Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr05

Orthogroup ID

OG0002529

Physical Location & Seq

Genomic Coordinates Reverse (-)

46891824 .. 46896802

Gene Structure 4979 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

MD05G1352500.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1161 bp

ATGGAAGGTGGTTCCAATGGCACTTGTAGTATGATGGCTTTTGGAGAAAGCAGCAGTAATGGAGGAGGAATGTGTCCAATGATGATGATGCCTCTAATGACTTCATCACATCATGCTGATCACTCTCACCATCATCATCATCATCATCAACCTATGAACCCTAATCCTAATGCAGATGCACACAATACTAGTACGACTCATCAGTTTCACCAGCTTCCCCAGTTGCCTCCGTCCAACAACCATCACGACCGGCATAACACAAGCGGCGGCTCCTCCTTCGTTCTCCACAACCCAGCTGCCGCCTCCTATTTCATGGACAACAACAACAATAATGAAGGTGTTGGCGGCAGCTCTTTTTCTTCTTCATCTTCAATTGTCAAGGCTAAGATCATGGCTCATCCTCACTATCACCGCCTCTTGGCCTCCTATATCAACTGTCAAAAGGTTGGAGCGCCGCCTGAAGTGGTGGCGAGGCTGGAAGAAGCGTGCGCATCGGCGGCGACAATAGGTCAAATGGTGAGTAGTAGTAGTGGATCAGGATCTCTCGGTGAAGATCCAGCTTTGGATCAGTTCATGGAGGCCTACTGCGAGATGCTCACCAAGTATGAGCAAGAACTCTCTAAACCCTTCAAGGAAGCCATGATCTTCTTCCAAAGAATCGAGTCCCAATTCAAAGCCCTTACTCTTTCTTCTTCTTCCGATTCTGCAGGTTATGGCGAGGGAATTGATAGGAATAACGGATCATCTGAAGAAGAGGTTGATGTTAACAACTTCATAGATCCGCAAGCGGAAGACAGGGAGCTTAAAGGTCAGCTATTGCGCAAGTACAGTGGATATTTGGGTAGTTTGAAGCAGGAGTTCATGAAGAAGAGGAAGAAGGGGAAGCTGCCTAAAGAAGCCAGGCAACAACTGCTTGATTGGTGGAGCCGTCATTACAAATGGCCTTATCCATCGGAGTCGCAGAAGCTAGCTCTGGCAGAATCAACGGGGCTGGACCAAAAGCAGATAAACAACTGGTTCATTAACCAAAGGAAGCGGCATTGGAAGCCGACGGAGGATATGCAGTTCGTGGTGATGGATGCTAGCCACCCCGGCCACTACTACATGGACGGTGTCTTGGGAAATCCATTTCCCATGGATATCTCTCCCACATTGCTCTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0003006 GO:0003674 GO:0003676 GO:0003700 GO:0003723 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005737 GO:0005856 GO:0005911 GO:0006355 GO:0006725 GO:0006807 GO:0006810 GO:0007275 GO:0008150 GO:0008152 GO:0009058 GO:0009308 GO:0009506 GO:0009690 GO:0009691 GO:0009791 GO:0009889 GO:0009908 GO:0009934 GO:0009987 GO:0010468 GO:0010496 GO:0010497 GO:0010556 GO:0010817 GO:0015630 GO:0019219 GO:0019222 GO:0019827 GO:0022414 GO:0022603 GO:0030054 GO:0031323 GO:0031326 GO:0032501 GO:0032502 GO:0034754 GO:0042445 GO:0042446 GO:0042802 GO:0042803 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0044237 GO:0044249 GO:0044424 GO:0044464 GO:0046483 GO:0046983 GO:0048367 GO:0048437 GO:0048438 GO:0048440 GO:0048467 GO:0048509 GO:0048608 GO:0048731 GO:0048827 GO:0048856 GO:0050789 GO:0050793 GO:0050794 GO:0051171 GO:0051179 GO:0051234 GO:0051252 GO:0055044 GO:0060255 GO:0061458 GO:0065007 GO:0065008 GO:0071704 GO:0080090 GO:0090567 GO:0097159 GO:0098727 GO:0099402 GO:0140110 GO:1901363 GO:1901564 GO:1903506 GO:2000112 GO:2001141

