Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr02

Orthogroup ID

OG0002476

Physical Location & Seq

Genomic Coordinates Forward (+)

10204376 .. 10205365

Gene Structure 990 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

MD02G1125500.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 630 bp

ATGATACAGAAAGGTGAACATCTTTCGGGTACCCTTTGTAAGGATACTCTTGGGATGTCCACGCATGGTCCAACACATGTGATATGGAAAGAATGTGGTCCAGATGCAGCCTGCAAATTTTTGGGCAATGCCCAGTTACTTGTGCACTATTGGTTTTTGCATAATGCCTATTCGATTGGAATTGGAGATACGATTGTTGATCCGGCAACAACGGAAAAAATCAAGCAGACAATTTCTGAGGCAAAAGATGAGTTGGGAGGGCTTATTAGTATAATAGCCCGGTCCAAGCAGCTGGAGGCTGAACCTGGACGAACTTTGGTGGACTCATTTGAAAACAAAGTGAACCAGGTGTTGAATAGGGCTCGTGATAATGATAAAGTTGGAAGTAGTGCTGAAAAGAGTCTATCCGAGATGAACAATCTTAAGGCCATGGTTACAACTGGATCCAAAGAGAATTTTATAAAAATGTCACAGATGATTGCTTGTGTAGGGCACCAGAACATTGAAGGTAAGAGAACCATGTATGGGTTGATAAACCACCTGCCATTGCCCCACTTTACTGAAGATGACTATGGACCAGAATGTCGTGGGTTCGTAAAGAATTCATACTTGCACGGTCAAACTCCATAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0003674 GO:0003676 GO:0003677 GO:0003824 GO:0003899 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0005737 GO:0005773 GO:0005911 GO:0006139 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009506 GO:0009507 GO:0009536 GO:0009987 GO:0016070 GO:0016591 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019438 GO:0030054 GO:0030880 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0046483 GO:0055029 GO:0055044 GO:0061695 GO:0070013 GO:0071704 GO:0090304 GO:0097159 GO:0097747 GO:0140098 GO:1901360 GO:1901362 GO:1901363 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko05016 ko05168 ko05169 map00230 map00240 map01100 map03020 map05016 map05168 map05169

Pfam Domains

Protein Families

RNA_pol_Rpb1_1 RNA_pol_Rpb1_2 RNA_pol_Rpb1_3 RNA_pol_Rpb1_4 RNA_pol_Rpb1_5 RNA_pol_Rpb1_6 RNA_pol_Rpb1_7 RNA_pol_Rpb1_R

Protein Analysis

210

Amino Acids

23.06

Weight (kDa)

6.5

Isoelectric Point (pI)

36.23

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb1_3	PF04983	1 - 64	2.2e-12	RNA polymerase Rpb1, domain 3
RNA_pol_Rpb1_4	PF05000	93 - 199	1.2e-25	RNA polymerase Rpb1, domain 4

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: OG0002476)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G35800 AT4G35800
fragaria_vesca	FvH4_1g11070 FvH4_1g11070 FvH4_1g11070 FvH4_1g11070 FvH4_1g11070 FvH4_1g11070 FvH4_1g11070 FvH4_1g11070
malus_domestica	MD02G1123200.v1.1 MD02G1123400.v1.1 MD02G1125500.v1.1 MD02G1125800.v1.1 MD15G1237200.v1.1
prunus_persica	Prupe.7G175200_v2.0.a1
pyrus_communis	pycom02g09610 pycom15g21110
rosa_chinensis	RchiOBHm_Chr2g0098321 RchiOBHm_Chr2g0098331
rosa_laevigata	RLG00000016790 RLG00000016791
rosa_multiflora	Rmu_co8358581.1_g000001 Rmu_sc0003434.1_g000008 Rmu_sc0023772.1_g000002 Rmu_sc0042863.1_g000001
rosa_roxburghii	Rroxscaffold_2G00144060 Rroxscaffold_2G00144070
rosa_rugosa	Rorug02G0072000 Rorug02G0072000 Rorug02G0072100
rosa_samantha	Rh2AG119100 Rh2AG119200 Rh2BG122300 Rh2BG122400 Rh2CG123900 Rh2CG124000 Rh2DG123900 Rh2DG124000
rosa_wichuraiana	Rw2G009330 Rw2G009340

