AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1113590


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1113590 MtrunA17_Chr7g0256851 93.162 117 6 1 1 117 1 115 7.23e-75 217
Msa1113590 MtrunA17_Chr3g0085831 49.524 105 51 2 1 104 1 104 5.16e-29 103
Msa1113590 MtrunA17_Chr5g0437861 44.872 78 40 1 1 75 1 78 1.21e-16 70.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1113590 AT2G41430.5 63.750 80 27 2 1 78 1 80 7.40e-30 105
Msa1113590 AT2G41430.4 63.750 80 27 2 1 78 1 80 7.40e-30 105
Msa1113590 AT2G41430.2 63.750 80 27 2 1 78 1 80 7.40e-30 105
Msa1113590 AT2G41430.1 63.750 80 27 2 1 78 1 80 7.40e-30 105
Msa1113590 AT2G41430.3 63.750 80 27 2 1 78 1 80 1.11e-29 103
Msa1113590 AT4G14270.1 55.000 60 27 0 2 61 3 62 1.19e-16 71.2
Msa1113590 AT4G14270.2 55.000 60 27 0 2 61 3 62 1.19e-16 71.2

Find 41 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGATAGGTAAGAAAGTTTA+TGG 0.140300 7_3:-60039554 None:intergenic
TTGATTAATGGTGTAGATTA+AGG 0.214432 7_3:+60038735 None:intergenic
TTTCTTACCTATCTTCAAAA+TGG 0.243229 7_3:+60039562 Msa1113590:three_prime_UTR
ATTGGTCAGTTGATTGCTTC+TGG 0.259967 7_3:-60039662 None:intergenic
TTCAAGATGGCATTAGTTTC+AGG 0.269984 7_3:+60038782 Msa1113590:exon
TTCCTTCTTACCAAAATCTA+TGG 0.308472 7_3:+60039396 Msa1113590:three_prime_UTR
ACTTTCTGTAACTTCTTGTA+TGG 0.314446 7_3:+60039351 Msa1113590:three_prime_UTR
TGAAATGGCACGATGATTAC+TGG 0.331014 7_3:+60038906 Msa1113590:CDS
GGAATGTAAAGTGGTGCATT+AGG 0.338731 7_3:-60038824 None:intergenic
ATTGCTTCTGGACATGTATC+TGG 0.341630 7_3:-60039650 None:intergenic
TTGACAGAACTTAGAATGTA+TGG 0.363844 7_3:+60039610 Msa1113590:three_prime_UTR
GACGGTCTTGCCTTAGCTTT+CGG 0.365977 7_3:+60039298 Msa1113590:three_prime_UTR
CAAGGAACAAAGAAATTTAC+TGG 0.369529 7_3:+60039226 Msa1113590:CDS
GTCACCAGCTGCCACCATTC+CGG 0.393504 7_3:-60038878 None:intergenic
AGCCTTCATCATCATGTTGC+TGG 0.408811 7_3:-60038934 None:intergenic
AGTAAGTTTAATATTACAAT+TGG 0.409046 7_3:-60039680 None:intergenic
TGTAACTTCTTGTATGGGCC+AGG 0.424773 7_3:+60039357 Msa1113590:three_prime_UTR
GAATGTAAAGTGGTGCATTA+GGG 0.425842 7_3:-60038823 None:intergenic
AGATAGGTAAGAAAGTTTAT+GGG 0.454817 7_3:-60039553 None:intergenic
TTCTCCGGAATGGTGGCAGC+TGG 0.463269 7_3:+60038874 Msa1113590:CDS
TCGACATAGCGAAATGCAGC+TGG 0.498421 7_3:-60038845 None:intergenic
GCATCAAGATCAAACGCATC+AGG 0.498917 7_3:-60039013 None:intergenic
CTTTCTGTAACTTCTTGTAT+GGG 0.504918 7_3:+60039352 Msa1113590:three_prime_UTR
TTCTGGACATGTATCTGGTA+TGG 0.513371 7_3:-60039645 None:intergenic
ATTTACTGGATGAGCTAAAG+AGG 0.519766 7_3:+60039240 Msa1113590:exon
