pycom01g15920

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
pyrus_communis
Chr1
OG0012533
Physical Location & Seq
Reverse (-)
15653285 .. 15654256
972 bp
Loading structure...
UTR
Exon/CDS
Intron
pycom01g15920.1

Sequence Viewer

Length: 972 bp
ATGGCGAATCGATGGTGGGCTGGAAATGTTTCCATGGGAGGAGGAGGAGGTCATGTGGACTCAATCTCCTCGACTCCGCCGTCTCTCCACCTCAGGAACACTGAGGAACAGCTGGACGACCAAAACAACACGACCACTCCCACCAACAGCAGCACCAGCCCTCACAAGCAGAACAAGAAACACCGCGAAGACGACCGGGACAACAATGATCAGGAAGGCGACGATCAGGGCCCCAACACCGGTAGCGGCAGCCATGACAGCCTCGAGCCTGGAAGCAGCAACCGGAGGCCGCGTGGCCGGCCGCCCGGGTCGAAGAACAAGCCTAAACCCCCCATAGTCATCACCAAAGAGAGCCCCAACGCTCTCCGAAGCCATGTGTTGGAAATCAGTAGCGGCAGCGACATTGTGGACAGCATTGCCACCTTTGCCCAAAGGCGGCATAGAGGGGTTTCGGTTCTCAGCGGAACTGGCATTGTCGCCAATGTCACTCTCCGACAACCAGCAGCACCAACTGGAGTGATCACATTGCACGGAAGGTTCGAGATACTATCGATGTCAGGGGCATTCCTGCCCTCCCCATCCCCACCTGGGGCGACAGGGCTGACCGTGTACTTGGCAGGCGGCCAAGGGCAGGTGGTGGGAGGCACCGTGATGGGAGCATTGGTGGCTTCCGGTCCAGTGATGGTTATAGCAGCTACCTTCACAAACGCGACATATGAGAGGCTGCCGCTTGAGGAGGAACAAGGTGGAGAAGGAGGAATGCAGTTGGAGCAACAACAGCAGCAGCAGCAGCAATCAGGTGTGAATTCGGCAGGGACAGGAGCAAATTCAAGTTCCCAAGGTTTGGGTGAGCATAGTAGTGCAATGGCTGTTTACAATTTGCCTTCAAATTTACTTGCGAACGGTGGTCAGATCCCTCAAGATATATTCTGGGGTCCTCCCCCTCCAAGACCCCCTCCTCCATCTTACTGA
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

324

Amino Acids

33.77

Weight (kDa)

5.98

Isoelectric Point (pI)

59.63

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PCC PF03479 123 - 236 5.8e-24 Plants and Prokaryotes Conserved (PCC) domain
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: OG0012533)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G55560
fragaria_vesca FvH4_7g22970
malus_domestica MD01G1138500.v1.1 MD07G1202700.v1.1
prunus_persica Prupe.2G239000_v2.0.a1
pyrus_communis pycom01g15920 pycom07g18970
rosa_chinensis RchiOBHm_Chr1g0368171
rosa_laevigata RLG00000027233
rosa_multiflora Rmu_sc0006814.1_g000001 Rmu_sc0020763.1_g000001 Rmu_sc0035888.1_g000001
rosa_roxburghii Rroxscaffold_4G00288830
rosa_rugosa Rorug01G0339100
rosa_samantha Rh1AG346600 Rh1BG309200 Rh1CG324700 Rh1DG341100
rosa_wichuraiana Rw1G030810

