Rroxscaffold_3G00270250

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000003
OG0000258
Physical Location & Seq
Reverse (-)
62868367 .. 62870651
2285 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_3G00270250.1

Sequence Viewer

Length: 939 bp
ATGACAAACTTAGATCAAGAGGCTCTTAGTGTTAAACCTGAAAAATTTAGTGGTCAACATTTCCGTAGATGGCAGAAACAGTTAAAATATTGGCTAACAGTTCTTGGGTATATTTCTGCCATTGAGGGGCATGATCAAAACAAAGCATCCTCTTCTTGGTTAACTCCGGAAGATATAGAATATCATTGTCATAATAGAATTTTAAGTGCTTTGTCTGACCACCTTTATGATGTGTATCACTCTACAACATCCACAGCCAAAGAACTTTGGGATGCATTAGAAGCCGAATATGGGATTGTAGATGCTGGAGTTGATAGGTTTACGGTCTCTAACTTTAATAGTTATAAGATGGTTGAAAACAAATCTGTAGATAGCCAAATCCATGAGTATCAAGAGCTTTTAAGGGGAATAGAAAAGAAAGGAACCAAGTTTAGTGAAGACTTCAAAGTGTCTTGCCTTATAGATAAATTGCCTCCTTCTTGGGATGAACATGCCAAGAGCCTTAGGCATAAACAAGGAGAGTTTACCCTTCGTCAAGCTATGAATAACCTTAGAGTTGAAGAAAAACAAAGGGTAGACCAAAAGGAAAAACCTGAGAAGACACCCATTGTGAACTTAATTGTGGGAAACAAAAACCATAACAAGACTAAATTCCACAACAGAAATCGAAGAAGCAATTTTCAGCCTAGGGGGATAAACTTTAAGAACAATAGAGCCAACCATAACAAACAGTTCCAAAAATCTAGGGATCAAGGGAGAGAAAAGATATCTTGCTTTGTTTGTGGAATGACCAACCATGTAGCAAGGAATTGCTTCTACAAAAGGACTGAGGAGAACAAGTCTCAAGCAAATAGGAATGGTCCAAAAGCTCAAGTGAATATGCTAATGGAGCAAGAGTCCTCTCAACCATTATTCAAAAATCAAGTGGAGGACGTGTAA
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

312

Amino Acids

36.51

Weight (kDa)

9.17

Isoelectric Point (pI)

