AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0885290


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0885290 MtrunA17_Chr8g0337671 80.342 117 23 0 5 121 27 143 2.83e-65 208
Msa0885290 MtrunA17_Chr4g0049181 79.339 121 24 1 1 121 41 160 9.89e-65 207
Msa0885290 MtrunA17_Chr7g0249841 69.231 117 35 1 5 121 26 141 4.43e-55 181
Msa0885290 MtrunA17_Chr4g0049171 80.612 98 19 0 23 120 35 132 1.37e-51 164
Msa0885290 MtrunA17_Chr6g0452221 43.697 119 65 2 4 121 21 138 2.97e-24 96.3
Msa0885290 MtrunA17_Chr3g0095181 37.607 117 66 4 11 124 36 148 4.26e-12 59.3
Msa0885290 MtrunA17_Chr3g0127671 38.333 120 65 5 1 120 61 171 7.12e-12 61.2
Msa0885290 MtrunA17_Chr3g0127701 39.496 119 63 5 2 120 20 129 9.97e-12 60.8
Msa0885290 MtrunA17_Chr5g0400861 30.469 128 81 4 1 125 17 139 4.34e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0885290 AT5G48380.1 48.739 119 60 1 7 125 27 144 1.75e-37 134
Msa0885290 AT3G28450.1 50.000 120 57 2 2 121 26 142 1.69e-32 120
Msa0885290 AT1G69990.1 46.667 120 62 2 1 120 11 128 4.67e-30 113
Msa0885290 AT1G27190.1 47.788 113 58 1 8 120 24 135 7.55e-29 109
Msa0885290 AT3G49750.2 34.746 118 70 4 11 125 28 141 1.20e-13 64.7
Msa0885290 AT3G49750.1 34.746 118 70 4 11 125 28 141 2.66e-13 64.7
Msa0885290 AT5G65830.1 34.211 114 67 4 11 121 35 143 2.75e-12 62.0
Msa0885290 AT1G28440.1 37.288 118 68 4 7 124 15 126 6.16e-12 61.6
Msa0885290 AT1G72300.1 39.744 78 47 0 44 121 79 156 2.65e-11 60.1

