Rroxscaffold_1G00033480

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000001
OG0000258
Physical Location & Seq
Forward (+)
48489062 .. 48491351
2290 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_1G00033480.1

Sequence Viewer

Length: 930 bp
ATGACAAACTTAGATCAAGAGGCTCTTAGTGTTAAACCTGAAAAATTTAGTGGTCAACATTTCCGTAGATGGCAGAAACAGTTAAAATATTGGCTAACAGTTCTTGGGTATATTTCTGCCATTGAGGGGCATGATCAAAACAAAGCATCCTCTTCTTGGTTAACTCCGGAAGATATAGAATATCATTGTCATAATAGAATTTTAAGTGCTTTGTCTGACCACCTTTATGATGTGTATCACTCTACAACATCCACAGCCAAAGAACTTTGGGATGCATTAGAAGCCGAATATGGGATTGTAGATGCTGGAGTTGATAGGTTTACGGTCTCTAACTTTAATAGTTATAAGATGGTTGAAAACAAATCTGTAGATAGCCAACTCCATGAGTATCAAGAGCTTTTAAGGGGAATAGAAAAGAAAGGAAGTGAAGACTTCAAAGTGTCTTGCCTTATAGATAAATTGCCTCCTTCTTGGGATGAACATGCCAAGAGCCTTAGGCATAAACAAGGAGAGTTTACCCTTCGTCAAGCTATGAATAACCTTAGAGTTGAAGAAAAACAAAGGGTAGACCAAAAGGAAAAACCTGAGAAAACACCCATTGTGAACTTAGTTGTGGGAAAGAAAAACCATAACAAGACTAAATTCCACAACAGAAATCGAAGAAGCAATTTTCAGCCTAGGGGGATAAACTTTAAGAACAATAGAGCCAACCGTAACAAACAGTTCCAGAAATCTAGGGATCAAGGGAGAGAAAAGATATCTTGCTTTGTTTGTGGGAGGACCAACCATGTAGCAAGGAATTGCTTCTACAAAAGGACTGAGGAGAACAAGTCTCAAGCAAATAGGAATGGTCCAAAAGCTCAAGTGAATATGCTAATGGAGCAAGAGTCCTCTCAACCATTATTCAAAAATCAAGTGGAGGACGTGTAA
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

309

Amino Acids

36.18

Weight (kDa)

9.31

Isoelectric Point (pI)

50.48

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 48 - 192 7.8e-17 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
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

