Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr05

Orthogroup ID

OG0003550

Physical Location & Seq

Genomic Coordinates Forward (+)

5943520 .. 5951021

Gene Structure 7502 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

MD05G1036800.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 984 bp

ATGGCATTACTTTTTGTTGCCATTTTGGAATTAGAGGTTGTGAATGCCAAATTGTCATCTCAACTTGCAAATTGTTGCTGTCATGAGAAAGAGAAAAAGCCTGATGGTTCTGTAAGTTTTGATAGTTCAGTTGAGAAAAGCAGGAAATCAAACTCTGGAAGTAAGAAGACCACCATTGAGAAAGTAAAAGAGACAGTGCCAGGTCATATCACAAGGATCATTAATCACCTCCCTAAGAGATATGTTGCTCTGAAAGTCATGTATTTTGGGCAGAGGTTTTATGGTTTTGCTTCAGAGGCACAAATGGATCCAACCATTGAGTCTGAAATTTTTAAAGCCCTTGAGAAGACAAGACTTTTAGTTGATGACAAGAAGGAATCACAATACTCAAGATGTGGTAGAACCGACAAGGGAGTATCTGCTGTTGGGCAAGTTATCGCTCTCTATTTACGATCAAACCTCAAGGAAACATGTGAGAATAATGAAGATTCCAACAAAATCGTTTACAATGAGCAATATGGTGAAATTGATTACGTGAGGGTGTTGAATCGGGCCCTTCCAGAGGATATTCGAGTTTTTGGCTGGTGTCCTGTTCCATTGGATTTCAATGCCAGGTTTAGCTGTTTAGGGAGGGAGTACTATTATTTATTTTGGGGGCAAAATCTGAATCTCTTGGCTATGGAGAGTGCTGGTAGGAAATTTGTTGGTGAACACGACTTCAGAAACTTTTGTAAAATGGATGCACTAAATGTACACAACTATAGGCGAAAAATCACTTCATTTGCAGTCTCTCCTTGTGATGTGAGGTTTGACGAGAACCAGCTTTGGGCGATTAAAATTAAAGGTAGTGCTTTCCTCTGGCACCAGGTCAGATGCATGGTTGCTGTGCTATTCTTGATCGGCCAAGGTCATGAATCTCCTGATGTGAGTATCAAATGTCAATTTGATAGATTGATTGCTGGAGTTTGGGTTATGCTTGTTTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0001522 GO:0003674 GO:0003824 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005737 GO:0006139 GO:0006396 GO:0006399 GO:0006400 GO:0006725 GO:0006807 GO:0008033 GO:0008150 GO:0008152 GO:0009451 GO:0009982 GO:0009987 GO:0010467 GO:0016070 GO:0016071 GO:0016556 GO:0016853 GO:0016866 GO:0031119 GO:0034470 GO:0034641 GO:0034660 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043412 GO:0044237 GO:0044238 GO:0044424 GO:0044464 GO:0046483 GO:0071704 GO:0090304 GO:1901360 GO:1990481

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PseudoU_synth_1

Protein Analysis

328

Amino Acids

37.46

Weight (kDa)

8.66

Isoelectric Point (pI)

38.06

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PseudoU_synth_1	PF01416	232 - 309	1.1e-21	tRNA pseudouridine synthase

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0003550)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G34150
fragaria_vesca	FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780 FvH4_2g12780
malus_domestica	MD05G1036800.v1.1 MD05G1036900.v1.1
prunus_persica	Prupe.8G045000_v2.0.a1 Prupe.8G045000_v2.0.a1
pyrus_communis	pycom05g02710 pycom05g02720
rosa_chinensis	RchiOBHm_Chr6g0273621
rosa_laevigata	RLG00000013608
rosa_multiflora	Rmu_sc0001419.1_g000001 Rmu_sc0015671.1_g000001
rosa_roxburghii	Rroxscaffold_7G00195210
rosa_rugosa	Rorug06G0076200 Rorug06G0076300 Rorug06G0076400
rosa_samantha	Rh6AG190900 Rh6BG194400 Rh6CG194300 Rh6DG186200
rosa_wichuraiana	Rw6G016710

