Rroxscaffold_3G00219320

ATP-dependent Clp protease proteolytic subunit

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000003
OG0016629
Physical Location & Seq
Reverse (-)
1453295 .. 1456502
3208 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_3G00219320.1

Sequence Viewer

Length: 936 bp
ATGGCGCAGACCTGCGTTTCCACATCGGCCTCCTCCTCCTCTCTCAGATTCAACTCCCTCGGCTTCGCTCTAAACCCTAGCTCTTGTTCCCAGCCACACAGCCTCACCGTCTCTCTCCCCTCTCAACGCTTTCCTTCAAGGAAGTTGAAGAAGTTAGTTGGGAATAGGAAAGGTCTCCAGAGTTCTCCGGTGAAGGCTGTCTATGATGAATTTTGGGCACCGGGTTCTCGTGAAGGAATTTGGTCCATAAGGGAGGATTTGCAAGTTCCATCTTCGCCATACTTTCCTGCTTGTGCACAGGGACAGGGTCCGCCGCCTATGGTGCAAGAACGCTTTCAGAGTGTTATTAGTCAGCTTTTCCAGCATAGAATCATTCGTTGTGGGGGAGCTGTGGATGATGATATGGCAAATATAATTGTCGCTCAGCTTCTTTACCTTGATGCTGTTGATCCTAAAAAGGACATTGTCATGTATGTGAATTCACCCGGAGGATCTGTTACTGCTGGTATGGCCATTTTCGACACTATGAGGCATATCCGACCTGATGTCTCTACTGTGTGTGTTGGACTAGCAGCTAGTATGGGGGCTTTCCTGCTTAGCGCTGGCACCAAGGGAAAACGGTACAGCTTGCCAAATTCAAGGATAATGATCCATCAGCCTCTTGGTGGAGCTCAAGGAGGGCAAACTGACATAGATATTCAGGCAAATGAAATGCTGCATCACAAGGCAAATTTAAATGGTTATCTCTCCTACCACACTGGTCAAAGTCTTGAAAAGATCAACCAAGACACGGATCGTGATTTCTTCATGAGTGCAAAGGAGGCTAAGGAGTATGGGCTTATAGATGGTGTGATATTGAATCCTCTCAAAGCTTTCCAACCGTTGCCAGTTGCGGTTGAGAGTACTGATGAATCCAGTGAGCAAGCTGTTGCCTAG

Protein Analysis

311

Amino Acids

33.69

Weight (kDa)

7.04

Isoelectric Point (pI)

49.08

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
CLP_protease PF00574 109 - 285 4.3e-81 Clp protease
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: OG0016629)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G02560
fragaria_vesca FvH4_5g39050
malus_domestica MD00G1140700.v1.1 MD03G1292800.v1.1
prunus_persica Prupe.8G265800_v2.0.a1
pyrus_communis pycom03g23210 pycom11g27350
rosa_chinensis RchiOBHm_Chr7g0241011
rosa_laevigata RLG00000000604
rosa_multiflora Rmu_sc0003187.1_g000009
rosa_roxburghii Rroxscaffold_3G00219320
rosa_rugosa Rorug07G0341200
rosa_samantha Rh7BG467700
rosa_wichuraiana Rw7G041930

