Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr12

Orthogroup ID

OG0005462

Physical Location & Seq

Genomic Coordinates Reverse (-)

1147011 .. 1151404

Gene Structure 4394 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

MD12G1011300.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1065 bp

ATGTTGTGGGTCGACAAGTACCGACCCAAAACCCTAGACCAGGCAATTGTCCACCAAGATATCGCCCAAAACCTCAAGAAACTTGTCGCGGAGCAGGACTGCCCCCATTTGCTCTTTTATGGCCCTTCTGGTTCCGGCAAGAAAACCCTAATCATCGCCCTTCTTCGTCAGATATTCGGACCCAGTGCCGACAAGGTGAAGGTGGAAAACAGGGCATGGAAAGTCGATGCTGGGAGTAGAACGATTGATATAGAGCTGACTACATTATCGAGCACCAACCATATTGAACTGAACCCCAGTGATGCAGGGTTTCAAGACAGATACATTGTTCAAGAGATAATTAAAGAAATGGCTAAAAATAGACCCATTGACACAAAAGGGAAAAAAGGATATAAAGTCCTAGTGCTGAATGAAGTTGACAAACTTTCAAGGGAAGCGCAGCATTCTCTTCGAAGAACTATGGAGAAATATAGTGCTTATTGCCGGCTAATACTATGCTGTAACAGTTCTTCAAGGGTTACTGAAGCAATCAGGTCTCGGTGTCTTAATGTGCGAATAAATTCACCAACAGAAGATCAGATTGTGAAGGTATTGGAGTTCATTGGAAAGAAAGAAGGGCTGCAACTTCCTTCGGGATTTGTTGCTCGTATAGCTGAAAAATCAAATAGGAGCTTAAGGAGAGCTATATTGTCATTGGAAACTTGTCGTGTTCAAGAGTATCCGTTTACAAGTAACCAGGCAATACCACCTATGGATTGGGAAGAATATGTTTCTGAAATTGCTTCTGATATAATGAAGGAGCAAAGCCCTAAAAGGCTTTATCAAGTGCGGCAAAAGTTGTATGAGCTGCTGCTTAATTGTATTCCTCCGGAGATCGTCTTGAAGAGACTTCTTTTTGAGTTATTGAAGAAGTTGGATGCGGAGTTGAAGCACGAGGTTTGTCATTGGGCTGCATATTATGAACATAGGATGCGTCTTGGGCAAAAAGCCATATTTCACCTTGAAGCGTTCGTGGCAAAGTTCATGAGCATTTATAAGGCTTTCCTCATCGAAGCGTTTGGCTGA

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

40.82

Weight (kDa)

9.2

Isoelectric Point (pI)

