Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr05

Orthogroup ID

OG0004063

Physical Location & Seq

Genomic Coordinates Forward (+)

9110809 .. 9113767

Gene Structure 2959 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

MD05G1053400.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 789 bp

ATGGCGCCGCCGATCCCAGGTCTCGATATCTCTTACAGTAGCTTTCAAGGTGGGAAGGTGAAAGAGGTGCCAGTTATAAGAATATTCGGCGCCACGCCGGCTGGTCAGAAGACTTGCTTGTACATTCATACAGCACTACCGTACTTATATGTGCCATGCGCTGATATCCCGATTCAGCTGCACCAGAAAGGTGATTCATACGCACATGATGTAGCTCTTGCTATAAAGAAAGCTTTGAAGCTCAAAGGCAATGCTGGTTCAAGGCGACAACATGTACATGGTTGCAGCCTTGTCCAGGCAGGAAGCTTTATGGTTACCACTCATCGGAGATCTACTATCCCCATGATGTCTCTCGTGCTGCAAGTCTTCTTCTGTTTTCAGGGAAGCTCAGTTTTTGATAAATGCTTACAGCCTCATGAATCTCACATTCCCTTCATTCTTCAATTTATGGTTGACTACAACTTGTATGGGATGGGTCATCTACATGTATCAAAGATTAAATTCCATCATCCAATACCAGATGTTTTTGTCCATAGAAGGTCTGTTTACAATGGACAGCCTAGTCAGGTCATAGATAAAACGACTTGCACGTCTGCTGTTTTGCAGCATGATTACATACATGGCCATCTGTCTTTGGGTTCACCCGTTTGGATATCTTCCACAATTCCAGTTGACTGGACATGGAATTCTCCTGTTGAATTTGAAGGTTCCTCAGATCCAGGCATTAACTGCATTAAACGTCAAAGTATTTGTGAACTTGAGGGCGATTCTACTGTAGATGATTCTTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000731 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006139 GO:0006259 GO:0006281 GO:0006301 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009314 GO:0009411 GO:0009416 GO:0009628 GO:0009987 GO:0010225 GO:0016035 GO:0018130 GO:0019438 GO:0019985 GO:0032991 GO:0033554 GO:0034641 GO:0034644 GO:0034645 GO:0034654 GO:0042276 GO:0042575 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044446 GO:0044464 GO:0046483 GO:0050896 GO:0051716 GO:0061695 GO:0071214 GO:0071478 GO:0071482 GO:0071494 GO:0071704 GO:0071897 GO:0090304 GO:0104004 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko01100 ko01524 ko03460 map01100 map01524 map03460

Pfam Domains

Protein Families

DNA_pol_B DNA_pol_B_exo1 RVT_2 zf-C4pol zf-RanBP

Protein Analysis

263

Amino Acids

29.04

Weight (kDa)

7.69

Isoelectric Point (pI)

46.66

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
REV3_N	PF24065	17 - 43	1.4e-10	DNA polymerase zeta catalytic subunit, N-terminal
POL3_N	PF24055	45 - 103	4e-08	DNA polymerase delta catalytic subunit-like, N-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: OG0004063)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G67500 AT1G67500 AT1G67500 AT1G67500 AT1G67500 AT1G67500 AT1G67500
fragaria_vesca	FvH4_6g06120 FvH4_6g06120 FvH4_6g06120 FvH4_6g06120 FvH4_6g06120
malus_domestica	MD05G1053400.v1.1 MD05G1053600.v1.1 MD05G1053700.v1.1 MD12G1217900.v1.1
prunus_persica	Prupe.6G324000_v2.0.a1 Prupe.6G324000_v2.0.a1 Prupe.6G324000_v2.0.a1
pyrus_communis	pycom05g04420 pycom12g20340
rosa_chinensis	RchiOBHm_Chr3g0455131
rosa_laevigata	RLG00000025385
rosa_multiflora	Rmu_co8200746.1_g000001 Rmu_sc0041669.1_g000001
rosa_roxburghii	Rroxscaffold_6G00424540
rosa_rugosa	Rorug01G0381700 Rorug03G0004000
rosa_samantha	Rh3AG064900 Rh3BG066900 Rh3CG065300 Rh3DG066800
rosa_wichuraiana	Rw3G005080

