Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr02

Orthogroup ID

OG0000701

Physical Location & Seq

Genomic Coordinates Forward (+)

7470290 .. 7472640

Gene Structure 2351 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

MD02G1093900.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 567 bp

ATGCAAATGCTGAAAGATCGGAATTACTTGGTTGGAGATTTTGAGATCAACATGTCAAAAGAACAGTTCAAGGACAAATACGGAGAGAACATGAAAAGGGAAGATCTTATCATCAATAAAACTAAGCGCAGTGATAGCAATGATCAGATTTATGTCTTCTTTCCTGATGAACCAAAGGTTGGGGTCAAGACAATGAAGACTTATACCAACCGCATGAAATCGGAGAATGTGTTCCGAGCAATCTTGGTTACTCAACAAAGTCTGACGCCCTTTGCAAAAACCTGTATCAGTGAGATATCGGGAAAGTTCCACTTGGAGGTTTTTCTGGAGGCAGAATTGTTGGTGAATATTAAAGAACACGTTCTAGTTCCTGAGCATCGGGTGCTTACAAGTGAGGAAAAGAAGACTTTGCTGGAGAGATACACCGTAAAAGAAACACAGCTCCCTCGGATTCAGGTGACTGATCCAATTGCGAAATACTACGGGCTTAAGCGCGCACAAGTTGTGAAGATAATTCGACCAAGTGAGACTGCAGGGCGATATGTCACCTACCGTTACGTTATATAA

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:0005665 GO:0005666 GO:0005730 GO:0005736 GO:0006139 GO:0006351 GO:0006366 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0010467 GO:0016070 GO:0016591 GO:0018130 GO:0019438 GO:0030880 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044452 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0090304 GO:0097659 GO:1901360 GO:1901362 GO:1901576 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

189

Amino Acids

22.12

Weight (kDa)

9.33

Isoelectric Point (pI)

31.57

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	1 - 72	7.6e-24	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	115 - 187	5.6e-35	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: OG0000701)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G22320
fragaria_vesca	FvH4_5g21560 FvH4_7g09301 FvH4_7g09301
malus_domestica	MD02G1080800.v1.1 MD02G1093900.v1.1 MD15G1208600.v1.1
prunus_persica	Prupe.2G121300_v2.0.a1 Prupe.2G121300_v2.0.a1 Prupe.2G121400_v2.0.a1 Prupe.2G121400_v2.0.a1
pyrus_communis	pycom02g06410 pycom02g07430 pycom15g18470
rosa_chinensis	RchiOBHm_Chr1g0332791 RchiOBHm_Chr1g0344101 RchiOBHm_Chr1g0344151 RchiOBHm_Chr1g0344171 RchiOBHm_Chr1g0345361 RchiOBHm_Chr1g0345421 RchiOBHm_Chr1g0345561 RchiOBHm_Chr1g0345591 RchiOBHm_Chr1g0345671 RchiOBHm_Chr1g0345701 RchiOBHm_Chr1g0345711 RchiOBHm_Chr1g0345721 RchiOBHm_Chr1g0345801 RchiOBHm_Chr1g0345851 RchiOBHm_Chr1g0345901 RchiOBHm_Chr1g0345921 RchiOBHm_Chr1g0345931 RchiOBHm_Chr1g0345951 RchiOBHm_Chr1g0345961 RchiOBHm_Chr7g0208981
rosa_laevigata	RLG00000003175 RLG00000029644
rosa_multiflora	Rmu_co8382943.1_g000001 Rmu_sc0000532.1_g000035 Rmu_sc0001292.1_g000003 Rmu_sc0001349.1_g000004 Rmu_sc0001692.1_g000006 Rmu_sc0001692.1_g000027 Rmu_sc0002329.1_g000024 Rmu_sc0002329.1_g000032 Rmu_sc0004239.1_g000023 Rmu_sc0008115.1_g000011
rosa_roxburghii	Rroxscaffold_3G00238160 Rroxscaffold_3G00249920 Rroxscaffold_4G00310020 Rroxscaffold_4G00317980 Rroxscaffold_5G00344600
rosa_rugosa	Rorug01G0103700 Rorug01G0103800 Rorug01G0103900 Rorug01G0171800 Rorug07G0107800
rosa_samantha	Rh1BG097500 Rh1BG161500 Rh1CG122000 Rh1CG173900 Rh1CG180700 Rh1CG181100 Rh1DG133900 Rh1DG191900 Rh7AG242600 Rh7BG237400 Rh7DG249500
rosa_wichuraiana	Rw1G010510 Rw1G016120 Rw1G016200 Rw1G016220 Rw1G016430 Rw1G016490 Rw7G020550

