Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr00

Orthogroup ID

OG0009947

Physical Location & Seq

Genomic Coordinates Reverse (-)

39303997 .. 39310160

Gene Structure 6164 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

MD00G1170800.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 690 bp

ATGGACGTGGAGGGAGAGCCGGCGAATGGGGAAACCAACGGGGAGATTCTGGGGCCTTGCCTGACCAGCCACATAGACGATGGTAGCGCAGAGAGCCACAGATACTACCTCTCACGGAGAACGGTGCTGGAGACGCTGAGGGACAGAGGCTATTCTGTTCCCGCCTCCGAAATCGACCTCTCTCTCCAAGACTTCCGCTTCCTCCACGGCCCCACTCCCGATATCGAGCGCCTACGCTTCTCCGCCACTCATTGCACCGACCCTTCTGACAGGATGCTGGTCATTTACTGTGGCCCTGGTATCGTGAAGGTTAATGTGATTCGTGGGCTACATTCTCAGATTGCTAATAAGGACACTTTGACGGGGCTCATGTTAATTACCCAAAACCAAGTAACAAACCAAGCTCTAAAAACTCTGGAACTTTATCCGTTTAAAACTGAAATATTCCAGATTACCGACTTGCTTGTTAACATCACGAAGCATGTCTTGAAGCCAAAGCATCAGGTGCTGACGGACAAAGAGAAAGGAAAACTCCTAAAGAAGTACAACGTAGAAGAAAAGCAGCTTCCTCGACTTTCACGAAAAGACGCAATTTCACGGTACCATGGACTTGAGAAGGGGCAGGTAGTGAAAGTTACTTGCACTGGTGATATTACCGAGTCTCATGTTACATACCGTTGCATCTGGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000418 GO:0000419 GO:0000428 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0005666 GO:0005730 GO:0005736 GO:0016591 GO:0030880 GO:0031974 GO:0031981 GO:0032991 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044452 GO:0044464 GO:0055029 GO:0061695 GO:0070013 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05016 ko05169 map00230 map00240 map01100 map03020 map04623 map05016 map05169

Pfam Domains

Protein Families

RNA_pol_Rpb5_C RNA_pol_Rpb5_N

Protein Analysis

230

Amino Acids

25.94

Weight (kDa)

7.69

Isoelectric Point (pI)

28.6

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	30 - 113	1.5e-19	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	156 - 228	3.9e-27	RNA polymerase Rpb5, C-terminal domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0009947)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G57080
fragaria_vesca	FvH4_6g25210
malus_domestica	MD00G1170800.v1.1 MD14G1084600.v1.1
prunus_persica	Prupe.7G043600_v2.0.a1 Prupe.7G043600_v2.0.a1 Prupe.7G043600_v2.0.a1
pyrus_communis	pycom12g07770 pycom14g07430
rosa_chinensis	RchiOBHm_Chr2g0125071
rosa_laevigata	RLG00000018847
rosa_multiflora	Rmu_sc0003505.1_g000022
rosa_roxburghii	Rroxscaffold_2G00118260 Rroxscaffold_2G00118720
rosa_rugosa	Rorug02G0255400 Rorug02G0255500.1
rosa_samantha	Rh2AG313900 Rh2BG322200 Rh2CG304500 Rh2DG340600
rosa_wichuraiana	Rw2G025400