42.17

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Rad17	PF03215	2 - 62	1e-05	Rad17 P-loop domain
DNA_pol3_delta2	PF13177	19 - 188	2e-12	DNA polymerase III, delta subunit
AAA	PF00004	37 - 182	4.2e-06	ATPase family associated with various cellular activities (AAA)
RCF1-5-like_lid	PF21960	196 - 236	5.7e-11	RCF1/5-like, AAA+ ATPase lid domain
RFC_C	PF22534	253 - 342	3.3e-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)
AanI	TTATAA	1 cut(s)	1035
AccI	GTMKAC	1 cut(s)	12
AccII	CGCG	1 cut(s)	89
AccIII	TCCGGA	1 cut(s)	868
AciI	CCGC	3 cut(s)	89, 829, 920
AcsI	RAATTY	1 cut(s)	559
AcuI	CTGAAG	1 cut(s)	543
AfaI	GTAC	1 cut(s)	20
AfiI	CCNNNNNNNGG	1 cut(s)	40
AflII	CTTAAG	1 cut(s)	673
AjnI	CCWGG	2 cut(s)	39, 735
AluBI	AGCT	5 cut(s)	256, 653, 672, 683, 847
AluI	AGCT	5 cut(s)	256, 653, 672, 683, 847
Alw21I	GWGCWC	1 cut(s)	275
Alw26I	GTCTC	2 cut(s)	540, 880
Aor13HI	TCCGGA	1 cut(s)	868
AoxI	GGCC	1 cut(s)	121
ApeKI	GCWGC	5 cut(s)	439, 619, 847, 850, 950
ApoI	RAATTY	1 cut(s)	559
Asp700I	GAANNNNTTC	1 cut(s)	559
AspLEI	GCGC	1 cut(s)	439
AspS9I	GGNCC	2 cut(s)	122, 179
AsuHPI	GGTGA	3 cut(s)	208, 555, 989
AsuII	TTCGAA	1 cut(s)	451
AvaII	GGWCC	1 cut(s)	179
BarI	GAAGNNNNNNTAC	2 cut(s)	493, 525
BauI	CACGAG	1 cut(s)	932
Bbv12I	GWGCWC	1 cut(s)	275
BbvI	GCAGC	5 cut(s)	451, 606, 834, 837, 937
BcgI	CGANNNNNNTGC	2 cut(s)	431, 465
BciT130I	CCWGG	2 cut(s)	41, 737
BciVI	GTATCC	1 cut(s)	729
BcoDI	GTCTC	2 cut(s)	540, 880
BfaI	CTAG	2 cut(s)	35, 401
BfrI	CTTAAG	1 cut(s)	673
BfuI	GTATCC	1 cut(s)	729
BisI	GCNGC	6 cut(s)	440, 620, 830, 848, 851, 951
BlsI	GCNGC	6 cut(s)	441, 621, 831, 849, 852, 952
Bme1390I	CCNGG	2 cut(s)	41, 737
Bme18I	GGWCC	1 cut(s)	179
BmgT120I	GGNCC	2 cut(s)	122, 179
BmiI	GGNNCC	2 cut(s)	133, 181
BmrFI	CCNGG	2 cut(s)	41, 737
BmrI	ACTGGG	2 cut(s)	177, 291
BmsI	GCATC	4 cut(s)	217, 292, 907, 960
BmuI	ACTGGG	2 cut(s)	177, 291
Bpu14I	TTCGAA	1 cut(s)	451
BpuEI	CTTGAG	1 cut(s)	59
BsaI	GGTCTC	1 cut(s)	540
BsaWI	WCCGGW	1 cut(s)	868
Bsc4I	CCNNNNNNNGG	1 cut(s)	40
Bse118I	RCCGGY	1 cut(s)	483
Bse1I	ACTGG	2 cut(s)	183, 297
BseAI	TCCGGA	1 cut(s)	868
BseBI	CCWGG	2 cut(s)	41, 737
BseGI	GGATG	2 cut(s)	922, 975
BseLI	CCNNNNNNNGG	1 cut(s)	40
BseNI	ACTGG	2 cut(s)	183, 297
BseXI	GCAGC	5 cut(s)	451, 606, 834, 837, 937
BseYI	CCCAGC	1 cut(s)	230
Bsh1236I	CGCG	1 cut(s)	89
BshFI	GGCC	1 cut(s)	123
BsiHKAI	GWGCWC	1 cut(s)	275
BsiSI	CCGG	3 cut(s)	135, 484, 869
BslI	CCNNNNNNNGG	1 cut(s)	40
BsmAI	GTCTC	2 cut(s)	540, 880
BsmI	GAATGC	1 cut(s)	442
BsnI	GGCC	1 cut(s)	123
Bso31I	GGTCTC	1 cut(s)	540
Bsp119I	TTCGAA	1 cut(s)	451
Bsp1286I	GDGCHC	1 cut(s)	275
Bsp13I	TCCGGA	1 cut(s)	868
