AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene051651


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051651.t1 MTR_1g017140 91.154 260 20 2 9 267 84 341 1.21e-175 488
MS.gene051651.t1 MTR_3g103570 42.146 261 110 13 9 256 84 316 3.59e-43 150
MS.gene051651.t1 MTR_5g014990 51.724 87 33 4 9 94 84 162 4.61e-17 79.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051651.t1 AT5G65790 44.186 86 43 3 9 92 84 166 1.45e-12 67.4
MS.gene051651.t1 AT3G49690 60.417 48 17 1 9 56 84 129 2.63e-12 66.2
MS.gene051651.t1 AT1G22640 53.191 47 22 0 1 47 1 47 2.19e-11 61.6
MS.gene051651.t1 AT4G37780 63.830 47 15 1 9 55 84 128 3.52e-11 62.8
MS.gene051651.t1 AT5G57620 56.250 48 19 1 9 56 84 129 6.99e-11 62.0

Find 50 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAATTTAACCTTGGTATT+TGG 0.131923 1.3:+5314418 None:intergenic
TACAAGGTTCTAGTATTAAT+TGG 0.175164 1.3:-5314481 MS.gene051651:CDS
GATACCATATGATCAATTTC+TGG 0.294149 1.3:+5314581 None:intergenic
AAACCATCAAAAGTAGTATT+AGG 0.306915 1.3:+5314779 None:intergenic
CTTGATCATTGAAGCCTTGT+TGG 0.313961 1.3:+5314858 None:intergenic
CTTGTTGTTGTTGATCTTTA+CGG 0.335397 1.3:+5315062 None:intergenic
ACAAGGTTCTAGTATTAATT+GGG 0.336603 1.3:-5314480 MS.gene051651:CDS
AATTATCCACCAAGATTTGA+TGG 0.368986 1.3:-5314554 MS.gene051651:CDS
ATAATGACATAAAGAACTAT+TGG 0.370430 1.3:-5315120 MS.gene051651:CDS
CATTCCAGAAATTGATCATA+TGG 0.373903 1.3:-5314585 MS.gene051651:CDS
TTGGTTGTGGTTGTTATCAT+TGG 0.385791 1.3:+5314667 None:intergenic
GATAATGTTATCTTCTTCTT+CGG 0.391795 1.3:+5315516 None:intergenic
ATGTCATTATCAGTTCTTCC+TGG 0.397545 1.3:+5315133 None:intergenic
TTCTTGAACCAAATTTGATA+AGG 0.407035 1.3:+5314961 None:intergenic
TGCATGACATGTGGTAAATA+TGG 0.407502 1.3:+5314935 None:intergenic
TGCAGCCTTTACATTAGTAT+TGG 0.421799 1.3:-5315493 MS.gene051651:CDS
GCACGTAATAGAGGCAATAA+TGG 0.443374 1.3:-5315040 MS.gene051651:CDS
AATTCCAACCCATCAAATCT+TGG 0.462721 1.3:+5314545 None:intergenic
TCCACCAAGATTTGATGGGT+TGG 0.464644 1.3:-5314549 MS.gene051651:CDS
CATTTGTTGCGAATTGTACT+TGG 0.466808 1.3:+5314648 None:intergenic
CAAGTACAATTCGCAACAAA+TGG 0.468082 1.3:-5314647 MS.gene051651:CDS
AGAAAACTTCTAATGAAGCT+TGG 0.468133 1.3:-5314827 MS.gene051651:CDS
TTGCGAATTGTACTTGGTTG+TGG 0.482944 1.3:+5314654 None:intergenic
CAACAACAAGCACGTAATAG+AGG 0.488651 1.3:-5315049 MS.gene051651:CDS
TTTACATTAGTATTGGAAGC+AGG 0.496580 1.3:-5315486 MS.gene051651:intron
AACATTGATTGTAGTGGAGG+TGG 0.509042 1.3:+5314893 None:intergenic
TGCTTCCAATACTAATGTAA+AGG 0.512738 1.3:+5315488 None:intergenic
CACAAATCACAATTTAACCT+TGG 0.527729 1.3:+5314411 None:intergenic
CCTTGGTATTTGGAATCAAG+AGG 0.548952 1.3:+5314428 None:intergenic
ATAATTGCAGCTCAATTGCC+AGG 0.552173 1.3:-5315151 MS.gene051651:intron
AAACTTCTAATGAAGCTTGG+AGG 0.553342 1.3:-5314824 MS.gene051651:CDS
ATTATCCACCAAGATTTGAT+GGG 0.556403 1.3:-5314553 MS.gene051651:CDS
ACATTGATTGTAGTGGAGGT+GGG 0.557868 1.3:+5314894 None:intergenic
CATTGATTGTAGTGGAGGTG+GGG 0.562307 1.3:+5314895 None:intergenic
TAAAGAACTATTGGAATACA+AGG 0.580554 1.3:-5315111 MS.gene051651:CDS
ATCGATAATAATAAGATACA+AGG 0.582126 1.3:-5314497 MS.gene051651:CDS
ATTGATTGTAGTGGAGGTGG+GGG 0.589201 1.3:+5314896 None:intergenic