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	77
AasI	GACNNNNNNGTC	2 cut(s)	561, 589
AccB1I	GGYRCC	3 cut(s)	4, 67, 89
AciI	CCGC	1 cut(s)	8
AclWI	GGATC	2 cut(s)	7, 710
AcoI	YGGCCR	1 cut(s)	622
AcsI	RAATTY	3 cut(s)	500, 685, 698
AcyI	GRCGYC	2 cut(s)	5, 90
AfaI	GTAC	3 cut(s)	122, 143, 276
AfiI	CCNNNNNNNGG	3 cut(s)	17, 295, 324
AflIII	ACRYGT	2 cut(s)	271, 484
AgsI	TTSAA	6 cut(s)	47, 238, 261, 443, 698, 704
AjiI	CACGTC	1 cut(s)	591
AjnI	CCWGG	3 cut(s)	16, 294, 718
AluBI	AGCT	7 cut(s)	42, 178, 215, 233, 241, 306, 387
AluI	AGCT	7 cut(s)	42, 178, 215, 233, 241, 306, 387
Alw26I	GTCTC	2 cut(s)	26, 354
AlwI	GGATC	2 cut(s)	7, 710
AoxI	GGCC	1 cut(s)	622
ApeKI	GCWGC	4 cut(s)	178, 285, 358, 604
ApoI	RAATTY	3 cut(s)	500, 685, 698
AspLEI	GCGC	3 cut(s)	7, 92, 161
AsuHPI	GGTGA	3 cut(s)	70, 203, 633
BalI	TGGCCA	1 cut(s)	624
BanI	GGYRCC	3 cut(s)	4, 67, 89
BauI	CACGAG	1 cut(s)	353
BbsI	GAAGAC	2 cut(s)	116, 358
BbvI	GCAGC	4 cut(s)	165, 297, 345, 616
BccI	CCATC	3 cut(s)	466, 513, 633
BcgI	CGANNNNNNTGC	2 cut(s)	160, 194
BciT130I	CCWGG	3 cut(s)	18, 296, 720
BcoDI	GTCTC	2 cut(s)	26, 354
BfaI	CTAG	1 cut(s)	561
BfmI	CTRYAG	1 cut(s)	774
BfoI	RGCGCY	2 cut(s)	8, 93
BglI	GCCNNNNNGGC	1 cut(s)	98
BglII	AGATCT	1 cut(s)	329
BisI	GCNGC	5 cut(s)	8, 179, 286, 359, 605
BlsI	GCNGC	5 cut(s)	9, 180, 287, 360, 606
Bme1390I	CCNGG	3 cut(s)	18, 296, 720
BmgBI	CACGTC	1 cut(s)	591
BmiI	GGNNCC	4 cut(s)	6, 69, 91, 709
BmrFI	CCNGG	3 cut(s)	18, 296, 720
BpiI	GAAGAC	2 cut(s)	116, 358
BpuEI	CTTGAG	1 cut(s)	779
BsaHI	GRCGYC	2 cut(s)	5, 90
BsaI	GGTCTC	1 cut(s)	26
BsaJI	CCNNGG	1 cut(s)	16
Bsc4I	CCNNNNNNNGG	3 cut(s)	17, 295, 324
Bse118I	RCCGGY	1 cut(s)	97
Bse1I	ACTGG	3 cut(s)	71, 668, 680
Bse3DI	GCAATG	1 cut(s)	256
BseBI	CCWGG	3 cut(s)	18, 296, 720
BseDI	CCNNGG	1 cut(s)	16
BseGI	GGATG	2 cut(s)	477, 508
BseLI	CCNNNNNNNGG	3 cut(s)	17, 295, 324
BseMI	GCAATG	1 cut(s)	256
BseMII	CTCAG	2 cut(s)	402, 726
BseNI	ACTGG	3 cut(s)	71, 668, 680
BseXI	GCAGC	4 cut(s)	165, 297, 345, 616
BsgI	GTGCAG	1 cut(s)	164
BshFI	GGCC	1 cut(s)	624
BshNI	GGYRCC	3 cut(s)	4, 67, 89
