Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr07

Orthogroup ID

OG0003607

Physical Location & Seq

Genomic Coordinates Reverse (-)

3025823 .. 3028668

Gene Structure 2846 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

MD07G1036700.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 696 bp

ATGGCTATCGTGAAAGGGGATGGCGTCGTTCCGGGCAGCGACGGAGGCAGCGGAAGGCCGGGGTGCATAACGAGCCACGTGGCAGAAGGGAGCGTGGAGAGCACCAGGTTCTACCTGTGCCGTCGTACAGTCATGGAAATGCTGAGGGACCGAGGCTGCAACGTCTCTGACTTGGACCTCAATCTCTCGCTCACTGAGTTCCTCTCCGAGTTCGGCCCCAACCCGGACCATGAACGCCTCAGCGTCTGCGTCCATCTACGCTCCAAGCCCTCCAAGAAGATTGTTGTCATCTTTTGTGGAACTGACGAGATAAGGAAACGCAACATGTGCGGTATCTATGCTGGCCTCCCGAACAAAGCAAGTATTCACCAGCTGATTCTTGTCTTACAAAGTAAAATGAACTGCTATGCTCGGAAAGAACTTGAAAAGTATCCATTTAAAGTTGACACCTTCCATATCTCGGACTTGCTGGTGAATATCACAAAGCATGTTTCACAGCCGAAGCTTGAGATGCTTACTGCTGAAGAAAAGAAGAAGCTGCTAATGAAATACAACTTGGAAGACAAGAAGCTCCCTCTGATGCTGGCAACTGATGCAACTGCACGATACTACGGATTGGAGAAGGGGCAGGTGGTAAAAGTCAATTACAGCGGGGGATTTGCTGGACCACTTGAAACTTACCGCTGCGTCGCTTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000419 GO:0000428 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0030880 GO:0032991 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0055029 GO:0061695 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

232

Amino Acids

25.79

Weight (kDa)

8.94

Isoelectric Point (pI)

36.81

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb5_N	PF03871	33 - 109	1.1e-19	RNA polymerase Rpb5, N-terminal domain
RNA_pol_Rpb5_C	PF01191	158 - 230	3.1e-25	RNA polymerase Rpb5, C-terminal domain

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

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Publication-ready

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Orthologous Genes (Group: OG0003607)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G54490
fragaria_vesca	FvH4_7g02710 FvH4_7g02710 FvH4_7g02710
malus_domestica	MD07G1036700.v1.1
prunus_persica	Prupe.2G032100_v2.0.a1
rosa_chinensis	RchiOBHm_Chr1g0321871 RchiOBHm_Chr1g0321951 RchiOBHm_Chr3g0472601
rosa_laevigata	RLG00000030400 RLG00000030402
rosa_multiflora	Rmu_sc0000427.1_g000005 Rmu_sc0002872.1_g000006 Rmu_sc0003510.1_g000023 Rmu_sc0015497.1_g000006
rosa_roxburghii	Rroxscaffold_4G00327410 Rroxscaffold_4G00327450
rosa_rugosa	Rorug01G0034400
rosa_samantha	Rh1AG047300 Rh1BG045400 Rh1CG051100 Rh1CG051500 Rh1DG055400 Rh1DG055800 Rh2CG536300 Rh3AG178800 Rh3BG204700 Rh3CG202100 Rh3CG224200 Rh5AG112100 Rh6AG330000
rosa_wichuraiana	Rw1G004250 Rw1G004290 Rw1G004310 Rw5G021040

