AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0278290


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0278290 MtrunA17_Chr1g0175161 97.059 136 4 0 4 139 121 256 2.98e-89 263
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0278290 AT3G57990.1 49.020 102 39 3 25 113 134 235 2.28e-22 91.3

Find 51 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCGTCGGCTGGGGCGATTGC+AGG 0.212071 2_3:-11253886 Msa0278290:CDS
GTCGGGAAGGTGCCGTCGGC+TGG 0.220747 2_3:-11253898 Msa0278290:CDS
TTTCTTGTGATGGATAAAAT+TGG 0.248063 2_3:-11253733 Msa0278290:CDS
TCCGCAAAACGGTGGCGTTT+TGG 0.257586 2_3:-11253977 Msa0278290:CDS
CTGAGGTTGCGGCGAGGACT+AGG 0.264777 2_3:-11253849 Msa0278290:CDS
TAGGGTTCCGGCTGAGGTTA+AGG 0.286798 2_3:-11253782 Msa0278290:CDS
GAGGACTAGGGTTCCGATTA+GGG 0.309618 2_3:-11253836 Msa0278290:CDS
CGAGGACTAGGGTTCCGATT+AGG 0.329022 2_3:-11253837 Msa0278290:CDS
GTTAAGGGCGAAAGCGCGTT+TGG 0.350617 2_3:-11253766 Msa0278290:CDS
TCGGGAAGGTGCCGTCGGCT+GGG 0.374474 2_3:-11253897 Msa0278290:CDS
AAAGGAAAGGTTGGTGCTGC+TGG 0.377756 2_3:-11253664 Msa0278290:CDS
CGGGAAGGTGCCGTCGGCTG+GGG 0.380207 2_3:-11253896 Msa0278290:CDS
ACCGCGGCACGTCCCCTAAT+CGG 0.411961 2_3:+11253823 None:intergenic
TTCTTGTGATGGATAAAATT+GGG 0.414031 2_3:-11253732 Msa0278290:CDS
TTTGTTGAATCTCCGGTGAT+TGG 0.435435 2_3:-11253931 Msa0278290:CDS
CAACATGTCGAAATCAAATC+AGG 0.441154 2_3:-11254330 None:intergenic
ATTTGAGTTTGTTGAATCTC+CGG 0.443909 2_3:-11253938 Msa0278290:CDS
AGGGTTCCGGCTGAGGTTAA+GGG 0.446628 2_3:-11253781 Msa0278290:CDS
TTAAGGGCGAAAGCGCGTTT+GGG 0.463653 2_3:-11253765 Msa0278290:CDS
CTTTCGCCCTTAACCTCAGC+CGG 0.466668 2_3:+11253775 None:intergenic
GTGATTGGTGGGTTTAGTGT+CGG 0.483284 2_3:-11253916 Msa0278290:CDS
GAGGGTTCTGTTTCTTGTGA+TGG 0.490125 2_3:-11253743 Msa0278290:CDS
GGTTATGCGTTTCCGCAAAA+CGG 0.490258 2_3:-11253988 Msa0278290:CDS
CTCGGCAACACAGCACTTGT+CGG 0.490850 2_3:+11253631 None:intergenic
TGATTGGTGGGTTTAGTGTC+GGG 0.491545 2_3:-11253915 Msa0278290:CDS
TTTAAATCCCCACACTCCGC+TGG 0.496695 2_3:+11253697 None:intergenic
AACATTTGCCAGCGGAGTGT+GGG 0.501336 2_3:-11253705 Msa0278290:CDS
AAGGTTGGTGCTGCTGGAGT+TGG 0.503818 2_3:-11253658 Msa0278290:CDS
GATTTAAAGAATTTGAAGAA+AGG 0.507692 2_3:-11253682 Msa0278290:CDS
GTTGAATCTCCGGTGATTGG+TGG 0.516218 2_3:-11253928 Msa0278290:CDS
