Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr02

Orthogroup ID

OG0000701

Physical Location & Seq

Genomic Coordinates Forward (+)

6364076 .. 6366910

Gene Structure 2835 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

MD02G1080800.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 939 bp

ATGACAAAAATTTATATATGTTGTCATTTTTGCATTCTTAAAGAGTATTACCCTTTTTTCAAGAAAAAAAAAAAAAAGGCAGAGAAAATAAAACGACGTCGTGGCTGTATAAAAGCTTCGGTTGGAAACCCTTTGCCTCTCTCTCGCAACGCGATCCTTGGCACAACACGCAGACAGCAGCTCTCGTTCTCGCGCCTTTTTTCTGTCCAAATCGAAAACCCTAATCACATCACTAACAATCTCCAAAGATCCTGTCAATTCAGCTGCGGTGATATCCTGTACGAGCATCCACTTCAACTTCCGACAACAAACGCTAATTTTTTCTGCCGAACAGAGGCGAAGATGGTTTTAACAGAAGAAGAAATCACAAGGCTTTACAGAGTCCGAAAGACTGTGATGCAAATGCTGAAAGATCGGAATTACTTGGTTGGAGATTTTGAGATCAACATGTCAAAAGAACAGTTCAAGGACAAATACGGAGAGAACATGAAAAGGGAAGATCTTATCATCAATAAAACAAAGAGAACTGACACAAACGATCAGATTTATGTCTTCTTTCCTGACGAACCAAAGGTTGGGGTCAAGACAATGAAGACTTATACCAATCGCATGAAATCGGAGAATGTGTTCAGAGCAATCTTGGTTACTCAACAAAGTCTGACGCCCTTTGCAAAGACCTGTATCAGTGAGATATCGGGAAAGTTCCACTTGGAGGAGGCAGAATTGTTGGTGAATATTAAAGAACACGTTCTAGTTCCTGAGCATCGGGTGCTTACAAATGAGGAAAAGAAGACTTTGCTGGAGAGGTATACTGTGAAAGAAACACAGGTGACTGATCCAATTGCGAAATACTACGGGCTTAAGCGTGCACAAGTTGTGAAGATAATTCGACCAAGCGAGACTGCAGGGCGATATGTCACCTACCGTTATGTTATATAA

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

313

Amino Acids

36.74

Weight (kDa)

9.63

Isoelectric Point (pI)

