MD16G1220100.v1.1

Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr16
OG0016485
Physical Location & Seq
Forward (+)
21916906 .. 21918043
1138 bp
Loading structure...
UTR
Exon/CDS
Intron
MD16G1220100.v1.1.491

Sequence Viewer

Length: 615 bp
ATGGATTCACTTCAAGAATTTGACCCTTCCAACCCATCAAATACTTCAAGCATTAACATCAACATCAACACTACCATCGCTACCAACTCATCCTCCTCCTCATCGTCATCATGCGCCACCCTCAGCCGCTATGAGAACCAAAAGCGGCGAGACTGGAACACCTTTGGGCAATACCTCCGTAACCACAGGCCGCCACTGTCCCTCTCGCGGTGCAGTGGGGCCCACGTGCTTGAGTTCCTCAGGTACCTGGACCAGTTTGGGAAGACCAAGGTGCACATCCAGCTGTGTCCCTTCTTCGGGAACCCTAACCCTCCTGCACCGTGCCCCTGCCCTCTGCGGCAAGCTTGGGGAAGCCTCGACGCCCTCATCGGCCGCCTCAGAGCCGCCTTTGAAGAGCACGGCGGGAAGCCTGAGGCAAACCCTTTTGGGGCTCGGGCTGTGAGGCTTTATCTGCGTGAGGTTCGAGATTCTCAGGCCAAAGCCAGAGGAATTAGCTACGAAAAGAAGAAGCGGAAGCGCCCACCAGAGAGTAGCACCAGTAGTACTAATAGTACTGCTAGTACTGTTCTTCCAGTTCAAGCAATACTGCCCCCTGCTCCTCCCAGTGCAAGCTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
DUF640

Protein Analysis

205

Amino Acids

22.44

Weight (kDa)

9.82

Isoelectric Point (pI)

64.85

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
ALOG_dom PF04852 33 - 156 1.4e-66 ALOG domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0016485)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G23290
fragaria_vesca FvH4_4g03750
malus_domestica MD13G1214900.v1.1 MD16G1220100.v1.1
prunus_persica Prupe.1G040300_v2.0.a1
rosa_chinensis RchiOBHm_Chr4g0393491
rosa_laevigata RLG00000009744 RLG00000009749
rosa_roxburghii Rroxscaffold_5G00338420
rosa_rugosa Rorug04G0001000
rosa_samantha Rh4AG047700 Rh4BG043600 Rh4CG050400
rosa_wichuraiana Rw4G003760

