Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr04

Orthogroup ID

OG0005462

Physical Location & Seq

Genomic Coordinates Forward (+)

4895148 .. 4906843

Gene Structure 11696 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

MD04G1041300.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1065 bp

ATGCTGTGGGTAGACAAGTACCGACCCAAAACCCTAGACCAGGCAATTGTCCACCAAGACATCGCCCAAAACCTCAAGAAACTCGTTGCAGAGCAGGATTGCCCCCATTTGCTCTTTTATGGCCCTTCCGGCTCCGGCAAGAAAACCCTCATCATCGCCCTCCTCCGTCAGGTTTTCGGTCCCAGCGCCGATAAGGTGAAAGTGGAAAATAGGGCATGGAAAGTTGATGCTGGGAGCAGAACCATTGATATAGAGCTGACTACATTGTCAAGCACAAACCATATTGAATTGAACCCCAGTGATGCAGGCTTTCAGGATAGATATATTGTCCAAGAGATAATTAAAGAAATGGCTAAAAATAGGCCCATTGACACAAAAGGGAAAAAAGGATATAAAATCTTAGTGCTGAATGAAGTTGACAAGCTTTCAAGAGAAGCGCAGCATTCTCTTCGAAGAACTATGGAGAAATATAGTGCTTATTGCCGGCTAATACTATGCTGTAACAGTTCTTCAAAGGTTACTGAAGCAATCCGGTCTCGGTGTCTAAATGTGCGAATAAATGCACCAACAGAAGACCAGATTGTTAAGGTATTGGAGTTCATTGGAAAGAAGGAAGTGCTGCAACTTCCTTCTGGATTCACTGCTCGTATAGCTGAAAAATCAAATAGGAGCTTAAGGAGAGCTATATTGTCCTTAGAAACTTGTCGTGTCCAACAGTATCCCTTTACAAGTAACCAATCGATACCCCCAATGGACTGGGAGGAATATGTTTCTGAAATCGCCTCTGATATAATGAAGGAGCAGAGCCCAAAAAGGCTTTATCAGGTGCGGCAGAAGCTGTATGAGCTACTTCTAAATTGTATTCCTCCAGAGATCATCTTGAAGAGGCTGCTTTATGAGTTATTGAAGAAATTGGATGCAGAACTGAAGCATGAGGTCTGCCATTGGGCTGCATATTACGAACACAGGATGCGTCTTGGGCAGAAAGCAATATTTCACCTGGAAGCATTCGTGGCGAAGTTCATGAGCATCTATAAGGCTTTCCTCATTGAAGCGTTTGGCTGA

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

355

Amino Acids

40.86

Weight (kDa)

9.24

Isoelectric Point (pI)

42.62

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DNA_pol3_delta2	PF13177	19 - 188	2.1e-12	DNA polymerase III, delta subunit
AAA	PF00004	37 - 182	2.8e-06	ATPase family associated with various cellular activities (AAA)
RCF1-5-like_lid	PF21960	196 - 236	1.5e-09	RCF1/5-like, AAA+ ATPase lid domain
RFC_C	PF22534	253 - 342	2.6e-32	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

