AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0885890

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0885890 MtrunA17_Chr1g0201251 69.231 52 15 1 1 52 86 136 1.20e-17 75.1
Msa0885890 MtrunA17_Chr6g0466891 63.462 52 18 1 1 52 86 136 1.96e-16 72.0
Msa0885890 MtrunA17_Chr3g0090241 72.340 47 12 1 1 47 86 131 9.59e-15 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0885890 AT1G07140.1 63.462 52 18 1 1 52 89 139 1.90e-14 67.4
Msa0885890 AT2G30060.1 65.957 47 15 1 1 47 91 136 4.03e-13 63.5
Msa0885890 AT5G58590.1 59.615 52 20 1 1 52 88 138 1.89e-12 61.6

Find 38 sgRNAs with CRISPR-Local

Find 120 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTATATGTTGGTGTGCTTTC+TGG 0.146976 6_1:-43377838 Msa0885890:CDS
GCTGCTTCAACTGTGTTTGC+AGG 0.266451 6_1:-43377862 Msa0885890:CDS
CCGAGAGAGTAGGGTGTATT+TGG 0.267050 6_1:-43378123 Msa0885890:intron
AGCGCAGATCTTGAGGGTTT+TGG 0.290367 6_1:+43378617 None:intergenic
CATTTCTGTTCGAGGAAGTT+GGG 0.301232 6_1:-43377953 Msa0885890:CDS
ATAAGGTTACTTGAAAAGTT+AGG 0.336456 6_1:-43378656 Msa0885890:five_prime_UTR
ACAACCGAGCCGTACTAAAC+TGG 0.359660 6_1:+43378743 None:intergenic
GATTCGGTTGCTAGCAGTTT+GGG 0.375277 6_1:-43377884 Msa0885890:CDS
TGATTCGGTTGCTAGCAGTT+TGG 0.405660 6_1:-43377885 Msa0885890:CDS
CGATGGAGTTCTTAAGCATA+AGG 0.412330 6_1:-43378673 Msa0885890:five_prime_UTR
GCATTTCTGTTCGAGGAAGT+TGG 0.423136 6_1:-43377954 Msa0885890:CDS
GAATTGAGAAATCGTGTGTT+TGG 0.437554 6_1:-43378451 Msa0885890:CDS
CTATCTTGTTAAAGTGGTGT+TGG 0.446382 6_1:-43378149 Msa0885890:CDS
GAAAAGTTAGGCTTCTTATG+AGG 0.446917 6_1:-43378644 Msa0885890:exon
TAACTTTATGAGTTCTTGAC+TGG 0.460076 6_1:-43378698 Msa0885890:five_prime_UTR
AATCGTGTGTTTGGCATGCT+AGG 0.466273 6_1:-43378442 Msa0885890:CDS
CGAGGAAGTTGGGGTCTAGT+TGG 0.485567 6_1:-43377943 Msa0885890:CDS
CTGCTTCAACTGTGTTTGCA+GGG 0.486018 6_1:-43377861 Msa0885890:CDS
ACGATTAGCGCAGATCTTGA+GGG 0.489998 6_1:+43378611 None:intergenic
TTCTCTTGCATACTCATCAT+AGG 0.492591 6_1:+43378479 None:intergenic
GACGATTAGCGCAGATCTTG+AGG 0.502484 6_1:+43378610 None:intergenic
TCTGCCATGAGATGGTGATT+CGG 0.523598 6_1:-43377900 Msa0885890:CDS
CATGCTAGGGATTCTGCTGA+TGG 0.533927 6_1:-43378428 Msa0885890:intron
TGATAACTATCTTGTTAAAG+TGG 0.534578 6_1:-43378155 Msa0885890:CDS
ATCGTGTGTTTGGCATGCTA+GGG 0.537370 6_1:-43378441 Msa0885890:CDS
TGTTGGAATCCGAGAGAGTA+GGG 0.545544 6_1:-43378132 Msa0885890:CDS
