Rw0G003940

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Contig00149
OG0000154
Physical Location & Seq
Forward (+)
9764 .. 10928
1165 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw0G003940.1

Sequence Viewer

Length: 1014 bp
ATGAGTGAAGACAAGACTCTGACGAAGATCCCTCACTTTGATGGTCATTATGACCACTGGAGTGAACTGATGGAGAATTTGCTAAGGGCAAAAGGTCTTTGGAGCTTGGTGGAGAATGGCTTTGAAAAGCCAAGAGCAAGGATGATGCTGACTGAGGTGCAGCAGACACAACTTGAAGATGCCAGAACCAAGGATCACCAAGTCAAGCATTATCTCTTCCAGGCACTTGATCTAACTGTCTTCAAACAAATCTTGGCCCATCGCACAATCAAGATTGTTTGGGACTCGATGAAGTGGAAGTTTGGAGGAAATATCAAGGTGAAGAGATCTCTTCTTAACTCACTAAGAAGAGAGTTTGAGGTTCTAGCGATGAAGAGGGATGAAACCATCACTGAGTATTTTGCAAGAATGATGACGGCCTCCAACAAGATAAGGAGCAATAGAGAAGATATGCCTGAATCAAAGATTAGGTTCACATATGTTGTAGTGTCCATTGAAGAATCAAAGGATACTAACATGTCCACCGATGAATTACGGAGTTCATTGGTGGTGCATGAACAAAATTTTCGAAGGGTGATCAATGAGGATGAGGATCAAGTTCTGAAGGACATTTTTCAATATGAATGTCCACAGTGGAACAAGGAGGCCAATTATGTAGAATTAGAAGAGGAAGATGAGCTGCTATTGATGGCATATGTAGAGCTACATGAAGCAAAGAGAAATGATGCGTGGTTTATAGACTCTGGATGCACAAATCACATGTGTGGGAATCAAGGTATGTGTACAAGTTTGGATACAACATTTTCACATATTGTCAAGCTTCGAAACAATACTAGAATAAAGGTTATTGGAAAGGGAGTTGTGAAGTTGGTTTTGAATGGAATTAGCTATGCCATTGGTGATGTGTATTGTGTACCTGAGCTCAAGAACAACCTCTTGAGCATGGGGCAACTTCAGGAAAAGGGATTGGCAGTGTTGTTTAAGGATGGTGTGTGCAGTGTTTATCATCCATAG
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

337

Amino Acids

39.3

Weight (kDa)

6.16

Isoelectric Point (pI)

46.82

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 24 - 187 1.4e-11 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 244 - 322 8.1e-23 Pol polyprotein, beta-barrel domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