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	461
AarI	CACCTGC	1 cut(s)	549
AasI	GACNNNNNNGTC	1 cut(s)	582
Acc36I	ACCTGC	1 cut(s)	549
Acc65I	GGTACC	1 cut(s)	29
AccB1I	GGYRCC	2 cut(s)	29, 492
AclWI	GGATC	3 cut(s)	194, 438, 451
AcsI	RAATTY	3 cut(s)	116, 454, 601
AcuI	CTGAAG	1 cut(s)	582
AfaI	GTAC	1 cut(s)	31
AfiI	CCNNNNNNNGG	2 cut(s)	40, 525
AflII	CTTAAG	1 cut(s)	422
AflIII	ACRYGT	1 cut(s)	76
AgsI	TTSAA	3 cut(s)	332, 355, 506
AjnI	CCWGG	2 cut(s)	304, 345
AluBI	AGCT	1 cut(s)	292
AluI	AGCT	1 cut(s)	292
Alw21I	GWGCWC	1 cut(s)	147
Alw44I	GTGCAC	1 cut(s)	143
AlwI	GGATC	3 cut(s)	194, 438, 451
AoxI	GGCC	1 cut(s)	426
ApaLI	GTGCAC	1 cut(s)	143
ApeKI	GCWGC	2 cut(s)	107, 289
ApoI	RAATTY	3 cut(s)	116, 454, 601
Asp718I	GGTACC	1 cut(s)	29
AspS9I	GGNCC	4 cut(s)	68, 98, 282, 575
AsuC2I	CCSGG	1 cut(s)	280
AsuHPI	GGTGA	1 cut(s)	26
AvaII	GGWCC	4 cut(s)	68, 98, 282, 575
BaeGI	GKGCMC	2 cut(s)	147, 495
BaeI	ACNNNNGTAYC	2 cut(s)	180, 213
BamHI	GGATCC	1 cut(s)	443
BanI	GGYRCC	2 cut(s)	29, 492
BanII	GRGCYC	1 cut(s)	364
BauI	CACGAG	1 cut(s)	363
Bbv12I	GWGCWC	1 cut(s)	147
BbvI	GCAGC	2 cut(s)	119, 301
BciT130I	CCWGG	2 cut(s)	306, 347
BciVI	GTATCC	1 cut(s)	37
BcnI	CCSGG	1 cut(s)	280
BfrI	CTTAAG	1 cut(s)	422
BfuAI	ACCTGC	1 cut(s)	549
BfuI	GTATCC	1 cut(s)	37
BisI	GCNGC	2 cut(s)	108, 290
BlsI	GCNGC	2 cut(s)	109, 291
Bme1390I	CCNGG	3 cut(s)	280, 306, 347
Bme18I	GGWCC	4 cut(s)	68, 98, 282, 575
BmgT120I	GGNCC	4 cut(s)	68, 98, 282, 575
BmiI	GGNNCC	3 cut(s)	31, 445, 494
BmrFI	CCNGG	3 cut(s)	280, 306, 347
BmrI	ACTGGG	1 cut(s)	127
BmsI	GCATC	1 cut(s)	94
BmuI	ACTGGG	1 cut(s)	127
BpmI	CTGGAG	1 cut(s)	314
BpuMI	CCSGG	1 cut(s)	280
BsaJI	CCNNGG	1 cut(s)	429
Bsc4I	CCNNNNNNNGG	2 cut(s)	40, 525
Bse1I	ACTGG	2 cut(s)	133, 445
Bse3DI	GCAATG	2 cut(s)	133, 545
BseBI	CCWGG	2 cut(s)	306, 347
BseDI	CCNNGG	1 cut(s)	429
BseGI	GGATG	1 cut(s)	60
BseLI	CCNNNNNNNGG	2 cut(s)	40, 525
BseMI	GCAATG	2 cut(s)	133, 545
BseMII	CTCAG	1 cut(s)	228
BseNI	ACTGG	2 cut(s)	133, 445
BseSI	GKGCMC	2 cut(s)	147, 495
BseXI	GCAGC	2 cut(s)	119, 301
BshFI	GGCC	1 cut(s)	428
BshNI	GGYRCC	2 cut(s)	29, 492
BsiHKAI	GWGCWC	1 cut(s)	147
BsiSI	CCGG	2 cut(s)	203, 280
BslI	CCNNNNNNNGG	2 cut(s)	40, 525
BsnI	GGCC	1 cut(s)	428
Bsp1286I	GDGCHC	3 cut(s)	147, 364, 495
Bsp143I	GATC	2 cut(s)	199, 443
Bsp19I	CCATGG	1 cut(s)	429
BspANI	GGCC	1 cut(s)	428
BspCNI	CTCAG	1 cut(s)	229