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	619
Acc36I	ACCTGC	1 cut(s)	619
AciI	CCGC	4 cut(s)	51, 330, 651, 682
AcuI	CTGAAG	1 cut(s)	543
AcvI	CACGTG	1 cut(s)	79
AcyI	GRCGYC	1 cut(s)	24
AfaI	GTAC	1 cut(s)	127
AfiI	CCNNNNNNNGG	2 cut(s)	223, 460
AflIII	ACRYGT	1 cut(s)	324
AgsI	TTSAA	2 cut(s)	425, 674
AjnI	CCWGG	1 cut(s)	104
AjuI	GAANNNNNNNTTGG	2 cut(s)	539, 571
AluBI	AGCT	4 cut(s)	373, 505, 538, 571
AluI	AGCT	4 cut(s)	373, 505, 538, 571
Alw21I	GWGCWC	1 cut(s)	104
Alw26I	GTCTC	1 cut(s)	169
AlwNI	CAGNNNCTG	1 cut(s)	246
AoxI	GGCC	3 cut(s)	56, 214, 343
ApeKI	GCWGC	5 cut(s)	36, 48, 156, 538, 684
AspS9I	GGNCC	5 cut(s)	148, 175, 215, 226, 665
AsuC2I	CCSGG	3 cut(s)	33, 60, 224
AsuHPI	GGTGA	2 cut(s)	359, 484
AvaII	GGWCC	4 cut(s)	148, 175, 226, 665
BbrPI	CACGTG	1 cut(s)	79
BbsI	GAAGAC	1 cut(s)	567
Bbv12I	GWGCWC	1 cut(s)	104
BbvCI	CCTCAGC	2 cut(s)	143, 239
BbvI	GCAGC	5 cut(s)	48, 60, 143, 525, 671
BccI	CCATC	2 cut(s)	14, 261
BceAI	ACGGC	1 cut(s)	105
BciT130I	CCWGG	1 cut(s)	106
BciVI	GTATCC	1 cut(s)	441
BcnI	CCSGG	3 cut(s)	33, 60, 224
BcoDI	GTCTC	1 cut(s)	169
BfuAI	ACCTGC	1 cut(s)	619
BfuI	GTATCC	1 cut(s)	441
BisI	GCNGC	5 cut(s)	37, 49, 157, 539, 685
BlsI	GCNGC	5 cut(s)	38, 50, 158, 540, 686
Bme1390I	CCNGG	4 cut(s)	33, 60, 106, 224
Bme18I	GGWCC	4 cut(s)	148, 175, 226, 665
BmgT120I	GGNCC	5 cut(s)	148, 175, 215, 226, 665
BmiI	GGNNCC	2 cut(s)	149, 217
BmrFI	CCNGG	4 cut(s)	33, 60, 106, 224
BmsI	GCATC	3 cut(s)	501, 570, 583
BpiI	GAAGAC	1 cut(s)	567
BplI	GAGNNNNNCTC	2 cut(s)	188, 220
Bpu10I	CCTNAGC	2 cut(s)	143, 239
BpuEI	CTTGAG	1 cut(s)	527
BpuMI	CCSGG	3 cut(s)	33, 60, 224
BsaAI	YACGTR	1 cut(s)	79
BsaHI	GRCGYC	1 cut(s)	24
BsaJI	CCNNGG	2 cut(s)	59, 151
Bsc4I	CCNNNNNNNGG	2 cut(s)	223, 460
BseBI	CCWGG	1 cut(s)	106
BseDI	CCNNGG	2 cut(s)	59, 151
BseGI	GGATG	1 cut(s)	25
BseLI	CCNNNNNNNGG	2 cut(s)	223, 460
BseMII	CTCAG	3 cut(s)	134, 186, 253
BseXI	GCAGC	5 cut(s)	48, 60, 143, 525, 671
BsgI	GTGCAG	1 cut(s)	585
BshFI	GGCC	3 cut(s)	58, 216, 345
BsiHKAI	GWGCWC	1 cut(s)	104
BsiSI	CCGG	3 cut(s)	32, 59, 224
BslFI	GGGAC	1 cut(s)	161
BslI	CCNNNNNNNGG	2 cut(s)	223, 460
BsmAI	GTCTC	1 cut(s)	169
BsmBI	CGTCTC	1 cut(s)	169
BsmFI	GGGAC	1 cut(s)	161
BsnI	GGCC	3 cut(s)	58, 216, 345
Bsp1286I	GDGCHC	1 cut(s)	104
BspACI	CCGC	4 cut(s)	51, 330, 651, 682
