AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0576110


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0576110 MtrunA17_Chr8g0393271 96.032 126 1 1 1 122 1 126 1.79e-83 247
Msa0576110 MtrunA17_Chr6g0479451 70.526 95 27 1 28 122 24 117 3.98e-42 141
Msa0576110 MtrunA17_Chr8g0375761 69.565 92 27 1 31 122 21 111 2.13e-39 134
Msa0576110 MtrunA17_Chr8g0375781 58.491 106 44 0 17 122 17 122 9.83e-38 130
Msa0576110 MtrunA17_Chr8g0375821 64.894 94 33 0 29 122 66 159 6.73e-37 129
Msa0576110 MtrunA17_Chr8g0375791 52.991 117 55 0 6 122 6 122 6.03e-35 123
Msa0576110 MtrunA17_Chr8g0375891 72.222 54 15 0 71 124 47 100 1.44e-20 81.3
Msa0576110 MtrunA17_Chr8g0375901 71.698 53 15 0 71 123 1 53 2.74e-19 79.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0576110 AT1G14700.2 63.107 103 37 1 21 123 48 149 1.29e-41 141
Msa0576110 AT1G14700.4 62.745 102 37 1 21 122 48 148 1.49e-41 139
Msa0576110 AT1G14700.1 62.745 102 37 1 21 122 48 148 8.31e-41 139
Msa0576110 AT3G17790.1 56.303 119 49 3 5 122 4 120 1.62e-39 135
Msa0576110 AT2G01880.1 59.813 107 41 2 17 122 10 115 2.74e-38 131
Msa0576110 AT2G01890.2 55.263 114 49 2 10 122 7 119 3.46e-37 128
Msa0576110 AT2G01890.1 55.263 114 49 2 10 122 7 119 7.55e-37 128
Msa0576110 AT1G25230.1 61.290 93 35 1 29 121 28 119 2.37e-35 124
Msa0576110 AT1G25230.3 61.290 93 35 1 29 121 51 142 3.07e-35 124
Msa0576110 AT1G14700.3 69.231 52 16 0 71 122 1 52 8.08e-20 82.4
Msa0576110 AT1G25230.2 62.745 51 19 0 71 121 1 51 2.33e-17 75.9
Msa0576110 AT2G01890.3 63.462 52 19 0 71 122 1 52 7.32e-17 74.3

