Rroxscaffold_3G00263220

TdcA1-ORF2 protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000003
OG0000224
Physical Location & Seq
Forward (+)
57179231 .. 57182364
3134 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_3G00263220.1

Sequence Viewer

Length: 795 bp
ATGTCGACTGTATTTTGTAATTTTCGTTATAAGTTGAAGAAACATTTTGAGAAATTTTCAACAATCGAGGAAGCAATTGAAAACAAACACGATGATGTCAAGACTCGGGAAGAATGGGAGTTTCCCCGTGCTCGTTTTTCTAGTGAAAAGTTTCAGATTCGTTCAGAGAAGAATGCTATAAATAGGTCAAAGTTGACACATCACCACAAAGCTGGGTCAAAGTCATTTATGTCTCACCAAGAGCAAATTGCAGCACAGACTGGAGAGATGCAAGGTGCAATTGATCGCTTTGAAACAGAGTACAAAAGCACTAAAAAAGGTTGGGACTTGGGAGCAAAAGCAAAGTGGGATGAAATGATTAAGATGCGAACCGAGACAACTCAACCTGATGGAACTCGGACAATGACGGACGATGAAATTTGTGCAAAAGTCCTCGGAGTCAAATCAGGATACATTAAGGGTTGTGGTTTTGGCCCTAGACCTCCACCATCAAGGGTCTCTCATTCGTCGATAAATGAAATGTCTGAAAAGAACAAAGAGTTGCAAGAACAGCTTCAAGAGACCCAACACCTTGTAGGGACTCAACAACAAAAGATTGATGCGCAAAATGAGGTGATCCAAAGATTGGAGGAGCAAGCCAAAAAGTTTGAGGAGTTCATGGCTAACTTTTCCAGGCAACATCCATCAAACTCGGGACTCAGCGTTCCATCAATGGCGGCCGGCACCGGTCTCCCTCCTAAGCCACTTGTTAATGGCCCTCCAACGCCGATCTTGTATGGCGACCACCAAAGTTAG
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

264

Amino Acids

30.07

Weight (kDa)

8.61

Isoelectric Point (pI)

