Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr06

Orthogroup ID

OG0002992

Physical Location & Seq

Genomic Coordinates Forward (+)

16763544 .. 16764455

Gene Structure 912 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

MD06G1069400.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 777 bp

ATGGCAATAATTAAAGCTCCTTCACTTAATAACACTGCTTGGATTGGAAAGCAAGTATTCAGCATGCTCCTACCTTCAGGTTTTTATTATGATTTTGCTCCAGATGGAGTTTGTATTCGAAATGGGGAGCTGCTATCCTCTGAAGGTTCTTCGTGGTTGCGAGATATGAGTGGAAATCTTTATCAGAGTCTCGTTAAACATTGCCAGGGTCAGGTACTTGACTTCCTACATGCTGCTCAGGAAGTTTTTTGTGAGTGGTTGTCAATGATGGGTTTGACTGTCTCTCTCTCGGACTTATACCTCACTTCTGACTCATGCTCAAGGAATAACTTGATGGAGGAAATTTTCTGTGGGTTGAGAGAAGCAGAGCAGGTACGTATATTTAAACAGTTGTTGGTGGATAGTAGTCGGGAACTTCTTATGGGATGTGCTGAAGAGAATCAAAGTCTCGTGACTTCGGATGTCGACTACTTCTGTCACGAGAAGCAGAAGTCTGCTGCCCTTAGTCAGGCTGGAAGTAAGGGTAACATACAGAAATTAGTGCTACACAGTATGTGCCTTGGTTTGCAAAACTCACTAGATCCATTATCTTTCAGAATTCCGAACCAGTTGTCGTGTGCTGCGTGGAATAATCAAAAGGTAATCAGTTCAGATCAGAAGGTTGAGGGAAGTGCTGAATGCGTTGAGTCCTACATCCCATCTGCTGTGGTTGAAAGCTCTTTCTTGACAGGCTTAAATCCGTTAGAATTGGAAATGCTGATCTTCCTGGGACTTTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000418 GO:0000428 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0006139 GO:0006396 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009892 GO:0009987 GO:0010033 GO:0010467 GO:0010468 GO:0010495 GO:0010605 GO:0010608 GO:0010629 GO:0014070 GO:0016070 GO:0016246 GO:0016441 GO:0016458 GO:0019222 GO:0030422 GO:0030880 GO:0031047 GO:0031050 GO:0031974 GO:0031981 GO:0032991 GO:0034641 GO:0035194 GO:0040029 GO:0042221 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0043331 GO:0044237 GO:0044238 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0046483 GO:0048519 GO:0050789 GO:0050896 GO:0051716 GO:0055029 GO:0060255 GO:0061695 GO:0065007 GO:0070013 GO:0070887 GO:0070918 GO:0071310 GO:0071359 GO:0071407 GO:0071704 GO:0090304 GO:1901360 GO:1901698 GO:1901699 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

DUF3223 RNA_pol_Rpb1_1 RNA_pol_Rpb1_2 RNA_pol_Rpb1_3 RNA_pol_Rpb1_4 RNA_pol_Rpb1_5

Protein Analysis

259

Amino Acids

28.55

Weight (kDa)

4.73

Isoelectric Point (pI)

42.4

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb1_3	PF04983	12 - 99	4.9e-11	RNA polymerase Rpb1, domain 3

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: OG0002992)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G63020 AT1G63020 AT1G63020 AT1G63020 AT1G63020
fragaria_vesca	FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400
malus_domestica	MD04G1068800.v1.1 MD06G1069300.v1.1 MD06G1069400.v1.1 MD06G1069500.v1.1 MD06G1069800.v1.1
prunus_persica	Prupe.5G089300_v2.0.a1
pyrus_communis	pycom04g06250
rosa_chinensis	RchiOBHm_Chr7g0199481
rosa_laevigata	RLG00000003790
rosa_multiflora	Rmu_co8411067.1_g000001 Rmu_sc0003890.1_g000001
rosa_roxburghii	Rroxscaffold_3G00256700
rosa_rugosa	Rorug07G0054300 Rorug07G0054400 Rorug07G0054500 Rorug07G0054500
rosa_samantha	Rh7AG179300 Rh7BG182800 Rh7CG188100 Rh7DG182200
rosa_wichuraiana	Rw7G015760