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 20
AccB1I GGYRCC 2 cut(s) 217, 605
AciI CCGC 3 cut(s) 311, 314, 893
AclWI GGATC 4 cut(s) 443, 499, 643, 801
AcoI YGGCCR 1 cut(s) 510
AcsI RAATTY 5 cut(s) 209, 237, 478, 634, 730
AfaI GTAC 2 cut(s) 623, 904
AfeI AGCGCT 1 cut(s) 601
AfiI CCNNNNNNNGG 2 cut(s) 665, 790
AgsI TTSAA 6 cut(s) 52, 138, 148, 639, 773, 859
AhdI GACNNNNNGTC 1 cut(s) 545
AluBI AGCT 9 cut(s) 81, 355, 389, 427, 575, 627, 671, 872, 926
AluI AGCT 9 cut(s) 81, 355, 389, 427, 575, 627, 671, 872, 926
Alw21I GWGCWC 2 cut(s) 298, 673
Alw26I GTCTC 3 cut(s) 115, 179, 553
Alw44I GTGCAC 1 cut(s) 294
AlwI GGATC 4 cut(s) 443, 499, 643, 801
Aor51HI AGCGCT 1 cut(s) 601
AoxI GGCC 2 cut(s) 27, 510
ApaLI GTGCAC 1 cut(s) 294
ApeKI GCWGC 2 cut(s) 572, 715
ApoI RAATTY 5 cut(s) 209, 237, 478, 634, 730
Asp700I GAANNNNTTC 1 cut(s) 333
AspLEI GCGC 2 cut(s) 7, 602
AspS9I GGNCC 2 cut(s) 243, 308
AsuC2I CCSGG 2 cut(s) 222, 486
AsuHPI GGTGA 3 cut(s) 97, 202, 474
AvaII GGWCC 2 cut(s) 243, 308
BaeGI GKGCMC 2 cut(s) 220, 298
BalI TGGCCA 1 cut(s) 512
BanI GGYRCC 2 cut(s) 217, 605
BanII GRGCYC 1 cut(s) 673
BauI CACGAG 1 cut(s) 228
Bbv12I GWGCWC 2 cut(s) 298, 673
BbvI GCAGC 2 cut(s) 584, 702
BccI CCATC 3 cut(s) 277, 660, 839
BcnI CCSGG 2 cut(s) 222, 486
BcoDI GTCTC 3 cut(s) 115, 179, 553
BfaI CTAG 4 cut(s) 78, 569, 576, 934
BfoI RGCGCY 1 cut(s) 603
BfuAI ACCTGC 1 cut(s) 20
BisI GCNGC 3 cut(s) 314, 573, 716
BlpI GCTNAGC 2 cut(s) 423, 596
BlsI GCNGC 3 cut(s) 315, 574, 717
BmcAI AGTACT 1 cut(s) 904
Bme1390I CCNGG 2 cut(s) 222, 486
Bme18I GGWCC 2 cut(s) 243, 308
BmeRI GACNNNNNGTC 1 cut(s) 545
BmgT120I GGNCC 2 cut(s) 243, 308
BmiI GGNNCC 3 cut(s) 219, 309, 607
BmrFI CCNGG 2 cut(s) 222, 486
BmsI GCATC 2 cut(s) 430, 727
BpmI CTGGAG 1 cut(s) 161
Bpu10I CCTNAGC 1 cut(s) 825
Bpu1102I GCTNAGC 2 cut(s) 423, 596
BpuEI CTTGAG 1 cut(s) 657
BpuMI CCSGG 2 cut(s) 222, 486
BsaBI GATNNNNATC 1 cut(s) 647
BsaI GGTCTC 1 cut(s) 179
BsaJI CCNNGG 2 cut(s) 58, 609
BsaWI WCCGGW 1 cut(s) 187
BsaXI ACNNNNNCTCC 2 cut(s) 480, 510
Bsc4I CCNNNNNNNGG 2 cut(s) 665, 790
Bse1I ACTGG 3 cut(s) 763, 887, 915
Bse8I GATNNNNATC 1 cut(s) 647
BseDI CCNNGG 2 cut(s) 58, 609
