AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1033830


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1033830 MtrunA17_Chr7g0256741 93.125 160 11 0 3 162 50 209 1.93e-108 311
Msa1033830 MtrunA17_Chr4g0004071 39.375 160 95 2 3 162 49 206 3.78e-36 127
Msa1033830 MtrunA17_Chr4g0004061 37.500 160 98 2 3 162 49 206 1.35e-34 123
Msa1033830 MtrunA17_Chr1g0148781 29.448 163 110 4 3 162 54 214 3.60e-19 82.4
Msa1033830 MtrunA17_Chr3g0138351 28.395 162 113 3 3 162 50 210 2.48e-15 71.6
Msa1033830 MtrunA17_Chr4g0009541 32.468 154 94 6 15 162 59 208 8.60e-15 70.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1033830 AT1G52820.2 42.949 156 87 2 7 162 56 209 2.38e-39 134
Msa1033830 AT1G52820.1 42.675 157 88 2 7 163 56 210 1.38e-38 134
Msa1033830 AT1G52800.1 38.994 159 95 2 4 162 52 208 2.48e-37 130
Msa1033830 AT1G52790.1 39.375 160 95 2 3 162 46 203 6.54e-36 126
Msa1033830 AT1G80320.1 36.646 161 99 3 4 162 50 209 2.35e-31 115
Msa1033830 AT4G03070.1 37.725 167 91 5 3 162 54 214 5.24e-26 100
Msa1033830 AT1G52810.1 40.000 105 63 0 3 107 52 156 1.55e-21 88.6
Msa1033830 AT4G03050.2 32.051 156 92 3 3 158 48 189 6.77e-18 79.7
Msa1033830 AT4G03050.1 32.051 156 92 3 3 158 48 189 6.77e-18 79.7
Msa1033830 AT1G15540.3 34.591 159 98 4 8 162 61 217 9.26e-18 79.0
Msa1033830 AT1G15540.2 34.591 159 98 4 8 162 57 213 9.90e-18 79.0
Msa1033830 AT1G15540.1 34.591 159 98 4 8 162 54 210 1.09e-17 78.6
Msa1033830 AT1G15540.4 34.591 159 98 4 8 162 54 210 1.09e-17 78.6

Find 34 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTTCTGACAATGTTATATT+TGG 0.130973 7_1:-69095407 Msa1033830:CDS
GTCTAATTCTCCCAACAATT+TGG 0.196750 7_1:+69094880 None:intergenic
TCCTTGAGGCCATATGATTT+TGG 0.205239 7_1:+69095229 None:intergenic
CTCAAGGAAATGATCGTTTC+TGG 0.227781 7_1:-69095214 Msa1033830:intron
ACTTCCCTTATATGAATCTT+TGG 0.231965 7_1:-69095294 Msa1033830:CDS
TGACATCCAAGCATAGTTAA+TGG 0.255056 7_1:+69095260 None:intergenic
AGAGATGGATGAGAAGGATT+TGG 0.277633 7_1:-69094747 Msa1033830:CDS
GATATCCAAAGATTCATATA+AGG 0.300354 7_1:+69095289 None:intergenic
AACATTGTCAGAAAGTTCTT+TGG 0.308306 7_1:+69095415 None:intergenic
GAGATGGATGAGAAGGATTT+GGG 0.312045 7_1:-69094746 Msa1033830:CDS
CATCAGCTAAATAATGTAAA+TGG 0.321665 7_1:-69094683 Msa1033830:CDS
ATACCATCCTCTTTGCTATA+TGG 0.351908 7_1:+69094858 None:intergenic
AGAATTCTTCAAACTCCCTT+TGG 0.356524 7_1:-69095378 Msa1033830:CDS
TAATTTCTTGATTCTATCAA+TGG 0.386845 7_1:+69094800 None:intergenic
CAAGCATAGTTAATGGATCT+TGG 0.392821 7_1:+69095267 None:intergenic
AATGAGTACTCCAAATTGTT+GGG 0.403546 7_1:-69094890 Msa1033830:CDS