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc36I	ACCTGC	1 cut(s)	361
AccI	GTMKAC	1 cut(s)	465
AclWI	GGATC	1 cut(s)	575
AcsI	RAATTY	2 cut(s)	342, 597
AcuI	CTGAAG	3 cut(s)	60, 162, 453
AfaI	GTAC	2 cut(s)	216, 375
AfiI	CCNNNNNNNGG	2 cut(s)	211, 508
AgsI	TTSAA	1 cut(s)	713
AjnI	CCWGG	2 cut(s)	204, 765
AluBI	AGCT	3 cut(s)	17, 130, 717
AluI	AGCT	3 cut(s)	17, 130, 717
Alw26I	GTCTC	3 cut(s)	194, 286, 452
AlwI	GGATC	1 cut(s)	575
ApeKI	GCWGC	4 cut(s)	130, 233, 497, 620
ApoI	RAATTY	2 cut(s)	342, 597
ArsI	GACNNNNNNTTYG	2 cut(s)	596, 628
AsuII	TTCGAA	1 cut(s)	118
BauI	CACGAG	2 cut(s)	449, 479
BbvI	GCAGC	4 cut(s)	117, 220, 484, 607
BccI	CCATC	4 cut(s)	98, 262, 328, 706
BciT130I	CCWGG	2 cut(s)	206, 767
BcoDI	GTCTC	3 cut(s)	194, 286, 452
BfaI	CTAG	1 cut(s)	578
BfuAI	ACCTGC	1 cut(s)	361
BisI	GCNGC	4 cut(s)	131, 234, 498, 621
BlsI	GCNGC	4 cut(s)	132, 235, 499, 622
Bme1390I	CCNGG	2 cut(s)	206, 767
BmrFI	CCNGG	2 cut(s)	206, 767
BpmI	CTGGAG	1 cut(s)	84
Bpu10I	CCTNAGC	1 cut(s)	237
Bpu14I	TTCGAA	1 cut(s)	118
BpuEI	CTTGAG	1 cut(s)	304
BsaAI	YACGTR	1 cut(s)	377
BsaJI	CCNNGG	3 cut(s)	205, 559, 766
Bsc4I	CCNNNNNNNGG	2 cut(s)	211, 508
Bse1I	ACTGG	1 cut(s)	607
Bse3DI	GCAATG	1 cut(s)	199
BseBI	CCWGG	2 cut(s)	206, 767
BseDI	CCNNGG	3 cut(s)	205, 559, 766
BseGI	GGATG	3 cut(s)	431, 466, 693
BseLI	CCNNNNNNNGG	2 cut(s)	211, 508
BseMI	GCAATG	1 cut(s)	199
BseMII	CTCAG	1 cut(s)	251
BseNI	ACTGG	1 cut(s)	607
BseXI	GCAGC	4 cut(s)	117, 220, 484, 607
BslI	CCNNNNNNNGG	2 cut(s)	211, 508
BsmAI	GTCTC	3 cut(s)	194, 286, 452
BsmI	GAATGC	1 cut(s)	683
Bsp119I	TTCGAA	1 cut(s)	118
Bsp143I	GATC	3 cut(s)	580, 652, 759
BspCNI	CTCAG	1 cut(s)	250
BspMI	ACCTGC	1 cut(s)	361
BspPI	GGATC	1 cut(s)	575
BspT104I	TTCGAA	1 cut(s)	118
BsrDI	GCAATG	1 cut(s)	199
BsrI	ACTGG	1 cut(s)	607
BssECI	CCNNGG	3 cut(s)	205, 559, 766
BssMI	GATC	3 cut(s)	580, 652, 759
BssSI	CACGAG	2 cut(s)	449, 479
BssT1I	CCWWGG	1 cut(s)	559
Bst2BI	CACGAG	2 cut(s)	449, 479
Bst2UI	CCWGG	2 cut(s)	206, 767
Bst4CI	ACNGT	3 cut(s)	280, 390, 551
Bst6I	CTCTTC	1 cut(s)	429
BstBAI	YACGTR	1 cut(s)	377
BstBI	TTCGAA	1 cut(s)	118
