(s) 119, 846
SmlI CTYRAG 3 cut(s) 549, 730, 874
SmoI CTYRAG 3 cut(s) 549, 730, 874
Sse9I AATT 4 cut(s) 44, 240, 682, 835
SseBI AGGCCT 2 cut(s) 293, 599
SsiI CCGC 1 cut(s) 514
SspMI CTAG 1 cut(s) 1051
SstI GAGCTC 1 cut(s) 93
StuI AGGCCT 2 cut(s) 293, 599
StyD4I CCNGG 3 cut(s) 145, 293, 993
TaaI ACNGT 3 cut(s) 369, 571, 932
TaqI TCGA 4 cut(s) 193, 284, 372, 499
TasI AATT 4 cut(s) 44, 240, 682, 835
TatI WGTACW 1 cut(s) 111
TfiI GAWTC 2 cut(s) 190, 245
Tru1I TTAA 3 cut(s) 558, 662, 834
Tru9I TTAA 3 cut(s) 558, 662, 834
TscAI CASTG 3 cut(s) 833, 937, 964
TseFI GTSAC 1 cut(s) 529
TseI GCWGC 1 cut(s) 870
Tsp45I GTSAC 1 cut(s) 529
TspDTI ATGAA 5 cut(s) 461, 618, 782, 879, 890
TspGWI ACGGA 1 cut(s) 524
TspRI CASTG 3 cut(s) 833, 937, 964
Van91I CCANNNNNTGG 1 cut(s) 484
XapI RAATTY 1 cut(s) 44
XceI RCATGY 1 cut(s) 275
XmnI GAANNNNTTC 1 cut(s) 189
XspI CTAG 1 cut(s) 1051
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.