Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr06

Orthogroup ID

OG0002992

Physical Location & Seq

Genomic Coordinates Forward (+)

16760513 .. 16763493

Gene Structure 2981 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

MD06G1069300.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1248 bp

ATGGCTCATATGCTTTGTTTTGCCATGTGTCAAAATCACATTGGCTCATGTCATTATGGGCGTATCCAATTTCCATGCTCAGTAGTTCATCCTTATTATCTTGTGGAAGTTGTTCAAATCTTAAACAAGATTTGTGTAGGATGTAAATCCGTTAAGCAGGATTTTAAGGTCAAGGGAAGTTCGTTAAGCTACCCAAGAATGAAGTTCAGAGTTTCTACGAGAGAACTCTTTAAAAGAAGTTGTACTATCATGGAAGCAAGCGGAATATTGCCTTCTGACTATTGGGATTTTATTCCAAAAGATGCACATCAAGATGAGAGTTGCACTAAACCAAACAAAAGAATTCTATCTCATGCGCAGGTTCATCATTTGTTGAAGGATGTTGATCCAAATTTCATTGCGAAGTTTGTCCCAATGACAGATTCACTTTCTATGGATTTATTCCTTGTAACTCCAAATAGTCATCGCGTGACAGAGTTTATGCATGCTTTTGCTAATGGGCAGCGGTTGATGTTTGACCATCGGACCAGGGCTTATAGGAAACTTTTCGATTTCAAAGGTGTAGCTAATGAGCTGGGTTCTCATTTGAACTCAGAGAAACCGGGCAATGATTTGATTGCTGCTCAGCTAAAAAATGTTAAAGATGATCGTTCAAAATCATCTGGTTTGAGATGGATCAAAGATGTTTTTCTTGGGAAGAGAACTGATCACTGTTTCCACATGGTGGTTGTTGGTGATCCAAACATTAAGCTCAGTGAAATTGGTATACCCTCTCATATTGCAGAGAGGATGCAGATAGCTGAGAATCTGAACAGATGGAACTTAGAAAGGTTGGGTGCCATCTGCAATCTACGCCTAATGTACAAACAAGTGATGCATGTTCGTAAAAAAGGTAGCATCATTCTCGTACGCCAGACAGACGAATTGCTGATGGGAGATACTATTTACAGGCCTCTGAGTGAAGGAGACATTTTGTTGATTAATAGGCATCCATCAATACATCAACACTCCCTCATTGCTTTATTCGTCAAGATACTTCCGGCAGCACCTGTTGTATCTATAAACCCACTCTGTTGCTCTCCATTTTGTGGTGACTTTGATGGTGATTGCCTTCATGGCTATGTTCCTCAATCAGCTGAGGCCAAAGTTGAGCTTAGCGAACTTGTTGCTTTAAATAAGCAATTGATTAATGTGCAGAGCGGTACCAACCTACTTCTTAACTGCTGCCCATTTGATCCTGGAGGATGA

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:0005666 GO:0006139 GO:0006396 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009892 GO:0009987 GO:0010033 GO:0010467 GO:0010468 GO:0010495 GO:0010605 GO:0010608 GO:0010629 GO:0014070 GO:0016070 GO:0016246 GO:0016441 GO:0016458 GO:0019222 GO:0030422 GO:0030880 GO:0031047 GO:0031050 GO:0031974 GO:0031981 GO:0032991 GO:0034641 GO:0035194 GO:0040029 GO:0042221 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0043331 GO:0044237 GO:0044238 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0046483 GO:0048519 GO:0050789 GO:0050896 GO:0051716 GO:0055029 GO:0060255 GO:0061695 GO:0065007 GO:0070013 GO:0070887 GO:0070918 GO:0071310 GO:0071359 GO:0071407 GO:0071704 GO:0090304 GO:1901360 GO:1901698 GO:1901699 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