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc65I GGTACC 1 cut(s) 243
AccB1I GGYRCC 1 cut(s) 243
AccII CGCG 1 cut(s) 208
AciI CCGC 9 cut(s) 127, 145, 191, 208, 337, 373, 384, 402, 511
AcoI YGGCCR 1 cut(s) 370
AcsI RAATTY 1 cut(s) 17
AcvI CACGTG 1 cut(s) 226
AcyI GRCGYC 1 cut(s) 360
AfaI GTAC 4 cut(s) 245, 544, 553, 562
AfiI CCNNNNNNNGG 4 cut(s) 207, 296, 297, 427
AgsI TTSAA 4 cut(s) 14, 48, 392, 578
AjnI CCWGG 1 cut(s) 246
AluBI AGCT 4 cut(s) 283, 344, 495, 612
AluI AGCT 4 cut(s) 283, 344, 495, 612
Alw21I GWGCWC 2 cut(s) 276, 399
Alw26I GTCTC 1 cut(s) 144
Alw44I GTGCAC 1 cut(s) 272
Ama87I CYCGRG 1 cut(s) 432
AoxI GGCC 4 cut(s) 188, 219, 370, 474
ApaI GGGCCC 1 cut(s) 223
ApaLI GTGCAC 1 cut(s) 272
ApoI RAATTY 1 cut(s) 17
Asp718I GGTACC 1 cut(s) 243
AspLEI GCGC 2 cut(s) 116, 519
AspS9I GGNCC 3 cut(s) 219, 220, 250
AvaI CYCGRG 1 cut(s) 432
AvaII GGWCC 1 cut(s) 250
AxyI CCTNAGG 2 cut(s) 239, 411
BaeGI GKGCMC 3 cut(s) 223, 276, 326
BanI GGYRCC 1 cut(s) 243
BanII GRGCYC 2 cut(s) 223, 433
BbrPI CACGTG 1 cut(s) 226
BbsI GAAGAC 1 cut(s) 269
Bbv12I GWGCWC 2 cut(s) 276, 399
BbvCI CCTCAGC 1 cut(s) 122
BccI CCATC 2 cut(s) 43, 83
BceAI ACGGC 1 cut(s) 415
BciT130I CCWGG 1 cut(s) 248
BcoDI GTCTC 1 cut(s) 144
BfaI CTAG 1 cut(s) 558
BfoI RGCGCY 1 cut(s) 520
BisI GCNGC 6 cut(s) 127, 146, 191, 338, 373, 384
BlsI GCNGC 6 cut(s) 128, 147, 192, 339, 374, 385
BmcAI AGTACT 3 cut(s) 544, 553, 562
Bme1390I CCNGG 1 cut(s) 248
Bme18I GGWCC 1 cut(s) 250
BmeT110I CYCGRG 1 cut(s) 432
BmgT120I GGNCC 3 cut(s) 219, 220, 250
BmiI GGNNCC 4 cut(s) 220, 221, 245, 302
BmrFI CCNGG 1 cut(s) 248
BmrI ACTGGG 1 cut(s) 597
BmuI ACTGGG 1 cut(s) 597
BpiI GAAGAC 1 cut(s) 269
Bpu10I CCTNAGC 1 cut(s) 122
BpuEI CTTGAG 1 cut(s) 251
BsaAI YACGTR 1 cut(s) 226
BsaHI GRCGYC 1 cut(s) 360
BsaJI CCNNGG 1 cut(s) 267
BsaXI ACNNNNNCTCC 2 cut(s) 77, 107
Bsc4I CCNNNNNNNGG 4 cut(s) 207, 296, 297, 427
Bse1I ACTGG 5 cut(s) 158, 253, 537, 572, 603
Bse21I CCTNAGG 2 cut(s) 239, 411
BseBI CCWGG 1 cut(s) 248
BseDI CCNNGG 1 cut(s) 267
BseGI GGATG 2 cut(s) 89, 276
BseLI CCNNNNNNNGG 4 cut(s) 207, 296, 297, 427
BseMII CTCAG 5 cut(s) 136, 253, 391, 402, 485
BseNI ACTGG 5 cut(s) 158, 253, 537, 572, 603
BseRI GAGGAG 3 cut(s) 85, 88, 588
BseSI GKGCMC 3 cut(s) 223, 276, 326
BseX3I CGGCCG 1 cut(s) 370
BsgI GTGCAG 2 cut(s) 232, 300
Bsh1236I CGCG 1 cut(s) 208
Bsh1285I CGRYCG 1 cut(s) 373
BshFI GGCC 4 cut(s) 190, 221, 372, 476
BshNI GGYRCC 1 cut(s) 243
BsiEI CGRYCG 1 cut(s) 373
BsiHKAI GWGCWC 2 cut(s) 276, 399
BsiHKCI CYCGRG 1 cut(s) 432
BslFI GGGAC 2 cut(s) 184, 273
BslI CCNNNNNNNGG 4 cut(s) 207, 296, 297, 427
BsmAI GTCTC 1 cut(s) 144
