Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr13

Orthogroup ID

OG0001390

Physical Location & Seq

Genomic Coordinates Forward (+)

17641165 .. 17646726

Gene Structure 5562 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

MD13G1198900.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 477 bp

ATGAAGATTTTACAGGCCAATTCCGGTGTGCTTACCAATTTTGATGTGCTCAACTTTCTAAAGGCCAAAGGGGCTTCAAAAGATCTAGCACGGGTTCTTGCTAATGTAGCGCCATCTGAGTATAAGATTTTCGATTACTTGGTTGCAACTCCTGCTTGTACTCAGACAAGAGAGAGTATCGATGAGTTCAAGGAGAAGTGTAGGGAATATGACCTTGCAGAAGCTGAGGTGCTCAATATAATCAACACTAGGCCATATAACGTCGTTGGAATCTTCCCGATGATAGAGGATATTGATAGCCGTTTAGGAGATAAAATTCAAGATCTAGTAGATATGGTGGTAGACGTGTTACCATCTCTACCTGTTCCAGCAGCAACTGATGAAAGTGGGGCAAACACCGCGGATGCAGAAAAAATTGAACATGAGAACGATAACAACGAAGAGGAACCTGAAAATGAGGAACCAATGGAGACATAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0003674 GO:0003824 GO:0003899 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005737 GO:0005886 GO:0006139 GO:0006351 GO:0006352 GO:0006383 GO:0006384 GO:0006725 GO:0006807 GO:0007568 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009360 GO:0009987 GO:0010467 GO:0016020 GO:0016070 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019438 GO:0030424 GO:0030425 GO:0030880 GO:0031974 GO:0031981 GO:0032502 GO:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034645 GO:0034654 GO:0036477 GO:0042575 GO:0042995 GO:0043005 GO:0043025 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044297 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044463 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0071944 GO:0090304 GO:0097447 GO:0097458 GO:0097659 GO:0097747 GO:0120025 GO:0120038 GO:0140098 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

RNA_pol_Rpb4

Protein Analysis

159

Amino Acids

17.56

Weight (kDa)

4.21

Isoelectric Point (pI)

46.0

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb4	PF03874	11 - 115	1.7e-09	RNA polymerase Rpb4

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: OG0001390)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT3G28956 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950 AT5G62950
fragaria_vesca	FvH4_4g01070 FvH4_4g01070 FvH4_5g27570
malus_domestica	MD13G1198900.v1.1
prunus_persica	Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1 Prupe.1G020700_v2.0.a1
pyrus_communis	pycom13g17270
rosa_chinensis	RchiOBHm_Chr4g0387641 RchiOBHm_Chr6g0280701
rosa_laevigata	RLG00000010104 RLG00000013035
rosa_multiflora	Rmu_sc0000976.1_g000021 Rmu_sc0003953.1_g000006
rosa_roxburghii	Rroxscaffold_7G00187720
rosa_rugosa	Rorug03G0311800 Rorug03G0311900 Rorug03G0312000 Rorug03G0312100 Rorug06G0133900 Rorug06G0133900 Rorug06G0133900 Rorug06G0134000
rosa_samantha	Rh4AG017400 Rh4BG012200 Rh4CG018600 Rh4DG013200 Rh6AG246600 Rh6BG248900 Rh6CG250000 Rh6DG241500
rosa_wichuraiana	Rw4G001120 Rw6G021350