DUF3223 RNA_pol_Rpb1_1 RNA_pol_Rpb1_2 RNA_pol_Rpb1_3 RNA_pol_Rpb1_4 RNA_pol_Rpb1_5

Protein Analysis

416

Amino Acids

46.93

Weight (kDa)

8.78

Isoelectric Point (pI)

43.75

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb1_2	PF00623	232 - 389	1.2e-31	RNA polymerase Rpb1, domain 2

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: OG0002992)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G63020 AT1G63020 AT1G63020 AT1G63020 AT1G63020
fragaria_vesca	FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400
malus_domestica	MD04G1068800.v1.1 MD06G1069300.v1.1 MD06G1069400.v1.1 MD06G1069500.v1.1 MD06G1069800.v1.1
prunus_persica	Prupe.5G089300_v2.0.a1
pyrus_communis	pycom04g06250
rosa_chinensis	RchiOBHm_Chr7g0199481
rosa_laevigata	RLG00000003790
rosa_multiflora	Rmu_co8411067.1_g000001 Rmu_sc0003890.1_g000001
rosa_roxburghii	Rroxscaffold_3G00256700
rosa_rugosa	Rorug07G0054300 Rorug07G0054400 Rorug07G0054500 Rorug07G0054500
rosa_samantha	Rh7AG179300 Rh7BG182800 Rh7CG188100 Rh7DG182200
rosa_wichuraiana	Rw7G015760