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AarI CACCTGC 1 cut(s) 622
AasI GACNNNNNNGTC 1 cut(s) 79
Acc36I ACCTGC 1 cut(s) 622
AccB1I GGYRCC 1 cut(s) 644
AccB7I CCANNNNNTGG 2 cut(s) 379, 844
AccII CGCG 3 cut(s) 186, 292, 710
AclWI GGATC 1 cut(s) 907
AcoI YGGCCR 3 cut(s) 295, 299, 622
AcsI RAATTY 3 cut(s) 805, 826, 889
AfaI GTAC 1 cut(s) 611
AfiI CCNNNNNNNGG 7 cut(s) 239, 379, 435, 588, 589, 631, 844
AgeI ACCGGT 1 cut(s) 239
AgsI TTSAA 2 cut(s) 831, 888
AjnI CCWGG 2 cut(s) 268, 586
AluBI AGCT 2 cut(s) 112, 695
AluI AGCT 2 cut(s) 112, 695
Alw26I GTCTC 1 cut(s) 87
AlwI GGATC 1 cut(s) 907
Ama87I CYCGRG 2 cut(s) 263, 305
AoxI GGCC 5 cut(s) 229, 287, 295, 299, 622
ApaI GGGCCC 1 cut(s) 233
ApoI RAATTY 3 cut(s) 805, 826, 889
AsiGI ACCGGT 1 cut(s) 239
Asp700I GAANNNNTTC 1 cut(s) 28
AspS9I GGNCC 4 cut(s) 229, 230, 674, 935
AsuC2I CCSGG 3 cut(s) 197, 306, 307
AsuHPI GGTGA 2 cut(s) 334, 860
AvaI CYCGRG 2 cut(s) 263, 305
AvaII GGWCC 2 cut(s) 674, 935
AxyI CCTNAGG 1 cut(s) 92
BaeGI GKGCMC 1 cut(s) 233
BanI GGYRCC 1 cut(s) 644
BanII GRGCYC 2 cut(s) 233, 356
BbsI GAAGAC 1 cut(s) 195
BccI CCATC 5 cut(s) 6, 586, 646, 676, 970
BceAI ACGGC 1 cut(s) 64
BciT130I CCWGG 2 cut(s) 270, 588
BclI TGATCA 2 cut(s) 208, 519
BcnI CCSGG 3 cut(s) 197, 306, 307
BcoDI GTCTC 1 cut(s) 87
BfuAI ACCTGC 1 cut(s) 622
Bme1390I CCNGG 5 cut(s) 197, 270, 306, 307, 588
Bme18I GGWCC 2 cut(s) 674, 935
BmeT110I CYCGRG 2 cut(s) 263, 305
BmgT120I GGNCC 4 cut(s) 229, 230, 674, 935
BmiI GGNNCC 4 cut(s) 231, 232, 646, 936
BmrFI CCNGG 5 cut(s) 197, 270, 306, 307, 588
BpiI GAAGAC 1 cut(s) 195
BpmI CTGGAG 1 cut(s) 534
BpuEI CTTGAG 2 cut(s) 752, 903
BpuMI CCSGG 3 cut(s) 197, 306, 307
Bsa29I ATCGAT 2 cut(s) 10, 551
BsaJI CCNNGG 5 cut(s) 33, 305, 587, 625, 838
BsaWI WCCGGW 3 cut(s) 239, 282, 671
Bsc4I CCNNNNNNNGG 7 cut(s) 239, 379, 435, 588, 589, 631, 844
Bse118I RCCGGY 2 cut(s) 239, 297
Bse1I ACTGG 3 cut(s) 472, 517, 677
Bse21I CCTNAGG 1 cut(s) 92
Bse3DI GCAATG 3 cut(s) 414, 524, 870
BseBI CCWGG 2 cut(s) 270, 588
BseCI ATCGAT 2 cut(s) 10, 551
BseDI CCNNGG 5 cut(s) 33, 305, 587, 625, 838
BseGI GGATG 1 cut(s) 578
BseLI CCNNNNNNNGG 7 cut(s) 239, 379, 435, 588, 589, 631, 844
BseMI GCAATG 3 cut(s) 414, 524, 870
BseMII CTCAG 3 cut(s) 93, 106, 472
BseNI ACTGG 3 cut(s) 472, 517, 677
BseRI GAGGAG 6 cut(s) 54, 57, 58, 60, 749, 948
