Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr01

Orthogroup ID

OG0003037

Physical Location & Seq

Genomic Coordinates Forward (+)

28033325 .. 28037281

Gene Structure 3957 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

MD01G1181300.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 981 bp

ATGGACAACGACGATCCCTTTCACCGTCGCAGAAGGTTCATTCCCAGAGTCCAGCCACGCAAGAAGCTTGGATCAACTGCCCCCACTCCCGACGTCGGTGACGGCGGCGATGGTGGTCAAGGAACTCGCCGGGCCCAGACTCTGCTGAGTCAGCACAATGAGAGAAGACGGGGAGTCGAAAAGAAATCTTCACTGCAAGTTGCATTTGGTCCTGGAGGAGCAGGTGCGTCCTCAACTTCTATCAGAACATTTGGAGCTGCAAAGGGTGGCGATGATGGTAAAAGCGGCAGCGTAGTTCTCAAAGACTCAAATGATGATGAGCAAAACCTCTCAACTCTGCCTTCAGCCTCTACTAAAGCTGAAACGGATGTAACCATGGAAGATGCTATCGATCCAGAAGCAGAACCACTTCAGGGTGTCAAGAATACAGAATGTTGGGATTATGAGAACACATACTATCCTACTACTCTTCCTCTCAGGCAACCCAACTCTGGAGACCCAGAAATCCTTAATGAGAATGAATTTGGGGAGGATGCTGAAAAAGAGTATGATGAGAACACTATAAACCCTGCTTCAGAACTCGGGCTGCTGGAGGAAAAAGAGCAAGCGAAGTTGTTATTCATTCAACTTCCTTCCATTTTGCCATCGACATCGAAGCCAGCAGCTACTGCAAAGGGCAAAGAGAAAGTTGGAAGCTCAACATCACTGGAGAGCACAGGTGCTCCAGAGAAGGGATGCAGTTTGGAAGAGTTGCCTGCCGGATATATGGGTAAAATGCTAGTTTCCAAGAGCGGAAAAGTCAAGCTGAGGCTAGGAGATACCTTCTATGATGTTGCACCTGGTTCAGATAGCAAGTTTGATCAAGATGTTGCGGTAGCCAACACTGTAGAGAAGAAATGCACCGTTCTCGGAGAGCTACGCCAGCGAGCTGTTGTAATTCCTGATGTGGATTCCCTCCTAAATGTGATTAACAGGAATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0001817 GO:0001819 GO:0002682 GO:0002684 GO:0003674 GO:0003682 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005737 GO:0005829 GO:0008150 GO:0016604 GO:0016607 GO:0030880 GO:0031347 GO:0031349 GO:0031974 GO:0031981 GO:0032479 GO:0032481 GO:0032648 GO:0032728 GO:0032991 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0045088 GO:0045089 GO:0048518 GO:0048583 GO:0048584 GO:0050776 GO:0050778 GO:0050789 GO:0051239 GO:0051240 GO:0055029 GO:0061695 GO:0065007 GO:0070013 GO:0080134 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05169 map00230 map00240 map01100 map03020 map04623 map05169

Pfam Domains

Protein Families

RNA_pol_Rpc4

Protein Analysis

327

Amino Acids

35.09

Weight (kDa)

4.96

Isoelectric Point (pI)

51.98

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpc4	PF05132	203 - 316	1.1e-25	RNA polymerase III RPC4

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: OG0003037)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G09380 AT5G09380 AT5G09380
fragaria_vesca	FvH4_1g08400 FvH4_1g08400 FvH4_7g27240 FvH4_7g27240
malus_domestica	MD01G1181300.v1.1 MD02G1088300.v1.1 MD07G1251400.v1.1
prunus_persica	Prupe.2G275200_v2.0.a1 Prupe.7G201300_v2.0.a1
pyrus_communis	pycom02g07090 pycom07g22410
rosa_chinensis	RchiOBHm_Chr1g0374021 RchiOBHm_Chr2g0094511 RchiOBHm_Chr3g0487921
rosa_laevigata	RLG00000016497 RLG00000026785
rosa_multiflora	Rmu_sc0004359.1_g000044 Rmu_sc0006924.1_g000006 Rmu_sc0009793.1_g000002
rosa_roxburghii	Rroxscaffold_2G00147110 Rroxscaffold_4G00283820
rosa_rugosa	Rorug01G0380300 Rorug02G0044300.1
rosa_samantha	Rh1AG390800 Rh1BG354900 Rh1CG368000 Rh1DG385600 Rh2AG092600 Rh2BG092800 Rh2CG095300 Rh2DG091700 Rh3AG285100 Rh6AG149200
rosa_wichuraiana	Rw1G034440 Rw6G012910

