Rroxscaffold_5G00349820

TdcA1-ORF2 protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000005
OG0000224
Physical Location & Seq
Forward (+)
23097837 .. 23099581
1745 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_5G00349820.1

Sequence Viewer

Length: 1029 bp
ATGACGGAGAAGATGAACAGTAATGCGGTTTTAGTTTTCGTGCCTCGAACCGCCAAAGAAAACTCGACGGTGGCATATTTTTACAGAAAAAAAGTGCGTGGAAAGACAAGAGGTTTAAATGCTGATAAGGTGCATGAGCAGCTTGGTACTAAAATACCTGTGACTTTCAAGAAAGAAAATGGCAGACCCACATGTCCATATGCAGAAATGTTTGCTAATGAAATTGGATTCACCATTCGGAACCATGCACCTCTAAATGTGAAAAAATGGAAGGAAACTAAGTACGACATTGACATGTCTCTACCTTGGGTTAAGAGATATGTGCATAAATCTTTTGGAACAGTGTTCGCTAACTTCCGTTATAAGCTGAAGAAGCATTTTGAGCAATTCTCAACAAAAGAGGAAGCATTAGAAAATAAACACAAAGATGTTAAAACTGAAGAAGAATGGGCTTTTCTGTGCACTTATTTTTCTAGTGAAGATTTTCAGATTGTTTCAGAGAAAAATTCTATTAATAGGTCACGTTTGAAATATCACCATAAAGCAGGGTCGAAGTCTTTTATGTCGCATCAAGAACAGATTGTAAGCTGCACAATCGGGGAGATGCTAGGTGCAATTGAACGCTTTGAAATGGAGTACAAAAGCATTAAAAAAGGTTGGGACTTGGGAGCGAAAGAATTATGGGATCAAATGGTTAAGATGCGAACTGAGACAACCCTTCTTGATGGGACTCGAACTATGAATGATGATGAAATATGTGCAAAGGTTCTTGGAGTAAAATCAGGCTACATCAAGGGTTGTGGTTTTGGCCCCAGGCCTCCACCATCTAGCACTTCTCGATCGTCAATAGATGAAATGTCTGAGAAGAATAAAGAGTTAGAAGATAAACTTGAAGAGACCCAAGATACTATAAAGGCTCAACAAGAAAAGATTGATGCACAAAACGTGCTGATCCAAGAATTGCAGGAGCAAGGCAAAAAGTTTGAGCAGTTCATGGCAACCTTTATGAACCAACAAGCATCAAGTTAG
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
DUF4216 DUF4218 Transpos_assoc Transposase_21 Transposase_24

Protein Analysis

342

Amino Acids

39.61

Weight (kDa)

8.99

Isoelectric Point (pI)

43.99

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Transposase_24 PF03004 148 - 237 3.5e-07 Plant transposase (Ptta/En/Spm family)
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: OG0000224)