50.97

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 48 - 195 6.3e-20 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) 345
AccI GTMKAC 1 cut(s) 576
AccIII TCCGGA 1 cut(s) 166
AclWI GGATC 1 cut(s) 756
AcsI RAATTY 3 cut(s) 44, 198, 650
AfiI CCNNNNNNNGG 3 cut(s) 126, 156, 291
AflIII ACRYGT 1 cut(s) 933
AgsI TTSAA 4 cut(s) 356, 445, 560, 916
AjiI CACGTC 1 cut(s) 934
AluBI AGCT 3 cut(s) 397, 539, 869
AluI AGCT 3 cut(s) 397, 539, 869
Alw26I GTCTC 2 cut(s) 331, 846
AlwI GGATC 1 cut(s) 756
Aor13HI TCCGGA 1 cut(s) 166
ApoI RAATTY 3 cut(s) 44, 198, 650
Asp700I GAANNNNTTC 1 cut(s) 812
AspA2I CCTAGG 1 cut(s) 686
AspS9I GGNCC 1 cut(s) 860
AvaII GGWCC 1 cut(s) 860
AvrII CCTAGG 1 cut(s) 686
AxyI CCTNAGG 1 cut(s) 503
BbsI GAAGAC 2 cut(s) 444, 605
BccI CCATC 2 cut(s) 63, 343
BclI TGATCA 1 cut(s) 133
BcoDI GTCTC 2 cut(s) 331, 846
BfaI CTAG 2 cut(s) 687, 744
BfmI CTRYAG 1 cut(s) 366
BlnI CCTAGG 1 cut(s) 686
Bme18I GGWCC 1 cut(s) 860
BmgBI CACGTC 1 cut(s) 934
BmgT120I GGNCC 1 cut(s) 860
BmiI GGNNCC 1 cut(s) 424
BmsI GCATC 3 cut(s) 155, 262, 292
BpiI GAAGAC 2 cut(s) 444, 605
BpmI CTGGAG 1 cut(s) 327
BpuEI CTTGAG 2 cut(s) 828, 855
BsaBI GATNNNNATC 1 cut(s) 234
BsaI GGTCTC 1 cut(s) 331
BsaJI CCNNGG 1 cut(s) 686
BsaWI WCCGGW 1 cut(s) 166
BsaXI ACNNNNNCTCC 5 cut(s) 824, 854, 881, 911, 920
Bsc4I CCNNNNNNNGG 3 cut(s) 126, 156, 291
Bse21I CCTNAGG 1 cut(s) 503
Bse8I GATNNNNATC 1 cut(s) 234
BseAI TCCGGA 1 cut(s) 166
BseDI CCNNGG 1 cut(s) 686
BseGI GGATG 4 cut(s) 146, 248, 277, 490
BseJI GATNNNNATC 1 cut(s) 234
BseLI CCNNNNNNNGG 3 cut(s) 126, 156, 291
BseMII CTCAG 2 cut(s) 585, 819
BseRI GAGGAG 1 cut(s) 845
BsiSI CCGG 1 cut(s) 167
BslI CCNNNNNNNGG 3 cut(s) 126, 156, 291
BsmAI GTCTC 2 cut(s) 331, 846
Bso31I GGTCTC 1 cut(s) 331
Bsp13I TCCGGA 1 cut(s) 166
Bsp143I GATC 3 cut(s) 13, 133, 748
BspCNI CTCAG 2 cut(s) 586, 820
BspEI TCCGGA 1 cut(s) 166
BspLI GGNNCC 1 cut(s) 424
BspPI GGATC 1 cut(s) 756
BspTNI GGTCTC 1 cut(s) 331
BssECI CCNNGG 1 cut(s) 686
BssMI GATC 3 cut(s) 13, 133, 748
BssT1I CCWWGG 1 cut(s) 686
Bst4CI ACNGT 4 cut(s) 81, 100, 325, 732
Bst6I CTCTTC 1 cut(s) 157
BstDEI CTNAG 6 cut(s) 10, 26, 503, 551, 594, 828
BstF5I GGATG 4 cut(s) 146, 248, 277, 490
BstKTI GATC 3 cut(s) 16, 136, 751
BstMAI GTCTC 2 cut(s) 331, 846
BstMBI GATC 3 cut(s) 13, 133, 748
BstMWI GCNNNNNNNGC 2 cut(s) 281, 889
BstNSI RCATGY 1 cut(s) 494
BstSFI CTRYAG 1 cut(s) 366
BstV2I GAAGAC 2 cut(s) 444, 605
Bsu36I CCTNAGG 1 cut(s) 503
BtrI CACGTC 1 cut(s) 934
BtsCI GGATG 4 cut(s) 146, 248, 277, 490
Cfr13I GGNCC 1 cut(s) 860
CviAII CATG 4 cut(s) 131, 383, 491, 797
DdeI CTNAG 6 cut(s) 10, 26, 503, 551, 594, 828
DpnI GATC 3 cut(s) 15, 135, 750
DpnII GATC 3 cut(s) 13, 133, 748
Eam1104I CTCTTC 1 cut(s) 157
EarI CTCTTC 1 cut(s) 157
Eco130I CCWWGG 1 cut(s) 686
Eco31I GGTCTC 1 cut(s) 331
Eco32I GATATC 1 cut(s) 768
Eco47I GGWCC 1 cut(s) 860
Eco81I CCTNAGG 1 cut(s) 503
EcoRV GATATC 1 cut(s) 768
EcoT14I CCWWGG 1 cut(s) 686
EcoT22I ATGCAT 1 cut(s) 277
ErhI CCWWGG 1 cut(s) 686
FaeI CATG 4 cut(s) 134, 386, 494, 800