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	342
AccII	CGCG	1 cut(s)	401
AciI	CCGC	2 cut(s)	399, 401
AcsI	RAATTY	1 cut(s)	315
AfaI	GTAC	1 cut(s)	160
AflIII	ACRYGT	1 cut(s)	345
AgsI	TTSAA	4 cut(s)	78, 190, 320, 419
AjiI	CACGTC	1 cut(s)	346
AluBI	AGCT	1 cut(s)	224
AluI	AGCT	1 cut(s)	224
Alw21I	GWGCWC	2 cut(s)	51, 234
Alw26I	GTCTC	1 cut(s)	464
AlwNI	CAGNNNCTG	2 cut(s)	224, 377
AoxI	GGCC	3 cut(s)	15, 63, 251
ApeKI	GCWGC	1 cut(s)	371
ApoI	RAATTY	1 cut(s)	315
AspLEI	GCGC	1 cut(s)	112
Bbv12I	GWGCWC	2 cut(s)	51, 234
BbvCI	CCTCAGC	1 cut(s)	225
BbvI	GCAGC	1 cut(s)	383
BccI	CCATC	2 cut(s)	121, 361
BceAI	ACGGC	1 cut(s)	285
BcoDI	GTCTC	1 cut(s)	464
BfaI	CTAG	3 cut(s)	86, 249, 326
BfoI	RGCGCY	1 cut(s)	113
BglI	GCCNNNNNGGC	1 cut(s)	71
BglII	AGATCT	2 cut(s)	82, 322
BisI	GCNGC	1 cut(s)	372
BlsI	GCNGC	1 cut(s)	373
BmgBI	CACGTC	1 cut(s)	346
BmiI	GGNNCC	2 cut(s)	447, 462
BmsI	GCATC	1 cut(s)	394
Bpu10I	CCTNAGC	1 cut(s)	225
Bsa29I	ATCGAT	1 cut(s)	180
BsaJI	CCNNGG	1 cut(s)	399
BsaWI	WCCGGW	1 cut(s)	23
BseCI	ATCGAT	1 cut(s)	180
BseDI	CCNNGG	1 cut(s)	399
BseGI	GGATG	1 cut(s)	409
BseMII	CTCAG	3 cut(s)	108, 176, 216
BseXI	GCAGC	1 cut(s)	383
Bsh1236I	CGCG	1 cut(s)	401
BshFI	GGCC	3 cut(s)	17, 65, 253
BshVI	ATCGAT	1 cut(s)	180
BsiHKAI	GWGCWC	2 cut(s)	51, 234
BsiSI	CCGG	1 cut(s)	24
BsmAI	GTCTC	1 cut(s)	464
BsnI	GGCC	3 cut(s)	17, 65, 253
Bsp1286I	GDGCHC	2 cut(s)	51, 234
Bsp143I	GATC	2 cut(s)	82, 322
BspACI	CCGC	2 cut(s)	399, 401
BspANI	GGCC	3 cut(s)	17, 65, 253
BspCNI	CTCAG	3 cut(s)	109, 175, 217
BspDI	ATCGAT	1 cut(s)	180
BspFNI	CGCG	1 cut(s)	401
BspLI	GGNNCC	2 cut(s)	447, 462
BssECI	CCNNGG	1 cut(s)	399
BssMI	GATC	2 cut(s)	82, 322
Bst6I	CTCTTC	1 cut(s)	435
BstAPI	GCANNNNNTGC	1 cut(s)	152
BstDEI	CTNAG	3 cut(s)	117, 162, 225
BstDSI	CCRYGG	1 cut(s)	399
BstF5I	GGATG	1 cut(s)	409
BstFNI	CGCG	1 cut(s)	401
BstH2I	RGCGCY	1 cut(s)	113
BstHHI	GCGC	1 cut(s)	112
BstKTI	GATC	2 cut(s)	85, 325
BstMAI	GTCTC	1 cut(s)	464
BstMBI	GATC	2 cut(s)	82, 322
BstMWI	GCNNNNNNNGC	4 cut(s)	71, 107, 152, 398
BstUI	CGCG	1 cut(s)	401
BstV1I	GCAGC	1 cut(s)	383
BstX2I	RGATCY	2 cut(s)	82, 322
BstYI	RGATCY	2 cut(s)	82, 322
Bsu15I	ATCGAT	1 cut(s)	180
BsuRI	GGCC	3 cut(s)	17, 65, 253
BsuTUI	ATCGAT	1 cut(s)	180
BtgI	CCRYGG	1 cut(s)	399
BtrI	CACGTC	1 cut(s)	346
BtsCI	GGATG	1 cut(s)	409
CaiI	CAGNNNCTG	2 cut(s)	224, 377
CfoI	GCGC	1 cut(s)	112
Cfr42I	CCGCGG	1 cut(s)	402
ClaI	ATCGAT	1 cut(s)	180
Csp6I	GTAC	1 cut(s)	159
CviAII	CATG	1 cut(s)	422
CviJI	RGCY	6 cut(s)	17, 65, 74, 224, 253, 300
CviKI_1	RGCY	6 cut(s)	17, 65, 74, 224, 253, 300
CviQI	GTAC	1 cut(s)	159
DdeI	CTNAG	3 cut(s)	117, 162, 225
