RLG00000002528

Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs)

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_laevigata
Chr1
OG0014937
Physical Location & Seq
Reverse (-)
35836791 .. 35837726
936 bp
Loading structure...
UTR
Exon/CDS
Intron
RLM00000002528

Sequence Viewer

Length: 936 bp
ATGGCGGGGTACAATGGCAGATCAGAATATATGCAACTTTTCCGTCCCGAACTGCACCTCCAGAGACCACCGTCACCATCCATCTCTGTTCCGCCGCAGCAACAACAACCTCAACCTTCTTCCGATTCTCAACAGCAAGAAGACTCGCCCGAAGGAGACCAAGAACACAAGATCGAGTCCGACACCGCTGCCACAAGTTCCGGAGGCGGCGGTGGCGGTAGCGGTGGGGGTTCAGGACGACGTCCGCGGGGGCGTCCGGCGGGGTCAAAGAACAAGCCGAAGCCGCCGATCATCGTGACGCGCGACAGCCCCAACGCGCTCCGCTCGCACGTGCTGGAGGTCTCTGCCGGGGCAGACGTGGTGGAGAGCGTGTCCCACTACGCGAGGCGGAGGGGGAGGGGAGTGTGCGTGCTCAGCGGCACCGGCACCGTCGCTAACGTCACCCTGCGTCAGCCGGCGGCGCCAGTGGGGAGCGTGGTCACTCTCCACGGGAGGTTCGAGATACTTTCGCTCTCAGGGACGGTGCTTCCGCCTCCGGCCCCTCCGGGCGCCGGGGGACTGTCGATTTTCCTGGCGGGCGGGCAGGGTCAGGTGGTTGGGGGCAGCGTGGTGGGCCCACTGCTGGCTTCGGGGCCAGTTGTTTTGATGGCTGCGTCGTTTGCGAATGCGGTGTTTGAGAGGCTGCCATTGGAGGAGGAAGAGGCAGCGGGCGGTGGTGGGTTACAAGTCCAGCAACCGACGGCTTCACAATCTTCAGGAGTGACAGGTGGTGGTGGTGGTGGTGGAGGACAACATCAGCAGCTTGGTGAGGGAAGCAGCGGCGGTCTCTTTAATCTGGGAGGGAACATGGGGGCGGGGAGCTATCCGGCGTTTTCGGGAACGGATTTGTACGGGTGGGGTAGCGGCGGAGCTACTCATCCGCGGCCTCCGTTTTAG
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
DUF296

Protein Analysis

312

Amino Acids

31.16

Weight (kDa)

6.66

Isoelectric Point (pI)

73.47

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 108 - 221 5e-23 Plants and Prokaryotes Conserved (PCC) domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0014937)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G20900 AT1G76500
fragaria_vesca FvH4_5g26230
malus_domestica MD06G1003000.v1.1
prunus_persica Prupe.5G004600_v2.0.a1
pyrus_communis pycom06g00310
rosa_chinensis RchiOBHm_Chr7g0216901
rosa_laevigata RLG00000002528
rosa_multiflora Rmu_sc0000854.1_g000020
rosa_roxburghii Rroxscaffold_3G00242760
rosa_rugosa Rorug07G0164300
rosa_samantha Rh7AG304600 Rh7BG296100 Rh7CG323000 Rh7DG304600
rosa_wichuraiana Rw7G025860

