AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene01360

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01360.t1 MTR_2g012450 100.000 146 0 0 1 146 1 146 1.04e-103 293
MS.gene01360.t1 MTR_5g015570 95.205 146 7 0 1 146 1 146 2.04e-90 259
MS.gene01360.t1 MTR_5g096540 91.096 146 13 0 1 146 1 146 4.27e-87 251
MS.gene01360.t1 MTR_4g126220 88.235 68 8 0 13 80 103 170 6.53e-38 127
MS.gene01360.t1 MTR_8g073140 56.977 86 10 1 30 115 1 59 2.66e-23 87.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01360.t1 AT5G67510 88.356 146 17 0 1 146 1 146 9.99e-93 265
MS.gene01360.t1 AT3G49910 85.616 146 21 0 1 146 1 146 1.18e-91 262

Find 50 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCGCAAGGACGACGAAGTTC+AGG 0.349938 2.2:+69940830 MS.gene01360:CDS
CGGAGAGCGGTGCGCTCATT+AGG 0.376828 2.2:-69940767 None:intergenic
CATTGAACGGACGTTGTACT+TGG 0.377101 2.2:-69940802 None:intergenic
TTAGTGATAACAACCTTTGA+AGG 0.395167 2.2:-69940981 None:intergenic
GGGTCGTGCTGCTGCTGATA+AGG 0.420559 2.2:+69941052 MS.gene01360:CDS
CTTGAGTAACCTTACCTTCA+CGG 0.428858 2.2:-69940875 None:intergenic
CACTAAGCTCAGATTGGATA+AGG 0.438891 2.2:+69940998 MS.gene01360:CDS
AGGATTAACACCAACATTAA+CGG 0.444745 2.2:-69940961 None:intergenic
ACTTCGTCGTCCTTGCGAAC+AGG 0.458496 2.2:-69940825 None:intergenic
AGGACACGGCGGACGCTTGA+TGG 0.458896 2.2:-69940747 None:intergenic
TGTTATCACTAAGCTCAGAT+TGG 0.466490 2.2:+69940992 MS.gene01360:CDS
CTCAAGTTTACCGACGCAAG+TGG 0.488086 2.2:+69940892 MS.gene01360:CDS
GGACACGGCGGACGCTTGAT+GGG 0.490566 2.2:-69940746 None:intergenic
ATTCAAAGGCCGTGAAGGTA+AGG 0.498862 2.2:+69940866 MS.gene01360:CDS
GACGAAGTTCAGGTTGTTCG+TGG 0.501347 2.2:+69940840 MS.gene01360:CDS
CTACGGCTGCTTGAAACTCG+TGG 0.513154 2.2:-69940696 None:intergenic
TGTTGGTGTTAATCCTTCAA+AGG 0.524932 2.2:+69940968 MS.gene01360:CDS
GCTACTTGATCGTAAGGCTA+AGG 0.528270 2.2:+69941031 MS.gene01360:CDS
GAGCCGTAAGGCTCATTTCA+CGG 0.531808 2.2:+69940722 MS.gene01360:CDS
TGCTGCTGCTGATAAGGAGA+AGG 0.537077 2.2:+69941058 MS.gene01360:CDS
ATCACAAGGGAGAAGGTGAA+TGG 0.545267 2.2:+69940933 MS.gene01360:CDS
CCGTTCAATGCCTGTTCGCA+AGG 0.545521 2.2:+69940815 MS.gene01360:CDS
GAGCCTTACGGCTCTTCCTA+CGG 0.547173 2.2:-69940713 None:intergenic
TACGGCTGCTTGAAACTCGT+GGG 0.549249 2.2:-69940695 None:intergenic
CTACTTGATCGTAAGGCTAA+GGG 0.553374 2.2:+69941032 MS.gene01360:CDS
TAAATCGCTACTTGATCGTA+AGG 0.555125 2.2:+69941025 MS.gene01360:CDS
GTTGTTCGTGGAACATTCAA+AGG 0.558204 2.2:+69940852 MS.gene01360:CDS
GGGCCGTGAAATGAGCCTTA+CGG 0.558279 2.2:-69940725 None:intergenic
GGGTACTAAGTTTGCTCCTG+AGG 0.563912 2.2:+69941079 MS.gene01360:CDS
AACGGACGTTGTACTTGGAT+CGG 0.564652 2.2:-69940797 None:intergenic
GTTGTACTTGGATCGGAGAT+CGG 0.572814 2.2:-69940790 None:intergenic
ACGGTCTGCATAATATCCTC+AGG 0.575139 2.2:-69941095 None:intergenic
CGAACGCATCACAAGGGAGA+AGG 0.580140 2.2:+69940926 MS.gene01360:CDS
TTCACATCGAACGCATCACA+AGG 0.588472 2.2:+69940919 MS.gene01360:CDS
GACACGGCGGACGCTTGATG+GGG 0.589940 2.2:-69940745 None:intergenic
CAGCCGTAGGAAGAGCCGTA+AGG 0.591177 2.2:+69940710 MS.gene01360:CDS
GGAACATTCAAAGGCCGTGA+AGG 0.606062 2.2:+69940861 MS.gene01360:CDS
CCTTGCGAACAGGCATTGAA+CGG 0.606739 2.2:-69940815 None:intergenic
GATCGGAGATCGGCGGAGAG+CGG 0.619426 2.2:-69940780 None:intergenic
AATGGATCCACCGTTAATGT+TGG 0.632764 2.2:+69940951 MS.gene01360:CDS
GCTGCTGCTGATAAGGAGAA+GGG 0.634378 2.2:+69941059 MS.gene01360:CDS
TCAAGTTTACCGACGCAAGT+GGG 0.644269 2.2:+69940893 MS.gene01360:CDS
GATTCAAGAATACTAATCAA+CGG 0.645334 2.2:-69941114 None:intergenic
ATTAACACCAACATTAACGG+TGG 0.662702 2.2:-69940958 None:intergenic
TGTGAATCACCCACTTGCGT+CGG 0.677070 2.2:-69940902 None:intergenic
CACGAGTTTCAAGCAGCCGT+AGG 0.686122 2.2:+69940697 MS.gene01360:CDS
GTACTTGGATCGGAGATCGG+CGG 0.709980 2.2:-69940787 None:intergenic
TCACATCGAACGCATCACAA+GGG 0.710980 2.2:+69940920 MS.gene01360:CDS
GCGGTGCGCTCATTAGGACA+CGG 0.711579 2.2:-69940761 None:intergenic
GTGCGCTCATTAGGACACGG+CGG 0.830011 2.2:-69940758 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AGGATTAACACCAACATTAA+CGG - chr2.2:69940964-69940983 None:intergenic 30.0%