BspANI	GGCC	3 cut(s)	58, 216, 345
BspCNI	CTCAG	3 cut(s)	135, 187, 252
BspLI	GGNNCC	2 cut(s)	149, 217
BspMI	ACCTGC	1 cut(s)	619
BssECI	CCNNGG	2 cut(s)	59, 151
BssNI	GRCGYC	1 cut(s)	24
Bst2UI	CCWGG	1 cut(s)	106
Bst4CI	ACNGT	1 cut(s)	130
BstACI	GRCGYC	1 cut(s)	24
BstAPI	GCANNNNNTGC	2 cut(s)	327, 593
BstBAI	YACGTR	1 cut(s)	79
BstC8I	GCNNGC	2 cut(s)	343, 585
BstDEI	CTNAG	3 cut(s)	143, 195, 239
BstF5I	GGATG	1 cut(s)	25
BstMAI	GTCTC	1 cut(s)	169
BstMWI	GCNNNNNNNGC	6 cut(s)	45, 72, 99, 327, 511, 593
BstNI	CCWGG	1 cut(s)	106
BstNSI	RCATGY	2 cut(s)	328, 491
BstSCI	CCNGG	4 cut(s)	31, 58, 104, 222
BstV1I	GCAGC	5 cut(s)	48, 60, 143, 525, 671
BstV2I	GAAGAC	1 cut(s)	567
BsuI	GTATCC	1 cut(s)	441
BsuRI	GGCC	3 cut(s)	58, 216, 345
BtsCI	GGATG	1 cut(s)	25
BtsIMutI	CAGTG	1 cut(s)	192
BveI	ACCTGC	1 cut(s)	619
Cac8I	GCNNGC	2 cut(s)	343, 585
CaiI	CAGNNNCTG	1 cut(s)	246
Cfr13I	GGNCC	5 cut(s)	148, 175, 215, 226, 665
CseI	GACGC	4 cut(s)	13, 232, 238, 676
CsiI	ACCWGGT	1 cut(s)	104
Csp6I	GTAC	1 cut(s)	126
CviAII	CATG	4 cut(s)	133, 230, 325, 488
CviQI	GTAC	1 cut(s)	126
DdeI	CTNAG	3 cut(s)	143, 195, 239
DraI	TTTAAA	1 cut(s)	439
Eco47I	GGWCC	4 cut(s)	148, 175, 226, 665
Eco57I	CTGAAG	1 cut(s)	543
Eco72I	CACGTG	1 cut(s)	79
EcoRII	CCWGG	1 cut(s)	104
Esp3I	CGTCTC	1 cut(s)	169
FaeI	CATG	4 cut(s)	136, 233, 328, 491
FaiI	YATR	8 cut(s)	68, 134, 231, 326, 339, 408, 456, 489
FaqI	GGGAC	1 cut(s)	161
FatI	CATG	4 cut(s)	132, 229, 324, 487
FauI	CCCGC	1 cut(s)	644
Fnu4HI	GCNGC	5 cut(s)	37, 49, 157, 539, 685
FokI	GGATG	1 cut(s)	32
Fsp4HI	GCNGC	5 cut(s)	37, 49, 157, 539, 685
GluI	GCNGC	5 cut(s)	37, 49, 157, 539, 685
HaeIII	GGCC	3 cut(s)	58, 216, 345
HapII	CCGG	3 cut(s)	32, 59, 224
HgaI	GACGC	4 cut(s)	13, 232, 238, 676
Hin1I	GRCGYC	1 cut(s)	24
Hin1II	CATG	4 cut(s)	136, 233, 328, 491
HincII	GTYRAC	1 cut(s)	445
HindII	GTYRAC	1 cut(s)	445
HindIII	AAGCTT	1 cut(s)	503
HinfI	GANTC	1 cut(s)	376
HpaII	CCGG	3 cut(s)	32, 59, 224
HphI	GGTGA	2 cut(s)	359, 484
Hpy166II	GTNNAC	1 cut(s)	445
Hpy188I	TCNGA	5 cut(s)	169, 208, 414, 463, 579
Hpy188III	TCNNGA	2 cut(s)	10, 349
Hpy8I	GTNNAC	1 cut(s)	445
Hpy99I	CGWCG	4 cut(s)	29, 44, 126, 692
HpyAV	CCTTC	4 cut(s)	48, 80, 460, 616
HpyCH4III	ACNGT	1 cut(s)	130
HpyCH4IV	ACGT	2 cut(s)	78, 162
HpyCH4V	TGCA	4 cut(s)	66, 159, 596, 602
HpyF10VI	GCNNNNNNNGC	6 cut(s)	45, 72, 99, 327, 511, 593