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AatII GACGTC 1 cut(s) 244
AccB1I GGYRCC 4 cut(s) 419, 425, 460, 548
AccBSI CCGCTC 1 cut(s) 324
AccII CGCG 6 cut(s) 247, 301, 303, 317, 383, 922
AccIII TCCGGA 1 cut(s) 200
AcuI CTGAAG 1 cut(s) 738
AcvI CACGTG 1 cut(s) 331
AcyI GRCGYC 4 cut(s) 241, 253, 461, 549
AfaI GTAC 2 cut(s) 11, 890
AfiI CCNNNNNNNGG 2 cut(s) 551, 622
AjiI CACGTC 1 cut(s) 358
AjnI CCWGG 1 cut(s) 570
AloI GAACNNNNNNTCC 2 cut(s) 42, 74
AluBI AGCT 3 cut(s) 802, 861, 911
AluI AGCT 3 cut(s) 802, 861, 911
Alw21I GWGCWC 1 cut(s) 414
Alw26I GTCTC 4 cut(s) 58, 150, 346, 830
Aor13HI TCCGGA 1 cut(s) 200
AoxI GGCC 4 cut(s) 537, 613, 632, 923
ApaI GGGCCC 1 cut(s) 617
ApeKI GCWGC 8 cut(s) 97, 188, 603, 650, 682, 704, 799, 816
AspLEI GCGC 4 cut(s) 303, 319, 463, 551
AspS9I GGNCC 4 cut(s) 538, 613, 614, 632
AsuC2I CCSGG 3 cut(s) 349, 546, 553
AsuHPI GGTGA 3 cut(s) 66, 433, 818
BaeGI GKGCMC 1 cut(s) 617
BanI GGYRCC 4 cut(s) 419, 425, 460, 548
BanII GRGCYC 1 cut(s) 617
BbrPI CACGTG 1 cut(s) 331
BbsI GAAGAC 1 cut(s) 147
Bbv12I GWGCWC 1 cut(s) 414
BbvI GCAGC 8 cut(s) 109, 175, 615, 637, 669, 716, 811, 828
BccI CCATC 3 cut(s) 85, 89, 640
BceAI ACGGC 1 cut(s) 756
BcgI CGANNNNNNTGC 2 cut(s) 170, 204
BciT130I CCWGG 1 cut(s) 572
BcnI CCSGG 3 cut(s) 349, 546, 553
BcoDI GTCTC 4 cut(s) 58, 150, 346, 830
BfoI RGCGCY 2 cut(s) 464, 552
BlpI GCTNAGC 1 cut(s) 413
Bme1390I CCNGG 4 cut(s) 349, 546, 553, 572
BmgBI CACGTC 1 cut(s) 358
BmgT120I GGNCC 4 cut(s) 538, 613, 614, 632
BmiI GGNNCC 7 cut(s) 421, 427, 462, 540, 550, 615, 633
BmrFI CCNGG 4 cut(s) 349, 546, 553, 572
BoxI GACNNNNGTC 1 cut(s) 70
BpiI GAAGAC 1 cut(s) 147
BpmI CTGGAG 2 cut(s) 44, 356
Bpu1102I GCTNAGC 1 cut(s) 413
BpuMI CCSGG 3 cut(s) 349, 546, 553
BsaAI YACGTR 1 cut(s) 331
BsaHI GRCGYC 4 cut(s) 241, 253, 461, 549
BsaI GGTCTC 4 cut(s) 58, 150, 346, 830
BsaJI CCNNGG 5 cut(s) 245, 348, 487, 552, 920
BsaWI WCCGGW 1 cut(s) 200
BsaXI ACNNNNNCTCC 6 cut(s) 42, 72, 356, 386, 393, 423
Bsc4I CCNNNNNNNGG 2 cut(s) 551, 622
Bse118I RCCGGY 2 cut(s) 422, 454
Bse1I ACTGG 2 cut(s) 464, 635
BseAI TCCGGA 1 cut(s) 200
BseBI CCWGG 1 cut(s) 572
BseDI CCNNGG 5 cut(s) 245, 348, 487, 552, 920
BseGI GGATG 2 cut(s) 77, 916
BseLI CCNNNNNNNGG 2 cut(s) 551, 622
BseMII CTCAG 2 cut(s) 427, 528
BseNI ACTGG 2 cut(s) 464, 635
BseRI GAGGAG 1 cut(s) 707
BseSI GKGCMC 1 cut(s) 617
BseXI GCAGC 8 cut(s) 109, 175, 615, 637, 669, 716, 811, 828
