AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0480400


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0480400 MtrunA17_Chr3g0137931 96.078 153 3 2 1 153 1 150 2.08e-106 300
Msa0480400 MtrunA17_Chr6g0477991 93.750 96 6 0 58 153 7 102 5.70e-65 193
Msa0480400 MtrunA17_Chr6g0476161 87.879 66 8 0 76 141 10 75 1.15e-38 127
Msa0480400 MtrunA17_Chr3g0138201 61.538 52 20 0 43 94 28 79 4.17e-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
Msa0480400 AT2G18660.1 37.879 132 68 5 23 151 7 127 2.05e-19 79.0
Msa0480400 AT4G30380.1 33.333 132 68 6 27 152 5 122 5.29e-11 57.0

Find 31 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTGGTACTGCTTCTTCTTA+TGG 0.173763 3_3:-85679763 Msa0480400:CDS
CAACATTGATATTTGCATTA+GGG 0.294856 3_3:+85678960 None:intergenic
TGCTCATTTGTTTGAGCAAT+AGG 0.304172 3_3:+85679800 None:intergenic
TCAACATTGATATTTGCATT+AGG 0.306005 3_3:+85678959 None:intergenic
ACTGCCACAAATATATTTCC+TGG 0.404012 3_3:+85679178 None:intergenic
CTACAGCTTGTGATGGGAAT+AGG 0.406360 3_3:-85679216 Msa0480400:CDS
TGGGTGTACTCACGTATATA+TGG 0.432788 3_3:+85679736 None:intergenic
AATGAAGGGTTGTGGGATAA+TGG 0.441192 3_3:-85679154 Msa0480400:CDS
AGCATTATTCTTGCAGATGT+TGG 0.481138 3_3:-85679781 Msa0480400:CDS
TGGCAGTGAATGAAGGGTTG+TGG 0.485625 3_3:-85679162 Msa0480400:CDS
ATATTTGTGGCAGTGAATGA+AGG 0.490865 3_3:-85679169 Msa0480400:CDS
TACAGAGTAAGGTGTGTAAG+TGG 0.500626 3_3:-85679112 Msa0480400:CDS
GGCAGTGAATGAAGGGTTGT+GGG 0.502397 3_3:-85679161 Msa0480400:CDS
ATCAATAAGCCATGCAAAGG+TGG 0.523686 3_3:-85679088 Msa0480400:CDS
TCCACCAGGAAATATATTTG+TGG 0.549161 3_3:-85679182 Msa0480400:CDS
AGTTGACATGTGGAAAGTGT+GGG 0.573051 3_3:+85679009 None:intergenic
CAGTTGACATGTGGAAAGTG+TGG 0.576339 3_3:+85679008 None:intergenic
ATACTACTACCACCTTTGCA+TGG 0.578652 3_3:+85679079 None:intergenic
GTGGAAGGAGATACAGAGTA+AGG 0.582766 3_3:-85679123 Msa0480400:CDS
TGGGATAATGGTGCAGCATG+TGG 0.603337 3_3:-85679142 Msa0480400:CDS
GGAATCAATAAGCCATGCAA+AGG 0.623535 3_3:-85679091 Msa0480400:CDS
TATTTGTGGCAGTGAATGAA+GGG 0.626127 3_3:-85679168 Msa0480400:CDS
TGTGCAGCTACAGCTTGTGA+TGG 0.627923 3_3:-85679223 Msa0480400:intron
GTGCAGCTACAGCTTGTGAT+GGG 0.628864 3_3:-85679222 Msa0480400:intron
GCCACAAATATATTTCCTGG+TGG 0.638508 3_3:+85679181 None:intergenic
CAAATGCTTCAGTTGACATG+TGG 0.644023 3_3:+85678999 None:intergenic
ATAATGGTGCAGCATGTGGA+AGG 0.648736 3_3:-85679138 Msa0480400:CDS
AGGAGACAACAGTTTCCACC+AGG 0.667613 3_3:-85679196 Msa0480400:CDS
GTGTACTCACGTATATATGG+AGG 0.706847 3_3:+85679739 None:intergenic
