Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr08

Orthogroup ID

OG0010170

Physical Location & Seq

Genomic Coordinates Forward (+)

29386656 .. 29392896

Gene Structure 6241 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

MD08G1227600.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 804 bp

ATGCTAAAACCCTTAAACCCGCGTATTATCCAAACTGCTACCCGAAAAGCTTCAGAAGAAGAAGAAGGGTCGGGAAGGAAGGAGGCAGTGACCTCGCCCTCTTTTGTGTTCCTCCTCCTCCATCACAATTTACAATTACAGTTTACAGCTCGACGCAGCAAGAAATTGTGTAGAGCACCCCAGATGTTCTACCTCAGCCGAATTGAGCACACGCTCCGTCTTCCACCTCATCTGCTCAGCCTTCGTCTAGAAGATGCGGTTAAGGGAGAGCTCGAGAAGATTTTCCTAGATAAGGTTATTGCCAAATTGGGGCTCTGCATTTCTGTCCACAGTATTCAATCCATTAAAGATGGATTTATCCTACCTAATGATGGTCATCCAACTTTTAGGGTGGAGTTCACACTAATTATGTTTCGTCCATTTGTGGGAGAGATAATTTCTGCAAAACTTAAAGAATCTACTGCAAATGGTTTACGCTTGTCGCTTGGATTTTTTGATGATATTTATGTACCAGTACATCTTTTGCCATCTCCATCCTGCTCCGAGCCTGACCCAGAAAAGAGGAACAACGTCATTTGGATATGGAAATGTCCTGATGCAGATGATCTTGCTGTTGAGTGGACGGATGAGATAAGATTCCAAGTTCAAAGTGTGACCTATCCACCAATTCCAATTGAGCAGCCGGAAGATGCGAAACCATTTGCTCCTATGGTGATTACTGGATCAATTGATTATGATGGTCTTGGCCCTCTTAGGTGGTGGGACAATGCGGAAGACAAGGATGAAGAACCTGAAGATCCTTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000228 GO:0000428 GO:0000785 GO:0000790 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005694 GO:0006139 GO:0006351 GO:0006352 GO:0006383 GO:0006384 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0010467 GO:0016070 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:0044427 GO:0044428 GO:0044446 GO:0044451 GO:0044454 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 ko05169 map00230 map00240 map01100 map03020 map04623 map05169

Pfam Domains

Protein Families

RNA_pol_Rbc25 SHS2_Rpb7-N

Protein Analysis

268

Amino Acids

30.42

Weight (kDa)

5.35

Isoelectric Point (pI)

57.71

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
SHS2_Rpb7-N	PF03876	69 - 125	5.2e-13	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
RNA_pol_Rbc25	PF08292	144 - 254	5.3e-18	RNA polymerase III subunit Rpc25

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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Orthologous Genes (Group: OG0010170)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G06790 AT1G06790
fragaria_vesca	FvH4_1g22880
malus_domestica	MD08G1227600.v1.1
prunus_persica	Prupe.2G103200_v2.0.a1 Prupe.2G103200_v2.0.a1 Prupe.2G103200_v2.0.a1 Prupe.2G103200_v2.0.a1 Prupe.2G103200_v2.0.a1 Prupe.7G016800_v2.0.a1
rosa_chinensis	RchiOBHm_Chr5g0063451
rosa_laevigata	RLG00000022776 RLG00000035635
rosa_multiflora	Rmu_sc0016394.1_g000005
rosa_roxburghii	Rroxscaffold_1G00017270
rosa_rugosa	Rorug05G0357400
rosa_samantha	Rh5AG416500 Rh5BG431600 Rh5CG454900 Rh5DG445100
rosa_wichuraiana	Rw5G039120

