AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0524930


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0524930 MtrunA17_Chr3g0137931 96.732 153 2 2 1 153 1 150 3.36e-107 301
Msa0524930 MtrunA17_Chr6g0477991 93.750 96 6 0 58 153 7 102 5.64e-65 193
Msa0524930 MtrunA17_Chr6g0476161 87.879 66 8 0 76 141 10 75 1.65e-38 127
Msa0524930 MtrunA17_Chr3g0138201 61.538 52 20 0 43 94 28 79 4.12e-19 76.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0524930 AT2G18660.1 37.879 132 68 5 23 151 7 127 1.78e-19 79.3
Msa0524930 AT4G30380.1 33.333 132 68 6 27 152 5 122 4.97e-11 57.0

Find 31 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTGGTACTGCTTCTTCTTA+TGG 0.173763 3_4:-78483622 Msa0524930:CDS
CAACATTGATATTTGCATTA+GGG 0.294856 3_4:+78482824 None:intergenic
TGCTCATTTGTTTGAGCAAT+AGG 0.304172 3_4:+78483659 None:intergenic
TCAACATTGATATTTGCATT+AGG 0.306005 3_4:+78482823 None:intergenic
ACTGCCACAAATATATTTCC+TGG 0.404012 3_4:+78483042 None:intergenic
CTACAGCTTGTGATGGGAAT+AGG 0.406360 3_4:-78483080 Msa0524930:CDS
TGGGTGTACTCACGTATATA+TGG 0.432788 3_4:+78483595 None:intergenic
AATGAAGGGTTGTGGGATAA+TGG 0.441192 3_4:-78483018 Msa0524930:CDS
AGCATTATTCTTGCAGATGT+TGG 0.481138 3_4:-78483640 Msa0524930:CDS
TGGCAGTGAATGAAGGGTTG+TGG 0.485625 3_4:-78483026 Msa0524930:CDS
ATATTTGTGGCAGTGAATGA+AGG 0.490865 3_4:-78483033 Msa0524930:CDS
TACAGAGTAAGGTGTGTAAG+TGG 0.500626 3_4:-78482976 Msa0524930:CDS
GGCAGTGAATGAAGGGTTGT+GGG 0.502397 3_4:-78483025 Msa0524930:CDS
ATCAATAAGCCATGCAAAGG+TGG 0.523686 3_4:-78482952 Msa0524930:CDS
TCCACCAGGAAATATATTTG+TGG 0.549161 3_4:-78483046 Msa0524930:CDS
AGTTGACATGTGGAAAGTGT+GGG 0.573051 3_4:+78482873 None:intergenic
CAGTTGACATGTGGAAAGTG+TGG 0.576339 3_4:+78482872 None:intergenic
ATACTACTACCACCTTTGCA+TGG 0.578652 3_4:+78482943 None:intergenic
GTGGAAGGAGATACAGAGTA+AGG 0.582766 3_4:-78482987 Msa0524930:CDS
TGGGATAATGGTGCAGCATG+TGG 0.603337 3_4:-78483006 Msa0524930:CDS
GGAATCAATAAGCCATGCAA+AGG 0.623535 3_4:-78482955 Msa0524930:CDS
TATTTGTGGCAGTGAATGAA+GGG 0.626127 3_4:-78483032 Msa0524930:CDS
TGTGCAGCTACAGCTTGTGA+TGG 0.627923 3_4:-78483087 Msa0524930:intron
GTGCAGCTACAGCTTGTGAT+GGG 0.628864 3_4:-78483086 Msa0524930:intron
GCCACAAATATATTTCCTGG+TGG 0.638508 3_4:+78483045 None:intergenic
CAAATGCTTCAGTTGACATG+TGG 0.644023 3_4:+78482863 None:intergenic
ATAATGGTGCAGCATGTGGA+AGG 0.648736 3_4:-78483002 Msa0524930:CDS
AGGAGACAACAGTTTCCACC+AGG 0.667613 3_4:-78483060 Msa0524930:CDS
