MD08G1056000.v1.1

YbaB/EbfC DNA-binding family

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr08
OG0003152
Physical Location & Seq
Forward (+)
4341568 .. 4344756
3189 bp
Loading structure...
UTR
Exon/CDS
Intron
MD08G1056000.v1.1.491

Sequence Viewer

Length: 573 bp
ATGGCGTCGACGAGTGCTTTAAGCTCCCGGCTTTCCAACTTCCACCGCCTCACCGACTCCCAGGAGCACCTCTCTTTCCGTGAAGTAGTAAACTCACATCCAGCATGTCCTTCAATTGTTTCTTGGCCTGGTGTTAAGACCAGGAGGGCGCCCCGTTCCTCCCGTGTGTATGGCTTATTTGGAGGAGGAAAAAAGGATAACGCTGAAAAGGGTGATGATGCAGCTTCAAAGGCTGGAATATTCGGTAATATGCAAAATCTGTATGAAACAGTTAAGAAAGCTCAAAATGTAGTACAAGTTGAAGCAGTGCGTGTGCAGAAAGAGCTTGCTGCGGCAGAGTTTGATGGTTACTGTGAAGGTGAGATAATAAAGGTAACCCTTTCTGGTAACCAGCAACCCGTACGCACTGAGATAACCGAGGCTGCTATGGAACTAGGAGCAGAAAAAGTCTCTGAATTGGTCACAGAAGCATACAAGGATGCGCATCAGAAGAGTGTCATGGCCATGAAGGAGAGAATGAGCAACCTTGCCCAGAGTTTAGGAATGCCACCAGGCCTGGGAGAATTGAAATGA
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
YbaB_DNA_bd

Protein Analysis

191

Amino Acids

20.64

Weight (kDa)

7.77

Isoelectric Point (pI)