TTAGTGATAACAACCTTTGA+AGG - chr2.2:69940984-69941003 None:intergenic 30.0%
ATTAACACCAACATTAACGG+TGG - chr2.2:69940961-69940980 None:intergenic 35.0%
TAAATCGCTACTTGATCGTA+AGG + chr2.2:69941025-69941044 MS.gene01360:CDS 35.0%
TGTTATCACTAAGCTCAGAT+TGG + chr2.2:69940992-69941011 MS.gene01360:CDS 35.0%
!! TGTTGGTGTTAATCCTTCAA+AGG + chr2.2:69940968-69940987 MS.gene01360:CDS 35.0%
AATGGATCCACCGTTAATGT+TGG + chr2.2:69940951-69940970 MS.gene01360:CDS 40.0%
CACTAAGCTCAGATTGGATA+AGG + chr2.2:69940998-69941017 MS.gene01360:CDS 40.0%
CTACTTGATCGTAAGGCTAA+GGG + chr2.2:69941032-69941051 MS.gene01360:CDS 40.0%
CTTGAGTAACCTTACCTTCA+CGG - chr2.2:69940878-69940897 None:intergenic 40.0%
GTTGTTCGTGGAACATTCAA+AGG + chr2.2:69940852-69940871 MS.gene01360:CDS 40.0%
AACGGACGTTGTACTTGGAT+CGG - chr2.2:69940800-69940819 None:intergenic 45.0%
ACGGTCTGCATAATATCCTC+AGG - chr2.2:69941098-69941117 None:intergenic 45.0%
ATCACAAGGGAGAAGGTGAA+TGG + chr2.2:69940933-69940952 MS.gene01360:CDS 45.0%
ATTCAAAGGCCGTGAAGGTA+AGG + chr2.2:69940866-69940885 MS.gene01360:CDS 45.0%
CATTGAACGGACGTTGTACT+TGG - chr2.2:69940805-69940824 None:intergenic 45.0%
GCTACTTGATCGTAAGGCTA+AGG + chr2.2:69941031-69941050 MS.gene01360:CDS 45.0%
GTTGTACTTGGATCGGAGAT+CGG - chr2.2:69940793-69940812 None:intergenic 45.0%
TCAAGTTTACCGACGCAAGT+GGG + chr2.2:69940893-69940912 MS.gene01360:CDS 45.0%
TCACATCGAACGCATCACAA+GGG + chr2.2:69940920-69940939 MS.gene01360:CDS 45.0%
TTCACATCGAACGCATCACA+AGG + chr2.2:69940919-69940938 MS.gene01360:CDS 45.0%
CTCAAGTTTACCGACGCAAG+TGG + chr2.2:69940892-69940911 MS.gene01360:CDS 50.0%
GAGCCGTAAGGCTCATTTCA+CGG + chr2.2:69940722-69940741 MS.gene01360:CDS 50.0%
GCTGCTGCTGATAAGGAGAA+GGG + chr2.2:69941059-69941078 MS.gene01360:CDS 50.0%
GGAACATTCAAAGGCCGTGA+AGG + chr2.2:69940861-69940880 MS.gene01360:CDS 50.0%
TACGGCTGCTTGAAACTCGT+GGG - chr2.2:69940698-69940717 None:intergenic 50.0%
TGCTGCTGCTGATAAGGAGA+AGG + chr2.2:69941058-69941077 MS.gene01360:CDS 50.0%
TGTGAATCACCCACTTGCGT+CGG - chr2.2:69940905-69940924 None:intergenic 50.0%
! GGGTACTAAGTTTGCTCCTG+AGG + chr2.2:69941079-69941098 MS.gene01360:CDS 50.0%
!! CCTTGCGAACAGGCATTGAA+CGG - chr2.2:69940818-69940837 None:intergenic 50.0%
!! GACGAAGTTCAGGTTGTTCG+TGG + chr2.2:69940840-69940859 MS.gene01360:CDS 50.0%
ACTTCGTCGTCCTTGCGAAC+AGG - chr2.2:69940828-69940847 None:intergenic 55.0%
CACGAGTTTCAAGCAGCCGT+AGG + chr2.2:69940697-69940716 MS.gene01360:CDS 55.0%
CCGTTCAATGCCTGTTCGCA+AGG + chr2.2:69940815-69940834 MS.gene01360:CDS 55.0%
CGAACGCATCACAAGGGAGA+AGG + chr2.2:69940926-69940945 MS.gene01360:CDS 55.0%
CTACGGCTGCTTGAAACTCG+TGG - chr2.2:69940699-69940718 None:intergenic 55.0%
GAGCCTTACGGCTCTTCCTA+CGG - chr2.2:69940716-69940735 None:intergenic 55.0%
GGGCCGTGAAATGAGCCTTA+CGG - chr2.2:69940728-69940747 None:intergenic 55.0%
GTACTTGGATCGGAGATCGG+CGG - chr2.2:69940790-69940809 None:intergenic 55.0%
TCGCAAGGACGACGAAGTTC+AGG + chr2.2:69940830-69940849 MS.gene01360:CDS 55.0%
CAGCCGTAGGAAGAGCCGTA+AGG + chr2.2:69940710-69940729 MS.gene01360:CDS 60.0%
GCGGTGCGCTCATTAGGACA+CGG - chr2.2:69940764-69940783 None:intergenic 60.0%
GTGCGCTCATTAGGACACGG+CGG - chr2.2:69940761-69940780 None:intergenic 60.0%
! GGGTCGTGCTGCTGCTGATA+AGG + chr2.2:69941052-69941071 MS.gene01360:CDS 60.0%
AGGACACGGCGGACGCTTGA+TGG - chr2.2:69940750-69940769 None:intergenic 65.0%
CGGAGAGCGGTGCGCTCATT+AGG - chr2.2:69940770-69940789 None:intergenic 65.0%
GACACGGCGGACGCTTGATG+GGG - chr2.2:69940748-69940767 None:intergenic 65.0%
GATCGGAGATCGGCGGAGAG+CGG - chr2.2:69940783-69940802 None:intergenic 65.0%
GGACACGGCGGACGCTTGAT+GGG - chr2.2:69940749-69940768 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 69940684 69941124 69940684 ID=MS.gene01360
chr2.2 mRNA 69940684 69941124 69940684 ID=MS.gene01360.t1;Parent=MS.gene01360
chr2.2 exon 69940684 69941124 69940684 ID=MS.gene01360.t1.exon1;Parent=MS.gene01360.t1
chr2.2 CDS 69940684 69941124 69940684 ID=cds.MS.gene01360.t1;Parent=MS.gene01360.t1
Gene Sequence