Find 29 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACACAACACAGATGTAAAT+TGG 0.249033 4_1:-80185003 None:intergenic
CAACATAACATGGGTGGTTT+AGG 0.292659 4_1:+80184943 None:intergenic
ACACTTAGCTTCCTCGTCAT+TGG 0.364659 4_1:+80185090 Msa0576110:CDS
GCTTCCTCGTCATTGGAGAC+TGG 0.404371 4_1:+80185097 Msa0576110:CDS
CAAGTTAAACATTGACTTTG+TGG 0.429435 4_1:+80185271 Msa0576110:CDS
ATTGACTTTGTGGTATCAAC+CGG 0.442770 4_1:+80185281 Msa0576110:CDS
GAGAAGGAATATTGAAAAGC+AGG 0.451116 4_1:-80185344 None:intergenic
CTTCCTCGTCATTGGAGACT+GGG 0.458606 4_1:+80185098 Msa0576110:CDS
GTGGCATCTGCTTTGACAGC+AGG 0.480379 4_1:-80185069 None:intergenic
CCTGAAAAGCAACTTGAGAC+TGG 0.496595 4_1:-80185140 None:intergenic
AGCAACTTGAGACTGGTTGT+AGG 0.500595 4_1:-80185133 None:intergenic
TTCTATGACGATGGATTGAC+TGG 0.514825 4_1:+80185311 Msa0576110:CDS
CAGATGTAAATTGGAATCCA+TGG 0.540833 4_1:-80184994 None:intergenic
CAGCAGGGTGCTCAATGCGT+TGG 0.541284 4_1:-80185053 None:intergenic
AAATTGGAATCCATGGCCAC+AGG 0.544307 4_1:-80184987 None:intergenic
GGAGACAATTTCTATGACGA+TGG 0.555932 4_1:+80185302 Msa0576110:CDS
AATTGGAATCCATGGCCACA+GGG 0.558266 4_1:-80184986 None:intergenic
TGGCATCTGCTTTGACAGCA+GGG 0.559566 4_1:-80185068 None:intergenic
ATTGGAGACTGGGGAAGGAA+AGG 0.574215 4_1:+80185108 Msa0576110:CDS
ATCGTCATAGAAATTGTCTC+CGG 0.579752 4_1:-80185300 None:intergenic
TCGTCATTGGAGACTGGGGA+AGG 0.599769 4_1:+80185103 Msa0576110:CDS
AGAAGGAATATTGAAAAGCA+GGG 0.612677 4_1:-80185343 None:intergenic
GGCGGTGTAGATATCTGAGA+AGG 0.631188 4_1:-80185360 None:intergenic
TTGGAATCCATGGCCACAGG+GGG 0.651995 4_1:-80184984 None:intergenic
ACACAACAACATAACATGGG+TGG 0.658211 4_1:+80184937 None:intergenic
TTCCTCGTCATTGGAGACTG+GGG 0.664337 4_1:+80185099 Msa0576110:CDS
TTCCCCAGTCTCCAATGACG+AGG 0.673800 4_1:-80185101 None:intergenic
AATGACGAGGAAGCTAAGTG+TGG 0.707391 4_1:-80185088 None:intergenic
ATTGGAATCCATGGCCACAG+GGG 0.738974 4_1:-80184985 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTAAAATAAAAATTCAGA+TGG + chr4_1:80185235-80185254 Msa0576110:intron 10.0%
!! ATTAAAATAAAAATTCAGAT+GGG + chr4_1:80185236-80185255 Msa0576110:intron 10.0%
!! TGTAAAAAAACTTGTCTTAA+AGG - chr4_1:80185196-80185215 None:intergenic 20.0%
! AAACTTGTCTTAAAGGAATT+TGG - chr4_1:80185189-80185208 None:intergenic 25.0%
!!! CATTATACCATTGTTTTTGA+AGG - chr4_1:80185391-80185410 None:intergenic 25.0%
! CTTCAAAAACAATGGTATAA+TGG + chr4_1:80185389-80185408 Msa0576110:CDS 25.0%
!! CAAGTTAAACATTGACTTTG+TGG + chr4_1:80185271-80185290 Msa0576110:CDS 30.0%
AGAAGGAATATTGAAAAGCA+GGG - chr4_1:80185346-80185365 None:intergenic 30.0%
CAGATGTAAATTGGAATCCA+TGG - chr4_1:80184997-80185016 None:intergenic 35.0%
CACACAACACAGATGTAAAT+TGG - chr4_1:80185006-80185025 None:intergenic 35.0%
AAAAATTCAGATGGGAAGAG+TGG + chr4_1:80185244-80185263 Msa0576110:intron 35.0%
! ATTGACTTTGTGGTATCAAC+CGG + chr4_1:80185281-80185300 Msa0576110:CDS 35.0%
ATCGTCATAGAAATTGTCTC+CGG - chr4_1:80185303-80185322 None:intergenic 35.0%
GAGAAGGAATATTGAAAAGC+AGG - chr4_1:80185347-80185366 None:intergenic 35.0%
GGAGACAATTTCTATGACGA+TGG + chr4_1:80185302-80185321 Msa0576110:CDS 40.0%
!! TTCTATGACGATGGATTGAC+TGG + chr4_1:80185311-80185330 Msa0576110:CDS 40.0%