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) 567
AccIII TCCGGA 1 cut(s) 166
AclWI GGATC 1 cut(s) 747
AcsI RAATTY 3 cut(s) 44, 198, 641
AfiI CCNNNNNNNGG 3 cut(s) 126, 156, 291
AflIII ACRYGT 1 cut(s) 924
AgsI TTSAA 4 cut(s) 356, 436, 551, 907
AjiI CACGTC 1 cut(s) 925
AluBI AGCT 3 cut(s) 397, 530, 860
AluI AGCT 3 cut(s) 397, 530, 860
Alw26I GTCTC 2 cut(s) 331, 837
AlwI GGATC 1 cut(s) 747
Aor13HI TCCGGA 1 cut(s) 166
ApoI RAATTY 3 cut(s) 44, 198, 641
Asp700I GAANNNNTTC 1 cut(s) 803
AspA2I CCTAGG 1 cut(s) 677
AspS9I GGNCC 2 cut(s) 780, 851
AvaII GGWCC 2 cut(s) 780, 851
AvrII CCTAGG 1 cut(s) 677
AxyI CCTNAGG 1 cut(s) 494
BbsI GAAGAC 1 cut(s) 435
BccI CCATC 2 cut(s) 63, 343
BclI TGATCA 1 cut(s) 133
BcoDI GTCTC 2 cut(s) 331, 837
BfaI CTAG 2 cut(s) 678, 735
BfmI CTRYAG 1 cut(s) 366
BlnI CCTAGG 1 cut(s) 677
Bme18I GGWCC 2 cut(s) 780, 851
BmgBI CACGTC 1 cut(s) 925
BmgT120I GGNCC 2 cut(s) 780, 851
BmsI GCATC 3 cut(s) 155, 262, 292
BpiI GAAGAC 1 cut(s) 435
BpmI CTGGAG 1 cut(s) 327
BpuEI CTTGAG 2 cut(s) 819, 846
BsaBI GATNNNNATC 1 cut(s) 234
BsaI GGTCTC 1 cut(s) 331
BsaJI CCNNGG 1 cut(s) 677
BsaWI WCCGGW 1 cut(s) 166
BsaXI ACNNNNNCTCC 5 cut(s) 815, 845, 872, 902, 911
Bsc4I CCNNNNNNNGG 3 cut(s) 126, 156, 291
Bse21I CCTNAGG 1 cut(s) 494
Bse8I GATNNNNATC 1 cut(s) 234
BseAI TCCGGA 1 cut(s) 166
BseDI CCNNGG 1 cut(s) 677
BseGI GGATG 4 cut(s) 146, 248, 277, 481
BseJI GATNNNNATC 1 cut(s) 234
BseLI CCNNNNNNNGG 3 cut(s) 126, 156, 291
BseMII CTCAG 2 cut(s) 576, 810
BseRI GAGGAG 1 cut(s) 836
BsiSI CCGG 1 cut(s) 167
BslI CCNNNNNNNGG 3 cut(s) 126, 156, 291
BsmAI GTCTC 2 cut(s) 331, 837
Bso31I GGTCTC 1 cut(s) 331
Bsp13I TCCGGA 1 cut(s) 166
Bsp143I GATC 3 cut(s) 13, 133, 739
BspCNI CTCAG 2 cut(s) 577, 811
BspEI TCCGGA 1 cut(s) 166
BspPI GGATC 1 cut(s) 747
BspTNI GGTCTC 1 cut(s) 331
BssECI CCNNGG 1 cut(s) 677
BssMI GATC 3 cut(s) 13, 133, 739
BssT1I CCWWGG 1 cut(s) 677
Bst4CI ACNGT 5 cut(s) 81, 100, 325, 713, 723
Bst6I CTCTTC 1 cut(s) 157
BstDEI CTNAG 7 cut(s) 10, 26, 494, 542, 585, 607, 819
BstF5I GGATG 4 cut(s) 146, 248, 277, 481
BstKTI GATC 3 cut(s) 16, 136, 742
BstMAI GTCTC 2 cut(s) 331, 837
BstMBI GATC 3 cut(s) 13, 133, 739
BstMWI GCNNNNNNNGC 2 cut(s) 281, 880
BstNSI RCATGY 1 cut(s) 485
BstSFI CTRYAG 1 cut(s) 366
BstV2I GAAGAC 1 cut(s) 435
Bsu36I CCTNAGG 1 cut(s) 494
BtrI CACGTC 1 cut(s) 925
BtsCI GGATG 4 cut(s) 146, 248, 277, 481
Cfr13I GGNCC 2 cut(s) 780, 851
CviAII CATG 4 cut(s) 131, 383, 482, 788
DdeI CTNAG 7 cut(s) 10, 26, 494, 542, 585, 607, 819
DpnI GATC 3 cut(s) 15, 135, 741
DpnII GATC 3 cut(s) 13, 133, 739
Eam1104I CTCTTC 1 cut(s) 157
EarI CTCTTC 1 cut(s) 157
Eco130I CCWWGG 1 cut(s) 677
Eco31I GGTCTC 1 cut(s) 331
Eco32I GATATC 1 cut(s) 759
Eco47I GGWCC 2 cut(s) 780, 851
Eco81I CCTNAGG 1 cut(s) 494
EcoRV GATATC 1 cut(s) 759
EcoT14I CCWWGG 1 cut(s) 677
EcoT22I ATGCAT 1 cut(s) 277
ErhI CCWWGG 1 cut(s) 677
FaeI CATG 4 cut(s) 134, 386, 485, 791
FalI AAGNNNNNCTT 2 cut(s) 9, 41