AGCTGGTGACAACACTGAAA+TGG 0.525245 7_3:+60038891 Msa1113590:CDS
AGCTGCATTTCGCTATGTCG+AGG 0.547833 7_3:+60038847 Msa1113590:CDS
AGCCAGCAACATGATGATGA+AGG 0.560493 7_3:+60038932 Msa1113590:CDS
ATCATAGACGCTGAATGCGA+CGG 0.570681 7_3:+60039280 Msa1113590:three_prime_UTR
AGCTAAATAACCGAAAGCTA+AGG 0.582950 7_3:-60039308 None:intergenic
GATGATGTAGATGAGTTTGA+CGG 0.592669 7_3:+60038968 Msa1113590:CDS
AGAGTTTATCAAGTCTTCTG+AGG 0.595138 7_3:+60039069 Msa1113590:CDS
GTCAAACAAAATTTGAAACA+AGG 0.599572 7_3:-60039592 None:intergenic
AGAGTGAAGGTGATTCAAGA+TGG 0.611938 7_3:+60038769 Msa1113590:exon
ATCAAGTCTTCTGAGGCACA+AGG 0.619098 7_3:+60039076 Msa1113590:CDS
AAATCTATGGTAAAATAGAG+AGG 0.627618 7_3:+60039409 Msa1113590:three_prime_UTR
AAGATGGCATTAGTTTCAGG+AGG 0.635369 7_3:+60038785 Msa1113590:exon
AATGATTGAAAATTGAAACC+TGG 0.642499 7_3:-60039375 None:intergenic
TGATGCGTTTGATCTTGATG+CGG 0.644823 7_3:+60039015 Msa1113590:CDS
AATGCAGCTGGAATGTAAAG+TGG 0.663728 7_3:-60038833 None:intergenic
ACAGAAAGTTAAAACTGACA+TGG 0.696360 7_3:-60039337 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACTTTCCTCTGAAAAATAA+CGG - chr7_3:60039198-60039217 None:intergenic 25.0%
! AATGATTGAAAATTGAAACC+TGG - chr7_3:60039378-60039397 None:intergenic 25.0%
!! CTCTATTTTACCATAGATTT+TGG - chr7_3:60039409-60039428 None:intergenic 25.0%
! AAATCTATGGTAAAATAGAG+AGG + chr7_3:60039409-60039428 Msa1113590:three_prime_UTR 25.0%
! AGATAGGTAAGAAAGTTTAT+GGG - chr7_3:60039556-60039575 None:intergenic 25.0%
! AAGATAGGTAAGAAAGTTTA+TGG - chr7_3:60039557-60039576 None:intergenic 25.0%
! TTTCTTACCTATCTTCAAAA+TGG + chr7_3:60039562-60039581 Msa1113590:three_prime_UTR 25.0%
!! GTCAAACAAAATTTGAAACA+AGG - chr7_3:60039595-60039614 None:intergenic 25.0%
!! AACTTTCCTCTGAAAAATAA+CGG - chr7_3:60039198-60039217 None:intergenic 25.0%
! AATGATTGAAAATTGAAACC+TGG - chr7_3:60039378-60039397 None:intergenic 25.0%
!! CTCTATTTTACCATAGATTT+TGG - chr7_3:60039409-60039428 None:intergenic 25.0%
! AAATCTATGGTAAAATAGAG+AGG + chr7_3:60039409-60039428 Msa1113590:three_prime_UTR 25.0%
! AGATAGGTAAGAAAGTTTAT+GGG - chr7_3:60039556-60039575 None:intergenic 25.0%
! AAGATAGGTAAGAAAGTTTA+TGG - chr7_3:60039557-60039576 None:intergenic 25.0%
! TTTCTTACCTATCTTCAAAA+TGG + chr7_3:60039562-60039581 Msa1113590:three_prime_UTR 25.0%
!! GTCAAACAAAATTTGAAACA+AGG - chr7_3:60039595-60039614 None:intergenic 25.0%
!!! AACATACCGTTATTTTTCAG+AGG + chr7_3:60039189-60039208 Msa1113590:intron 30.0%
!! TTTTTCAGAGGAAAGTTTTG+TGG + chr7_3:60039201-60039220 Msa1113590:intron 30.0%