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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)	265
AccI	GTMKAC	1 cut(s)	12
AciI	CCGC	1 cut(s)	829
AcuI	CTGAAG	2 cut(s)	543, 947
AfaI	GTAC	1 cut(s)	20
AfiI	CCNNNNNNNGG	2 cut(s)	40, 169
AflII	CTTAAG	1 cut(s)	673
AgsI	TTSAA	7 cut(s)	287, 292, 429, 513, 883, 907, 1052
AjnI	CCWGG	2 cut(s)	39, 999
AluBI	AGCT	7 cut(s)	256, 424, 653, 672, 683, 838, 847
AluI	AGCT	7 cut(s)	256, 424, 653, 672, 683, 838, 847
Alw26I	GTCTC	1 cut(s)	540
AlwNI	CAGNNNCTG	1 cut(s)	838
AoxI	GGCC	2 cut(s)	121, 362
ApeKI	GCWGC	4 cut(s)	439, 619, 889, 950
AspLEI	GCGC	2 cut(s)	188, 439
AspS9I	GGNCC	3 cut(s)	122, 179, 363
AsuHPI	GGTGA	2 cut(s)	208, 989
AsuII	TTCGAA	1 cut(s)	451
AvaII	GGWCC	1 cut(s)	179
BanII	GRGCYC	1 cut(s)	809
BarI	GAAGNNNNNNTAC	2 cut(s)	493, 525
BbsI	GAAGAC	1 cut(s)	579
BbvI	GCAGC	4 cut(s)	451, 606, 876, 937
BcgI	CGANNNNNNTGC	2 cut(s)	431, 465
BciT130I	CCWGG	2 cut(s)	41, 1001
BciVI	GTATCC	1 cut(s)	729
BcoDI	GTCTC	1 cut(s)	540
BfaI	CTAG	1 cut(s)	35
BfoI	RGCGCY	1 cut(s)	189
BfrI	CTTAAG	1 cut(s)	673
BfuI	GTATCC	1 cut(s)	729
BglI	GCCNNNNNGGC	1 cut(s)	129
BisI	GCNGC	5 cut(s)	440, 620, 830, 890, 951
BlsI	GCNGC	5 cut(s)	441, 621, 831, 891, 952
Bme1390I	CCNGG	2 cut(s)	41, 1001
Bme18I	GGWCC	1 cut(s)	179
BmgT120I	GGNCC	3 cut(s)	122, 179, 363
BmiI	GGNNCC	2 cut(s)	133, 181
BmrFI	CCNGG	2 cut(s)	41, 1001
BmrI	ACTGGG	2 cut(s)	291, 766
BmsI	GCATC	5 cut(s)	217, 292, 907, 960, 1038
BmuI	ACTGGG	2 cut(s)	291, 766
BpiI	GAAGAC	1 cut(s)	579
BpmI	CTGGAG	1 cut(s)	852
Bpu14I	TTCGAA	1 cut(s)	451
BpuEI	CTTGAG	1 cut(s)	59
Bsa29I	ATCGAT	1 cut(s)	740
BsaI	GGTCTC	1 cut(s)	540
BsaWI	WCCGGW	1 cut(s)	531
Bsc4I	CCNNNNNNNGG	2 cut(s)	40, 169
Bse118I	RCCGGY	1 cut(s)	483
Bse1I	ACTGG	2 cut(s)	297, 761
BseBI	CCWGG	2 cut(s)	41, 1001
BseCI	ATCGAT	1 cut(s)	740
BseGI	GGATG	2 cut(s)	922, 975
BseLI	CCNNNNNNNGG	2 cut(s)	40, 169
BseNI	ACTGG	2 cut(s)	297, 761
BseRI	GAGGAG	1 cut(s)	152
BseXI	GCAGC	4 cut(s)	451, 606, 876, 937
BseYI	CCCAGC	2 cut(s)	182, 230
BshFI	GGCC	2 cut(s)	123, 364
BshVI	ATCGAT	1 cut(s)	740
BsiSI	CCGG	4 cut(s)	129, 135, 484, 532
BslFI	GGGAC	1 cut(s)	165
BslI	CCNNNNNNNGG	2 cut(s)	40, 169
BsmAI	GTCTC	1 cut(s)	540
BsmFI	GGGAC	1 cut(s)	165
BsmI	GAATGC	2 cut(s)	442, 1007
BsnI	GGCC	2 cut(s)	123, 364
Bso31I	GGTCTC	1 cut(s)	540
Bsp119I	TTCGAA	1 cut(s)	451
Bsp1286I	GDGCHC	1 cut(s)	809
Bsp143I	GATC	1 cut(s)	873
BspACI	CCGC	1 cut(s)	829
BspANI	GGCC	2 cut(s)	123, 364
BspDI	ATCGAT	1 cut(s)	740
BspHI	TCATGA	1 cut(s)	1023
BspLI	GGNNCC	2 cut(s)	133, 181
BspT104I	TTCGAA	1 cut(s)	451
BspTI	CTTAAG	1 cut(s)	673
BspTNI	GGTCTC	1 cut(s)	540
BsrFI	RCCGGY	1 cut(s)	483
BsrI	ACTGG	2 cut(s)	297, 761
BssAI	RCCGGY	1 cut(s)	483