BseGI GGATG 1 cut(s) 400
BseJI GATNNNNATC 1 cut(s) 647
BseLI CCNNNNNNNGG 2 cut(s) 665, 790
BseMII CTCAG 2 cut(s) 58, 437
BseNI ACTGG 3 cut(s) 763, 887, 915
BseRI GAGGAG 3 cut(s) 22, 25, 28
BseSI GKGCMC 2 cut(s) 220, 298
BseXI GCAGC 2 cut(s) 584, 702
BseYI CCCAGC 1 cut(s) 90
BshFI GGCC 2 cut(s) 29, 512
BshNI GGYRCC 2 cut(s) 217, 605
BsiHKAI GWGCWC 2 cut(s) 298, 673
BsiSI CCGG 3 cut(s) 188, 221, 486
BslFI GGGAC 1 cut(s) 315
BslI CCNNNNNNNGG 2 cut(s) 665, 790
BsmAI GTCTC 3 cut(s) 115, 179, 553
BsmBI CGTCTC 1 cut(s) 115
BsmFI GGGAC 1 cut(s) 315
BsnI GGCC 2 cut(s) 29, 512
Bso31I GGTCTC 1 cut(s) 179
Bsp1286I GDGCHC 3 cut(s) 220, 298, 673
Bsp143I GATC 5 cut(s) 448, 491, 648, 777, 793
Bsp1720I GCTNAGC 2 cut(s) 423, 596
BspACI CCGC 3 cut(s) 311, 314, 893
BspANI GGCC 2 cut(s) 29, 512
BspCNI CTCAG 2 cut(s) 57, 436
BspHI TCATGA 1 cut(s) 807
BspLI GGNNCC 3 cut(s) 219, 309, 607
BspMI ACCTGC 1 cut(s) 20
BspPI GGATC 4 cut(s) 443, 499, 643, 801
BspT107I GGYRCC 2 cut(s) 217, 605
BspTNI GGTCTC 1 cut(s) 179
BsrI ACTGG 3 cut(s) 763, 887, 915
BssECI CCNNGG 2 cut(s) 58, 609
BssMI GATC 5 cut(s) 448, 491, 648, 777, 793
BssSI CACGAG 1 cut(s) 228
BssT1I CCWWGG 1 cut(s) 609
Bst2BI CACGAG 1 cut(s) 228
Bst4CI ACNGT 4 cut(s) 109, 556, 621, 882
BstC8I GCNNGC 3 cut(s) 604, 629, 924
BstDEI CTNAG 4 cut(s) 44, 423, 596, 825
BstF5I GGATG 1 cut(s) 400
BstH2I RGCGCY 1 cut(s) 603
BstHHI GCGC 2 cut(s) 7, 602
BstKTI GATC 5 cut(s) 451, 494, 651, 780, 796
BstMAI GTCTC 3 cut(s) 115, 179, 553
BstMBI GATC 5 cut(s) 448, 491, 648, 777, 793
BstMWI GCNNNNNNNGC 4 cut(s) 322, 361, 509, 821
BstSCI CCNGG 2 cut(s) 220, 484
BstSLI GKGCMC 2 cut(s) 220, 298
BstV1I GCAGC 2 cut(s) 584, 702
BstX2I RGATCY 1 cut(s) 491
BstYI RGATCY 1 cut(s) 491
BsuRI GGCC 2 cut(s) 29, 512
BtsCI GGATG 1 cut(s) 400
BtsIMutI CAGTG 2 cut(s) 756, 922
BveI ACCTGC 1 cut(s) 20
Cac8I GCNNGC 3 cut(s) 604, 629, 924
CciI TCATGA 1 cut(s) 807
CfoI GCGC 2 cut(s) 7, 602
Cfr13I GGNCC 2 cut(s) 243, 308
Csp6I GTAC 2 cut(s) 622, 903
CviAII CATG 2 cut(s) 469, 808
CviQI GTAC 2 cut(s) 622, 903
DdeI CTNAG 4 cut(s) 44, 423, 596, 825
DpnI GATC 5 cut(s) 450, 493, 650, 779, 795
DpnII GATC 5 cut(s) 448, 491, 648, 777, 793
DraI TTTAAA 1 cut(s) 735
