RchiOBHm_Chr3g0496001

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
3
OG0000077
Physical Location & Seq
Forward (+)
46485938 .. 46489043
3106 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ45834

Sequence Viewer

Length: 873 bp
ATGAACGAATCAAGTTCTTCAACCATTCATTTCCCTTTGAGTATCAGCCAAATTGAGCTTCTGAATGGCTCTAACTTCAGAAAATGGAAATCGGACATTGAGCTCAACTTGGGAATACTTGACTATGATCATGTGCTCAAGGAGGATCCACCTGAGGAATTGACACCAACTGCAAGTAGGGAGGCCAAAGAGAAGTTTGAAAAATGGCACAAACACAACAAAATGGCTTTGATCATGATCAAGAAAAGCATACCTGATAATGTGAGAGGAGGCATTCCAGATTCTGAGTATGCCAAGGAGTTCTTCAACTCCATTGCTGAGAAGTTTAAAATCTCAGATAAGGCTGAGATAAATAATCTCATGAAATCACTCATGAGAATGGAGTTCAATGGGAAAGGCAGTGTTAGAGAATTCATCATGAGAGGTTCTAATGTTGCTGGAAAACTAAGGGGACTGAATATGGCTGTGGAAGATTCATTTCTGGTTTACATGCTTCTAAACAAACTACCAGAAGAGTATGATAATCTGAAATCACTCTACAAGACTCAAAAGGAGCAGTGGACTGTGAATGAATTGATCTCACTCTGTGTTGAAGTCGAAGATGAAGTCAAGAAGAAAGGAAAAGAGATTTCAGTGAATTTAGTCACCAAAATGCAACATAAGAAAAGGTTTGGAAACAATTGCAACAAAGGCAGCACCTCAAAACTTACAGTTAAGACTGACAACAATAAGGGTAAGTCTTCTAAGCCTGCTATAGTGATGAAATGTTTCTTTTGCAAGAAATCAGGGCATTTTAAGAAAGATTGTGAGGGTTTCAAGGCTTGGCTAACTAAGAAAGGGATTATCAAGAATAACAATCCCAAACAGGAATGA
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
Retrotran_gag_2 zf-CCHC

Protein Analysis

290

Amino Acids

33.25

Weight (kDa)

9.38

Isoelectric Point (pI)

33.35

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 50 - 206 1e-17 gag-polypeptide of LTR copia-type
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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Orthologous Genes (Group: OG0000077)

