RchiOBHm_Chr1g0322851

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
1
OG0000562
Physical Location & Seq
Forward (+)
10278594 .. 10280476
1883 bp
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UTR
Exon/CDS
Intron
PRQ55282

Sequence Viewer

Length: 1131 bp
ATGACAAAAGGAGAAGGTTCCCTCGTTGCAAAGATAGAAAGCCCAGAAGGAAATCCAAATCAGCGTCTGTGCTCAGTGCTTCTAAATGAGTTCAACTACCTTCCTTGGTCAAGAGCAATCACTCTAGCCCTTGGTGGAAGATCAAAGCTCAGCTTCATCAACAACAAAAGCAAAATCCCAGATGCCTCATCATCTGAATATGAAAGTTGGTTATCCAACGATCAACTTGTCATGTCATGGCTCCTTAATTCAATGGAGCCAAAACTTGCAGAAATCTTTAGCTATTCAGAGTCATCTCGACATCTTTGGGATGCTGTCAAAGACATGTATGGCAACCTAAACAATGCAGCAAGAGTGTTTCAACTCAAAAAGGATCTTGCAGGGATTCAACAAGGTAATCTCTCATTTGTTCAACATCTTGGCAACCTAAAGGCCAAGTGGAATGAGCTTGATATGTATAGGCCTCACACCACTGATGCCACCATATTGTTGAAACGAGCTGAAGAAGATAAAATATTCCAATTGCTTGCAAGTCTGGGATCTGAATATGAGGATCTCAAAAGCCATCTTTTGATGACCCCGGAGCTTCCTTCATTCGCAACGGTATGCAACTCCATTCAACGTGAAGAAGTGCGCAAAATGGTGATGAATGTGAACACCAGTATTAGAGGGTCAGAAGCTAGAGCATTTGCTGCAAACAAAAGTGTCACAAGCGACAGAACATACAAGGGCAAGAGGCCAGATCTAAAGTGCACACATTGTGAAGGCATTGGACGAGCTGGTATAGGCCACATAAGAGAGAGATGTTGGATATTGCATCCAGAACTGAAACCTAAGTTCAATGAGGAGCAAAAAAATCAAAGAGGCACCACTCAGAGAAGCCCTTACATCTCTAATCCAAAGGGAAACCTCAGCAACACTTCTGAAGGTATGATGAACTTCACATCCAATCCAATAAGTCTTATAAATGAGTTTGCTACATATCTTGAAAAGAAGCAAGGCAGTTTAGAGAGAAATGAAAATGGAAGCACAACTGCTATGCTTGGAAAGTTTGCTGGTTTTTTGGCGAAATCAAACATGGCTTCTTCAGAGGATATACCAGGATCGAGTGTCCAAGGAGAAGATTGGTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00940 ko01110 map00940 map01110
Pfam Domains
Protein Families
Retrotran_gag_2

Protein Analysis

376

Amino Acids

42.14

Weight (kDa)

8.44

Isoelectric Point (pI)

36.65

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 17 - 60 5.9e-11 gag-polypeptide of LTR copia-type
Retrotran_gag_2 PF14223 56 - 213 5.3e-11 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: OG0000562)

Species Orthologous Gene IDs
fragaria_vesca FvH4_2g17331 FvH4_3g36541
malus_domestica MD07G1078600.v1.1 MD10G1237700.v1.1 MD10G1333400.v1.1 MD11G1102200.v1.1 MD13G1138400.v1.1 MD14G1033400.v1.1 MD15G1053300.v1.1
prunus_persica Prupe.1G465400_v2.0.a1 Prupe.3G136000_v2.0.a1 Prupe.7G119900_v2.0.a1
pyrus_communis pycom01g04630 pycom03g13050 pycom04g21190 pycom05g04910 pycom05g05510 pycom08g15850 pycom09g15040 pycom1094g00010 pycom11g02000 pycom12g06150 pycom13g24110 pycom13g24910 pycom14g00050 pycom15g21970 pycom15g35170 pycom15g35180 pycom16g14620 pycom16g14630 pycom808g00110
rosa_chinensis RchiOBHm_Chr1g0322851 RchiOBHm_Chr1g0365941 RchiOBHm_Chr3g0453341 RchiOBHm_Chr4g0388371 RchiOBHm_Chr4g0394021 RchiOBHm_Chr5g0013181 RchiOBHm_Chr6g0261721 RchiOBHm_Chr6g0261731 RchiOBHm_Chr7g0188861 RchiOBHm_Chr7g0192331 RchiOBHm_Chr7g0231721
rosa_multiflora Rmu_sc0002521.1_g000006 Rmu_sc0003255.1_g000026 Rmu_sc0004191.1_g000036 Rmu_sc0004414.1_g000014 Rmu_sc0005670.1_g000006 Rmu_sc0006081.1_g000001 Rmu_sc0007215.1_g000004 Rmu_sc0010088.1_g000010 Rmu_sc0020285.1_g000003 Rmu_sc0026896.1_g000002 Rmu_ssc0000019.1_g000029
rosa_roxburghii Rroxscaffold_3G00224890 Rroxscaffold_6G00400640 Rroxscaffold_7G00176590 Rroxscaffold_7G00189230
rosa_samantha Rh4BG046700
rosa_wichuraiana Rw1G012690 Rw1G031370 Rw2G042180 Rw2G043670 Rw2G046240 Rw2G049890 Rw2G050760 Rw2G051280 Rw2G053590 Rw3G007590 Rw3G026850 Rw4G001540 Rw4G009760 Rw4G019270 Rw5G000720 Rw5G005620 Rw5G041560 Rw6G007370 Rw6G009830 Rw6G015360 Rw6G031160 Rw7G004930 Rw7G011010 Rw7G024230 Rw7G028240

