Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr16

Orthogroup ID

OG0005882

Physical Location & Seq

Genomic Coordinates Forward (+)

14070828 .. 14079134

Gene Structure 8307 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

MD16G1169300.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 420 bp

ATGAATACGGGTGATAAGATACATACACTAAAAGATAAGATAGCTTATATGCCATGGGAAGGTTACAATTTTGAAGATGCGGTACTCATTAGTGAGCATCTGGTATATGGAGATATTTATACTTCTTTTCATATACGGAAATATGAAATTCAGACTCATGTAACAAGCAATGGCCCTGAAAGAATCACTAACGAAATACAGCATCTAGAAGCCCATTTACTTTGCAATTTAGACAAAAATGGAATTGTGAGGTTGGGATATTGGGTAAAGACATGTGATATTTTAGTAGGCAAATTAACACCTCAAATGGCGAAAGAATCGTTGTATGCTCCGGCAGATAGATTATTACGAGCCATACTTGGCATTCATGTATCCACTTCAAAGGAAACTTGTCTAAAATCGAAACTTAATAAGGGATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0009507 GO:0009536 GO:0030880 GO:0032991 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044444 GO:0044464 GO:0061695 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 map00230 map00240 map01100 map03020

Pfam Domains

Protein Families

RNA_pol_Rpb2_2 RNA_pol_Rpb2_3 RNA_pol_Rpb2_6 RNA_pol_Rpb2_7

Protein Analysis

140

Amino Acids

15.84

Weight (kDa)

7.76

Isoelectric Point (pI)

21.28

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb2_6	PF00562	14 - 121	8.2e-23	RNA polymerase Rpb2, domain 6

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Orthologous Genes (Group: OG0005882)

Species	Orthologous Gene IDs
arabidopsis_thaliana	ATCG00190
malus_domestica	MD01G1093300.v1.1 MD16G1169300.v1.1
pyrus_communis	pycom12397g00320 pycom14g07090
rosa_chinensis	RchiOBHm_CPg0502401
rosa_laevigata	RLG00000000047 RLG00000000087 RLG00000000116 RLG00000000175 RLG00000000231 RLG00000000246 RLG00000000284 RLG00000000299 RLG00000000300 RLG00000000314 RLG00000000318 RLG00000000340
rosa_multiflora	Rmu_sc0002986.1_g000010 Rmu_sc0008812.1_g000013 Rmu_sc0011830.1_g000003
rosa_roxburghii	Rroxscaffold_2G00119070
rosa_rugosa	Rorug02G0490800 RorugMtG0001900
rosa_samantha	Rh2AG293900 Rh2AG294000 Rh2DG317800 Rh2DG317900