TGAGGTTGCGGCGAGGACTA+GGG 0.516942 2_3:-11253848 Msa0278290:CDS
CGTCGGCTGGGGCGATTGCA+GGG 0.524791 2_3:-11253885 Msa0278290:CDS
AATTTGAAGAAAGGAAAGGT+TGG 0.524993 2_3:-11253673 Msa0278290:CDS
GAACATTTGCCAGCGGAGTG+TGG 0.526006 2_3:-11253706 Msa0278290:CDS
AAAGAATTTGAAGAAAGGAA+AGG 0.540260 2_3:-11253677 Msa0278290:CDS
TCCGATTAGGGGACGTGCCG+CGG 0.544241 2_3:-11253824 Msa0278290:CDS
AGGGCGAAAGCGCGTTTGGG+AGG 0.549372 2_3:-11253762 Msa0278290:CDS
CCTGCAATCGCCCCAGCCGA+CGG 0.550116 2_3:+11253886 None:intergenic
TTGAATCTCCGGTGATTGGT+GGG 0.555286 2_3:-11253927 Msa0278290:CDS
GGGCGAAAGCGCGTTTGGGA+GGG 0.557564 2_3:-11253761 Msa0278290:CDS
TCTTGTGATGGATAAAATTG+GGG 0.562838 2_3:-11253731 Msa0278290:CDS
TAGTGTCGGGAAGGTGCCGT+CGG 0.576506 2_3:-11253902 Msa0278290:CDS
ACACTAAACCCACCAATCAC+CGG 0.580138 2_3:+11253919 None:intergenic
TGGTGGGTTTAGTGTCGGGA+AGG 0.594609 2_3:-11253911 Msa0278290:CDS
ACATTTGCCAGCGGAGTGTG+GGG 0.619702 2_3:-11253704 Msa0278290:CDS
CTTCACTGCAAAACTCGTCT+CGG 0.621132 2_3:+11253613 None:intergenic
TATGCGTTTCCGCAAAACGG+TGG 0.624687 2_3:-11253985 Msa0278290:CDS
TGTGATGGATAAAATTGGGG+TGG 0.626777 2_3:-11253728 Msa0278290:CDS
CGGGGACTGAGGTTGCGGCG+AGG 0.653848 2_3:-11253855 Msa0278290:CDS
TGGGGTGGAACATTTGCCAG+CGG 0.659065 2_3:-11253713 Msa0278290:CDS
AGGACTAGGGTTCCGATTAG+GGG 0.661644 2_3:-11253835 Msa0278290:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAGAAAATTTGATTTCAATT+TGG - chr2_3:11253736-11253755 Msa0278290:CDS 15.0%
!!! AGAAAATTTGATTTCAATTT+GGG - chr2_3:11253737-11253756 Msa0278290:CDS 15.0%
!!! GTGTTTTTGTTAGTTTAAAA+TGG - chr2_3:11253676-11253695 Msa0278290:CDS 20.0%
!! TCTCAATTTGAAAATTGTAT+TGG - chr2_3:11253812-11253831 Msa0278290:CDS 20.0%
!! GATTTAAAGAATTTGAAGAA+AGG - chr2_3:11254259-11254278 Msa0278290:intron 20.0%
!!! TGGTTTTGTTTAGATCAATA+AGG - chr2_3:11253696-11253715 Msa0278290:CDS 25.0%
! CACATTAATCAGTCAATTTA+GGG + chr2_3:11253780-11253799 None:intergenic 25.0%
!! ACAAAAACCATTTTAAACCT+AGG - chr2_3:11253879-11253898 Msa0278290:CDS 25.0%
!! AGTTCGATTTTAGATGTTAA+GGG - chr2_3:11253932-11253951 Msa0278290:CDS 25.0%
!!! TTTCTTGTGATGGATAAAAT+TGG - chr2_3:11254208-11254227 Msa0278290:intron 25.0%
!!! TTCTTGTGATGGATAAAATT+GGG - chr2_3:11254209-11254228 Msa0278290:intron 25.0%
! AAAGAATTTGAAGAAAGGAA+AGG - chr2_3:11254264-11254283 Msa0278290:intron 25.0%