BseSI GKGCMC 1 cut(s) 233
BseX3I CGGCCG 1 cut(s) 299
Bsh1236I CGCG 3 cut(s) 186, 292, 710
Bsh1285I CGRYCG 2 cut(s) 196, 302
BshFI GGCC 5 cut(s) 231, 289, 297, 301, 624
BshNI GGYRCC 1 cut(s) 644
BshTI ACCGGT 1 cut(s) 239
BshVI ATCGAT 2 cut(s) 10, 551
BsiEI CGRYCG 2 cut(s) 196, 302
BsiHKCI CYCGRG 2 cut(s) 263, 305
BsiSI CCGG 6 cut(s) 196, 240, 283, 298, 306, 672
BslFI GGGAC 2 cut(s) 212, 829
BslI CCNNNNNNNGG 7 cut(s) 239, 379, 435, 588, 589, 631, 844
BsmAI GTCTC 1 cut(s) 87
BsmBI CGTCTC 1 cut(s) 87
BsmFI GGGAC 2 cut(s) 212, 829
BsmI GAATGC 2 cut(s) 563, 765
BsnI GGCC 5 cut(s) 231, 289, 297, 301, 624
BsoBI CYCGRG 2 cut(s) 263, 305
Bsp120I GGGCCC 1 cut(s) 229
Bsp1286I GDGCHC 2 cut(s) 233, 356
Bsp143I GATC 4 cut(s) 208, 223, 519, 912
Bsp19I CCATGG 1 cut(s) 33
BspANI GGCC 5 cut(s) 231, 289, 297, 301, 624
BspCNI CTCAG 3 cut(s) 94, 105, 471
BspDI ATCGAT 2 cut(s) 10, 551
BspFNI CGCG 3 cut(s) 186, 292, 710
BspLI GGNNCC 4 cut(s) 231, 232, 646, 936
BspMI ACCTGC 1 cut(s) 622
BspPI GGATC 1 cut(s) 907
BspT107I GGYRCC 1 cut(s) 644
BsrDI GCAATG 3 cut(s) 414, 524, 870
BsrFI RCCGGY 2 cut(s) 239, 297
BsrI ACTGG 3 cut(s) 472, 517, 677
BssAI RCCGGY 2 cut(s) 239, 297
BssECI CCNNGG 5 cut(s) 33, 305, 587, 625, 838
BssMI GATC 4 cut(s) 208, 223, 519, 912
BssT1I CCWWGG 3 cut(s) 33, 625, 838
Bst2UI CCWGG 2 cut(s) 270, 588
Bst4CI ACNGT 3 cut(s) 607, 649, 905
BstC8I GCNNGC 2 cut(s) 299, 619
BstDEI CTNAG 3 cut(s) 92, 102, 458
BstDSI CCRYGG 1 cut(s) 33
BstF5I GGATG 1 cut(s) 578
BstFNI CGCG 3 cut(s) 186, 292, 710
BstKTI GATC 4 cut(s) 211, 226, 522, 915
BstMAI GTCTC 1 cut(s) 87
BstMBI GATC 4 cut(s) 208, 223, 519, 912
BstMCI CGRYCG 2 cut(s) 196, 302
BstNI CCWGG 2 cut(s) 270, 588
BstSCI CCNGG 5 cut(s) 195, 268, 304, 305, 586
BstSLI GKGCMC 1 cut(s) 233
BstUI CGCG 3 cut(s) 186, 292, 710
BstV2I GAAGAC 1 cut(s) 195
BstX2I RGATCY 1 cut(s) 912
BstYI RGATCY 1 cut(s) 912
BstZI CGGCCG 1 cut(s) 299
Bsu15I ATCGAT 2 cut(s) 10, 551
Bsu36I CCTNAGG 1 cut(s) 92
BsuRI GGCC 5 cut(s) 231, 289, 297, 301, 624
BsuTUI ATCGAT 2 cut(s) 10, 551
BtgI CCRYGG 1 cut(s) 33
BtsCI GGATG 1 cut(s) 578
BtsIMutI CAGTG 2 cut(s) 99, 684
BveI ACCTGC 1 cut(s) 622
Cac8I GCNNGC 2 cut(s) 299, 619
Cfr10I RCCGGY 2 cut(s) 239, 297
Cfr13I GGNCC 4 cut(s) 229, 230, 674, 935
Cfr9I CCCGGG 1 cut(s) 305
ClaI ATCGAT 2 cut(s) 10, 551