Species Orthologous Gene IDs
arabidopsis_thaliana AT5G53670
fragaria_vesca FvH4_1g12751 FvH4_1g13491 FvH4_1g13491 FvH4_1g16302 FvH4_1g16303 FvH4_1g29161 FvH4_1g29941 FvH4_2g02290 FvH4_2g05985 FvH4_2g15841 FvH4_2g18261 FvH4_2g22761 FvH4_2g22761 FvH4_2g22761 FvH4_3g13432 FvH4_3g14801 FvH4_3g28581 FvH4_3g30611 FvH4_3g30611 FvH4_3g30611 FvH4_3g32571 FvH4_3g32571 FvH4_3g32571 FvH4_3g33631 FvH4_3g36663 FvH4_3g36664 FvH4_4g00961 FvH4_4g17672 FvH4_5g13441 FvH4_5g30231 FvH4_5g39263 FvH4_6g06661 FvH4_6g06662 FvH4_6g40841 FvH4_7g00732 FvH4_7g11331 FvH4_7g12361
malus_domestica MD02G1100700.v1.1 MD02G1280000.v1.1 MD03G1045100.v1.1 MD04G1043300.v1.1 MD05G1061800.v1.1 MD05G1118300.v1.1 MD05G1334900.v1.1 MD08G1232100.v1.1 MD10G1202700.v1.1 MD11G1016600.v1.1 MD11G1271900.v1.1 MD15G1002900.v1.1 MD15G1059300.v1.1
prunus_persica Prupe.1G445900_v2.0.a1 Prupe.4G244000_v2.0.a1 Prupe.6G221400_v2.0.a1 Prupe.6G301400_v2.0.a1 Prupe.7G031600_v2.0.a1 Prupe.8G017100_v2.0.a1
pyrus_communis pycom01g08140 pycom01g19130 pycom02g09810 pycom03g12420 pycom05g09140 pycom05g22780 pycom06g17440 pycom07g04850 pycom07g08300 pycom08g09110 pycom08g10760 pycom09g15580 pycom09g18260 pycom09g18400 pycom11g07380 pycom11g20370 pycom12g01630 pycom12g11730 pycom13g21040 pycom14g00290 pycom14g10520 pycom15g16640 pycom15g18720 pycom15g24540 pycom15g26360 pycom16g08100 pycom16g09950 pycom16g11700 pycom16g19690 pycom17g20400
rosa_chinensis RchiOBHm_Chr1g0317481 RchiOBHm_Chr1g0322601 RchiOBHm_Chr1g0324761 RchiOBHm_Chr1g0335001 RchiOBHm_Chr1g0336961 RchiOBHm_Chr1g0345341 RchiOBHm_Chr1g0348501 RchiOBHm_Chr1g0352591 RchiOBHm_Chr1g0354901 RchiOBHm_Chr1g0365141 RchiOBHm_Chr1g0365511 RchiOBHm_Chr1g0368471 RchiOBHm_Chr1g0373471 RchiOBHm_Chr1g0373951 RchiOBHm_Chr1g0375621 RchiOBHm_Chr1g0378491 RchiOBHm_Chr1g0383431 RchiOBHm_Chr2g0086291 RchiOBHm_Chr2g0096681 RchiOBHm_Chr2g0117391 RchiOBHm_Chr2g0121511 RchiOBHm_Chr2g0128511 RchiOBHm_Chr2g0159591 RchiOBHm_Chr2g0173271 RchiOBHm_Chr3g0453771 RchiOBHm_Chr3g0462071 RchiOBHm_Chr3g0467151 RchiOBHm_Chr3g0468531 RchiOBHm_Chr3g0478981 RchiOBHm_Chr3g0488371 RchiOBHm_Chr3g0496001 RchiOBHm_Chr3g0496651 RchiOBHm_Chr4g0390941 RchiOBHm_Chr4g0431251 RchiOBHm_Chr4g0441691 RchiOBHm_Chr5g0001181 RchiOBHm_Chr5g0001671 RchiOBHm_Chr5g0021461 RchiOBHm_Chr5g0045101 RchiOBHm_Chr5g0045461 RchiOBHm_Chr5g0063421 RchiOBHm_Chr5g0068061 RchiOBHm_Chr5g0069541 RchiOBHm_Chr5g0073131 RchiOBHm_Chr5g0076631 RchiOBHm_Chr5g0079181 RchiOBHm_Chr5g0082051 RchiOBHm_Chr6g0248451 RchiOBHm_Chr6g0255561 RchiOBHm_Chr6g0266491 RchiOBHm_Chr6g0268111 RchiOBHm_Chr6g0304521 RchiOBHm_Chr6g0306511 RchiOBHm_Chr7g0181641 RchiOBHm_Chr7g0181791 RchiOBHm_Chr7g0188321 RchiOBHm_Chr7g0194951 RchiOBHm_Chr7g0195071 RchiOBHm_Chr7g0199671 RchiOBHm_Chr7g0204631 RchiOBHm_Chr7g0231771 RchiOBHm_Chr7g0231831 RchiOBHm_Chr7g0242511
rosa_laevigata RLG00000015596 RLG00000021778 RLG00000028187