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	861
AclWI	GGATC	3 cut(s)	224, 302, 315
AcoI	YGGCCR	1 cut(s)	901
AcsI	RAATTY	2 cut(s)	327, 698
AcuI	CTGAAG	2 cut(s)	276, 703
AfaI	GTAC	2 cut(s)	638, 753
AfiI	CCNNNNNNNGG	2 cut(s)	562, 826
AflIII	ACRYGT	1 cut(s)	470
AgsI	TTSAA	2 cut(s)	547, 607
AjnI	CCWGG	3 cut(s)	199, 611, 864
AluBI	AGCT	2 cut(s)	621, 823
AluI	AGCT	2 cut(s)	621, 823
Alw26I	GTCTC	2 cut(s)	185, 793
AlwI	GGATC	3 cut(s)	224, 302, 315
AoxI	GGCC	2 cut(s)	552, 901
ApaI	GGGCCC	1 cut(s)	556
ApoI	RAATTY	2 cut(s)	327, 698
AseI	ATTAAT	1 cut(s)	222
AspS9I	GGNCC	2 cut(s)	552, 553
AsuHPI	GGTGA	3 cut(s)	218, 533, 719
BaeGI	GKGCMC	1 cut(s)	556
BamHI	GGATCC	1 cut(s)	307
BanI	GGYRCC	1 cut(s)	861
BanII	GRGCYC	1 cut(s)	556
BbsI	GAAGAC	2 cut(s)	173, 353
BccI	CCATC	1 cut(s)	98
BciT130I	CCWGG	3 cut(s)	201, 613, 866
BcoDI	GTCTC	2 cut(s)	185, 793
BfmI	CTRYAG	1 cut(s)	760
BmcAI	AGTACT	1 cut(s)	638
Bme1390I	CCNGG	3 cut(s)	201, 613, 866
BmgT120I	GGNCC	2 cut(s)	552, 553
BmiI	GGNNCC	3 cut(s)	309, 554, 863
BmrFI	CCNGG	3 cut(s)	201, 613, 866
BmsI	GCATC	2 cut(s)	730, 863
BpiI	GAAGAC	2 cut(s)	173, 353
BpmI	CTGGAG	1 cut(s)	981
BpuEI	CTTGAG	3 cut(s)	362, 373, 446
BsaAI	YACGTR	1 cut(s)	535
BsaJI	CCNNGG	1 cut(s)	904
BsaXI	ACNNNNNCTCC	2 cut(s)	954, 984
Bsc4I	CCNNNNNNNGG	2 cut(s)	562, 826
BseBI	CCWGG	3 cut(s)	201, 613, 866
BseDI	CCNNGG	1 cut(s)	904
BseGI	GGATG	1 cut(s)	745
BseLI	CCNNNNNNNGG	2 cut(s)	562, 826
BseSI	GKGCMC	1 cut(s)	556
BshFI	GGCC	2 cut(s)	554, 903
BshNI	GGYRCC	1 cut(s)	861
BslI	CCNNNNNNNGG	2 cut(s)	562, 826
BsmAI	GTCTC	2 cut(s)	185, 793
BsmI	GAATGC	1 cut(s)	49
BsnI	GGCC	2 cut(s)	554, 903
Bsp120I	GGGCCC	1 cut(s)	552
Bsp1286I	GDGCHC	1 cut(s)	556
Bsp1407I	TGTACA	1 cut(s)	751
Bsp143I	GATC	4 cut(s)	216, 307, 452, 897
BspANI	GGCC	2 cut(s)	554, 903
BspHI	TCATGA	2 cut(s)	82, 910
BspLI	GGNNCC	3 cut(s)	309, 554, 863
BspPI	GGATC	3 cut(s)	224, 302, 315
BspT107I	GGYRCC	1 cut(s)	861
BsrGI	TGTACA	1 cut(s)	751
BssECI	CCNNGG	1 cut(s)	904
BssMI	GATC	4 cut(s)	216, 307, 452, 897
BssT1I	CCWWGG	1 cut(s)	904
Bst2UI	CCWGG	3 cut(s)	201, 613, 866
Bst4CI	ACNGT	1 cut(s)	196
BstAUI	TGTACA	1 cut(s)	751
BstBAI	YACGTR	1 cut(s)	535
BstDEI	CTNAG	1 cut(s)	234
BstENI	CCTNNNNNAGG	1 cut(s)	560