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 965
Acc16I TGCGCA 1 cut(s) 635
AccB1I GGYRCC 1 cut(s) 866
AclWI GGATC 4 cut(s) 381, 547, 561, 1111
AcuI CTGAAG 3 cut(s) 522, 945, 1071
AdeI CACNNNGTG 1 cut(s) 761
AflIII ACRYGT 1 cut(s) 324
AgsI TTSAA 9 cut(s) 94, 252, 362, 389, 413, 493, 620, 841, 989
AjnI CCWGG 1 cut(s) 1099
AloI GAACNNNNNNTCC 2 cut(s) 929, 961
AluBI AGCT 8 cut(s) 148, 153, 282, 448, 500, 586, 680, 779
AluI AGCT 8 cut(s) 148, 153, 282, 448, 500, 586, 680, 779
Alw21I GWGCWC 2 cut(s) 74, 755
Alw44I GTGCAC 1 cut(s) 751
AlwI GGATC 4 cut(s) 381, 547, 561, 1111
AlwNI CAGNNNCTG 1 cut(s) 67
AoxI GGCC 4 cut(s) 432, 461, 737, 787
ApaLI GTGCAC 1 cut(s) 751
ApeKI GCWGC 2 cut(s) 347, 692
AspLEI GCGC 1 cut(s) 636
AsuC2I CCSGG 1 cut(s) 581
AsuHPI GGTGA 1 cut(s) 655
BaeGI GKGCMC 1 cut(s) 755
BanI GGYRCC 1 cut(s) 866
Bbv12I GWGCWC 2 cut(s) 74, 755
BbvCI CCTCAGC 1 cut(s) 911
BbvI GCAGC 2 cut(s) 359, 679
BccI CCATC 1 cut(s) 573
BciT130I CCWGG 1 cut(s) 1101
BcnI CCSGG 1 cut(s) 581
BfaI CTAG 2 cut(s) 125, 681
BglII AGATCT 1 cut(s) 742
BisI GCNGC 2 cut(s) 348, 693
BlpI GCTNAGC 1 cut(s) 149
BlsI GCNGC 2 cut(s) 349, 694
Bme1390I CCNGG 2 cut(s) 581, 1101
BmiI GGNNCC 4 cut(s) 19, 242, 258, 868
BmrFI CCNGG 2 cut(s) 581, 1101
BmsI GCATC 4 cut(s) 172, 301, 466, 826
Bpu10I CCTNAGC 1 cut(s) 911
Bpu1102I GCTNAGC 1 cut(s) 149
BpuMI CCSGG 1 cut(s) 581
BsaJI CCNNGG 4 cut(s) 104, 130, 579, 1114
Bse1I ACTGG 1 cut(s) 660
BseBI CCWGG 1 cut(s) 1101
BseDI CCNNGG 4 cut(s) 104, 130, 579, 1114
BseGI GGATG 3 cut(s) 316, 817, 944
BseMII CTCAG 4 cut(s) 87, 163, 887, 925
BseNI ACTGG 1 cut(s) 660
BseRI GAGGAG 1 cut(s) 860
BseSI GKGCMC 1 cut(s) 755
BseXI GCAGC 2 cut(s) 359, 679
BshFI GGCC 4 cut(s) 434, 463, 739, 789
BshNI GGYRCC 1 cut(s) 866
BsiHKAI GWGCWC 2 cut(s) 74, 755
BsiSI CCGG 1 cut(s) 581
BsnI GGCC 4 cut(s) 434, 463, 739, 789
Bsp1286I GDGCHC 2 cut(s) 74, 755
Bsp143I GATC 7 cut(s) 140, 220, 373, 539, 553, 742, 1103
Bsp1720I GCTNAGC 1 cut(s) 149
BspANI GGCC 4 cut(s) 434, 463, 739, 789
BspCNI CTCAG 4 cut(s) 86, 162, 886, 924
BspLI GGNNCC 4 cut(s) 19, 242, 258, 868
BspPI GGATC 4 cut(s) 381, 547, 561, 1111
BspT107I GGYRCC 1 cut(s) 866
BsrI ACTGG 1 cut(s) 660
BssECI CCNNGG 4 cut(s) 104, 130, 579, 1114
BssMI GATC 7 cut(s) 140, 220, 373, 539, 553, 742, 1103
BssT1I CCWWGG 3 cut(s) 104, 130, 1114