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc36I	ACCTGC	1 cut(s)	613
Acc65I	GGTACC	1 cut(s)	600
AccB1I	GGYRCC	1 cut(s)	600
AciI	CCGC	3 cut(s)	162, 196, 243
AfaI	GTAC	2 cut(s)	545, 602
AfiI	CCNNNNNNNGG	1 cut(s)	26
AgsI	TTSAA	1 cut(s)	490
AjiI	CACGTC	1 cut(s)	7
AjnI	CCWGG	1 cut(s)	295
AluBI	AGCT	2 cut(s)	404, 565
AluI	AGCT	2 cut(s)	404, 565
Alw26I	GTCTC	2 cut(s)	125, 666
AlwNI	CAGNNNCTG	1 cut(s)	508
AoxI	GGCC	3 cut(s)	53, 208, 292
ApeKI	GCWGC	1 cut(s)	562
Asp718I	GGTACC	1 cut(s)	600
AspLEI	GCGC	2 cut(s)	89, 231
AspS9I	GGNCC	3 cut(s)	53, 209, 293
AsuHPI	GGTGA	1 cut(s)	659
BanI	GGYRCC	1 cut(s)	600
BanII	GRGCYC	1 cut(s)	369
BbvCI	CCTCAGC	1 cut(s)	137
BbvI	GCAGC	1 cut(s)	574
BccI	CCATC	1 cut(s)	74
BceAI	ACGGC	1 cut(s)	223
BcgI	CGANNNNNNTGC	2 cut(s)	551, 585
BciT130I	CCWGG	1 cut(s)	297
BcoDI	GTCTC	2 cut(s)	125, 666
BfoI	RGCGCY	1 cut(s)	232
BfuAI	ACCTGC	1 cut(s)	613
BisI	GCNGC	1 cut(s)	563
BlsI	GCNGC	1 cut(s)	564
Bme1390I	CCNGG	1 cut(s)	297
BmgBI	CACGTC	1 cut(s)	7
BmgT120I	GGNCC	3 cut(s)	53, 209, 293
BmiI	GGNNCC	3 cut(s)	54, 211, 602
BmrFI	CCNGG	1 cut(s)	297
BmsI	GCATC	2 cut(s)	264, 508
BpmI	CTGGAG	1 cut(s)	149
Bpu10I	CCTNAGC	1 cut(s)	137
BpuEI	CTTGAG	1 cut(s)	632
BsaJI	CCNNGG	3 cut(s)	205, 295, 604
Bsc4I	CCNNNNNNNGG	1 cut(s)	26
Bse118I	RCCGGY	1 cut(s)	19
Bse1I	ACTGG	1 cut(s)	649
Bse3DI	GCAATG	1 cut(s)	250
BseBI	CCWGG	1 cut(s)	297
BseDI	CCNNGG	3 cut(s)	205, 295, 604
BseGI	GGATG	1 cut(s)	279
BseLI	CCNNNNNNNGG	1 cut(s)	26
BseMI	GCAATG	1 cut(s)	250
BseMII	CTCAG	2 cut(s)	128, 350
BseNI	ACTGG	1 cut(s)	649
BseXI	GCAGC	1 cut(s)	574
BshFI	GGCC	3 cut(s)	55, 210, 294
BshNI	GGYRCC	1 cut(s)	600
BsiSI	CCGG	1 cut(s)	20
BslFI	GGGAC	1 cut(s)	155
BslI	CCNNNNNNNGG	1 cut(s)	26
BsmAI	GTCTC	2 cut(s)	125, 666
BsmBI	CGTCTC	1 cut(s)	125
BsmFI	GGGAC	1 cut(s)	155
BsnI	GGCC	3 cut(s)	55, 210, 294
Bsp1286I	GDGCHC	1 cut(s)	369
Bsp19I	CCATGG	1 cut(s)	604
BspACI	CCGC	3 cut(s)	162, 196, 243
BspANI	GGCC	3 cut(s)	55, 210, 294
BspCNI	CTCAG	2 cut(s)	129, 349
BspLI	GGNNCC	3 cut(s)	54, 211, 602
BspMI	ACCTGC	1 cut(s)	613
BspT107I	GGYRCC	1 cut(s)	600
BsrDI	GCAATG	1 cut(s)	250
BsrFI	RCCGGY	1 cut(s)	19
BsrI	ACTGG	1 cut(s)	649
BssAI	RCCGGY	1 cut(s)	19
BssECI	CCNNGG	3 cut(s)	205, 295, 604
BssT1I	CCWWGG	1 cut(s)	604
Bst2UI	CCWGG	1 cut(s)	297
