AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0443700


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0443700 MtrunA17_Chr4g0054501 85.526 76 11 0 29 104 12 87 1.12e-43 137
Msa0443700 MtrunA17_Chr1g0158721 73.333 60 13 1 30 89 13 69 1.96e-25 93.2
Msa0443700 MtrunA17_Chr6g0449691 77.049 61 12 1 16 76 181 239 2.17e-24 95.5
Msa0443700 MtrunA17_Chr3g0113101 48.684 76 27 1 1 76 106 169 3.40e-15 69.3
Msa0443700 MtrunA17_Chr6g0487231 57.447 47 20 0 29 75 175 221 9.70e-13 62.4
Msa0443700 MtrunA17_Chr4g0070851 56.818 44 19 0 30 73 177 220 1.57e-11 58.9
Msa0443700 MtrunA17_Chr2g0299991 51.111 45 22 0 29 73 176 220 3.45e-11 58.2
Msa0443700 MtrunA17_Chr5g0410861 62.791 43 15 1 29 71 29 70 4.93e-11 54.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0443700 AT5G40440.5 87.234 47 6 0 30 76 110 156 2.79e-23 92.8
Msa0443700 AT5G40440.4 87.234 47 6 0 30 76 192 238 2.92e-23 92.8
Msa0443700 AT5G40440.1 87.234 47 6 0 30 76 192 238 2.92e-23 92.8
Msa0443700 AT5G40440.6 87.234 47 6 0 30 76 174 220 3.59e-23 92.4
Msa0443700 AT5G40440.3 87.234 47 6 0 30 76 174 220 3.59e-23 92.4
Msa0443700 AT5G40440.2 87.234 47 6 0 30 76 174 220 3.59e-23 92.4
Msa0443700 AT3G55800.1 60.870 46 18 0 1 46 113 158 2.61e-13 64.7
Msa0443700 AT5G56580.1 60.000 45 18 0 31 75 179 223 1.00e-12 62.8
Msa0443700 AT4G29810.3 53.191 47 22 0 30 76 186 232 6.57e-12 60.5
Msa0443700 AT4G29810.1 53.191 47 22 0 30 76 177 223 7.22e-12 60.5
Msa0443700 AT4G29810.2 53.191 47 22 0 30 76 186 232 7.38e-12 60.5

Find 14 sgRNAs with CRISPR-Local

Find 118 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACACAATGTGTTAACTCTTT+TGG 0.201562 3_3:+15587508 Msa0443700:CDS
GAGCCGAAAATTACTGATTT+TGG 0.210770 3_3:+15588529 Msa0443700:CDS
ATTTACTTGTAAACCTCAAA+GGG 0.420841 3_3:+15588506 Msa0443700:CDS
AGGTTTACAAGTAAATTAGC+AGG 0.487423 3_3:-15588499 None:intergenic
AATTTACTTGTAAACCTCAA+AGG 0.501450 3_3:+15588505 Msa0443700:CDS
CATAGAGAATTCAATTGCAA+TGG 0.556755 3_3:+15588564 Msa0443700:CDS
GCTCAACAAGATCCTCAATA+CGG 0.592189 3_3:-15588829 None:intergenic
TGGGGATGAGCAGCTTGCAG+TGG 0.595661 3_3:+15587528 Msa0443700:CDS
AGATGAGCAAGTCCGTATTG+AGG 0.604364 3_3:+15588817 Msa0443700:CDS
GCAGCTTGCAGTGGATATGA+TGG 0.623243 3_3:+15587537 Msa0443700:CDS
GTGAAGACAACTTCTTGTGG+TGG 0.628890 3_3:+15587484 None:intergenic
AAAGTGAAGACAACTTCTTG+TGG 0.638471 3_3:+15587481 None:intergenic
AAGGGTCTAAGTTATCTGCA+CGG 0.655190 3_3:+15588445 Msa0443700:intron
TTTACTTGTAAACCTCAAAG+GGG 0.694553 3_3:+15588507 Msa0443700:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTTTTAATCTTTTTGAA+GGG + chr3_3:15588427-15588446 Msa0443700:intron 15.0%