CCAAATACACCCTACTCTCT+CGG 0.552355 6_1:+43378123 None:intergenic
ATGAGTATGCAAGAGAATGT+TGG 0.553283 6_1:-43378473 Msa0885890:CDS
TGAGTTCTTGACTGGTACGA+TGG 0.554894 6_1:-43378690 Msa0885890:five_prime_UTR
TGCTTCAACTGTGTTTGCAG+GGG 0.555834 6_1:-43377860 Msa0885890:CDS
ATTTCTGTTCGAGGAAGTTG+GGG 0.577830 6_1:-43377952 Msa0885890:CDS
GTGTTGGAATCCGAGAGAGT+AGG 0.584549 6_1:-43378133 Msa0885890:CDS
GCGGAGGATCCAGTTTAGTA+CGG 0.588858 6_1:-43378752 Msa0885890:five_prime_UTR
AGCAAAGATATTAGCTGCGG+AGG 0.590198 6_1:-43378768 None:intergenic
GGATCCAGTTTAGTACGGCT+CGG 0.590569 6_1:-43378747 Msa0885890:five_prime_UTR
GTGTTTGCAGGGGTATATGT+TGG 0.608820 6_1:-43377850 Msa0885890:CDS
AGCAGCAAAGATATTAGCTG+CGG 0.638123 6_1:-43378771 None:intergenic
GCAACCGAATCACCATCTCA+TGG 0.649274 6_1:+43377896 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGTTAGATGATGTTTTATTT+TGG - chr6_1:43378297-43378316 Msa0885890:intron 20.0%
!!! GTTAGATGATGTTTTATTTT+GGG - chr6_1:43378298-43378317 Msa0885890:intron 20.0%
!!! TTAGATGATGTTTTATTTTG+GGG - chr6_1:43378299-43378318 Msa0885890:intron 20.0%
!!! TGTTAGATGATGTTTTATTT+TGG - chr6_1:43378297-43378316 Msa0885890:intron 20.0%
!!! GTTAGATGATGTTTTATTTT+GGG - chr6_1:43378298-43378317 Msa0885890:intron 20.0%
!!! TTAGATGATGTTTTATTTTG+GGG - chr6_1:43378299-43378318 Msa0885890:intron 20.0%
! ATAAGGTTACTTGAAAAGTT+AGG - chr6_1:43377922-43377941 Msa0885890:CDS 25.0%
!!! TTTTGTGATTTTGATTGTTG+TGG - chr6_1:43378053-43378072 Msa0885890:intron 25.0%
!!! CAGATTTTTTGTAGTTAGAT+TGG - chr6_1:43378251-43378270 Msa0885890:intron 25.0%
!! ATTGGTTTAGATGAATATTG+TGG - chr6_1:43378269-43378288 Msa0885890:intron 25.0%
! TTGGTTTAGATGAATATTGT+GGG - chr6_1:43378270-43378289 Msa0885890:intron 25.0%
!!! TAGATGATGTTTTATTTTGG+GGG - chr6_1:43378300-43378319 Msa0885890:intron 25.0%
! TGATAACTATCTTGTTAAAG+TGG - chr6_1:43378423-43378442 Msa0885890:intron 25.0%
! AAATGAGTAAAATTACAGAC+CGG + chr6_1:43378511-43378530 None:intergenic 25.0%
! GTTTACTTATCCAAAAAGAT+AGG - chr6_1:43378543-43378562 Msa0885890:intron 25.0%
!! AGGAAAAATTCCTATCTTTT+TGG + chr6_1:43378556-43378575 None:intergenic 25.0%
! ATAAGGTTACTTGAAAAGTT+AGG - chr6_1:43377922-43377941 Msa0885890:CDS 25.0%
!!! TTTTGTGATTTTGATTGTTG+TGG - chr6_1:43378053-43378072 Msa0885890:intron 25.0%
!!! CAGATTTTTTGTAGTTAGAT+TGG - chr6_1:43378251-43378270 Msa0885890:intron 25.0%