TCCAACCCATCAAATCTTGG+TGG 0.591459 1.3:+5314548 None:intergenic
AGTTTATGATCAAGAACATG+TGG 0.602665 1.3:-5314714 MS.gene051651:CDS
AATAATAGAGTGATGAGTAG+TGG 0.606658 1.3:-5314992 MS.gene051651:CDS
TATGACAACATTGATTGTAG+TGG 0.610396 1.3:+5314887 None:intergenic
GACTCGGTGCAAGAAGAGCA+AGG 0.613143 1.3:-5314614 MS.gene051651:CDS
CAAGGTTCTAGTATTAATTG+GGG 0.621220 1.3:-5314479 MS.gene051651:CDS
CCTCTTGATTCCAAATACCA+AGG 0.634631 1.3:-5314428 MS.gene051651:CDS
AGGATGATGATAACTTGAAG+TGG 0.634882 1.3:+5314448 None:intergenic
GACAACATTGATTGTAGTGG+AGG 0.641566 1.3:+5314890 None:intergenic
TTGTCATACACAAACCAACA+AGG 0.660089 1.3:-5314872 MS.gene051651:CDS
GTTTATGATCAAGAACATGT+GGG 0.665568 1.3:-5314713 MS.gene051651:CDS
AAATGGTCAATACTTTGACT+CGG 0.679619 1.3:-5314630 MS.gene051651:CDS
AGCAAAGGTTGCATGACATG+TGG 0.714384 1.3:+5314926 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAATTCAAACACTAT+TGG + chr1.3:5314692-5314711 None:intergenic 15.0%
!! ATAATGACATAAAGAACTAT+TGG - chr1.3:5314832-5314851 MS.gene051651:CDS 20.0%
!! ATCGATAATAATAAGATACA+AGG - chr1.3:5315455-5315474 MS.gene051651:intron 20.0%
!! TATCTATAAAATCAAGACAT+AGG + chr1.3:5314616-5314635 None:intergenic 20.0%
!!! TGAATTTTCCTTATCAAATT+TGG - chr1.3:5314983-5315002 MS.gene051651:CDS 20.0%
! AAACCATCAAAAGTAGTATT+AGG + chr1.3:5315176-5315195 None:intergenic 25.0%
! GATAATGTTATCTTCTTCTT+CGG + chr1.3:5314439-5314458 None:intergenic 25.0%
! TAAAGAACTATTGGAATACA+AGG - chr1.3:5314841-5314860 MS.gene051651:CDS 25.0%
! TTCTTGAACCAAATTTGATA+AGG + chr1.3:5314994-5315013 None:intergenic 25.0%
!! ACAAGGTTCTAGTATTAATT+GGG - chr1.3:5315472-5315491 MS.gene051651:intron 25.0%
!! TACAAGGTTCTAGTATTAAT+TGG - chr1.3:5315471-5315490 MS.gene051651:intron 25.0%
AAATGGTCAATACTTTGACT+CGG - chr1.3:5315322-5315341 MS.gene051651:intron 30.0%
AATAATAGAGTGATGAGTAG+TGG - chr1.3:5314960-5314979 MS.gene051651:CDS 30.0%
AATTATCCACCAAGATTTGA+TGG - chr1.3:5315398-5315417 MS.gene051651:intron 30.0%
ACAAAAAGTAGCATAGCATA+TGG + chr1.3:5314659-5314678 None:intergenic 30.0%
AGAAAACTTCTAATGAAGCT+TGG - chr1.3:5315125-5315144 MS.gene051651:CDS 30.0%
AGTTTATGATCAAGAACATG+TGG - chr1.3:5315238-5315257 MS.gene051651:intron 30.0%
ATTATCCACCAAGATTTGAT+GGG - chr1.3:5315399-5315418 MS.gene051651:intron 30.0%
CATTCCAGAAATTGATCATA+TGG - chr1.3:5315367-5315386 MS.gene051651:intron 30.0%
CTTTCATACCAAACCAAAAA+GGG + chr1.3:5314771-5314790 None:intergenic 30.0%
GATACCATATGATCAATTTC+TGG + chr1.3:5315374-5315393 None:intergenic 30.0%
GTTTATGATCAAGAACATGT+GGG - chr1.3:5315239-5315258 MS.gene051651:intron 30.0%
TGCTTCCAATACTAATGTAA+AGG + chr1.3:5314467-5314486 None:intergenic 30.0%
! AAGGTTGAAAAAGAAGCTTT+TGG - chr1.3:5314860-5314879 MS.gene051651:CDS 30.0%
! AGGTTGAAAAAGAAGCTTTT+GGG - chr1.3:5314861-5314880 MS.gene051651:CDS 30.0%
! CAAGGTTCTAGTATTAATTG+GGG - chr1.3:5315473-5315492 MS.gene051651:intron 30.0%
! TATGACAACATTGATTGTAG+TGG + chr1.3:5315068-5315087 None:intergenic 30.0%
! TTTACATTAGTATTGGAAGC+AGG - chr1.3:5314466-5314485 MS.gene051651:CDS 30.0%
!! CATCCTAATACTACTTTTGA+TGG - chr1.3:5315170-5315189 MS.gene051651:intron 30.0%
!! CTTGTTGTTGTTGATCTTTA+CGG + chr1.3:5314893-5314912 None:intergenic 30.0%