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AciI	CCGC	1 cut(s)	80
AcsI	RAATTY	1 cut(s)	147
AfaI	GTAC	1 cut(s)	84
AfiI	CCNNNNNNNGG	1 cut(s)	59
AflIII	ACRYGT	1 cut(s)	272
AgsI	TTSAA	2 cut(s)	74, 381
AluBI	AGCT	1 cut(s)	44
AluI	AGCT	1 cut(s)	44
AoxI	GGCC	1 cut(s)	172
ApoI	RAATTY	1 cut(s)	147
AspS9I	GGNCC	1 cut(s)	173
AsuHPI	GGTGA	1 cut(s)	23
BarI	GAAGNNNNNNTAC	4 cut(s)	66, 98, 201, 233
BciVI	GTATCC	1 cut(s)	382
BfaI	CTAG	1 cut(s)	206
BfuI	GTATCC	1 cut(s)	382
BmgT120I	GGNCC	1 cut(s)	173
BmsI	GCATC	3 cut(s)	67, 106, 211
BsaJI	CCNNGG	1 cut(s)	53
Bsc4I	CCNNNNNNNGG	1 cut(s)	59
Bse3DI	GCAATG	1 cut(s)	175
BseDI	CCNNGG	1 cut(s)	53
BseLI	CCNNNNNNNGG	1 cut(s)	59
BseMI	GCAATG	1 cut(s)	175
BshFI	GGCC	1 cut(s)	174
BsiSI	CCGG	1 cut(s)	332
BslI	CCNNNNNNNGG	1 cut(s)	59
BsmI	GAATGC	1 cut(s)	363
BsnI	GGCC	1 cut(s)	174
Bsp19I	CCATGG	1 cut(s)	53
BspACI	CCGC	1 cut(s)	80
BspANI	GGCC	1 cut(s)	174
BsrDI	GCAATG	1 cut(s)	175
BssECI	CCNNGG	1 cut(s)	53
BssT1I	CCWWGG	1 cut(s)	53
BstDSI	CCRYGG	1 cut(s)	53
BstNSI	RCATGY	1 cut(s)	276
BsuI	GTATCC	1 cut(s)	382
BsuRI	GGCC	1 cut(s)	174
BtgI	CCRYGG	1 cut(s)	53
Cfr13I	GGNCC	1 cut(s)	173
Csp6I	GTAC	1 cut(s)	83
CviAII	CATG	4 cut(s)	54, 158, 273, 368
CviJI	RGCY	4 cut(s)	44, 174, 212, 353
CviKI_1	RGCY	4 cut(s)	44, 174, 212, 353
CviQI	GTAC	1 cut(s)	83
Eco130I	CCWWGG	1 cut(s)	53
EcoT14I	CCWWGG	1 cut(s)	53
ErhI	CCWWGG	1 cut(s)	53
FaeI	CATG	4 cut(s)	57, 161, 276, 371
FatI	CATG	4 cut(s)	53, 157, 272, 367
FspBI	CTAG	1 cut(s)	206
HaeIII	GGCC	1 cut(s)	174
HapII	CCGG	1 cut(s)	332
Hin1II	CATG	4 cut(s)	57, 161, 276, 371
HinfI	GANTC	3 cut(s)	154, 183, 317
HpaII	CCGG	1 cut(s)	332
HphI	GGTGA	1 cut(s)	23
Hpy188I	TCNGA	1 cut(s)	153
Hpy188III	TCNNGA	1 cut(s)	206
HpyAV	CCTTC	1 cut(s)	53
HpyCH4V	TGCA	1 cut(s)	225
Hsp92II	CATG	4 cut(s)	57, 161, 276, 371
LmnI	GCTCC	1 cut(s)	334
LpnPI	CCDG	3 cut(s)	86, 189, 345
LweI	GCATC	3 cut(s)	67, 106, 211
MaeI	CTAG	1 cut(s)	206
MaeIII	GTNAC	2 cut(s)	62, 160
MboII	GAAGA	1 cut(s)	86
MluCI	AATT	5 cut(s)	67, 147, 226, 243, 293
MlyI	GAGTC	1 cut(s)	148
MnlI	CCTC	2 cut(s)	243, 312
MseI	TTAA	2 cut(s)	296, 408
MspI	CCGG	1 cut(s)	332
Mva1269I	GAATGC	1 cut(s)	363
NcoI	CCATGG	1 cut(s)	53
NlaIII	CATG	4 cut(s)	57, 161, 276, 371
NspI	RCATGY	1 cut(s)	276
PciI	ACATGT	1 cut(s)	272
PctI	GAATGC	1 cut(s)	363
PfeI	GAWTC	2 cut(s)	183, 317
PleI	GAGTC	1 cut(s)	148
PpsI	GAGTC	1 cut(s)	148
PscI	ACATGT	1 cut(s)	272
PspPI	GGNCC	1 cut(s)	173
RsaI	GTAC	1 cut(s)	84
RsaNI	GTAC	1 cut(s)	83
SaqAI	TTAA	2 cut(s)	296, 408
Sau96I	GGNCC	1 cut(s)	173
SchI	GAGTC	1 cut(s)	148
SetI	ASST	4 cut(s)	46, 64, 254, 304
SfaNI	GCATC	3 cut(s)	67, 106, 211
Sse9I	AATT	5 cut(s)	67, 147, 226, 243, 293
SsiI	CCGC	1 cut(s)	80
SspMI	CTAG	1 cut(s)	206
StyI	CCWWGG	1 cut(s)	53
TaqI	TCGA	1 cut(s)	401
TasI	AATT	5 cut(s)	67, 147, 226, 243, 293
TfiI	GAWTC	2 cut(s)	183, 317
Tru1I	TTAA	2 cut(s)	296, 408
Tru9I	TTAA	2 cut(s)	296, 408
TspDTI	ATGAA	4 cut(s)	17, 119, 159, 356
TspGWI	ACGGA	1 cut(s)	151
XapI	RAATTY	1 cut(s)	147
XbaI	TCTAGA	1 cut(s)	205
XceI	RCATGY	1 cut(s)	276
XspI	CTAG	1 cut(s)	206

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