Bst4CI	ACNGT	4 cut(s)	124, 290, 600, 677
BstAPI	GCANNNNNTGC	1 cut(s)	505
BstC8I	GCNNGC	1 cut(s)	21
BstDEI	CTNAG	2 cut(s)	137, 336
BstDSI	CCRYGG	2 cut(s)	205, 604
BstF5I	GGATG	1 cut(s)	279
BstH2I	RGCGCY	1 cut(s)	232
BstHHI	GCGC	2 cut(s)	89, 231
BstMAI	GTCTC	2 cut(s)	125, 666
BstMWI	GCNNNNNNNGC	4 cut(s)	66, 93, 133, 505
BstNI	CCWGG	1 cut(s)	297
BstNSI	RCATGY	1 cut(s)	485
BstSCI	CCNGG	1 cut(s)	295
BstV1I	GCAGC	1 cut(s)	574
BsuRI	GGCC	3 cut(s)	55, 210, 294
BtgI	CCRYGG	2 cut(s)	205, 604
BtrI	CACGTC	1 cut(s)	7
BtsCI	GGATG	1 cut(s)	279
BtsIMutI	CAGTG	1 cut(s)	642
BveI	ACCTGC	1 cut(s)	613
Cac8I	GCNNGC	1 cut(s)	21
CaiI	CAGNNNCTG	1 cut(s)	508
CfoI	GCGC	2 cut(s)	89, 231
Cfr10I	RCCGGY	1 cut(s)	19
Cfr13I	GGNCC	3 cut(s)	53, 209, 293
CseI	GACGC	2 cut(s)	142, 596
Csp6I	GTAC	2 cut(s)	544, 601
CviAII	CATG	4 cut(s)	370, 482, 605, 665
CviQI	GTAC	2 cut(s)	544, 601
DdeI	CTNAG	2 cut(s)	137, 336
DraI	TTTAAA	1 cut(s)	433
EciI	GGCGGA	1 cut(s)	232
Eco130I	CCWWGG	1 cut(s)	604
Eco24I	GRGCYC	1 cut(s)	369
Eco32I	GATATC	1 cut(s)	223
EcoO109I	RGGNCCY	1 cut(s)	53
EcoRII	CCWGG	1 cut(s)	295
EcoRV	GATATC	1 cut(s)	223
EcoT14I	CCWWGG	1 cut(s)	604
EcoT38I	GRGCYC	1 cut(s)	369
ErhI	CCWWGG	1 cut(s)	604
Esp3I	CGTCTC	1 cut(s)	125
FaeI	CATG	4 cut(s)	373, 485, 608, 668
FaiI	YATR	6 cut(s)	74, 371, 483, 606, 666, 673
FalI	AAGNNNNNCTT	2 cut(s)	470, 502
FaqI	GGGAC	1 cut(s)	155
FatI	CATG	4 cut(s)	369, 481, 604, 664
FauI	CCCGC	1 cut(s)	169
Fnu4HI	GCNGC	1 cut(s)	563
FokI	GGATG	1 cut(s)	286
FriOI	GRGCYC	1 cut(s)	369
Fsp4HI	GCNGC	1 cut(s)	563
GlaI	GCGC	2 cut(s)	88, 230
GluI	GCNGC	1 cut(s)	563
GsuI	CTGGAG	1 cut(s)	149
HaeII	RGCGCY	1 cut(s)	232
HaeIII	GGCC	3 cut(s)	55, 210, 294
HapII	CCGG	1 cut(s)	20
HgaI	GACGC	2 cut(s)	142, 596
HhaI	GCGC	2 cut(s)	89, 231
Hin1II	CATG	4 cut(s)	373, 485, 608, 668
Hin6I	GCGC	2 cut(s)	87, 229
HinP1I	GCGC	2 cut(s)	87, 229
HincII	GTYRAC	1 cut(s)	469
HindII	GTYRAC	1 cut(s)	469
HinfI	GANTC	3 cut(s)	46, 319, 659
HpaI	GTTAAC	1 cut(s)	469
HpaII	CCGG	1 cut(s)	20
HphI	GGTGA	1 cut(s)	659
Hpy166II	GTNNAC	1 cut(s)	469
Hpy188I	TCNGA	3 cut(s)	169, 268, 339
Hpy188III	TCNNGA	7 cut(s)	218, 304, 416, 448, 475, 487, 579
Hpy8I	GTNNAC	1 cut(s)	469
HpyAV	CCTTC	3 cut(s)	273, 301, 610
HpyCH4III	ACNGT	4 cut(s)	124, 290, 600, 677
HpyCH4IV	ACGT	2 cut(s)	6, 549