46.72

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Transposase_24 PF03004 48 - 159 6.4e-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) 30
Acc16I TGCGCA 1 cut(s) 603
AccB1I GGYRCC 1 cut(s) 722
AccB7I CCANNNNNTGG 1 cut(s) 625
AccI GTMKAC 1 cut(s) 5
AciI CCGC 1 cut(s) 716
AclWI GGATC 1 cut(s) 610
AcoI YGGCCR 1 cut(s) 717
AcsI RAATTY 2 cut(s) 53, 417
AfaI GTAC 1 cut(s) 302
AfiI CCNNNNNNNGG 1 cut(s) 625
AgeI ACCGGT 1 cut(s) 725
AgsI TTSAA 5 cut(s) 37, 60, 80, 293, 557
AjnI CCWGG 1 cut(s) 671
AloI GAACNNNNNNTCC 2 cut(s) 687, 719
AluBI AGCT 2 cut(s) 212, 553
AluI AGCT 2 cut(s) 212, 553
Alw21I GWGCWC 1 cut(s) 133
Alw26I GTCTC 5 cut(s) 237, 368, 502, 554, 734
AlwI GGATC 1 cut(s) 610
Ama87I CYCGRG 2 cut(s) 105, 691
AoxI GGCC 3 cut(s) 472, 717, 754
ApeKI GCWGC 1 cut(s) 251
ApoI RAATTY 2 cut(s) 53, 417
AsiGI ACCGGT 1 cut(s) 725
Asp700I GAANNNNTTC 2 cut(s) 150, 552
AspLEI GCGC 1 cut(s) 604
AspS9I GGNCC 2 cut(s) 473, 755
AsuHPI GGTGA 3 cut(s) 194, 227, 625
AvaI CYCGRG 2 cut(s) 105, 691
BanI GGYRCC 1 cut(s) 722
Bbv12I GWGCWC 1 cut(s) 133
BbvI GCAGC 1 cut(s) 263
BccI CCATC 4 cut(s) 383, 496, 691, 715
BciT130I CCWGG 1 cut(s) 673
BciVI GTATCC 1 cut(s) 443
BcoDI GTCTC 5 cut(s) 237, 368, 502, 554, 734
BfaI CTAG 2 cut(s) 141, 477
BfuI GTATCC 1 cut(s) 443
BisI GCNGC 2 cut(s) 252, 717
BlsI GCNGC 2 cut(s) 253, 718
Bme1390I CCNGG 1 cut(s) 673
BmeT110I CYCGRG 2 cut(s) 105, 691
BmgT120I GGNCC 2 cut(s) 473, 755
BmiI GGNNCC 1 cut(s) 724
BmrFI CCNGG 1 cut(s) 673
BmsI GCATC 3 cut(s) 258, 354, 589
BpmI CTGGAG 1 cut(s) 282
Bpu10I CCTNAGC 1 cut(s) 738
BsaI GGTCTC 3 cut(s) 502, 554, 734
BsaJI CCNNGG 1 cut(s) 433
BsaWI WCCGGW 1 cut(s) 725
Bsc4I CCNNNNNNNGG 1 cut(s) 625
Bse118I RCCGGY 2 cut(s) 719, 725
Bse1I ACTGG 1 cut(s) 265
BseBI CCWGG 1 cut(s) 673
BseDI CCNNGG 1 cut(s) 433
BseGI GGATG 2 cut(s) 355, 679
BseLI CCNNNNNNNGG 1 cut(s) 625
BseMII CTCAG 1 cut(s) 712
BseNI ACTGG 1 cut(s) 265
BseRI GAGGAG 2 cut(s) 644, 665
BseX3I CGGCCG 1 cut(s) 717
BseXI GCAGC 1 cut(s) 263
BseYI CCCAGC 1 cut(s) 212
Bsh1285I CGRYCG 1 cut(s) 720
BshFI GGCC 3 cut(s) 474, 719, 756
BshNI GGYRCC 1 cut(s) 722
BshTI ACCGGT 1 cut(s) 725
BsiEI CGRYCG 1 cut(s) 720
BsiHKAI GWGCWC 1 cut(s) 133
BsiHKCI CYCGRG 2 cut(s) 105, 691
BsiSI CCGG 2 cut(s) 720, 726
BslFI GGGAC 3 cut(s) 338, 592, 708
BslI CCNNNNNNNGG 1 cut(s) 625
BsmAI GTCTC 5 cut(s) 237, 368, 502, 554, 734
BsmFI GGGAC 3 cut(s) 338, 592, 708
BsmI GAATGC 1 cut(s) 178
BsnI GGCC 3 cut(s) 474, 719, 756
Bso31I GGTCTC 3 cut(s) 502, 554, 734
BsoBI CYCGRG 2 cut(s) 105, 691
Bsp1286I GDGCHC 1 cut(s) 133
Bsp143I GATC 3 cut(s) 283, 615, 768
BspACI CCGC 1 cut(s) 716
