AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1419700


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1419700 MtrunA17_Chr4g0062601 85.263 95 6 2 1 94 79 166 1.32e-38 126
Msa1419700 MtrunA17_Chr8g0372741 68.367 98 26 3 1 94 82 178 1.25e-34 116
Msa1419700 MtrunA17_Chr1g0198831 46.269 67 21 2 29 94 52 104 1.77e-11 55.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1419700 AT1G73965.1 50.000 66 20 2 29 94 55 107 2.39e-13 60.8
Msa1419700 AT1G68795.1 51.429 70 16 3 28 94 64 118 9.26e-13 59.7

Find 31 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACTAGCAACACCAAGTTTC+AGG 0.222084 tig0024723:+11962 Msa1419700:CDS
CATTAATGGTGCAATGGATT+TGG 0.262090 tig0024723:-12176 None:intergenic
AGTTTCAGGTTTATCAAAAT+AGG 0.287858 tig0024723:+11976 Msa1419700:CDS
ACTTCACTCCATTTCTTAAT+CGG 0.308385 tig0024723:+12021 Msa1419700:CDS
ACTGAGATCGATCCGCGTTA+TGG 0.417933 tig0024723:+12125 Msa1419700:CDS
GATACTCTTTCATATGTGCT+TGG 0.418515 tig0024723:+11899 None:intergenic
AATAGGAAAATCTTAGCAAC+CGG 0.463874 tig0024723:+11993 Msa1419700:CDS
GATAAACGCCTTGTTCCATC+TGG 0.473410 tig0024723:+12152 Msa1419700:CDS
AAATCCAATATTAGTACTAG+TGG 0.494292 tig0024723:+11927 Msa1419700:CDS
TCAGTTTCCTTCGGCTCATG+AGG 0.494458 tig0024723:-12107 None:intergenic
TGGTGGTGCCGATTAAGAAA+TGG 0.504177 tig0024723:-12029 None:intergenic
AAATGGAGTGAAGTCAAATC+CGG 0.507048 tig0024723:-12012 None:intergenic
CCGGCATGTGACTCCGGTGG+TGG 0.514190 tig0024723:-12076 None:intergenic
GAGTCACCGGCATGTGACTC+CGG 0.517907 tig0024723:-12082 None:intergenic
GGCTCATGAGGGTGAGTCAC+CGG 0.520168 tig0024723:-12095 None:intergenic
ACCACGGTCATCGTCATCAT+CGG 0.529578 tig0024723:+12048 Msa1419700:CDS
GGATCGATCTCAGTTTCCTT+CGG 0.540255 tig0024723:-12116 None:intergenic
CCACGGTCATCGTCATCATC+GGG 0.543735 tig0024723:+12049 Msa1419700:CDS
TGCAATGGATTTGGACCAGA+TGG 0.557410 tig0024723:-12167 None:intergenic
GAACCTCATTAATGGTGCAA+TGG 0.574590 tig0024723:-12182 None:intergenic
CCACCACCGGAGTCACATGC+CGG 0.579118 tig0024723:+12076 Msa1419700:CDS
AAACTTGGTGTTGCTAGTAA+TGG 0.582271 tig0024723:-11958 None:intergenic
CAGTTTCCTTCGGCTCATGA+GGG 0.590230 tig0024723:-12106 None:intergenic
GACTCACCCTCATGAGCCGA+AGG 0.604155 tig0024723:+12100 Msa1419700:CDS
GATTTGGACCAGATGGAACA+AGG 0.607957 tig0024723:-12160 None:intergenic
ATCATCGGGATCACCACCAC+CGG 0.629549 tig0024723:+12063 Msa1419700:CDS
TCACCGGCATGTGACTCCGG+TGG 0.690195 tig0024723:-12079 None:intergenic
TTTCTTAATCGGCACCACCA+CGG 0.698743 tig0024723:+12032 Msa1419700:CDS
CGTTTATCAACACCATAACG+CGG 0.733230 tig0024723:-12137 None:intergenic
CCCGATGATGACGATGACCG+TGG 0.746981 tig0024723:-12049 None:intergenic
GATGATGACGATGACCGTGG+TGG 0.778203 tig0024723:-12046 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAATCCAATATTAGTACTAG+TGG + tig0024723:11927-11946 Msa1419700:CDS 25.0%
!! TTTTCCACTAGTACTAATAT+TGG - tig0024723:11934-11953 None:intergenic 25.0%