BspLI	GGNNCC	3 cut(s)	31, 445, 494
BspMI	ACCTGC	1 cut(s)	549
BspPI	GGATC	3 cut(s)	194, 438, 451
BspT107I	GGYRCC	2 cut(s)	29, 492
BspTI	CTTAAG	1 cut(s)	422
BsrDI	GCAATG	2 cut(s)	133, 545
BsrI	ACTGG	2 cut(s)	133, 445
BssECI	CCNNGG	1 cut(s)	429
BssMI	GATC	2 cut(s)	199, 443
BssSI	CACGAG	1 cut(s)	363
BssT1I	CCWWGG	1 cut(s)	429
Bst2BI	CACGAG	1 cut(s)	363
Bst2UI	CCWGG	2 cut(s)	306, 347
Bst4CI	ACNGT	1 cut(s)	617
BstAFI	CTTAAG	1 cut(s)	422
BstC8I	GCNNGC	1 cut(s)	112
BstDEI	CTNAG	1 cut(s)	237
BstDSI	CCRYGG	1 cut(s)	429
BstENI	CCTNNNNNAGG	1 cut(s)	38
BstF5I	GGATG	1 cut(s)	60
BstKTI	GATC	2 cut(s)	202, 446
BstMBI	GATC	2 cut(s)	199, 443
BstNI	CCWGG	2 cut(s)	306, 347
BstNSI	RCATGY	1 cut(s)	80
BstSCI	CCNGG	3 cut(s)	278, 304, 345
BstSLI	GKGCMC	2 cut(s)	147, 495
BstV1I	GCAGC	2 cut(s)	119, 301
BstX2I	RGATCY	1 cut(s)	443
BstXI	CCANNNNNNTGG	1 cut(s)	292
BstYI	RGATCY	1 cut(s)	443
BsuI	GTATCC	1 cut(s)	37
BsuRI	GGCC	1 cut(s)	428
BtgI	CCRYGG	1 cut(s)	429
BtsCI	GGATG	1 cut(s)	60
BveI	ACCTGC	1 cut(s)	549
Cac8I	GCNNGC	1 cut(s)	112
Cfr13I	GGNCC	4 cut(s)	68, 98, 282, 575
CsiI	ACCWGGT	1 cut(s)	345
Csp6I	GTAC	1 cut(s)	30
CviAII	CATG	4 cut(s)	65, 77, 430, 520
CviJI	RGCY	7 cut(s)	110, 262, 278, 292, 299, 362, 428
CviKI_1	RGCY	7 cut(s)	110, 262, 278, 292, 299, 362, 428
CviQI	GTAC	1 cut(s)	30
DdeI	CTNAG	1 cut(s)	237
DpnI	GATC	2 cut(s)	201, 445
DpnII	GATC	2 cut(s)	199, 443
DrdI	GACNNNNNNGTC	1 cut(s)	582
DseDI	GACNNNNNNGTC	1 cut(s)	582
Eco130I	CCWWGG	1 cut(s)	429
Eco24I	GRGCYC	1 cut(s)	364
Eco47I	GGWCC	4 cut(s)	68, 98, 282, 575
Eco57I	CTGAAG	1 cut(s)	582
EcoNI	CCTNNNNNAGG	1 cut(s)	38
EcoRI	GAATTC	1 cut(s)	601
EcoRII	CCWGG	2 cut(s)	304, 345
EcoT14I	CCWWGG	1 cut(s)	429
EcoT38I	GRGCYC	1 cut(s)	364
ErhI	CCWWGG	1 cut(s)	429
FaeI	CATG	4 cut(s)	68, 80, 433, 523
FatI	CATG	4 cut(s)	64, 76, 429, 519
Fnu4HI	GCNGC	2 cut(s)	108, 290
FokI	GGATG	1 cut(s)	67
FriOI	GRGCYC	1 cut(s)	364
Fsp4HI	GCNGC	2 cut(s)	108, 290
GluI	GCNGC	2 cut(s)	108, 290
GsuI	CTGGAG	1 cut(s)	314
HaeIII	GGCC	1 cut(s)	428
HapII	CCGG	2 cut(s)	203, 280
Hin1II	CATG	4 cut(s)	68, 80, 433, 523
HinfI	GANTC	2 cut(s)	323, 400
HpaII	CCGG	2 cut(s)	203, 280
HphI	GGTGA	1 cut(s)	26
Hpy166II	GTNNAC	5 cut(s)	17, 60, 145, 322, 343
Hpy188I	TCNGA	2 cut(s)	238, 409
Hpy188III	TCNNGA	2 cut(s)	101, 365
Hpy8I	GTNNAC	5 cut(s)	17, 60, 145, 322, 343
HpyAV	CCTTC	1 cut(s)	500
HpyCH4III	ACNGT	1 cut(s)	617
HpyCH4V	TGCA	5 cut(s)	107, 114, 145, 160, 613