CTGATGTACTACAGATATAA+TGG 0.431408 7_1:+69094700 None:intergenic
CAATGAGTACTCCAAATTGT+TGG 0.439455 7_1:-69094891 Msa1033830:CDS
CAAGATCCATTAACTATGCT+TGG 0.444301 7_1:-69095266 Msa1033830:CDS
AAATATTCACCAAAATCATA+TGG 0.463691 7_1:-69095238 Msa1033830:CDS
ATATCCAAAGATTCATATAA+GGG 0.472934 7_1:+69095290 None:intergenic
AACAAGAGAGATGGATGAGA+AGG 0.485145 7_1:-69094753 Msa1033830:CDS
AGACCTTTCCATGGCTACTC+AGG 0.493237 7_1:-69095329 Msa1033830:CDS
GTAGCACACTATGATAAAGT+TGG 0.526616 7_1:-69095438 None:intergenic
ACCAAAATCATATGGCCTCA+AGG 0.544014 7_1:-69095230 Msa1033830:CDS
AGAGTTGTCCTGAGTAGCCA+TGG 0.568925 7_1:+69095321 None:intergenic
GAAATATAGAACAAGAGAGA+TGG 0.576102 7_1:-69094762 Msa1033830:CDS
AGGATGGTATTTGAAAGCTA+TGG 0.598356 7_1:-69094845 Msa1033830:CDS
ATAATGGTCAAGTCTGAATG+AGG 0.623723 7_1:+69094716 None:intergenic
TGTCCTGAGTAGCCATGGAA+AGG 0.627328 7_1:+69095326 None:intergenic
ATAAGTGATAGACCTTTCCA+TGG 0.632144 7_1:-69095338 Msa1033830:CDS
AGACCATATAGCAAAGAGGA+TGG 0.638381 7_1:-69094861 Msa1033830:CDS
CAGAAACGATCATTTCCTTG+AGG 0.669988 7_1:+69095215 None:intergenic
AATTAGACCATATAGCAAAG+AGG 0.678010 7_1:-69094865 Msa1033830:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCAATAAATATATATTTTGA+TGG + chr7_1:69095142-69095161 None:intergenic 10.0%
!!! TCAATAAATATATATTTTGA+TGG + chr7_1:69095142-69095161 None:intergenic 10.0%
!! ATATCCAAAGATTCATATAA+GGG + chr7_1:69094808-69094827 None:intergenic 20.0%
!! AAATATTCACCAAAATCATA+TGG - chr7_1:69094857-69094876 Msa1033830:CDS 20.0%
!! TAATTTCTTGATTCTATCAA+TGG + chr7_1:69095298-69095317 None:intergenic 20.0%
!! ATATCCAAAGATTCATATAA+GGG + chr7_1:69094808-69094827 None:intergenic 20.0%
!! AAATATTCACCAAAATCATA+TGG - chr7_1:69094857-69094876 Msa1033830:CDS 20.0%
!! TAATTTCTTGATTCTATCAA+TGG + chr7_1:69095298-69095317 None:intergenic 20.0%
! CTTTCTGACAATGTTATATT+TGG - chr7_1:69094688-69094707 Msa1033830:CDS 25.0%
! GATATCCAAAGATTCATATA+AGG + chr7_1:69094809-69094828 None:intergenic 25.0%
! TGCTTCATGAATCTATATTA+TGG + chr7_1:69094921-69094940 None:intergenic 25.0%
! TCTCAAATTATTAGTGATGT+CGG - chr7_1:69095041-69095060 Msa1033830:intron 25.0%
! CATCAGCTAAATAATGTAAA+TGG - chr7_1:69095412-69095431 Msa1033830:CDS 25.0%
! CTTTCTGACAATGTTATATT+TGG - chr7_1:69094688-69094707 Msa1033830:CDS 25.0%
! GATATCCAAAGATTCATATA+AGG + chr7_1:69094809-69094828 None:intergenic 25.0%
! TGCTTCATGAATCTATATTA+TGG + chr7_1:69094921-69094940 None:intergenic 25.0%
! TCTCAAATTATTAGTGATGT+CGG - chr7_1:69095041-69095060 Msa1033830:intron 25.0%
! CATCAGCTAAATAATGTAAA+TGG - chr7_1:69095412-69095431 Msa1033830:CDS 25.0%