!! ATTGGTTTAGATGAATATTG+TGG - chr6_1:43378269-43378288 Msa0885890:intron 25.0%
! TTGGTTTAGATGAATATTGT+GGG - chr6_1:43378270-43378289 Msa0885890:intron 25.0%
!!! TAGATGATGTTTTATTTTGG+GGG - chr6_1:43378300-43378319 Msa0885890:intron 25.0%
! TGATAACTATCTTGTTAAAG+TGG - chr6_1:43378423-43378442 Msa0885890:intron 25.0%
! AAATGAGTAAAATTACAGAC+CGG + chr6_1:43378511-43378530 None:intergenic 25.0%
! GTTTACTTATCCAAAAAGAT+AGG - chr6_1:43378543-43378562 Msa0885890:intron 25.0%
!! AGGAAAAATTCCTATCTTTT+TGG + chr6_1:43378556-43378575 None:intergenic 25.0%
TAACTTTATGAGTTCTTGAC+TGG - chr6_1:43377880-43377899 Msa0885890:CDS 30.0%
ACTCAACAACTATTGACATA+TGG - chr6_1:43378368-43378387 Msa0885890:intron 30.0%
! AAGATAGGAATTTTTCCTTG+TGG - chr6_1:43378558-43378577 Msa0885890:intron 30.0%
AAAGGAAAATATGTACCACA+AGG + chr6_1:43378576-43378595 None:intergenic 30.0%
! TTGTGGTACATATTTTCCTT+TGG - chr6_1:43378575-43378594 Msa0885890:intron 30.0%
TAACTTTATGAGTTCTTGAC+TGG - chr6_1:43377880-43377899 Msa0885890:CDS 30.0%
ACTCAACAACTATTGACATA+TGG - chr6_1:43378368-43378387 Msa0885890:intron 30.0%
! AAGATAGGAATTTTTCCTTG+TGG - chr6_1:43378558-43378577 Msa0885890:intron 30.0%
AAAGGAAAATATGTACCACA+AGG + chr6_1:43378576-43378595 None:intergenic 30.0%
! TTGTGGTACATATTTTCCTT+TGG - chr6_1:43378575-43378594 Msa0885890:intron 30.0%
GAAAAGTTAGGCTTCTTATG+AGG - chr6_1:43377934-43377953 Msa0885890:CDS 35.0%
TTCTCTTGCATACTCATCAT+AGG + chr6_1:43378102-43378121 None:intergenic 35.0%
ATGAGTATGCAAGAGAATGT+TGG - chr6_1:43378105-43378124 Msa0885890:intron 35.0%
GAATTGAGAAATCGTGTGTT+TGG - chr6_1:43378127-43378146 Msa0885890:CDS 35.0%
! AGGATGCACTTTTCTGTTTT+CGG - chr6_1:43378182-43378201 Msa0885890:intron 35.0%
CTATCTTGTTAAAGTGGTGT+TGG - chr6_1:43378429-43378448 Msa0885890:CDS 35.0%
! TTTCCTTTGGTAATTGTAGC+AGG - chr6_1:43378588-43378607 Msa0885890:intron 35.0%
! TTCCTTTGGTAATTGTAGCA+GGG - chr6_1:43378589-43378608 Msa0885890:intron 35.0%
GAAAAGTTAGGCTTCTTATG+AGG - chr6_1:43377934-43377953 Msa0885890:CDS 35.0%
TTCTCTTGCATACTCATCAT+AGG + chr6_1:43378102-43378121 None:intergenic 35.0%
ATGAGTATGCAAGAGAATGT+TGG - chr6_1:43378105-43378124 Msa0885890:intron 35.0%
GAATTGAGAAATCGTGTGTT+TGG - chr6_1:43378127-43378146 Msa0885890:CDS 35.0%
! AGGATGCACTTTTCTGTTTT+CGG - chr6_1:43378182-43378201 Msa0885890:intron 35.0%
CTATCTTGTTAAAGTGGTGT+TGG - chr6_1:43378429-43378448 Msa0885890:CDS 35.0%