HpyF3I	CTNAG	1 cut(s)	237
Hsp92II	CATG	4 cut(s)	68, 80, 433, 523
KpnI	GGTACC	1 cut(s)	33
Kzo9I	GATC	2 cut(s)	199, 443
Lsp1109I	GCAGC	2 cut(s)	119, 301
LweI	GCATC	1 cut(s)	94
MabI	ACCWGGT	1 cut(s)	345
MaeIII	GTNAC	3 cut(s)	135, 433, 468
MalI	GATC	2 cut(s)	201, 445
MboI	GATC	2 cut(s)	199, 443
MboII	GAAGA	1 cut(s)	575
MflI	RGATCY	1 cut(s)	443
MhlI	GDGCHC	3 cut(s)	147, 364, 495
MluCI	AATT	5 cut(s)	116, 180, 231, 454, 601
MlyI	GAGTC	2 cut(s)	317, 409
MmeI	TCCRAC	2 cut(s)	95, 361
MnlI	CCTC	3 cut(s)	232, 251, 289
MseI	TTAA	1 cut(s)	423
MspA1I	CMGCKG	1 cut(s)	292
MspCI	CTTAAG	1 cut(s)	422
MspI	CCGG	2 cut(s)	203, 280
MspR9I	CCNGG	3 cut(s)	280, 306, 347
MvaI	CCWGG	2 cut(s)	306, 347
NciI	CCSGG	1 cut(s)	280
NcoI	CCATGG	1 cut(s)	429
NdeII	GATC	2 cut(s)	199, 443
NlaIII	CATG	4 cut(s)	68, 80, 433, 523
NlaIV	GGNNCC	3 cut(s)	31, 445, 494
NmuCI	GTSAC	1 cut(s)	468
NspI	RCATGY	1 cut(s)	80
PaqCI	CACCTGC	1 cut(s)	549
PciI	ACATGT	1 cut(s)	76
PkrI	GCNGC	2 cut(s)	109, 291
PleI	GAGTC	2 cut(s)	317, 408
PpsI	GAGTC	2 cut(s)	317, 408
PscI	ACATGT	1 cut(s)	76
PsiI	TTATAA	1 cut(s)	461
Psp6I	CCWGG	2 cut(s)	304, 345
PspGI	CCWGG	2 cut(s)	304, 345
PspN4I	GGNNCC	3 cut(s)	31, 445, 494
PspPI	GGNCC	4 cut(s)	68, 98, 282, 575
PsuI	RGATCY	1 cut(s)	443
PvuII	CAGCTG	1 cut(s)	292
RsaI	GTAC	1 cut(s)	31
RsaNI	GTAC	1 cut(s)	30
SaqAI	TTAA	1 cut(s)	423
SatI	GCNGC	2 cut(s)	108, 290
Sau3AI	GATC	2 cut(s)	199, 443
Sau96I	GGNCC	4 cut(s)	68, 98, 282, 575
SchI	GAGTC	2 cut(s)	317, 409
ScrFI	CCNGG	3 cut(s)	280, 306, 347
SduI	GDGCHC	3 cut(s)	147, 364, 495
SetI	ASST	6 cut(s)	16, 294, 307, 351, 511, 543
SexAI	ACCWGGT	1 cut(s)	345
SfaNI	GCATC	1 cut(s)	94
SinI	GGWCC	4 cut(s)	68, 98, 282, 575
SmlI	CTYRAG	1 cut(s)	422
SmoI	CTYRAG	1 cut(s)	422
Sse9I	AATT	5 cut(s)	116, 180, 231, 454, 601
StyD4I	CCNGG	3 cut(s)	278, 304, 345
StyI	CCWWGG	1 cut(s)	429
TaaI	ACNGT	1 cut(s)	617
TaqI	TCGA	1 cut(s)	173
TasI	AATT	5 cut(s)	116, 180, 231, 454, 601
Tru1I	TTAA	1 cut(s)	423
Tru9I	TTAA	1 cut(s)	423
TseFI	GTSAC	1 cut(s)	468
TseI	GCWGC	2 cut(s)	107, 289
Tsp45I	GTSAC	1 cut(s)	468
TspDTI	ATGAA	2 cut(s)	428, 594
TspGWI	ACGGA	1 cut(s)	227
Vha464I	CTTAAG	1 cut(s)	422
VneI	GTGCAC	1 cut(s)	143
VpaK11BI	GGWCC	4 cut(s)	68, 98, 282, 575
XagI	CCTNNNNNAGG	1 cut(s)	38
XapI	RAATTY	3 cut(s)	116, 454, 601
XceI	RCATGY	1 cut(s)	80

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