BstC8I	GCNNGC	1 cut(s)	65
BstDEI	CTNAG	2 cut(s)	237, 503
BstENI	CCTNNNNNAGG	1 cut(s)	506
BstF5I	GGATG	3 cut(s)	431, 466, 693
BstKTI	GATC	3 cut(s)	583, 655, 762
BstMAI	GTCTC	3 cut(s)	194, 286, 452
BstMBI	GATC	3 cut(s)	580, 652, 759
BstNI	CCWGG	2 cut(s)	206, 767
BstNSI	RCATGY	2 cut(s)	67, 233
BstSCI	CCNGG	2 cut(s)	204, 765
BstSNI	TACGTA	1 cut(s)	377
BstV1I	GCAGC	4 cut(s)	117, 220, 484, 607
BstX2I	RGATCY	1 cut(s)	580
BstYI	RGATCY	1 cut(s)	580
BtsCI	GGATG	3 cut(s)	431, 466, 693
BtsI	GCAGTG	1 cut(s)	33
BtsIMutI	CAGTG	1 cut(s)	33
BveI	ACCTGC	1 cut(s)	361
Cac8I	GCNNGC	1 cut(s)	65
Csp6I	GTAC	2 cut(s)	215, 374
CviAII	CATG	3 cut(s)	64, 230, 315
CviJI	RGCY	5 cut(s)	17, 130, 512, 717, 732
CviKI_1	RGCY	5 cut(s)	17, 130, 512, 717, 732
CviQI	GTAC	2 cut(s)	215, 374
DdeI	CTNAG	2 cut(s)	237, 503
DpnI	GATC	3 cut(s)	582, 654, 761
DpnII	GATC	3 cut(s)	580, 652, 759
DraI	TTTAAA	1 cut(s)	385
Eam1104I	CTCTTC	1 cut(s)	429
EarI	CTCTTC	1 cut(s)	429
Eco105I	TACGTA	1 cut(s)	377
Eco130I	CCWWGG	1 cut(s)	559
Eco57I	CTGAAG	3 cut(s)	60, 162, 453
EcoNI	CCTNNNNNAGG	1 cut(s)	506
EcoRI	GAATTC	1 cut(s)	597
EcoRII	CCWGG	2 cut(s)	204, 765
EcoT14I	CCWWGG	1 cut(s)	559
ErhI	CCWWGG	1 cut(s)	559
FaeI	CATG	3 cut(s)	67, 233, 318
FatI	CATG	3 cut(s)	63, 229, 314
FblI	GTMKAC	1 cut(s)	465
Fnu4HI	GCNGC	4 cut(s)	131, 234, 498, 621
FokI	GGATG	3 cut(s)	438, 473, 680
Fsp4HI	GCNGC	4 cut(s)	131, 234, 498, 621
FspBI	CTAG	1 cut(s)	578
GluI	GCNGC	4 cut(s)	131, 234, 498, 621
GsuI	CTGGAG	1 cut(s)	84
Hin1II	CATG	3 cut(s)	67, 233, 318
HincII	GTYRAC	1 cut(s)	466
HindII	GTYRAC	1 cut(s)	466
HinfI	GANTC	4 cut(s)	187, 311, 439, 686
Hpy166II	GTNNAC	1 cut(s)	466
Hpy188I	TCNGA	9 cut(s)	142, 186, 292, 310, 460, 596, 603, 652, 657
Hpy188III	TCNNGA	6 cut(s)	101, 239, 410, 451, 479, 724
Hpy8I	GTNNAC	1 cut(s)	466
HpyAV	CCTTC	4 cut(s)	30, 84, 137, 652
HpyCH4III	ACNGT	3 cut(s)	280, 390, 551
HpyCH4IV	ACGT	1 cut(s)	376
HpyCH4V	TGCA	1 cut(s)	568
HpyF3I	CTNAG	2 cut(s)	237, 503
HpySE526I	ACGT	1 cut(s)	376
Hsp92II	CATG	3 cut(s)	67, 233, 318
Kzo9I	GATC	3 cut(s)	580, 652, 759
LmnI	GCTCC	4 cut(s)	22, 72, 103, 127