BsgI GTGCAG 1 cut(s) 38
Bsh1236I CGCG 6 cut(s) 247, 301, 303, 317, 383, 922
BshFI GGCC 4 cut(s) 539, 615, 634, 925
BshNI GGYRCC 4 cut(s) 419, 425, 460, 548
BsiHKAI GWGCWC 1 cut(s) 414
BsiSI CCGG 9 cut(s) 201, 257, 348, 423, 455, 536, 545, 552, 866
BslFI GGGAC 4 cut(s) 30, 358, 532, 570
BslI CCNNNNNNNGG 2 cut(s) 551, 622
BsmAI GTCTC 4 cut(s) 58, 150, 346, 830
BsmFI GGGAC 4 cut(s) 30, 358, 532, 570
BsmI GAATGC 1 cut(s) 670
BsnI GGCC 4 cut(s) 539, 615, 634, 925
Bso31I GGTCTC 4 cut(s) 58, 150, 346, 830
Bsp120I GGGCCC 1 cut(s) 613
Bsp1286I GDGCHC 2 cut(s) 414, 617
Bsp13I TCCGGA 1 cut(s) 200
Bsp143I GATC 3 cut(s) 20, 171, 288
Bsp1720I GCTNAGC 1 cut(s) 413
BspANI GGCC 4 cut(s) 539, 615, 634, 925
BspCNI CTCAG 2 cut(s) 426, 527
BspEI TCCGGA 1 cut(s) 200
BspFNI CGCG 6 cut(s) 247, 301, 303, 317, 383, 922
BspLI GGNNCC 7 cut(s) 421, 427, 462, 540, 550, 615, 633
BspT107I GGYRCC 4 cut(s) 419, 425, 460, 548
BspTNI GGTCTC 4 cut(s) 58, 150, 346, 830
BsrBI CCGCTC 1 cut(s) 324
BsrFI RCCGGY 2 cut(s) 422, 454
BsrI ACTGG 2 cut(s) 464, 635
BssAI RCCGGY 2 cut(s) 422, 454
BssECI CCNNGG 5 cut(s) 245, 348, 487, 552, 920
BssMI GATC 3 cut(s) 20, 171, 288
BssNI GRCGYC 4 cut(s) 241, 253, 461, 549
Bst2UI CCWGG 1 cut(s) 572
Bst4CI ACNGT 4 cut(s) 72, 430, 523, 561
Bst6I CTCTTC 1 cut(s) 693
BstACI GRCGYC 4 cut(s) 241, 253, 461, 549
BstBAI YACGTR 1 cut(s) 331
BstC8I GCNNGC 7 cut(s) 326, 410, 456, 577, 581, 624, 709
BstDEI CTNAG 2 cut(s) 413, 514
BstDSI CCRYGG 3 cut(s) 245, 487, 920
BstF5I GGATG 2 cut(s) 77, 916
BstFNI CGCG 6 cut(s) 247, 301, 303, 317, 383, 922
BstH2I RGCGCY 2 cut(s) 464, 552
BstHHI GCGC 4 cut(s) 303, 319, 463, 551
BstKTI GATC 3 cut(s) 23, 174, 291
BstMAI GTCTC 4 cut(s) 58, 150, 346, 830
BstMBI GATC 3 cut(s) 20, 171, 288
BstMWI GCNNNNNNNGC 8 cut(s) 213, 283, 325, 414, 423, 460, 612, 659
BstNI CCWGG 1 cut(s) 572
BstPAI GACNNNNGTC 1 cut(s) 70
BstSCI CCNGG 4 cut(s) 347, 544, 551, 570
BstSLI GKGCMC 1 cut(s) 617
BstUI CGCG 6 cut(s) 247, 301, 303, 317, 383, 922
BstV1I GCAGC 8 cut(s) 109, 175, 615, 637, 669, 716, 811, 828
BstV2I GAAGAC 1 cut(s) 147
BsuRI GGCC 4 cut(s) 539, 615, 634, 925
BtgI CCRYGG 3 cut(s) 245, 487, 920
BtrI CACGTC 1 cut(s) 358
BtsCI GGATG 2 cut(s) 77, 916
BtsI GCAGTG 1 cut(s) 617
BtsIMutI CAGTG 2 cut(s) 471, 617
Cac8I GCNNGC 7 cut(s) 326, 410, 456, 577, 581, 624, 709
CfoI GCGC 4 cut(s) 303, 319, 463, 551
Cfr10I RCCGGY 2 cut(s) 422, 454
Cfr13I GGNCC 4 cut(s) 538, 613, 614, 632