AATAAGGTTTCTCTGTTAGT+TGG - chr2_3:11253712-11253731 Msa0278290:CDS 30.0%
GCACATTAATCAGTCAATTT+AGG + chr2_3:11253781-11253800 None:intergenic 30.0%
! AACCATTTTAAACCTAGGTT+TGG - chr2_3:11253884-11253903 Msa0278290:CDS 30.0%
! ACCATTTTAAACCTAGGTTT+GGG - chr2_3:11253885-11253904 Msa0278290:CDS 30.0%
! GAGTTCGATTTTAGATGTTA+AGG - chr2_3:11253931-11253950 Msa0278290:CDS 30.0%
!! ATTTGAGTTTGTTGAATCTC+CGG - chr2_3:11254003-11254022 Msa0278290:CDS 30.0%
!! TCTTGTGATGGATAAAATTG+GGG - chr2_3:11254210-11254229 Msa0278290:intron 30.0%
AATTTGAAGAAAGGAAAGGT+TGG - chr2_3:11254268-11254287 Msa0278290:intron 30.0%
! AATCAGTCAATTTAGGGCAT+CGG + chr2_3:11253774-11253793 None:intergenic 35.0%
! CCATTTTAAACCTAGGTTTG+GGG - chr2_3:11253886-11253905 Msa0278290:CDS 35.0%
AAAGAAAAATCCCCAAACCT+AGG + chr2_3:11253899-11253918 None:intergenic 35.0%
CCCCAAACCTAGGTTTAAAA+TGG + chr2_3:11253889-11253908 None:intergenic 40.0%
TTTGTTGAATCTCCGGTGAT+TGG - chr2_3:11254010-11254029 Msa0278290:CDS 40.0%
!! TGTGATGGATAAAATTGGGG+TGG - chr2_3:11254213-11254232 Msa0278290:intron 40.0%
GGTTATGCGTTTCCGCAAAA+CGG - chr2_3:11253953-11253972 Msa0278290:CDS 45.0%
TTGAATCTCCGGTGATTGGT+GGG - chr2_3:11254014-11254033 Msa0278290:CDS 45.0%
ACACTAAACCCACCAATCAC+CGG + chr2_3:11254025-11254044 None:intergenic 45.0%
!! GTGATTGGTGGGTTTAGTGT+CGG - chr2_3:11254025-11254044 Msa0278290:intron 45.0%
!! TGATTGGTGGGTTTAGTGTC+GGG - chr2_3:11254026-11254045 Msa0278290:intron 45.0%
!! TGAATTTTAGGTGGGGGGTT+AGG - chr2_3:11254140-11254159 Msa0278290:intron 45.0%
!! GAATTTTAGGTGGGGGGTTA+GGG - chr2_3:11254141-11254160 Msa0278290:intron 45.0%
! GAGGGTTCTGTTTCTTGTGA+TGG - chr2_3:11254198-11254217 Msa0278290:intron 45.0%
!!! TTTGTATAATTTTTAATTTT+TGG + chr2_3:11253864-11253883 None:intergenic 5.0%
TATGCGTTTCCGCAAAACGG+TGG - chr2_3:11253956-11253975 Msa0278290:CDS 50.0%
GTTGAATCTCCGGTGATTGG+TGG - chr2_3:11254013-11254032 Msa0278290:CDS 50.0%
!! GGCGATTGCAGGGTTGTTTT+CGG - chr2_3:11254066-11254085 Msa0278290:intron 50.0%
!! GCGATTGCAGGGTTGTTTTC+GGG - chr2_3:11254067-11254086 Msa0278290:intron 50.0%
!! CGATTGCAGGGTTGTTTTCG+GGG - chr2_3:11254068-11254087 Msa0278290:intron 50.0%
GAGGACTAGGGTTCCGATTA+GGG - chr2_3:11254105-11254124 Msa0278290:intron 50.0%
AGGACTAGGGTTCCGATTAG+GGG - chr2_3:11254106-11254125 Msa0278290:intron 50.0%