!!! GTTTTTTTAATCTTTTTGAA+GGG + chr3_3:15588427-15588446 Msa0443700:intron 15.0%
!! TAATTAAACTGATTATGTAG+TGG + chr3_3:15587649-15587668 Msa0443700:intron 20.0%
!! AAATTAAACAATACAACATG+TGG + chr3_3:15587830-15587849 Msa0443700:intron 20.0%
!! ACTCTATTAGTGATATAATT+AGG + chr3_3:15588124-15588143 Msa0443700:intron 20.0%
!! AACATGAAACAATTATGATT+TGG - chr3_3:15588199-15588218 None:intergenic 20.0%
!!! GGTTTTTTTAATCTTTTTGA+AGG + chr3_3:15588426-15588445 Msa0443700:intron 20.0%
!!! ATACCAAAATCAGTAATTTT+CGG - chr3_3:15588535-15588554 None:intergenic 20.0%
!! TAATTAAACTGATTATGTAG+TGG + chr3_3:15587649-15587668 Msa0443700:intron 20.0%
!! AAATTAAACAATACAACATG+TGG + chr3_3:15587830-15587849 Msa0443700:intron 20.0%
!! ACTCTATTAGTGATATAATT+AGG + chr3_3:15588124-15588143 Msa0443700:intron 20.0%
!! AACATGAAACAATTATGATT+TGG - chr3_3:15588199-15588218 None:intergenic 20.0%
!!! GGTTTTTTTAATCTTTTTGA+AGG + chr3_3:15588426-15588445 Msa0443700:intron 20.0%
!!! ATACCAAAATCAGTAATTTT+CGG - chr3_3:15588535-15588554 None:intergenic 20.0%
!!! TCATAATTTGTTGTGTCATT+AGG - chr3_3:15587694-15587713 None:intergenic 25.0%
!!! ACAAAAGTATCAGAATCTTA+CGG - chr3_3:15587754-15587773 None:intergenic 25.0%
!!! TTGATTTGTGTTCATATAAC+AGG + chr3_3:15587902-15587921 Msa0443700:intron 25.0%
! AATAGAGTCACACAAATAAA+GGG - chr3_3:15588112-15588131 None:intergenic 25.0%
! TAATAGAGTCACACAAATAA+AGG - chr3_3:15588113-15588132 None:intergenic 25.0%
! ATCATTTCCACACAAATAAA+GGG - chr3_3:15588158-15588177 None:intergenic 25.0%
! ATGATCTCAAACATTTAAGA+AGG + chr3_3:15588173-15588192 Msa0443700:intron 25.0%
! TGAAACATGGATGATAAAAT+AGG - chr3_3:15588311-15588330 None:intergenic 25.0%
! AATTTACTTGTAAACCTCAA+AGG + chr3_3:15588505-15588524 Msa0443700:CDS 25.0%
! ATTTACTTGTAAACCTCAAA+GGG + chr3_3:15588506-15588525 Msa0443700:CDS 25.0%
!!! TCATAATTTGTTGTGTCATT+AGG - chr3_3:15587694-15587713 None:intergenic 25.0%
!!! ACAAAAGTATCAGAATCTTA+CGG - chr3_3:15587754-15587773 None:intergenic 25.0%
!!! TTGATTTGTGTTCATATAAC+AGG + chr3_3:15587902-15587921 Msa0443700:intron 25.0%
! AATAGAGTCACACAAATAAA+GGG - chr3_3:15588112-15588131 None:intergenic 25.0%
! TAATAGAGTCACACAAATAA+AGG - chr3_3:15588113-15588132 None:intergenic 25.0%
! ATCATTTCCACACAAATAAA+GGG - chr3_3:15588158-15588177 None:intergenic 25.0%
! ATGATCTCAAACATTTAAGA+AGG + chr3_3:15588173-15588192 Msa0443700:intron 25.0%
! TGAAACATGGATGATAAAAT+AGG - chr3_3:15588311-15588330 None:intergenic 25.0%
! AATTTACTTGTAAACCTCAA+AGG + chr3_3:15588505-15588524 Msa0443700:CDS 25.0%
! ATTTACTTGTAAACCTCAAA+GGG + chr3_3:15588506-15588525 Msa0443700:CDS 25.0%