41.34

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	119 - 204	1.8e-31	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	244 - 311	1.3e-26	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)
AatII	GACGTC	1 cut(s)	100
AccB7I	CCANNNNNTGG	1 cut(s)	575
AccI	GTMKAC	1 cut(s)	809
AccII	CGCG	2 cut(s)	152, 193
AciI	CCGC	1 cut(s)	267
AclWI	GGATC	3 cut(s)	148, 243, 830
AcsI	RAATTY	1 cut(s)	9
AcyI	GRCGYC	2 cut(s)	97, 662
AfaI	GTAC	1 cut(s)	281
AfiI	CCNNNNNNNGG	3 cut(s)	334, 575, 712
AflII	CTTAAG	1 cut(s)	860
AflIII	ACRYGT	2 cut(s)	447, 745
AgsI	TTSAA	3 cut(s)	61, 296, 466
AjuI	GAANNNNNNNTTGG	2 cut(s)	558, 590
AloI	GAACNNNNNNTCC	2 cut(s)	611, 643
AluBI	AGCT	3 cut(s)	116, 181, 264
AluI	AGCT	3 cut(s)	116, 181, 264
Alw21I	GWGCWC	1 cut(s)	871
Alw26I	GTCTC	1 cut(s)	893
Alw44I	GTGCAC	1 cut(s)	867
AlwI	GGATC	3 cut(s)	148, 243, 830
ApaLI	GTGCAC	1 cut(s)	867
ApeKI	GCWGC	2 cut(s)	178, 264
ApoI	RAATTY	1 cut(s)	9
ArsI	GACNNNNNNTTYG	2 cut(s)	238, 270
Asp700I	GAANNNNTTC	2 cut(s)	626, 747
AspLEI	GCGC	1 cut(s)	195
AsuHPI	GGTGA	4 cut(s)	281, 742, 841, 910
BaeGI	GKGCMC	1 cut(s)	871
BarI	GAAGNNNNNNTAC	2 cut(s)	100, 132
BbsI	GAAGAC	3 cut(s)	544, 599, 797
Bbv12I	GWGCWC	1 cut(s)	871
BbvI	GCAGC	2 cut(s)	190, 251
BccI	CCATC	1 cut(s)	337
BcoDI	GTCTC	1 cut(s)	893
BfaI	CTAG	1 cut(s)	752
BfmI	CTRYAG	1 cut(s)	903
BfrI	CTTAAG	1 cut(s)	860
BglII	AGATCT	1 cut(s)	499
BisI	GCNGC	2 cut(s)	179, 265
BlsI	GCNGC	2 cut(s)	180, 266
BmsI	GCATC	3 cut(s)	295, 387, 772
BpiI	GAAGAC	3 cut(s)	544, 599, 797
BpmI	CTGGAG	1 cut(s)	821
Bpu10I	CCTNAGC	1 cut(s)	759
BsaHI	GRCGYC	2 cut(s)	97, 662
BsaJI	CCNNGG	1 cut(s)	157
BsaXI	ACNNNNNCTCC	2 cut(s)	611, 641
Bsc4I	CCNNNNNNNGG	3 cut(s)	334, 575, 712
BseDI	CCNNGG	1 cut(s)	157
BseGI	GGATG	1 cut(s)	286
BseLI	CCNNNNNNNGG	3 cut(s)	334, 575, 712
BseMII	CTCAG	1 cut(s)	750
BseRI	GAGGAG	1 cut(s)	728
BseSI	GKGCMC	1 cut(s)	871
BseXI	GCAGC	2 cut(s)	190, 251
Bsh1236I	CGCG	2 cut(s)	152, 193
BsiHKAI	GWGCWC	1 cut(s)	871
BslI	CCNNNNNNNGG	3 cut(s)	334, 575, 712
BsmAI	GTCTC	1 cut(s)	893
BsmI	GAATGC	1 cut(s)	33
Bsp1286I	GDGCHC	1 cut(s)	871
Bsp143I	GATC	7 cut(s)	153, 248, 412, 441, 499, 538, 835
BspACI	CCGC	1 cut(s)	267
BspCNI	CTCAG	1 cut(s)	751
BspFNI	CGCG	2 cut(s)	152, 193
BspMAI	CTGCAG	1 cut(s)	907
BspPI	GGATC	3 cut(s)	148, 243, 830
BspTI	CTTAAG	1 cut(s)	860
BssECI	CCNNGG	1 cut(s)	157
BssMI	GATC	7 cut(s)	153, 248, 412, 441, 499, 538, 835
BssNAI	GTATAC	1 cut(s)	810
BssNI	GRCGYC	2 cut(s)	97, 662
BssT1I	CCWWGG	1 cut(s)	157
Bst1107I	GTATAC	1 cut(s)	810