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	212
AatII	GACGTC	1 cut(s)	96
Acc36I	ACCTGC	1 cut(s)	212
AccBSI	CCGCTC	1 cut(s)	792
AciI	CCGC	4 cut(s)	105, 285, 792, 872
AclWI	GGATC	3 cut(s)	8, 79, 386
AcsI	RAATTY	1 cut(s)	521
AcuI	CTGAAG	3 cut(s)	327, 395, 558
AcyI	GRCGYC	1 cut(s)	93
AfiI	CCNNNNNNNGG	4 cut(s)	95, 413, 491, 731
AgsI	TTSAA	1 cut(s)	626
AhdI	GACNNNNNGTC	1 cut(s)	173
AjnI	CCWGG	2 cut(s)	211, 838
AluBI	AGCT	8 cut(s)	67, 257, 359, 665, 696, 805, 916, 929
AluI	AGCT	8 cut(s)	67, 257, 359, 665, 696, 805, 916, 929
Alw21I	GWGCWC	2 cut(s)	716, 724
Alw26I	GTCTC	1 cut(s)	489
AlwI	GGATC	3 cut(s)	8, 79, 386
AlwNI	CAGNNNCTG	2 cut(s)	142, 668
Ama87I	CYCGRG	1 cut(s)	581
AoxI	GGCC	1 cut(s)	132
ApaI	GGGCCC	1 cut(s)	136
ApeKI	GCWGC	4 cut(s)	257, 288, 586, 662
ApoI	RAATTY	1 cut(s)	521
Asp700I	GAANNNNTTC	1 cut(s)	408
AspS9I	GGNCC	3 cut(s)	132, 133, 209
AsuC2I	CCSGG	1 cut(s)	131
AsuHPI	GGTGA	2 cut(s)	14, 110
AvaI	CYCGRG	1 cut(s)	581
AvaII	GGWCC	1 cut(s)	209
BaeGI	GKGCMC	1 cut(s)	136
BanII	GRGCYC	1 cut(s)	136
BbsI	GAAGAC	1 cut(s)	172
Bbv12I	GWGCWC	2 cut(s)	716, 724
BbvCI	CCTCAGC	1 cut(s)	806
BbvI	GCAGC	4 cut(s)	244, 300, 573, 674
BccI	CCATC	3 cut(s)	104, 269, 652
BceAI	ACGGC	1 cut(s)	118
BcgI	CGANNNNNNTGC	2 cut(s)	889, 923
BciT130I	CCWGG	2 cut(s)	213, 840
BclI	TGATCA	1 cut(s)	859
BcnI	CCSGG	1 cut(s)	131
BcoDI	GTCTC	1 cut(s)	489
BfaI	CTAG	2 cut(s)	779, 812
BfmI	CTRYAG	1 cut(s)	885
BfuAI	ACCTGC	1 cut(s)	212
BisI	GCNGC	6 cut(s)	106, 258, 286, 289, 587, 663
BlsI	GCNGC	6 cut(s)	107, 259, 287, 290, 588, 664
Bme1390I	CCNGG	3 cut(s)	131, 213, 840
Bme18I	GGWCC	1 cut(s)	209
BmeRI	GACNNNNNGTC	1 cut(s)	173
BmeT110I	CYCGRG	1 cut(s)	581
BmgT120I	GGNCC	3 cut(s)	132, 133, 209
BmiI	GGNNCC	1 cut(s)	134
BmrFI	CCNGG	3 cut(s)	131, 213, 840
BmsI	GCATC	3 cut(s)	373, 523, 725
BpiI	GAAGAC	1 cut(s)	172
BpmI	CTGGAG	5 cut(s)	234, 513, 611, 708, 728
Bpu10I	CCTNAGC	1 cut(s)	806
BpuMI	CCSGG	1 cut(s)	131
Bsa29I	ATCGAT	1 cut(s)	390
BsaHI	GRCGYC	1 cut(s)	93
BsaI	GGTCTC	1 cut(s)	489
BsaJI	CCNNGG	1 cut(s)	375
BsaXI	ACNNNNNCTCC	2 cut(s)	706, 736
Bsc4I	CCNNNNNNNGG	4 cut(s)	95, 413, 491, 731
Bse1I	ACTGG	1 cut(s)	711
BseBI	CCWGG	2 cut(s)	213, 840