Species Orthologous Gene IDs
fragaria_vesca FvH4_2g08145 FvH4_4g05492 FvH4_4g15892
pyrus_communis pycom07g09690 pycom16g18380
rosa_chinensis RchiOBHm_Chr0c17g0499961 RchiOBHm_Chr1g0345631 RchiOBHm_Chr1g0345641 RchiOBHm_Chr1g0381191 RchiOBHm_Chr2g0102381 RchiOBHm_Chr2g0106131 RchiOBHm_Chr2g0148461 RchiOBHm_Chr2g0148471 RchiOBHm_Chr2g0157121 RchiOBHm_Chr3g0476041 RchiOBHm_Chr3g0476051 RchiOBHm_Chr3g0486961 RchiOBHm_Chr3g0487551 RchiOBHm_Chr4g0385011 RchiOBHm_Chr4g0410891 RchiOBHm_Chr4g0415291 RchiOBHm_Chr4g0427801 RchiOBHm_Chr4g0427811 RchiOBHm_Chr5g0001961 RchiOBHm_Chr5g0009841 RchiOBHm_Chr5g0025231 RchiOBHm_Chr6g0272461 RchiOBHm_Chr7g0199391 RchiOBHm_Chr7g0214031
rosa_laevigata RLG00000000706 RLG00000000749 RLG00000000750 RLG00000001166 RLG00000001748 RLG00000008952 RLG00000009088 RLG00000009090 RLG00000009094 RLG00000015391 RLG00000016519 RLG00000016520 RLG00000017174 RLG00000018887 RLG00000023058 RLG00000023059 RLG00000028282 RLG00000028531 RLG00000030444 RLG00000034592 RLG00000036555
rosa_multiflora Rmu_sc0000045.1_g000015 Rmu_sc0000157.1_g000011 Rmu_sc0000493.1_g000080 Rmu_sc0001307.1_g000027 Rmu_sc0001470.1_g000010 Rmu_sc0002277.1_g000022 Rmu_sc0002365.1_g000027 Rmu_sc0002693.1_g000008 Rmu_sc0002833.1_g000051 Rmu_sc0003275.1_g000066 Rmu_sc0003286.1_g000008 Rmu_sc0004234.1_g000035 Rmu_sc0004546.1_g000001 Rmu_sc0005058.1_g000004 Rmu_sc0007025.1_g000015 Rmu_sc0008144.1_g000006 Rmu_sc0008688.1_g000001 Rmu_sc0009185.1_g000010 Rmu_sc0020638.1_g000001
rosa_roxburghii Rroxscaffold_158G00443750 Rroxscaffold_1G00001770 Rroxscaffold_1G00002620 Rroxscaffold_1G00024490 Rroxscaffold_1G00035180 Rroxscaffold_1G00035190 Rroxscaffold_1G00061370 Rroxscaffold_1G00075590 Rroxscaffold_2G00110960 Rroxscaffold_2G00121340 Rroxscaffold_2G00128850 Rroxscaffold_2G00142580 Rroxscaffold_2G00142590 Rroxscaffold_3G00223630 Rroxscaffold_3G00263220 Rroxscaffold_4G00310820 Rroxscaffold_5G00336270 Rroxscaffold_5G00336280 Rroxscaffold_5G00336320 Rroxscaffold_5G00349820 Rroxscaffold_6G00395720 Rroxscaffold_6G00395910 Rroxscaffold_6G00415660 Rroxscaffold_7G00179770 Rroxscaffold_7G00184390 Rroxscaffold_7G00189270 Rroxscaffold_7G00197240 Rroxscaffold_8G00436850 Rroxscaffold_8G00436860 Rroxscaffold_8G00436880
rosa_rugosa Rorug01G0118400 Rorug02G0048900 Rorug02G0185600 Rorug02G0222600 Rorug03G0152800 Rorug04G0047600 Rorug04G0446400 Rorug05G0118900 Rorug05G0359700 Rorug05G0374800 Rorug05G0374900 Rorug05G0375000 Rorug05G0375100 Rorug05G0418900 Rorug05G0540000 Rorug05G0540000 Rorug05G0540100 Rorug06G0358700 Rorug06G0358700 Rorug06G0408700 Rorug06G0408700 Rorug06G0408800 Rorug06G0408900 Rorug07G0203000
rosa_samantha Rh1CG190700 Rh1CG196300 Rh2BG566600 Rh2CG188900 Rh3AG090900 Rh3AG278200 Rh3BG233900 Rh3CG094300 Rh4BG202100 Rh5BG543100 Rh5CG566000 Rh5DG397500 Rh7CG432800
rosa_wichuraiana Rw0G017850 Rw1G010340 Rw1G016290 Rw2G018520 Rw3G008970 Rw5G028090 Rw5G043930 Rw6G014660 Rw6G030340 Rw7G038240