DriI GACNNNNNGTC 1 cut(s) 545
EaeI YGGCCR 1 cut(s) 510
Eam1105I GACNNNNNGTC 1 cut(s) 545
EciI GGCGGA 1 cut(s) 300
Ecl136II GAGCTC 1 cut(s) 671
Eco130I CCWWGG 1 cut(s) 609
Eco24I GRGCYC 1 cut(s) 673
Eco31I GGTCTC 1 cut(s) 179
Eco47I GGWCC 2 cut(s) 243, 308
Eco47III AGCGCT 1 cut(s) 601
Eco53kI GAGCTC 1 cut(s) 671
EcoICRI GAGCTC 1 cut(s) 671
EcoRI GAATTC 1 cut(s) 478
EcoT14I CCWWGG 1 cut(s) 609
EcoT38I GRGCYC 1 cut(s) 673
ErhI CCWWGG 1 cut(s) 609
Esp3I CGTCTC 1 cut(s) 115
FaeI CATG 2 cut(s) 472, 811
FaqI GGGAC 1 cut(s) 315
FatI CATG 2 cut(s) 468, 807
Fnu4HI GCNGC 3 cut(s) 314, 573, 716
FokI GGATG 1 cut(s) 407
FriOI GRGCYC 1 cut(s) 673
Fsp4HI GCNGC 3 cut(s) 314, 573, 716
FspBI CTAG 4 cut(s) 78, 569, 576, 934
GlaI GCGC 2 cut(s) 6, 601
GluI GCNGC 3 cut(s) 314, 573, 716
GsaI CCCAGC 1 cut(s) 94
GsuI CTGGAG 1 cut(s) 161
HaeII RGCGCY 1 cut(s) 603
HaeIII GGCC 2 cut(s) 29, 512
HapII CCGG 3 cut(s) 188, 221, 486
HhaI GCGC 2 cut(s) 7, 602
Hin1II CATG 2 cut(s) 472, 811
Hin6I GCGC 2 cut(s) 5, 600
HinP1I GCGC 2 cut(s) 5, 600
HindIII AAGCTT 1 cut(s) 870
HinfI GANTC 4 cut(s) 48, 369, 859, 911
HpaII CCGG 3 cut(s) 188, 221, 486
HphI GGTGA 3 cut(s) 97, 202, 474
Hpy166II GTNNAC 1 cut(s) 296
Hpy188I TCNGA 3 cut(s) 47, 339, 539
Hpy188III TCNNGA 5 cut(s) 178, 230, 770, 797, 808
Hpy8I GTNNAC 1 cut(s) 296
HpyAV CCTTC 3 cut(s) 144, 187, 227
HpyCH4III ACNGT 4 cut(s) 109, 556, 621, 882
HpyCH4V TGCA 5 cut(s) 262, 296, 325, 718, 815
HpyF10VI GCNNNNNNNGC 4 cut(s) 322, 361, 509, 821
HpyF3I CTNAG 4 cut(s) 44, 423, 596, 825
Hsp92II CATG 2 cut(s) 472, 811
HspAI GCGC 2 cut(s) 5, 600
Kzo9I GATC 5 cut(s) 448, 491, 648, 777, 793
LmnI GCTCC 2 cut(s) 386, 668
Lsp1109I GCAGC 2 cut(s) 584, 702
LweI GCATC 2 cut(s) 430, 727
MaeI CTAG 4 cut(s) 78, 569, 576, 934
MaeIII GTNAC 1 cut(s) 496
MalI GATC 5 cut(s) 450, 493, 650, 779, 795
MboI GATC 5 cut(s) 448, 491, 648, 777, 793
MboII GAAGA 3 cut(s) 160, 264, 796
MflI RGATCY 1 cut(s) 491
MhlI GDGCHC 3 cut(s) 220, 298, 673
MlsI TGGCCA 1 cut(s) 512
MluCI AATT 6 cut(s) 209, 237, 414, 478, 634, 730
MluNI TGGCCA 1 cut(s) 512
MmeI TCCRAC 3 cut(s) 544, 562, 901
Mox20I TGGCCA 1 cut(s) 512
MroXI GAANNNNTTC 1 cut(s) 333
MscI TGGCCA 1 cut(s) 512