BssMI	GATC	1 cut(s)	873
Bst2UI	CCWGG	2 cut(s)	41, 1001
Bst4CI	ACNGT	2 cut(s)	506, 717
Bst6I	CTCTTC	2 cut(s)	453, 878
BstAFI	CTTAAG	1 cut(s)	673
BstBI	TTCGAA	1 cut(s)	451
BstC8I	GCNNGC	2 cut(s)	307, 485
BstDEI	CTNAG	2 cut(s)	400, 694
BstENI	CCTNNNNNAGG	2 cut(s)	38, 167
BstF5I	GGATG	2 cut(s)	922, 975
BstH2I	RGCGCY	1 cut(s)	189
BstHHI	GCGC	2 cut(s)	188, 439
BstKTI	GATC	1 cut(s)	876
BstMAI	GTCTC	1 cut(s)	540
BstMBI	GATC	1 cut(s)	873
BstMWI	GCNNNNNNNGC	6 cut(s)	129, 650, 835, 844, 979, 1013
BstNI	CCWGG	2 cut(s)	41, 1001
BstSCI	CCNGG	2 cut(s)	39, 999
BstV1I	GCAGC	4 cut(s)	451, 606, 876, 937
BstV2I	GAAGAC	1 cut(s)	579
BstXI	CCANNNNNNTGG	1 cut(s)	756
Bsu15I	ATCGAT	1 cut(s)	740
BsuI	GTATCC	1 cut(s)	729
BsuRI	GGCC	2 cut(s)	123, 364
BsuTUI	ATCGAT	1 cut(s)	740
BtgZI	GCGATG	2 cut(s)	46, 139
BtsCI	GGATG	2 cut(s)	922, 975
BtsI	GCAGTG	1 cut(s)	639
BtsIMutI	CAGTG	2 cut(s)	304, 639
Cac8I	GCNNGC	2 cut(s)	307, 485
CaiI	CAGNNNCTG	1 cut(s)	838
CciI	TCATGA	1 cut(s)	1023
CfoI	GCGC	2 cut(s)	188, 439
Cfr10I	RCCGGY	1 cut(s)	483
Cfr13I	GGNCC	3 cut(s)	122, 179, 363
ClaI	ATCGAT	1 cut(s)	740
CseI	GACGC	1 cut(s)	962
Csp6I	GTAC	1 cut(s)	19
CviAII	CATG	3 cut(s)	216, 932, 1024
CviQI	GTAC	1 cut(s)	19
DdeI	CTNAG	2 cut(s)	400, 694
DpnI	GATC	1 cut(s)	875
DpnII	GATC	1 cut(s)	873
DrdI	GACNNNNNNGTC	1 cut(s)	265
DseDI	GACNNNNNNGTC	1 cut(s)	265
Eam1104I	CTCTTC	2 cut(s)	453, 878
EarI	CTCTTC	2 cut(s)	453, 878
Eco24I	GRGCYC	1 cut(s)	809
Eco31I	GGTCTC	1 cut(s)	540
Eco47I	GGWCC	1 cut(s)	179
Eco57I	CTGAAG	2 cut(s)	543, 947
EcoNI	CCTNNNNNAGG	2 cut(s)	38, 167
EcoRII	CCWGG	2 cut(s)	39, 999
EcoT38I	GRGCYC	1 cut(s)	809
FaeI	CATG	3 cut(s)	219, 935, 1027
FaqI	GGGAC	1 cut(s)	165
FatI	CATG	3 cut(s)	215, 931, 1023
FblI	GTMKAC	1 cut(s)	12
Fnu4HI	GCNGC	5 cut(s)	440, 620, 830, 890, 951
FokI	GGATG	2 cut(s)	929, 982
FriOI	GRGCYC	1 cut(s)	809
Fsp4HI	GCNGC	5 cut(s)	440, 620, 830, 890, 951
FspBI	CTAG	1 cut(s)	35
GlaI	GCGC	2 cut(s)	187, 438
GluI	GCNGC	5 cut(s)	440, 620, 830, 890, 951
GsaI	CCCAGC	2 cut(s)	186, 234
GsuI	CTGGAG	1 cut(s)	852
HaeII	RGCGCY	1 cut(s)	189
HaeIII	GGCC	2 cut(s)	123, 364
HapII	CCGG	4 cut(s)	129, 135, 484, 532
HgaI	GACGC	1 cut(s)	962
HhaI	GCGC	2 cut(s)	188, 439
Hin1II	CATG	3 cut(s)	219, 935, 1027
Hin6I	GCGC	2 cut(s)	186, 437
HinP1I	GCGC	2 cut(s)	186, 437
HincII	GTYRAC	1 cut(s)	418
HindII	GTYRAC	1 cut(s)	418
HindIII	AAGCTT	1 cut(s)	422
HinfI	GANTC	1 cut(s)	636
HpaII	CCGG	4 cut(s)	129, 135, 484, 532
HphI	GGTGA	2 cut(s)	208, 989
Hpy166II	GTNNAC	3 cut(s)	13, 52, 418
Hpy188I	TCNGA	2 cut(s)	775, 787
Hpy188III	TCNNGA	7 cut(s)	76, 314, 429, 633, 869, 880, 1024
Hpy8I	GTNNAC	3 cut(s)	13, 52, 418
HpyAV	CCTTC	4 cut(s)	135, 604, 639, 790