AACATTGTCAGAAAGTTCTT+TGG + chr7_1:69094683-69094702 None:intergenic 30.0%
ACTTCCCTTATATGAATCTT+TGG - chr7_1:69094801-69094820 Msa1033830:CDS 30.0%
CTCAAATTATTAGTGATGTC+GGG - chr7_1:69095042-69095061 Msa1033830:intron 30.0%
AGATAAGAGAATATGAAGCA+CGG + chr7_1:69095112-69095131 None:intergenic 30.0%
AATGAGTACTCCAAATTGTT+GGG - chr7_1:69095205-69095224 Msa1033830:intron 30.0%
AATTAGACCATATAGCAAAG+AGG - chr7_1:69095230-69095249 Msa1033830:CDS 30.0%
GAAATATAGAACAAGAGAGA+TGG - chr7_1:69095333-69095352 Msa1033830:CDS 30.0%
CTGATGTACTACAGATATAA+TGG + chr7_1:69095398-69095417 None:intergenic 30.0%
AACATTGTCAGAAAGTTCTT+TGG + chr7_1:69094683-69094702 None:intergenic 30.0%
ACTTCCCTTATATGAATCTT+TGG - chr7_1:69094801-69094820 Msa1033830:CDS 30.0%
CTCAAATTATTAGTGATGTC+GGG - chr7_1:69095042-69095061 Msa1033830:intron 30.0%
AGATAAGAGAATATGAAGCA+CGG + chr7_1:69095112-69095131 None:intergenic 30.0%
AATGAGTACTCCAAATTGTT+GGG - chr7_1:69095205-69095224 Msa1033830:intron 30.0%
AATTAGACCATATAGCAAAG+AGG - chr7_1:69095230-69095249 Msa1033830:CDS 30.0%
GAAATATAGAACAAGAGAGA+TGG - chr7_1:69095333-69095352 Msa1033830:CDS 30.0%
CTGATGTACTACAGATATAA+TGG + chr7_1:69095398-69095417 None:intergenic 30.0%
AGAATTCTTCAAACTCCCTT+TGG - chr7_1:69094717-69094736 Msa1033830:CDS 35.0%
!! TTTGCGCTTTTGTTTCCAAA+GGG + chr7_1:69094735-69094754 None:intergenic 35.0%
!! TTTTGCGCTTTTGTTTCCAA+AGG + chr7_1:69094736-69094755 None:intergenic 35.0%
ATAAGTGATAGACCTTTCCA+TGG - chr7_1:69094757-69094776 Msa1033830:CDS 35.0%
! CAAGCATAGTTAATGGATCT+TGG + chr7_1:69094831-69094850 None:intergenic 35.0%
CAAGATCCATTAACTATGCT+TGG - chr7_1:69094829-69094848 Msa1033830:CDS 35.0%
TGACATCCAAGCATAGTTAA+TGG + chr7_1:69094838-69094857 None:intergenic 35.0%
AAATTATTAGTGATGTCGGG+CGG - chr7_1:69095045-69095064 Msa1033830:intron 35.0%
CAATGAGTACTCCAAATTGT+TGG - chr7_1:69095204-69095223 Msa1033830:intron 35.0%
GTCTAATTCTCCCAACAATT+TGG + chr7_1:69095218-69095237 None:intergenic 35.0%
! ATACCATCCTCTTTGCTATA+TGG + chr7_1:69095240-69095259 None:intergenic 35.0%
AGGATGGTATTTGAAAGCTA+TGG - chr7_1:69095250-69095269 Msa1033830:CDS 35.0%
ATAATGGTCAAGTCTGAATG+AGG + chr7_1:69095382-69095401 None:intergenic 35.0%
AGAATTCTTCAAACTCCCTT+TGG - chr7_1:69094717-69094736 Msa1033830:CDS 35.0%
!! TTTGCGCTTTTGTTTCCAAA+GGG + chr7_1:69094735-69094754 None:intergenic 35.0%
!! TTTTGCGCTTTTGTTTCCAA+AGG + chr7_1:69094736-69094755 None:intergenic 35.0%
ATAAGTGATAGACCTTTCCA+TGG - chr7_1:69094757-69094776 Msa1033830:CDS 35.0%
! CAAGCATAGTTAATGGATCT+TGG + chr7_1:69094831-69094850 None:intergenic 35.0%
CAAGATCCATTAACTATGCT+TGG - chr7_1:69094829-69094848 Msa1033830:CDS 35.0%