! ACACAATGTGTTAACTCTTT+TGG + chr3_3:15587508-15587527 Msa0443700:CDS 30.0%
! CACAATGTGTTAACTCTTTT+GGG + chr3_3:15587509-15587528 Msa0443700:CDS 30.0%
! ACAATGTGTTAACTCTTTTG+GGG + chr3_3:15587510-15587529 Msa0443700:CDS 30.0%
! TACCATGCAATAGTAGTTTT+AGG + chr3_3:15587979-15587998 Msa0443700:intron 30.0%
! ACTTATTCATGATAGCGTTA+AGG + chr3_3:15588019-15588038 Msa0443700:intron 30.0%
GATCATTTCCACACAAATAA+AGG - chr3_3:15588159-15588178 None:intergenic 30.0%
! AATTGTTTCATGTTGACTGA+TGG + chr3_3:15588205-15588224 Msa0443700:intron 30.0%
! GTGATACTTTTGTGACAATT+AGG + chr3_3:15588227-15588246 Msa0443700:intron 30.0%
TTTGTGACAATTAGGAGATA+AGG + chr3_3:15588235-15588254 Msa0443700:intron 30.0%
ATGGATGATAAAATAGGTTC+GGG - chr3_3:15588305-15588324 None:intergenic 30.0%
CATGGATGATAAAATAGGTT+CGG - chr3_3:15588306-15588325 None:intergenic 30.0%
ATTGAGATATGCTACTAACT+TGG + chr3_3:15588401-15588420 Msa0443700:intron 30.0%
AGGTTTACAAGTAAATTAGC+AGG - chr3_3:15588502-15588521 None:intergenic 30.0%
TTTACTTGTAAACCTCAAAG+GGG + chr3_3:15588507-15588526 Msa0443700:CDS 30.0%
!! ACTGATTTTGGTATTAGTGT+TGG + chr3_3:15588541-15588560 Msa0443700:CDS 30.0%
CATAGAGAATTCAATTGCAA+TGG + chr3_3:15588564-15588583 Msa0443700:CDS 30.0%
GAAGTGCAATTTCTATCTAT+AGG - chr3_3:15588794-15588813 None:intergenic 30.0%
! ACACAATGTGTTAACTCTTT+TGG + chr3_3:15587508-15587527 Msa0443700:CDS 30.0%
! CACAATGTGTTAACTCTTTT+GGG + chr3_3:15587509-15587528 Msa0443700:CDS 30.0%
! ACAATGTGTTAACTCTTTTG+GGG + chr3_3:15587510-15587529 Msa0443700:CDS 30.0%
! TACCATGCAATAGTAGTTTT+AGG + chr3_3:15587979-15587998 Msa0443700:intron 30.0%
! ACTTATTCATGATAGCGTTA+AGG + chr3_3:15588019-15588038 Msa0443700:intron 30.0%
GATCATTTCCACACAAATAA+AGG - chr3_3:15588159-15588178 None:intergenic 30.0%
! AATTGTTTCATGTTGACTGA+TGG + chr3_3:15588205-15588224 Msa0443700:intron 30.0%
! GTGATACTTTTGTGACAATT+AGG + chr3_3:15588227-15588246 Msa0443700:intron 30.0%
TTTGTGACAATTAGGAGATA+AGG + chr3_3:15588235-15588254 Msa0443700:intron 30.0%
ATGGATGATAAAATAGGTTC+GGG - chr3_3:15588305-15588324 None:intergenic 30.0%
CATGGATGATAAAATAGGTT+CGG - chr3_3:15588306-15588325 None:intergenic 30.0%
ATTGAGATATGCTACTAACT+TGG + chr3_3:15588401-15588420 Msa0443700:intron 30.0%
AGGTTTACAAGTAAATTAGC+AGG - chr3_3:15588502-15588521 None:intergenic 30.0%
TTTACTTGTAAACCTCAAAG+GGG + chr3_3:15588507-15588526 Msa0443700:CDS 30.0%
!! ACTGATTTTGGTATTAGTGT+TGG + chr3_3:15588541-15588560 Msa0443700:CDS 30.0%
CATAGAGAATTCAATTGCAA+TGG + chr3_3:15588564-15588583 Msa0443700:CDS 30.0%