! TTTCCTTTGGTAATTGTAGC+AGG - chr6_1:43378588-43378607 Msa0885890:intron 35.0%
! TTCCTTTGGTAATTGTAGCA+GGG - chr6_1:43378589-43378608 Msa0885890:intron 35.0%
CGATGGAGTTCTTAAGCATA+AGG - chr6_1:43377905-43377924 Msa0885890:CDS 40.0%
GAGTAAAATTACAGACCGGA+TGG + chr6_1:43378507-43378526 None:intergenic 40.0%
! GTCTTTTGCATTTCTGTTCG+AGG - chr6_1:43378617-43378636 Msa0885890:CDS 40.0%
CATTTCTGTTCGAGGAAGTT+GGG - chr6_1:43378625-43378644 Msa0885890:CDS 40.0%
ATTTCTGTTCGAGGAAGTTG+GGG - chr6_1:43378626-43378645 Msa0885890:CDS 40.0%
!!! CAGTTTTTTCTGCCATGAGA+TGG - chr6_1:43378670-43378689 Msa0885890:five_prime_UTR 40.0%
GTATATGTTGGTGTGCTTTC+TGG - chr6_1:43378740-43378759 Msa0885890:five_prime_UTR 40.0%
CGATGGAGTTCTTAAGCATA+AGG - chr6_1:43377905-43377924 Msa0885890:CDS 40.0%
GAGTAAAATTACAGACCGGA+TGG + chr6_1:43378507-43378526 None:intergenic 40.0%
! GTCTTTTGCATTTCTGTTCG+AGG - chr6_1:43378617-43378636 Msa0885890:CDS 40.0%
CATTTCTGTTCGAGGAAGTT+GGG - chr6_1:43378625-43378644 Msa0885890:CDS 40.0%
ATTTCTGTTCGAGGAAGTTG+GGG - chr6_1:43378626-43378645 Msa0885890:CDS 40.0%
!!! CAGTTTTTTCTGCCATGAGA+TGG - chr6_1:43378670-43378689 Msa0885890:five_prime_UTR 40.0%
GTATATGTTGGTGTGCTTTC+TGG - chr6_1:43378740-43378759 Msa0885890:five_prime_UTR 40.0%
TGAGTTCTTGACTGGTACGA+TGG - chr6_1:43377888-43377907 Msa0885890:CDS 45.0%
ACGATTAGCGCAGATCTTGA+GGG + chr6_1:43377970-43377989 None:intergenic 45.0%
AATCGTGTGTTTGGCATGCT+AGG - chr6_1:43378136-43378155 Msa0885890:CDS 45.0%
ATCGTGTGTTTGGCATGCTA+GGG - chr6_1:43378137-43378156 Msa0885890:CDS 45.0%
! TCTGCTGATGGTGAGCTTAA+AGG - chr6_1:43378162-43378181 Msa0885890:CDS 45.0%
TGTTGGAATCCGAGAGAGTA+GGG - chr6_1:43378446-43378465 Msa0885890:CDS 45.0%
CCAAATACACCCTACTCTCT+CGG + chr6_1:43378458-43378477 None:intergenic 45.0%
CACCCTGCTACAATTACCAA+AGG + chr6_1:43378594-43378613 None:intergenic 45.0%
GCATTTCTGTTCGAGGAAGT+TGG - chr6_1:43378624-43378643 Msa0885890:CDS 45.0%
TCTGCCATGAGATGGTGATT+CGG - chr6_1:43378678-43378697 Msa0885890:five_prime_UTR 45.0%
!! TGATTCGGTTGCTAGCAGTT+TGG - chr6_1:43378693-43378712 Msa0885890:five_prime_UTR 45.0%
! GATTCGGTTGCTAGCAGTTT+GGG - chr6_1:43378694-43378713 Msa0885890:five_prime_UTR 45.0%
CTGCTTCAACTGTGTTTGCA+GGG - chr6_1:43378717-43378736 Msa0885890:five_prime_UTR 45.0%
TGCTTCAACTGTGTTTGCAG+GGG - chr6_1:43378718-43378737 Msa0885890:five_prime_UTR 45.0%