CAAGGAACAAAGAAATTTAC+TGG + chr7_3:60039226-60039245 Msa1113590:CDS 30.0%
ACAGAAAGTTAAAACTGACA+TGG - chr7_3:60039340-60039359 None:intergenic 30.0%
ACTTTCTGTAACTTCTTGTA+TGG + chr7_3:60039351-60039370 Msa1113590:three_prime_UTR 30.0%
CTTTCTGTAACTTCTTGTAT+GGG + chr7_3:60039352-60039371 Msa1113590:three_prime_UTR 30.0%
TTCCTTCTTACCAAAATCTA+TGG + chr7_3:60039396-60039415 Msa1113590:three_prime_UTR 30.0%
!! TACCATAGATTTTGGTAAGA+AGG - chr7_3:60039401-60039420 None:intergenic 30.0%
!! AATGCATCCATTTTGAAGAT+AGG - chr7_3:60039572-60039591 None:intergenic 30.0%
TTGACAGAACTTAGAATGTA+TGG + chr7_3:60039610-60039629 Msa1113590:three_prime_UTR 30.0%
!!! AACATACCGTTATTTTTCAG+AGG + chr7_3:60039189-60039208 Msa1113590:intron 30.0%
!! TTTTTCAGAGGAAAGTTTTG+TGG + chr7_3:60039201-60039220 Msa1113590:intron 30.0%
CAAGGAACAAAGAAATTTAC+TGG + chr7_3:60039226-60039245 Msa1113590:CDS 30.0%
ACAGAAAGTTAAAACTGACA+TGG - chr7_3:60039340-60039359 None:intergenic 30.0%
ACTTTCTGTAACTTCTTGTA+TGG + chr7_3:60039351-60039370 Msa1113590:three_prime_UTR 30.0%
CTTTCTGTAACTTCTTGTAT+GGG + chr7_3:60039352-60039371 Msa1113590:three_prime_UTR 30.0%
TTCCTTCTTACCAAAATCTA+TGG + chr7_3:60039396-60039415 Msa1113590:three_prime_UTR 30.0%
!! TACCATAGATTTTGGTAAGA+AGG - chr7_3:60039401-60039420 None:intergenic 30.0%
!! AATGCATCCATTTTGAAGAT+AGG - chr7_3:60039572-60039591 None:intergenic 30.0%
TTGACAGAACTTAGAATGTA+TGG + chr7_3:60039610-60039629 Msa1113590:three_prime_UTR 30.0%
GGAAAAAGTGATAAGAGTGA+AGG + chr7_3:60038756-60038775 Msa1113590:five_prime_UTR 35.0%
! TTCAAGATGGCATTAGTTTC+AGG + chr7_3:60038782-60038801 Msa1113590:exon 35.0%
GAATGTAAAGTGGTGCATTA+GGG - chr7_3:60038826-60038845 None:intergenic 35.0%
GATGATGTAGATGAGTTTGA+CGG + chr7_3:60038968-60038987 Msa1113590:CDS 35.0%
AGAGTTTATCAAGTCTTCTG+AGG + chr7_3:60039069-60039088 Msa1113590:CDS 35.0%
ATTTACTGGATGAGCTAAAG+AGG + chr7_3:60039240-60039259 Msa1113590:exon 35.0%
AGCTAAATAACCGAAAGCTA+AGG - chr7_3:60039311-60039330 None:intergenic 35.0%
GGAAAAAGTGATAAGAGTGA+AGG + chr7_3:60038756-60038775 Msa1113590:five_prime_UTR 35.0%
! TTCAAGATGGCATTAGTTTC+AGG + chr7_3:60038782-60038801 Msa1113590:exon 35.0%
GAATGTAAAGTGGTGCATTA+GGG - chr7_3:60038826-60038845 None:intergenic 35.0%
GATGATGTAGATGAGTTTGA+CGG + chr7_3:60038968-60038987 Msa1113590:CDS 35.0%
AGAGTTTATCAAGTCTTCTG+AGG + chr7_3:60039069-60039088 Msa1113590:CDS 35.0%
ATTTACTGGATGAGCTAAAG+AGG + chr7_3:60039240-60039259 Msa1113590:exon 35.0%
AGCTAAATAACCGAAAGCTA+AGG - chr7_3:60039311-60039330 None:intergenic 35.0%
AGAGTGAAGGTGATTCAAGA+TGG + chr7_3:60038769-60038788 Msa1113590:exon 40.0%
