Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr04

Orthogroup ID

OG0005462

Physical Location & Seq

Genomic Coordinates Forward (+)

4787069 .. 4792507

Gene Structure 5439 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

MD04G1041000.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1023 bp

ATGGTGCTGTGGGTAGACAAGTACCGACCCAAAACCCTAGACCAGGCAATTGTCCACCAAGACATCGCCCAAAACCTCAAGAAACTCGTTGCAGAGCAAGATTGCCCCCATTTGCTTTTTTATGGCCCTTCCGGCTCCGGCAAGAAAACCCTCATCATCGCCCTCCTCCGTCAGGTTTTCGGTCCCAGCGCCGATAAGGTGAAGGTGGAAAATAGGACATGGAAAGTTGATGCTGGGAGTAGGACCATTGATATAGAGCTGACTACAATGTCAAGCACAAACCATATTGAACTGAACCCCAGTGATGCAGGCTTTCAGGACAGATGTATTGTCCAAGAGATAATTAAAGAAATGGTTAAAAATAGGCCCATTGACACAAAAGGGAAAAAAGGATACAAAATCTTAGTGCTGAATGAAGTTGACAAGCTTTCAAGAGAAGCGCAGCATTCTCTTCGAAGAACTATGGAGAAATATAGTGCTTATTGCCAGCTAATACTATGCTGTAACAGTTCTTCAAGGGTTACTGAAGCAATCTGGTCTCAGTGTCTAAATGTGCGAATAAATGCGCCAACAGAAGACCAGATTGTTAAGGTATTGGAGTTCATTGGAAAGAAGGAAGCGCTGCAACTTCCTTCTGGATTCGCTGCTCGTATAGCTGAAAAATCAAATAGGAGCTTAAGGAGAGCTATATTGTCATTAGAAACTTGTCTTGTTCAACAGTTAAGTGCCAGAGTTCTAATTGGTCATCAGTTGTGTGAAGCAGTATCCCTTAACAAGTACCCAATGGACTGGGAGGAATATGTTTCTGAAATCGCCTCTGATATAATGAAGGAGCAGAGCCCAAAAAGGCTTTATCAGGTGCGGCAGAAGCTGTATGAGCTACTTTTAAATTGTATTCCTCCAGAGATCATCTTGAAGAGGCTGCTTTATGAGTTATTGAAGAAATTGGATGCAGAACTGAAGCATGAGGTCTGCCATTGGCTTCGTATTGCCATTCGTGGCGAAGTTCATGAGCATCTATAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005657 GO:0005663 GO:0005694 GO:0006139 GO:0006259 GO:0006260 GO:0006261 GO:0006275 GO:0006281 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009889 GO:0009891 GO:0009893 GO:0009987 GO:0010556 GO:0010557 GO:0010604 GO:0019219 GO:0019222 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0031390 GO:0032991 GO:0033554 GO:0034641 GO:0034645 GO:0043085 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0044093 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044422 GO:0044424 GO:0044427 GO:0044446 GO:0044464 GO:0045935 GO:0046483 GO:0048518 GO:0048522 GO:0050789 GO:0050790 GO:0050794 GO:0050896 GO:0051052 GO:0051054 GO:0051171 GO:0051173 GO:0051338 GO:0051347 GO:0051716 GO:0060255 GO:0065007 GO:0065009 GO:0071704 GO:0080090 GO:0090304 GO:0090329 GO:1900262 GO:1900264 GO:1901360 GO:1901576 GO:2000112 GO:2000278 GO:2000573

KEGG Pathways

Metabolic & Signaling

ko03030 ko03420 ko03430 map03030 map03420 map03430

Pfam Domains

Protein Families

DNA_pol3_delta2

Protein Analysis

341

Amino Acids

39.01

Weight (kDa)

8.88

Isoelectric Point (pI)

41.43

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Rad17	PF03215	3 - 63	1e-05	Rad17 P-loop domain
DNA_pol3_delta2	PF13177	20 - 189	2e-10	DNA polymerase III, delta subunit
RCF1-5-like_lid	PF21960	197 - 236	6.3e-10	RCF1/5-like, AAA+ ATPase lid domain
RFC_C	PF22534	264 - 327	9.6e-16	Replication factor C subunit 3, C-terminal domain