FatI CATG 4 cut(s) 130, 382, 481, 787
FbaI TGATCA 1 cut(s) 133
FblI GTMKAC 1 cut(s) 567
FokI GGATG 4 cut(s) 133, 235, 284, 488
FspBI CTAG 2 cut(s) 678, 735
GsuI CTGGAG 1 cut(s) 327
HapII CCGG 1 cut(s) 167
Hin1II CATG 4 cut(s) 134, 386, 485, 791
HincII GTYRAC 2 cut(s) 56, 162
HindII GTYRAC 2 cut(s) 56, 162
HinfI GANTC 1 cut(s) 887
HpaI GTTAAC 1 cut(s) 162
HpaII CCGG 1 cut(s) 167
Hpy166II GTNNAC 6 cut(s) 56, 162, 321, 516, 568, 604
Hpy188I TCNGA 1 cut(s) 217
Hpy188III TCNNGA 4 cut(s) 17, 167, 392, 727
Hpy8I GTNNAC 6 cut(s) 56, 162, 321, 516, 568, 604
HpyAV CCTTC 2 cut(s) 477, 530
HpyCH4III ACNGT 5 cut(s) 81, 100, 325, 713, 723
HpyCH4IV ACGT 1 cut(s) 924
HpyCH4V TGCA 1 cut(s) 275
HpyF10VI GCNNNNNNNGC 2 cut(s) 281, 880
HpyF3I CTNAG 7 cut(s) 10, 26, 494, 542, 585, 607, 819
HpySE526I ACGT 1 cut(s) 924
Hsp92II CATG 4 cut(s) 134, 386, 485, 791
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, 739
LmnI GCTCC 1 cut(s) 880
LpnPI CCDG 5 cut(s) 51, 180, 291, 597, 740
LweI GCATC 3 cut(s) 155, 262, 292
MaeI CTAG 2 cut(s) 678, 735
MaeII ACGT 1 cut(s) 924
MaeIII GTNAC 1 cut(s) 713
MalI GATC 3 cut(s) 15, 135, 741
MboI GATC 3 cut(s) 13, 133, 739
MboII GAAGA 5 cut(s) 144, 182, 440, 563, 672
MluCI AATT 6 cut(s) 44, 198, 458, 641, 667, 799
MlyI GAGTC 1 cut(s) 896
MnlI CCTC 8 cut(s) 13, 118, 160, 474, 771, 814, 901, 913
Mph1103I ATGCAT 1 cut(s) 277
MroI TCCGGA 1 cut(s) 166
MroXI GAANNNNTTC 1 cut(s) 803
MseI TTAA 7 cut(s) 33, 83, 161, 203, 336, 401, 693
MslI CAYNNNNRTG 1 cut(s) 225
MspI CCGG 1 cut(s) 167
MwoI GCNNNNNNNGC 2 cut(s) 281, 880
NdeII GATC 3 cut(s) 13, 133, 739
NlaIII CATG 4 cut(s) 134, 386, 485, 791
NsiI ATGCAT 1 cut(s) 277
NspI RCATGY 1 cut(s) 485
PdmI GAANNNNTTC 1 cut(s) 803
PleI GAGTC 1 cut(s) 895
PpsI GAGTC 1 cut(s) 895
PsiI TTATAA 1 cut(s) 345
PspPI GGNCC 2 cut(s) 780, 851
RseI CAYNNNNRTG 1 cut(s) 225
SaqAI TTAA 7 cut(s) 33, 83, 161, 203, 336, 401, 693
Sau3AI GATC 3 cut(s) 13, 133, 739
Sau96I GGNCC 2 cut(s) 780, 851
SchI GAGTC 1 cut(s) 896
SetI ASST 9 cut(s) 40, 225, 320, 399, 532, 543, 586, 862, 927
SfaNI GCATC 3 cut(s) 155, 262, 292
SfcI CTRYAG 1 cut(s) 366
SinI GGWCC 2 cut(s) 780, 851
SmiMI CAYNNNNRTG 1 cut(s) 225
SmlI CTYRAG 2 cut(s) 834, 861
SmoI CTYRAG 2 cut(s) 834, 861
Sse9I AATT 6 cut(s) 44, 198, 458, 641, 667, 799
SspI AATATT 1 cut(s) 89
SspMI CTAG 2 cut(s) 678, 735
StyI CCWWGG 1 cut(s) 677
TaaI ACNGT 5 cut(s) 81, 100, 325, 713, 723
TaiI ACGT 1 cut(s) 927
TaqI TCGA 1 cut(s) 658
TasI AATT 6 cut(s) 44, 198, 458, 641, 667, 799
Tru1I TTAA 7 cut(s) 33, 83, 161, 203, 336, 401, 693
Tru9I TTAA 7 cut(s) 33, 83, 161, 203, 336, 401, 693
TspDTI ATGAA 2 cut(s) 492, 548
TspGWI ACGGA 1 cut(s) 53
VpaK11BI GGWCC 2 cut(s) 780, 851
XapI RAATTY 3 cut(s) 44, 198, 641
XceI RCATGY 1 cut(s) 485
XmaJI CCTAGG 1 cut(s) 677
XmiI GTMKAC 1 cut(s) 567
XmnI GAANNNNTTC 1 cut(s) 803
XspI CTAG 2 cut(s) 678, 735
Zsp2I ATGCAT 1 cut(s) 277
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.