BsmFI GGGAC 2 cut(s) 184, 273
BsnI GGCC 4 cut(s) 190, 221, 372, 476
BsoBI CYCGRG 1 cut(s) 432
Bsp120I GGGCCC 1 cut(s) 219
Bsp1286I GDGCHC 5 cut(s) 223, 276, 326, 399, 433
BspACI CCGC 9 cut(s) 127, 145, 191, 208, 337, 373, 384, 402, 511
BspANI GGCC 4 cut(s) 190, 221, 372, 476
BspCNI CTCAG 5 cut(s) 135, 252, 390, 403, 484
BspFNI CGCG 1 cut(s) 208
BspLI GGNNCC 4 cut(s) 220, 221, 245, 302
BspQI GCTCTTC 1 cut(s) 387
BspT107I GGYRCC 1 cut(s) 243
BsrI ACTGG 5 cut(s) 158, 253, 537, 572, 603
BssECI CCNNGG 1 cut(s) 267
BssNI GRCGYC 1 cut(s) 360
BssT1I CCWWGG 1 cut(s) 267
Bst2UI CCWGG 1 cut(s) 248
Bst4CI ACNGT 3 cut(s) 198, 321, 565
Bst6I CTCTTC 1 cut(s) 387
BstACI GRCGYC 1 cut(s) 360
BstBAI YACGTR 1 cut(s) 226
BstC8I GCNNGC 2 cut(s) 342, 610
BstDEI CTNAG 5 cut(s) 122, 239, 377, 411, 471
BstF5I GGATG 2 cut(s) 89, 276
BstFNI CGCG 1 cut(s) 208
BstH2I RGCGCY 1 cut(s) 520
BstHHI GCGC 2 cut(s) 116, 519
BstMAI GTCTC 1 cut(s) 144
BstMCI CGRYCG 1 cut(s) 373
BstMWI GCNNNNNNNGC 2 cut(s) 280, 451
BstNI CCWGG 1 cut(s) 248
BstSCI CCNGG 1 cut(s) 246
BstSLI GKGCMC 3 cut(s) 223, 276, 326
BstUI CGCG 1 cut(s) 208
BstV2I GAAGAC 1 cut(s) 269
BstZI CGGCCG 1 cut(s) 370
Bsu36I CCTNAGG 2 cut(s) 239, 411
BsuRI GGCC 4 cut(s) 190, 221, 372, 476
BtgZI GCGATG 1 cut(s) 61
BtsCI GGATG 2 cut(s) 89, 276
BtsI GCAGTG 1 cut(s) 220
BtsIMutI CAGTG 3 cut(s) 194, 220, 610
Cac8I GCNNGC 2 cut(s) 342, 610
CfoI GCGC 2 cut(s) 116, 519
Cfr13I GGNCC 3 cut(s) 219, 220, 250
CseI GACGC 1 cut(s) 368
Csp6I GTAC 4 cut(s) 244, 543, 552, 561
CviAII CATG 1 cut(s) 111
CviQI GTAC 4 cut(s) 244, 543, 552, 561
DdeI CTNAG 5 cut(s) 122, 239, 377, 411, 471
EaeI YGGCCR 1 cut(s) 370
EagI CGGCCG 1 cut(s) 370
Eam1104I CTCTTC 1 cut(s) 387
EarI CTCTTC 1 cut(s) 387
EclXI CGGCCG 1 cut(s) 370
Eco130I CCWWGG 1 cut(s) 267
Eco24I GRGCYC 2 cut(s) 223, 433
Eco47I GGWCC 1 cut(s) 250
Eco52I CGGCCG 1 cut(s) 370
Eco72I CACGTG 1 cut(s) 226
Eco81I CCTNAGG 2 cut(s) 239, 411
Eco88I CYCGRG 1 cut(s) 432
EcoO109I RGGNCCY 1 cut(s) 219
EcoRII CCWGG 1 cut(s) 246
EcoT14I CCWWGG 1 cut(s) 267
EcoT38I GRGCYC 2 cut(s) 223, 433
ErhI CCWWGG 1 cut(s) 267
FaeI CATG 1 cut(s) 114
FaiI YATR 2 cut(s) 112, 132
FaqI GGGAC 2 cut(s) 184, 273
FatI CATG 1 cut(s) 110
FauI CCCGC 1 cut(s) 395
Fnu4HI GCNGC 6 cut(s) 127, 146, 191, 338, 373, 384
FokI GGATG 2 cut(s) 76, 263
FriOI GRGCYC 2 cut(s) 223, 433
Fsp4HI GCNGC 6 cut(s) 127, 146, 191, 338, 373, 384
FspBI CTAG 1 cut(s) 558
GlaI GCGC 2 cut(s) 115, 518
GluI GCNGC 6 cut(s) 127, 146, 191, 338, 373, 384
HaeII RGCGCY 1 cut(s) 520
HaeIII GGCC 4 cut(s) 190, 221, 372, 476
HgaI GACGC 1 cut(s) 368
HhaI GCGC 2 cut(s) 116, 519
Hin1I GRCGYC 1 cut(s) 360