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

ELK Homeobox_KN KNOX1 KNOX2

Protein Analysis

387

Amino Acids

43.04

Weight (kDa)

6.3

Isoelectric Point (pI)

44.81

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
KNOX1	PF03790	126 - 164	1e-20	KNOX1 domain
KNOX2	PF03791	182 - 228	1.3e-21	KNOX2 domain
ELK	PF03789	267 - 288	4.6e-11	ELK domain
Homeobox_KN	PF05920	307 - 346	1.1e-18	Homeobox KN domain
Homeodomain	PF00046	314 - 347	9.2e-07	Homeodomain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0002529)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G62360
fragaria_vesca	FvH4_3g01400 FvH4_3g01400 FvH4_3g01400 FvH4_3g01400 FvH4_6g42570 FvH4_6g42570
malus_domestica	MD05G1352500.v1.1 MD09G1112500.v1.1 MD10G1276200.v1.1 MD10G1326500.v1.1 MD17G1102600.v1.1
prunus_persica	Prupe.3G212100_v2.0.a1 Prupe.4G015200_v2.0.a1 Prupe.4G015200_v2.0.a1
pyrus_communis	pycom05g31940 pycom09g03690 pycom10g27650 pycom17g09700
rosa_chinensis	RchiOBHm_Chr2g0158421 RchiOBHm_Chr5g0002121
rosa_laevigata	RLG00000021086 RLG00000030997
rosa_multiflora	Rmu_sc0004855.1_g000009 Rmu_ssc0000001.1_g000013
rosa_roxburghii	Rroxscaffold_1G00073790 Rroxscaffold_2G00091400
rosa_rugosa	Rorug02G0468500 Rorug02G0468600 Rorug04G0394500 Rorug04G0394500
rosa_samantha	Rh2AG534700 Rh2BG548100 Rh2CG518500 Rh2DG557700 Rh5AG016200 Rh5BG019600 Rh5CG017500 Rh5DG017700
rosa_wichuraiana	Rw2G044280 Rw5G001580