Csp6I GTAC 1 cut(s) 610
CspAI ACCGGT 1 cut(s) 239
CviAII CATG 4 cut(s) 34, 53, 254, 374
CviQI GTAC 1 cut(s) 610
DdeI CTNAG 3 cut(s) 92, 102, 458
DpnI GATC 4 cut(s) 210, 225, 521, 914
DpnII GATC 4 cut(s) 208, 223, 519, 912
DrdI GACNNNNNNGTC 1 cut(s) 79
DseDI GACNNNNNNGTC 1 cut(s) 79
EaeI YGGCCR 3 cut(s) 295, 299, 622
EagI CGGCCG 1 cut(s) 299
EciI GGCGGA 1 cut(s) 66
EclXI CGGCCG 1 cut(s) 299
Eco130I CCWWGG 3 cut(s) 33, 625, 838
Eco24I GRGCYC 2 cut(s) 233, 356
Eco47I GGWCC 2 cut(s) 674, 935
Eco52I CGGCCG 1 cut(s) 299
Eco81I CCTNAGG 1 cut(s) 92
Eco88I CYCGRG 2 cut(s) 263, 305
EcoO109I RGGNCCY 3 cut(s) 229, 230, 935
EcoRI GAATTC 1 cut(s) 805
EcoRII CCWGG 2 cut(s) 268, 586
EcoT14I CCWWGG 3 cut(s) 33, 625, 838
EcoT38I GRGCYC 2 cut(s) 233, 356
ErhI CCWWGG 3 cut(s) 33, 625, 838
Esp3I CGTCTC 1 cut(s) 87
FaeI CATG 4 cut(s) 37, 56, 257, 377
FaqI GGGAC 2 cut(s) 212, 829
FatI CATG 4 cut(s) 33, 52, 253, 373
FauNDI CATATG 1 cut(s) 715
FbaI TGATCA 2 cut(s) 208, 519
FokI GGATG 1 cut(s) 565
FriOI GRGCYC 2 cut(s) 233, 356
FseI GGCCGGCC 1 cut(s) 301
GsuI CTGGAG 1 cut(s) 534
HaeIII GGCC 5 cut(s) 231, 289, 297, 301, 624
HapII CCGG 6 cut(s) 196, 240, 283, 298, 306, 672
Hin1II CATG 4 cut(s) 37, 56, 257, 377
HinfI GANTC 3 cut(s) 7, 59, 73
HpaII CCGG 6 cut(s) 196, 240, 283, 298, 306, 672
HphI GGTGA 2 cut(s) 334, 860
Hpy166II GTNNAC 4 cut(s) 58, 409, 610, 874
Hpy188I TCNGA 3 cut(s) 368, 494, 912
Hpy188III TCNNGA 4 cut(s) 94, 212, 541, 920
Hpy8I GTNNAC 4 cut(s) 58, 409, 610, 874
Hpy99I CGWCG 1 cut(s) 224
HpyAV CCTTC 5 cut(s) 209, 528, 709, 746, 894
HpyCH4III ACNGT 3 cut(s) 607, 649, 905
HpyCH4V TGCA 3 cut(s) 529, 763, 863
HpyF3I CTNAG 3 cut(s) 92, 102, 458
Hsp92II CATG 4 cut(s) 37, 56, 257, 377
KroI GCCGGC 1 cut(s) 297
KroNI GCCGGC 1 cut(s) 299
Ksp22I TGATCA 2 cut(s) 208, 519
Kzo9I GATC 4 cut(s) 208, 223, 519, 912
LmnI GCTCC 3 cut(s) 656, 769, 821
MaeIII GTNAC 1 cut(s) 484
MalI GATC 4 cut(s) 210, 225, 521, 914
MboI GATC 4 cut(s) 208, 223, 519, 912
MboII GAAGA 2 cut(s) 200, 325
MflI RGATCY 1 cut(s) 912
MhlI GDGCHC 2 cut(s) 233, 356
MluCI AATT 4 cut(s) 805, 826, 877, 889
MlyI GAGTC 2 cut(s) 53, 67
MmeI TCCRAC 3 cut(s) 360, 517, 747
MroNI GCCGGC 1 cut(s) 297
MroXI GAANNNNTTC 1 cut(s) 28
MslI CAYNNNNRTG 2 cut(s) 650, 858
MspA1I CMGCKG 2 cut(s) 112, 462
MspI CCGG 6 cut(s) 196, 240, 283, 298, 306, 672