HpyCH4III	ACNGT	2 cut(s)	506, 717
HpyCH4V	TGCA	6 cut(s)	89, 305, 563, 622, 920, 953
HpyF10VI	GCNNNNNNNGC	6 cut(s)	129, 650, 835, 844, 979, 1013
HpyF3I	CTNAG	2 cut(s)	400, 694
Hsp92II	CATG	3 cut(s)	219, 935, 1027
HspAI	GCGC	2 cut(s)	186, 437
KroI	GCCGGC	1 cut(s)	483
KroNI	GCCGGC	1 cut(s)	485
Kzo9I	GATC	1 cut(s)	873
LmnI	GCTCC	4 cut(s)	137, 234, 669, 799
Lsp1109I	GCAGC	4 cut(s)	451, 606, 876, 937
LweI	GCATC	5 cut(s)	217, 292, 907, 960, 1038
MaeI	CTAG	1 cut(s)	35
MaeIII	GTNAC	3 cut(s)	500, 517, 731
MalI	GATC	1 cut(s)	875
MboI	GATC	1 cut(s)	873
MboII	GAAGA	6 cut(s)	440, 465, 501, 584, 895, 919
MfeI	CAATTG	1 cut(s)	45
MhlI	GDGCHC	1 cut(s)	809
MluCI	AATT	5 cut(s)	45, 287, 339, 856, 911
MmeI	TCCRAC	1 cut(s)	736
MroNI	GCCGGC	1 cut(s)	483
MseI	TTAA	3 cut(s)	342, 585, 674
MspCI	CTTAAG	1 cut(s)	673
MspI	CCGG	4 cut(s)	129, 135, 484, 532
MspR9I	CCNGG	2 cut(s)	41, 1001
MunI	CAATTG	1 cut(s)	45
Mva1269I	GAATGC	2 cut(s)	442, 1007
MvaI	CCWGG	2 cut(s)	41, 1001
MwoI	GCNNNNNNNGC	6 cut(s)	129, 650, 835, 844, 979, 1013
NaeI	GCCGGC	1 cut(s)	485
NdeII	GATC	1 cut(s)	873
NgoMIV	GCCGGC	1 cut(s)	483
NlaIII	CATG	3 cut(s)	219, 935, 1027
NlaIV	GGNNCC	2 cut(s)	133, 181
NspV	TTCGAA	1 cut(s)	451
PagI	TCATGA	1 cut(s)	1023
PctI	GAATGC	2 cut(s)	442, 1007
PdiI	GCCGGC	1 cut(s)	485
PfeI	GAWTC	1 cut(s)	636
PkrI	GCNGC	5 cut(s)	441, 621, 831, 891, 952
Psp6I	CCWGG	2 cut(s)	39, 999
PspFI	CCCAGC	2 cut(s)	182, 230
PspGI	CCWGG	2 cut(s)	39, 999
PspN4I	GGNNCC	2 cut(s)	133, 181
PspPI	GGNCC	3 cut(s)	122, 179, 363
PstNI	CAGNNNCTG	1 cut(s)	838
RsaI	GTAC	1 cut(s)	20
RsaNI	GTAC	1 cut(s)	19
SaqAI	TTAA	3 cut(s)	342, 585, 674
SatI	GCNGC	5 cut(s)	440, 620, 830, 890, 951
Sau3AI	GATC	1 cut(s)	873
Sau96I	GGNCC	3 cut(s)	122, 179, 363
ScrFI	CCNGG	2 cut(s)	41, 1001
SduI	GDGCHC	1 cut(s)	809
SfaNI	GCATC	5 cut(s)	217, 292, 907, 960, 1038
SfuI	TTCGAA	1 cut(s)	451
SinI	GGWCC	1 cut(s)	179
SmlI	CTYRAG	2 cut(s)	74, 673
SmoI	CTYRAG	2 cut(s)	74, 673
Sse9I	AATT	5 cut(s)	45, 287, 339, 856, 911
SsiI	CCGC	1 cut(s)	829
SspI	AATATT	1 cut(s)	993
SspMI	CTAG	1 cut(s)	35
StyD4I	CCNGG	2 cut(s)	39, 999
TaaI	ACNGT	2 cut(s)	506, 717
TaqI	TCGA	2 cut(s)	451, 740
TaqII	GACCGA	1 cut(s)	167
TasI	AATT	5 cut(s)	45, 287, 339, 856, 911
TauI	GCSGC	1 cut(s)	832
TfiI	GAWTC	1 cut(s)	636
Tru1I	TTAA	3 cut(s)	342, 585, 674
Tru9I	TTAA	3 cut(s)	342, 585, 674
TscAI	CASTG	2 cut(s)	304, 646
TseI	GCWGC	4 cut(s)	439, 619, 889, 950
TspDTI	ATGAA	4 cut(s)	426, 589, 809, 1012
TspGWI	ACGGA	1 cut(s)	155
TspRI	CASTG	2 cut(s)	304, 646
Vha464I	CTTAAG	1 cut(s)	673
VpaK11BI	GGWCC	1 cut(s)	179
XagI	CCTNNNNNAGG	2 cut(s)	38, 167
XmiI	GTMKAC	1 cut(s)	12
XspI	CTAG	1 cut(s)	35

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