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 363
AasI GACNNNNNNGTC 1 cut(s) 192
AciI CCGC 2 cut(s) 26, 51
AclWI GGATC 2 cut(s) 693, 946
AcsI RAATTY 1 cut(s) 505
AcuI CTGAAG 2 cut(s) 389, 459
AfaI GTAC 3 cut(s) 148, 284, 638
AflIII ACRYGT 2 cut(s) 191, 294
AgsI TTSAA 5 cut(s) 169, 529, 620, 629, 893
AjnI CCWGG 1 cut(s) 812
AluBI AGCT 3 cut(s) 142, 367, 588
AluI AGCT 3 cut(s) 142, 367, 588
Alw21I GWGCWC 1 cut(s) 464
Alw26I GTCTC 3 cut(s) 303, 704, 890
Alw44I GTGCAC 1 cut(s) 460
AlwI GGATC 2 cut(s) 693, 946
AoxI GGCC 2 cut(s) 808, 815
ApaLI GTGCAC 1 cut(s) 460
ApeKI GCWGC 2 cut(s) 139, 588
ApoI RAATTY 1 cut(s) 505
AseI ATTAAT 1 cut(s) 513
Asp700I GAANNNNTTC 1 cut(s) 483
AspS9I GGNCC 1 cut(s) 809
AsuHPI GGTGA 2 cut(s) 223, 527
BaeGI GKGCMC 1 cut(s) 464
Bbv12I GWGCWC 1 cut(s) 464
BbvI GCAGC 2 cut(s) 151, 575
BccI CCATC 2 cut(s) 719, 832
BciT130I CCWGG 1 cut(s) 814
BcoDI GTCTC 3 cut(s) 303, 704, 890
BfaI CTAG 3 cut(s) 474, 608, 828
BisI GCNGC 2 cut(s) 140, 589
BlsI GCNGC 2 cut(s) 141, 590
Bme1390I CCNGG 1 cut(s) 814
BmgT120I GGNCC 1 cut(s) 809
BmiI GGNNCC 2 cut(s) 242, 811
BmrFI CCNGG 1 cut(s) 814
BmsI GCATC 4 cut(s) 577, 594, 690, 925
BplI GAGNNNNNCTC 2 cut(s) 374, 406
BsaI GGTCTC 1 cut(s) 890
BsaJI CCNNGG 2 cut(s) 305, 812
BseBI CCWGG 1 cut(s) 814
BseDI CCNNGG 2 cut(s) 305, 812
BseMII CTCAG 2 cut(s) 699, 852
BseSI GKGCMC 1 cut(s) 464
BseXI GCAGC 2 cut(s) 151, 575
BsgI GTGCAG 1 cut(s) 574
Bsh1285I CGRYCG 1 cut(s) 842
BshFI GGCC 2 cut(s) 810, 817
BsiEI CGRYCG 1 cut(s) 842
BsiHKAI GWGCWC 1 cut(s) 464
BslFI GGGAC 2 cut(s) 674, 742
BsmAI GTCTC 3 cut(s) 303, 704, 890
BsmFI GGGAC 2 cut(s) 674, 742
BsnI GGCC 2 cut(s) 810, 817
Bso31I GGTCTC 1 cut(s) 890
Bsp1286I GDGCHC 1 cut(s) 464
Bsp143I GATC 3 cut(s) 685, 839, 951
BspACI CCGC 2 cut(s) 26, 51
BspANI GGCC 2 cut(s) 810, 817
BspCNI CTCAG 2 cut(s) 700, 853
BspLI GGNNCC 2 cut(s) 242, 811
BspPI GGATC 2 cut(s) 693, 946
BspTNI GGTCTC 1 cut(s) 890
BssECI CCNNGG 2 cut(s) 305, 812
BssMI GATC 3 cut(s) 685, 839, 951
BssT1I CCWWGG 1 cut(s) 305
Bst2UI CCWGG 1 cut(s) 814
Bst4CI ACNGT 3 cut(s) 20, 70, 343
Bst6I CTCTTC 1 cut(s) 888
BstDEI CTNAG 3 cut(s) 279, 708, 861
BstKTI GATC 3 cut(s) 688, 842, 954
BstMAI GTCTC 3 cut(s) 303, 704, 890
BstMBI GATC 3 cut(s) 685, 839, 951
BstMCI CGRYCG 1 cut(s) 842