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc16I	TGCGCA	1 cut(s)	357
Acc36I	ACCTGC	1 cut(s)	349
Acc65I	GGTACC	1 cut(s)	1202
AccB1I	GGYRCC	2 cut(s)	836, 1202
AccB7I	CCANNNNNTGG	2 cut(s)	724, 1088
AccBSI	CCGCTC	1 cut(s)	1200
AccI	GTMKAC	1 cut(s)	766
AccII	CGCG	1 cut(s)	468
AciI	CCGC	3 cut(s)	261, 505, 1200
AclWI	GGATC	4 cut(s)	380, 683, 731, 1229
AcsI	RAATTY	2 cut(s)	342, 391
AdeI	CACNNNGTG	1 cut(s)	724
AfaI	GTAC	4 cut(s)	244, 863, 909, 1204
AfiI	CCNNNNNNNGG	2 cut(s)	724, 1088
AgsI	TTSAA	5 cut(s)	116, 376, 556, 589, 654
AjnI	CCWGG	2 cut(s)	527, 1237
AjuI	GAANNNNNNNTTGG	2 cut(s)	406, 438
AluBI	AGCT	8 cut(s)	189, 566, 574, 628, 751, 800, 1136, 1153
AluI	AGCT	8 cut(s)	189, 566, 574, 628, 751, 800, 1136, 1153
Alw26I	GTCTC	1 cut(s)	960
AlwI	GGATC	4 cut(s)	380, 683, 731, 1229
AlwNI	CAGNNNCTG	1 cut(s)	1049
AoxI	GGCC	2 cut(s)	950, 1140
ApeKI	GCWGC	4 cut(s)	502, 620, 1043, 1224
ApoI	RAATTY	2 cut(s)	342, 391
AseI	ATTAAT	2 cut(s)	981, 1188
Asp700I	GAANNNNTTC	2 cut(s)	111, 545
Asp718I	GGTACC	1 cut(s)	1202
AspLEI	GCGC	1 cut(s)	358
AspS9I	GGNCC	1 cut(s)	525
AsuC2I	CCSGG	1 cut(s)	603
AsuHPI	GGTGA	3 cut(s)	746, 1103, 1115
AvaII	GGWCC	1 cut(s)	525
BanI	GGYRCC	2 cut(s)	836, 1202
BbvCI	CCTCAGC	1 cut(s)	1137
BbvI	GCAGC	4 cut(s)	514, 607, 1055, 1211
BccI	CCATC	7 cut(s)	528, 666, 810, 848, 925, 1000, 1094
BcgI	CGANNNNNNTGC	4 cut(s)	886, 920, 1148, 1182
BciT130I	CCWGG	2 cut(s)	529, 1239
BciVI	GTATCC	1 cut(s)	74
BclI	TGATCA	1 cut(s)	706
BcnI	CCSGG	1 cut(s)	603
BcoDI	GTCTC	1 cut(s)	960
BfuAI	ACCTGC	1 cut(s)	349
BfuI	GTATCC	1 cut(s)	74
BglI	GCCNNNNNGGC	1 cut(s)	1116
BisI	GCNGC	4 cut(s)	503, 621, 1044, 1225
BlpI	GCTNAGC	2 cut(s)	624, 1154
BlsI	GCNGC	4 cut(s)	504, 622, 1045, 1226
Bme1390I	CCNGG	3 cut(s)	529, 603, 1239
Bme18I	GGWCC	1 cut(s)	525
BmgT120I	GGNCC	1 cut(s)	525
BmiI	GGNNCC	2 cut(s)	838, 1204
BmrFI	CCNGG	3 cut(s)	529, 603, 1239
BmsI	GCATC	5 cut(s)	292, 780, 864, 906, 997
Bpu10I	CCTNAGC	1 cut(s)	1137
Bpu1102I	GCTNAGC	2 cut(s)	624, 1154
BpuMI	CCSGG	1 cut(s)	603
BsaBI	GATNNNNATC	3 cut(s)	145, 306, 384
BsaJI	CCNNGG	1 cut(s)	528
Bsc4I	CCNNNNNNNGG	2 cut(s)	724, 1088
Bse3DI	GCAATG	3 cut(s)	396, 613, 1014
Bse8I	GATNNNNATC	3 cut(s)	145, 306, 384
BseBI	CCWGG	2 cut(s)	529, 1239
BseDI	CCNNGG	1 cut(s)	528
BseGI	GGATG	5 cut(s)	88, 146, 385, 795, 988
BseJI	GATNNNNATC	3 cut(s)	145, 306, 384