FalI AAGNNNNNCTT 2 cut(s) 9, 41
FatI CATG 4 cut(s) 130, 382, 490, 796
FbaI TGATCA 1 cut(s) 133
FblI GTMKAC 1 cut(s) 576
FokI GGATG 4 cut(s) 133, 235, 284, 497
FspBI CTAG 2 cut(s) 687, 744
GsuI CTGGAG 1 cut(s) 327
HapII CCGG 1 cut(s) 167
Hin1II CATG 4 cut(s) 134, 386, 494, 800
HincII GTYRAC 2 cut(s) 56, 162
HindII GTYRAC 2 cut(s) 56, 162
HinfI GANTC 1 cut(s) 896
HpaI GTTAAC 1 cut(s) 162
HpaII CCGG 1 cut(s) 167
Hpy166II GTNNAC 6 cut(s) 56, 162, 321, 525, 577, 613
Hpy188I TCNGA 1 cut(s) 217
Hpy188III TCNNGA 3 cut(s) 17, 167, 392
Hpy8I GTNNAC 6 cut(s) 56, 162, 321, 525, 577, 613
HpyAV CCTTC 2 cut(s) 486, 539
HpyCH4III ACNGT 4 cut(s) 81, 100, 325, 732
HpyCH4IV ACGT 1 cut(s) 933
HpyCH4V TGCA 1 cut(s) 275
HpyF10VI GCNNNNNNNGC 2 cut(s) 281, 889
HpyF3I CTNAG 6 cut(s) 10, 26, 503, 551, 594, 828
HpySE526I ACGT 1 cut(s) 933
Hsp92II CATG 4 cut(s) 134, 386, 494, 800
Kpn2I TCCGGA 1 cut(s) 166
Ksp22I TGATCA 1 cut(s) 133
KspAI GTTAAC 1 cut(s) 162
Kzo9I GATC 3 cut(s) 13, 133, 748
LmnI GCTCC 1 cut(s) 889
LpnPI CCDG 4 cut(s) 51, 180, 291, 606
LweI GCATC 3 cut(s) 155, 262, 292
MaeI CTAG 2 cut(s) 687, 744
MaeII ACGT 1 cut(s) 933
MalI GATC 3 cut(s) 15, 135, 750
MboI GATC 3 cut(s) 13, 133, 748
MboII GAAGA 6 cut(s) 144, 182, 449, 572, 610, 681
MluCI AATT 7 cut(s) 44, 198, 467, 618, 650, 676, 808
MlyI GAGTC 1 cut(s) 905
MnlI CCTC 7 cut(s) 13, 118, 160, 483, 823, 910, 922
Mph1103I ATGCAT 1 cut(s) 277
MroI TCCGGA 1 cut(s) 166
MroXI GAANNNNTTC 1 cut(s) 812
MseI TTAA 8 cut(s) 33, 83, 161, 203, 336, 401, 617, 702
MslI CAYNNNNRTG 1 cut(s) 225
MspI CCGG 1 cut(s) 167
MwoI GCNNNNNNNGC 2 cut(s) 281, 889
NdeII GATC 3 cut(s) 13, 133, 748
NlaIII CATG 4 cut(s) 134, 386, 494, 800
NlaIV GGNNCC 1 cut(s) 424
NsiI ATGCAT 1 cut(s) 277
NspI RCATGY 1 cut(s) 494
PdmI GAANNNNTTC 1 cut(s) 812
PleI GAGTC 1 cut(s) 904
PpsI GAGTC 1 cut(s) 904
PsiI TTATAA 1 cut(s) 345
PspN4I GGNNCC 1 cut(s) 424
PspPI GGNCC 1 cut(s) 860
RseI CAYNNNNRTG 1 cut(s) 225
SaqAI TTAA 8 cut(s) 33, 83, 161, 203, 336, 401, 617, 702
Sau3AI GATC 3 cut(s) 13, 133, 748
Sau96I GGNCC 1 cut(s) 860
SchI GAGTC 1 cut(s) 905
SetI ASST 9 cut(s) 40, 225, 320, 399, 541, 552, 595, 871, 936
SfaNI GCATC 3 cut(s) 155, 262, 292
SfcI CTRYAG 1 cut(s) 366
SinI GGWCC 1 cut(s) 860
SmiMI CAYNNNNRTG 1 cut(s) 225
SmlI CTYRAG 2 cut(s) 843, 870
SmoI CTYRAG 2 cut(s) 843, 870
Sse9I AATT 7 cut(s) 44, 198, 467, 618, 650, 676, 808
SspI AATATT 1 cut(s) 89
SspMI CTAG 2 cut(s) 687, 744
StyI CCWWGG 1 cut(s) 686
TaaI ACNGT 4 cut(s) 81, 100, 325, 732
TaiI ACGT 1 cut(s) 936
TaqI TCGA 1 cut(s) 667
TasI AATT 7 cut(s) 44, 198, 467, 618, 650, 676, 808
Tru1I TTAA 8 cut(s) 33, 83, 161, 203, 336, 401, 617, 702
Tru9I TTAA 8 cut(s) 33, 83, 161, 203, 336, 401, 617, 702
TspDTI ATGAA 2 cut(s) 501, 557
TspGWI ACGGA 1 cut(s) 53
VpaK11BI GGWCC 1 cut(s) 860
XapI RAATTY 3 cut(s) 44, 198, 650
XceI RCATGY 1 cut(s) 494
XmaJI CCTAGG 1 cut(s) 686
XmiI GTMKAC 1 cut(s) 576
XmnI GAANNNNTTC 1 cut(s) 812
XspI CTAG 2 cut(s) 687, 744
Zsp2I ATGCAT 1 cut(s) 277
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.