37.09

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
YbaB_DNA_bd PF02575 92 - 179 1.6e-14 YbaB/EbfC DNA-binding 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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc16I TGCGCA 1 cut(s) 483
AccB1I GGYRCC 1 cut(s) 148
AccI GTMKAC 1 cut(s) 8
AciI CCGC 2 cut(s) 46, 332
AcoI YGGCCR 1 cut(s) 501
AcyI GRCGYC 2 cut(s) 5, 149
AfaI GTAC 2 cut(s) 294, 402
AfiI CCNNNNNNNGG 1 cut(s) 557
AgsI TTSAA 4 cut(s) 114, 228, 302, 568
AjnI CCWGG 5 cut(s) 60, 127, 140, 550, 555
AluBI AGCT 4 cut(s) 24, 224, 281, 325
AluI AGCT 4 cut(s) 24, 224, 281, 325
Alw21I GWGCWC 1 cut(s) 69
Alw26I GTCTC 1 cut(s) 454
AoxI GGCC 3 cut(s) 125, 501, 553
ApeKI GCWGC 3 cut(s) 221, 329, 422
AspLEI GCGC 2 cut(s) 151, 484
AsuC2I CCSGG 1 cut(s) 28
AsuHPI GGTGA 3 cut(s) 43, 224, 371
BalI TGGCCA 1 cut(s) 503
BanI GGYRCC 1 cut(s) 148
Bbv12I GWGCWC 1 cut(s) 69
BbvI GCAGC 3 cut(s) 233, 316, 409
BccI CCATC 1 cut(s) 338
BciT130I CCWGG 5 cut(s) 62, 129, 142, 552, 557
BcnI CCSGG 1 cut(s) 28
BcoDI GTCTC 1 cut(s) 454
BfaI CTAG 1 cut(s) 434
BfoI RGCGCY 1 cut(s) 152
BisI GCNGC 4 cut(s) 222, 330, 333, 423
BlsI GCNGC 4 cut(s) 223, 331, 334, 424
Bme1390I CCNGG 6 cut(s) 28, 62, 129, 142, 552, 557
BmiI GGNNCC 1 cut(s) 150
BmrFI CCNGG 6 cut(s) 28, 62, 129, 142, 552, 557
BmsI GCATC 3 cut(s) 208, 469, 493
BplI GAGNNNNNCTC 2 cut(s) 56, 88
BpuMI CCSGG 1 cut(s) 28
BsaBI GATNNNNATC 1 cut(s) 483
BsaHI GRCGYC 2 cut(s) 5, 149
BsaJI CCNNGG 3 cut(s) 60, 417, 556
Bsc4I CCNNNNNNNGG 1 cut(s) 557
Bse8I GATNNNNATC 1 cut(s) 483
BseBI CCWGG 5 cut(s) 62, 129, 142, 552, 557
BseDI CCNNGG 3 cut(s) 60, 417, 556
BseGI GGATG 2 cut(s) 97, 484
BseJI GATNNNNATC 1 cut(s) 483
BseLI CCNNNNNNNGG 1 cut(s) 557
BseMII CTCAG 1 cut(s) 399
BseRI GAGGAG 1 cut(s) 198
BseXI GCAGC 3 cut(s) 233, 316, 409
BsgI GTGCAG 1 cut(s) 335
BshFI GGCC 3 cut(s) 127, 503, 555
BshNI GGYRCC 1 cut(s) 148
BsiHKAI GWGCWC 1 cut(s) 69
BsiSI CCGG 1 cut(s) 28
BsiWI CGTACG 1 cut(s) 400
BslI CCNNNNNNNGG 1 cut(s) 557
BsmAI GTCTC 1 cut(s) 454
BsmI GAATGC 1 cut(s) 549
BsnI GGCC 3 cut(s) 127, 503, 555
Bsp1286I GDGCHC 1 cut(s) 69
BspACI CCGC 2 cut(s) 46, 332
BspANI GGCC 3 cut(s) 127, 503, 555
BspCNI CTCAG 1 cut(s) 400
BspLI GGNNCC 1 cut(s) 150
BspT107I GGYRCC 1 cut(s) 148
BssECI CCNNGG 3 cut(s) 60, 417, 556
BssNI GRCGYC 2 cut(s) 5, 149
Bst2UI CCWGG 5 cut(s) 62, 129, 142, 552, 557
Bst4CI ACNGT 2 cut(s) 271, 353
Bst6I CTCTTC 1 cut(s) 485