>MS.gene01360

ATGAAGTTCAACCCACGAGTTTCAAGCAGCCGTAGGAAGAGCCGTAAGGCTCATTTCACGGCCCCATCAAGCGTCCGCCGTGTCCTAATGAGCGCACCGCTCTCCGCCGATCTCCGATCCAAGTACAACGTCCGTTCAATGCCTGTTCGCAAGGACGACGAAGTTCAGGTTGTTCGTGGAACATTCAAAGGCCGTGAAGGTAAGGTTACTCAAGTTTACCGACGCAAGTGGGTGATTCACATCGAACGCATCACAAGGGAGAAGGTGAATGGATCCACCGTTAATGTTGGTGTTAATCCTTCAAAGGTTGTTATCACTAAGCTCAGATTGGATAAGGATCGTAAATCGCTACTTGATCGTAAGGCTAAGGGTCGTGCTGCTGCTGATAAGGAGAAGGGTACTAAGTTTGCTCCTGAGGATATTATGCAGACCGTTGATTAG
Protein sequence

>MS.gene01360.t1

MKFNPRVSSSRRKSRKAHFTAPSSVRRVLMSAPLSADLRSKYNVRSMPVRKDDEVQVVRGTFKGREGKVTQVYRRKWVIHIERITREKVNGSTVNVGVNPSKVVITKLRLDKDRKSLLDRKAKGRAAADKEKGTKFAPEDIMQTVD