! AAGATGGCATTAGTTTCAGG+AGG + chr7_3:60038785-60038804 Msa1113590:exon 40.0%
GGAATGTAAAGTGGTGCATT+AGG - chr7_3:60038827-60038846 None:intergenic 40.0%
AATGCAGCTGGAATGTAAAG+TGG - chr7_3:60038836-60038855 None:intergenic 40.0%
! CTATGTCGAGGATTTTTCTC+CGG + chr7_3:60038859-60038878 Msa1113590:CDS 40.0%
TGAAATGGCACGATGATTAC+TGG + chr7_3:60038906-60038925 Msa1113590:CDS 40.0%
TGATGCGTTTGATCTTGATG+CGG + chr7_3:60039015-60039034 Msa1113590:CDS 40.0%
TTCTGGACATGTATCTGGTA+TGG - chr7_3:60039648-60039667 None:intergenic 40.0%
ATTGCTTCTGGACATGTATC+TGG - chr7_3:60039653-60039672 None:intergenic 40.0%
ATTGGTCAGTTGATTGCTTC+TGG - chr7_3:60039665-60039684 None:intergenic 40.0%
AGAGTGAAGGTGATTCAAGA+TGG + chr7_3:60038769-60038788 Msa1113590:exon 40.0%
! AAGATGGCATTAGTTTCAGG+AGG + chr7_3:60038785-60038804 Msa1113590:exon 40.0%
GGAATGTAAAGTGGTGCATT+AGG - chr7_3:60038827-60038846 None:intergenic 40.0%
AATGCAGCTGGAATGTAAAG+TGG - chr7_3:60038836-60038855 None:intergenic 40.0%
! CTATGTCGAGGATTTTTCTC+CGG + chr7_3:60038859-60038878 Msa1113590:CDS 40.0%
TGAAATGGCACGATGATTAC+TGG + chr7_3:60038906-60038925 Msa1113590:CDS 40.0%
TGATGCGTTTGATCTTGATG+CGG + chr7_3:60039015-60039034 Msa1113590:CDS 40.0%
TTCTGGACATGTATCTGGTA+TGG - chr7_3:60039648-60039667 None:intergenic 40.0%
ATTGCTTCTGGACATGTATC+TGG - chr7_3:60039653-60039672 None:intergenic 40.0%
ATTGGTCAGTTGATTGCTTC+TGG - chr7_3:60039665-60039684 None:intergenic 40.0%
! TCGAGGATTTTTCTCCGGAA+TGG + chr7_3:60038864-60038883 Msa1113590:CDS 45.0%
! AGGATTTTTCTCCGGAATGG+TGG + chr7_3:60038867-60038886 Msa1113590:CDS 45.0%
AGCTGGTGACAACACTGAAA+TGG + chr7_3:60038891-60038910 Msa1113590:CDS 45.0%
! AGCCAGCAACATGATGATGA+AGG + chr7_3:60038932-60038951 Msa1113590:CDS 45.0%
AGCCTTCATCATCATGTTGC+TGG - chr7_3:60038937-60038956 None:intergenic 45.0%
GCATCAAGATCAAACGCATC+AGG - chr7_3:60039016-60039035 None:intergenic 45.0%
!! ATCAAGTCTTCTGAGGCACA+AGG + chr7_3:60039076-60039095 Msa1113590:CDS 45.0%
!! GAGGAAAGTTTTGTGGAGCA+AGG + chr7_3:60039208-60039227 Msa1113590:intron 45.0%
ATCATAGACGCTGAATGCGA+CGG + chr7_3:60039280-60039299 Msa1113590:three_prime_UTR 45.0%
TGTAACTTCTTGTATGGGCC+AGG + chr7_3:60039357-60039376 Msa1113590:three_prime_UTR 45.0%
! TCGAGGATTTTTCTCCGGAA+TGG + chr7_3:60038864-60038883 Msa1113590:CDS 45.0%
! AGGATTTTTCTCCGGAATGG+TGG + chr7_3:60038867-60038886 Msa1113590:CDS 45.0%
AGCTGGTGACAACACTGAAA+TGG + chr7_3:60038891-60038910 Msa1113590:CDS 45.0%
! AGCCAGCAACATGATGATGA+AGG + chr7_3:60038932-60038951 Msa1113590:CDS 45.0%
AGCCTTCATCATCATGTTGC+TGG - chr7_3:60038937-60038956 None:intergenic 45.0%