TTGACATGTGGAAAGTGTGG+GGG 0.720155 3_3:+85679011 None:intergenic
GTTGACATGTGGAAAGTGTG+GGG 0.728941 3_3:+85679010 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAATATTGAATGAATAAA+TGG + chr3_3:85679131-85679150 None:intergenic 15.0%
!! AGAAATATTGAATGAATAAA+TGG + chr3_3:85679131-85679150 None:intergenic 15.0%
!!! AACTATAATTTTTTGCTTGA+TGG + chr3_3:85678954-85678973 None:intergenic 20.0%
!! ATATTGAATGAATAAATGGT+GGG + chr3_3:85679127-85679146 None:intergenic 20.0%
!! AATATTGAATGAATAAATGG+TGG + chr3_3:85679128-85679147 None:intergenic 20.0%
!! ATTTAACGTGGAAAAAAAAT+TGG + chr3_3:85679189-85679208 None:intergenic 20.0%
!!! GTTCCAAACATTTTAAAAAT+GGG + chr3_3:85679441-85679460 None:intergenic 20.0%
!! ATTAATATGTGAAATTTGTG+TGG + chr3_3:85679463-85679482 None:intergenic 20.0%
!!! AACTATAATTTTTTGCTTGA+TGG + chr3_3:85678954-85678973 None:intergenic 20.0%
!! ATATTGAATGAATAAATGGT+GGG + chr3_3:85679127-85679146 None:intergenic 20.0%
!! AATATTGAATGAATAAATGG+TGG + chr3_3:85679128-85679147 None:intergenic 20.0%
!! ATTTAACGTGGAAAAAAAAT+TGG + chr3_3:85679189-85679208 None:intergenic 20.0%
!!! GTTCCAAACATTTTAAAAAT+GGG + chr3_3:85679441-85679460 None:intergenic 20.0%
!! ATTAATATGTGAAATTTGTG+TGG + chr3_3:85679463-85679482 None:intergenic 20.0%
! TAGCTCAAAAACAAATAATG+AGG - chr3_3:85678989-85679008 Msa0480400:CDS 25.0%
! ATGATATATCATGTATACGT+AGG + chr3_3:85679158-85679177 None:intergenic 25.0%
! AGTGTTAAACTAAATGTTGA+TGG + chr3_3:85679373-85679392 None:intergenic 25.0%
!!! AGTCCCATTTTTAAAATGTT+TGG - chr3_3:85679435-85679454 Msa0480400:intron 25.0%
!!! GGTTCCAAACATTTTAAAAA+TGG + chr3_3:85679442-85679461 None:intergenic 25.0%
! CAACATTGATATTTGCATTA+GGG + chr3_3:85679884-85679903 None:intergenic 25.0%
! TCAACATTGATATTTGCATT+AGG + chr3_3:85679885-85679904 None:intergenic 25.0%
! TAGCTCAAAAACAAATAATG+AGG - chr3_3:85678989-85679008 Msa0480400:CDS 25.0%
! ATGATATATCATGTATACGT+AGG + chr3_3:85679158-85679177 None:intergenic 25.0%
! AGTGTTAAACTAAATGTTGA+TGG + chr3_3:85679373-85679392 None:intergenic 25.0%
!!! AGTCCCATTTTTAAAATGTT+TGG - chr3_3:85679435-85679454 Msa0480400:intron 25.0%
!!! GGTTCCAAACATTTTAAAAA+TGG + chr3_3:85679442-85679461 None:intergenic 25.0%
! CAACATTGATATTTGCATTA+GGG + chr3_3:85679884-85679903 None:intergenic 25.0%
! TCAACATTGATATTTGCATT+AGG + chr3_3:85679885-85679904 None:intergenic 25.0%
!! AAAGAGATTAGTCTCCTATA+AGG + chr3_3:85679243-85679262 None:intergenic 30.0%
AACCAATCGGTATCATTATA+GGG + chr3_3:85679272-85679291 None:intergenic 30.0%