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	179
AccII	CGCG	1 cut(s)	495
AciI	CCGC	1 cut(s)	211
AclWI	GGATC	1 cut(s)	458
AcyI	GRCGYC	1 cut(s)	266
AfiI	CCNNNNNNNGG	2 cut(s)	179, 316
AflII	CTTAAG	1 cut(s)	488
AflIII	ACRYGT	2 cut(s)	51, 358
AgsI	TTSAA	1 cut(s)	70
AjuI	GAANNNNNNNTTGG	2 cut(s)	162, 194
AloI	GAACNNNNNNTCC	2 cut(s)	215, 247
AluBI	AGCT	1 cut(s)	442
AluI	AGCT	1 cut(s)	442
Alw26I	GTCTC	1 cut(s)	521
AlwI	GGATC	1 cut(s)	458
Asp700I	GAANNNNTTC	2 cut(s)	230, 360
AspLEI	GCGC	3 cut(s)	129, 495, 497
AsuHPI	GGTGA	3 cut(s)	355, 469, 538
BbsI	GAAGAC	3 cut(s)	148, 203, 410
BclI	TGATCA	1 cut(s)	142
BcoDI	GTCTC	1 cut(s)	521
BfaI	CTAG	1 cut(s)	365
BfmI	CTRYAG	1 cut(s)	531
BfrI	CTTAAG	1 cut(s)	488
BglII	AGATCT	1 cut(s)	103
BmsI	GCATC	1 cut(s)	385
BpiI	GAAGAC	3 cut(s)	148, 203, 410
BpmI	CTGGAG	2 cut(s)	347, 434
Bpu10I	CCTNAGC	1 cut(s)	372
BsaHI	GRCGYC	1 cut(s)	266
BsaJI	CCNNGG	1 cut(s)	446
BsaXI	ACNNNNNCTCC	2 cut(s)	215, 245
Bsc4I	CCNNNNNNNGG	2 cut(s)	179, 316
Bse3DI	GCAATG	1 cut(s)	145
BseDI	CCNNGG	1 cut(s)	446
BseLI	CCNNNNNNNGG	2 cut(s)	179, 316
BseMI	GCAATG	1 cut(s)	145
BseMII	CTCAG	1 cut(s)	363
BsePI	GCGCGC	1 cut(s)	493
Bsh1236I	CGCG	1 cut(s)	495
BslI	CCNNNNNNNGG	2 cut(s)	179, 316
BsmAI	GTCTC	1 cut(s)	521
Bsp143I	GATC	5 cut(s)	16, 45, 103, 142, 463
BspACI	CCGC	1 cut(s)	211
BspCNI	CTCAG	1 cut(s)	364
BspFNI	CGCG	1 cut(s)	495
BspMAI	CTGCAG	1 cut(s)	535
BspPI	GGATC	1 cut(s)	458
BspTI	CTTAAG	1 cut(s)	488
BsrDI	GCAATG	1 cut(s)	145
BssECI	CCNNGG	1 cut(s)	446
BssHII	GCGCGC	1 cut(s)	493
BssMI	GATC	5 cut(s)	16, 45, 103, 142, 463
BssNI	GRCGYC	1 cut(s)	266
Bst4CI	ACNGT	3 cut(s)	66, 427, 554
BstACI	GRCGYC	1 cut(s)	266
BstAFI	CTTAAG	1 cut(s)	488
BstAPI	GCANNNNNTGC	1 cut(s)	382
BstC8I	GCNNGC	1 cut(s)	495
BstDEI	CTNAG	2 cut(s)	123, 372
BstFNI	CGCG	1 cut(s)	495
BstHHI	GCGC	3 cut(s)	129, 495, 497