Lsp1109I	GCAGC	4 cut(s)	117, 220, 484, 607
MaeI	CTAG	1 cut(s)	578
MaeII	ACGT	1 cut(s)	376
MaeIII	GTNAC	3 cut(s)	451, 476, 524
MalI	GATC	3 cut(s)	582, 654, 761
MboI	GATC	3 cut(s)	580, 652, 759
MboII	GAAGA	3 cut(s)	141, 446, 754
MflI	RGATCY	1 cut(s)	580
MluCI	AATT	5 cut(s)	9, 342, 536, 597, 746
MlyI	GAGTC	3 cut(s)	196, 305, 695
MnlI	CCTC	4 cut(s)	148, 311, 331, 658
MseI	TTAA	5 cut(s)	12, 27, 195, 384, 734
MspR9I	CCNGG	2 cut(s)	206, 767
Mva1269I	GAATGC	1 cut(s)	683
MvaI	CCWGG	2 cut(s)	206, 767
NdeII	GATC	3 cut(s)	580, 652, 759
NlaIII	CATG	3 cut(s)	67, 233, 318
NmuCI	GTSAC	2 cut(s)	451, 476
NspI	RCATGY	2 cut(s)	67, 233
NspV	TTCGAA	1 cut(s)	118
PaeI	GCATGC	1 cut(s)	67
PcsI	WCGNNNNNNNCGW	1 cut(s)	620
PctI	GAATGC	1 cut(s)	683
PfeI	GAWTC	1 cut(s)	439
PkrI	GCNGC	4 cut(s)	132, 235, 499, 622
PleI	GAGTC	3 cut(s)	195, 305, 694
PpsI	GAGTC	3 cut(s)	195, 305, 694
Ppu21I	YACGTR	1 cut(s)	377
Psp6I	CCWGG	2 cut(s)	204, 765
PspGI	CCWGG	2 cut(s)	204, 765
PsuI	RGATCY	1 cut(s)	580
RsaI	GTAC	2 cut(s)	216, 375
RsaNI	GTAC	2 cut(s)	215, 374
SalI	GTCGAC	1 cut(s)	464
SaqAI	TTAA	5 cut(s)	12, 27, 195, 384, 734
SatI	GCNGC	4 cut(s)	131, 234, 498, 621
Sau3AI	GATC	3 cut(s)	580, 652, 759
SchI	GAGTC	3 cut(s)	196, 305, 695
ScrFI	CCNGG	2 cut(s)	206, 767
SfuI	TTCGAA	1 cut(s)	118
SmlI	CTYRAG	1 cut(s)	319
SmoI	CTYRAG	1 cut(s)	319
SnaBI	TACGTA	1 cut(s)	377
SphI	GCATGC	1 cut(s)	67
Sse9I	AATT	5 cut(s)	9, 342, 536, 597, 746
SspMI	CTAG	1 cut(s)	578
StyD4I	CCNGG	2 cut(s)	204, 765
StyI	CCWWGG	1 cut(s)	559
TaaI	ACNGT	3 cut(s)	280, 390, 551
TaiI	ACGT	1 cut(s)	379
TaqI	TCGA	2 cut(s)	118, 465
TasI	AATT	5 cut(s)	9, 342, 536, 597, 746
TfiI	GAWTC	1 cut(s)	439
Tru1I	TTAA	5 cut(s)	12, 27, 195, 384, 734
Tru9I	TTAA	5 cut(s)	12, 27, 195, 384, 734
TscAI	CASTG	1 cut(s)	40
TseFI	GTSAC	2 cut(s)	451, 476
TseI	GCWGC	4 cut(s)	130, 233, 497, 620
Tsp45I	GTSAC	2 cut(s)	451, 476
TspGWI	ACGGA	1 cut(s)	729
TspRI	CASTG	1 cut(s)	40
XagI	CCTNNNNNAGG	1 cut(s)	506
XapI	RAATTY	2 cut(s)	342, 597
XceI	RCATGY	2 cut(s)	67, 233
XmiI	GTMKAC	1 cut(s)	465
XspI	CTAG	1 cut(s)	578

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