!!! ATTTTGATAAACCTGAAACT+TGG - tig0024723:11976-11995 None:intergenic 25.0%
!!! AGTTTCAGGTTTATCAAAAT+AGG + tig0024723:11976-11995 Msa1419700:CDS 25.0%
AATAGGAAAATCTTAGCAAC+CGG + tig0024723:11993-12012 Msa1419700:CDS 30.0%
ACTTCACTCCATTTCTTAAT+CGG + tig0024723:12021-12040 Msa1419700:CDS 30.0%
!! AAACTTGGTGTTGCTAGTAA+TGG - tig0024723:11961-11980 None:intergenic 35.0%
AAATGGAGTGAAGTCAAATC+CGG - tig0024723:12015-12034 None:intergenic 35.0%
TACTAGCAACACCAAGTTTC+AGG + tig0024723:11962-11981 Msa1419700:CDS 40.0%
CGTTTATCAACACCATAACG+CGG - tig0024723:12140-12159 None:intergenic 40.0%
!! TGGTGGTGCCGATTAAGAAA+TGG - tig0024723:12032-12051 None:intergenic 45.0%
TTTCTTAATCGGCACCACCA+CGG + tig0024723:12032-12051 Msa1419700:CDS 45.0%
GGATCGATCTCAGTTTCCTT+CGG - tig0024723:12119-12138 None:intergenic 45.0%
! GATAAACGCCTTGTTCCATC+TGG + tig0024723:12152-12171 Msa1419700:CDS 45.0%
GATTTGGACCAGATGGAACA+AGG - tig0024723:12163-12182 None:intergenic 45.0%
! TGCAATGGATTTGGACCAGA+TGG - tig0024723:12170-12189 None:intergenic 45.0%
ACCACGGTCATCGTCATCAT+CGG + tig0024723:12048-12067 Msa1419700:CDS 50.0%
CAGTTTCCTTCGGCTCATGA+GGG - tig0024723:12109-12128 None:intergenic 50.0%
TCAGTTTCCTTCGGCTCATG+AGG - tig0024723:12110-12129 None:intergenic 50.0%
ACTGAGATCGATCCGCGTTA+TGG + tig0024723:12125-12144 Msa1419700:CDS 50.0%
! GATGATGACGATGACCGTGG+TGG - tig0024723:12049-12068 None:intergenic 55.0%
CCACGGTCATCGTCATCATC+GGG + tig0024723:12049-12068 Msa1419700:CDS 55.0%
ATCATCGGGATCACCACCAC+CGG + tig0024723:12063-12082 Msa1419700:CDS 55.0%
! CCCGATGATGACGATGACCG+TGG - tig0024723:12052-12071 None:intergenic 60.0%
GAGTCACCGGCATGTGACTC+CGG - tig0024723:12085-12104 None:intergenic 60.0%
GGCTCATGAGGGTGAGTCAC+CGG - tig0024723:12098-12117 None:intergenic 60.0%
GACTCACCCTCATGAGCCGA+AGG + tig0024723:12100-12119 Msa1419700:CDS 60.0%
CCACCACCGGAGTCACATGC+CGG + tig0024723:12076-12095 Msa1419700:CDS 65.0%
TCACCGGCATGTGACTCCGG+TGG - tig0024723:12082-12101 None:intergenic 65.0%
CCGGCATGTGACTCCGGTGG+TGG - tig0024723:12079-12098 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
tig0024723 gene 11912 12196 11912 ID=Msa1419700;Name=Msa1419700
tig0024723 mRNA 11912 12196 11912 ID=Msa1419700-mRNA-1;Parent=Msa1419700;Name=Msa1419700-mRNA-1;_AED=0.10;_eAED=0.10;_QI=0|-1|0|1|-1|1|1|0|94
tig0024723 exon 11912 12196 11912 ID=Msa1419700-mRNA-1:exon:1048;Parent=Msa1419700-mRNA-1
tig0024723 CDS 11912 12196 11912 ID=Msa1419700-mRNA-1:cds;Parent=Msa1419700-mRNA-1
Gene Sequence

>Msa1419700

ATGTGCTTGGATTTCAAATCCAATATTAGTACTAGTGGAAAAATCACCATTACTAGCAACACCAAGTTTCAGGTTTATCAAAATAGGAAAATCTTAGCAACCGGATTTGACTTCACTCCATTTCTTAATCGGCACCACCACGGTCATCGTCATCATCGGGATCACCACCACCGGAGTCACATGCCGGTGACTCACCCTCATGAGCCGAAGGAAACTGAGATCGATCCGCGTTATGGTGTTGATAAACGCCTTGTTCCATCTGGTCCAAATCCATTGCACCATTAA

Protein sequence

>Msa1419700

MCLDFKSNISTSGKITITSNTKFQVYQNRKILATGFDFTPFLNRHHHGHRHHRDHHHRSHMPVTHPHEPKETEIDPRYGVDKRLVPSGPNPLHH*