BstMWI GCNNNNNNNGC 3 cut(s) 139, 373, 382
BstNI CCWGG 1 cut(s) 814
BstNSI RCATGY 2 cut(s) 195, 298
BstSCI CCNGG 1 cut(s) 812
BstSLI GKGCMC 1 cut(s) 464
BstV1I GCAGC 2 cut(s) 151, 575
BsuRI GGCC 2 cut(s) 810, 817
BtsIMutI CAGTG 1 cut(s) 348
Cfr13I GGNCC 1 cut(s) 809
Csp6I GTAC 3 cut(s) 147, 283, 637
CspCI CAANNNNNGTGG 2 cut(s) 781, 816
CviAII CATG 5 cut(s) 134, 192, 245, 295, 994
CviJI RGCY 8 cut(s) 142, 367, 452, 588, 786, 810, 817, 917
CviKI_1 RGCY 8 cut(s) 142, 367, 452, 588, 786, 810, 817, 917
CviQI GTAC 3 cut(s) 147, 283, 637
DdeI CTNAG 3 cut(s) 279, 708, 861
DpnI GATC 3 cut(s) 687, 841, 953
DpnII GATC 3 cut(s) 685, 839, 951
DraI TTTAAA 1 cut(s) 117
DrdI GACNNNNNNGTC 1 cut(s) 192
DseDI GACNNNNNNGTC 1 cut(s) 192
Eam1104I CTCTTC 1 cut(s) 888
EarI CTCTTC 1 cut(s) 888
Eco130I CCWWGG 1 cut(s) 305
Eco147I AGGCCT 1 cut(s) 817
Eco31I GGTCTC 1 cut(s) 890
Eco57I CTGAAG 2 cut(s) 389, 459
EcoRII CCWGG 1 cut(s) 812
EcoT14I CCWWGG 1 cut(s) 305
ErhI CCWWGG 1 cut(s) 305
FaeI CATG 5 cut(s) 137, 195, 248, 298, 997
FalI AAGNNNNNCTT 2 cut(s) 873, 905
FaqI GGGAC 2 cut(s) 674, 742
FatI CATG 5 cut(s) 133, 191, 244, 294, 993
FauNDI CATATG 1 cut(s) 199
Fnu4HI GCNGC 2 cut(s) 140, 589
Fsp4HI GCNGC 2 cut(s) 140, 589
FspBI CTAG 3 cut(s) 474, 608, 828
GluI GCNGC 2 cut(s) 140, 589
HaeIII GGCC 2 cut(s) 810, 817
Hin1II CATG 5 cut(s) 137, 195, 248, 298, 997
HinfI GANTC 2 cut(s) 228, 730
HphI GGTGA 2 cut(s) 223, 527
Hpy166II GTNNAC 1 cut(s) 462
Hpy188I TCNGA 4 cut(s) 240, 489, 499, 862
Hpy188III TCNNGA 4 cut(s) 169, 572, 722, 837
Hpy8I GTNNAC 1 cut(s) 462
Hpy99I CGWCG 1 cut(s) 70
HpyAV CCTTC 2 cut(s) 265, 728
HpyCH4III ACNGT 3 cut(s) 20, 70, 343
HpyCH4IV ACGT 2 cut(s) 523, 945
HpyF10VI GCNNNNNNNGC 3 cut(s) 139, 373, 382
HpyF3I CTNAG 3 cut(s) 279, 708, 861
HpySE526I ACGT 2 cut(s) 523, 945
Hsp92II CATG 5 cut(s) 137, 195, 248, 298, 997
Kzo9I GATC 3 cut(s) 685, 839, 951
LmnI GCTCC 2 cut(s) 668, 967
LpnPI CCDG 6 cut(s) 171, 531, 768, 799, 826, 950
Lsp1109I GCAGC 2 cut(s) 151, 575
LweI GCATC 4 cut(s) 577, 594, 690, 925
MaeI CTAG 3 cut(s) 474, 608, 828
MaeII ACGT 2 cut(s) 523, 945
MaeIII GTNAC 2 cut(s) 160, 519
MalI GATC 3 cut(s) 687, 841, 953
MboI GATC 3 cut(s) 685, 839, 951
MboII GAAGA 8 cut(s) 22, 382, 452, 455, 491, 877, 893, 905
MfeI CAATTG 1 cut(s) 615
MhlI GDGCHC 1 cut(s) 464