Bst2UI CCWGG 1 cut(s) 1101
Bst4CI ACNGT 1 cut(s) 604
BstAPI GCANNNNNTGC 1 cut(s) 692
BstC8I GCNNGC 1 cut(s) 528
BstDEI CTNAG 5 cut(s) 73, 149, 834, 873, 911
BstF5I GGATG 3 cut(s) 316, 817, 944
BstHHI GCGC 1 cut(s) 636
BstKTI GATC 7 cut(s) 143, 223, 376, 542, 556, 745, 1106
BstMBI GATC 7 cut(s) 140, 220, 373, 539, 553, 742, 1103
BstMWI GCNNNNNNNGC 1 cut(s) 692
BstNI CCWGG 1 cut(s) 1101
BstNSI RCATGY 1 cut(s) 328
BstSCI CCNGG 2 cut(s) 579, 1099
BstSLI GKGCMC 1 cut(s) 755
BstV1I GCAGC 2 cut(s) 359, 679
BstX2I RGATCY 4 cut(s) 373, 539, 553, 742
BstYI RGATCY 4 cut(s) 373, 539, 553, 742
BsuRI GGCC 4 cut(s) 434, 463, 739, 789
BtsCI GGATG 3 cut(s) 316, 817, 944
BtsIMutI CAGTG 2 cut(s) 81, 471
Cac8I GCNNGC 1 cut(s) 528
CaiI CAGNNNCTG 1 cut(s) 67
CfoI GCGC 1 cut(s) 636
CseI GACGC 1 cut(s) 53
CviAII CATG 4 cut(s) 232, 237, 325, 1078
DdeI CTNAG 5 cut(s) 73, 149, 834, 873, 911
DpnI GATC 7 cut(s) 142, 222, 375, 541, 555, 744, 1105
DpnII GATC 7 cut(s) 140, 220, 373, 539, 553, 742, 1103
DraIII CACNNNGTG 1 cut(s) 761
Eco130I CCWWGG 3 cut(s) 104, 130, 1114
Eco147I AGGCCT 1 cut(s) 463
Eco57I CTGAAG 3 cut(s) 522, 945, 1071
EcoRII CCWGG 1 cut(s) 1099
EcoT14I CCWWGG 3 cut(s) 104, 130, 1114
ErhI CCWWGG 3 cut(s) 104, 130, 1114
FaeI CATG 4 cut(s) 235, 240, 328, 1081
FalI AAGNNNNNCTT 2 cut(s) 137, 169
FatI CATG 4 cut(s) 231, 236, 324, 1077
Fnu4HI GCNGC 2 cut(s) 348, 693
FokI GGATG 3 cut(s) 323, 804, 931
Fsp4HI GCNGC 2 cut(s) 348, 693
FspBI CTAG 2 cut(s) 125, 681
FspI TGCGCA 1 cut(s) 635
GlaI GCGC 1 cut(s) 635
GluI GCNGC 2 cut(s) 348, 693
HaeIII GGCC 4 cut(s) 434, 463, 739, 789
HapII CCGG 1 cut(s) 581
HgaI GACGC 1 cut(s) 53
HhaI GCGC 1 cut(s) 636
Hin1II CATG 4 cut(s) 235, 240, 328, 1081
Hin6I GCGC 1 cut(s) 634
HinP1I GCGC 1 cut(s) 634
HinfI GANTC 2 cut(s) 290, 385
HpaII CCGG 1 cut(s) 581
HphI GGTGA 1 cut(s) 655
Hpy166II GTNNAC 2 cut(s) 655, 753
Hpy188I TCNGA 7 cut(s) 196, 289, 544, 676, 876, 925, 1090
Hpy188III TCNNGA 4 cut(s) 111, 297, 821, 986
Hpy8I GTNNAC 2 cut(s) 655, 753
HpyAV CCTTC 6 cut(s) 8, 41, 110, 600, 758, 920
HpyCH4III ACNGT 1 cut(s) 604
HpyCH4IV ACGT 1 cut(s) 622
HpyCH4V TGCA 9 cut(s) 29, 269, 347, 380, 530, 609, 695, 753, 817
HpyF10VI GCNNNNNNNGC 1 cut(s) 692
HpyF3I CTNAG 5 cut(s) 73, 149, 834, 873, 911
HpySE526I ACGT 1 cut(s) 622
Hsp92II CATG 4 cut(s) 235, 240, 328, 1081