BsiSI	CCGG	1 cut(s)	98
BslI	CCNNNNNNNGG	3 cut(s)	17, 295, 324
BsmAI	GTCTC	2 cut(s)	26, 354
BsnI	GGCC	1 cut(s)	624
Bso31I	GGTCTC	1 cut(s)	26
Bsp1407I	TGTACA	2 cut(s)	120, 274
Bsp143I	GATC	3 cut(s)	12, 329, 715
BspACI	CCGC	1 cut(s)	8
BspANI	GGCC	1 cut(s)	624
BspCNI	CTCAG	2 cut(s)	401, 725
BspHI	TCATGA	1 cut(s)	415
BspLI	GGNNCC	4 cut(s)	6, 69, 91, 709
BspPI	GGATC	2 cut(s)	7, 710
BspT107I	GGYRCC	3 cut(s)	4, 67, 89
BspTNI	GGTCTC	1 cut(s)	26
BsrDI	GCAATG	1 cut(s)	256
BsrFI	RCCGGY	1 cut(s)	97
BsrGI	TGTACA	2 cut(s)	120, 274
BsrI	ACTGG	3 cut(s)	71, 668, 680
BssAI	RCCGGY	1 cut(s)	97
BssECI	CCNNGG	1 cut(s)	16
BssMI	GATC	3 cut(s)	12, 329, 715
BssNI	GRCGYC	2 cut(s)	5, 90
BssSI	CACGAG	1 cut(s)	353
Bst2BI	CACGAG	1 cut(s)	353
Bst2UI	CCWGG	3 cut(s)	18, 296, 720
Bst4CI	ACNGT	3 cut(s)	38, 141, 775
BstACI	GRCGYC	2 cut(s)	5, 90
BstAPI	GCANNNNNTGC	1 cut(s)	729
BstAUI	TGTACA	2 cut(s)	120, 274
BstC8I	GCNNGC	1 cut(s)	99
BstDEI	CTNAG	2 cut(s)	388, 712
BstEII	GGTNACC	1 cut(s)	313
BstENI	CCTNNNNNAGG	1 cut(s)	293
BstF5I	GGATG	2 cut(s)	477, 508
BstH2I	RGCGCY	2 cut(s)	8, 93
BstHHI	GCGC	3 cut(s)	7, 92, 161
BstKTI	GATC	3 cut(s)	15, 332, 718
BstMAI	GTCTC	2 cut(s)	26, 354
BstMBI	GATC	3 cut(s)	12, 329, 715
BstMWI	GCNNNNNNNGC	2 cut(s)	98, 729
BstNI	CCWGG	3 cut(s)	18, 296, 720
BstNSI	RCATGY	2 cut(s)	275, 488
BstPI	GGTNACC	1 cut(s)	313
BstSCI	CCNGG	3 cut(s)	16, 294, 718
BstSFI	CTRYAG	1 cut(s)	774
BstV1I	GCAGC	4 cut(s)	165, 297, 345, 616
BstV2I	GAAGAC	2 cut(s)	116, 358
BstX2I	RGATCY	2 cut(s)	329, 715
BstXI	CCANNNNNNTGG	1 cut(s)	675
BstYI	RGATCY	2 cut(s)	329, 715
BsuRI	GGCC	1 cut(s)	624
BtrI	CACGTC	1 cut(s)	591
BtsCI	GGATG	2 cut(s)	477, 508
Cac8I	GCNNGC	1 cut(s)	99
CciI	TCATGA	1 cut(s)	415
CfoI	GCGC	3 cut(s)	7, 92, 161
Cfr10I	RCCGGY	1 cut(s)	97
Csp6I	GTAC	3 cut(s)	121, 142, 275
CviQI	GTAC	3 cut(s)	121, 142, 275
DdeI	CTNAG	2 cut(s)	388, 712
DinI	GGCGCC	2 cut(s)	6, 91
DpnI	GATC	3 cut(s)	14, 331, 717
DpnII	GATC	3 cut(s)	12, 329, 715
DrdI	GACNNNNNNGTC	2 cut(s)	561, 589
DseDI	GACNNNNNNGTC	2 cut(s)	561, 589
EaeI	YGGCCR	1 cut(s)	622