BstKTI	GATC	5 cut(s)	19, 48, 106, 145, 466
BstMAI	GTCTC	1 cut(s)	521
BstMBI	GATC	5 cut(s)	16, 45, 103, 142, 463
BstMWI	GCNNNNNNNGC	2 cut(s)	135, 382
BstNSI	RCATGY	1 cut(s)	55
BstSFI	CTRYAG	1 cut(s)	531
BstUI	CGCG	1 cut(s)	495
BstV2I	GAAGAC	3 cut(s)	148, 203, 410
BstX2I	RGATCY	1 cut(s)	103
BstYI	RGATCY	1 cut(s)	103
BtsI	GCAGTG	1 cut(s)	136
BtsIMutI	CAGTG	2 cut(s)	136, 295
Cac8I	GCNNGC	1 cut(s)	495
CfoI	GCGC	3 cut(s)	129, 495, 497
CseI	GACGC	1 cut(s)	274
CviAII	CATG	3 cut(s)	52, 91, 214
CviJI	RGCY	2 cut(s)	442, 487
CviKI_1	RGCY	2 cut(s)	442, 487
DdeI	CTNAG	2 cut(s)	123, 372
DpnI	GATC	5 cut(s)	18, 47, 105, 144, 465
DpnII	GATC	5 cut(s)	16, 45, 103, 142, 463
Eco32I	GATATC	1 cut(s)	297
EcoRV	GATATC	1 cut(s)	297
FaeI	CATG	3 cut(s)	55, 94, 217
FaiI	YATR	8 cut(s)	53, 92, 153, 204, 215, 543, 563, 565
FalI	AAGNNNNNCTT	2 cut(s)	296, 328
FatI	CATG	3 cut(s)	51, 90, 213
FbaI	TGATCA	1 cut(s)	142
FspBI	CTAG	1 cut(s)	365
GlaI	GCGC	3 cut(s)	128, 494, 496
GsuI	CTGGAG	2 cut(s)	347, 434
HgaI	GACGC	1 cut(s)	274
HhaI	GCGC	3 cut(s)	129, 495, 497
Hin1I	GRCGYC	1 cut(s)	266
Hin1II	CATG	3 cut(s)	55, 94, 217
Hin6I	GCGC	3 cut(s)	127, 493, 495
HinP1I	GCGC	3 cut(s)	127, 493, 495
HinfI	GANTC	1 cut(s)	451
HphI	GGTGA	3 cut(s)	355, 469, 538
Hpy188I	TCNGA	6 cut(s)	21, 147, 223, 236, 264, 450
Hpy188III	TCNNGA	5 cut(s)	164, 187, 300, 326, 371
HpyCH4III	ACNGT	3 cut(s)	66, 427, 554
HpyCH4IV	ACGT	2 cut(s)	360, 558
HpyCH4V	TGCA	3 cut(s)	4, 275, 533
HpyF10VI	GCNNNNNNNGC	2 cut(s)	135, 382
HpyF3I	CTNAG	2 cut(s)	123, 372
HpySE526I	ACGT	2 cut(s)	360, 558
Hsp92I	GRCGYC	1 cut(s)	266
Hsp92II	CATG	3 cut(s)	55, 94, 217
HspAI	GCGC	3 cut(s)	127, 493, 495
Ksp22I	TGATCA	1 cut(s)	142
Kzo9I	GATC	5 cut(s)	16, 45, 103, 142, 463
LmnI	GCTCC	1 cut(s)	447
LpnPI	CCDG	7 cut(s)	177, 295, 311, 384, 398, 440, 519
LweI	GCATC	1 cut(s)	385
MaeI	CTAG	1 cut(s)	365