BstACI GRCGYC 2 cut(s) 5, 149
BstC8I GCNNGC 1 cut(s) 327
BstDEI CTNAG 1 cut(s) 408
BstEII GGTNACC 2 cut(s) 373, 386
BstF5I GGATG 2 cut(s) 97, 484
BstH2I RGCGCY 1 cut(s) 152
BstHHI GCGC 2 cut(s) 151, 484
BstMAI GTCTC 1 cut(s) 454
BstMWI GCNNNNNNNGC 2 cut(s) 230, 322
BstNI CCWGG 5 cut(s) 62, 129, 142, 552, 557
BstNSI RCATGY 1 cut(s) 108
BstPI GGTNACC 2 cut(s) 373, 386
BstSCI CCNGG 6 cut(s) 26, 60, 127, 140, 550, 555
BstV1I GCAGC 3 cut(s) 233, 316, 409
BsuRI GGCC 3 cut(s) 127, 503, 555
BtsCI GGATG 2 cut(s) 97, 484
BtsI GCAGTG 1 cut(s) 312
BtsIMutI CAGTG 2 cut(s) 312, 405
Cac8I GCNNGC 1 cut(s) 327
CfoI GCGC 2 cut(s) 151, 484
Csp6I GTAC 2 cut(s) 293, 401
CviAII CATG 3 cut(s) 105, 499, 505
CviQI GTAC 2 cut(s) 293, 401
DdeI CTNAG 1 cut(s) 408
DinI GGCGCC 1 cut(s) 150
EaeI YGGCCR 1 cut(s) 501
Eam1104I CTCTTC 1 cut(s) 485
EarI CTCTTC 1 cut(s) 485
Eco147I AGGCCT 1 cut(s) 555
Eco91I GGTNACC 2 cut(s) 373, 386
EcoO65I GGTNACC 2 cut(s) 373, 386
EcoRII CCWGG 5 cut(s) 60, 127, 140, 550, 555
EgeI GGCGCC 1 cut(s) 150
EheI GGCGCC 1 cut(s) 150
FaeI CATG 3 cut(s) 108, 502, 508
FaiI YATR 8 cut(s) 106, 171, 251, 264, 428, 472, 500, 506
FatI CATG 3 cut(s) 104, 498, 504
FblI GTMKAC 1 cut(s) 8
Fnu4HI GCNGC 4 cut(s) 222, 330, 333, 423
FokI GGATG 2 cut(s) 84, 491
Fsp4HI GCNGC 4 cut(s) 222, 330, 333, 423
FspAI RTGCGCAY 1 cut(s) 483
FspBI CTAG 1 cut(s) 434
FspI TGCGCA 1 cut(s) 483
GlaI GCGC 2 cut(s) 150, 483
GluI GCNGC 4 cut(s) 222, 330, 333, 423
HaeII RGCGCY 1 cut(s) 152
HaeIII GGCC 3 cut(s) 127, 503, 555
HapII CCGG 1 cut(s) 28
HhaI GCGC 2 cut(s) 151, 484
Hin1I GRCGYC 2 cut(s) 5, 149
Hin1II CATG 3 cut(s) 108, 502, 508
Hin6I GCGC 2 cut(s) 149, 482
HinP1I GCGC 2 cut(s) 149, 482
HincII GTYRAC 1 cut(s) 9
HindII GTYRAC 1 cut(s) 9
HinfI GANTC 1 cut(s) 56
HpaII CCGG 1 cut(s) 28
HphI GGTGA 3 cut(s) 43, 224, 371
Hpy166II GTNNAC 2 cut(s) 9, 91
Hpy188I TCNGA 2 cut(s) 454, 489
Hpy8I GTNNAC 2 cut(s) 9, 91
Hpy99I CGWCG 2 cut(s) 10, 13
HpyAV CCTTC 3 cut(s) 120, 350, 502
HpyCH4III ACNGT 2 cut(s) 271, 353
HpyCH4V TGCA 3 cut(s) 221, 253, 316
HpyF10VI GCNNNNNNNGC 2 cut(s) 230, 322
HpyF3I CTNAG 1 cut(s) 408
Hsp92I GRCGYC 2 cut(s) 5, 149
Hsp92II CATG 3 cut(s) 108, 502, 508
HspAI GCGC 2 cut(s) 149, 482
KasI GGCGCC 1 cut(s) 148
LmnI GCTCC 3 cut(s) 29, 64, 437
Lsp1109I GCAGC 3 cut(s) 233, 316, 409
LweI GCATC 3 cut(s) 208, 469, 493
MaeI CTAG 1 cut(s) 434
MaeIII GTNAC 4 cut(s) 347, 373, 386, 460