Eco31I	GGTCTC	1 cut(s)	26
Eco32I	GATATC	3 cut(s)	28, 166, 654
Eco91I	GGTNACC	1 cut(s)	313
EcoNI	CCTNNNNNAGG	1 cut(s)	293
EcoO65I	GGTNACC	1 cut(s)	313
EcoRI	GAATTC	1 cut(s)	685
EcoRII	CCWGG	3 cut(s)	16, 294, 718
EcoRV	GATATC	3 cut(s)	28, 166, 654
EgeI	GGCGCC	2 cut(s)	6, 91
EheI	GGCGCC	2 cut(s)	6, 91
FalI	AAGNNNNNCTT	2 cut(s)	101, 133
Fnu4HI	GCNGC	5 cut(s)	8, 179, 286, 359, 605
FokI	GGATG	2 cut(s)	484, 495
Fsp4HI	GCNGC	5 cut(s)	8, 179, 286, 359, 605
FspBI	CTAG	1 cut(s)	561
GlaI	GCGC	3 cut(s)	6, 91, 160
GluI	GCNGC	5 cut(s)	8, 179, 286, 359, 605
HaeII	RGCGCY	2 cut(s)	8, 93
HaeIII	GGCC	1 cut(s)	624
HapII	CCGG	1 cut(s)	98
HhaI	GCGC	3 cut(s)	7, 92, 161
Hin1I	GRCGYC	2 cut(s)	5, 90
Hin6I	GCGC	3 cut(s)	5, 90, 159
HinP1I	GCGC	3 cut(s)	5, 90, 159
HincII	GTYRAC	2 cut(s)	454, 673
HindII	GTYRAC	2 cut(s)	454, 673
HindIII	AAGCTT	2 cut(s)	231, 304
HinfI	GANTC	5 cut(s)	172, 194, 419, 767, 782
HpaII	CCGG	1 cut(s)	98
HphI	GGTGA	3 cut(s)	70, 203, 633
Hpy166II	GTNNAC	5 cut(s)	454, 547, 641, 673, 755
Hpy188I	TCNGA	3 cut(s)	108, 327, 715
Hpy188III	TCNNGA	3 cut(s)	23, 169, 416
Hpy8I	GTNNAC	5 cut(s)	454, 547, 641, 673, 755
HpyAV	CCTTC	4 cut(s)	49, 442, 531, 698
HpyCH4III	ACNGT	3 cut(s)	38, 141, 775
HpyCH4IV	ACGT	2 cut(s)	590, 739
HpyCH4V	TGCA	6 cut(s)	181, 285, 361, 588, 604, 732
HpyF10VI	GCNNNNNNNGC	2 cut(s)	98, 729
HpyF3I	CTNAG	2 cut(s)	388, 712
HpySE526I	ACGT	2 cut(s)	590, 739
Hsp92I	GRCGYC	2 cut(s)	5, 90
HspAI	GCGC	3 cut(s)	5, 90, 159
KasI	GGCGCC	2 cut(s)	4, 89
KroI	GCCGGC	1 cut(s)	97
KroNI	GCCGGC	1 cut(s)	99
Kzo9I	GATC	3 cut(s)	12, 329, 715
Lsp1109I	GCAGC	4 cut(s)	165, 297, 345, 616
MaeI	CTAG	1 cut(s)	561
MaeII	ACGT	2 cut(s)	590, 739
MaeIII	GTNAC	1 cut(s)	313
MalI	GATC	3 cut(s)	14, 331, 717
MboI	GATC	3 cut(s)	12, 329, 715
MboII	GAAGA	5 cut(s)	121, 358, 361, 431, 648
MflI	RGATCY	2 cut(s)	329, 715
MlsI	TGGCCA	1 cut(s)	624
MluCI	AATT	5 cut(s)	443, 500, 663, 685, 698
MluNI	TGGCCA	1 cut(s)	624
Mly113I	GGCGCC	2 cut(s)	5, 90
MnlI	CCTC	4 cut(s)	58, 423, 721, 754
Mox20I	TGGCCA	1 cut(s)	624
MroNI	GCCGGC	1 cut(s)	97