TGACATCCAAGCATAGTTAA+TGG + chr7_1:69094838-69094857 None:intergenic 35.0%
AAATTATTAGTGATGTCGGG+CGG - chr7_1:69095045-69095064 Msa1033830:intron 35.0%
CAATGAGTACTCCAAATTGT+TGG - chr7_1:69095204-69095223 Msa1033830:intron 35.0%
GTCTAATTCTCCCAACAATT+TGG + chr7_1:69095218-69095237 None:intergenic 35.0%
! ATACCATCCTCTTTGCTATA+TGG + chr7_1:69095240-69095259 None:intergenic 35.0%
AGGATGGTATTTGAAAGCTA+TGG - chr7_1:69095250-69095269 Msa1033830:CDS 35.0%
ATAATGGTCAAGTCTGAATG+AGG + chr7_1:69095382-69095401 None:intergenic 35.0%
ACCAAAATCATATGGCCTCA+AGG - chr7_1:69094865-69094884 Msa1033830:CDS 40.0%
! TCCTTGAGGCCATATGATTT+TGG + chr7_1:69094869-69094888 None:intergenic 40.0%
CAGAAACGATCATTTCCTTG+AGG + chr7_1:69094883-69094902 None:intergenic 40.0%
CTCAAGGAAATGATCGTTTC+TGG - chr7_1:69094881-69094900 Msa1033830:CDS 40.0%
!! AGGAAATGATCGTTTCTGGT+TGG - chr7_1:69094885-69094904 Msa1033830:CDS 40.0%
TATCAGTGTCGTGTTTGTGT+CGG + chr7_1:69094993-69095012 None:intergenic 40.0%
GAGAATATGAAGCACGGATA+TGG + chr7_1:69095106-69095125 None:intergenic 40.0%
AGACCATATAGCAAAGAGGA+TGG - chr7_1:69095234-69095253 Msa1033830:CDS 40.0%
AACAAGAGAGATGGATGAGA+AGG - chr7_1:69095342-69095361 Msa1033830:CDS 40.0%
AGAGATGGATGAGAAGGATT+TGG - chr7_1:69095348-69095367 Msa1033830:CDS 40.0%
GAGATGGATGAGAAGGATTT+GGG - chr7_1:69095349-69095368 Msa1033830:CDS 40.0%
ACCAAAATCATATGGCCTCA+AGG - chr7_1:69094865-69094884 Msa1033830:CDS 40.0%
! TCCTTGAGGCCATATGATTT+TGG + chr7_1:69094869-69094888 None:intergenic 40.0%
CAGAAACGATCATTTCCTTG+AGG + chr7_1:69094883-69094902 None:intergenic 40.0%
CTCAAGGAAATGATCGTTTC+TGG - chr7_1:69094881-69094900 Msa1033830:CDS 40.0%
!! AGGAAATGATCGTTTCTGGT+TGG - chr7_1:69094885-69094904 Msa1033830:CDS 40.0%
TATCAGTGTCGTGTTTGTGT+CGG + chr7_1:69094993-69095012 None:intergenic 40.0%
GAGAATATGAAGCACGGATA+TGG + chr7_1:69095106-69095125 None:intergenic 40.0%
AGACCATATAGCAAAGAGGA+TGG - chr7_1:69095234-69095253 Msa1033830:CDS 40.0%
AACAAGAGAGATGGATGAGA+AGG - chr7_1:69095342-69095361 Msa1033830:CDS 40.0%
AGAGATGGATGAGAAGGATT+TGG - chr7_1:69095348-69095367 Msa1033830:CDS 40.0%
GAGATGGATGAGAAGGATTT+GGG - chr7_1:69095349-69095368 Msa1033830:CDS 40.0%
! TCCACGGATTAAACATGTCC+CGG - chr7_1:69094948-69094967 Msa1033830:intron 45.0%
ACACAACACATGTCTGACAC+CGG + chr7_1:69094970-69094989 None:intergenic 45.0%
ACGGATATGGATACAGACAC+CGG + chr7_1:69095093-69095112 None:intergenic 45.0%
! TCCACGGATTAAACATGTCC+CGG - chr7_1:69094948-69094967 Msa1033830:intron 45.0%
ACACAACACATGTCTGACAC+CGG + chr7_1:69094970-69094989 None:intergenic 45.0%