!!! TGCTATGCTACTTTTTGTTT+AGG - chr1.3:5314661-5314680 MS.gene051651:CDS 30.0%
AAACTTCTAATGAAGCTTGG+AGG - chr1.3:5315128-5315147 MS.gene051651:CDS 35.0%
AATTCCAACCCATCAAATCT+TGG + chr1.3:5315410-5315429 None:intergenic 35.0%
AGGATGATGATAACTTGAAG+TGG + chr1.3:5315507-5315526 None:intergenic 35.0%
ATGTCATTATCAGTTCTTCC+TGG + chr1.3:5314822-5314841 None:intergenic 35.0%
CAAGTACAATTCGCAACAAA+TGG - chr1.3:5315305-5315324 MS.gene051651:intron 35.0%
GCTTTCATACCAAACCAAAA+AGG + chr1.3:5314772-5314791 None:intergenic 35.0%
TGCAGCCTTTACATTAGTAT+TGG - chr1.3:5314459-5314478 MS.gene051651:CDS 35.0%
TGCATGACATGTGGTAAATA+TGG + chr1.3:5315020-5315039 None:intergenic 35.0%
TTGGTTGTGGTTGTTATCAT+TGG + chr1.3:5315288-5315307 None:intergenic 35.0%
TTGTCATACACAAACCAACA+AGG - chr1.3:5315080-5315099 MS.gene051651:CDS 35.0%
! CATTTGTTGCGAATTGTACT+TGG + chr1.3:5315307-5315326 None:intergenic 35.0%
! GGTTGAAAAAGAAGCTTTTG+GGG - chr1.3:5314862-5314881 MS.gene051651:CDS 35.0%
! TGAAAAGTGAAGACCCTTTT+TGG - chr1.3:5314755-5314774 MS.gene051651:CDS 35.0%
!!! GATGGGTTGGAATTCTTTTA+TGG - chr1.3:5315416-5315435 MS.gene051651:intron 35.0%
!!! TTTTGGTTTGGTATGAAAGC+AGG - chr1.3:5314772-5314791 MS.gene051651:CDS 35.0%
ATAATTGCAGCTCAATTGCC+AGG - chr1.3:5314801-5314820 MS.gene051651:CDS 40.0%
CAACAACAAGCACGTAATAG+AGG - chr1.3:5314903-5314922 MS.gene051651:CDS 40.0%
CCTCTTGATTCCAAATACCA+AGG - chr1.3:5315524-5315543 MS.gene051651:CDS 40.0%
GCACGTAATAGAGGCAATAA+TGG - chr1.3:5314912-5314931 MS.gene051651:CDS 40.0%
TTGCGAATTGTACTTGGTTG+TGG + chr1.3:5315301-5315320 None:intergenic 40.0%
! AACATTGATTGTAGTGGAGG+TGG + chr1.3:5315062-5315081 None:intergenic 40.0%
! AAGCTTGGAGGAAGATTTTC+AGG - chr1.3:5315140-5315159 MS.gene051651:CDS 40.0%
! ACATTGATTGTAGTGGAGGT+GGG + chr1.3:5315061-5315080 None:intergenic 40.0%
! CCTTGGTATTTGGAATCAAG+AGG + chr1.3:5315527-5315546 None:intergenic 40.0%
! CTTGATCATTGAAGCCTTGT+TGG + chr1.3:5315097-5315116 None:intergenic 40.0%
! GACAACATTGATTGTAGTGG+AGG + chr1.3:5315065-5315084 None:intergenic 40.0%
!!! AGTGAAGACCCTTTTTGGTT+TGG - chr1.3:5314760-5314779 MS.gene051651:CDS 40.0%
AGCAAAGGTTGCATGACATG+TGG + chr1.3:5315029-5315048 None:intergenic 45.0%
TCCAACCCATCAAATCTTGG+TGG + chr1.3:5315407-5315426 None:intergenic 45.0%
! ATTGATTGTAGTGGAGGTGG+GGG + chr1.3:5315059-5315078 None:intergenic 45.0%
! CATTGATTGTAGTGGAGGTG+GGG + chr1.3:5315060-5315079 None:intergenic 45.0%
! TCCACCAAGATTTGATGGGT+TGG - chr1.3:5315403-5315422 MS.gene051651:intron 45.0%
!! TGGTTTGGTATGAAAGCAGG+TGG - chr1.3:5314775-5314794 MS.gene051651:CDS 45.0%
!! GACTCGGTGCAAGAAGAGCA+AGG - chr1.3:5315338-5315357 MS.gene051651:intron 55.0%
!! GGTGGGGGTGTTGATAGCAA+AGG + chr1.3:5315044-5315063 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 5314424 5315550 5314424 ID=MS.gene051651
chr1.3 mRNA 5314424 5315550 5314424 ID=MS.gene051651.t1;Parent=MS.gene051651
chr1.3 exon 5315487 5315550 5315487 ID=MS.gene051651.t1.exon1;Parent=MS.gene051651.t1
chr1.3 CDS 5315487 5315550 5315487 ID=cds.MS.gene051651.t1;Parent=MS.gene051651.t1
chr1.3 exon 5314424 5315163 5314424 ID=MS.gene051651.t1.exon2;Parent=MS.gene051651.t1
chr1.3 CDS 5314424 5315163 5314424 ID=cds.MS.gene051651.t1;Parent=MS.gene051651.t1
Gene Sequence