BspANI GGCC 3 cut(s) 474, 719, 756
BspCNI CTCAG 1 cut(s) 711
BspLI GGNNCC 1 cut(s) 724
BspPI GGATC 1 cut(s) 610
BspT107I GGYRCC 1 cut(s) 722
BspTNI GGTCTC 3 cut(s) 502, 554, 734
BsrFI RCCGGY 2 cut(s) 719, 725
BsrI ACTGG 1 cut(s) 265
BssAI RCCGGY 2 cut(s) 719, 725
BssECI CCNNGG 1 cut(s) 433
BssMI GATC 3 cut(s) 283, 615, 768
Bst2UI CCWGG 1 cut(s) 673
Bst4CI ACNGT 1 cut(s) 10
BstC8I GCNNGC 2 cut(s) 636, 721
BstDEI CTNAG 2 cut(s) 698, 738
BstF5I GGATG 2 cut(s) 355, 679
BstHHI GCGC 1 cut(s) 604
BstKTI GATC 3 cut(s) 286, 618, 771
BstMAI GTCTC 5 cut(s) 237, 368, 502, 554, 734
BstMBI GATC 3 cut(s) 283, 615, 768
BstMCI CGRYCG 1 cut(s) 720
BstMWI GCNNNNNNNGC 1 cut(s) 550
BstNI CCWGG 1 cut(s) 673
BstSCI CCNGG 1 cut(s) 671
BstV1I GCAGC 1 cut(s) 263
BstXI CCANNNNNNTGG 1 cut(s) 212
BstZI CGGCCG 1 cut(s) 717
BsuI GTATCC 1 cut(s) 443
BsuRI GGCC 3 cut(s) 474, 719, 756
BtsCI GGATG 2 cut(s) 355, 679
Cac8I GCNNGC 2 cut(s) 636, 721
CfoI GCGC 1 cut(s) 604
Cfr10I RCCGGY 2 cut(s) 719, 725
Cfr13I GGNCC 2 cut(s) 473, 755
Csp6I GTAC 1 cut(s) 301
CspAI ACCGGT 1 cut(s) 725
CviAII CATG 1 cut(s) 658
CviJI RGCY 8 cut(s) 212, 474, 553, 638, 662, 719, 742, 756
CviKI_1 RGCY 8 cut(s) 212, 474, 553, 638, 662, 719, 742, 756
CviQI GTAC 1 cut(s) 301
DdeI CTNAG 2 cut(s) 698, 738
DpnI GATC 3 cut(s) 285, 617, 770
DpnII GATC 3 cut(s) 283, 615, 768
EaeI YGGCCR 1 cut(s) 717
EagI CGGCCG 1 cut(s) 717
EclXI CGGCCG 1 cut(s) 717
Eco31I GGTCTC 3 cut(s) 502, 554, 734
Eco52I CGGCCG 1 cut(s) 717
Eco88I CYCGRG 2 cut(s) 105, 691
EcoRII CCWGG 1 cut(s) 671
FaeI CATG 1 cut(s) 661
FaiI YATR 5 cut(s) 30, 179, 230, 659, 777
FalI AAGNNNNNCTT 2 cut(s) 537, 569
FaqI GGGAC 3 cut(s) 338, 592, 708
FatI CATG 1 cut(s) 657
FblI GTMKAC 1 cut(s) 5
Fnu4HI GCNGC 2 cut(s) 252, 717
FokI GGATG 2 cut(s) 362, 666
Fsp4HI GCNGC 2 cut(s) 252, 717
FspBI CTAG 2 cut(s) 141, 477
FspI TGCGCA 1 cut(s) 603
GlaI GCGC 1 cut(s) 603
GluI GCNGC 2 cut(s) 252, 717
GsaI CCCAGC 1 cut(s) 216
GsuI CTGGAG 1 cut(s) 282
HaeIII GGCC 3 cut(s) 474, 719, 756
HapII CCGG 2 cut(s) 720, 726
HhaI GCGC 1 cut(s) 604
Hin1II CATG 1 cut(s) 661
Hin6I GCGC 1 cut(s) 602
HinP1I GCGC 1 cut(s) 602
HincII GTYRAC 2 cut(s) 6, 195
HindII GTYRAC 2 cut(s) 6, 195
HinfI GANTC 5 cut(s) 103, 157, 438, 580, 696
HpaII CCGG 2 cut(s) 720, 726
HphI GGTGA 3 cut(s) 194, 227, 625
Hpy166II GTNNAC 2 cut(s) 6, 195
Hpy188I TCNGA 5 cut(s) 156, 166, 399, 437, 526
Hpy188III TCNNGA 5 cut(s) 100, 107, 447, 557, 693
Hpy8I GTNNAC 2 cut(s) 6, 195
Hpy99I CGWCG 1 cut(s) 511
HpyCH4III ACNGT 1 cut(s) 10
HpyCH4V TGCA 5 cut(s) 251, 271, 278, 425, 544
HpyF10VI GCNNNNNNNGC 1 cut(s) 550
HpyF3I CTNAG 2 cut(s) 698, 738