HpyF3I	CTNAG	3 cut(s)	143, 195, 239
HpySE526I	ACGT	2 cut(s)	78, 162
Hsp92I	GRCGYC	1 cut(s)	24
Hsp92II	CATG	4 cut(s)	136, 233, 328, 491
LmnI	GCTCC	3 cut(s)	90, 266, 576
Lsp1109I	GCAGC	5 cut(s)	48, 60, 143, 525, 671
LweI	GCATC	3 cut(s)	501, 570, 583
MabI	ACCWGGT	1 cut(s)	104
MaeII	ACGT	2 cut(s)	78, 162
MboII	GAAGA	4 cut(s)	289, 536, 544, 572
MhlI	GDGCHC	1 cut(s)	104
MluCI	AATT	1 cut(s)	643
MnlI	CCTC	9 cut(s)	38, 138, 146, 188, 212, 248, 280, 356, 585
MseI	TTAA	1 cut(s)	438
MslI	CAYNNNNRTG	1 cut(s)	137
MspA1I	CMGCKG	4 cut(s)	51, 373, 651, 684
MspI	CCGG	3 cut(s)	32, 59, 224
MspR9I	CCNGG	4 cut(s)	33, 60, 106, 224
MvaI	CCWGG	1 cut(s)	106
MwoI	GCNNNNNNNGC	6 cut(s)	45, 72, 99, 327, 511, 593
NciI	CCSGG	3 cut(s)	33, 60, 224
NlaIII	CATG	4 cut(s)	136, 233, 328, 491
NlaIV	GGNNCC	2 cut(s)	149, 217
NspI	RCATGY	2 cut(s)	328, 491
PaqCI	CACCTGC	1 cut(s)	619
PciI	ACATGT	1 cut(s)	324
PfeI	GAWTC	1 cut(s)	376
PkrI	GCNGC	5 cut(s)	38, 50, 158, 540, 686
PmaCI	CACGTG	1 cut(s)	79
PmlI	CACGTG	1 cut(s)	79
Ppu21I	YACGTR	1 cut(s)	79
PscI	ACATGT	1 cut(s)	324
Psp6I	CCWGG	1 cut(s)	104
PspCI	CACGTG	1 cut(s)	79
PspGI	CCWGG	1 cut(s)	104
PspN4I	GGNNCC	2 cut(s)	149, 217
PspPI	GGNCC	5 cut(s)	148, 175, 215, 226, 665
PstNI	CAGNNNCTG	1 cut(s)	246
PvuII	CAGCTG	1 cut(s)	373
RsaI	GTAC	1 cut(s)	127
RsaNI	GTAC	1 cut(s)	126
RseI	CAYNNNNRTG	1 cut(s)	137
SaqAI	TTAA	1 cut(s)	438
SatI	GCNGC	5 cut(s)	37, 49, 157, 539, 685
Sau96I	GGNCC	5 cut(s)	148, 175, 215, 226, 665
ScrFI	CCNGG	4 cut(s)	33, 60, 106, 224
SduI	GDGCHC	1 cut(s)	104
SexAI	ACCWGGT	1 cut(s)	104
SfaNI	GCATC	3 cut(s)	501, 570, 583
SinI	GGWCC	4 cut(s)	148, 175, 226, 665
SmiMI	CAYNNNNRTG	1 cut(s)	137
SmlI	CTYRAG	1 cut(s)	506
SmoI	CTYRAG	1 cut(s)	506
Sse9I	AATT	1 cut(s)	643
SsiI	CCGC	4 cut(s)	51, 330, 651, 682
StyD4I	CCNGG	4 cut(s)	31, 58, 104, 222
TaaI	ACNGT	1 cut(s)	130
TaiI	ACGT	2 cut(s)	81, 165
TaqII	GACCGA	1 cut(s)	165
TasI	AATT	1 cut(s)	643
TfiI	GAWTC	1 cut(s)	376
Tru1I	TTAA	1 cut(s)	438
Tru9I	TTAA	1 cut(s)	438
TscAI	CASTG	1 cut(s)	199
TseI	GCWGC	5 cut(s)	36, 48, 156, 538, 684
TspDTI	ATGAA	3 cut(s)	246, 413, 560
TspGWI	ACGGA	2 cut(s)	57, 627
TspRI	CASTG	1 cut(s)	199
VpaK11BI	GGWCC	4 cut(s)	148, 175, 226, 665
XceI	RCATGY	2 cut(s)	328, 491

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