!! AAAGAGATTAGTCTCCTATA+AGG + chr3_3:85679243-85679262 None:intergenic 30.0%
AACCAATCGGTATCATTATA+GGG + chr3_3:85679272-85679291 None:intergenic 30.0%
TGCTCATTTGTTTGAGCAAT+AGG + chr3_3:85679044-85679063 None:intergenic 35.0%
AGCATTATTCTTGCAGATGT+TGG - chr3_3:85679060-85679079 Msa0480400:CDS 35.0%
!! AGAGGTGTTGATATTTAACG+TGG + chr3_3:85679201-85679220 None:intergenic 35.0%
AGTTTAGTGCATCACCTTAT+AGG - chr3_3:85679226-85679245 Msa0480400:intron 35.0%
ACCAATCGGTATCATTATAG+GGG + chr3_3:85679271-85679290 None:intergenic 35.0%
CAACCAATCGGTATCATTAT+AGG + chr3_3:85679273-85679292 None:intergenic 35.0%
! CTATAATGATACCGATTGGT+TGG - chr3_3:85679271-85679290 Msa0480400:intron 35.0%
TCCACCAGGAAATATATTTG+TGG - chr3_3:85679659-85679678 Msa0480400:intron 35.0%
ACTGCCACAAATATATTTCC+TGG + chr3_3:85679666-85679685 None:intergenic 35.0%
ATATTTGTGGCAGTGAATGA+AGG - chr3_3:85679672-85679691 Msa0480400:intron 35.0%
TATTTGTGGCAGTGAATGAA+GGG - chr3_3:85679673-85679692 Msa0480400:intron 35.0%
TGCTCATTTGTTTGAGCAAT+AGG + chr3_3:85679044-85679063 None:intergenic 35.0%
AGCATTATTCTTGCAGATGT+TGG - chr3_3:85679060-85679079 Msa0480400:CDS 35.0%
!! AGAGGTGTTGATATTTAACG+TGG + chr3_3:85679201-85679220 None:intergenic 35.0%
AGTTTAGTGCATCACCTTAT+AGG - chr3_3:85679226-85679245 Msa0480400:intron 35.0%
ACCAATCGGTATCATTATAG+GGG + chr3_3:85679271-85679290 None:intergenic 35.0%
CAACCAATCGGTATCATTAT+AGG + chr3_3:85679273-85679292 None:intergenic 35.0%
! CTATAATGATACCGATTGGT+TGG - chr3_3:85679271-85679290 Msa0480400:intron 35.0%
TCCACCAGGAAATATATTTG+TGG - chr3_3:85679659-85679678 Msa0480400:intron 35.0%
ACTGCCACAAATATATTTCC+TGG + chr3_3:85679666-85679685 None:intergenic 35.0%
ATATTTGTGGCAGTGAATGA+AGG - chr3_3:85679672-85679691 Msa0480400:intron 35.0%
TATTTGTGGCAGTGAATGAA+GGG - chr3_3:85679673-85679692 Msa0480400:intron 35.0%
GTTGGTACTGCTTCTTCTTA+TGG - chr3_3:85679078-85679097 Msa0480400:CDS 40.0%
GTGTACTCACGTATATATGG+AGG + chr3_3:85679105-85679124 None:intergenic 40.0%
TGGGTGTACTCACGTATATA+TGG + chr3_3:85679108-85679127 None:intergenic 40.0%
GATGCACTAAACTACAAGAG+AGG + chr3_3:85679219-85679238 None:intergenic 40.0%
ACCCCTATAATGATACCGAT+TGG - chr3_3:85679267-85679286 Msa0480400:intron 40.0%
! TAATGATACCGATTGGTTGG+AGG - chr3_3:85679274-85679293 Msa0480400:intron 40.0%
! TTTTACCACCTCCAACCAAT+CGG + chr3_3:85679285-85679304 None:intergenic 40.0%
GCCACAAATATATTTCCTGG+TGG + chr3_3:85679663-85679682 None:intergenic 40.0%
AATGAAGGGTTGTGGGATAA+TGG - chr3_3:85679687-85679706 Msa0480400:intron 40.0%