Cfr42I CCGCGG 2 cut(s) 248, 923
CseI GACGC 4 cut(s) 242, 307, 437, 642
Csp6I GTAC 2 cut(s) 10, 889
CviAII CATG 1 cut(s) 847
CviQI GTAC 2 cut(s) 10, 889
DdeI CTNAG 2 cut(s) 413, 514
DinI GGCGCC 2 cut(s) 462, 550
DpnI GATC 3 cut(s) 22, 173, 290
DpnII GATC 3 cut(s) 20, 171, 288
Eam1104I CTCTTC 1 cut(s) 693
EarI CTCTTC 1 cut(s) 693
EciI GGCGGA 4 cut(s) 81, 403, 519, 921
Eco24I GRGCYC 1 cut(s) 617
Eco31I GGTCTC 4 cut(s) 58, 150, 346, 830
Eco57I CTGAAG 1 cut(s) 738
Eco72I CACGTG 1 cut(s) 331
EcoRII CCWGG 1 cut(s) 570
EcoT38I GRGCYC 1 cut(s) 617
EgeI GGCGCC 2 cut(s) 462, 550
EheI GGCGCC 2 cut(s) 462, 550
FaeI CATG 1 cut(s) 850
FaiI YATR 3 cut(s) 30, 32, 848
FaqI GGGAC 4 cut(s) 30, 358, 532, 570
FatI CATG 1 cut(s) 846
FauI CCCGC 6 cut(s) 240, 253, 568, 572, 700, 847
FokI GGATG 2 cut(s) 64, 903
FriOI GRGCYC 1 cut(s) 617
GlaI GCGC 4 cut(s) 302, 318, 462, 550
GsuI CTGGAG 2 cut(s) 44, 356
HaeII RGCGCY 2 cut(s) 464, 552
HaeIII GGCC 4 cut(s) 539, 615, 634, 925
HapII CCGG 9 cut(s) 201, 257, 348, 423, 455, 536, 545, 552, 866
HgaI GACGC 4 cut(s) 242, 307, 437, 642
HhaI GCGC 4 cut(s) 303, 319, 463, 551
Hin1I GRCGYC 4 cut(s) 241, 253, 461, 549
Hin1II CATG 1 cut(s) 850
Hin6I GCGC 4 cut(s) 301, 317, 461, 549
HinP1I GCGC 4 cut(s) 301, 317, 461, 549
HinfI GANTC 3 cut(s) 125, 143, 176
HpaII CCGG 9 cut(s) 201, 257, 348, 423, 455, 536, 545, 552, 866
HphI GGTGA 3 cut(s) 66, 433, 818
Hpy188I TCNGA 3 cut(s) 25, 124, 181
Hpy188III TCNNGA 8 cut(s) 47, 61, 201, 234, 295, 499, 756, 876
Hpy99I CGWCG 4 cut(s) 243, 434, 658, 742
HpyAV CCTTC 2 cut(s) 126, 146
HpyCH4III ACNGT 4 cut(s) 72, 430, 523, 561
HpyCH4IV ACGT 4 cut(s) 241, 330, 357, 438
HpyCH4V TGCA 2 cut(s) 34, 55
HpyF10VI GCNNNNNNNGC 8 cut(s) 213, 283, 325, 414, 423, 460, 612, 659
HpyF3I CTNAG 2 cut(s) 413, 514
HpySE526I ACGT 4 cut(s) 241, 330, 357, 438
Hsp92I GRCGYC 4 cut(s) 241, 253, 461, 549
Hsp92II CATG 1 cut(s) 850
HspAI GCGC 4 cut(s) 301, 317, 461, 549
KasI GGCGCC 2 cut(s) 460, 548
Kpn2I TCCGGA 1 cut(s) 200
KroI GCCGGC 1 cut(s) 454
KroNI GCCGGC 1 cut(s) 456
KspI CCGCGG 2 cut(s) 248, 923
Kzo9I GATC 3 cut(s) 20, 171, 288
LmnI GCTCC 4 cut(s) 324, 471, 858, 908
Lsp1109I GCAGC 8 cut(s) 109, 175, 615, 637, 669, 716, 811, 828
MaeII ACGT 4 cut(s) 241, 330, 357, 438
MaeIII GTNAC 6 cut(s) 72, 295, 439, 478, 720, 760
MalI GATC 3 cut(s) 22, 173, 290
MbiI CCGCTC 1 cut(s) 324
MboI GATC 3 cut(s) 20, 171, 288
MboII GAAGA 4 cut(s) 111, 152, 710, 744