rosa_multiflora Rmu_co8285397.1_g000001 Rmu_co8301931.1_g000001 Rmu_co8376351.1_g000001 Rmu_co8412043.1_g000001 Rmu_sc0000079.1_g000006 Rmu_sc0000160.1_g000007 Rmu_sc0000208.1_g000006 Rmu_sc0000258.1_g000016 Rmu_sc0000295.1_g000008 Rmu_sc0000302.1_g000025 Rmu_sc0000423.1_g000039 Rmu_sc0000441.1_g000040 Rmu_sc0000538.1_g000074 Rmu_sc0000603.1_g000019 Rmu_sc0000611.1_g000018 Rmu_sc0000729.1_g000002 Rmu_sc0000837.1_g000044 Rmu_sc0000903.1_g000015 Rmu_sc0000924.1_g000029 Rmu_sc0001173.1_g000021 Rmu_sc0001289.1_g000004 Rmu_sc0001347.1_g000005 Rmu_sc0001464.1_g000020 Rmu_sc0001618.1_g000015 Rmu_sc0002014.1_g000002 Rmu_sc0002047.1_g000002 Rmu_sc0002160.1_g000029 Rmu_sc0002310.1_g000011 Rmu_sc0002416.1_g000002 Rmu_sc0002417.1_g000008 Rmu_sc0002445.1_g000008 Rmu_sc0002691.1_g000026 Rmu_sc0002700.1_g000021 Rmu_sc0002748.1_g000032 Rmu_sc0002792.1_g000048 Rmu_sc0002831.1_g000012 Rmu_sc0002928.1_g000025 Rmu_sc0002956.1_g000001 Rmu_sc0003170.1_g000039 Rmu_sc0003232.1_g000024 Rmu_sc0003391.1_g000014 Rmu_sc0003600.1_g000009 Rmu_sc0003630.1_g000064 Rmu_sc0003633.1_g000035 Rmu_sc0003802.1_g000001 Rmu_sc0003881.1_g000001 Rmu_sc0003989.1_g000001 Rmu_sc0004208.1_g000021 Rmu_sc0004815.1_g000004 Rmu_sc0004821.1_g000002 Rmu_sc0005237.1_g000004 Rmu_sc0005638.1_g000006 Rmu_sc0005996.1_g000004 Rmu_sc0006604.1_g000005 Rmu_sc0007023.1_g000007 Rmu_sc0007084.1_g000004 Rmu_sc0007239.1_g000001 Rmu_sc0007338.1_g000010 Rmu_sc0007398.1_g000004 Rmu_sc0007630.1_g000001 Rmu_sc0008067.1_g000001 Rmu_sc0008114.1_g000001 Rmu_sc0008623.1_g000008 Rmu_sc0009777.1_g000010 Rmu_sc0012719.1_g000001 Rmu_sc0014173.1_g000001 Rmu_sc0015338.1_g000002 Rmu_sc0015804.1_g000002 Rmu_sc0023779.1_g000001 Rmu_sc0024140.1_g000001 Rmu_sc0024833.1_g000006 Rmu_ssc0000087.1_g000013 Rmu_ssc0000400.1_g000088 Rmu_ssc0000400.1_g000089
rosa_roxburghii Rroxscaffold_175G00432540 Rroxscaffold_1G00003260 Rroxscaffold_1G00032490 Rroxscaffold_1G00035100 Rroxscaffold_1G00051960 Rroxscaffold_1G00056120 Rroxscaffold_2G00091260 Rroxscaffold_2G00097580 Rroxscaffold_2G00100910 Rroxscaffold_2G00101000 Rroxscaffold_2G00104370 Rroxscaffold_2G00154020 Rroxscaffold_3G00219010 Rroxscaffold_3G00241360 Rroxscaffold_3G00265190 Rroxscaffold_4G00328620 Rroxscaffold_5G00338660 Rroxscaffold_5G00339430 Rroxscaffold_5G00346490 Rroxscaffold_5G00360740 Rroxscaffold_5G00373490 Rroxscaffold_5G00373950 Rroxscaffold_5G00379290 Rroxscaffold_6G00390000 Rroxscaffold_6G00406560 Rroxscaffold_7G00163660 Rroxscaffold_7G00172220 Rroxscaffold_7G00182760 Rroxscaffold_7G00217680 Rroxscaffold_7G00217910
rosa_rugosa Rorug03G0299400 Rorug04G0048800 Rorug05G0503600 Rorug07G0090800 Rorug07G0090900 Rorug07G0294700
rosa_samantha Rh3BG243300 Rh4BG398100
rosa_wichuraiana Rw0G005950 Rw0G023070 Rw1G003680 Rw1G004130 Rw1G007910 Rw1G013940 Rw1G018710 Rw1G022140 Rw1G031170 Rw1G041420 Rw2G024950 Rw2G045000 Rw2G049360 Rw3G007370 Rw3G009120 Rw3G011780 Rw3G027830 Rw4G001510 Rw4G003110 Rw4G008370 Rw4G022100 Rw4G035490 Rw5G001650 Rw5G002000 Rw5G002590 Rw5G017930 Rw5G020530 Rw5G024010 Rw5G024710 Rw5G025620 Rw5G027980 Rw5G030200 Rw5G036530 Rw5G044700 Rw6G006860 Rw6G018940 Rw6G019810 Rw6G029740 Rw7G009360 Rw7G017280 Rw7G017540 Rw7G020090 Rw7G022500 Rw7G031420