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc16I	TGCGCA	2 cut(s)	490, 821
Acc36I	ACCTGC	1 cut(s)	698
AclWI	GGATC	6 cut(s)	541, 547, 548, 573, 748, 773
AcoI	YGGCCR	1 cut(s)	1093
AcuI	CTGAAG	2 cut(s)	480, 768
AfaI	GTAC	2 cut(s)	193, 827
AfiI	CCNNNNNNNGG	1 cut(s)	418
AgsI	TTSAA	4 cut(s)	372, 631, 673, 850
AhdI	GACNNNNNGTC	1 cut(s)	507
AhlI	ACTAGT	1 cut(s)	188
AjnI	CCWGG	1 cut(s)	899
AloI	GAACNNNNNNTCC	2 cut(s)	1049, 1081
AluBI	AGCT	9 cut(s)	214, 296, 351, 560, 802, 814, 886, 967, 971
AluI	AGCT	9 cut(s)	214, 296, 351, 560, 802, 814, 886, 967, 971
AlwI	GGATC	6 cut(s)	541, 547, 548, 573, 748, 773
AoxI	GGCC	4 cut(s)	420, 579, 941, 1093
ApeKI	GCWGC	4 cut(s)	51, 296, 348, 886
AspLEI	GCGC	3 cut(s)	454, 491, 822
AspS9I	GGNCC	1 cut(s)	994
AsuC2I	CCSGG	1 cut(s)	1092
AsuHPI	GGTGA	7 cut(s)	119, 200, 401, 529, 560, 589, 1084
AsuNHI	GCTAGC	2 cut(s)	967, 1082
AvaII	GGWCC	1 cut(s)	994
BbsI	GAAGAC	1 cut(s)	798
BbvI	GCAGC	4 cut(s)	63, 283, 360, 873
BccI	CCATC	5 cut(s)	28, 138, 249, 958, 1069
BceAI	ACGGC	1 cut(s)	912
BciT130I	CCWGG	1 cut(s)	901
BclI	TGATCA	1 cut(s)	118
BcnI	CCSGG	1 cut(s)	1092
BcuI	ACTAGT	1 cut(s)	188
BfaI	CTAG	3 cut(s)	189, 968, 1083
BfmI	CTRYAG	1 cut(s)	705
BfoI	RGCGCY	1 cut(s)	455
BfuAI	ACCTGC	1 cut(s)	698
BglI	GCCNNNNNGGC	1 cut(s)	1092
Bme1390I	CCNGG	2 cut(s)	901, 1092
Bme18I	GGWCC	1 cut(s)	994
BmeRI	GACNNNNNGTC	1 cut(s)	507
BmgT120I	GGNCC	1 cut(s)	994
BmiI	GGNNCC	3 cut(s)	13, 271, 926
BmrFI	CCNGG	2 cut(s)	901, 1092
BmrI	ACTGGG	1 cut(s)	214
BmsI	GCATC	5 cut(s)	78, 166, 500, 582, 1069
BmtI	GCTAGC	2 cut(s)	971, 1086
BmuI	ACTGGG	1 cut(s)	214
BpiI	GAAGAC	1 cut(s)	798
BpuMI	CCSGG	1 cut(s)	1092
BsaBI	GATNNNNATC	1 cut(s)	538
BsaJI	CCNNGG	2 cut(s)	1090, 1134
Bsc4I	CCNNNNNNNGG	1 cut(s)	418
Bse118I	RCCGGY	1 cut(s)	249
Bse1I	ACTGG	2 cut(s)	220, 1019
Bse3DI	GCAATG	1 cut(s)	1151
Bse8I	GATNNNNATC	1 cut(s)	538
BseBI	CCWGG	1 cut(s)	901
BseDI	CCNNGG	2 cut(s)	1090, 1134
BseGI	GGATG	2 cut(s)	397, 1084
BseJI	GATNNNNATC	1 cut(s)	538
BseLI	CCNNNNNNNGG	1 cut(s)	418
BseMI	GCAATG	1 cut(s)	1151
BseNI	ACTGG	2 cut(s)	220, 1019
BseRI	GAGGAG	2 cut(s)	78, 262
BseXI	GCAGC	4 cut(s)	63, 283, 360, 873
BseYI	CCCAGC	1 cut(s)	292