MaeII	ACGT	2 cut(s)	360, 558
MaeIII	GTNAC	4 cut(s)	247, 457, 544, 554
MalI	GATC	5 cut(s)	18, 47, 105, 144, 465
MboI	GATC	5 cut(s)	16, 45, 103, 142, 463
MboII	GAAGA	5 cut(s)	113, 148, 208, 415, 520
MfeI	CAATTG	1 cut(s)	468
MflI	RGATCY	1 cut(s)	103
MluCI	AATT	4 cut(s)	22, 335, 468, 513
MmeI	TCCRAC	1 cut(s)	13
MnlI	CCTC	4 cut(s)	310, 322, 388, 456
MroXI	GAANNNNTTC	2 cut(s)	230, 360
MseI	TTAA	2 cut(s)	351, 489
MspCI	CTTAAG	1 cut(s)	488
MunI	CAATTG	1 cut(s)	468
MvnI	CGCG	1 cut(s)	495
MwoI	GCNNNNNNNGC	2 cut(s)	135, 382
NdeII	GATC	5 cut(s)	16, 45, 103, 142, 463
NlaIII	CATG	3 cut(s)	55, 94, 217
NmuCI	GTSAC	2 cut(s)	457, 544
NspI	RCATGY	1 cut(s)	55
PauI	GCGCGC	1 cut(s)	493
PciI	ACATGT	1 cut(s)	51
PdmI	GAANNNNTTC	2 cut(s)	230, 360
PfeI	GAWTC	1 cut(s)	451
PflMI	CCANNNNNTGG	1 cut(s)	179
PscI	ACATGT	1 cut(s)	51
PstI	CTGCAG	1 cut(s)	535
PsuI	RGATCY	1 cut(s)	103
PteI	GCGCGC	1 cut(s)	493
SaqAI	TTAA	2 cut(s)	351, 489
Sau3AI	GATC	5 cut(s)	16, 45, 103, 142, 463
SetI	ASST	8 cut(s)	180, 284, 321, 363, 444, 459, 551, 561
SfaNI	GCATC	1 cut(s)	385
SfcI	CTRYAG	1 cut(s)	531
SmlI	CTYRAG	1 cut(s)	488
SmoI	CTYRAG	1 cut(s)	488
Sse9I	AATT	4 cut(s)	22, 335, 468, 513
SsiI	CCGC	1 cut(s)	211
SspI	AATATT	1 cut(s)	349
SspMI	CTAG	1 cut(s)	365
TaaI	ACNGT	3 cut(s)	66, 427, 554
TaiI	ACGT	2 cut(s)	363, 561
TaqI	TCGA	1 cut(s)	517
TasI	AATT	4 cut(s)	22, 335, 468, 513
TfiI	GAWTC	1 cut(s)	451
Tru1I	TTAA	2 cut(s)	351, 489
Tru9I	TTAA	2 cut(s)	351, 489
TscAI	CASTG	2 cut(s)	136, 295
TseFI	GTSAC	2 cut(s)	457, 544
Tsp45I	GTSAC	2 cut(s)	457, 544
TspDTI	ATGAA	4 cut(s)	107, 183, 209, 230
TspGWI	ACGGA	1 cut(s)	96
TspRI	CASTG	2 cut(s)	136, 295
Van91I	CCANNNNNTGG	1 cut(s)	179
Vha464I	CTTAAG	1 cut(s)	488
XceI	RCATGY	1 cut(s)	55
XmnI	GAANNNNTTC	2 cut(s)	230, 360
XspI	CTAG	1 cut(s)	365

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