Bst4CI	ACNGT	4 cut(s)	394, 462, 814, 926
BstACI	GRCGYC	2 cut(s)	97, 662
BstAFI	CTTAAG	1 cut(s)	860
BstAPI	GCANNNNNTGC	1 cut(s)	769
BstC8I	GCNNGC	1 cut(s)	867
BstDEI	CTNAG	1 cut(s)	759
BstF5I	GGATG	1 cut(s)	286
BstFNI	CGCG	2 cut(s)	152, 193
BstHHI	GCGC	1 cut(s)	195
BstKTI	GATC	7 cut(s)	156, 251, 415, 444, 502, 541, 838
BstMAI	GTCTC	1 cut(s)	893
BstMBI	GATC	7 cut(s)	153, 248, 412, 441, 499, 538, 835
BstMWI	GCNNNNNNNGC	2 cut(s)	168, 769
BstNSI	RCATGY	1 cut(s)	451
BstSFI	CTRYAG	1 cut(s)	903
BstSLI	GKGCMC	1 cut(s)	871
BstUI	CGCG	2 cut(s)	152, 193
BstV1I	GCAGC	2 cut(s)	190, 251
BstV2I	GAAGAC	3 cut(s)	544, 599, 797
BstX2I	RGATCY	2 cut(s)	248, 499
BstYI	RGATCY	2 cut(s)	248, 499
BstZ17I	GTATAC	1 cut(s)	810
BtsCI	GGATG	1 cut(s)	286
BtsIMutI	CAGTG	1 cut(s)	691
Cac8I	GCNNGC	1 cut(s)	867
CfoI	GCGC	1 cut(s)	195
CseI	GACGC	1 cut(s)	670
Csp6I	GTAC	1 cut(s)	280
CviAII	CATG	3 cut(s)	448, 487, 610
CviJI	RGCY	6 cut(s)	105, 116, 181, 264, 373, 859
CviKI_1	RGCY	6 cut(s)	105, 116, 181, 264, 373, 859
CviQI	GTAC	1 cut(s)	280
DdeI	CTNAG	1 cut(s)	759
DpnI	GATC	7 cut(s)	155, 250, 414, 443, 501, 540, 837
DpnII	GATC	7 cut(s)	153, 248, 412, 441, 499, 538, 835
Eco130I	CCWWGG	1 cut(s)	157
Eco32I	GATATC	2 cut(s)	274, 693
EcoRV	GATATC	2 cut(s)	274, 693
EcoT14I	CCWWGG	1 cut(s)	157
ErhI	CCWWGG	1 cut(s)	157
FaeI	CATG	3 cut(s)	451, 490, 613
FalI	AAGNNNNNCTT	2 cut(s)	692, 724
FatI	CATG	3 cut(s)	447, 486, 609
FblI	GTMKAC	1 cut(s)	809
Fnu4HI	GCNGC	2 cut(s)	179, 265
FokI	GGATG	1 cut(s)	273
Fsp4HI	GCNGC	2 cut(s)	179, 265
FspBI	CTAG	1 cut(s)	752
GlaI	GCGC	1 cut(s)	194
GluI	GCNGC	2 cut(s)	179, 265
GsuI	CTGGAG	1 cut(s)	821
HgaI	GACGC	1 cut(s)	670
HhaI	GCGC	1 cut(s)	195
Hin1I	GRCGYC	2 cut(s)	97, 662
Hin1II	CATG	3 cut(s)	451, 490, 613
Hin6I	GCGC	1 cut(s)	193
HinP1I	GCGC	1 cut(s)	193
HindIII	AAGCTT	1 cut(s)	114
HinfI	GANTC	1 cut(s)	381
HphI	GGTGA	4 cut(s)	281, 742, 841, 910
Hpy166II	GTNNAC	2 cut(s)	810, 869
Hpy188I	TCNGA	7 cut(s)	303, 386, 417, 543, 619, 632, 660
Hpy188III	TCNNGA	5 cut(s)	61, 560, 583, 696, 758
Hpy8I	GTNNAC	2 cut(s)	810, 869
Hpy99I	CGWCG	2 cut(s)	99, 102
HpyCH4III	ACNGT	4 cut(s)	394, 462, 814, 926
HpyCH4IV	ACGT	2 cut(s)	97, 747
HpyCH4V	TGCA	5 cut(s)	33, 400, 671, 869, 905
HpyF10VI	GCNNNNNNNGC	2 cut(s)	168, 769
HpyF3I	CTNAG	1 cut(s)	759
HpySE526I	ACGT	2 cut(s)	97, 747
Hsp92I	GRCGYC	2 cut(s)	97, 662
Hsp92II	CATG	3 cut(s)	451, 490, 613
HspAI	GCGC	1 cut(s)	193
Kzo9I	GATC	7 cut(s)	153, 248, 412, 441, 499, 538, 835
LpnPI	CCDG	8 cut(s)	265, 290, 573, 691, 771, 785, 812, 891