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)
AclWI GGATC 3 cut(s) 22, 201, 600
AcsI RAATTY 2 cut(s) 76, 562
AcuI CTGAAG 2 cut(s) 623, 938
AfaI GTAC 2 cut(s) 784, 915
AflIII ACRYGT 2 cut(s) 516, 759
AgsI TTSAA 6 cut(s) 125, 176, 244, 497, 617, 877
AjnI CCWGG 1 cut(s) 219
AleI CACNNNNGTG 2 cut(s) 60, 762
AluBI AGCT 6 cut(s) 105, 679, 703, 820, 888, 922
AluI AGCT 6 cut(s) 105, 679, 703, 820, 888, 922
Alw21I GWGCWC 1 cut(s) 924
AlwI GGATC 3 cut(s) 22, 201, 600
AoxI GGCC 3 cut(s) 255, 417, 645
ApeKI GCWGC 2 cut(s) 160, 679
ApoI RAATTY 2 cut(s) 76, 562
AspS9I GGNCC 1 cut(s) 256
AsuHPI GGTGA 4 cut(s) 188, 331, 586, 911
AsuII TTCGAA 2 cut(s) 568, 823
BanII GRGCYC 1 cut(s) 924
BbsI GAAGAC 2 cut(s) 15, 232
Bbv12I GWGCWC 1 cut(s) 924
BbvI GCAGC 2 cut(s) 172, 666
BccI CCATC 6 cut(s) 35, 64, 267, 395, 682, 980
BceAI ACGGC 1 cut(s) 432
BciT130I CCWGG 1 cut(s) 221
BciVI GTATCC 2 cut(s) 502, 787
BclI TGATCA 1 cut(s) 576
BfaI CTAG 2 cut(s) 365, 834
BfuI GTATCC 2 cut(s) 502, 787
BglII AGATCT 1 cut(s) 326
BisI GCNGC 2 cut(s) 161, 680
BlsI GCNGC 2 cut(s) 162, 681
Bme1390I CCNGG 1 cut(s) 221
BmgT120I GGNCC 1 cut(s) 256
BmrFI CCNGG 1 cut(s) 221
BmsI GCATC 4 cut(s) 135, 169, 715, 737
BpiI GAAGAC 2 cut(s) 15, 232
BpmI CTGGAG 1 cut(s) 79
Bpu10I CCTNAGC 2 cut(s) 83, 918
Bpu14I TTCGAA 2 cut(s) 568, 823
BpuEI CTTGAG 2 cut(s) 908, 958
BsaBI GATNNNNATC 1 cut(s) 591
BsaJI CCNNGG 1 cut(s) 189
Bse1I ACTGG 1 cut(s) 62
Bse8I GATNNNNATC 1 cut(s) 591
BseBI CCWGG 1 cut(s) 221
BseDI CCNNGG 1 cut(s) 189
BseGI GGATG 6 cut(s) 147, 385, 592, 752, 991, 1006
BseJI GATNNNNATC 1 cut(s) 591
BseMII CTCAG 3 cut(s) 144, 384, 909
BseNI ACTGG 1 cut(s) 62
BseXI GCAGC 2 cut(s) 172, 666
BsgI GTGCAG 1 cut(s) 179
BshFI GGCC 3 cut(s) 257, 419, 647
BsiHKAI GWGCWC 1 cut(s) 924
BslFI GGGAC 1 cut(s) 296
BsmFI GGGAC 1 cut(s) 296
BsnI GGCC 3 cut(s) 257, 419, 647
Bsp119I TTCGAA 2 cut(s) 568, 823
Bsp1286I GDGCHC 1 cut(s) 924
Bsp1407I TGTACA 1 cut(s) 782
Bsp143I GATC 6 cut(s) 27, 193, 229, 326, 576, 592
BspANI GGCC 3 cut(s) 257, 419, 647
BspCNI CTCAG 3 cut(s) 145, 385, 910
BspPI GGATC 3 cut(s) 22, 201, 600
BspT104I TTCGAA 2 cut(s) 568, 823
BsrGI TGTACA 1 cut(s) 782
BsrI ACTGG 1 cut(s) 62
BssECI CCNNGG 1 cut(s) 189
BssMI GATC 6 cut(s) 27, 193, 229, 326, 576, 592
BssT1I CCWWGG 1 cut(s) 189
Bst2UI CCWGG 1 cut(s) 221
Bst4CI ACNGT 2 cut(s) 238, 633
Bst6I CTCTTC 6 cut(s) 221, 317, 336, 343, 368, 660