TACAGAGTAAGGTGTGTAAG+TGG - chr3_3:85679729-85679748 Msa0480400:intron 40.0%
GGAATCAATAAGCCATGCAA+AGG - chr3_3:85679750-85679769 Msa0480400:CDS 40.0%
ATCAATAAGCCATGCAAAGG+TGG - chr3_3:85679753-85679772 Msa0480400:CDS 40.0%
ATACTACTACCACCTTTGCA+TGG + chr3_3:85679765-85679784 None:intergenic 40.0%
! AGTTGACATGTGGAAAGTGT+GGG + chr3_3:85679835-85679854 None:intergenic 40.0%
CAAATGCTTCAGTTGACATG+TGG + chr3_3:85679845-85679864 None:intergenic 40.0%
GTTGGTACTGCTTCTTCTTA+TGG - chr3_3:85679078-85679097 Msa0480400:CDS 40.0%
GTGTACTCACGTATATATGG+AGG + chr3_3:85679105-85679124 None:intergenic 40.0%
TGGGTGTACTCACGTATATA+TGG + chr3_3:85679108-85679127 None:intergenic 40.0%
GATGCACTAAACTACAAGAG+AGG + chr3_3:85679219-85679238 None:intergenic 40.0%
ACCCCTATAATGATACCGAT+TGG - chr3_3:85679267-85679286 Msa0480400:intron 40.0%
! TAATGATACCGATTGGTTGG+AGG - chr3_3:85679274-85679293 Msa0480400:intron 40.0%
! TTTTACCACCTCCAACCAAT+CGG + chr3_3:85679285-85679304 None:intergenic 40.0%
GCCACAAATATATTTCCTGG+TGG + chr3_3:85679663-85679682 None:intergenic 40.0%
AATGAAGGGTTGTGGGATAA+TGG - chr3_3:85679687-85679706 Msa0480400:intron 40.0%
TACAGAGTAAGGTGTGTAAG+TGG - chr3_3:85679729-85679748 Msa0480400:intron 40.0%
GGAATCAATAAGCCATGCAA+AGG - chr3_3:85679750-85679769 Msa0480400:CDS 40.0%
ATCAATAAGCCATGCAAAGG+TGG - chr3_3:85679753-85679772 Msa0480400:CDS 40.0%
ATACTACTACCACCTTTGCA+TGG + chr3_3:85679765-85679784 None:intergenic 40.0%
! AGTTGACATGTGGAAAGTGT+GGG + chr3_3:85679835-85679854 None:intergenic 40.0%
CAAATGCTTCAGTTGACATG+TGG + chr3_3:85679845-85679864 None:intergenic 40.0%
! CTACAGCTTGTGATGGGAAT+AGG - chr3_3:85679625-85679644 Msa0480400:intron 45.0%
ATAATGGTGCAGCATGTGGA+AGG - chr3_3:85679703-85679722 Msa0480400:intron 45.0%
GTGGAAGGAGATACAGAGTA+AGG - chr3_3:85679718-85679737 Msa0480400:intron 45.0%
! TTGACATGTGGAAAGTGTGG+GGG + chr3_3:85679833-85679852 None:intergenic 45.0%
! GTTGACATGTGGAAAGTGTG+GGG + chr3_3:85679834-85679853 None:intergenic 45.0%
CAGTTGACATGTGGAAAGTG+TGG + chr3_3:85679836-85679855 None:intergenic 45.0%
! CTACAGCTTGTGATGGGAAT+AGG - chr3_3:85679625-85679644 Msa0480400:intron 45.0%
ATAATGGTGCAGCATGTGGA+AGG - chr3_3:85679703-85679722 Msa0480400:intron 45.0%
GTGGAAGGAGATACAGAGTA+AGG - chr3_3:85679718-85679737 Msa0480400:intron 45.0%
! TTGACATGTGGAAAGTGTGG+GGG + chr3_3:85679833-85679852 None:intergenic 45.0%
! GTTGACATGTGGAAAGTGTG+GGG + chr3_3:85679834-85679853 None:intergenic 45.0%
CAGTTGACATGTGGAAAGTG+TGG + chr3_3:85679836-85679855 None:intergenic 45.0%