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: OG0005462)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G27740
fragaria_vesca	FvH4_1g23560 FvH4_2g04970 FvH4_2g04970 FvH4_2g04970
malus_domestica	MD04G1041000.v1.1 MD04G1041300.v1.1 MD12G1011300.v1.1
prunus_persica	Prupe.1G194700_v2.0.a1 Prupe.1G194700_v2.0.a1 Prupe.4G268900_v2.0.a1 Prupe.4G268900_v2.0.a1 Prupe.7G013300_v2.0.a1 Prupe.7G013300_v2.0.a1 Prupe.7G013300_v2.0.a1
pyrus_communis	pycom12g00880
rosa_chinensis	RchiOBHm_Chr3g0496081
rosa_laevigata	RLG00000022564
rosa_multiflora	Rmu_sc0002392.1_g000001
rosa_roxburghii	Rroxscaffold_6G00389580
rosa_rugosa	Rorug03G0279300 Rorug03G0279400 Rorug03G0279400 Rorug03G0279400 Rorug03G0279500
rosa_samantha	Rh3AG326500 Rh3BG362800 Rh3DG362200
rosa_wichuraiana	Rw3G028590

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AasI	GACNNNNNNGTC	1 cut(s)	268
AccI	GTMKAC	1 cut(s)	15
AciI	CCGC	1 cut(s)	862
AcuI	CTGAAG	2 cut(s)	546, 980
AfaI	GTAC	2 cut(s)	23, 779
AfeI	AGCGCT	1 cut(s)	621
AfiI	CCNNNNNNNGG	2 cut(s)	43, 172
AflII	CTTAAG	1 cut(s)	676
AgsI	TTSAA	6 cut(s)	290, 432, 516, 716, 916, 940
AjnI	CCWGG	1 cut(s)	42
AluBI	AGCT	8 cut(s)	259, 427, 490, 656, 675, 686, 871, 880
AluI	AGCT	8 cut(s)	259, 427, 490, 656, 675, 686, 871, 880
Alw26I	GTCTC	1 cut(s)	543
AlwNI	CAGNNNCTG	1 cut(s)	871
Aor51HI	AGCGCT	1 cut(s)	621
AoxI	GGCC	2 cut(s)	124, 365
ApeKI	GCWGC	4 cut(s)	442, 622, 644, 922
AspLEI	GCGC	4 cut(s)	191, 442, 568, 622
AspS9I	GGNCC	4 cut(s)	125, 182, 243, 366
AsuHPI	GGTGA	1 cut(s)	211
AsuII	TTCGAA	1 cut(s)	454
AvaII	GGWCC	2 cut(s)	182, 243
BanII	GRGCYC	1 cut(s)	842
BarI	GAAGNNNNNNTAC	2 cut(s)	496, 528
BbsI	GAAGAC	1 cut(s)	582
BbvI	GCAGC	4 cut(s)	454, 609, 631, 909
BcgI	CGANNNNNNTGC	2 cut(s)	434, 468
BciT130I	CCWGG	1 cut(s)	44
BciVI	GTATCC	2 cut(s)	386, 775
BcoDI	GTCTC	1 cut(s)	543
BfaI	CTAG	1 cut(s)	38
BfoI	RGCGCY	2 cut(s)	192, 623
BfrI	CTTAAG	1 cut(s)	676
BfuI	GTATCC	2 cut(s)	386, 775
BglI	GCCNNNNNGGC	1 cut(s)	132
BisI	GCNGC	5 cut(s)	443, 623, 645, 863, 923
BlsI	GCNGC	5 cut(s)	444, 624, 646, 864, 924
Bme1390I	CCNGG	1 cut(s)	44
Bme18I	GGWCC	2 cut(s)	182, 243