Bsh1285I	CGRYCG	1 cut(s)	250
BshFI	GGCC	4 cut(s)	422, 581, 943, 1095
BsiEI	CGRYCG	1 cut(s)	250
BsiSI	CCGG	2 cut(s)	250, 1092
BslFI	GGGAC	1 cut(s)	649
BslI	CCNNNNNNNGG	1 cut(s)	418
BsmFI	GGGAC	1 cut(s)	649
BsnI	GGCC	4 cut(s)	422, 581, 943, 1095
Bsp143I	GATC	9 cut(s)	118, 387, 533, 539, 553, 565, 642, 740, 778
Bsp19I	CCATGG	1 cut(s)	1134
BspANI	GGCC	4 cut(s)	422, 581, 943, 1095
BspHI	TCATGA	1 cut(s)	861
BspLI	GGNNCC	3 cut(s)	13, 271, 926
BspMAI	CTGCAG	1 cut(s)	709
BspMI	ACCTGC	1 cut(s)	698
BspOI	GCTAGC	2 cut(s)	971, 1086
BspPI	GGATC	6 cut(s)	541, 547, 548, 573, 748, 773
BsrDI	GCAATG	1 cut(s)	1151
BsrFI	RCCGGY	1 cut(s)	249
BsrI	ACTGG	2 cut(s)	220, 1019
BssAI	RCCGGY	1 cut(s)	249
BssECI	CCNNGG	2 cut(s)	1090, 1134
BssMI	GATC	9 cut(s)	118, 387, 533, 539, 553, 565, 642, 740, 778
BssT1I	CCWWGG	1 cut(s)	1134
Bst2UI	CCWGG	1 cut(s)	901
Bst4CI	ACNGT	3 cut(s)	437, 830, 1112
Bst6I	CTCTTC	2 cut(s)	747, 863
BstAPI	GCANNNNNTGC	1 cut(s)	910
BstC8I	GCNNGC	4 cut(s)	487, 786, 969, 1084
BstDEI	CTNAG	1 cut(s)	384
BstDSI	CCRYGG	1 cut(s)	1134
BstF5I	GGATG	2 cut(s)	397, 1084
BstH2I	RGCGCY	1 cut(s)	455
BstHHI	GCGC	3 cut(s)	454, 491, 822
BstKTI	GATC	9 cut(s)	121, 390, 536, 542, 556, 568, 645, 743, 781
BstMBI	GATC	9 cut(s)	118, 387, 533, 539, 553, 565, 642, 740, 778
BstMCI	CGRYCG	1 cut(s)	250
BstMWI	GCNNNNNNNGC	4 cut(s)	497, 910, 1045, 1092
BstNI	CCWGG	1 cut(s)	901
BstSCI	CCNGG	2 cut(s)	899, 1090
BstSFI	CTRYAG	1 cut(s)	705
BstV1I	GCAGC	4 cut(s)	63, 283, 360, 873
BstV2I	GAAGAC	1 cut(s)	798
BstX2I	RGATCY	3 cut(s)	539, 553, 778
BstYI	RGATCY	3 cut(s)	539, 553, 778
BsuRI	GGCC	4 cut(s)	422, 581, 943, 1095
BtgI	CCRYGG	1 cut(s)	1134
BtsCI	GGATG	2 cut(s)	397, 1084
BtsIMutI	CAGTG	1 cut(s)	835
BveI	ACCTGC	1 cut(s)	698
Cac8I	GCNNGC	4 cut(s)	487, 786, 969, 1084
CciI	TCATGA	1 cut(s)	861
CfoI	GCGC	3 cut(s)	454, 491, 822
Cfr10I	RCCGGY	1 cut(s)	249
Cfr13I	GGNCC	1 cut(s)	994
Csp6I	GTAC	2 cut(s)	192, 826
CspCI	CAANNNNNGTGG	2 cut(s)	811, 846
CviAII	CATG	8 cut(s)	113, 313, 391, 574, 640, 862, 1105, 1135
CviQI	GTAC	2 cut(s)	192, 826
DdeI	CTNAG	1 cut(s)	384
DpnI	GATC	9 cut(s)	120, 389, 535, 541, 555, 567, 644, 742, 780
DpnII	GATC	9 cut(s)	118, 387, 533, 539, 553, 565, 642, 740, 778