HpyCH4V	TGCA	3 cut(s)	255, 642, 681
HpyF10VI	GCNNNNNNNGC	4 cut(s)	66, 93, 133, 505
HpyF3I	CTNAG	2 cut(s)	137, 336
HpySE526I	ACGT	2 cut(s)	6, 549
Hsp92II	CATG	4 cut(s)	373, 485, 608, 668
HspAI	GCGC	2 cut(s)	87, 229
KpnI	GGTACC	1 cut(s)	604
KroI	GCCGGC	1 cut(s)	19
KroNI	GCCGGC	1 cut(s)	21
KspAI	GTTAAC	1 cut(s)	469
Lsp1109I	GCAGC	1 cut(s)	574
LweI	GCATC	2 cut(s)	264, 508
MaeII	ACGT	2 cut(s)	6, 549
MaeIII	GTNAC	3 cut(s)	391, 634, 667
MboII	GAAGA	1 cut(s)	566
MhlI	GDGCHC	1 cut(s)	369
MluCI	AATT	2 cut(s)	375, 591
MlyI	GAGTC	1 cut(s)	668
MnlI	CCTC	8 cut(s)	4, 119, 132, 140, 175, 188, 212, 579
MroNI	GCCGGC	1 cut(s)	19
MseI	TTAA	4 cut(s)	312, 374, 432, 468
MspI	CCGG	1 cut(s)	20
MspR9I	CCNGG	1 cut(s)	297
MvaI	CCWGG	1 cut(s)	297
MwoI	GCNNNNNNNGC	4 cut(s)	66, 93, 133, 505
NaeI	GCCGGC	1 cut(s)	21
NcoI	CCATGG	1 cut(s)	604
NgoMIV	GCCGGC	1 cut(s)	19
NlaIII	CATG	4 cut(s)	373, 485, 608, 668
NlaIV	GGNNCC	3 cut(s)	54, 211, 602
NspI	RCATGY	1 cut(s)	485
PcsI	WCGNNNNNNNCGW	1 cut(s)	577
PdiI	GCCGGC	1 cut(s)	21
PfeI	GAWTC	2 cut(s)	46, 319
PkrI	GCNGC	1 cut(s)	564
PleI	GAGTC	1 cut(s)	667
PpsI	GAGTC	1 cut(s)	667
Psp6I	CCWGG	1 cut(s)	295
PspGI	CCWGG	1 cut(s)	295
PspN4I	GGNNCC	3 cut(s)	54, 211, 602
PspPI	GGNCC	3 cut(s)	53, 209, 293
PstNI	CAGNNNCTG	1 cut(s)	508
RsaI	GTAC	2 cut(s)	545, 602
RsaNI	GTAC	2 cut(s)	544, 601
SaqAI	TTAA	4 cut(s)	312, 374, 432, 468
SatI	GCNGC	1 cut(s)	563
Sau96I	GGNCC	3 cut(s)	53, 209, 293
SchI	GAGTC	1 cut(s)	668
ScrFI	CCNGG	1 cut(s)	297
SduI	GDGCHC	1 cut(s)	369
SetI	ASST	9 cut(s)	9, 111, 180, 312, 406, 507, 552, 567, 627
SfaNI	GCATC	2 cut(s)	264, 508
SmlI	CTYRAG	1 cut(s)	611
SmoI	CTYRAG	1 cut(s)	611
Sse9I	AATT	2 cut(s)	375, 591
SsiI	CCGC	3 cut(s)	162, 196, 243
SspI	AATATT	1 cut(s)	444
StyD4I	CCNGG	1 cut(s)	295
StyI	CCWWGG	1 cut(s)	604
TaaI	ACNGT	4 cut(s)	124, 290, 600, 677
TaiI	ACGT	2 cut(s)	9, 552
TaqI	TCGA	3 cut(s)	174, 225, 571
TasI	AATT	2 cut(s)	375, 591
TatI	WGTACW	1 cut(s)	543
TfiI	GAWTC	2 cut(s)	46, 319
Tru1I	TTAA	4 cut(s)	312, 374, 432, 468
Tru9I	TTAA	4 cut(s)	312, 374, 432, 468
TscAI	CASTG	1 cut(s)	649
TseI	GCWGC	1 cut(s)	562
TspGWI	ACGGA	3 cut(s)	130, 417, 527
TspRI	CASTG	1 cut(s)	649
XceI	RCATGY	1 cut(s)	485
XcmI	CCANNNNNNNNNTGG	1 cut(s)	77

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