Hin1II CATG 1 cut(s) 114
Hin6I GCGC 2 cut(s) 114, 517
HinP1I GCGC 2 cut(s) 114, 517
HindIII AAGCTT 1 cut(s) 342
HinfI GANTC 2 cut(s) 5, 467
Hpy166II GTNNAC 1 cut(s) 274
Hpy188I TCNGA 1 cut(s) 380
Hpy188III TCNNGA 3 cut(s) 14, 298, 464
Hpy8I GTNNAC 1 cut(s) 274
Hpy99I CGWCG 1 cut(s) 362
HpyAV CCTTC 2 cut(s) 36, 301
HpyCH4III ACNGT 3 cut(s) 198, 321, 565
HpyCH4IV ACGT 1 cut(s) 225
HpyCH4V TGCA 4 cut(s) 213, 274, 317, 608
HpyF10VI GCNNNNNNNGC 2 cut(s) 280, 451
HpyF3I CTNAG 5 cut(s) 122, 239, 377, 411, 471
HpySE526I ACGT 1 cut(s) 225
Hsp92I GRCGYC 1 cut(s) 360
Hsp92II CATG 1 cut(s) 114
HspAI GCGC 2 cut(s) 114, 517
KpnI GGTACC 1 cut(s) 247
LguI GCTCTTC 1 cut(s) 387
LmnI GCTCC 1 cut(s) 601
MaeI CTAG 1 cut(s) 558
MaeII ACGT 1 cut(s) 225
MaeIII GTNAC 1 cut(s) 179
MboII GAAGA 5 cut(s) 274, 286, 404, 517, 560
MhlI GDGCHC 5 cut(s) 223, 276, 326, 399, 433
MluCI AATT 2 cut(s) 17, 489
MmeI TCCRAC 1 cut(s) 54
MseI TTAA 1 cut(s) 54
MspA1I CMGCKG 1 cut(s) 283
MspR9I CCNGG 1 cut(s) 248
MvaI CCWGG 1 cut(s) 248
MvnI CGCG 1 cut(s) 208
MwoI GCNNNNNNNGC 2 cut(s) 280, 451
NlaIII CATG 1 cut(s) 114
NlaIV GGNNCC 4 cut(s) 220, 221, 245, 302
PciSI GCTCTTC 1 cut(s) 387
PfeI GAWTC 2 cut(s) 5, 467
PkrI GCNGC 6 cut(s) 128, 147, 192, 339, 374, 385
PmaCI CACGTG 1 cut(s) 226
PmlI CACGTG 1 cut(s) 226
Ppu21I YACGTR 1 cut(s) 226
Psp6I CCWGG 1 cut(s) 246
PspCI CACGTG 1 cut(s) 226
PspGI CCWGG 1 cut(s) 246
PspN4I GGNNCC 4 cut(s) 220, 221, 245, 302
PspOMI GGGCCC 1 cut(s) 219
PspPI GGNCC 3 cut(s) 219, 220, 250
PvuII CAGCTG 1 cut(s) 283
RsaI GTAC 4 cut(s) 245, 544, 553, 562
RsaNI GTAC 4 cut(s) 244, 543, 552, 561
SapI GCTCTTC 1 cut(s) 387
SaqAI TTAA 1 cut(s) 54
SatI GCNGC 6 cut(s) 127, 146, 191, 338, 373, 384
Sau96I GGNCC 3 cut(s) 219, 220, 250
ScaI AGTACT 3 cut(s) 544, 553, 562
ScrFI CCNGG 1 cut(s) 248
SduI GDGCHC 5 cut(s) 223, 276, 326, 399, 433
SinI GGWCC 1 cut(s) 250
SmlI CTYRAG 1 cut(s) 230
SmoI CTYRAG 1 cut(s) 230
Sse9I AATT 2 cut(s) 17, 489
SsiI CCGC 9 cut(s) 127, 145, 191, 208, 337, 373, 384, 402, 511
SspMI CTAG 1 cut(s) 558
StyD4I CCNGG 1 cut(s) 246
StyI CCWWGG 1 cut(s) 267
TaaI ACNGT 3 cut(s) 198, 321, 565
TaiI ACGT 1 cut(s) 228
TaqI TCGA 2 cut(s) 357, 463
TasI AATT 2 cut(s) 17, 489
TatI WGTACW 3 cut(s) 542, 551, 560
TauI GCSGC 6 cut(s) 129, 148, 193, 340, 375, 386
TfiI GAWTC 2 cut(s) 5, 467
Tru1I TTAA 1 cut(s) 54
Tru9I TTAA 1 cut(s) 54
TscAI CASTG 3 cut(s) 201, 220, 610
TspGWI ACGGA 1 cut(s) 167
TspRI CASTG 3 cut(s) 201, 220, 610
VneI GTGCAC 1 cut(s) 272
VpaK11BI GGWCC 1 cut(s) 250
XapI RAATTY 1 cut(s) 17
XspI CTAG 1 cut(s) 558
ZrmI AGTACT 3 cut(s) 544, 553, 562
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.