DpnI	GATC	2 cut(s)	84, 324
DpnII	GATC	2 cut(s)	82, 322
Eam1104I	CTCTTC	1 cut(s)	435
EarI	CTCTTC	1 cut(s)	435
FaeI	CATG	1 cut(s)	425
FaiI	YATR	8 cut(s)	123, 210, 239, 256, 258, 335, 423, 475
FatI	CATG	1 cut(s)	421
FblI	GTMKAC	1 cut(s)	342
Fnu4HI	GCNGC	1 cut(s)	372
FokI	GGATG	1 cut(s)	416
Fsp4HI	GCNGC	1 cut(s)	372
FspBI	CTAG	3 cut(s)	86, 249, 326
GlaI	GCGC	1 cut(s)	111
GluI	GCNGC	1 cut(s)	372
HaeII	RGCGCY	1 cut(s)	113
HaeIII	GGCC	3 cut(s)	17, 65, 253
HapII	CCGG	1 cut(s)	24
HhaI	GCGC	1 cut(s)	112
Hin1II	CATG	1 cut(s)	425
Hin6I	GCGC	1 cut(s)	110
HinP1I	GCGC	1 cut(s)	110
HinfI	GANTC	1 cut(s)	270
HpaII	CCGG	1 cut(s)	24
Hpy166II	GTNNAC	1 cut(s)	343
Hpy188I	TCNGA	2 cut(s)	118, 165
Hpy188III	TCNNGA	2 cut(s)	277, 320
Hpy8I	GTNNAC	1 cut(s)	343
Hpy99I	CGWCG	1 cut(s)	266
HpyCH4IV	ACGT	2 cut(s)	261, 345
HpyCH4V	TGCA	3 cut(s)	146, 218, 407
HpyF10VI	GCNNNNNNNGC	4 cut(s)	71, 107, 152, 398
HpyF3I	CTNAG	3 cut(s)	117, 162, 225
HpySE526I	ACGT	2 cut(s)	261, 345
Hsp92II	CATG	1 cut(s)	425
HspAI	GCGC	1 cut(s)	110
KspI	CCGCGG	1 cut(s)	402
Kzo9I	GATC	2 cut(s)	82, 322
LpnPI	CCDG	5 cut(s)	37, 165, 375, 381, 462
Lsp1109I	GCAGC	1 cut(s)	383
LweI	GCATC	1 cut(s)	394
MaeI	CTAG	3 cut(s)	86, 249, 326
MaeII	ACGT	2 cut(s)	261, 345
MaeIII	GTNAC	1 cut(s)	348
MalI	GATC	2 cut(s)	84, 324
MboI	GATC	2 cut(s)	82, 322
MboII	GAAGA	3 cut(s)	16, 265, 452
MflI	RGATCY	2 cut(s)	82, 322
MhlI	GDGCHC	2 cut(s)	51, 234
MluCI	AATT	4 cut(s)	19, 37, 315, 414
MmeI	TCCRAC	1 cut(s)	247
MnlI	CCTC	4 cut(s)	220, 280, 436, 451
MspA1I	CMGCKG	1 cut(s)	401
MspI	CCGG	1 cut(s)	24
MvnI	CGCG	1 cut(s)	401
MwoI	GCNNNNNNNGC	4 cut(s)	71, 107, 152, 398
NdeII	GATC	2 cut(s)	82, 322
NlaIII	CATG	1 cut(s)	425
NlaIV	GGNNCC	2 cut(s)	447, 462
PcsI	WCGNNNNNNNCGW	1 cut(s)	435
PfeI	GAWTC	1 cut(s)	270
PkrI	GCNGC	1 cut(s)	373
PspN4I	GGNNCC	2 cut(s)	447, 462
PstNI	CAGNNNCTG	2 cut(s)	224, 377
PsuI	RGATCY	2 cut(s)	82, 322
RsaI	GTAC	1 cut(s)	160
RsaNI	GTAC	1 cut(s)	159
SacII	CCGCGG	1 cut(s)	402
SatI	GCNGC	1 cut(s)	372
Sau3AI	GATC	2 cut(s)	82, 322
SduI	GDGCHC	2 cut(s)	51, 234
SetI	ASST	7 cut(s)	216, 226, 231, 264, 348, 364, 451
SfaNI	GCATC	1 cut(s)	394
Sfr303I	CCGCGG	1 cut(s)	402
SgrBI	CCGCGG	1 cut(s)	402
Sse9I	AATT	4 cut(s)	19, 37, 315, 414
SsiI	CCGC	2 cut(s)	399, 401
SspMI	CTAG	3 cut(s)	86, 249, 326
TaiI	ACGT	2 cut(s)	264, 348
TaqI	TCGA	2 cut(s)	132, 180
TasI	AATT	4 cut(s)	19, 37, 315, 414
TatI	WGTACW	1 cut(s)	158
TfiI	GAWTC	1 cut(s)	270
TseI	GCWGC	1 cut(s)	371
TspDTI	ATGAA	2 cut(s)	17, 396
XapI	RAATTY	1 cut(s)	315
XmiI	GTMKAC	1 cut(s)	342
XspI	CTAG	3 cut(s)	86, 249, 326

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