GTGTACTCACGTATATATGG+AGG 0.706847 3_4:+78483598 None:intergenic
TTGACATGTGGAAAGTGTGG+GGG 0.720155 3_4:+78482875 None:intergenic
GTTGACATGTGGAAAGTGTG+GGG 0.728941 3_4:+78482874 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAATATTGAATGAATAAA+TGG + chr3_4:78482995-78483014 None:intergenic 15.0%
!! AGAAATATTGAATGAATAAA+TGG + chr3_4:78482995-78483014 None:intergenic 15.0%
!! ATATTGAATGAATAAATGGT+GGG + chr3_4:78482991-78483010 None:intergenic 20.0%
!! AATATTGAATGAATAAATGG+TGG + chr3_4:78482992-78483011 None:intergenic 20.0%
!!! GTTCCAAACATTTTAAAAAT+GGG + chr3_4:78483305-78483324 None:intergenic 20.0%
!! ATTAATATGTGAAATTTGTG+TGG + chr3_4:78483327-78483346 None:intergenic 20.0%
!! ATATTGAATGAATAAATGGT+GGG + chr3_4:78482991-78483010 None:intergenic 20.0%
!! AATATTGAATGAATAAATGG+TGG + chr3_4:78482992-78483011 None:intergenic 20.0%
!!! GTTCCAAACATTTTAAAAAT+GGG + chr3_4:78483305-78483324 None:intergenic 20.0%
!! ATTAATATGTGAAATTTGTG+TGG + chr3_4:78483327-78483346 None:intergenic 20.0%
!!! AACTATGATTTTTTGCTTGA+TGG + chr3_4:78482818-78482837 None:intergenic 25.0%
! TAGCTCAAAAACAAATAATG+AGG - chr3_4:78482853-78482872 Msa0524930:CDS 25.0%
! ATGATATATCATGTATACGT+AGG + chr3_4:78483022-78483041 None:intergenic 25.0%
! AGTGTTAAACTAAATGTTGA+TGG + chr3_4:78483237-78483256 None:intergenic 25.0%
!!! AGTCCCATTTTTAAAATGTT+TGG - chr3_4:78483299-78483318 Msa0524930:intron 25.0%
!!! GGTTCCAAACATTTTAAAAA+TGG + chr3_4:78483306-78483325 None:intergenic 25.0%
! CAACATTGATATTTGCATTA+GGG + chr3_4:78483743-78483762 None:intergenic 25.0%
! TCAACATTGATATTTGCATT+AGG + chr3_4:78483744-78483763 None:intergenic 25.0%
!!! AACTATGATTTTTTGCTTGA+TGG + chr3_4:78482818-78482837 None:intergenic 25.0%
! TAGCTCAAAAACAAATAATG+AGG - chr3_4:78482853-78482872 Msa0524930:CDS 25.0%
! ATGATATATCATGTATACGT+AGG + chr3_4:78483022-78483041 None:intergenic 25.0%
! AGTGTTAAACTAAATGTTGA+TGG + chr3_4:78483237-78483256 None:intergenic 25.0%
!!! AGTCCCATTTTTAAAATGTT+TGG - chr3_4:78483299-78483318 Msa0524930:intron 25.0%
!!! GGTTCCAAACATTTTAAAAA+TGG + chr3_4:78483306-78483325 None:intergenic 25.0%
! CAACATTGATATTTGCATTA+GGG + chr3_4:78483743-78483762 None:intergenic 25.0%
! TCAACATTGATATTTGCATT+AGG + chr3_4:78483744-78483763 None:intergenic 25.0%
!! AAAGAGATTAGTCTCCTATA+AGG + chr3_4:78483107-78483126 None:intergenic 30.0%
!! AAAGAGATTAGTCTCCTATA+AGG + chr3_4:78483107-78483126 None:intergenic 30.0%
TGCTCATTTGTTTGAGCAAT+AGG + chr3_4:78482908-78482927 None:intergenic 35.0%