MluCI AATT 6 cut(s) 222, 386, 505, 615, 677, 959
MlyI GAGTC 1 cut(s) 724
MnlI CCTC 5 cut(s) 54, 104, 261, 394, 828
MroXI GAANNNNTTC 1 cut(s) 483
MseI TTAA 6 cut(s) 116, 312, 432, 513, 648, 696
MslI CAYNNNNRTG 2 cut(s) 293, 426
MspR9I CCNGG 1 cut(s) 814
MunI CAATTG 1 cut(s) 615
MvaI CCWGG 1 cut(s) 814
MwoI GCNNNNNNNGC 3 cut(s) 139, 373, 382
NdeI CATATG 1 cut(s) 199
NdeII GATC 3 cut(s) 685, 839, 951
NlaIII CATG 5 cut(s) 137, 195, 248, 298, 997
NlaIV GGNNCC 2 cut(s) 242, 811
NmuCI GTSAC 2 cut(s) 160, 519
NspI RCATGY 2 cut(s) 195, 298
PceI AGGCCT 1 cut(s) 817
PciI ACATGT 2 cut(s) 191, 294
PdmI GAANNNNTTC 1 cut(s) 483
PfeI GAWTC 1 cut(s) 228
PkrI GCNGC 2 cut(s) 141, 590
Ple19I CGATCG 1 cut(s) 842
PleI GAGTC 1 cut(s) 724
PpsI GAGTC 1 cut(s) 724
PscI ACATGT 2 cut(s) 191, 294
PshBI ATTAAT 1 cut(s) 513
PsiI TTATAA 1 cut(s) 363
Psp6I CCWGG 1 cut(s) 812
PspGI CCWGG 1 cut(s) 812
PspN4I GGNNCC 2 cut(s) 242, 811
PspPI GGNCC 1 cut(s) 809
PvuI CGATCG 1 cut(s) 842
RsaI GTAC 3 cut(s) 148, 284, 638
RsaNI GTAC 3 cut(s) 147, 283, 637
RseI CAYNNNNRTG 2 cut(s) 293, 426
SaqAI TTAA 6 cut(s) 116, 312, 432, 513, 648, 696
SatI GCNGC 2 cut(s) 140, 589
Sau3AI GATC 3 cut(s) 685, 839, 951
Sau96I GGNCC 1 cut(s) 809
SchI GAGTC 1 cut(s) 724
ScrFI CCNGG 1 cut(s) 814
SduI GDGCHC 1 cut(s) 464
SfaNI GCATC 4 cut(s) 577, 594, 690, 925
SmiMI CAYNNNNRTG 2 cut(s) 293, 426
Sse9I AATT 6 cut(s) 222, 386, 505, 615, 677, 959
SseBI AGGCCT 1 cut(s) 817
SsiI CCGC 2 cut(s) 26, 51
SspMI CTAG 3 cut(s) 474, 608, 828
StuI AGGCCT 1 cut(s) 817
StyD4I CCNGG 1 cut(s) 812
StyI CCWWGG 1 cut(s) 305
TaaI ACNGT 3 cut(s) 20, 70, 343
TaiI ACGT 2 cut(s) 526, 948
TaqI TCGA 5 cut(s) 46, 65, 551, 733, 838
TasI AATT 6 cut(s) 222, 386, 505, 615, 677, 959
TatI WGTACW 1 cut(s) 636
TfiI GAWTC 1 cut(s) 228
Tru1I TTAA 6 cut(s) 116, 312, 432, 513, 648, 696
Tru9I TTAA 6 cut(s) 116, 312, 432, 513, 648, 696
TscAI CASTG 1 cut(s) 348
TseFI GTSAC 2 cut(s) 160, 519
TseI GCWGC 2 cut(s) 139, 588
Tsp45I GTSAC 2 cut(s) 160, 519
TspDTI ATGAA 7 cut(s) 29, 234, 755, 765, 867, 982, 1022
TspGWI ACGGA 2 cut(s) 20, 347
TspRI CASTG 1 cut(s) 348
VneI GTGCAC 1 cut(s) 460
VspI ATTAAT 1 cut(s) 513
XapI RAATTY 1 cut(s) 505
XceI RCATGY 2 cut(s) 195, 298
XmnI GAANNNNTTC 1 cut(s) 483
XspI CTAG 3 cut(s) 474, 608, 828
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.