Bsp143I	GATC	2 cut(s)	574, 873
BspACI	CCGC	3 cut(s)	89, 829, 920
BspANI	GGCC	1 cut(s)	123
BspEI	TCCGGA	1 cut(s)	868
BspFNI	CGCG	1 cut(s)	89
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)	183, 297
BssAI	RCCGGY	1 cut(s)	483
BssMI	GATC	2 cut(s)	574, 873
BssSI	CACGAG	1 cut(s)	932
Bst2BI	CACGAG	1 cut(s)	932
Bst2UI	CCWGG	2 cut(s)	41, 737
Bst4CI	ACNGT	1 cut(s)	506
Bst6I	CTCTTC	2 cut(s)	453, 878
BstAFI	CTTAAG	1 cut(s)	673
BstBI	TTCGAA	1 cut(s)	451
BstC8I	GCNNGC	1 cut(s)	485
BstENI	CCTNNNNNAGG	1 cut(s)	38
BstF5I	GGATG	2 cut(s)	922, 975
BstFNI	CGCG	1 cut(s)	89
BstHHI	GCGC	1 cut(s)	439
BstKTI	GATC	2 cut(s)	577, 876
BstMAI	GTCTC	2 cut(s)	540, 880
BstMBI	GATC	2 cut(s)	574, 873
BstMWI	GCNNNNNNNGC	3 cut(s)	650, 979, 1013
BstNI	CCWGG	2 cut(s)	41, 737
BstSCI	CCNGG	2 cut(s)	39, 735
BstUI	CGCG	1 cut(s)	89
BstV1I	GCAGC	5 cut(s)	451, 606, 834, 837, 937
BsuI	GTATCC	1 cut(s)	729
BsuRI	GGCC	1 cut(s)	123
BtgZI	GCGATG	1 cut(s)	139
BtsCI	GGATG	2 cut(s)	922, 975
BtsIMutI	CAGTG	2 cut(s)	190, 304
Cac8I	GCNNGC	1 cut(s)	485
CciI	TCATGA	1 cut(s)	1023
CfoI	GCGC	1 cut(s)	439
Cfr10I	RCCGGY	1 cut(s)	483
Cfr13I	GGNCC	2 cut(s)	122, 179
CseI	GACGC	1 cut(s)	962
Csp6I	GTAC	1 cut(s)	19
CviAII	CATG	2 cut(s)	216, 1024
CviQI	GTAC	1 cut(s)	19
DpnI	GATC	2 cut(s)	576, 875
DpnII	GATC	2 cut(s)	574, 873
Eam1104I	CTCTTC	2 cut(s)	453, 878
EarI	CTCTTC	2 cut(s)	453, 878
Eco31I	GGTCTC	1 cut(s)	540
Eco32I	GATATC	1 cut(s)	61
Eco47I	GGWCC	1 cut(s)	179
Eco57I	CTGAAG	1 cut(s)	543
EcoNI	CCTNNNNNAGG	1 cut(s)	38
EcoRII	CCWGG	2 cut(s)	39, 735
EcoRV	GATATC	1 cut(s)	61
FaeI	CATG	2 cut(s)	219, 1027
FatI	CATG	2 cut(s)	215, 1023
FblI	GTMKAC	1 cut(s)	12
Fnu4HI	GCNGC	6 cut(s)	440, 620, 830, 848, 851, 951
FokI	GGATG	2 cut(s)	929, 982
Fsp4HI	GCNGC	6 cut(s)	440, 620, 830, 848, 851, 951
FspBI	CTAG	2 cut(s)	35, 401
GlaI	GCGC	1 cut(s)	438
GluI	GCNGC	6 cut(s)	440, 620, 830, 848, 851, 951
GsaI	CCCAGC	1 cut(s)	234
HaeIII	GGCC	1 cut(s)	123
HapII	CCGG	3 cut(s)	135, 484, 869
HgaI	GACGC	1 cut(s)	962
HhaI	GCGC	1 cut(s)	439
Hin1II	CATG	2 cut(s)	219, 1027
Hin6I	GCGC	1 cut(s)	437
HinP1I	GCGC	1 cut(s)	437
HincII	GTYRAC	2 cut(s)	13, 418
HindII	GTYRAC	2 cut(s)	13, 418
HpaII	CCGG	3 cut(s)	135, 484, 869
HphI	GGTGA	3 cut(s)	208, 555, 989
Hpy166II	GTNNAC	4 cut(s)	13, 52, 418, 726
Hpy188I	TCNGA	5 cut(s)	171, 179, 579, 775, 787
Hpy188III	TCNNGA	8 cut(s)	76, 314, 332, 633, 713, 869, 880, 1024
Hpy8I	GTNNAC	4 cut(s)	13, 52, 418, 726
HpyAV	CCTTC	7 cut(s)	135, 170, 193, 580, 608, 639, 790
HpyCH4III	ACNGT	1 cut(s)	506
HpyCH4V	TGCA	3 cut(s)	305, 622, 953
HpyF10VI	GCNNNNNNNGC	3 cut(s)	650, 979, 1013
Hsp92II	CATG	2 cut(s)	219, 1027