AGCATTATTCTTGCAGATGT+TGG - chr3_4:78482924-78482943 Msa0524930:CDS 35.0%
!! AGAGGTGTTGATATTTAACG+TGG + chr3_4:78483065-78483084 None:intergenic 35.0%
AGTTTAGTGCATCACCTTAT+AGG - chr3_4:78483090-78483109 Msa0524930:intron 35.0%
AACCAATCGGTATCATTGTA+GGG + chr3_4:78483136-78483155 None:intergenic 35.0%
TCCACCAGGAAATATATTTG+TGG - chr3_4:78483518-78483537 Msa0524930:intron 35.0%
ACTGCCACAAATATATTTCC+TGG + chr3_4:78483525-78483544 None:intergenic 35.0%
ATATTTGTGGCAGTGAATGA+AGG - chr3_4:78483531-78483550 Msa0524930:intron 35.0%
TATTTGTGGCAGTGAATGAA+GGG - chr3_4:78483532-78483551 Msa0524930:intron 35.0%
TGCTCATTTGTTTGAGCAAT+AGG + chr3_4:78482908-78482927 None:intergenic 35.0%
AGCATTATTCTTGCAGATGT+TGG - chr3_4:78482924-78482943 Msa0524930:CDS 35.0%
!! AGAGGTGTTGATATTTAACG+TGG + chr3_4:78483065-78483084 None:intergenic 35.0%
AGTTTAGTGCATCACCTTAT+AGG - chr3_4:78483090-78483109 Msa0524930:intron 35.0%
AACCAATCGGTATCATTGTA+GGG + chr3_4:78483136-78483155 None:intergenic 35.0%
TCCACCAGGAAATATATTTG+TGG - chr3_4:78483518-78483537 Msa0524930:intron 35.0%
ACTGCCACAAATATATTTCC+TGG + chr3_4:78483525-78483544 None:intergenic 35.0%
ATATTTGTGGCAGTGAATGA+AGG - chr3_4:78483531-78483550 Msa0524930:intron 35.0%
TATTTGTGGCAGTGAATGAA+GGG - chr3_4:78483532-78483551 Msa0524930:intron 35.0%
GTTGGTACTGCTTCTTCTTA+TGG - chr3_4:78482942-78482961 Msa0524930:CDS 40.0%
GTGTACTCACGTATATATGG+AGG + chr3_4:78482969-78482988 None:intergenic 40.0%
TGGGTGTACTCACGTATATA+TGG + chr3_4:78482972-78482991 None:intergenic 40.0%
GATGCACTAAACTACAAGAG+AGG + chr3_4:78483083-78483102 None:intergenic 40.0%
ACCAATCGGTATCATTGTAG+GGG + chr3_4:78483135-78483154 None:intergenic 40.0%
CAACCAATCGGTATCATTGT+AGG + chr3_4:78483137-78483156 None:intergenic 40.0%
! CTACAATGATACCGATTGGT+TGG - chr3_4:78483135-78483154 Msa0524930:intron 40.0%
! TTTTACCACCTCCAACCAAT+CGG + chr3_4:78483149-78483168 None:intergenic 40.0%
GCCACAAATATATTTCCTGG+TGG + chr3_4:78483522-78483541 None:intergenic 40.0%
AATGAAGGGTTGTGGGATAA+TGG - chr3_4:78483546-78483565 Msa0524930:intron 40.0%
TACAGAGTAAGGTGTGTAAG+TGG - chr3_4:78483588-78483607 Msa0524930:intron 40.0%
GGAATCAATAAGCCATGCAA+AGG - chr3_4:78483609-78483628 Msa0524930:CDS 40.0%
ATCAATAAGCCATGCAAAGG+TGG - chr3_4:78483612-78483631 Msa0524930:CDS 40.0%
ATACTACTACCACCTTTGCA+TGG + chr3_4:78483624-78483643 None:intergenic 40.0%
! AGTTGACATGTGGAAAGTGT+GGG + chr3_4:78483694-78483713 None:intergenic 40.0%
CAAATGCTTCAGTTGACATG+TGG + chr3_4:78483704-78483723 None:intergenic 40.0%