BseCI	ATCGAT	1 cut(s)	390
BseDI	CCNNGG	1 cut(s)	375
BseGI	GGATG	3 cut(s)	373, 538, 740
BseLI	CCNNNNNNNGG	4 cut(s)	95, 413, 491, 731
BseMII	CTCAG	3 cut(s)	137, 490, 797
BseNI	ACTGG	1 cut(s)	711
BseRI	GAGGAG	1 cut(s)	231
BseSI	GKGCMC	1 cut(s)	136
BseXI	GCAGC	4 cut(s)	244, 300, 573, 674
BshFI	GGCC	1 cut(s)	134
BshVI	ATCGAT	1 cut(s)	390
BsiHKAI	GWGCWC	2 cut(s)	716, 724
BsiHKCI	CYCGRG	1 cut(s)	581
BsiSI	CCGG	2 cut(s)	130, 759
BslI	CCNNNNNNNGG	4 cut(s)	95, 413, 491, 731
BsmAI	GTCTC	1 cut(s)	489
BsnI	GGCC	1 cut(s)	134
Bso31I	GGTCTC	1 cut(s)	489
BsoBI	CYCGRG	1 cut(s)	581
Bsp120I	GGGCCC	1 cut(s)	132
Bsp1286I	GDGCHC	3 cut(s)	136, 716, 724
Bsp143I	GATC	4 cut(s)	13, 71, 391, 859
Bsp19I	CCATGG	1 cut(s)	375
BspACI	CCGC	4 cut(s)	105, 285, 792, 872
BspANI	GGCC	1 cut(s)	134
BspCNI	CTCAG	3 cut(s)	138, 489, 798
BspDI	ATCGAT	1 cut(s)	390
BspLI	GGNNCC	1 cut(s)	134
BspMI	ACCTGC	1 cut(s)	212
BspPI	GGATC	3 cut(s)	8, 79, 386
BspTNI	GGTCTC	1 cut(s)	489
BsrBI	CCGCTC	1 cut(s)	792
BsrI	ACTGG	1 cut(s)	711
BssECI	CCNNGG	1 cut(s)	375
BssMI	GATC	4 cut(s)	13, 71, 391, 859
BssNI	GRCGYC	1 cut(s)	93
BssT1I	CCWWGG	1 cut(s)	375
Bst2UI	CCWGG	2 cut(s)	213, 840
Bst4CI	ACNGT	3 cut(s)	26, 886, 904
Bst6I	CTCTTC	2 cut(s)	474, 741
BstACI	GRCGYC	1 cut(s)	93
BstAPI	GCANNNNNTGC	1 cut(s)	668
BstC8I	GCNNGC	5 cut(s)	606, 660, 756, 923, 927
BstDEI	CTNAG	3 cut(s)	146, 476, 806
BstDSI	CCRYGG	1 cut(s)	375
BstF5I	GGATG	3 cut(s)	373, 538, 740
BstKTI	GATC	4 cut(s)	16, 74, 394, 862
BstMAI	GTCTC	1 cut(s)	489
BstMBI	GATC	4 cut(s)	13, 71, 391, 859
BstMWI	GCNNNNNNNGC	3 cut(s)	151, 668, 922
BstNI	CCWGG	2 cut(s)	213, 840
BstSCI	CCNGG	3 cut(s)	129, 211, 838
BstSFI	CTRYAG	1 cut(s)	885
BstSLI	GKGCMC	1 cut(s)	136
BstV1I	GCAGC	4 cut(s)	244, 300, 573, 674
BstV2I	GAAGAC	1 cut(s)	172
Bsu15I	ATCGAT	1 cut(s)	390
BsuRI	GGCC	1 cut(s)	134
BsuTUI	ATCGAT	1 cut(s)	390
BtgI	CCRYGG	1 cut(s)	375
BtgZI	GCGATG	2 cut(s)	123, 285
BtsCI	GGATG	3 cut(s)	373, 538, 740
BtsI	GCAGTG	1 cut(s)	191
BtsIMutI	CAGTG	3 cut(s)	191, 704, 882
BveI	ACCTGC	1 cut(s)	212
Cac8I	GCNNGC	5 cut(s)	606, 660, 756, 923, 927
CaiI	CAGNNNCTG	2 cut(s)	142, 668
Cfr13I	GGNCC	3 cut(s)	132, 133, 209
ClaI	ATCGAT	1 cut(s)	390
CseI	GACGC	1 cut(s)	216