HspAI	GCGC	1 cut(s)	437
Kpn2I	TCCGGA	1 cut(s)	868
KroI	GCCGGC	1 cut(s)	483
KroNI	GCCGGC	1 cut(s)	485
Kzo9I	GATC	2 cut(s)	574, 873
LmnI	GCTCC	3 cut(s)	91, 669, 799
Lsp1109I	GCAGC	5 cut(s)	451, 606, 834, 837, 937
LweI	GCATC	4 cut(s)	217, 292, 907, 960
MaeI	CTAG	2 cut(s)	35, 401
MaeIII	GTNAC	3 cut(s)	500, 517, 731
MalI	GATC	2 cut(s)	576, 875
MboI	GATC	2 cut(s)	574, 873
MboII	GAAGA	8 cut(s)	155, 440, 465, 501, 584, 773, 895, 919
MfeI	CAATTG	1 cut(s)	45
MhlI	GDGCHC	1 cut(s)	275
MluCI	AATT	5 cut(s)	45, 339, 559, 777, 856
MmeI	TCCRAC	1 cut(s)	894
MnlI	CCTC	4 cut(s)	83, 876, 928, 1055
MroI	TCCGGA	1 cut(s)	868
MroNI	GCCGGC	1 cut(s)	483
MroXI	GAANNNNTTC	1 cut(s)	559
MseI	TTAA	4 cut(s)	342, 546, 674, 855
MspCI	CTTAAG	1 cut(s)	673
MspI	CCGG	3 cut(s)	135, 484, 869
MspR9I	CCNGG	2 cut(s)	41, 737
MunI	CAATTG	1 cut(s)	45
Mva1269I	GAATGC	1 cut(s)	442
MvaI	CCWGG	2 cut(s)	41, 737
MvnI	CGCG	1 cut(s)	89
MwoI	GCNNNNNNNGC	3 cut(s)	650, 979, 1013
NaeI	GCCGGC	1 cut(s)	485
NdeII	GATC	2 cut(s)	574, 873
NgoMIV	GCCGGC	1 cut(s)	483
NlaIII	CATG	2 cut(s)	219, 1027
NlaIV	GGNNCC	2 cut(s)	133, 181
NspV	TTCGAA	1 cut(s)	451
PagI	TCATGA	1 cut(s)	1023
PctI	GAATGC	1 cut(s)	442
PdiI	GCCGGC	1 cut(s)	485
PdmI	GAANNNNTTC	1 cut(s)	559
PkrI	GCNGC	6 cut(s)	441, 621, 831, 849, 852, 952
PsiI	TTATAA	1 cut(s)	1035
Psp6I	CCWGG	2 cut(s)	39, 735
PspFI	CCCAGC	1 cut(s)	230
PspGI	CCWGG	2 cut(s)	39, 735
PspN4I	GGNNCC	2 cut(s)	133, 181
PspPI	GGNCC	2 cut(s)	122, 179
RsaI	GTAC	1 cut(s)	20
RsaNI	GTAC	1 cut(s)	19
SalI	GTCGAC	1 cut(s)	11
SaqAI	TTAA	4 cut(s)	342, 546, 674, 855
SatI	GCNGC	6 cut(s)	440, 620, 830, 848, 851, 951
Sau3AI	GATC	2 cut(s)	574, 873
Sau96I	GGNCC	2 cut(s)	122, 179
ScrFI	CCNGG	2 cut(s)	41, 737
SduI	GDGCHC	1 cut(s)	275
SfaNI	GCATC	4 cut(s)	217, 292, 907, 960
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, 339, 559, 777, 856
SsiI	CCGC	3 cut(s)	89, 829, 920
SspMI	CTAG	2 cut(s)	35, 401
StyD4I	CCNGG	2 cut(s)	39, 735
TaaI	ACNGT	1 cut(s)	506
TaqI	TCGA	5 cut(s)	12, 225, 269, 451, 1050
TasI	AATT	5 cut(s)	45, 339, 559, 777, 856
TauI	GCSGC	1 cut(s)	832
Tru1I	TTAA	4 cut(s)	342, 546, 674, 855
Tru9I	TTAA	4 cut(s)	342, 546, 674, 855
TscAI	CASTG	2 cut(s)	190, 304
TseI	GCWGC	5 cut(s)	439, 619, 847, 850, 950
TspDTI	ATGAA	5 cut(s)	426, 589, 809, 975, 1012
TspGWI	ACGGA	1 cut(s)	711
TspRI	CASTG	2 cut(s)	190, 304
Vha464I	CTTAAG	1 cut(s)	673
VpaK11BI	GGWCC	1 cut(s)	179
XagI	CCTNNNNNAGG	1 cut(s)	38
XapI	RAATTY	1 cut(s)	559
XcmI	CCANNNNNNNNNTGG	1 cut(s)	753
XmiI	GTMKAC	1 cut(s)	12
XmnI	GAANNNNTTC	1 cut(s)	559
XspI	CTAG	2 cut(s)	35, 401

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