BseLI	CCNNNNNNNGG	2 cut(s)	724, 1088
BseMI	GCAATG	3 cut(s)	396, 613, 1014
BseMII	CTCAG	7 cut(s)	93, 606, 638, 766, 792, 947, 1128
BseXI	GCAGC	4 cut(s)	514, 607, 1055, 1211
BseYI	CCCAGC	1 cut(s)	574
BsgI	GTGCAG	1 cut(s)	1214
Bsh1236I	CGCG	1 cut(s)	468
BshFI	GGCC	2 cut(s)	952, 1142
BshNI	GGYRCC	2 cut(s)	836, 1202
BsiSI	CCGG	2 cut(s)	602, 1040
BsiWI	CGTACG	1 cut(s)	907
BslFI	GGGAC	1 cut(s)	395
BslI	CCNNNNNNNGG	2 cut(s)	724, 1088
BsmAI	GTCTC	1 cut(s)	960
BsmFI	GGGAC	1 cut(s)	395
BsnI	GGCC	2 cut(s)	952, 1142
Bsp1407I	TGTACA	1 cut(s)	861
Bsp143I	GATC	6 cut(s)	385, 646, 675, 706, 736, 1234
Bsp1720I	GCTNAGC	2 cut(s)	624, 1154
BspACI	CCGC	3 cut(s)	261, 505, 1200
BspANI	GGCC	2 cut(s)	952, 1142
BspCNI	CTCAG	7 cut(s)	92, 605, 637, 765, 793, 948, 1129
BspFNI	CGCG	1 cut(s)	468
BspLI	GGNNCC	2 cut(s)	838, 1204
BspMI	ACCTGC	1 cut(s)	349
BspPI	GGATC	4 cut(s)	380, 683, 731, 1229
BspT107I	GGYRCC	2 cut(s)	836, 1202
BsrBI	CCGCTC	1 cut(s)	1200
BsrDI	GCAATG	3 cut(s)	396, 613, 1014
BsrGI	TGTACA	1 cut(s)	861
BssECI	CCNNGG	1 cut(s)	528
BssMI	GATC	6 cut(s)	385, 646, 675, 706, 736, 1234
BssNAI	GTATAC	1 cut(s)	767
Bst1107I	GTATAC	1 cut(s)	767
Bst2UI	CCWGG	2 cut(s)	529, 1239
Bst4CI	ACNGT	1 cut(s)	713
Bst6I	CTCTTC	1 cut(s)	692
BstAUI	TGTACA	1 cut(s)	861
BstC8I	GCNNGC	2 cut(s)	259, 486
BstDEI	CTNAG	9 cut(s)	79, 592, 624, 752, 801, 823, 956, 1137, 1154
BstF5I	GGATG	5 cut(s)	88, 146, 385, 795, 988
BstFNI	CGCG	1 cut(s)	468
BstHHI	GCGC	1 cut(s)	358
BstKTI	GATC	6 cut(s)	388, 649, 678, 709, 739, 1237
BstMAI	GTCTC	1 cut(s)	960
BstMBI	GATC	6 cut(s)	385, 646, 675, 706, 736, 1234
BstMWI	GCNNNNNNNGC	2 cut(s)	852, 1116
BstNI	CCWGG	2 cut(s)	529, 1239
BstNSI	RCATGY	2 cut(s)	488, 881
BstSCI	CCNGG	3 cut(s)	527, 601, 1237
BstUI	CGCG	1 cut(s)	468
BstV1I	GCAGC	4 cut(s)	514, 607, 1055, 1211
BstZ17I	GTATAC	1 cut(s)	767
BsuI	GTATCC	1 cut(s)	74
BsuRI	GGCC	2 cut(s)	952, 1142
BtgZI	GCGATG	1 cut(s)	449
BtsCI	GGATG	5 cut(s)	88, 146, 385, 795, 988
BtsIMutI	CAGTG	2 cut(s)	709, 760
BveI	ACCTGC	1 cut(s)	349
Cac8I	GCNNGC	2 cut(s)	259, 486
CaiI	CAGNNNCTG	1 cut(s)	1049
CfoI	GCGC	1 cut(s)	358
Cfr13I	GGNCC	1 cut(s)	525
Csp6I	GTAC	4 cut(s)	243, 862, 908, 1203
CviAII	CATG	9 cut(s)	25, 48, 75, 250, 353, 485, 721, 878, 1115
CviQI	GTAC	4 cut(s)	243, 862, 908, 1203
DdeI	CTNAG	9 cut(s)	79, 592, 624, 752, 801, 823, 956, 1137, 1154