DriI	GACNNNNNGTC	1 cut(s)	507
EaeI	YGGCCR	1 cut(s)	1093
Eam1104I	CTCTTC	2 cut(s)	747, 863
Eam1105I	GACNNNNNGTC	1 cut(s)	507
EarI	CTCTTC	2 cut(s)	747, 863
Eco130I	CCWWGG	1 cut(s)	1134
Eco147I	AGGCCT	1 cut(s)	581
Eco32I	GATATC	1 cut(s)	1141
Eco47I	GGWCC	1 cut(s)	994
Eco57I	CTGAAG	2 cut(s)	480, 768
EcoRII	CCWGG	1 cut(s)	899
EcoRV	GATATC	1 cut(s)	1141
EcoT14I	CCWWGG	1 cut(s)	1134
ErhI	CCWWGG	1 cut(s)	1134
FaeI	CATG	8 cut(s)	116, 316, 394, 577, 643, 865, 1108, 1138
FaqI	GGGAC	1 cut(s)	649
FatI	CATG	8 cut(s)	112, 312, 390, 573, 639, 861, 1104, 1134
FbaI	TGATCA	1 cut(s)	118
FokI	GGATG	2 cut(s)	384, 1091
FspAI	RTGCGCAY	1 cut(s)	490
FspBI	CTAG	3 cut(s)	189, 968, 1083
FspI	TGCGCA	2 cut(s)	490, 821
GlaI	GCGC	3 cut(s)	453, 490, 821
GsaI	CCCAGC	1 cut(s)	296
HaeII	RGCGCY	1 cut(s)	455
HaeIII	GGCC	4 cut(s)	422, 581, 943, 1095
HapII	CCGG	2 cut(s)	250, 1092
HhaI	GCGC	3 cut(s)	454, 491, 822
Hin1II	CATG	8 cut(s)	116, 316, 394, 577, 643, 865, 1108, 1138
Hin6I	GCGC	3 cut(s)	452, 489, 820
HinP1I	GCGC	3 cut(s)	452, 489, 820
HincII	GTYRAC	1 cut(s)	766
HindII	GTYRAC	1 cut(s)	766
HinfI	GANTC	6 cut(s)	196, 657, 662, 701, 956, 980
HpaI	GTTAAC	1 cut(s)	766
HpaII	CCGG	2 cut(s)	250, 1092
HphI	GGTGA	7 cut(s)	119, 200, 401, 529, 560, 589, 1084
Hpy166II	GTNNAC	1 cut(s)	766
Hpy188I	TCNGA	4 cut(s)	700, 748, 955, 1160
Hpy188III	TCNNGA	3 cut(s)	245, 537, 862
Hpy8I	GTNNAC	1 cut(s)	766
Hpy99I	CGWCG	1 cut(s)	1054
HpyAV	CCTTC	4 cut(s)	286, 329, 637, 871
HpyCH4III	ACNGT	3 cut(s)	437, 830, 1112
HpyCH4V	TGCA	4 cut(s)	173, 179, 707, 1063
HpyF10VI	GCNNNNNNNGC	4 cut(s)	497, 910, 1045, 1092
HpyF3I	CTNAG	1 cut(s)	384
Hsp92II	CATG	8 cut(s)	116, 316, 394, 577, 643, 865, 1108, 1138
HspAI	GCGC	3 cut(s)	452, 489, 820
Ksp22I	TGATCA	1 cut(s)	118
KspAI	GTTAAC	1 cut(s)	766
Kzo9I	GATC	9 cut(s)	118, 387, 533, 539, 553, 565, 642, 740, 778
LmnI	GCTCC	4 cut(s)	275, 449, 799, 924
Lsp1109I	GCAGC	4 cut(s)	63, 283, 360, 873
LweI	GCATC	5 cut(s)	78, 166, 500, 582, 1069
MaeI	CTAG	3 cut(s)	189, 968, 1083
MalI	GATC	9 cut(s)	120, 389, 535, 541, 555, 567, 644, 742, 780
MboI	GATC	9 cut(s)	118, 387, 533, 539, 553, 565, 642, 740, 778
MfeI	CAATTG	1 cut(s)	372