CsiI	ACCWGGT	1 cut(s)	838
CviAII	CATG	1 cut(s)	376
DdeI	CTNAG	3 cut(s)	146, 476, 806
DpnI	GATC	4 cut(s)	15, 73, 393, 861
DpnII	GATC	4 cut(s)	13, 71, 391, 859
DriI	GACNNNNNGTC	1 cut(s)	173
Eam1104I	CTCTTC	2 cut(s)	474, 741
Eam1105I	GACNNNNNGTC	1 cut(s)	173
EarI	CTCTTC	2 cut(s)	474, 741
Eco130I	CCWWGG	1 cut(s)	375
Eco24I	GRGCYC	1 cut(s)	136
Eco31I	GGTCTC	1 cut(s)	489
Eco47I	GGWCC	1 cut(s)	209
Eco57I	CTGAAG	3 cut(s)	327, 395, 558
Eco88I	CYCGRG	1 cut(s)	581
EcoRII	CCWGG	2 cut(s)	211, 838
EcoT14I	CCWWGG	1 cut(s)	375
EcoT38I	GRGCYC	1 cut(s)	136
ErhI	CCWWGG	1 cut(s)	375
FaeI	CATG	1 cut(s)	379
FaiI	YATR	8 cut(s)	377, 444, 454, 549, 563, 765, 767, 828
FatI	CATG	1 cut(s)	375
FbaI	TGATCA	1 cut(s)	859
Fnu4HI	GCNGC	6 cut(s)	106, 258, 286, 289, 587, 663
FokI	GGATG	3 cut(s)	380, 545, 747
FriOI	GRGCYC	1 cut(s)	136
Fsp4HI	GCNGC	6 cut(s)	106, 258, 286, 289, 587, 663
FspBI	CTAG	2 cut(s)	779, 812
GluI	GCNGC	6 cut(s)	106, 258, 286, 289, 587, 663
GsuI	CTGGAG	5 cut(s)	234, 513, 611, 708, 728
HaeIII	GGCC	1 cut(s)	134
HapII	CCGG	2 cut(s)	130, 759
HgaI	GACGC	1 cut(s)	216
Hin1I	GRCGYC	1 cut(s)	93
Hin1II	CATG	1 cut(s)	379
HindIII	AAGCTT	1 cut(s)	65
HinfI	GANTC	6 cut(s)	48, 139, 148, 174, 305, 950
HpaII	CCGG	2 cut(s)	130, 759
HphI	GGTGA	2 cut(s)	14, 110
Hpy188I	TCNGA	4 cut(s)	245, 577, 847, 911
Hpy188III	TCNNGA	7 cut(s)	89, 395, 421, 492, 725, 863, 941
Hpy99I	CGWCG	4 cut(s)	14, 30, 95, 98
HpyAV	CCTTC	5 cut(s)	27, 351, 642, 724, 832
HpyCH4III	ACNGT	3 cut(s)	26, 886, 904
HpyCH4IV	ACGT	1 cut(s)	93
HpyCH4V	TGCA	7 cut(s)	196, 203, 260, 671, 738, 836, 900
HpyF10VI	GCNNNNNNNGC	3 cut(s)	151, 668, 922
HpyF3I	CTNAG	3 cut(s)	146, 476, 806
HpySE526I	ACGT	1 cut(s)	93
Hsp92I	GRCGYC	1 cut(s)	93
Hsp92II	CATG	1 cut(s)	379
Ksp22I	TGATCA	1 cut(s)	859
Kzo9I	GATC	4 cut(s)	13, 71, 391, 859
LmnI	GCTCC	3 cut(s)	218, 254, 727
Lsp1109I	GCAGC	4 cut(s)	244, 300, 573, 674
LweI	GCATC	3 cut(s)	373, 523, 725
MabI	ACCWGGT	1 cut(s)	838
MaeI	CTAG	2 cut(s)	779, 812
MaeII	ACGT	1 cut(s)	93
MaeIII	GTNAC	2 cut(s)	98, 370
MalI	GATC	4 cut(s)	15, 73, 393, 861
MbiI	CCGCTC	1 cut(s)	792
MboI	GATC	4 cut(s)	13, 71, 391, 859
MboII	GAAGA	6 cut(s)	177, 180, 392, 461, 758, 904