DpnI	GATC	6 cut(s)	387, 648, 677, 708, 738, 1236
DpnII	GATC	6 cut(s)	385, 646, 675, 706, 736, 1234
DraI	TTTAAA	2 cut(s)	232, 1173
DraIII	CACNNNGTG	1 cut(s)	724
Eam1104I	CTCTTC	1 cut(s)	692
EarI	CTCTTC	1 cut(s)	692
Eco147I	AGGCCT	1 cut(s)	952
Eco47I	GGWCC	1 cut(s)	525
EcoRI	GAATTC	1 cut(s)	342
EcoRII	CCWGG	2 cut(s)	527, 1237
EcoT22I	ATGCAT	2 cut(s)	486, 879
FaeI	CATG	9 cut(s)	28, 51, 78, 253, 356, 488, 724, 881, 1118
FalI	AAGNNNNNCTT	2 cut(s)	1137, 1169
FaqI	GGGAC	1 cut(s)	395
FatI	CATG	9 cut(s)	24, 47, 74, 249, 352, 484, 720, 877, 1114
FauNDI	CATATG	1 cut(s)	9
FbaI	TGATCA	1 cut(s)	706
FblI	GTMKAC	1 cut(s)	766
Fnu4HI	GCNGC	4 cut(s)	503, 621, 1044, 1225
FokI	GGATG	5 cut(s)	75, 153, 392, 802, 975
Fsp4HI	GCNGC	4 cut(s)	503, 621, 1044, 1225
FspI	TGCGCA	1 cut(s)	357
GlaI	GCGC	1 cut(s)	357
GluI	GCNGC	4 cut(s)	503, 621, 1044, 1225
GsaI	CCCAGC	1 cut(s)	578
HaeIII	GGCC	2 cut(s)	952, 1142
HapII	CCGG	2 cut(s)	602, 1040
HhaI	GCGC	1 cut(s)	358
Hin1II	CATG	9 cut(s)	28, 51, 78, 253, 356, 488, 724, 881, 1118
Hin6I	GCGC	1 cut(s)	356
HinP1I	GCGC	1 cut(s)	356
HinfI	GANTC	2 cut(s)	422, 805
HpaII	CCGG	2 cut(s)	602, 1040
HphI	GGTGA	3 cut(s)	746, 1103, 1115
Hpy166II	GTNNAC	1 cut(s)	767
Hpy188I	TCNGA	6 cut(s)	209, 277, 525, 595, 810, 957
Hpy188III	TCNNGA	2 cut(s)	311, 1030
Hpy8I	GTNNAC	1 cut(s)	767
HpyAV	CCTTC	4 cut(s)	282, 370, 956, 1121
HpyCH4III	ACNGT	1 cut(s)	713
HpyCH4V	TGCA	8 cut(s)	305, 324, 484, 782, 793, 846, 877, 1195
HpyF10VI	GCNNNNNNNGC	2 cut(s)	852, 1116
HpyF3I	CTNAG	9 cut(s)	79, 592, 624, 752, 801, 823, 956, 1137, 1154
Hsp92II	CATG	9 cut(s)	28, 51, 78, 253, 356, 488, 724, 881, 1118
HspAI	GCGC	1 cut(s)	356
KpnI	GGTACC	1 cut(s)	1206
Ksp22I	TGATCA	1 cut(s)	706
Kzo9I	GATC	6 cut(s)	385, 646, 675, 706, 736, 1234
Lsp1109I	GCAGC	4 cut(s)	514, 607, 1055, 1211
LweI	GCATC	5 cut(s)	292, 780, 864, 906, 997
MaeIII	GTNAC	3 cut(s)	448, 469, 1091
MalI	GATC	6 cut(s)	387, 648, 677, 708, 738, 1236
MbiI	CCGCTC	1 cut(s)	1200
MboI	GATC	6 cut(s)	385, 646, 675, 706, 736, 1234
MboII	GAAGA	1 cut(s)	709
MfeI	CAATTG	1 cut(s)	1181
MluCI	AATT	6 cut(s)	68, 342, 391, 759, 923, 1181
MnlI	CCTC	7 cut(s)	780, 781, 963, 1022, 1132, 1137, 1235
Mph1103I	ATGCAT	2 cut(s)	486, 879
MroXI	GAANNNNTTC	2 cut(s)	111, 545
MslI	CAYNNNNRTG	2 cut(s)	312, 1119
MspA1I	CMGCKG	2 cut(s)	505, 1136