! GTGTTTGCAGGGGTATATGT+TGG - chr6_1:43378728-43378747 Msa0885890:five_prime_UTR 45.0%
TGAGTTCTTGACTGGTACGA+TGG - chr6_1:43377888-43377907 Msa0885890:CDS 45.0%
ACGATTAGCGCAGATCTTGA+GGG + chr6_1:43377970-43377989 None:intergenic 45.0%
AATCGTGTGTTTGGCATGCT+AGG - chr6_1:43378136-43378155 Msa0885890:CDS 45.0%
ATCGTGTGTTTGGCATGCTA+GGG - chr6_1:43378137-43378156 Msa0885890:CDS 45.0%
! TCTGCTGATGGTGAGCTTAA+AGG - chr6_1:43378162-43378181 Msa0885890:CDS 45.0%
TGTTGGAATCCGAGAGAGTA+GGG - chr6_1:43378446-43378465 Msa0885890:CDS 45.0%
CCAAATACACCCTACTCTCT+CGG + chr6_1:43378458-43378477 None:intergenic 45.0%
CACCCTGCTACAATTACCAA+AGG + chr6_1:43378594-43378613 None:intergenic 45.0%
GCATTTCTGTTCGAGGAAGT+TGG - chr6_1:43378624-43378643 Msa0885890:CDS 45.0%
TCTGCCATGAGATGGTGATT+CGG - chr6_1:43378678-43378697 Msa0885890:five_prime_UTR 45.0%
!! TGATTCGGTTGCTAGCAGTT+TGG - chr6_1:43378693-43378712 Msa0885890:five_prime_UTR 45.0%
! GATTCGGTTGCTAGCAGTTT+GGG - chr6_1:43378694-43378713 Msa0885890:five_prime_UTR 45.0%
CTGCTTCAACTGTGTTTGCA+GGG - chr6_1:43378717-43378736 Msa0885890:five_prime_UTR 45.0%
TGCTTCAACTGTGTTTGCAG+GGG - chr6_1:43378718-43378737 Msa0885890:five_prime_UTR 45.0%
! GTGTTTGCAGGGGTATATGT+TGG - chr6_1:43378728-43378747 Msa0885890:five_prime_UTR 45.0%
GCGGAGGATCCAGTTTAGTA+CGG - chr6_1:43377826-43377845 Msa0885890:CDS 50.0%
GGATCCAGTTTAGTACGGCT+CGG - chr6_1:43377831-43377850 Msa0885890:CDS 50.0%
ACAACCGAGCCGTACTAAAC+TGG + chr6_1:43377838-43377857 None:intergenic 50.0%
! AGCGCAGATCTTGAGGGTTT+TGG + chr6_1:43377964-43377983 None:intergenic 50.0%
GACGATTAGCGCAGATCTTG+AGG + chr6_1:43377971-43377990 None:intergenic 50.0%
CATGCTAGGGATTCTGCTGA+TGG - chr6_1:43378150-43378169 Msa0885890:CDS 50.0%
GTGTTGGAATCCGAGAGAGT+AGG - chr6_1:43378445-43378464 Msa0885890:CDS 50.0%
CCGAGAGAGTAGGGTGTATT+TGG - chr6_1:43378455-43378474 Msa0885890:CDS 50.0%
! CACTTGTTGCACATGCCATC+CGG - chr6_1:43378489-43378508 Msa0885890:intron 50.0%
GCAACCGAATCACCATCTCA+TGG + chr6_1:43378685-43378704 None:intergenic 50.0%
GCTGCTTCAACTGTGTTTGC+AGG - chr6_1:43378716-43378735 Msa0885890:five_prime_UTR 50.0%
GCGGAGGATCCAGTTTAGTA+CGG - chr6_1:43377826-43377845 Msa0885890:CDS 50.0%
GGATCCAGTTTAGTACGGCT+CGG - chr6_1:43377831-43377850 Msa0885890:CDS 50.0%
ACAACCGAGCCGTACTAAAC+TGG + chr6_1:43377838-43377857 None:intergenic 50.0%
! AGCGCAGATCTTGAGGGTTT+TGG + chr6_1:43377964-43377983 None:intergenic 50.0%