>MS.gene051651

ATGGTGGTTTTTCCGAAGAAGAAGATAACATTATCTGCAGCCTTTACATTAGTATTGGAAGCAGGTACATATACATACTCATATACATACATATGCTTAGTTTCTTGCATAACACAATTGATCATTTGCAACTGCAATTCAAGCAGCATAGATTAAGAATCAAGATGTAATTGTAACTGTGATTTAAAACCTATGTCTTGATTTTATAGATACACTATGATTAATATTATAACCATATGCTATGCTACTTTTTGTTTAGGTGCAACCAATAGTGTTTGAATTTTTTTTAACTGTCTATATATAATAATTATTATATATAGATATATATGTATGAAAAGTGAAGACCCTTTTTGGTTTGGTATGAAAGCAGGTGGTCGATAATTGCAGCTCAATTGCCAGGAAGAACTGATAATGACATAAAGAACTATTGGAATACAAGGTTGAAAAAGAAGCTTTTGGGGAAACACCGTAAAGATCAACAACAACAAGCACGTAATAGAGGCAATAATGGTGTTATTGTTAAGCAAGAAAGCAATAATAATAGAGTGATGAGTAGTGGTGAATTTTCCTTATCAAATTTGGTTCAAGAACAACCATATTTACCACATGTCATGCAACCTTTGCTATCAACACCCCCACCTCCACTACAATCAATGTTGTCATACACAAACCAACAAGGCTTCAATGATCAAGATTCTATTAGAAAACTTCTAATGAAGCTTGGAGGAAGATTTTCAGGTGATTATCATCCTAATACTACTTTTGATGGTTTGAATCTTCAATTTTCAAATGCTACTTCTTCAACTCATGAACAAGTTTATGATCAAGAACATGTGGGTTCTTCTACTTGTGTTAATTCTTCCAATGATAACAACCACAACCAAGTACAATTCGCAACAAATGGTCAATACTTTGACTCGGTGCAAGAAGAGCAAGGTAAATTCATTCCAGAAATTGATCATATGGTATCTACTAATTATCCACCAAGATTTGATGGGTTGGAATTCTTTTATGGTGAAGAAGACTTGAATATCGATAATAATAAGATACAAGGTTCTAGTATTAATTGGGGTGAAGCTACCACTTCAAGTTATCATCATCCTCTTGATTCCAAATACCAAGGTTAA

Protein sequence

>MS.gene051651.t1

MVVFPKKKITLSAAFTLVLEAAQLPGRTDNDIKNYWNTRLKKKLLGKHRKDQQQQARNRGNNGVIVKQESNNNRVMSSGEFSLSNLVQEQPYLPHVMQPLLSTPPPPLQSMLSYTNQQGFNDQDSIRKLLMKLGGRFSGDYHPNTTFDGLNLQFSNATSSTHEQVYDQEHVGSSTCVNSSNDNNHNQVQFATNGQYFDSVQEEQGKFIPEIDHMVSTNYPPRFDGLEFFYGEEDLNIDNNKIQGSSINWGEATTSSYHHPLDSKYQG