!!! TTGTTTTTGAAGGCTGTTGG+CGG - chr4_1:80185381-80185400 None:intergenic 40.0%
!!! CCATTGTTTTTGAAGGCTGT+TGG - chr4_1:80185384-80185403 None:intergenic 40.0%
CCAACAGCCTTCAAAAACAA+TGG + chr4_1:80185381-80185400 Msa0576110:CDS 40.0%
AATTGGAATCCATGGCCACA+GGG - chr4_1:80184989-80185008 None:intergenic 45.0%
AAATTGGAATCCATGGCCAC+AGG - chr4_1:80184990-80185009 None:intergenic 45.0%
AATGACGAGGAAGCTAAGTG+TGG - chr4_1:80185091-80185110 None:intergenic 45.0%
ACACTTAGCTTCCTCGTCAT+TGG + chr4_1:80185090-80185109 Msa0576110:CDS 45.0%
! AGCAACTTGAGACTGGTTGT+AGG - chr4_1:80185136-80185155 None:intergenic 45.0%
CCTGAAAAGCAACTTGAGAC+TGG - chr4_1:80185143-80185162 None:intergenic 45.0%
!!! CCAGTCTCAAGTTGCTTTTC+AGG + chr4_1:80185140-80185159 Msa0576110:CDS 45.0%
!! TTAATAAATAATGATAAAAA+TGG - chr4_1:80185221-80185240 None:intergenic 5.0%
ATTGGAATCCATGGCCACAG+GGG - chr4_1:80184988-80185007 None:intergenic 50.0%
TGGCATCTGCTTTGACAGCA+GGG - chr4_1:80185071-80185090 None:intergenic 50.0%
CTTCCTCGTCATTGGAGACT+GGG + chr4_1:80185098-80185117 Msa0576110:CDS 50.0%
TTCCTCGTCATTGGAGACTG+GGG + chr4_1:80185099-80185118 Msa0576110:CDS 50.0%
ATTGGAGACTGGGGAAGGAA+AGG + chr4_1:80185108-80185127 Msa0576110:CDS 50.0%
GGCGGTGTAGATATCTGAGA+AGG - chr4_1:80185363-80185382 None:intergenic 50.0%
TTGGAATCCATGGCCACAGG+GGG - chr4_1:80184987-80185006 None:intergenic 55.0%
GTGGCATCTGCTTTGACAGC+AGG - chr4_1:80185072-80185091 None:intergenic 55.0%
GCTTCCTCGTCATTGGAGAC+TGG + chr4_1:80185097-80185116 Msa0576110:CDS 55.0%
TTCCCCAGTCTCCAATGACG+AGG - chr4_1:80185104-80185123 None:intergenic 55.0%
TCGTCATTGGAGACTGGGGA+AGG + chr4_1:80185103-80185122 Msa0576110:CDS 55.0%
CAAGTAGCCTAAGCCCCCTG+TGG + chr4_1:80184971-80184990 Msa0576110:CDS 60.0%
! CAGCAGGGTGCTCAATGCGT+TGG - chr4_1:80185056-80185075 None:intergenic 60.0%
TCCATGGCCACAGGGGGCTT+AGG - chr4_1:80184981-80185000 None:intergenic 65.0%
GCCTAAGCCCCCTGTGGCCA+TGG + chr4_1:80184977-80184996 Msa0576110:CDS 70.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 80184952 80185418 80184952 ID=Msa0576110;Name=Msa0576110
chr4_1 mRNA 80184952 80185418 80184952 ID=Msa0576110-mRNA-1;Parent=Msa0576110;Name=Msa0576110-mRNA-1;_AED=0.15;_eAED=0.15;_QI=0|0|0|1|1|1|2|0|125
chr4_1 exon 80184952 80185161 80184952 ID=Msa0576110-mRNA-1:exon:28622;Parent=Msa0576110-mRNA-1
chr4_1 exon 80185254 80185418 80185254 ID=Msa0576110-mRNA-1:exon:28623;Parent=Msa0576110-mRNA-1
chr4_1 CDS 80184952 80185161 80184952 ID=Msa0576110-mRNA-1:cds;Parent=Msa0576110-mRNA-1
chr4_1 CDS 80185254 80185418 80185254 ID=Msa0576110-mRNA-1:cds;Parent=Msa0576110-mRNA-1
Gene Sequence

>Msa0576110

ATGGGTGGTTTAGGAAGAACAAGTAGCCTAAGCCCCCTGTGGCCATGGATTCCAATTTACATCTGTGTTGTGTGTGTAAGTGTAAATGTATCAGCTGAGCTCCAACGCATTGAGCACCCTGCTGTCAAAGCAGATGCCACACTTAGCTTCCTCGTCATTGGAGACTGGGGAAGGAAAGGAACCTACAACCAGTCTCAAGTTGCTTTTCAGATGGGAAGAGTGGCTGACAAGTTAAACATTGACTTTGTGGTATCAACCGGAGACAATTTCTATGACGATGGATTGACTGGTGTACATGACCCTGCTTTTCAATATTCCTTCTCAGATATCTACACCGCCAACAGCCTTCAAAAACAATGGTATAATGGTCAGTGT

Protein sequence

>Msa0576110

MGGLGRTSSLSPLWPWIPIYICVVCVSVNVSAELQRIEHPAVKADATLSFLVIGDWGRKGTYNQSQVAFQMGRVADKLNIDFVVSTGDNFYDDGLTGVHDPAFQYSFSDIYTANSLQKQWYNGQC