BmgT120I	GGNCC	4 cut(s)	125, 182, 243, 366
BmiI	GGNNCC	2 cut(s)	136, 184
BmrFI	CCNGG	1 cut(s)	44
BmrI	ACTGGG	2 cut(s)	294, 799
BmsI	GCATC	3 cut(s)	220, 295, 940
BmuI	ACTGGG	2 cut(s)	294, 799
BpiI	GAAGAC	1 cut(s)	582
BpmI	CTGGAG	1 cut(s)	885
Bpu14I	TTCGAA	1 cut(s)	454
BpuEI	CTTGAG	1 cut(s)	62
BsaI	GGTCTC	1 cut(s)	543
Bsc4I	CCNNNNNNNGG	2 cut(s)	43, 172
Bse1I	ACTGG	2 cut(s)	300, 794
BseBI	CCWGG	1 cut(s)	44
BseGI	GGATG	1 cut(s)	955
BseLI	CCNNNNNNNGG	2 cut(s)	43, 172
BseMII	CTCAG	1 cut(s)	554
BseNI	ACTGG	2 cut(s)	300, 794
BseRI	GAGGAG	1 cut(s)	155
BseXI	GCAGC	4 cut(s)	454, 609, 631, 909
BseYI	CCCAGC	2 cut(s)	185, 233
BshFI	GGCC	2 cut(s)	126, 367
BsiSI	CCGG	2 cut(s)	132, 138
BslFI	GGGAC	1 cut(s)	168
BslI	CCNNNNNNNGG	2 cut(s)	43, 172
BsmAI	GTCTC	1 cut(s)	543
BsmFI	GGGAC	1 cut(s)	168
BsmI	GAATGC	1 cut(s)	445
BsnI	GGCC	2 cut(s)	126, 367
Bso31I	GGTCTC	1 cut(s)	543
Bsp119I	TTCGAA	1 cut(s)	454
Bsp1286I	GDGCHC	1 cut(s)	842
Bsp143I	GATC	1 cut(s)	906
BspACI	CCGC	1 cut(s)	862
BspANI	GGCC	2 cut(s)	126, 367
BspCNI	CTCAG	1 cut(s)	553
BspHI	TCATGA	1 cut(s)	1009
BspLI	GGNNCC	2 cut(s)	136, 184
BspT104I	TTCGAA	1 cut(s)	454
BspTI	CTTAAG	1 cut(s)	676
BspTNI	GGTCTC	1 cut(s)	543
BsrI	ACTGG	2 cut(s)	300, 794
BssMI	GATC	1 cut(s)	906
Bst2UI	CCWGG	1 cut(s)	44
Bst4CI	ACNGT	2 cut(s)	509, 720
Bst6I	CTCTTC	2 cut(s)	456, 911
BstAFI	CTTAAG	1 cut(s)	676
BstBI	TTCGAA	1 cut(s)	454
BstC8I	GCNNGC	2 cut(s)	310, 488
BstDEI	CTNAG	2 cut(s)	403, 540
BstENI	CCTNNNNNAGG	2 cut(s)	41, 170
BstF5I	GGATG	1 cut(s)	955
BstH2I	RGCGCY	2 cut(s)	192, 623
BstHHI	GCGC	4 cut(s)	191, 442, 568, 622
BstKTI	GATC	1 cut(s)	909
BstMAI	GTCTC	1 cut(s)	543
BstMBI	GATC	1 cut(s)	906
BstMWI	GCNNNNNNNGC	4 cut(s)	132, 653, 868, 877
BstNI	CCWGG	1 cut(s)	44
BstSCI	CCNGG	1 cut(s)	42
BstV1I	GCAGC	4 cut(s)	454, 609, 631, 909
BstV2I	GAAGAC	1 cut(s)	582
BstXI	CCANNNNNNTGG	1 cut(s)	789
BsuI	GTATCC	2 cut(s)	386, 775
BsuRI	GGCC	2 cut(s)	126, 367
BtgZI	GCGATG	2 cut(s)	49, 142
BtsCI	GGATG	1 cut(s)	955
BtsIMutI	CAGTG	2 cut(s)	307, 548
Cac8I	GCNNGC	2 cut(s)	310, 488
CaiI	CAGNNNCTG	1 cut(s)	871
CciI	TCATGA	1 cut(s)	1009