GTTGGTACTGCTTCTTCTTA+TGG - chr3_4:78482942-78482961 Msa0524930:CDS 40.0%
GTGTACTCACGTATATATGG+AGG + chr3_4:78482969-78482988 None:intergenic 40.0%
TGGGTGTACTCACGTATATA+TGG + chr3_4:78482972-78482991 None:intergenic 40.0%
GATGCACTAAACTACAAGAG+AGG + chr3_4:78483083-78483102 None:intergenic 40.0%
ACCAATCGGTATCATTGTAG+GGG + chr3_4:78483135-78483154 None:intergenic 40.0%
CAACCAATCGGTATCATTGT+AGG + chr3_4:78483137-78483156 None:intergenic 40.0%
! CTACAATGATACCGATTGGT+TGG - chr3_4:78483135-78483154 Msa0524930:intron 40.0%
! TTTTACCACCTCCAACCAAT+CGG + chr3_4:78483149-78483168 None:intergenic 40.0%
GCCACAAATATATTTCCTGG+TGG + chr3_4:78483522-78483541 None:intergenic 40.0%
AATGAAGGGTTGTGGGATAA+TGG - chr3_4:78483546-78483565 Msa0524930:intron 40.0%
TACAGAGTAAGGTGTGTAAG+TGG - chr3_4:78483588-78483607 Msa0524930:intron 40.0%
GGAATCAATAAGCCATGCAA+AGG - chr3_4:78483609-78483628 Msa0524930:CDS 40.0%
ATCAATAAGCCATGCAAAGG+TGG - chr3_4:78483612-78483631 Msa0524930:CDS 40.0%
ATACTACTACCACCTTTGCA+TGG + chr3_4:78483624-78483643 None:intergenic 40.0%
! AGTTGACATGTGGAAAGTGT+GGG + chr3_4:78483694-78483713 None:intergenic 40.0%
CAAATGCTTCAGTTGACATG+TGG + chr3_4:78483704-78483723 None:intergenic 40.0%
ACCCCTACAATGATACCGAT+TGG - chr3_4:78483131-78483150 Msa0524930:intron 45.0%
! CAATGATACCGATTGGTTGG+AGG - chr3_4:78483138-78483157 Msa0524930:intron 45.0%
! CTACAGCTTGTGATGGGAAT+AGG - chr3_4:78483484-78483503 Msa0524930:intron 45.0%
ATAATGGTGCAGCATGTGGA+AGG - chr3_4:78483562-78483581 Msa0524930:intron 45.0%
GTGGAAGGAGATACAGAGTA+AGG - chr3_4:78483577-78483596 Msa0524930:intron 45.0%
! TTGACATGTGGAAAGTGTGG+GGG + chr3_4:78483692-78483711 None:intergenic 45.0%
! GTTGACATGTGGAAAGTGTG+GGG + chr3_4:78483693-78483712 None:intergenic 45.0%
CAGTTGACATGTGGAAAGTG+TGG + chr3_4:78483695-78483714 None:intergenic 45.0%
ACCCCTACAATGATACCGAT+TGG - chr3_4:78483131-78483150 Msa0524930:intron 45.0%
! CAATGATACCGATTGGTTGG+AGG - chr3_4:78483138-78483157 Msa0524930:intron 45.0%
! CTACAGCTTGTGATGGGAAT+AGG - chr3_4:78483484-78483503 Msa0524930:intron 45.0%
ATAATGGTGCAGCATGTGGA+AGG - chr3_4:78483562-78483581 Msa0524930:intron 45.0%
GTGGAAGGAGATACAGAGTA+AGG - chr3_4:78483577-78483596 Msa0524930:intron 45.0%
! TTGACATGTGGAAAGTGTGG+GGG + chr3_4:78483692-78483711 None:intergenic 45.0%
! GTTGACATGTGGAAAGTGTG+GGG + chr3_4:78483693-78483712 None:intergenic 45.0%
CAGTTGACATGTGGAAAGTG+TGG + chr3_4:78483695-78483714 None:intergenic 45.0%
! TGATACCGATTGGTTGGAGG+TGG - chr3_4:78483141-78483160 Msa0524930:intron 50.0%