BstF5I	GGATG	1 cut(s)	745
BstKTI	GATC	4 cut(s)	219, 310, 455, 900
BstMAI	GTCTC	2 cut(s)	185, 793
BstMBI	GATC	4 cut(s)	216, 307, 452, 897
BstMWI	GCNNNNNNNGC	1 cut(s)	296
BstNI	CCWGG	3 cut(s)	201, 613, 866
BstNSI	RCATGY	1 cut(s)	474
BstSCI	CCNGG	3 cut(s)	199, 611, 864
BstSFI	CTRYAG	1 cut(s)	760
BstSLI	GKGCMC	1 cut(s)	556
BstV2I	GAAGAC	2 cut(s)	173, 353
BstX2I	RGATCY	1 cut(s)	307
BstYI	RGATCY	1 cut(s)	307
BsuRI	GGCC	2 cut(s)	554, 903
BtsCI	GGATG	1 cut(s)	745
BtsIMutI	CAGTG	1 cut(s)	201
CciI	TCATGA	2 cut(s)	82, 910
Cfr13I	GGNCC	2 cut(s)	552, 553
CsiI	ACCWGGT	1 cut(s)	864
Csp6I	GTAC	2 cut(s)	637, 752
CviAII	CATG	5 cut(s)	83, 259, 471, 877, 911
CviJI	RGCY	8 cut(s)	100, 338, 554, 582, 621, 677, 823, 903
CviKI_1	RGCY	8 cut(s)	100, 338, 554, 582, 621, 677, 823, 903
CviQI	GTAC	2 cut(s)	637, 752
DdeI	CTNAG	1 cut(s)	234
DpnI	GATC	4 cut(s)	218, 309, 454, 899
DpnII	GATC	4 cut(s)	216, 307, 452, 897
DraI	TTTAAA	1 cut(s)	334
EaeI	YGGCCR	1 cut(s)	901
Eco130I	CCWWGG	1 cut(s)	904
Eco24I	GRGCYC	1 cut(s)	556
Eco57I	CTGAAG	2 cut(s)	276, 703
EcoNI	CCTNNNNNAGG	1 cut(s)	560
EcoO109I	RGGNCCY	1 cut(s)	553
EcoRII	CCWGG	3 cut(s)	199, 611, 864
EcoT14I	CCWWGG	1 cut(s)	904
EcoT22I	ATGCAT	1 cut(s)	878
EcoT38I	GRGCYC	1 cut(s)	556
ErhI	CCWWGG	1 cut(s)	904
FaeI	CATG	5 cut(s)	86, 262, 474, 880, 914
FatI	CATG	5 cut(s)	82, 258, 470, 876, 910
FokI	GGATG	1 cut(s)	752
FriOI	GRGCYC	1 cut(s)	556
GsuI	CTGGAG	1 cut(s)	981
HaeIII	GGCC	2 cut(s)	554, 903
Hin1II	CATG	5 cut(s)	86, 262, 474, 880, 914
HinfI	GANTC	6 cut(s)	320, 377, 488, 547, 667, 914
HphI	GGTGA	3 cut(s)	218, 533, 719
Hpy166II	GTNNAC	3 cut(s)	505, 710, 754
Hpy188I	TCNGA	6 cut(s)	252, 295, 325, 666, 722, 872
Hpy188III	TCNNGA	7 cut(s)	83, 156, 390, 560, 895, 911, 920
Hpy8I	GTNNAC	3 cut(s)	505, 710, 754
HpyAV	CCTTC	2 cut(s)	367, 566
HpyCH4III	ACNGT	1 cut(s)	196
HpyCH4IV	ACGT	1 cut(s)	534
HpyCH4V	TGCA	4 cut(s)	68, 743, 785, 876
HpyF10VI	GCNNNNNNNGC	1 cut(s)	296
HpyF3I	CTNAG	1 cut(s)	234
HpySE526I	ACGT	1 cut(s)	534
Hsp92II	CATG	5 cut(s)	86, 262, 474, 880, 914
Kzo9I	GATC	4 cut(s)	216, 307, 452, 897
LweI	GCATC	2 cut(s)	730, 863
MabI	ACCWGGT	1 cut(s)	864
MaeII	ACGT	1 cut(s)	534
MalI	GATC	4 cut(s)	218, 309, 454, 899