MflI	RGATCY	3 cut(s)	539, 553, 778
MluCI	AATT	3 cut(s)	372, 668, 723
MlyI	GAGTC	3 cut(s)	190, 671, 965
MmeI	TCCRAC	2 cut(s)	258, 427
MseI	TTAA	3 cut(s)	765, 804, 1023
MspA1I	CMGCKG	1 cut(s)	296
MspI	CCGG	2 cut(s)	250, 1092
MspR9I	CCNGG	2 cut(s)	901, 1092
MunI	CAATTG	1 cut(s)	372
MvaI	CCWGG	1 cut(s)	901
MwoI	GCNNNNNNNGC	4 cut(s)	497, 910, 1045, 1092
NciI	CCSGG	1 cut(s)	1092
NcoI	CCATGG	1 cut(s)	1134
NdeII	GATC	9 cut(s)	118, 387, 533, 539, 553, 565, 642, 740, 778
NheI	GCTAGC	2 cut(s)	967, 1082
NlaIII	CATG	8 cut(s)	116, 316, 394, 577, 643, 865, 1108, 1138
NlaIV	GGNNCC	3 cut(s)	13, 271, 926
NsbI	TGCGCA	2 cut(s)	490, 821
PagI	TCATGA	1 cut(s)	861
PceI	AGGCCT	1 cut(s)	581
PfeI	GAWTC	3 cut(s)	657, 701, 980
PflFI	GACNNNGTC	1 cut(s)	1112
PleI	GAGTC	3 cut(s)	190, 670, 964
PpsI	GAGTC	3 cut(s)	190, 670, 964
Psp6I	CCWGG	1 cut(s)	899
PspFI	CCCAGC	1 cut(s)	292
PspGI	CCWGG	1 cut(s)	899
PspN4I	GGNNCC	3 cut(s)	13, 271, 926
PspPI	GGNCC	1 cut(s)	994
PstI	CTGCAG	1 cut(s)	709
PsuI	RGATCY	3 cut(s)	539, 553, 778
PsyI	GACNNNGTC	1 cut(s)	1112
PvuII	CAGCTG	1 cut(s)	296
RsaI	GTAC	2 cut(s)	193, 827
RsaNI	GTAC	2 cut(s)	192, 826
SaqAI	TTAA	3 cut(s)	765, 804, 1023
Sau3AI	GATC	9 cut(s)	118, 387, 533, 539, 553, 565, 642, 740, 778
Sau96I	GGNCC	1 cut(s)	994
SchI	GAGTC	3 cut(s)	190, 671, 965
ScrFI	CCNGG	2 cut(s)	901, 1092
SfaNI	GCATC	5 cut(s)	78, 166, 500, 582, 1069
SfcI	CTRYAG	1 cut(s)	705
SinI	GGWCC	1 cut(s)	994
SpeI	ACTAGT	1 cut(s)	188
Sse9I	AATT	3 cut(s)	372, 668, 723
SseBI	AGGCCT	1 cut(s)	581
SspMI	CTAG	3 cut(s)	189, 968, 1083
StuI	AGGCCT	1 cut(s)	581
StyD4I	CCNGG	2 cut(s)	899, 1090
StyI	CCWWGG	1 cut(s)	1134
TaaI	ACNGT	3 cut(s)	437, 830, 1112
TaqI	TCGA	1 cut(s)	660
TasI	AATT	3 cut(s)	372, 668, 723
TatI	WGTACW	1 cut(s)	825
TauI	GCSGC	7 cut(s)	267, 270, 302, 348, 457, 500, 1039
TfiI	GAWTC	3 cut(s)	657, 701, 980
Tru1I	TTAA	3 cut(s)	765, 804, 1023
Tru9I	TTAA	3 cut(s)	765, 804, 1023
TscAI	CASTG	1 cut(s)	835
TseI	GCWGC	4 cut(s)	51, 296, 348, 886
TspGWI	ACGGA	3 cut(s)	219, 753, 1067
TspRI	CASTG	1 cut(s)	835
Tth111I	GACNNNGTC	1 cut(s)	1112
VpaK11BI	GGWCC	1 cut(s)	994
XspI	CTAG	3 cut(s)	189, 968, 1083

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.