Find 24 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGAGGTTAAGTAATTATT+TGG 0.115459 6_1:+40780999 None:intergenic
GTCTTGCAAGGAATTCTTAA+TGG 0.231983 6_1:+40781022 None:intergenic
GGTTTCATATGTAGATTTAA+TGG 0.295617 6_1:-40780951 Msa0885290:CDS
CTCTCTTATAACAAATTTAC+TGG 0.305708 6_1:-40780735 Msa0885290:CDS
TTGAGGTTAAGTAATTATTT+GGG 0.409710 6_1:+40781000 None:intergenic
ACTATCTAACATGGGGTTGA+AGG 0.419371 6_1:-40780883 Msa0885290:CDS
TGAAAACTGCTCATCAATTA+CGG 0.435476 6_1:-40780841 Msa0885290:CDS
CTTGTGCCTCAGTATGATAA+TGG 0.461438 6_1:-40781084 None:intergenic
CTTTCAATCAATGAGCTCTC+AGG 0.472919 6_1:-40780810 Msa0885290:CDS
GATTTAATGGTGTTGAATGC+TGG 0.504838 6_1:-40780938 Msa0885290:CDS
AGTATACTTGATATATCAGA+TGG 0.505360 6_1:+40780780 None:intergenic
CTGAGAGCTCATTGATTGAA+AGG 0.524706 6_1:+40780811 None:intergenic
CTATCTAACATGGGGTTGAA+GGG 0.528422 6_1:-40780882 Msa0885290:CDS
GTAATTATTTGGGTCTTGCA+AGG 0.531394 6_1:+40781010 None:intergenic
ATAATTACTTAACCTCAAGC+TGG 0.542997 6_1:-40780995 Msa0885290:CDS
AAATCTCAAACTATCTAACA+TGG 0.543158 6_1:-40780892 Msa0885290:CDS
TTTGTTATAAGAGAGATCAA+TGG 0.548617 6_1:+40780743 None:intergenic
GTTGTTGAAGTTCCAGCTTG+AGG 0.552303 6_1:+40780983 None:intergenic
AACTTCAACAACAAAACTGA+AGG 0.560611 6_1:-40780972 Msa0885290:CDS
AATCTCAAACTATCTAACAT+GGG 0.565321 6_1:-40780891 Msa0885290:CDS
ATCTCAAACTATCTAACATG+GGG 0.631175 6_1:-40780890 Msa0885290:CDS
CAATCAATGAGCTCTCAGGA+CGG 0.648181 6_1:-40780806 Msa0885290:CDS
GTATACTTGATATATCAGAT+GGG 0.696920 6_1:+40780781 None:intergenic
TTGAAGGGTCAGTTTCCACG+TGG 0.735953 6_1:-40780867 Msa0885290:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGAGGTTAAGTAATTATTT+GGG + chr6_1:40780790-40780809 None:intergenic 20.0%
! CTTGAGGTTAAGTAATTATT+TGG + chr6_1:40780791-40780810 None:intergenic 25.0%
! GGTTTCATATGTAGATTTAA+TGG - chr6_1:40780836-40780855 Msa0885290:CDS 25.0%
!! TTTAGTACTCTATTTTCATC+TGG + chr6_1:40780878-40780897 None:intergenic 25.0%
! AAATCTCAAACTATCTAACA+TGG - chr6_1:40780895-40780914 Msa0885290:CDS 25.0%
! AATCTCAAACTATCTAACAT+GGG - chr6_1:40780896-40780915 Msa0885290:CDS 25.0%
! GTATACTTGATATATCAGAT+GGG + chr6_1:40781009-40781028 None:intergenic 25.0%
! AGTATACTTGATATATCAGA+TGG + chr6_1:40781010-40781029 None:intergenic 25.0%
!! TTTGTTATAAGAGAGATCAA+TGG + chr6_1:40781047-40781066 None:intergenic 25.0%
! CTCTCTTATAACAAATTTAC+TGG - chr6_1:40781052-40781071 Msa0885290:CDS 25.0%
ATAATTACTTAACCTCAAGC+TGG - chr6_1:40780792-40780811 Msa0885290:CDS 30.0%
AACTTCAACAACAAAACTGA+AGG - chr6_1:40780815-40780834 Msa0885290:CDS 30.0%
ATCTCAAACTATCTAACATG+GGG - chr6_1:40780897-40780916 Msa0885290:CDS 30.0%
TGAAAACTGCTCATCAATTA+CGG - chr6_1:40780946-40780965 Msa0885290:CDS 30.0%
GTCTTGCAAGGAATTCTTAA+TGG + chr6_1:40780768-40780787 None:intergenic 35.0%
GTAATTATTTGGGTCTTGCA+AGG + chr6_1:40780780-40780799 None:intergenic 35.0%
! GATTTAATGGTGTTGAATGC+TGG - chr6_1:40780849-40780868 Msa0885290:CDS 35.0%
ACTATCTAACATGGGGTTGA+AGG - chr6_1:40780904-40780923 Msa0885290:CDS 40.0%
CTATCTAACATGGGGTTGAA+GGG - chr6_1:40780905-40780924 Msa0885290:CDS 40.0%
! CTGAGAGCTCATTGATTGAA+AGG + chr6_1:40780979-40780998 None:intergenic 40.0%
CTTTCAATCAATGAGCTCTC+AGG - chr6_1:40780977-40780996 Msa0885290:CDS 40.0%
GTTGTTGAAGTTCCAGCTTG+AGG + chr6_1:40780807-40780826 None:intergenic 45.0%
CAATCAATGAGCTCTCAGGA+CGG - chr6_1:40780981-40781000 Msa0885290:CDS 45.0%
TTGAAGGGTCAGTTTCCACG+TGG - chr6_1:40780920-40780939 Msa0885290:CDS 50.0%
!! GAGCAGTTTTCAAGACCACG+TGG + chr6_1:40780938-40780957 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 40780716 40781093 40780716 ID=Msa0885290;Name=Msa0885290
chr6_1 mRNA 40780716 40781093 40780716 ID=Msa0885290-mRNA-1;Parent=Msa0885290;Name=Msa0885290-mRNA-1;_AED=0.47;_eAED=0.49;_QI=0|-1|0|1|-1|1|1|0|125
chr6_1 exon 40780716 40781093 40780716 ID=Msa0885290-mRNA-1:exon:9157;Parent=Msa0885290-mRNA-1
chr6_1 CDS 40780716 40781093 40780716 ID=Msa0885290-mRNA-1:cds;Parent=Msa0885290-mRNA-1
Gene Sequence

>Msa0885290

ATGATAATGGCTAGTCAGAGTACTGAGACTGATATCTTCTGTTTAAAATCCATTAAGAATTCCTTGCAAGACCCAAATAATTACTTAACCTCAAGCTGGAACTTCAACAACAAAACTGAAGGTTTCATATGTAGATTTAATGGTGTTGAATGCTGGCATCCAGATGAAAATAGAGTACTAAATCTCAAACTATCTAACATGGGGTTGAAGGGTCAGTTTCCACGTGGTCTTGAAAACTGCTCATCAATTACGGACGTAGACCTTTCAATCAATGAGCTCTCAGGACGGATCCCATCTGATATATCAAGTATACTTTCATTTGTTTCGACCATTGATCTCTCTTATAACAAATTTACTGGCGAAACTCAACAACTATAG

Protein sequence

>Msa0885290

MIMASQSTETDIFCLKSIKNSLQDPNNYLTSSWNFNNKTEGFICRFNGVECWHPDENRVLNLKLSNMGLKGQFPRGLENCSSITDVDLSINELSGRIPSDISSILSFVSTIDLSYNKFTGETQQL*