MboI	GATC	4 cut(s)	216, 307, 452, 897
MboII	GAAGA	3 cut(s)	178, 358, 497
MflI	RGATCY	1 cut(s)	307
MhlI	GDGCHC	1 cut(s)	556
MluCI	AATT	8 cut(s)	29, 50, 70, 327, 525, 698, 837, 941
MlyI	GAGTC	1 cut(s)	329
MmeI	TCCRAC	2 cut(s)	335, 516
Mph1103I	ATGCAT	1 cut(s)	878
MseI	TTAA	5 cut(s)	222, 333, 834, 840, 982
MspR9I	CCNGG	3 cut(s)	201, 613, 866
Mva1269I	GAATGC	1 cut(s)	49
MvaI	CCWGG	3 cut(s)	201, 613, 866
MwoI	GCNNNNNNNGC	1 cut(s)	296
NdeII	GATC	4 cut(s)	216, 307, 452, 897
NlaIII	CATG	5 cut(s)	86, 262, 474, 880, 914
NlaIV	GGNNCC	3 cut(s)	309, 554, 863
NsiI	ATGCAT	1 cut(s)	878
NspI	RCATGY	1 cut(s)	474
PagI	TCATGA	2 cut(s)	82, 910
PciI	ACATGT	1 cut(s)	470
PctI	GAATGC	1 cut(s)	49
PfeI	GAWTC	5 cut(s)	377, 488, 547, 667, 914
PleI	GAGTC	1 cut(s)	328
PpsI	GAGTC	1 cut(s)	328
Ppu21I	YACGTR	1 cut(s)	535
PscI	ACATGT	1 cut(s)	470
PshBI	ATTAAT	1 cut(s)	222
Psp6I	CCWGG	3 cut(s)	199, 611, 864
PspGI	CCWGG	3 cut(s)	199, 611, 864
PspN4I	GGNNCC	3 cut(s)	309, 554, 863
PspOMI	GGGCCC	1 cut(s)	552
PspPI	GGNCC	2 cut(s)	552, 553
PsuI	RGATCY	1 cut(s)	307
RsaI	GTAC	2 cut(s)	638, 753
RsaNI	GTAC	2 cut(s)	637, 752
SaqAI	TTAA	5 cut(s)	222, 333, 834, 840, 982
Sau3AI	GATC	4 cut(s)	216, 307, 452, 897
Sau96I	GGNCC	2 cut(s)	552, 553
ScaI	AGTACT	1 cut(s)	638
SchI	GAGTC	1 cut(s)	329
ScrFI	CCNGG	3 cut(s)	201, 613, 866
SduI	GDGCHC	1 cut(s)	556
SexAI	ACCWGGT	1 cut(s)	864
SfaNI	GCATC	2 cut(s)	730, 863
SfcI	CTRYAG	1 cut(s)	760
SmlI	CTYRAG	3 cut(s)	341, 388, 461
SmoI	CTYRAG	3 cut(s)	341, 388, 461
Sse9I	AATT	8 cut(s)	29, 50, 70, 327, 525, 698, 837, 941
StyD4I	CCNGG	3 cut(s)	199, 611, 864
StyI	CCWWGG	1 cut(s)	904
TaaI	ACNGT	1 cut(s)	196
TaiI	ACGT	1 cut(s)	537
TaqI	TCGA	1 cut(s)	571
TasI	AATT	8 cut(s)	29, 50, 70, 327, 525, 698, 837, 941
TatI	WGTACW	2 cut(s)	636, 751
TfiI	GAWTC	5 cut(s)	377, 488, 547, 667, 914
Tru1I	TTAA	5 cut(s)	222, 333, 834, 840, 982
Tru9I	TTAA	5 cut(s)	222, 333, 834, 840, 982
TscAI	CASTG	1 cut(s)	201
TspDTI	ATGAA	3 cut(s)	498, 768, 927
TspRI	CASTG	1 cut(s)	201
VspI	ATTAAT	1 cut(s)	222
XagI	CCTNNNNNAGG	1 cut(s)	560
XapI	RAATTY	2 cut(s)	327, 698
XceI	RCATGY	1 cut(s)	474
ZrmI	AGTACT	1 cut(s)	638
Zsp2I	ATGCAT	1 cut(s)	878

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