MspR9I CCNGG 5 cut(s) 197, 270, 306, 307, 588
Mva1269I GAATGC 2 cut(s) 563, 765
MvaI CCWGG 2 cut(s) 270, 588
MvnI CGCG 3 cut(s) 186, 292, 710
NaeI GCCGGC 1 cut(s) 299
NciI CCSGG 3 cut(s) 197, 306, 307
NcoI CCATGG 1 cut(s) 33
NdeI CATATG 1 cut(s) 715
NdeII GATC 4 cut(s) 208, 223, 519, 912
NgoMIV GCCGGC 1 cut(s) 297
NlaIII CATG 4 cut(s) 37, 56, 257, 377
NlaIV GGNNCC 4 cut(s) 231, 232, 646, 936
NmuCI GTSAC 1 cut(s) 484
PaeR7I CTCGAG 1 cut(s) 263
PaqCI CACCTGC 1 cut(s) 622
PcsI WCGNNNNNNNCGW 2 cut(s) 77, 537
PctI GAATGC 2 cut(s) 563, 765
PdiI GCCGGC 1 cut(s) 299
PdmI GAANNNNTTC 1 cut(s) 28
PfeI GAWTC 1 cut(s) 7
PflMI CCANNNNNTGG 2 cut(s) 379, 844
PinAI ACCGGT 1 cut(s) 239
PleI GAGTC 2 cut(s) 53, 67
PpsI GAGTC 2 cut(s) 53, 67
PpuMI RGGWCCY 1 cut(s) 935
Psp5II RGGWCCY 1 cut(s) 935
Psp6I CCWGG 2 cut(s) 268, 586
PspGI CCWGG 2 cut(s) 268, 586
PspN4I GGNNCC 4 cut(s) 231, 232, 646, 936
PspOMI GGGCCC 1 cut(s) 229
PspPI GGNCC 4 cut(s) 229, 230, 674, 935
PspPPI RGGWCCY 1 cut(s) 935
PspXI VCTCGAGB 1 cut(s) 263
PsuI RGATCY 1 cut(s) 912
PvuII CAGCTG 1 cut(s) 112
RigI GGCCGGCC 1 cut(s) 301
RsaI GTAC 1 cut(s) 611
RsaNI GTAC 1 cut(s) 610
RseI CAYNNNNRTG 2 cut(s) 650, 858
Sau3AI GATC 4 cut(s) 208, 223, 519, 912
Sau96I GGNCC 4 cut(s) 229, 230, 674, 935
SchI GAGTC 2 cut(s) 53, 67
ScrFI CCNGG 5 cut(s) 197, 270, 306, 307, 588
SduI GDGCHC 2 cut(s) 233, 356
Sfr274I CTCGAG 1 cut(s) 263
SinI GGWCC 2 cut(s) 674, 935
SlaI CTCGAG 1 cut(s) 263
SmaI CCCGGG 1 cut(s) 307
SmiMI CAYNNNNRTG 2 cut(s) 650, 858
SmlI CTYRAG 3 cut(s) 263, 731, 918
SmoI CTYRAG 3 cut(s) 263, 731, 918
Sse9I AATT 4 cut(s) 805, 826, 877, 889
StyD4I CCNGG 5 cut(s) 195, 268, 304, 305, 586
StyI CCWWGG 3 cut(s) 33, 625, 838
TaaI ACNGT 3 cut(s) 607, 649, 905
TaqI TCGA 6 cut(s) 10, 71, 264, 311, 540, 551
TasI AATT 4 cut(s) 805, 826, 877, 889
TatI WGTACW 1 cut(s) 609
TauI GCSGC 7 cut(s) 249, 292, 304, 396, 439, 624, 730
TfiI GAWTC 1 cut(s) 7
TscAI CASTG 2 cut(s) 106, 684
TseFI GTSAC 1 cut(s) 484
Tsp45I GTSAC 1 cut(s) 484
TspGWI ACGGA 1 cut(s) 546
TspMI CCCGGG 1 cut(s) 305
TspRI CASTG 2 cut(s) 106, 684
Van91I CCANNNNNTGG 2 cut(s) 379, 844
VpaK11BI GGWCC 2 cut(s) 674, 935
XapI RAATTY 3 cut(s) 805, 826, 889
XhoI CTCGAG 1 cut(s) 263
XmaI CCCGGG 1 cut(s) 305
XmnI GAANNNNTTC 1 cut(s) 28
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.