MseI TTAA 1 cut(s) 734
MslI CAYNNNNRTG 2 cut(s) 467, 473
Msp20I TGGCCA 1 cut(s) 512
MspI CCGG 3 cut(s) 188, 221, 486
MspR9I CCNGG 2 cut(s) 222, 486
MwoI GCNNNNNNNGC 4 cut(s) 322, 361, 509, 821
NciI CCSGG 2 cut(s) 222, 486
NdeII GATC 5 cut(s) 448, 491, 648, 777, 793
NlaIII CATG 2 cut(s) 472, 811
NlaIV GGNNCC 3 cut(s) 219, 309, 607
NmeAIII GCCGAG 1 cut(s) 39
PagI TCATGA 1 cut(s) 807
PdmI GAANNNNTTC 1 cut(s) 333
PfeI GAWTC 4 cut(s) 48, 369, 859, 911
PflFI GACNNNGTC 2 cut(s) 306, 464
PkrI GCNGC 3 cut(s) 315, 574, 717
Psp124BI GAGCTC 1 cut(s) 673
PspFI CCCAGC 1 cut(s) 90
PspN4I GGNNCC 3 cut(s) 219, 309, 607
PspPI GGNCC 2 cut(s) 243, 308
PsuI RGATCY 1 cut(s) 491
PsyI GACNNNGTC 2 cut(s) 306, 464
RsaI GTAC 2 cut(s) 623, 904
RsaNI GTAC 2 cut(s) 622, 903
RseI CAYNNNNRTG 2 cut(s) 467, 473
SacI GAGCTC 1 cut(s) 673
SaqAI TTAA 1 cut(s) 734
SatI GCNGC 3 cut(s) 314, 573, 716
Sau3AI GATC 5 cut(s) 448, 491, 648, 777, 793
Sau96I GGNCC 2 cut(s) 243, 308
ScaI AGTACT 1 cut(s) 904
ScrFI CCNGG 2 cut(s) 222, 486
SduI GDGCHC 3 cut(s) 220, 298, 673
SfaNI GCATC 2 cut(s) 430, 727
SinI GGWCC 2 cut(s) 243, 308
SmiI ATTTAAAT 1 cut(s) 735
SmiMI CAYNNNNRTG 2 cut(s) 467, 473
SmlI CTYRAG 1 cut(s) 672
SmoI CTYRAG 1 cut(s) 672
Sse9I AATT 6 cut(s) 209, 237, 414, 478, 634, 730
SsiI CCGC 3 cut(s) 311, 314, 893
SspMI CTAG 4 cut(s) 78, 569, 576, 934
SstI GAGCTC 1 cut(s) 673
StyD4I CCNGG 2 cut(s) 220, 484
StyI CCWWGG 1 cut(s) 609
SwaI ATTTAAAT 1 cut(s) 735
TaaI ACNGT 4 cut(s) 109, 556, 621, 882
TaqI TCGA 1 cut(s) 519
TasI AATT 6 cut(s) 209, 237, 414, 478, 634, 730
TatI WGTACW 1 cut(s) 902
TauI GCSGC 1 cut(s) 316
TfiI GAWTC 4 cut(s) 48, 369, 859, 911
Tru1I TTAA 1 cut(s) 734
Tru9I TTAA 1 cut(s) 734
TscAI CASTG 2 cut(s) 763, 922
TseI GCWGC 2 cut(s) 572, 715
TspDTI ATGAA 4 cut(s) 222, 723, 796, 924
TspGWI ACGGA 1 cut(s) 806
TspRI CASTG 2 cut(s) 763, 922
Tth111I GACNNNGTC 2 cut(s) 306, 464
VneI GTGCAC 1 cut(s) 294
VpaK11BI GGWCC 2 cut(s) 243, 308
XapI RAATTY 5 cut(s) 209, 237, 478, 634, 730
XcmI CCANNNNNNNNNTGG 1 cut(s) 659
XmnI GAANNNNTTC 1 cut(s) 333
XspI CTAG 4 cut(s) 78, 569, 576, 934
ZrmI AGTACT 1 cut(s) 904
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.