MhlI	GDGCHC	3 cut(s)	136, 716, 724
MluCI	AATT	3 cut(s)	521, 936, 976
MlyI	GAGTC	5 cut(s)	57, 133, 157, 183, 299
MmeI	TCCRAC	1 cut(s)	670
MnlI	CCTC	9 cut(s)	209, 241, 338, 358, 483, 523, 586, 801, 965
MroXI	GAANNNNTTC	1 cut(s)	408
MseI	TTAA	2 cut(s)	510, 969
MspI	CCGG	2 cut(s)	130, 759
MspR9I	CCNGG	3 cut(s)	131, 213, 840
MvaI	CCWGG	2 cut(s)	213, 840
MwoI	GCNNNNNNNGC	3 cut(s)	151, 668, 922
NciI	CCSGG	1 cut(s)	131
NcoI	CCATGG	1 cut(s)	375
NdeII	GATC	4 cut(s)	13, 71, 391, 859
NlaIII	CATG	1 cut(s)	379
NlaIV	GGNNCC	1 cut(s)	134
NmuCI	GTSAC	1 cut(s)	98
PaqCI	CACCTGC	1 cut(s)	212
PdmI	GAANNNNTTC	1 cut(s)	408
PfeI	GAWTC	1 cut(s)	950
PfoI	TCCNGGA	1 cut(s)	211
PkrI	GCNGC	6 cut(s)	107, 259, 287, 290, 588, 664
PleI	GAGTC	5 cut(s)	56, 133, 156, 182, 299
PpsI	GAGTC	5 cut(s)	56, 133, 156, 182, 299
Psp6I	CCWGG	2 cut(s)	211, 838
PspGI	CCWGG	2 cut(s)	211, 838
PspN4I	GGNNCC	1 cut(s)	134
PspOMI	GGGCCC	1 cut(s)	132
PspPI	GGNCC	3 cut(s)	132, 133, 209
PstNI	CAGNNNCTG	2 cut(s)	142, 668
SaqAI	TTAA	2 cut(s)	510, 969
SatI	GCNGC	6 cut(s)	106, 258, 286, 289, 587, 663
Sau3AI	GATC	4 cut(s)	13, 71, 391, 859
Sau96I	GGNCC	3 cut(s)	132, 133, 209
SchI	GAGTC	5 cut(s)	57, 133, 157, 183, 299
ScrFI	CCNGG	3 cut(s)	131, 213, 840
SduI	GDGCHC	3 cut(s)	136, 716, 724
SexAI	ACCWGGT	1 cut(s)	838
SfaNI	GCATC	3 cut(s)	373, 523, 725
SfcI	CTRYAG	1 cut(s)	885
SinI	GGWCC	1 cut(s)	209
Sse9I	AATT	3 cut(s)	521, 936, 976
SsiI	CCGC	4 cut(s)	105, 285, 792, 872
SspMI	CTAG	2 cut(s)	779, 812
StyD4I	CCNGG	3 cut(s)	129, 211, 838
StyI	CCWWGG	1 cut(s)	375
TaaI	ACNGT	3 cut(s)	26, 886, 904
TaiI	ACGT	1 cut(s)	96
TaqI	TCGA	4 cut(s)	177, 390, 647, 653
TasI	AATT	3 cut(s)	521, 936, 976
TauI	GCSGC	2 cut(s)	108, 288
TfiI	GAWTC	1 cut(s)	950
Tru1I	TTAA	2 cut(s)	510, 969
Tru9I	TTAA	2 cut(s)	510, 969
TscAI	CASTG	3 cut(s)	198, 711, 889
TseFI	GTSAC	1 cut(s)	98
TseI	GCWGC	4 cut(s)	257, 288, 586, 662
Tsp45I	GTSAC	1 cut(s)	98
TspDTI	ATGAA	3 cut(s)	28, 534, 610
TspGWI	ACGGA	1 cut(s)	380
TspRI	CASTG	3 cut(s)	198, 711, 889
VpaK11BI	GGWCC	1 cut(s)	209
XapI	RAATTY	1 cut(s)	521
XmnI	GAANNNNTTC	1 cut(s)	408
XspI	CTAG	2 cut(s)	779, 812
ZraI	GACGTC	1 cut(s)	94

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