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccII	CGCG	1 cut(s)	22
AciI	CCGC	3 cut(s)	20, 257, 770
AclWI	GGATC	2 cut(s)	730, 791
AcuI	CTGAAG	1 cut(s)	36
AfaI	GTAC	2 cut(s)	510, 516
AfiI	CCNNNNNNNGG	4 cut(s)	292, 309, 371, 425
AgsI	TTSAA	2 cut(s)	338, 647
AluBI	AGCT	3 cut(s)	50, 149, 271
AluI	AGCT	3 cut(s)	50, 149, 271
Alw21I	GWGCWC	3 cut(s)	178, 210, 273
AlwI	GGATC	2 cut(s)	730, 791
Ama87I	CYCGRG	1 cut(s)	272
AoxI	GGCC	1 cut(s)	745
ApeKI	GCWGC	2 cut(s)	156, 679
Asp700I	GAANNNNTTC	2 cut(s)	49, 281
AspS9I	GGNCC	1 cut(s)	746
AsuHPI	GGTGA	1 cut(s)	724
AvaI	CYCGRG	1 cut(s)	272
BanII	GRGCYC	2 cut(s)	273, 315
BbsI	GAAGAC	2 cut(s)	212, 780
Bbv12I	GWGCWC	3 cut(s)	178, 210, 273
BbvCI	CCTCAGC	1 cut(s)	194
BbvI	GCAGC	2 cut(s)	168, 691
BccI	CCATC	6 cut(s)	129, 344, 365, 535, 541, 731
BcgI	CGANNNNNNTGC	2 cut(s)	75, 109
BfaI	CTAG	2 cut(s)	248, 287
BisI	GCNGC	2 cut(s)	157, 680
BlpI	GCTNAGC	1 cut(s)	236
BlsI	GCNGC	2 cut(s)	158, 681
BmeT110I	CYCGRG	1 cut(s)	272
BmgT120I	GGNCC	1 cut(s)	746
BmsI	GCATC	3 cut(s)	244, 586, 679
BpiI	GAAGAC	2 cut(s)	212, 780
Bpu10I	CCTNAGC	1 cut(s)	194
Bpu1102I	GCTNAGC	1 cut(s)	236
BsaBI	GATNNNNATC	1 cut(s)	375
Bsc4I	CCNNNNNNNGG	4 cut(s)	292, 309, 371, 425
Bse1I	ACTGG	2 cut(s)	512, 724
Bse8I	GATNNNNATC	1 cut(s)	375
BseGI	GGATG	4 cut(s)	376, 533, 631, 787
BseJI	GATNNNNATC	1 cut(s)	375
BseLI	CCNNNNNNNGG	4 cut(s)	292, 309, 371, 425
BseMII	CTCAG	2 cut(s)	208, 250
BseNI	ACTGG	2 cut(s)	512, 724
BseRI	GAGGAG	2 cut(s)	104, 107
BseXI	GCAGC	2 cut(s)	168, 691
Bsh1236I	CGCG	1 cut(s)	22
BshFI	GGCC	1 cut(s)	747
BsiHKAI	GWGCWC	3 cut(s)	178, 210, 273
BsiHKCI	CYCGRG	1 cut(s)	272
BsiSI	CCGG	1 cut(s)	683
BslFI	GGGAC	1 cut(s)	776
BslI	CCNNNNNNNGG	4 cut(s)	292, 309, 371, 425
BsmFI	GGGAC	1 cut(s)	776
BsnI	GGCC	1 cut(s)	747
BsoBI	CYCGRG	1 cut(s)	272
Bsp1286I	GDGCHC	4 cut(s)	178, 210, 273, 315
Bsp143I	GATC	3 cut(s)	604, 722, 796
Bsp1720I	GCTNAGC	1 cut(s)	236
BspACI	CCGC	3 cut(s)	20, 257, 770
BspANI	GGCC	1 cut(s)	747
BspCNI	CTCAG	2 cut(s)	207, 249
BspFNI	CGCG	1 cut(s)	22