MspI	CCGG	2 cut(s)	602, 1040
MspR9I	CCNGG	3 cut(s)	529, 603, 1239
MunI	CAATTG	1 cut(s)	1181
MvaI	CCWGG	2 cut(s)	529, 1239
MvnI	CGCG	1 cut(s)	468
MwoI	GCNNNNNNNGC	2 cut(s)	852, 1116
NciI	CCSGG	1 cut(s)	603
NdeI	CATATG	1 cut(s)	9
NdeII	GATC	6 cut(s)	385, 646, 675, 706, 736, 1234
NlaIII	CATG	9 cut(s)	28, 51, 78, 253, 356, 488, 724, 881, 1118
NlaIV	GGNNCC	2 cut(s)	838, 1204
NmuCI	GTSAC	2 cut(s)	469, 1091
NsbI	TGCGCA	1 cut(s)	357
NsiI	ATGCAT	2 cut(s)	486, 879
NspI	RCATGY	2 cut(s)	488, 881
PaeI	GCATGC	1 cut(s)	488
PceI	AGGCCT	1 cut(s)	952
PdmI	GAANNNNTTC	2 cut(s)	111, 545
PfeI	GAWTC	2 cut(s)	422, 805
Pfl23II	CGTACG	1 cut(s)	907
PflMI	CCANNNNNTGG	2 cut(s)	724, 1088
PfoI	TCCNGGA	1 cut(s)	1237
PkrI	GCNGC	4 cut(s)	504, 622, 1045, 1226
PshBI	ATTAAT	2 cut(s)	981, 1188
Psp6I	CCWGG	2 cut(s)	527, 1237
PspFI	CCCAGC	1 cut(s)	574
PspGI	CCWGG	2 cut(s)	527, 1237
PspLI	CGTACG	1 cut(s)	907
PspN4I	GGNNCC	2 cut(s)	838, 1204
PspPI	GGNCC	1 cut(s)	525
PstNI	CAGNNNCTG	1 cut(s)	1049
PvuII	CAGCTG	1 cut(s)	1136
RsaI	GTAC	4 cut(s)	244, 863, 909, 1204
RsaNI	GTAC	4 cut(s)	243, 862, 908, 1203
RseI	CAYNNNNRTG	2 cut(s)	312, 1119
SatI	GCNGC	4 cut(s)	503, 621, 1044, 1225
Sau3AI	GATC	6 cut(s)	385, 646, 675, 706, 736, 1234
Sau96I	GGNCC	1 cut(s)	525
ScrFI	CCNGG	3 cut(s)	529, 603, 1239
SfaNI	GCATC	5 cut(s)	292, 780, 864, 906, 997
SinI	GGWCC	1 cut(s)	525
SmiMI	CAYNNNNRTG	2 cut(s)	312, 1119
SphI	GCATGC	1 cut(s)	488
Sse9I	AATT	6 cut(s)	68, 342, 391, 759, 923, 1181
SseBI	AGGCCT	1 cut(s)	952
SsiI	CCGC	3 cut(s)	261, 505, 1200
SspI	AATATT	1 cut(s)	267
StuI	AGGCCT	1 cut(s)	952
StyD4I	CCNGG	3 cut(s)	527, 601, 1237
TaaI	ACNGT	1 cut(s)	713
TaqI	TCGA	1 cut(s)	549
TasI	AATT	6 cut(s)	68, 342, 391, 759, 923, 1181
TatI	WGTACW	2 cut(s)	242, 861
TfiI	GAWTC	2 cut(s)	422, 805
TscAI	CASTG	2 cut(s)	716, 760
TseFI	GTSAC	2 cut(s)	469, 1091
TseI	GCWGC	4 cut(s)	502, 620, 1043, 1224
Tsp45I	GTSAC	2 cut(s)	469, 1091
TspDTI	ATGAA	5 cut(s)	77, 215, 353, 385, 1103
TspGWI	ACGGA	1 cut(s)	139
TspRI	CASTG	2 cut(s)	716, 760
Van91I	CCANNNNNTGG	2 cut(s)	724, 1088
VpaK11BI	GGWCC	1 cut(s)	525
VspI	ATTAAT	2 cut(s)	981, 1188
XapI	RAATTY	2 cut(s)	342, 391
XceI	RCATGY	2 cut(s)	488, 881
XmiI	GTMKAC	1 cut(s)	766
XmnI	GAANNNNTTC	2 cut(s)	111, 545
Zsp2I	ATGCAT	2 cut(s)	486, 879

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