Hsp92II CATG 1 cut(s) 661
HspAI GCGC 1 cut(s) 602
KroI GCCGGC 1 cut(s) 719
KroNI GCCGGC 1 cut(s) 721
Kzo9I GATC 3 cut(s) 283, 615, 768
LmnI GCTCC 2 cut(s) 332, 631
LpnPI CCDG 8 cut(s) 198, 246, 399, 432, 658, 685, 733, 739
Lsp1109I GCAGC 1 cut(s) 263
LweI GCATC 3 cut(s) 258, 354, 589
MaeI CTAG 2 cut(s) 141, 477
MalI GATC 3 cut(s) 285, 617, 770
MboI GATC 3 cut(s) 283, 615, 768
MboII GAAGA 3 cut(s) 49, 122, 181
MfeI CAATTG 2 cut(s) 75, 279
MhlI GDGCHC 1 cut(s) 133
MluCI AATT 6 cut(s) 19, 53, 75, 246, 279, 417
MlyI GAGTC 4 cut(s) 97, 447, 574, 690
MmeI TCCRAC 1 cut(s) 785
MnlI CCTC 8 cut(s) 61, 443, 492, 604, 622, 643, 744, 768
MroNI GCCGGC 1 cut(s) 719
MroXI GAANNNNTTC 2 cut(s) 150, 552
MseI TTAA 3 cut(s) 360, 456, 750
MslI CAYNNNNRTG 1 cut(s) 93
MspI CCGG 2 cut(s) 720, 726
MspR9I CCNGG 1 cut(s) 673
MunI CAATTG 2 cut(s) 75, 279
Mva1269I GAATGC 1 cut(s) 178
MvaI CCWGG 1 cut(s) 673
MwoI GCNNNNNNNGC 1 cut(s) 550
NaeI GCCGGC 1 cut(s) 721
NdeII GATC 3 cut(s) 283, 615, 768
NgoMIV GCCGGC 1 cut(s) 719
NlaIII CATG 1 cut(s) 661
NlaIV GGNNCC 1 cut(s) 724
NsbI TGCGCA 1 cut(s) 603
PctI GAATGC 1 cut(s) 178
PdiI GCCGGC 1 cut(s) 721
PdmI GAANNNNTTC 2 cut(s) 150, 552
PfeI GAWTC 1 cut(s) 157
PflMI CCANNNNNTGG 1 cut(s) 625
PinAI ACCGGT 1 cut(s) 725
PkrI GCNGC 2 cut(s) 253, 718
PleI GAGTC 4 cut(s) 97, 446, 574, 690
PpsI GAGTC 4 cut(s) 97, 446, 574, 690
PsiI TTATAA 1 cut(s) 30
Psp6I CCWGG 1 cut(s) 671
PspFI CCCAGC 1 cut(s) 212
PspGI CCWGG 1 cut(s) 671
PspN4I GGNNCC 1 cut(s) 724
PspPI GGNCC 2 cut(s) 473, 755
RsaI GTAC 1 cut(s) 302
RsaNI GTAC 1 cut(s) 301
RseI CAYNNNNRTG 1 cut(s) 93
SalI GTCGAC 1 cut(s) 4
SaqAI TTAA 3 cut(s) 360, 456, 750
SatI GCNGC 2 cut(s) 252, 717
Sau3AI GATC 3 cut(s) 283, 615, 768
Sau96I GGNCC 2 cut(s) 473, 755
SchI GAGTC 4 cut(s) 97, 447, 574, 690
ScrFI CCNGG 1 cut(s) 673
SduI GDGCHC 1 cut(s) 133
SetI ASST 9 cut(s) 188, 214, 277, 322, 388, 484, 555, 573, 615
SfaNI GCATC 3 cut(s) 258, 354, 589
SmiMI CAYNNNNRTG 1 cut(s) 93
Sse9I AATT 6 cut(s) 19, 53, 75, 246, 279, 417
SsiI CCGC 1 cut(s) 716
SspMI CTAG 2 cut(s) 141, 477
StyD4I CCNGG 1 cut(s) 671
TaaI ACNGT 1 cut(s) 10
TaqI TCGA 3 cut(s) 5, 66, 509
TasI AATT 6 cut(s) 19, 53, 75, 246, 279, 417
TatI WGTACW 1 cut(s) 300
TauI GCSGC 1 cut(s) 719
TfiI GAWTC 1 cut(s) 157
Tru1I TTAA 3 cut(s) 360, 456, 750
Tru9I TTAA 3 cut(s) 360, 456, 750
TseI GCWGC 1 cut(s) 251
TspDTI ATGAA 4 cut(s) 366, 429, 531, 646
TspGWI ACGGA 1 cut(s) 422
Van91I CCANNNNNTGG 1 cut(s) 625
XapI RAATTY 2 cut(s) 53, 417
XmiI GTMKAC 1 cut(s) 5
XmnI GAANNNNTTC 2 cut(s) 150, 552
XspI CTAG 2 cut(s) 141, 477
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.