ACGGATATGGATACAGACAC+CGG + chr7_1:69095093-69095112 None:intergenic 45.0%
AGACCTTTCCATGGCTACTC+AGG - chr7_1:69094766-69094785 Msa1033830:CDS 50.0%
TGTCCTGAGTAGCCATGGAA+AGG + chr7_1:69094772-69094791 None:intergenic 50.0%
AGAGTTGTCCTGAGTAGCCA+TGG + chr7_1:69094777-69094796 None:intergenic 50.0%
CATGAAGCACAGACACTCCA+CGG - chr7_1:69094932-69094951 Msa1033830:intron 50.0%
ACCGGGACATGTTTAATCCG+TGG + chr7_1:69094952-69094971 None:intergenic 50.0%
CACAACACATGTCTGACACC+GGG + chr7_1:69094969-69094988 None:intergenic 50.0%
AGACCTTTCCATGGCTACTC+AGG - chr7_1:69094766-69094785 Msa1033830:CDS 50.0%
TGTCCTGAGTAGCCATGGAA+AGG + chr7_1:69094772-69094791 None:intergenic 50.0%
AGAGTTGTCCTGAGTAGCCA+TGG + chr7_1:69094777-69094796 None:intergenic 50.0%
CATGAAGCACAGACACTCCA+CGG - chr7_1:69094932-69094951 Msa1033830:intron 50.0%
ACCGGGACATGTTTAATCCG+TGG + chr7_1:69094952-69094971 None:intergenic 50.0%
CACAACACATGTCTGACACC+GGG + chr7_1:69094969-69094988 None:intergenic 50.0%
TACAGACACCGGACGCGACA+CGG + chr7_1:69095082-69095101 None:intergenic 60.0%
TACAGACACCGGACGCGACA+CGG + chr7_1:69095082-69095101 None:intergenic 60.0%
GTCAGTGTCCGTGTCGCGTC+CGG - chr7_1:69095071-69095090 Msa1033830:intron 65.0%
GTCAGTGTCCGTGTCGCGTC+CGG - chr7_1:69095071-69095090 Msa1033830:intron 65.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 69094667 69095450 69094667 ID=Msa1033830;Name=Msa1033830
chr7_1 mRNA 69094667 69095450 69094667 ID=Msa1033830-mRNA-1;Parent=Msa1033830;Name=Msa1033830-mRNA-1;_AED=0.40;_eAED=0.41;_QI=0|0|0|1|1|1|2|0|163
chr7_1 exon 69095215 69095450 69095215 ID=Msa1033830-mRNA-1:exon:16245;Parent=Msa1033830-mRNA-1
chr7_1 exon 69094667 69094922 69094667 ID=Msa1033830-mRNA-1:exon:16244;Parent=Msa1033830-mRNA-1
chr7_1 CDS 69095215 69095450 69095215 ID=Msa1033830-mRNA-1:cds;Parent=Msa1033830-mRNA-1
chr7_1 CDS 69094667 69094922 69094667 ID=Msa1033830-mRNA-1:cds;Parent=Msa1033830-mRNA-1
Gene Sequence

>Msa1033830

ATGATAAAGTTGGCCAAAGAACTTTCTGACAATGTTATATTTGGAATTGAAGAATTCTTCAAACTCCCTTTGGAAACAAAAGCGCAAAAGATAAGTGATAGACCTTTCCATGGCTACTCAGGACAACTCTCAACACTTCCCTTATATGAATCTTTGGATATCCAAGATCCATTAACTATGCTTGGATGTCAAATATTCACCAAAATCATATGGCCTCAAGGAAATGATCGTTTCTGCGAAAGTTTCAATGAGTACTCCAAATTGTTGGGAGAATTAGACCATATAGCAAAGAGGATGGTATTTGAAAGCTATGGTGTTGATATGAAAATATGTGAACCATTGATAGAATCAAGAAATTATCTCATTCGATGCTTGAAATATAGAACAAGAGAGATGGATGAGAAGGATTTGGGATTAACACCTCATTCAGACTTGACCATTATATCTGTAGTACATCAGCTAAATAATGTAAATGGCTTGCAAATCAATTGA

Protein sequence

>Msa1033830

MIKLAKELSDNVIFGIEEFFKLPLETKAQKISDRPFHGYSGQLSTLPLYESLDIQDPLTMLGCQIFTKIIWPQGNDRFCESFNEYSKLLGELDHIAKRMVFESYGVDMKICEPLIESRNYLIRCLKYRTREMDEKDLGLTPHSDLTIISVVHQLNNVNGLQIN*