AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054307

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054307.t1 MTR_1g101810 66.667 117 38 1 2 117 43 159 1.82e-48 157
MS.gene054307.t1 MTR_1g101810 66.667 117 38 1 2 117 73 189 5.51e-48 157
MS.gene054307.t1 MTR_8g033070 66.304 92 30 1 22 113 80 170 2.29e-36 126
MS.gene054307.t1 MTR_7g028160 56.044 91 40 0 10 100 38 128 1.02e-29 108
MS.gene054307.t1 MTR_1g038650 61.644 73 28 0 12 84 22 94 3.12e-27 100
MS.gene054307.t1 MTR_2g006150 57.143 91 39 0 19 109 127 217 9.56e-27 103
MS.gene054307.t1 MTR_2g006150 57.143 91 39 0 19 109 127 217 1.55e-26 102
MS.gene054307.t1 MTR_1g114380 58.228 79 31 1 6 84 19 95 4.95e-26 98.2
MS.gene054307.t1 MTR_1g063870 68.254 63 20 0 22 84 49 111 2.78e-25 94.7
MS.gene054307.t1 MTR_5g039600 55.435 92 35 1 18 103 57 148 3.59e-25 98.2
MS.gene054307.t1 MTR_4g108370 63.750 80 23 1 11 84 80 159 5.11e-25 97.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054307.t1 AT2G45680 67.010 97 31 1 22 117 75 171 9.06e-38 130
MS.gene054307.t1 AT5G51910 64.000 100 35 1 1 99 35 134 2.38e-36 125
MS.gene054307.t1 AT5G51910 64.000 100 35 1 1 99 35 134 2.38e-36 125
MS.gene054307.t1 AT1G69690 73.016 63 17 0 22 84 52 114 6.59e-28 104
MS.gene054307.t1 AT1G58100 69.697 66 20 0 19 84 57 122 1.83e-27 104
MS.gene054307.t1 AT1G35560 71.212 66 19 0 19 84 52 117 2.24e-27 103
MS.gene054307.t1 AT3G47620 57.955 88 32 1 2 84 92 179 3.04e-27 104
MS.gene054307.t1 AT5G23280 60.526 76 30 0 9 84 26 101 4.82e-27 100
MS.gene054307.t1 AT3G27010 63.889 72 26 0 12 83 68 139 9.17e-27 101
MS.gene054307.t1 AT3G27010 63.889 72 26 0 12 83 68 139 9.17e-27 101
MS.gene054307.t1 AT1G72010 72.464 69 19 0 16 84 57 125 1.08e-26 102
MS.gene054307.t1 AT5G08330 63.768 69 25 0 16 84 25 93 4.44e-26 97.8
MS.gene054307.t1 AT5G41030 60.870 69 27 0 19 87 65 133 4.27e-24 92.8
MS.gene054307.t1 AT2G37000 69.492 59 18 0 22 80 43 101 4.23e-23 89.0
MS.gene054307.t1 AT3G45150 49.231 65 32 1 17 81 13 76 9.46e-17 72.0