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AclWI GGATC 2 cut(s) 140, 153
AcsI RAATTY 2 cut(s) 410, 637
AcuI CTGAAG 1 cut(s) 61
AdeI CACNNNGTG 1 cut(s) 587
AgsI TTSAA 6 cut(s) 21, 200, 307, 388, 593, 817
AjuI GAANNNNNNNTTGG 4 cut(s) 42, 74, 287, 319
AluBI AGCT 2 cut(s) 58, 103
AluI AGCT 2 cut(s) 58, 103
Alw21I GWGCWC 2 cut(s) 105, 138
AlwI GGATC 2 cut(s) 140, 153
AlwNI CAGNNNCTG 1 cut(s) 284
AoxI GGCC 1 cut(s) 183
ApeKI GCWGC 1 cut(s) 693
ApoI RAATTY 2 cut(s) 410, 637
ArsI GACNNNNNNTTYG 2 cut(s) 591, 623
Asp700I GAANNNNTTC 1 cut(s) 767
AsuHPI GGTGA 1 cut(s) 637
AxyI CCTNAGG 1 cut(s) 153
BamHI GGATCC 1 cut(s) 145
BanII GRGCYC 1 cut(s) 105
BbsI GAAGAC 1 cut(s) 732
Bbv12I GWGCWC 2 cut(s) 105, 138
BbvI GCAGC 1 cut(s) 705
BclI TGATCA 3 cut(s) 127, 231, 237
BfmI CTRYAG 1 cut(s) 753
BisI GCNGC 1 cut(s) 694
BlsI GCNGC 1 cut(s) 695
BmiI GGNNCC 1 cut(s) 147
BpiI GAAGAC 1 cut(s) 732
BpuEI CTTGAG 1 cut(s) 122
BsaBI GATNNNNATC 1 cut(s) 236
BsaJI CCNNGG 1 cut(s) 294
Bse21I CCTNAGG 1 cut(s) 153
Bse3DI GCAATG 1 cut(s) 312
Bse8I GATNNNNATC 1 cut(s) 236
BseDI CCNNGG 1 cut(s) 294
BseJI GATNNNNATC 1 cut(s) 236
BseMI GCAATG 1 cut(s) 312
BseMII CTCAG 5 cut(s) 144, 276, 309, 336, 348
BseRI GAGGAG 1 cut(s) 282
BseXI GCAGC 1 cut(s) 705
BshFI GGCC 1 cut(s) 185
BsiHKAI GWGCWC 2 cut(s) 105, 138
BslFI GGGAC 1 cut(s) 465
BsmFI GGGAC 1 cut(s) 465
BsmI GAATGC 1 cut(s) 273
BsnI GGCC 1 cut(s) 185
Bsp1286I GDGCHC 2 cut(s) 105, 138
Bsp143I GATC 5 cut(s) 127, 145, 231, 237, 576
BspANI GGCC 1 cut(s) 185
BspCNI CTCAG 5 cut(s) 145, 277, 310, 337, 347
BspHI TCATGA 4 cut(s) 234, 360, 372, 417
BspLI GGNNCC 1 cut(s) 147
BspPI GGATC 2 cut(s) 140, 153
BsrDI GCAATG 1 cut(s) 312
BssECI CCNNGG 1 cut(s) 294
BssMI GATC 5 cut(s) 127, 145, 231, 237, 576
BssT1I CCWWGG 1 cut(s) 294
Bst4CI ACNGT 2 cut(s) 565, 712
Bst6I CTCTTC 1 cut(s) 507
BstC8I GCNNGC 1 cut(s) 750
BstDEI CTNAG 8 cut(s) 153, 285, 318, 334, 345, 446, 744, 831
BstKTI GATC 5 cut(s) 130, 148, 234, 240, 579
BstMBI GATC 5 cut(s) 127, 145, 231, 237, 576
BstMWI GCNNNNNNNGC 1 cut(s) 690