! TGATACCGATTGGTTGGAGG+TGG - chr3_3:85679277-85679296 Msa0480400:intron 50.0%
TGTGCAGCTACAGCTTGTGA+TGG - chr3_3:85679618-85679637 Msa0480400:intron 50.0%
GTGCAGCTACAGCTTGTGAT+GGG - chr3_3:85679619-85679638 Msa0480400:intron 50.0%
AGGAGACAACAGTTTCCACC+AGG - chr3_3:85679645-85679664 Msa0480400:intron 50.0%
TGGCAGTGAATGAAGGGTTG+TGG - chr3_3:85679679-85679698 Msa0480400:intron 50.0%
GGCAGTGAATGAAGGGTTGT+GGG - chr3_3:85679680-85679699 Msa0480400:intron 50.0%
! TGGGATAATGGTGCAGCATG+TGG - chr3_3:85679699-85679718 Msa0480400:intron 50.0%
! TGATACCGATTGGTTGGAGG+TGG - chr3_3:85679277-85679296 Msa0480400:intron 50.0%
TGTGCAGCTACAGCTTGTGA+TGG - chr3_3:85679618-85679637 Msa0480400:intron 50.0%
GTGCAGCTACAGCTTGTGAT+GGG - chr3_3:85679619-85679638 Msa0480400:intron 50.0%
AGGAGACAACAGTTTCCACC+AGG - chr3_3:85679645-85679664 Msa0480400:intron 50.0%
TGGCAGTGAATGAAGGGTTG+TGG - chr3_3:85679679-85679698 Msa0480400:intron 50.0%
GGCAGTGAATGAAGGGTTGT+GGG - chr3_3:85679680-85679699 Msa0480400:intron 50.0%
! TGGGATAATGGTGCAGCATG+TGG - chr3_3:85679699-85679718 Msa0480400:intron 50.0%
! GTGGAAAGTGTGGGGGCATG+AGG + chr3_3:85679826-85679845 None:intergenic 60.0%
! GTGGAAAGTGTGGGGGCATG+AGG + chr3_3:85679826-85679845 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 85678946 85679917 85678946 ID=Msa0480400;Name=Msa0480400
chr3_3 mRNA 85678946 85679917 85678946 ID=Msa0480400-mRNA-1;Parent=Msa0480400;Name=Msa0480400-mRNA-1;_AED=0.00;_eAED=0.01;_QI=0|0|0|1|1|1|2|0|153
chr3_3 exon 85679749 85679917 85679749 ID=Msa0480400-mRNA-1:exon:24679;Parent=Msa0480400-mRNA-1
chr3_3 exon 85678946 85679238 85678946 ID=Msa0480400-mRNA-1:exon:24678;Parent=Msa0480400-mRNA-1
chr3_3 CDS 85679749 85679917 85679749 ID=Msa0480400-mRNA-1:cds;Parent=Msa0480400-mRNA-1
chr3_3 CDS 85678946 85679238 85678946 ID=Msa0480400-mRNA-1:cds;Parent=Msa0480400-mRNA-1
Gene Sequence

>Msa0480400

ATGTACCATCAAGCAAAAAATTATAGTTTGCGTATATCAATCATAGCTCAAAAACAAATAATGAGGTCATTTATGCTTGTTGTAATAATTTCAAGCCTATTGCTCAAACAAATGAGCATTATTCTTGCAGATGTTGGTACTGCTTCTTCTTATGGTCCTCCATATATACCTACAGCTTGTGATGGGAATAGGAGACAACAGTTTCCACCAGGAAATATATTTGTGGCAGTGAATGAAGGGTTGTGGGATAATGGTGCAGCATGTGGAAGGAGATACAGAGTAAGGTGTGTAAGTGGAATCAATAAGCCATGCAAAGGTGGTAGTAGTATTGATGTTAAAGTTGTTGATTCTATTACTTGTACAAGATCCTCATGCCCCCACACTTTCCACATGTCAACTGAAGCATTTGCAGCTATCTCACGCTTCCCTAATGCAAATATCAATGTTGAATACATTCAGTAA

Protein sequence

>Msa0480400

MYHQAKNYSLRISIIAQKQIMRSFMLVVIISSLLLKQMSIILADVGTASSYGPPYIPTACDGNRRQQFPPGNIFVAVNEGLWDNGAACGRRYRVRCVSGINKPCKGGSSIDVKVVDSITCTRSSCPHTFHMSTEAFAAISRFPNANINVEYIQ*