BstAUI TGTACA 1 cut(s) 782
BstBI TTCGAA 2 cut(s) 568, 823
BstDEI CTNAG 5 cut(s) 83, 153, 344, 393, 918
BstF5I GGATG 6 cut(s) 147, 385, 592, 752, 991, 1006
BstKTI GATC 6 cut(s) 30, 196, 232, 329, 579, 595
BstMBI GATC 6 cut(s) 27, 193, 229, 326, 576, 592
BstNI CCWGG 1 cut(s) 221
BstNSI RCATGY 2 cut(s) 520, 763
BstSCI CCNGG 1 cut(s) 219
BstV1I GCAGC 2 cut(s) 172, 666
BstV2I GAAGAC 2 cut(s) 15, 232
BstX2I RGATCY 2 cut(s) 27, 326
BstYI RGATCY 2 cut(s) 27, 326
BsuI GTATCC 2 cut(s) 502, 787
BsuRI GGCC 3 cut(s) 257, 419, 647
BtgZI GCGATG 2 cut(s) 245, 383
BtsCI GGATG 6 cut(s) 147, 385, 592, 752, 991, 1006
BtsI GCAGTG 2 cut(s) 978, 1003
BtsIMutI CAGTG 5 cut(s) 55, 390, 638, 978, 1003
Cfr13I GGNCC 1 cut(s) 256
Csp6I GTAC 2 cut(s) 783, 914
CviAII CATG 5 cut(s) 517, 554, 707, 760, 943
CviQI GTAC 2 cut(s) 783, 914
DdeI CTNAG 5 cut(s) 83, 153, 344, 393, 918
DpnI GATC 6 cut(s) 29, 195, 231, 328, 578, 594
DpnII GATC 6 cut(s) 27, 193, 229, 326, 576, 592
Eam1104I CTCTTC 6 cut(s) 221, 317, 336, 343, 368, 660
EarI CTCTTC 6 cut(s) 221, 317, 336, 343, 368, 660
Ecl136II GAGCTC 1 cut(s) 922
Eco130I CCWWGG 1 cut(s) 189
Eco24I GRGCYC 1 cut(s) 924
Eco53kI GAGCTC 1 cut(s) 922
Eco57I CTGAAG 2 cut(s) 623, 938
EcoICRI GAGCTC 1 cut(s) 922
EcoRII CCWGG 1 cut(s) 219
EcoT14I CCWWGG 1 cut(s) 189
EcoT38I GRGCYC 1 cut(s) 924
ErhI CCWWGG 1 cut(s) 189
FaeI CATG 5 cut(s) 520, 557, 710, 763, 946
FaqI GGGAC 1 cut(s) 296
FatI CATG 5 cut(s) 516, 553, 706, 759, 942
FauNDI CATATG 2 cut(s) 478, 694
FbaI TGATCA 1 cut(s) 576
Fnu4HI GCNGC 2 cut(s) 161, 680
FokI GGATG 6 cut(s) 154, 392, 599, 759, 993, 998
FriOI GRGCYC 1 cut(s) 924
Fsp4HI GCNGC 2 cut(s) 161, 680
FspBI CTAG 2 cut(s) 365, 834
GluI GCNGC 2 cut(s) 161, 680
GsuI CTGGAG 1 cut(s) 79
HaeIII GGCC 3 cut(s) 257, 419, 647
Hin1II CATG 5 cut(s) 520, 557, 710, 763, 946
HindIII AAGCTT 1 cut(s) 818
HinfI GANTC 6 cut(s) 16, 284, 458, 500, 740, 769
HphI GGTGA 4 cut(s) 188, 331, 586, 911
Hpy166II GTNNAC 6 cut(s) 65, 474, 522, 629, 783, 914
Hpy188I TCNGA 2 cut(s) 21, 603
Hpy188III TCNNGA 5 cut(s) 271, 744, 925, 937, 956
Hpy8I GTNNAC 6 cut(s) 65, 474, 522, 629, 783, 914
HpyAV CCTTC 2 cut(s) 564, 598
HpyCH4III ACNGT 2 cut(s) 238, 633
HpyCH4V TGCA 5 cut(s) 160, 404, 553, 750, 996
HpyF3I CTNAG 5 cut(s) 83, 153, 344, 393, 918
Hsp92II CATG 5 cut(s) 520, 557, 710, 763, 946
Ksp22I TGATCA 1 cut(s) 576