BstNSI RCATGY 1 cut(s) 493
BstSFI CTRYAG 1 cut(s) 753
BstV1I GCAGC 1 cut(s) 705
BstV2I GAAGAC 1 cut(s) 732
BstX2I RGATCY 1 cut(s) 145
BstYI RGATCY 1 cut(s) 145
Bsu36I CCTNAGG 1 cut(s) 153
BsuRI GGCC 1 cut(s) 185
BtsI GCAGTG 2 cut(s) 406, 563
BtsIMutI CAGTG 3 cut(s) 406, 563, 639
Cac8I GCNNGC 1 cut(s) 750
CaiI CAGNNNCTG 1 cut(s) 284
CciI TCATGA 4 cut(s) 234, 360, 372, 417
CviAII CATG 6 cut(s) 131, 235, 361, 373, 418, 490
DdeI CTNAG 8 cut(s) 153, 285, 318, 334, 345, 446, 744, 831
DpnI GATC 5 cut(s) 129, 147, 233, 239, 578
DpnII GATC 5 cut(s) 127, 145, 231, 237, 576
DraI TTTAAA 1 cut(s) 328
DraIII CACNNNGTG 1 cut(s) 587
Eam1104I CTCTTC 1 cut(s) 507
EarI CTCTTC 1 cut(s) 507
Ecl136II GAGCTC 1 cut(s) 103
Eco130I CCWWGG 1 cut(s) 294
Eco24I GRGCYC 1 cut(s) 105
Eco53kI GAGCTC 1 cut(s) 103
Eco57I CTGAAG 1 cut(s) 61
Eco81I CCTNAGG 1 cut(s) 153
EcoICRI GAGCTC 1 cut(s) 103
EcoRI GAATTC 1 cut(s) 410
EcoT14I CCWWGG 1 cut(s) 294
EcoT38I GRGCYC 1 cut(s) 105
ErhI CCWWGG 1 cut(s) 294
FaeI CATG 6 cut(s) 134, 238, 364, 376, 421, 493
FalI AAGNNNNNCTT 2 cut(s) 287, 319
FaqI GGGAC 1 cut(s) 465
FatI CATG 6 cut(s) 130, 234, 360, 372, 417, 489
FbaI TGATCA 3 cut(s) 127, 231, 237
Fnu4HI GCNGC 1 cut(s) 694
FriOI GRGCYC 1 cut(s) 105
Fsp4HI GCNGC 1 cut(s) 694
GluI GCNGC 1 cut(s) 694
HaeIII GGCC 1 cut(s) 185
Hin1II CATG 6 cut(s) 134, 238, 364, 376, 421, 493
HinfI GANTC 4 cut(s) 8, 281, 473, 544
HphI GGTGA 1 cut(s) 637
Hpy166II GTNNAC 2 cut(s) 487, 561
Hpy188I TCNGA 6 cut(s) 63, 80, 94, 286, 337, 528
Hpy188III TCNNGA 8 cut(s) 235, 241, 278, 361, 373, 418, 610, 847
Hpy8I GTNNAC 2 cut(s) 487, 561
HpyCH4III ACNGT 2 cut(s) 565, 712
HpyCH4V TGCA 4 cut(s) 173, 655, 684, 777
HpyF10VI GCNNNNNNNGC 1 cut(s) 690
HpyF3I CTNAG 8 cut(s) 153, 285, 318, 334, 345, 446, 744, 831
Hsp92II CATG 6 cut(s) 134, 238, 364, 376, 421, 493
Ksp22I TGATCA 3 cut(s) 127, 231, 237
Kzo9I GATC 5 cut(s) 127, 145, 231, 237, 576
LmnI GCTCC 1 cut(s) 553
LpnPI CCDG 9 cut(s) 165, 267, 291, 423, 467, 522, 762, 771, 851
Lsp1109I GCAGC 1 cut(s) 705
MaeIII GTNAC 1 cut(s) 643