Lsp1109I	GCAGC	2 cut(s)	190, 251
LweI	GCATC	3 cut(s)	295, 387, 772
MaeI	CTAG	1 cut(s)	752
MaeII	ACGT	2 cut(s)	97, 747
MaeIII	GTNAC	3 cut(s)	643, 829, 916
MalI	GATC	7 cut(s)	155, 250, 414, 443, 501, 540, 837
MboI	GATC	7 cut(s)	153, 248, 412, 441, 499, 538, 835
MboII	GAAGA	8 cut(s)	352, 368, 371, 509, 544, 604, 802, 892
MfeI	CAATTG	1 cut(s)	840
MflI	RGATCY	2 cut(s)	248, 499
MhlI	GDGCHC	1 cut(s)	871
MluCI	AATT	7 cut(s)	9, 257, 316, 418, 722, 840, 885
MlyI	GAGTC	1 cut(s)	390
MmeI	TCCRAC	3 cut(s)	103, 326, 409
MnlI	CCTC	6 cut(s)	147, 328, 706, 709, 775, 798
MroXI	GAANNNNTTC	2 cut(s)	626, 747
MseI	TTAA	4 cut(s)	39, 350, 738, 861
MspA1I	CMGCKG	1 cut(s)	264
MspCI	CTTAAG	1 cut(s)	860
MunI	CAATTG	1 cut(s)	840
Mva1269I	GAATGC	1 cut(s)	33
MvnI	CGCG	2 cut(s)	152, 193
MwoI	GCNNNNNNNGC	2 cut(s)	168, 769
NdeII	GATC	7 cut(s)	153, 248, 412, 441, 499, 538, 835
NlaIII	CATG	3 cut(s)	451, 490, 613
NmuCI	GTSAC	2 cut(s)	829, 916
NspI	RCATGY	1 cut(s)	451
PciI	ACATGT	1 cut(s)	447
PctI	GAATGC	1 cut(s)	33
PdmI	GAANNNNTTC	2 cut(s)	626, 747
PflMI	CCANNNNNTGG	1 cut(s)	575
PkrI	GCNGC	2 cut(s)	180, 266
PleI	GAGTC	1 cut(s)	389
PpsI	GAGTC	1 cut(s)	389
PscI	ACATGT	1 cut(s)	447
PstI	CTGCAG	1 cut(s)	907
PsuI	RGATCY	2 cut(s)	248, 499
PvuII	CAGCTG	1 cut(s)	264
RsaI	GTAC	1 cut(s)	281
RsaNI	GTAC	1 cut(s)	280
SaqAI	TTAA	4 cut(s)	39, 350, 738, 861
SatI	GCNGC	2 cut(s)	179, 265
Sau3AI	GATC	7 cut(s)	153, 248, 412, 441, 499, 538, 835
SchI	GAGTC	1 cut(s)	390
SduI	GDGCHC	1 cut(s)	871
SfaNI	GCATC	3 cut(s)	295, 387, 772
SfcI	CTRYAG	1 cut(s)	903
SmlI	CTYRAG	1 cut(s)	860
SmoI	CTYRAG	1 cut(s)	860
Sse9I	AATT	7 cut(s)	9, 257, 316, 418, 722, 840, 885
SsiI	CCGC	1 cut(s)	267
SspI	AATATT	1 cut(s)	736
SspMI	CTAG	1 cut(s)	752
StyI	CCWWGG	1 cut(s)	157
TaaI	ACNGT	4 cut(s)	394, 462, 814, 926
TaiI	ACGT	2 cut(s)	100, 750
TaqI	TCGA	2 cut(s)	213, 889
TasI	AATT	7 cut(s)	9, 257, 316, 418, 722, 840, 885
Tru1I	TTAA	4 cut(s)	39, 350, 738, 861
Tru9I	TTAA	4 cut(s)	39, 350, 738, 861
TscAI	CASTG	1 cut(s)	691
TseFI	GTSAC	2 cut(s)	829, 916
TseI	GCWGC	2 cut(s)	178, 264
Tsp45I	GTSAC	2 cut(s)	829, 916
TspDTI	ATGAA	3 cut(s)	503, 605, 626
TspGWI	ACGGA	1 cut(s)	492
TspRI	CASTG	1 cut(s)	691
Van91I	CCANNNNNTGG	1 cut(s)	575
Vha464I	CTTAAG	1 cut(s)	860
VneI	GTGCAC	1 cut(s)	867
XapI	RAATTY	1 cut(s)	9
XceI	RCATGY	1 cut(s)	451
XmiI	GTMKAC	1 cut(s)	809
XmnI	GAANNNNTTC	2 cut(s)	626, 747
XspI	CTAG	1 cut(s)	752
ZraI	GACGTC	1 cut(s)	98

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