MhlI GDGCHC 2 cut(s) 414, 617
Mly113I GGCGCC 2 cut(s) 461, 549
MlyI GAGTC 2 cut(s) 137, 185
MmeI TCCRAC 1 cut(s) 204
MroI TCCGGA 1 cut(s) 200
MroNI GCCGGC 1 cut(s) 454
MseI TTAA 1 cut(s) 831
MspA1I CMGCKG 6 cut(s) 188, 247, 417, 707, 819, 922
MspI CCGG 9 cut(s) 201, 257, 348, 423, 455, 536, 545, 552, 866
MspR9I CCNGG 4 cut(s) 349, 546, 553, 572
Mva1269I GAATGC 1 cut(s) 670
MvaI CCWGG 1 cut(s) 572
MvnI CGCG 6 cut(s) 247, 301, 303, 317, 383, 922
MwoI GCNNNNNNNGC 8 cut(s) 213, 283, 325, 414, 423, 460, 612, 659
NaeI GCCGGC 1 cut(s) 456
NarI GGCGCC 2 cut(s) 461, 549
NciI CCSGG 3 cut(s) 349, 546, 553
NdeII GATC 3 cut(s) 20, 171, 288
NgoMIV GCCGGC 1 cut(s) 454
NlaIII CATG 1 cut(s) 850
NlaIV GGNNCC 7 cut(s) 421, 427, 462, 540, 550, 615, 633
NmuCI GTSAC 5 cut(s) 72, 295, 439, 478, 760
PcsI WCGNNNNNNNCGW 2 cut(s) 300, 495
PctI GAATGC 1 cut(s) 670
PdiI GCCGGC 1 cut(s) 456
PfeI GAWTC 1 cut(s) 125
PflFI GACNNNGTC 1 cut(s) 240
PleI GAGTC 2 cut(s) 137, 184
PluTI GGCGCC 2 cut(s) 464, 552
PmaCI CACGTG 1 cut(s) 331
PmlI CACGTG 1 cut(s) 331
PpsI GAGTC 2 cut(s) 137, 184
Ppu21I YACGTR 1 cut(s) 331
PshAI GACNNNNGTC 1 cut(s) 70
Psp6I CCWGG 1 cut(s) 570
PspCI CACGTG 1 cut(s) 331
PspGI CCWGG 1 cut(s) 570
PspN4I GGNNCC 7 cut(s) 421, 427, 462, 540, 550, 615, 633
PspOMI GGGCCC 1 cut(s) 613
PspPI GGNCC 4 cut(s) 538, 613, 614, 632
PsyI GACNNNGTC 1 cut(s) 240
RsaI GTAC 2 cut(s) 11, 890
RsaNI GTAC 2 cut(s) 10, 889
SacII CCGCGG 2 cut(s) 248, 923
SaqAI TTAA 1 cut(s) 831
Sau3AI GATC 3 cut(s) 20, 171, 288
Sau96I GGNCC 4 cut(s) 538, 613, 614, 632
SchI GAGTC 2 cut(s) 137, 185
ScrFI CCNGG 4 cut(s) 349, 546, 553, 572
SduI GDGCHC 2 cut(s) 414, 617
SfoI GGCGCC 2 cut(s) 462, 550
Sfr303I CCGCGG 2 cut(s) 248, 923
SgrBI CCGCGG 2 cut(s) 248, 923
SspDI GGCGCC 2 cut(s) 460, 548
StyD4I CCNGG 4 cut(s) 347, 544, 551, 570
TaaI ACNGT 4 cut(s) 72, 430, 523, 561
TaiI ACGT 4 cut(s) 244, 333, 360, 441
TaqI TCGA 3 cut(s) 174, 498, 563
TauI GCSGC 8 cut(s) 97, 210, 286, 420, 461, 822, 906, 925
TfiI GAWTC 1 cut(s) 125
Tru1I TTAA 1 cut(s) 831
Tru9I TTAA 1 cut(s) 831
TscAI CASTG 2 cut(s) 471, 624
TseFI GTSAC 5 cut(s) 72, 295, 439, 478, 760
TseI GCWGC 8 cut(s) 97, 188, 603, 650, 682, 704, 799, 816
Tsp45I GTSAC 5 cut(s) 72, 295, 439, 478, 760
TspGWI ACGGA 3 cut(s) 32, 896, 918
TspRI CASTG 2 cut(s) 471, 624
Tth111I GACNNNGTC 1 cut(s) 240
ZraI GACGTC 1 cut(s) 242
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.