GAAGTGCAATTTCTATCTAT+AGG - chr3_3:15588794-15588813 None:intergenic 30.0%
! GGCTAATAATCTTCGTTTTG+AGG + chr3_3:15587558-15587577 Msa0443700:CDS 35.0%
CATCAATAACTCATCTGCTT+CGG + chr3_3:15587722-15587741 Msa0443700:intron 35.0%
ATCAATAACTCATCTGCTTC+GGG + chr3_3:15587723-15587742 Msa0443700:intron 35.0%
GTCCTAAAACTACTATTGCA+TGG - chr3_3:15587984-15588003 None:intergenic 35.0%
AATATATGCTCCTTACACGT+AGG - chr3_3:15588340-15588359 None:intergenic 35.0%
AGATATGCTACTAACTTGGT+TGG + chr3_3:15588405-15588424 Msa0443700:intron 35.0%
!!! GAGCCGAAAATTACTGATTT+TGG + chr3_3:15588529-15588548 Msa0443700:CDS 35.0%
AACAAAGTGTGGAAGCAAAT+CGG - chr3_3:15588630-15588649 None:intergenic 35.0%
! GGCTAATAATCTTCGTTTTG+AGG + chr3_3:15587558-15587577 Msa0443700:CDS 35.0%
CATCAATAACTCATCTGCTT+CGG + chr3_3:15587722-15587741 Msa0443700:intron 35.0%
ATCAATAACTCATCTGCTTC+GGG + chr3_3:15587723-15587742 Msa0443700:intron 35.0%
GTCCTAAAACTACTATTGCA+TGG - chr3_3:15587984-15588003 None:intergenic 35.0%
AATATATGCTCCTTACACGT+AGG - chr3_3:15588340-15588359 None:intergenic 35.0%
AGATATGCTACTAACTTGGT+TGG + chr3_3:15588405-15588424 Msa0443700:intron 35.0%
!!! GAGCCGAAAATTACTGATTT+TGG + chr3_3:15588529-15588548 Msa0443700:CDS 35.0%
AACAAAGTGTGGAAGCAAAT+CGG - chr3_3:15588630-15588649 None:intergenic 35.0%
ACATATCTCGTGTACACCAT+TGG - chr3_3:15588047-15588066 None:intergenic 40.0%
TTCCACACAAATAAAGGGTC+TGG - chr3_3:15588153-15588172 None:intergenic 40.0%
GGAGATAAGGACATTATGTG+AGG + chr3_3:15588248-15588267 Msa0443700:intron 40.0%
TCTACAAGACCCTCATAACA+AGG - chr3_3:15588276-15588295 None:intergenic 40.0%
AAGGGTCTAAGTTATCTGCA+CGG + chr3_3:15588445-15588464 Msa0443700:intron 40.0%
TCAGTCAAGCAAACAAAGTG+TGG - chr3_3:15588641-15588660 None:intergenic 40.0%
GCTCAACAAGATCCTCAATA+CGG - chr3_3:15588832-15588851 None:intergenic 40.0%
ACATATCTCGTGTACACCAT+TGG - chr3_3:15588047-15588066 None:intergenic 40.0%
TTCCACACAAATAAAGGGTC+TGG - chr3_3:15588153-15588172 None:intergenic 40.0%
GGAGATAAGGACATTATGTG+AGG + chr3_3:15588248-15588267 Msa0443700:intron 40.0%
TCTACAAGACCCTCATAACA+AGG - chr3_3:15588276-15588295 None:intergenic 40.0%
AAGGGTCTAAGTTATCTGCA+CGG + chr3_3:15588445-15588464 Msa0443700:intron 40.0%
TCAGTCAAGCAAACAAAGTG+TGG - chr3_3:15588641-15588660 None:intergenic 40.0%
GCTCAACAAGATCCTCAATA+CGG - chr3_3:15588832-15588851 None:intergenic 40.0%
! TGCCAGACCCTTTATTTGTG+TGG + chr3_3:15588148-15588167 Msa0443700:intron 45.0%
! ATGTGAGGCACCTTGTTATG+AGG + chr3_3:15588263-15588282 Msa0443700:intron 45.0%
! TGTGAGGCACCTTGTTATGA+GGG + chr3_3:15588264-15588283 Msa0443700:intron 45.0%