HspAI GCGC 1 cut(s) 634
Kzo9I GATC 7 cut(s) 140, 220, 373, 539, 553, 742, 1103
LmnI GCTCC 4 cut(s) 246, 256, 583, 847
Lsp1109I GCAGC 2 cut(s) 359, 679
LweI GCATC 4 cut(s) 172, 301, 466, 826
MaeI CTAG 2 cut(s) 125, 681
MaeII ACGT 1 cut(s) 622
MaeIII GTNAC 1 cut(s) 706
MalI GATC 7 cut(s) 142, 222, 375, 541, 555, 744, 1105
MboI GATC 7 cut(s) 140, 220, 373, 539, 553, 742, 1103
MboII GAAGA 5 cut(s) 150, 515, 518, 638, 1077
MfeI CAATTG 1 cut(s) 521
MflI RGATCY 4 cut(s) 373, 539, 553, 742
MhlI GDGCHC 2 cut(s) 74, 755
MluCI AATT 2 cut(s) 247, 521
MlyI GAGTC 1 cut(s) 299
MmeI TCCRAC 2 cut(s) 240, 788
MseI TTAA 1 cut(s) 246
MspI CCGG 1 cut(s) 581
MspR9I CCNGG 2 cut(s) 581, 1101
MunI CAATTG 1 cut(s) 521
MvaI CCWGG 1 cut(s) 1101
MwoI GCNNNNNNNGC 1 cut(s) 692
NciI CCSGG 1 cut(s) 581
NdeII GATC 7 cut(s) 140, 220, 373, 539, 553, 742, 1103
NlaIII CATG 4 cut(s) 235, 240, 328, 1081
NlaIV GGNNCC 4 cut(s) 19, 242, 258, 868
NmuCI GTSAC 1 cut(s) 706
NsbI TGCGCA 1 cut(s) 635
NspI RCATGY 1 cut(s) 328
PceI AGGCCT 1 cut(s) 463
PciI ACATGT 1 cut(s) 324
PfeI GAWTC 1 cut(s) 385
PkrI GCNGC 2 cut(s) 349, 694
PleI GAGTC 1 cut(s) 298
PpsI GAGTC 1 cut(s) 298
PscI ACATGT 1 cut(s) 324
PsiI TTATAA 1 cut(s) 965
Psp6I CCWGG 1 cut(s) 1099
PspGI CCWGG 1 cut(s) 1099
PspN4I GGNNCC 4 cut(s) 19, 242, 258, 868
PstNI CAGNNNCTG 1 cut(s) 67
PsuI RGATCY 4 cut(s) 373, 539, 553, 742
SaqAI TTAA 1 cut(s) 246
SatI GCNGC 2 cut(s) 348, 693
Sau3AI GATC 7 cut(s) 140, 220, 373, 539, 553, 742, 1103
SchI GAGTC 1 cut(s) 299
ScrFI CCNGG 2 cut(s) 581, 1101
SduI GDGCHC 2 cut(s) 74, 755
SfaNI GCATC 4 cut(s) 172, 301, 466, 826
Sse9I AATT 2 cut(s) 247, 521
SseBI AGGCCT 1 cut(s) 463
SspI AATATT 1 cut(s) 516
SspMI CTAG 2 cut(s) 125, 681
StuI AGGCCT 1 cut(s) 463
StyD4I CCNGG 2 cut(s) 579, 1099
StyI CCWWGG 3 cut(s) 104, 130, 1114
TaaI ACNGT 1 cut(s) 604
TaiI ACGT 1 cut(s) 625
TaqI TCGA 2 cut(s) 298, 1106
TasI AATT 2 cut(s) 247, 521
TfiI GAWTC 1 cut(s) 385
Tru1I TTAA 1 cut(s) 246
Tru9I TTAA 1 cut(s) 246
TscAI CASTG 2 cut(s) 81, 478
TseFI GTSAC 1 cut(s) 706
TseI GCWGC 2 cut(s) 347, 692
Tsp45I GTSAC 1 cut(s) 706
TspDTI ATGAA 6 cut(s) 145, 216, 582, 662, 950, 1032
TspRI CASTG 2 cut(s) 81, 478
VneI GTGCAC 1 cut(s) 751
XceI RCATGY 1 cut(s) 328
XspI CTAG 2 cut(s) 125, 681
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.