TGTGCAGCTACAGCTTGTGA+TGG - chr3_4:78483477-78483496 Msa0524930:intron 50.0%
GTGCAGCTACAGCTTGTGAT+GGG - chr3_4:78483478-78483497 Msa0524930:intron 50.0%
AGGAGACAACAGTTTCCACC+AGG - chr3_4:78483504-78483523 Msa0524930:intron 50.0%
TGGCAGTGAATGAAGGGTTG+TGG - chr3_4:78483538-78483557 Msa0524930:intron 50.0%
GGCAGTGAATGAAGGGTTGT+GGG - chr3_4:78483539-78483558 Msa0524930:intron 50.0%
! TGGGATAATGGTGCAGCATG+TGG - chr3_4:78483558-78483577 Msa0524930:intron 50.0%
! TGATACCGATTGGTTGGAGG+TGG - chr3_4:78483141-78483160 Msa0524930:intron 50.0%
TGTGCAGCTACAGCTTGTGA+TGG - chr3_4:78483477-78483496 Msa0524930:intron 50.0%
GTGCAGCTACAGCTTGTGAT+GGG - chr3_4:78483478-78483497 Msa0524930:intron 50.0%
AGGAGACAACAGTTTCCACC+AGG - chr3_4:78483504-78483523 Msa0524930:intron 50.0%
TGGCAGTGAATGAAGGGTTG+TGG - chr3_4:78483538-78483557 Msa0524930:intron 50.0%
GGCAGTGAATGAAGGGTTGT+GGG - chr3_4:78483539-78483558 Msa0524930:intron 50.0%
! TGGGATAATGGTGCAGCATG+TGG - chr3_4:78483558-78483577 Msa0524930:intron 50.0%
! GTGGAAAGTGTGGGGGCATG+AGG + chr3_4:78483685-78483704 None:intergenic 60.0%
! GTGGAAAGTGTGGGGGCATG+AGG + chr3_4:78483685-78483704 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 78482810 78483776 78482810 ID=Msa0524930;Name=Msa0524930
chr3_4 mRNA 78482810 78483776 78482810 ID=Msa0524930-mRNA-1;Parent=Msa0524930;Name=Msa0524930-mRNA-1;_AED=0.00;_eAED=0.01;_QI=0|0|0|1|1|1|2|0|153
chr3_4 exon 78483608 78483776 78483608 ID=Msa0524930-mRNA-1:exon:23261;Parent=Msa0524930-mRNA-1
chr3_4 exon 78482810 78483102 78482810 ID=Msa0524930-mRNA-1:exon:23260;Parent=Msa0524930-mRNA-1
chr3_4 CDS 78483608 78483776 78483608 ID=Msa0524930-mRNA-1:cds;Parent=Msa0524930-mRNA-1
chr3_4 CDS 78482810 78483102 78482810 ID=Msa0524930-mRNA-1:cds;Parent=Msa0524930-mRNA-1
Gene Sequence

>Msa0524930

ATGTACCATCAAGCAAAAAATCATAGTTTGCGTATATCAATCATAGCTCAAAAACAAATAATGAGGTCATTTATGCTTGTTGTAATAATTTCAAGCCTATTGCTCAAACAAATGAGCATTATTCTTGCAGATGTTGGTACTGCTTCTTCTTATGGTCCTCCATATATACCTACAGCTTGTGATGGGAATAGGAGACAACAGTTTCCACCAGGAAATATATTTGTGGCAGTGAATGAAGGGTTGTGGGATAATGGTGCAGCATGTGGAAGGAGATACAGAGTAAGGTGTGTAAGTGGAATCAATAAGCCATGCAAAGGTGGTAGTAGTATTGATGTTAAAGTTGTTGATTCTATTACTTGTACAAGATCCTCATGCCCCCACACTTTCCACATGTCAACTGAAGCATTTGCAGCTATCTCACGCTTCCCTAATGCAAATATCAATGTTGAATACATTCAGTAA

Protein sequence

>Msa0524930

MYHQAKNHSLRISIIAQKQIMRSFMLVVIISSLLLKQMSIILADVGTASSYGPPYIPTACDGNRRQQFPPGNIFVAVNEGLWDNGAACGRRYRVRCVSGINKPCKGGSSIDVKVVDSITCTRSSCPHTFHMSTEAFAAISRFPNANINVEYIQ*