GCATCAAGATCAAACGCATC+AGG - chr7_3:60039016-60039035 None:intergenic 45.0%
!! ATCAAGTCTTCTGAGGCACA+AGG + chr7_3:60039076-60039095 Msa1113590:CDS 45.0%
!! GAGGAAAGTTTTGTGGAGCA+AGG + chr7_3:60039208-60039227 Msa1113590:intron 45.0%
ATCATAGACGCTGAATGCGA+CGG + chr7_3:60039280-60039299 Msa1113590:three_prime_UTR 45.0%
TGTAACTTCTTGTATGGGCC+AGG + chr7_3:60039357-60039376 Msa1113590:three_prime_UTR 45.0%
TCGACATAGCGAAATGCAGC+TGG - chr7_3:60038848-60038867 None:intergenic 50.0%
AGCTGCATTTCGCTATGTCG+AGG + chr7_3:60038847-60038866 Msa1113590:CDS 50.0%
! GACGGTCTTGCCTTAGCTTT+CGG + chr7_3:60039298-60039317 Msa1113590:three_prime_UTR 50.0%
TCGACATAGCGAAATGCAGC+TGG - chr7_3:60038848-60038867 None:intergenic 50.0%
AGCTGCATTTCGCTATGTCG+AGG + chr7_3:60038847-60038866 Msa1113590:CDS 50.0%
! GACGGTCTTGCCTTAGCTTT+CGG + chr7_3:60039298-60039317 Msa1113590:three_prime_UTR 50.0%
TTCTCCGGAATGGTGGCAGC+TGG + chr7_3:60038874-60038893 Msa1113590:CDS 60.0%
GTCACCAGCTGCCACCATTC+CGG - chr7_3:60038881-60038900 None:intergenic 60.0%
TTCTCCGGAATGGTGGCAGC+TGG + chr7_3:60038874-60038893 Msa1113590:CDS 60.0%
GTCACCAGCTGCCACCATTC+CGG - chr7_3:60038881-60038900 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 60038750 60039700 60038750 ID=Msa1113590;Name=Msa1113590
chr7_3 mRNA 60038750 60039700 60038750 ID=Msa1113590-mRNA-1;Parent=Msa1113590;Name=Msa1113590-mRNA-1;_AED=0.00;_eAED=0.00;_QI=38|1|1|1|1|1|2|448|117
chr7_3 exon 60038750 60039097 60038750 ID=Msa1113590-mRNA-1:exon:13411;Parent=Msa1113590-mRNA-1
chr7_3 exon 60039209 60039700 60039209 ID=Msa1113590-mRNA-1:exon:13412;Parent=Msa1113590-mRNA-1
chr7_3 five_prime_UTR 60038750 60038787 60038750 ID=Msa1113590-mRNA-1:five_prime_utr;Parent=Msa1113590-mRNA-1
chr7_3 CDS 60038788 60039097 60038788 ID=Msa1113590-mRNA-1:cds;Parent=Msa1113590-mRNA-1
chr7_3 CDS 60039209 60039252 60039209 ID=Msa1113590-mRNA-1:cds;Parent=Msa1113590-mRNA-1
chr7_3 three_prime_UTR 60039253 60039700 60039253 ID=Msa1113590-mRNA-1:three_prime_utr;Parent=Msa1113590-mRNA-1
Gene Sequence

>Msa1113590

ATGGCATTAGTTTCAGGAGGAAGATCAACACTAAACCCTAATGCACCACTTTACATTCCAGCTGCATTTCGCTATGTCGAGGATTTTTCTCCGGAATGGTGGCAGCTGGTGACAACACTGAAATGGCACGATGATTACTGGCTTAGCCAGCAACATGATGATGAAGGCTTTTATGATGATGATGATGTAGATGAGTTTGACGGCAATGATGTCGTTGATTTGCTTCCTGATGCGTTTGATCTTGATGCGGATGAAGATCTTTTGATTGAAGCTCAGCTTGAAGAGTTTATCAAGTCTTCTGAGGCACAAGAGGAAAGTTTTGTGGAGCAAGGAACAAAGAAATTTACTGGATGA

Protein sequence

>Msa1113590

MALVSGGRSTLNPNAPLYIPAAFRYVEDFSPEWWQLVTTLKWHDDYWLSQQHDDEGFYDDDDVDEFDGNDVVDLLPDAFDLDADEDLLIEAQLEEFIKSSEAQEESFVEQGTKKFTG*