Kzo9I GATC 6 cut(s) 27, 193, 229, 326, 576, 592
LmnI GCTCC 2 cut(s) 102, 435
LpnPI CCDG 8 cut(s) 43, 196, 206, 233, 468, 729, 930, 941
Lsp1109I GCAGC 2 cut(s) 172, 666
LweI GCATC 4 cut(s) 135, 169, 715, 737
MaeI CTAG 2 cut(s) 365, 834
MalI GATC 6 cut(s) 29, 195, 231, 328, 578, 594
MboI GATC 6 cut(s) 27, 193, 229, 326, 576, 592
MflI RGATCY 2 cut(s) 27, 326
MhlI GDGCHC 1 cut(s) 924
MluCI AATT 6 cut(s) 76, 530, 562, 649, 659, 882
MlyI GAGTC 3 cut(s) 10, 278, 734
MmeI TCCRAC 1 cut(s) 447
MseI TTAA 2 cut(s) 336, 981
MslI CAYNNNNRTG 3 cut(s) 39, 60, 762
MspR9I CCNGG 1 cut(s) 221
MvaI CCWGG 1 cut(s) 221
NdeI CATATG 2 cut(s) 478, 694
NdeII GATC 6 cut(s) 27, 193, 229, 326, 576, 592
NlaIII CATG 5 cut(s) 520, 557, 710, 763, 946
NspI RCATGY 2 cut(s) 520, 763
NspV TTCGAA 2 cut(s) 568, 823
OliI CACNNNNGTG 2 cut(s) 60, 762
PciI ACATGT 2 cut(s) 516, 759
PfeI GAWTC 3 cut(s) 458, 500, 769
PkrI GCNGC 2 cut(s) 162, 681
PleI GAGTC 3 cut(s) 10, 278, 734
PpsI GAGTC 3 cut(s) 10, 278, 734
PscI ACATGT 2 cut(s) 516, 759
Psp124BI GAGCTC 1 cut(s) 924
Psp6I CCWGG 1 cut(s) 219
PspGI CCWGG 1 cut(s) 219
PspPI GGNCC 1 cut(s) 256
PsuI RGATCY 2 cut(s) 27, 326
RsaI GTAC 2 cut(s) 784, 915
RsaNI GTAC 2 cut(s) 783, 914
RseI CAYNNNNRTG 3 cut(s) 39, 60, 762
SacI GAGCTC 1 cut(s) 924
SaqAI TTAA 2 cut(s) 336, 981
SatI GCNGC 2 cut(s) 161, 680
Sau3AI GATC 6 cut(s) 27, 193, 229, 326, 576, 592
Sau96I GGNCC 1 cut(s) 256
SchI GAGTC 3 cut(s) 10, 278, 734
ScrFI CCNGG 1 cut(s) 221
SduI GDGCHC 1 cut(s) 924
SfaNI GCATC 4 cut(s) 135, 169, 715, 737
SfuI TTCGAA 2 cut(s) 568, 823
SmiMI CAYNNNNRTG 3 cut(s) 39, 60, 762
SmlI CTYRAG 2 cut(s) 923, 937
SmoI CTYRAG 2 cut(s) 923, 937
Sse9I AATT 6 cut(s) 76, 530, 562, 649, 659, 882
SspMI CTAG 2 cut(s) 365, 834
SstI GAGCTC 1 cut(s) 924
StyD4I CCNGG 1 cut(s) 219
StyI CCWWGG 1 cut(s) 189
TaaI ACNGT 2 cut(s) 238, 633
TaqI TCGA 3 cut(s) 287, 568, 823
TasI AATT 6 cut(s) 76, 530, 562, 649, 659, 882
TatI WGTACW 1 cut(s) 782
TfiI GAWTC 3 cut(s) 458, 500, 769
Tru1I TTAA 2 cut(s) 336, 981
Tru9I TTAA 2 cut(s) 336, 981
TscAI CASTG 5 cut(s) 62, 397, 638, 978, 1003
TseI GCWGC 2 cut(s) 160, 679
TspDTI ATGAA 8 cut(s) 305, 386, 396, 531, 543, 570, 636, 723
TspGWI ACGGA 1 cut(s) 550
TspRI CASTG 5 cut(s) 62, 397, 638, 978, 1003
XapI RAATTY 2 cut(s) 76, 562
XceI RCATGY 2 cut(s) 520, 763
XspI CTAG 2 cut(s) 365, 834
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.