CfoI	GCGC	4 cut(s)	191, 442, 568, 622
Cfr13I	GGNCC	4 cut(s)	125, 182, 243, 366
Csp6I	GTAC	2 cut(s)	22, 778
CviAII	CATG	3 cut(s)	219, 965, 1010
CviQI	GTAC	2 cut(s)	22, 778
DdeI	CTNAG	2 cut(s)	403, 540
DpnI	GATC	1 cut(s)	908
DpnII	GATC	1 cut(s)	906
DraI	TTTAAA	1 cut(s)	888
DrdI	GACNNNNNNGTC	1 cut(s)	268
DseDI	GACNNNNNNGTC	1 cut(s)	268
Eam1104I	CTCTTC	2 cut(s)	456, 911
EarI	CTCTTC	2 cut(s)	456, 911
Eco24I	GRGCYC	1 cut(s)	842
Eco31I	GGTCTC	1 cut(s)	543
Eco47I	GGWCC	2 cut(s)	182, 243
Eco47III	AGCGCT	1 cut(s)	621
Eco57I	CTGAAG	2 cut(s)	546, 980
EcoNI	CCTNNNNNAGG	2 cut(s)	41, 170
EcoRII	CCWGG	1 cut(s)	42
EcoT38I	GRGCYC	1 cut(s)	842
FaeI	CATG	3 cut(s)	222, 968, 1013
FaqI	GGGAC	1 cut(s)	168
FatI	CATG	3 cut(s)	218, 964, 1009
FblI	GTMKAC	1 cut(s)	15
Fnu4HI	GCNGC	5 cut(s)	443, 623, 645, 863, 923
FokI	GGATG	1 cut(s)	962
FriOI	GRGCYC	1 cut(s)	842
Fsp4HI	GCNGC	5 cut(s)	443, 623, 645, 863, 923
FspBI	CTAG	1 cut(s)	38
GlaI	GCGC	4 cut(s)	190, 441, 567, 621
GluI	GCNGC	5 cut(s)	443, 623, 645, 863, 923
GsaI	CCCAGC	2 cut(s)	189, 237
GsuI	CTGGAG	1 cut(s)	885
HaeII	RGCGCY	2 cut(s)	192, 623
HaeIII	GGCC	2 cut(s)	126, 367
HapII	CCGG	2 cut(s)	132, 138
HhaI	GCGC	4 cut(s)	191, 442, 568, 622
Hin1II	CATG	3 cut(s)	222, 968, 1013
Hin6I	GCGC	4 cut(s)	189, 440, 566, 620
HinP1I	GCGC	4 cut(s)	189, 440, 566, 620
HincII	GTYRAC	1 cut(s)	421
HindII	GTYRAC	1 cut(s)	421
HindIII	AAGCTT	1 cut(s)	425
HinfI	GANTC	1 cut(s)	639
HpaII	CCGG	2 cut(s)	132, 138
HphI	GGTGA	1 cut(s)	211
Hpy166II	GTNNAC	3 cut(s)	16, 55, 421
Hpy188I	TCNGA	2 cut(s)	808, 820
Hpy188III	TCNNGA	7 cut(s)	79, 317, 432, 636, 902, 913, 1010
Hpy8I	GTNNAC	3 cut(s)	16, 55, 421
HpyAV	CCTTC	5 cut(s)	138, 196, 607, 642, 823
HpyCH4III	ACNGT	2 cut(s)	509, 720
HpyCH4V	TGCA	4 cut(s)	92, 308, 625, 953
HpyF10VI	GCNNNNNNNGC	4 cut(s)	132, 653, 868, 877
HpyF3I	CTNAG	2 cut(s)	403, 540
Hsp92II	CATG	3 cut(s)	222, 968, 1013
HspAI	GCGC	4 cut(s)	189, 440, 566, 620
Kzo9I	GATC	1 cut(s)	906
LmnI	GCTCC	3 cut(s)	140, 672, 832
Lsp1109I	GCAGC	4 cut(s)	454, 609, 631, 909
LweI	GCATC	3 cut(s)	220, 295, 940
MaeI	CTAG	1 cut(s)	38
MaeIII	GTNAC	2 cut(s)	503, 520