MboII GAAGA 1 cut(s) 502
MfeI CAATTG 1 cut(s) 114
MhlI GDGCHC 1 cut(s) 69
MlsI TGGCCA 1 cut(s) 503
MluCI AATT 3 cut(s) 114, 455, 563
MluNI TGGCCA 1 cut(s) 503
Mly113I GGCGCC 1 cut(s) 149
MlyI GAGTC 1 cut(s) 50
MmeI TCCRAC 1 cut(s) 60
MnlI CCTC 7 cut(s) 59, 80, 138, 169, 176, 179, 412
Mox20I TGGCCA 1 cut(s) 503
MscI TGGCCA 1 cut(s) 503
MseI TTAA 3 cut(s) 20, 135, 273
MslI CAYNNNNRTG 1 cut(s) 503
Msp20I TGGCCA 1 cut(s) 503
MspI CCGG 1 cut(s) 28
MspR9I CCNGG 6 cut(s) 28, 62, 129, 142, 552, 557
MunI CAATTG 1 cut(s) 114
Mva1269I GAATGC 1 cut(s) 549
MvaI CCWGG 5 cut(s) 62, 129, 142, 552, 557
MwoI GCNNNNNNNGC 2 cut(s) 230, 322
NarI GGCGCC 1 cut(s) 149
NciI CCSGG 1 cut(s) 28
NlaIII CATG 3 cut(s) 108, 502, 508
NlaIV GGNNCC 1 cut(s) 150
NmuCI GTSAC 1 cut(s) 460
NsbI TGCGCA 1 cut(s) 483
NspI RCATGY 1 cut(s) 108
PceI AGGCCT 1 cut(s) 555
PctI GAATGC 1 cut(s) 549
Pfl23II CGTACG 1 cut(s) 400
PkrI GCNGC 4 cut(s) 223, 331, 334, 424
PleI GAGTC 1 cut(s) 50
PluTI GGCGCC 1 cut(s) 152
PpsI GAGTC 1 cut(s) 50
Psp6I CCWGG 5 cut(s) 60, 127, 140, 550, 555
PspEI GGTNACC 2 cut(s) 373, 386
PspGI CCWGG 5 cut(s) 60, 127, 140, 550, 555
PspLI CGTACG 1 cut(s) 400
PspN4I GGNNCC 1 cut(s) 150
RsaI GTAC 2 cut(s) 294, 402
RsaNI GTAC 2 cut(s) 293, 401
RseI CAYNNNNRTG 1 cut(s) 503
SalI GTCGAC 1 cut(s) 7
SaqAI TTAA 3 cut(s) 20, 135, 273
SatI GCNGC 4 cut(s) 222, 330, 333, 423
SchI GAGTC 1 cut(s) 50
ScrFI CCNGG 6 cut(s) 28, 62, 129, 142, 552, 557
SduI GDGCHC 1 cut(s) 69
SetI ASST 8 cut(s) 26, 72, 226, 283, 327, 361, 375, 528
SfaNI GCATC 3 cut(s) 208, 469, 493
SfoI GGCGCC 1 cut(s) 150
SgrDI CGTCGACG 1 cut(s) 7
SmiMI CAYNNNNRTG 1 cut(s) 503
Sse9I AATT 3 cut(s) 114, 455, 563
SseBI AGGCCT 1 cut(s) 555
SsiI CCGC 2 cut(s) 46, 332
SspDI GGCGCC 1 cut(s) 148
SspI AATATT 1 cut(s) 240
SspMI CTAG 1 cut(s) 434
StuI AGGCCT 1 cut(s) 555
StyD4I CCNGG 6 cut(s) 26, 60, 127, 140, 550, 555
TaaI ACNGT 2 cut(s) 271, 353
TaqI TCGA 1 cut(s) 8
TasI AATT 3 cut(s) 114, 455, 563
TatI WGTACW 1 cut(s) 292
TauI GCSGC 1 cut(s) 335
Tru1I TTAA 3 cut(s) 20, 135, 273
Tru9I TTAA 3 cut(s) 20, 135, 273
TscAI CASTG 2 cut(s) 312, 412
TseFI GTSAC 1 cut(s) 460
TseI GCWGC 3 cut(s) 221, 329, 422
Tsp45I GTSAC 1 cut(s) 460
TspDTI ATGAA 2 cut(s) 279, 521
TspGWI ACGGA 1 cut(s) 68
TspRI CASTG 2 cut(s) 312, 412
XceI RCATGY 1 cut(s) 108
XmiI GTMKAC 1 cut(s) 8
XspI CTAG 1 cut(s) 434
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.