Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr04

Orthogroup ID

OG0003142

Physical Location & Seq

Genomic Coordinates Forward (+)

6307538 .. 6307720

Gene Structure 183 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

MD04G1053300.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 183 bp

ATGATGGTTGATCGTTTGTTCGAGGACATATTTCAGATTCTGCGATTGAACCCAGATGGCGAAAAGTTCGATAAAGTTACTCGAGTAGAAGCAAAGAGTGAGACTTGCGAGATGTTCATGCACCTGGATGTGAATTCAGAGGTTTATCTGATGAGGGAAGGGCAATCGCAAGACATTGGCTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0003674 GO:0003676 GO:0003677 GO:0003697 GO:0005488 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:0032993 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:0097159 GO:0097659 GO:1901360 GO:1901362 GO:1901363 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_Rpb8

Protein Analysis

61

Amino Acids

7.09

Weight (kDa)

4.49

Isoelectric Point (pI)

37.24

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb8	PF03870	8 - 56	3.2e-14	RNA polymerase Rpb8

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Publication-ready

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Orthologous Genes (Group: OG0003142)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G54250 AT3G59600
fragaria_vesca	FvH4_7g05580 FvH4_7g05580 FvH4_7g05580 FvH4_7g05580 FvH4_7g05580 FvH4_7g05580 FvH4_7g05580
malus_domestica	MD03G1174900.v1.1 MD04G1053300.v1.1 MD05G1057600.v1.1 MD11G1193000.v1.1
prunus_persica	Prupe.4G249600_v2.0.a1 Prupe.4G249600_v2.0.a1
pyrus_communis	pycom03g13240 pycom11g16850
rosa_chinensis	RchiOBHm_Chr1g0332731 RchiOBHm_Chr5g0052071 RchiOBHm_Chr6g0273601
rosa_laevigata	RLG00000034845
rosa_multiflora	Rmu_sc0001587.1_g000001 Rmu_sc0032204.1_g000001 Rmu_ssc0000098.1_g000004
rosa_roxburghii	Rroxscaffold_1G00027860 Rroxscaffold_4G00318050
rosa_rugosa	Rorug01G0104600 Rorug05G0275000 Rorug05G0275100
rosa_samantha	Rh1AG127600 Rh1BG097000 Rh1CG121400 Rh5BG358000 Rh5CG383500 Rh5DG373400 Rh6CG194200
rosa_wichuraiana	Rw5G032800

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AcsI	RAATTY	1 cut(s)	133
AgsI	TTSAA	1 cut(s)	49
AjnI	CCWGG	1 cut(s)	123
Alw26I	GTCTC	1 cut(s)	95
AlwNI	CAGNNNCTG	1 cut(s)	40
Ama87I	CYCGRG	1 cut(s)	81
ApoI	RAATTY	1 cut(s)	133
AvaI	CYCGRG	1 cut(s)	81
BccI	CCATC	1 cut(s)	50
BciT130I	CCWGG	1 cut(s)	125
BcoDI	GTCTC	1 cut(s)	95
Bme1390I	CCNGG	1 cut(s)	125
BmeT110I	CYCGRG	1 cut(s)	81
BmrFI	CCNGG	1 cut(s)	125
BseBI	CCWGG	1 cut(s)	125
BseGI	GGATG	1 cut(s)	133
BsiHKCI	CYCGRG	1 cut(s)	81
BsmAI	GTCTC	1 cut(s)	95
BsoBI	CYCGRG	1 cut(s)	81
Bsp143I	GATC	1 cut(s)	10
BssMI	GATC	1 cut(s)	10
Bst2UI	CCWGG	1 cut(s)	125
BstF5I	GGATG	1 cut(s)	133
BstKTI	GATC	1 cut(s)	13
BstMAI	GTCTC	1 cut(s)	95
BstMBI	GATC	1 cut(s)	10
BstNI	CCWGG	1 cut(s)	125
BstSCI	CCNGG	1 cut(s)	123
BtsCI	GGATG	1 cut(s)	133
CaiI	CAGNNNCTG	1 cut(s)	40
CviAII	CATG	1 cut(s)	118
CviJI	RGCY	1 cut(s)	180
CviKI_1	RGCY	1 cut(s)	180
DpnI	GATC	1 cut(s)	12
DpnII	GATC	1 cut(s)	10
Eco88I	CYCGRG	1 cut(s)	81
EcoRI	GAATTC	1 cut(s)	133
EcoRII	CCWGG	1 cut(s)	123
FaeI	CATG	1 cut(s)	121
FaiI	YATR	2 cut(s)	29, 119
FatI	CATG	1 cut(s)	117
FokI	GGATG	1 cut(s)	140
Hin1II	CATG	1 cut(s)	121
HinfI	GANTC	1 cut(s)	37
Hpy188I	TCNGA	3 cut(s)	36, 139, 150
HpyAV	CCTTC	1 cut(s)	152
HpyCH4V	TGCA	1 cut(s)	121
Hsp92II	CATG	1 cut(s)	121
Kzo9I	GATC	1 cut(s)	10
LpnPI	CCDG	3 cut(s)	66, 110, 137
MaeIII	GTNAC	1 cut(s)	76
MalI	GATC	1 cut(s)	12
MboI	GATC	1 cut(s)	10
MluCI	AATT	1 cut(s)	133
MnlI	CCTC	3 cut(s)	16, 133, 147
MslI	CAYNNNNRTG	1 cut(s)	126
MspR9I	CCNGG	1 cut(s)	125
MvaI	CCWGG	1 cut(s)	125
NdeII	GATC	1 cut(s)	10
NlaIII	CATG	1 cut(s)	121
PaeR7I	CTCGAG	1 cut(s)	81
PfeI	GAWTC	1 cut(s)	37
Psp6I	CCWGG	1 cut(s)	123
PspGI	CCWGG	1 cut(s)	123
PspXI	VCTCGAGB	1 cut(s)	81
PstNI	CAGNNNCTG	1 cut(s)	40
RseI	CAYNNNNRTG	1 cut(s)	126
Sau3AI	GATC	1 cut(s)	10
ScrFI	CCNGG	1 cut(s)	125
SetI	ASST	2 cut(s)	126, 144
Sfr274I	CTCGAG	1 cut(s)	81
SgeI	CNNG	9 cut(s)	34, 65, 93, 95, 117, 121, 130, 136, 137
SlaI	CTCGAG	1 cut(s)	81
SmiMI	CAYNNNNRTG	1 cut(s)	126
SmlI	CTYRAG	1 cut(s)	81
SmoI	CTYRAG	1 cut(s)	81
Sse9I	AATT	1 cut(s)	133
StyD4I	CCNGG	1 cut(s)	123
TaqI	TCGA	3 cut(s)	21, 69, 82
TasI	AATT	1 cut(s)	133
TfiI	GAWTC	1 cut(s)	37
TspDTI	ATGAA	1 cut(s)	106
XapI	RAATTY	1 cut(s)	133
XhoI	CTCGAG	1 cut(s)	81

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