BspPI	GGATC	2 cut(s)	730, 791
BsrI	ACTGG	2 cut(s)	512, 724
BssMI	GATC	3 cut(s)	604, 722, 796
Bst4CI	ACNGT	2 cut(s)	141, 332
BstDEI	CTNAG	3 cut(s)	194, 236, 752
BstENI	CCTNNNNNAGG	1 cut(s)	290
BstF5I	GGATG	4 cut(s)	376, 533, 631, 787
BstFNI	CGCG	1 cut(s)	22
BstKTI	GATC	3 cut(s)	607, 725, 799
BstMBI	GATC	3 cut(s)	604, 722, 796
BstUI	CGCG	1 cut(s)	22
BstV1I	GCAGC	2 cut(s)	168, 691
BstV2I	GAAGAC	2 cut(s)	212, 780
BstX2I	RGATCY	1 cut(s)	796
BstYI	RGATCY	1 cut(s)	796
BsuRI	GGCC	1 cut(s)	747
BtsCI	GGATG	4 cut(s)	376, 533, 631, 787
BtsI	GCAGTG	1 cut(s)	93
BtsIMutI	CAGTG	1 cut(s)	93
Cfr13I	GGNCC	1 cut(s)	746
CseI	GACGC	1 cut(s)	162
Csp6I	GTAC	2 cut(s)	509, 515
CviJI	RGCY	9 cut(s)	50, 149, 198, 240, 271, 313, 547, 682, 747
CviKI_1	RGCY	9 cut(s)	50, 149, 198, 240, 271, 313, 547, 682, 747
CviQI	GTAC	2 cut(s)	509, 515
DdeI	CTNAG	3 cut(s)	194, 236, 752
DpnI	GATC	3 cut(s)	606, 724, 798
DpnII	GATC	3 cut(s)	604, 722, 796
Ecl136II	GAGCTC	1 cut(s)	271
Eco24I	GRGCYC	2 cut(s)	273, 315
Eco53kI	GAGCTC	1 cut(s)	271
Eco57I	CTGAAG	1 cut(s)	36
Eco88I	CYCGRG	1 cut(s)	272
EcoICRI	GAGCTC	1 cut(s)	271
EcoNI	CCTNNNNNAGG	1 cut(s)	290
EcoT38I	GRGCYC	2 cut(s)	273, 315
FaiI	YATR	5 cut(s)	410, 507, 583, 710, 735
FaqI	GGGAC	1 cut(s)	776
FauI	CCCGC	1 cut(s)	27
Fnu4HI	GCNGC	2 cut(s)	157, 680
FokI	GGATG	4 cut(s)	363, 520, 638, 794
FriOI	GRGCYC	2 cut(s)	273, 315
Fsp4HI	GCNGC	2 cut(s)	157, 680
FspBI	CTAG	2 cut(s)	248, 287
GluI	GCNGC	2 cut(s)	157, 680
HaeIII	GGCC	1 cut(s)	747
HapII	CCGG	1 cut(s)	683
HgaI	GACGC	1 cut(s)	162
HindIII	AAGCTT	1 cut(s)	48
HinfI	GANTC	2 cut(s)	455, 636
HpaII	CCGG	1 cut(s)	683
HphI	GGTGA	1 cut(s)	724
Hpy166II	GTNNAC	5 cut(s)	144, 328, 399, 473, 621
Hpy188I	TCNGA	2 cut(s)	55, 544
Hpy188III	TCNNGA	4 cut(s)	72, 248, 274, 593
Hpy8I	GTNNAC	5 cut(s)	144, 328, 399, 473, 621
Hpy99I	CGWCG	1 cut(s)	156
HpyAV	CCTTC	4 cut(s)	59, 69, 73, 251
HpyCH4III	ACNGT	2 cut(s)	141, 332
HpyCH4IV	ACGT	1 cut(s)	570
HpyCH4V	TGCA	4 cut(s)	318, 443, 464, 599
HpyF3I	CTNAG	3 cut(s)	194, 236, 752
HpySE526I	ACGT	1 cut(s)	570