Find 40 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCGGTGGCTTTGATGATTGC+AGG 0.311422 6.1:+24690716 None:intergenic
GGCTATGGCCGGAATTATTC+CGG 0.369975 6.1:+24690691 None:intergenic
AGAAACAATAGGGTGGTTAC+TGG 0.376057 6.1:-24690750 MS.gene054307:CDS
CAACTTTCCGCCCTCTGAAA+TGG 0.397867 6.1:+24690670 None:intergenic
CACCGGCACCGGAATAATTC+CGG 0.398178 6.1:-24690699 MS.gene054307:CDS
GACCAAGATCTCTCGTCAAC+TGG 0.398427 6.1:+24690786 None:intergenic
AAGTCTGATGGAGAAACAAT+AGG 0.400346 6.1:-24690761 MS.gene054307:CDS
TTCCAGTTGACGAGAGATCT+TGG 0.406107 6.1:-24690788 MS.gene054307:CDS
GGTCTAGCTGCCGATGTTGT+TGG 0.412258 6.1:+24690641 None:intergenic
TCGGCTGACACTGTCATTTG+TGG 0.434746 6.1:+24690896 None:intergenic
CTGTCATTTGTGGTTCCAGC+GGG 0.459106 6.1:+24690906 None:intergenic
TTCAGAGGGCGGAAAGTTGA+AGG 0.466569 6.1:-24690666 MS.gene054307:CDS
TTGCTGACAGTGTGACTCTT+CGG 0.478708 6.1:+24690828 None:intergenic
ATCATCAAAGCCACCGGCAC+CGG 0.497106 6.1:-24690710 MS.gene054307:CDS
TTCGTGTGACGGTCCTCTGA+TGG 0.498844 6.1:+24690866 None:intergenic
AGCTAGACCAGACGGCCAAA+AGG 0.501805 6.1:-24690627 MS.gene054307:CDS
CCCTCTGAAATGGCTATGGC+CGG 0.502325 6.1:+24690680 None:intergenic
TGTCAGCAACATGTGCATCT+AGG 0.504146 6.1:-24690814 MS.gene054307:CDS
GGCCGGAATTATTCCGGTGC+CGG 0.511782 6.1:+24690697 None:intergenic
AGTCTGATGGAGAAACAATA+GGG 0.517180 6.1:-24690760 MS.gene054307:CDS
TCCGCCCTCTGAAATGGCTA+TGG 0.528278 6.1:+24690676 None:intergenic
CGGAATTATTCCGGTGCCGG+TGG 0.529649 6.1:+24690700 None:intergenic
AAAAGCAAGAGAGACTCAAT+TGG 0.530473 6.1:-24690593 MS.gene054307:CDS
AAAACAGACGTTGAACCCGC+TGG 0.542316 6.1:-24690921 MS.gene054307:CDS
GGACCGTCACACGAAGGTGG+AGG 0.555419 6.1:-24690858 MS.gene054307:CDS
ATCCCTCCACCTTCGTGTGA+CGG 0.556037 6.1:+24690855 None:intergenic
GATCTTGGTCACAAGTCTGA+TGG 0.556205 6.1:-24690773 MS.gene054307:CDS
CAGACGGCCAAAAGGCCCCA+AGG 0.564342 6.1:-24690619 MS.gene054307:CDS
GACCGTCACACGAAGGTGGA+GGG 0.605599 6.1:-24690857 MS.gene054307:CDS
TCCGGCCATAGCCATTTCAG+AGG 0.619818 6.1:-24690681 MS.gene054307:CDS
GCCATAGCCATTTCAGAGGG+CGG 0.621097 6.1:-24690677 MS.gene054307:CDS
CCTGCAATCATCAAAGCCAC+CGG 0.628378 6.1:-24690716 MS.gene054307:CDS
AGAGGACCGTCACACGAAGG+TGG 0.628436 6.1:-24690861 MS.gene054307:CDS
CCGGCCATAGCCATTTCAGA+GGG 0.636688 6.1:-24690680 MS.gene054307:CDS
ACATCGGCAGCTAGACCAGA+CGG 0.655173 6.1:-24690635 MS.gene054307:CDS
ACTGTCATTTGTGGTTCCAG+CGG 0.655351 6.1:+24690905 None:intergenic
GTTGAAGGTTCCAACAACAT+CGG 0.665250 6.1:-24690651 MS.gene054307:CDS
AGCCGAAAAGAAACCATCAG+AGG 0.683646 6.1:-24690879 MS.gene054307:CDS
ATCAGAGGACCGTCACACGA+AGG 0.685962 6.1:-24690864 MS.gene054307:CDS
CTGATGGAGAAACAATAGGG+TGG 0.705438 6.1:-24690757 MS.gene054307:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAAAGCAAGAGAGACTCAAT+TGG - chr6.1:24690922-24690941 MS.gene054307:CDS 35.0%
AAGTCTGATGGAGAAACAAT+AGG - chr6.1:24690754-24690773 MS.gene054307:CDS 35.0%
AGTCTGATGGAGAAACAATA+GGG - chr6.1:24690755-24690774 MS.gene054307:CDS 35.0%
AGAAACAATAGGGTGGTTAC+TGG - chr6.1:24690765-24690784 MS.gene054307:CDS 40.0%
GTTGAAGGTTCCAACAACAT+CGG - chr6.1:24690864-24690883 MS.gene054307:CDS 40.0%
! GTCCTCTGATGGTTTCTTTT+CGG + chr6.1:24690641-24690660 None:intergenic 40.0%
!! CTCTCTTGCTTTTCTTCCTT+GGG + chr6.1:24690915-24690934 None:intergenic 40.0%
!! TCTCTCTTGCTTTTCTTCCT+TGG + chr6.1:24690916-24690935 None:intergenic 40.0%
!! TCTCTTGCTTTTCTTCCTTG+GGG + chr6.1:24690914-24690933 None:intergenic 40.0%
AGCCGAAAAGAAACCATCAG+AGG - chr6.1:24690636-24690655 MS.gene054307:CDS 45.0%
CTGATGGAGAAACAATAGGG+TGG - chr6.1:24690758-24690777 MS.gene054307:CDS 45.0%