MalI	GATC	1 cut(s)	908
MboI	GATC	1 cut(s)	906
MboII	GAAGA	6 cut(s)	443, 468, 504, 587, 928, 952
MfeI	CAATTG	1 cut(s)	48
MhlI	GDGCHC	1 cut(s)	842
MluCI	AATT	5 cut(s)	48, 342, 738, 889, 944
MnlI	CCTC	9 cut(s)	86, 161, 173, 176, 787, 826, 909, 912, 961
MseI	TTAA	7 cut(s)	345, 357, 588, 677, 722, 771, 887
MspCI	CTTAAG	1 cut(s)	676
MspI	CCGG	2 cut(s)	132, 138
MspR9I	CCNGG	1 cut(s)	44
MunI	CAATTG	1 cut(s)	48
Mva1269I	GAATGC	1 cut(s)	445
MvaI	CCWGG	1 cut(s)	44
MwoI	GCNNNNNNNGC	4 cut(s)	132, 653, 868, 877
NdeII	GATC	1 cut(s)	906
NlaIII	CATG	3 cut(s)	222, 968, 1013
NlaIV	GGNNCC	2 cut(s)	136, 184
NspV	TTCGAA	1 cut(s)	454
PagI	TCATGA	1 cut(s)	1009
PctI	GAATGC	1 cut(s)	445
PfeI	GAWTC	1 cut(s)	639
PkrI	GCNGC	5 cut(s)	444, 624, 646, 864, 924
Psp6I	CCWGG	1 cut(s)	42
PspFI	CCCAGC	2 cut(s)	185, 233
PspGI	CCWGG	1 cut(s)	42
PspN4I	GGNNCC	2 cut(s)	136, 184
PspPI	GGNCC	4 cut(s)	125, 182, 243, 366
PstNI	CAGNNNCTG	1 cut(s)	871
RsaI	GTAC	2 cut(s)	23, 779
RsaNI	GTAC	2 cut(s)	22, 778
SaqAI	TTAA	7 cut(s)	345, 357, 588, 677, 722, 771, 887
SatI	GCNGC	5 cut(s)	443, 623, 645, 863, 923
Sau3AI	GATC	1 cut(s)	906
Sau96I	GGNCC	4 cut(s)	125, 182, 243, 366
ScrFI	CCNGG	1 cut(s)	44
SduI	GDGCHC	1 cut(s)	842
SfaNI	GCATC	3 cut(s)	220, 295, 940
SfuI	TTCGAA	1 cut(s)	454
SinI	GGWCC	2 cut(s)	182, 243
SmlI	CTYRAG	2 cut(s)	77, 676
SmoI	CTYRAG	2 cut(s)	77, 676
Sse9I	AATT	5 cut(s)	48, 342, 738, 889, 944
SsiI	CCGC	1 cut(s)	862
SspMI	CTAG	1 cut(s)	38
StyD4I	CCNGG	1 cut(s)	42
TaaI	ACNGT	2 cut(s)	509, 720
TaqI	TCGA	1 cut(s)	454
TaqII	GACCGA	1 cut(s)	170
TasI	AATT	5 cut(s)	48, 342, 738, 889, 944
TauI	GCSGC	1 cut(s)	865
TfiI	GAWTC	1 cut(s)	639
Tru1I	TTAA	7 cut(s)	345, 357, 588, 677, 722, 771, 887
Tru9I	TTAA	7 cut(s)	345, 357, 588, 677, 722, 771, 887
TscAI	CASTG	2 cut(s)	307, 548
TseI	GCWGC	4 cut(s)	442, 622, 644, 922
TspDTI	ATGAA	4 cut(s)	429, 592, 842, 998
TspGWI	ACGGA	1 cut(s)	158
TspRI	CASTG	2 cut(s)	307, 548
Vha464I	CTTAAG	1 cut(s)	676
VpaK11BI	GGWCC	2 cut(s)	182, 243
XagI	CCTNNNNNAGG	2 cut(s)	41, 170
XmiI	GTMKAC	1 cut(s)	15
XspI	CTAG	1 cut(s)	38

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