Kzo9I	GATC	3 cut(s)	604, 722, 796
LmnI	GCTCC	3 cut(s)	219, 545, 709
LpnPI	CCDG	8 cut(s)	194, 525, 550, 561, 567, 606, 696, 705
Lsp1109I	GCAGC	2 cut(s)	168, 691
LweI	GCATC	3 cut(s)	244, 586, 679
MaeI	CTAG	2 cut(s)	248, 287
MaeII	ACGT	1 cut(s)	570
MaeIII	GTNAC	2 cut(s)	88, 652
MalI	GATC	3 cut(s)	606, 724, 798
MboI	GATC	3 cut(s)	604, 722, 796
MboII	GAAGA	9 cut(s)	68, 71, 74, 212, 263, 289, 698, 785, 797
MfeI	CAATTG	2 cut(s)	672, 726
MflI	RGATCY	1 cut(s)	796
MhlI	GDGCHC	4 cut(s)	178, 210, 273, 315
MmeI	TCCRAC	1 cut(s)	404
MroXI	GAANNNNTTC	2 cut(s)	49, 281
MseI	TTAA	5 cut(s)	14, 261, 345, 450, 802
MspI	CCGG	1 cut(s)	683
MunI	CAATTG	2 cut(s)	672, 726
MvnI	CGCG	1 cut(s)	22
NdeII	GATC	3 cut(s)	604, 722, 796
NmuCI	GTSAC	2 cut(s)	88, 652
PaeR7I	CTCGAG	1 cut(s)	272
PdmI	GAANNNNTTC	2 cut(s)	49, 281
PfeI	GAWTC	2 cut(s)	455, 636
PkrI	GCNGC	2 cut(s)	158, 681
Psp124BI	GAGCTC	1 cut(s)	273
PspPI	GGNCC	1 cut(s)	746
PsuI	RGATCY	1 cut(s)	796
RsaI	GTAC	2 cut(s)	510, 516
RsaNI	GTAC	2 cut(s)	509, 515
SacI	GAGCTC	1 cut(s)	273
SaqAI	TTAA	5 cut(s)	14, 261, 345, 450, 802
SatI	GCNGC	2 cut(s)	157, 680
Sau3AI	GATC	3 cut(s)	604, 722, 796
Sau96I	GGNCC	1 cut(s)	746
SduI	GDGCHC	4 cut(s)	178, 210, 273, 315
SfaNI	GCATC	3 cut(s)	244, 586, 679
Sfr274I	CTCGAG	1 cut(s)	272
SlaI	CTCGAG	1 cut(s)	272
SmlI	CTYRAG	1 cut(s)	272
SmoI	CTYRAG	1 cut(s)	272
SsiI	CCGC	3 cut(s)	20, 257, 770
SspMI	CTAG	2 cut(s)	248, 287
SstI	GAGCTC	1 cut(s)	273
TaaI	ACNGT	2 cut(s)	141, 332
TaiI	ACGT	1 cut(s)	573
TaqI	TCGA	2 cut(s)	151, 273
TatI	WGTACW	1 cut(s)	514
TfiI	GAWTC	2 cut(s)	455, 636
Tru1I	TTAA	5 cut(s)	14, 261, 345, 450, 802
Tru9I	TTAA	5 cut(s)	14, 261, 345, 450, 802
TscAI	CASTG	1 cut(s)	93
TseFI	GTSAC	2 cut(s)	88, 652
TseI	GCWGC	2 cut(s)	156, 679
Tsp45I	GTSAC	2 cut(s)	88, 652
TspDTI	ATGAA	1 cut(s)	798
TspGWI	ACGGA	2 cut(s)	206, 638
TspRI	CASTG	1 cut(s)	93
XagI	CCTNNNNNAGG	1 cut(s)	290
XbaI	TCTAGA	1 cut(s)	247
XhoI	CTCGAG	1 cut(s)	272
XmnI	GAANNNNTTC	2 cut(s)	49, 281
XspI	CTAG	2 cut(s)	248, 287

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