GATCTTGGTCACAAGTCTGA+TGG - chr6.1:24690742-24690761 MS.gene054307:CDS 45.0%
TGTCAGCAACATGTGCATCT+AGG - chr6.1:24690701-24690720 MS.gene054307:CDS 45.0%
TTCCAGTTGACGAGAGATCT+TGG - chr6.1:24690727-24690746 MS.gene054307:CDS 45.0%
TTGCTGACAGTGTGACTCTT+CGG + chr6.1:24690690-24690709 None:intergenic 45.0%
! ACTGTCATTTGTGGTTCCAG+CGG + chr6.1:24690613-24690632 None:intergenic 45.0%
! TTTTCTTCCTTGGGGCCTTT+TGG + chr6.1:24690906-24690925 None:intergenic 45.0%
AAAACAGACGTTGAACCCGC+TGG - chr6.1:24690594-24690613 MS.gene054307:CDS 50.0%
CCTGCAATCATCAAAGCCAC+CGG - chr6.1:24690799-24690818 MS.gene054307:CDS 50.0%
GACCAAGATCTCTCGTCAAC+TGG + chr6.1:24690732-24690751 None:intergenic 50.0%
GGCTATGGCCGGAATTATTC+CGG + chr6.1:24690827-24690846 None:intergenic 50.0%
TTCAGAGGGCGGAAAGTTGA+AGG - chr6.1:24690849-24690868 MS.gene054307:CDS 50.0%
! CAACTTTCCGCCCTCTGAAA+TGG + chr6.1:24690848-24690867 None:intergenic 50.0%
! CTGTCATTTGTGGTTCCAGC+GGG + chr6.1:24690612-24690631 None:intergenic 50.0%
! TCGGCTGACACTGTCATTTG+TGG + chr6.1:24690622-24690641 None:intergenic 50.0%
ACATCGGCAGCTAGACCAGA+CGG - chr6.1:24690880-24690899 MS.gene054307:CDS 55.0%
AGCTAGACCAGACGGCCAAA+AGG - chr6.1:24690888-24690907 MS.gene054307:CDS 55.0%
ATCAGAGGACCGTCACACGA+AGG - chr6.1:24690651-24690670 MS.gene054307:CDS 55.0%
ATCATCAAAGCCACCGGCAC+CGG - chr6.1:24690805-24690824 MS.gene054307:CDS 55.0%
ATCCCTCCACCTTCGTGTGA+CGG + chr6.1:24690663-24690682 None:intergenic 55.0%
CCGGCCATAGCCATTTCAGA+GGG - chr6.1:24690835-24690854 MS.gene054307:CDS 55.0%
GCCATAGCCATTTCAGAGGG+CGG - chr6.1:24690838-24690857 MS.gene054307:CDS 55.0%
GGTCTAGCTGCCGATGTTGT+TGG + chr6.1:24690877-24690896 None:intergenic 55.0%
TCCGGCCATAGCCATTTCAG+AGG - chr6.1:24690834-24690853 MS.gene054307:CDS 55.0%
TTCGTGTGACGGTCCTCTGA+TGG + chr6.1:24690652-24690671 None:intergenic 55.0%
! CACCGGCACCGGAATAATTC+CGG - chr6.1:24690816-24690835 MS.gene054307:CDS 55.0%
!! CCCTCTGAAATGGCTATGGC+CGG + chr6.1:24690838-24690857 None:intergenic 55.0%
!! CCGGTGGCTTTGATGATTGC+AGG + chr6.1:24690802-24690821 None:intergenic 55.0%
!! TCCGCCCTCTGAAATGGCTA+TGG + chr6.1:24690842-24690861 None:intergenic 55.0%
AGAGGACCGTCACACGAAGG+TGG - chr6.1:24690654-24690673 MS.gene054307:CDS 60.0%
GACCGTCACACGAAGGTGGA+GGG - chr6.1:24690658-24690677 MS.gene054307:CDS 60.0%
GGCCGGAATTATTCCGGTGC+CGG + chr6.1:24690821-24690840 None:intergenic 60.0%
! CGGAATTATTCCGGTGCCGG+TGG + chr6.1:24690818-24690837 None:intergenic 60.0%
CAGACGGCCAAAAGGCCCCA+AGG - chr6.1:24690896-24690915 MS.gene054307:CDS 65.0%
GGACCGTCACACGAAGGTGG+AGG - chr6.1:24690657-24690676 MS.gene054307:CDS 65.0%
! CTTGGGGCCTTTTGGCCGTC+TGG + chr6.1:24690898-24690917 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 24690589 24690948 24690589 ID=MS.gene054307
chr6.1 mRNA 24690589 24690948 24690589 ID=MS.gene054307.t1;Parent=MS.gene054307
chr6.1 exon 24690589 24690948 24690589 ID=MS.gene054307.t1.exon1;Parent=MS.gene054307.t1
chr6.1 CDS 24690589 24690948 24690589 ID=cds.MS.gene054307.t1;Parent=MS.gene054307.t1
Gene Sequence

>MS.gene054307

ATGGAAAAACAGACGTTGAACCCGCTGGAACCACAAATGACAGTGTCAGCCGAAAAGAAACCATCAGAGGACCGTCACACGAAGGTGGAGGGATGTGTCCGAAGAGTCACACTGTCAGCAACATGTGCATCTAGGATCTTCCAGTTGACGAGAGATCTTGGTCACAAGTCTGATGGAGAAACAATAGGGTGGTTACTGGAACAAGCTGAACCTGCAATCATCAAAGCCACCGGCACCGGAATAATTCCGGCCATAGCCATTTCAGAGGGCGGAAAGTTGAAGGTTCCAACAACATCGGCAGCTAGACCAGACGGCCAAAAGGCCCCAAGGAAGAAAAGCAAGAGAGACTCAATTGGTTAA
Protein sequence

>MS.gene054307.t1

MEKQTLNPLEPQMTVSAEKKPSEDRHTKVEGCVRRVTLSATCASRIFQLTRDLGHKSDGETIGWLLEQAEPAIIKATGTGIIPAIAISEGGKLKVPTTSAARPDGQKAPRKKSKRDSIG