MscI	TGGCCA	1 cut(s)	624
MseI	TTAA	4 cut(s)	498, 726, 735, 787
MslI	CAYNNNNRTG	2 cut(s)	276, 483
Msp20I	TGGCCA	1 cut(s)	624
MspA1I	CMGCKG	1 cut(s)	178
MspI	CCGG	1 cut(s)	98
MspR9I	CCNGG	3 cut(s)	18, 296, 720
MvaI	CCWGG	3 cut(s)	18, 296, 720
MwoI	GCNNNNNNNGC	2 cut(s)	98, 729
NaeI	GCCGGC	1 cut(s)	99
NarI	GGCGCC	2 cut(s)	5, 90
NdeII	GATC	3 cut(s)	12, 329, 715
NgoMIV	GCCGGC	1 cut(s)	97
NlaIV	GGNNCC	4 cut(s)	6, 69, 91, 709
NspI	RCATGY	2 cut(s)	275, 488
PagI	TCATGA	1 cut(s)	415
PciI	ACATGT	2 cut(s)	271, 484
PcsI	WCGNNNNNNNCGW	1 cut(s)	587
PdiI	GCCGGC	1 cut(s)	99
PfeI	GAWTC	5 cut(s)	172, 194, 419, 767, 782
PkrI	GCNGC	5 cut(s)	9, 180, 287, 360, 606
PluTI	GGCGCC	2 cut(s)	8, 93
PscI	ACATGT	2 cut(s)	271, 484
PsiI	TTATAA	1 cut(s)	77
Psp6I	CCWGG	3 cut(s)	16, 294, 718
PspEI	GGTNACC	1 cut(s)	313
PspGI	CCWGG	3 cut(s)	16, 294, 718
PspN4I	GGNNCC	4 cut(s)	6, 69, 91, 709
PsuI	RGATCY	2 cut(s)	329, 715
PvuII	CAGCTG	1 cut(s)	178
RsaI	GTAC	3 cut(s)	122, 143, 276
RsaNI	GTAC	3 cut(s)	121, 142, 275
RseI	CAYNNNNRTG	2 cut(s)	276, 483
SaqAI	TTAA	4 cut(s)	498, 726, 735, 787
SatI	GCNGC	5 cut(s)	8, 179, 286, 359, 605
Sau3AI	GATC	3 cut(s)	12, 329, 715
ScrFI	CCNGG	3 cut(s)	18, 296, 720
SfcI	CTRYAG	1 cut(s)	774
SfoI	GGCGCC	2 cut(s)	6, 91
SmiMI	CAYNNNNRTG	2 cut(s)	276, 483
SmlI	CTYRAG	1 cut(s)	758
SmoI	CTYRAG	1 cut(s)	758
Sse9I	AATT	5 cut(s)	443, 500, 663, 685, 698
SsiI	CCGC	1 cut(s)	8
SspDI	GGCGCC	2 cut(s)	4, 89
SspI	AATATT	1 cut(s)	84
SspMI	CTAG	1 cut(s)	561
StyD4I	CCNGG	3 cut(s)	16, 294, 718
TaaI	ACNGT	3 cut(s)	38, 141, 775
TaiI	ACGT	2 cut(s)	593, 742
TaqI	TCGA	1 cut(s)	24
TasI	AATT	5 cut(s)	443, 500, 663, 685, 698
TatI	WGTACW	2 cut(s)	120, 274
TauI	GCSGC	1 cut(s)	10
TfiI	GAWTC	5 cut(s)	172, 194, 419, 767, 782
Tru1I	TTAA	4 cut(s)	498, 726, 735, 787
Tru9I	TTAA	4 cut(s)	498, 726, 735, 787
TseI	GCWGC	4 cut(s)	178, 285, 358, 604
TspDTI	ATGAA	4 cut(s)	116, 186, 424, 432
XagI	CCTNNNNNAGG	1 cut(s)	293
XapI	RAATTY	3 cut(s)	500, 685, 698
XceI	RCATGY	2 cut(s)	275, 488
XspI	CTAG	1 cut(s)	561

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