GACGATTAGCGCAGATCTTG+AGG + chr6_1:43377971-43377990 None:intergenic 50.0%
CATGCTAGGGATTCTGCTGA+TGG - chr6_1:43378150-43378169 Msa0885890:CDS 50.0%
GTGTTGGAATCCGAGAGAGT+AGG - chr6_1:43378445-43378464 Msa0885890:CDS 50.0%
CCGAGAGAGTAGGGTGTATT+TGG - chr6_1:43378455-43378474 Msa0885890:CDS 50.0%
! CACTTGTTGCACATGCCATC+CGG - chr6_1:43378489-43378508 Msa0885890:intron 50.0%
GCAACCGAATCACCATCTCA+TGG + chr6_1:43378685-43378704 None:intergenic 50.0%
GCTGCTTCAACTGTGTTTGC+AGG - chr6_1:43378716-43378735 Msa0885890:five_prime_UTR 50.0%
CGAGGAAGTTGGGGTCTAGT+TGG - chr6_1:43378635-43378654 Msa0885890:exon 55.0%
CGAGGAAGTTGGGGTCTAGT+TGG - chr6_1:43378635-43378654 Msa0885890:exon 55.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 43377816 43378784 43377816 ID=Msa0885890;Name=Msa0885890
chr6_1 mRNA 43377816 43378784 43377816 ID=Msa0885890-mRNA-1;Parent=Msa0885890;Name=Msa0885890-mRNA-1;_AED=0.43;_eAED=0.43;_QI=135|0.33|0.25|0.75|1|1|4|0|122
chr6_1 exon 43377816 43377990 43377816 ID=Msa0885890-mRNA-1:exon:9417;Parent=Msa0885890-mRNA-1
chr6_1 exon 43378124 43378193 43378124 ID=Msa0885890-mRNA-1:exon:9416;Parent=Msa0885890-mRNA-1
chr6_1 exon 43378429 43378506 43378429 ID=Msa0885890-mRNA-1:exon:9415;Parent=Msa0885890-mRNA-1
chr6_1 exon 43378607 43378784 43378607 ID=Msa0885890-mRNA-1:exon:9414;Parent=Msa0885890-mRNA-1
chr6_1 five_prime_UTR 43378650 43378784 43378650 ID=Msa0885890-mRNA-1:five_prime_utr;Parent=Msa0885890-mRNA-1
chr6_1 CDS 43378607 43378649 43378607 ID=Msa0885890-mRNA-1:cds;Parent=Msa0885890-mRNA-1
chr6_1 CDS 43378429 43378506 43378429 ID=Msa0885890-mRNA-1:cds;Parent=Msa0885890-mRNA-1
chr6_1 CDS 43378124 43378193 43378124 ID=Msa0885890-mRNA-1:cds;Parent=Msa0885890-mRNA-1
chr6_1 CDS 43377816 43377990 43377816 ID=Msa0885890-mRNA-1:cds;Parent=Msa0885890-mRNA-1
Gene Sequence

>Msa0885890

ATGAGGCAATCCAAAACCCTCAAGATCTGCGCTAATCGTCTTATTATACCTATGATGAGTATGCAAGAGAATGTTGGAATTGAGAAATCGTGTGTTTGGCATGCTAGGGATTCTGCTGATGTGAATGAATTAATTGATGATAACTATCTTGTTAAAGTGGTGTTGGAATCCGAGAGAGTAGGGTGTATTTGGGTGTTTGTCTTTTGCATTTCTGTTCGAGGAAGTTGGGGTCTAGTTGGCGATAGATCAATCAGTTTTTTCTGCCATGAGATGGTGATTCGGTTGCTAGCAGTTTGGGCTGCTTCAACTGTGTTTGCAGGGGTATATGTTGGTGTGCTTTCTGGTTTGATTTCTGCTGCAGTCCAT
Protein sequence

>Msa0885890

MRQSKTLKICANRLIIPMMSMQENVGIEKSCVWHARDSADVNELIDDNYLVKVVLESERVGCIWVFVFCISVRGSWGLVGDRSISFFCHEMVIRLLAVWAASTVFAGVYVGVLSGLISAAVH