!! ACGTAGGAGCTTCTGAAACA+TGG - chr3_3:15588324-15588343 None:intergenic 45.0%
TTCAGAAGCTCCTACGTGTA+AGG + chr3_3:15588327-15588346 Msa0443700:intron 45.0%
! TAATTTTCGGCTCCCCTTTG+AGG - chr3_3:15588522-15588541 None:intergenic 45.0%
AGATGAGCAAGTCCGTATTG+AGG + chr3_3:15588817-15588836 Msa0443700:CDS 45.0%
! TGCCAGACCCTTTATTTGTG+TGG + chr3_3:15588148-15588167 Msa0443700:intron 45.0%
! ATGTGAGGCACCTTGTTATG+AGG + chr3_3:15588263-15588282 Msa0443700:intron 45.0%
! TGTGAGGCACCTTGTTATGA+GGG + chr3_3:15588264-15588283 Msa0443700:intron 45.0%
!! ACGTAGGAGCTTCTGAAACA+TGG - chr3_3:15588324-15588343 None:intergenic 45.0%
TTCAGAAGCTCCTACGTGTA+AGG + chr3_3:15588327-15588346 Msa0443700:intron 45.0%
! TAATTTTCGGCTCCCCTTTG+AGG - chr3_3:15588522-15588541 None:intergenic 45.0%
AGATGAGCAAGTCCGTATTG+AGG + chr3_3:15588817-15588836 Msa0443700:CDS 45.0%
GCAGCTTGCAGTGGATATGA+TGG + chr3_3:15587537-15587556 Msa0443700:CDS 50.0%
! TGATAGCGTTAAGGCGCCAA+TGG + chr3_3:15588028-15588047 Msa0443700:intron 50.0%
GCAGCTTGCAGTGGATATGA+TGG + chr3_3:15587537-15587556 Msa0443700:CDS 50.0%
! TGATAGCGTTAAGGCGCCAA+TGG + chr3_3:15588028-15588047 Msa0443700:intron 50.0%
TGGGGATGAGCAGCTTGCAG+TGG + chr3_3:15587528-15587547 Msa0443700:CDS 60.0%
TGGGGATGAGCAGCTTGCAG+TGG + chr3_3:15587528-15587547 Msa0443700:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 15587490 15588884 15587490 ID=Msa0443700;Name=Msa0443700
chr3_3 mRNA 15587490 15588884 15587490 ID=Msa0443700-mRNA-1;Parent=Msa0443700;Name=Msa0443700-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|0|0|0.66|0.5|0.33|3|0|104
chr3_3 exon 15587490 15587579 15587490 ID=Msa0443700-mRNA-1:exon:3274;Parent=Msa0443700-mRNA-1
chr3_3 exon 15588448 15588585 15588448 ID=Msa0443700-mRNA-1:exon:3275;Parent=Msa0443700-mRNA-1
chr3_3 exon 15588798 15588884 15588798 ID=Msa0443700-mRNA-1:exon:3276;Parent=Msa0443700-mRNA-1
chr3_3 CDS 15587490 15587579 15587490 ID=Msa0443700-mRNA-1:cds;Parent=Msa0443700-mRNA-1
chr3_3 CDS 15588448 15588585 15588448 ID=Msa0443700-mRNA-1:cds;Parent=Msa0443700-mRNA-1
chr3_3 CDS 15588798 15588884 15588798 ID=Msa0443700-mRNA-1:cds;Parent=Msa0443700-mRNA-1
Gene Sequence

>Msa0443700

ACAACTTCTTGTGGTGGAACACAATGTGTTAACTCTTTTGGGGATGAGCAGCTTGCAGTGGATATGATGGCTAATAATCTTCGTTTTGAGGGTCTAAGTTATCTGCACGGAGTCAGATATTTAGTTCACAGAGACATAAAGCCTGCTAATTTACTTGTAAACCTCAAAGGGGAGCCGAAAATTACTGATTTTGGTATTAGTGTTGGCATAGAGAATTCAATTGCAATGATAGAAATTGCACTTCAAAAGATGAGCAAGTCCGTATTGAGGATCTTGTTGAGCTGTGAGAGAACGACTAGATTATCTCATTGTTGA

Protein sequence

>Msa0443700

TTSCGGTQCVNSFGDEQLAVDMMANNLRFEGLSYLHGVRYLVHRDIKPANLLVNLKGEPKITDFGISVGIENSIAMIEIALQKMSKSVLRILLSCERTTRLSHC*