MalI GATC 5 cut(s) 129, 147, 233, 239, 578
MboI GATC 5 cut(s) 127, 145, 231, 237, 576
MboII GAAGA 7 cut(s) 9, 295, 482, 524, 611, 625, 732
MfeI CAATTG 1 cut(s) 679
MflI RGATCY 1 cut(s) 145
MhlI GDGCHC 2 cut(s) 105, 138
MluCI AATT 6 cut(s) 51, 158, 410, 572, 637, 679
MlyI GAGTC 1 cut(s) 538
MnlI CCTC 8 cut(s) 136, 148, 175, 260, 263, 416, 709, 802
MroXI GAANNNNTTC 1 cut(s) 767
MseI TTAA 3 cut(s) 327, 714, 795
MslI CAYNNNNRTG 2 cut(s) 377, 650
MunI CAATTG 1 cut(s) 679
Mva1269I GAATGC 1 cut(s) 273
MwoI GCNNNNNNNGC 1 cut(s) 690
NdeII GATC 5 cut(s) 127, 145, 231, 237, 576
NlaIII CATG 6 cut(s) 134, 238, 364, 376, 421, 493
NlaIV GGNNCC 1 cut(s) 147
NmuCI GTSAC 1 cut(s) 643
NspI RCATGY 1 cut(s) 493
PagI TCATGA 4 cut(s) 234, 360, 372, 417
PctI GAATGC 1 cut(s) 273
PdmI GAANNNNTTC 1 cut(s) 767
PfeI GAWTC 3 cut(s) 8, 281, 473
PkrI GCNGC 1 cut(s) 695
PleI GAGTC 1 cut(s) 538
PpsI GAGTC 1 cut(s) 538
Psp124BI GAGCTC 1 cut(s) 105
PspN4I GGNNCC 1 cut(s) 147
PstNI CAGNNNCTG 1 cut(s) 284
PsuI RGATCY 1 cut(s) 145
RseI CAYNNNNRTG 2 cut(s) 377, 650
SacI GAGCTC 1 cut(s) 105
SaqAI TTAA 3 cut(s) 327, 714, 795
SatI GCNGC 1 cut(s) 694
Sau3AI GATC 5 cut(s) 127, 145, 231, 237, 576
SchI GAGTC 1 cut(s) 538
SduI GDGCHC 2 cut(s) 105, 138
SetI ASST 7 cut(s) 60, 105, 154, 256, 427, 671, 701
SfcI CTRYAG 1 cut(s) 753
SmiMI CAYNNNNRTG 2 cut(s) 377, 650
SmlI CTYRAG 1 cut(s) 137
SmoI CTYRAG 1 cut(s) 137
Sse9I AATT 6 cut(s) 51, 158, 410, 572, 637, 679
SstI GAGCTC 1 cut(s) 105
StyI CCWWGG 1 cut(s) 294
TaaI ACNGT 2 cut(s) 565, 712
TaqI TCGA 1 cut(s) 597
TasI AATT 6 cut(s) 51, 158, 410, 572, 637, 679
TfiI GAWTC 3 cut(s) 8, 281, 473
Tru1I TTAA 3 cut(s) 327, 714, 795
Tru9I TTAA 3 cut(s) 327, 714, 795
TscAI CASTG 3 cut(s) 406, 563, 639
TseFI GTSAC 1 cut(s) 643
TseI GCWGC 1 cut(s) 693
Tsp45I GTSAC 1 cut(s) 643
TspDTI ATGAA 8 cut(s) 17, 17, 377, 403, 465, 585, 618, 776
TspRI CASTG 3 cut(s) 406, 563, 639
XapI RAATTY 2 cut(s) 410, 637
XceI RCATGY 1 cut(s) 493
XmnI GAANNNNTTC 1 cut(s) 767
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.