!! TGCCGCGGTGAATTTTAGGT+GGG - chr2_3:11254132-11254151 Msa0278290:intron 50.0%
! TTAAGGGCGAAAGCGCGTTT+GGG - chr2_3:11254176-11254195 Msa0278290:intron 50.0%
AACATTTGCCAGCGGAGTGT+GGG - chr2_3:11254236-11254255 Msa0278290:intron 50.0%
TTTAAATCCCCACACTCCGC+TGG + chr2_3:11254247-11254266 None:intergenic 50.0%
!! AAAGGAAAGGTTGGTGCTGC+TGG - chr2_3:11254277-11254296 Msa0278290:intron 50.0%
! TCCGCAAAACGGTGGCGTTT+TGG - chr2_3:11253964-11253983 Msa0278290:CDS 55.0%
! CCCAAAACGCCACCGTTTTG+CGG + chr2_3:11253968-11253987 None:intergenic 55.0%
! CCGCAAAACGGTGGCGTTTT+GGG - chr2_3:11253965-11253984 Msa0278290:CDS 55.0%
! CGCAAAACGGTGGCGTTTTG+GGG - chr2_3:11253966-11253985 Msa0278290:CDS 55.0%
!! TGGTGGGTTTAGTGTCGGGA+AGG - chr2_3:11254030-11254049 Msa0278290:intron 55.0%
!! AGGGTTGTTTTCGGGGACTG+AGG - chr2_3:11254075-11254094 Msa0278290:intron 55.0%
!! GTTTTCGGGGACTGAGGTTG+CGG - chr2_3:11254081-11254100 Msa0278290:intron 55.0%
CGAGGACTAGGGTTCCGATT+AGG - chr2_3:11254104-11254123 Msa0278290:intron 55.0%
! GACGTGCCGCGGTGAATTTT+AGG - chr2_3:11254128-11254147 Msa0278290:intron 55.0%
! GTGCCGCGGTGAATTTTAGG+TGG - chr2_3:11254131-11254150 Msa0278290:intron 55.0%
!! GCCGCGGTGAATTTTAGGTG+GGG - chr2_3:11254133-11254152 Msa0278290:intron 55.0%
CCCCCACCTAAAATTCACCG+CGG + chr2_3:11254137-11254156 None:intergenic 55.0%
!! CCGCGGTGAATTTTAGGTGG+GGG - chr2_3:11254134-11254153 Msa0278290:intron 55.0%
!! CGCGGTGAATTTTAGGTGGG+GGG - chr2_3:11254135-11254154 Msa0278290:intron 55.0%
TAGGGTTCCGGCTGAGGTTA+AGG - chr2_3:11254159-11254178 Msa0278290:intron 55.0%
AGGGTTCCGGCTGAGGTTAA+GGG - chr2_3:11254160-11254179 Msa0278290:intron 55.0%
CTTTCGCCCTTAACCTCAGC+CGG + chr2_3:11254169-11254188 None:intergenic 55.0%
! GTTAAGGGCGAAAGCGCGTT+TGG - chr2_3:11254175-11254194 Msa0278290:intron 55.0%
TGGGGTGGAACATTTGCCAG+CGG - chr2_3:11254228-11254247 Msa0278290:intron 55.0%
GAACATTTGCCAGCGGAGTG+TGG - chr2_3:11254235-11254254 Msa0278290:intron 55.0%
ACATTTGCCAGCGGAGTGTG+GGG - chr2_3:11254237-11254256 Msa0278290:intron 55.0%
!! AAGGTTGGTGCTGCTGGAGT+TGG - chr2_3:11254283-11254302 Msa0278290:intron 55.0%
CTCGGCAACACAGCACTTGT+CGG + chr2_3:11254313-11254332 None:intergenic 55.0%
!! TAGTGTCGGGAAGGTGCCGT+CGG - chr2_3:11254039-11254058 Msa0278290:intron 60.0%
TGAGGTTGCGGCGAGGACTA+GGG - chr2_3:11254093-11254112 Msa0278290:intron 60.0%
TAGGTGGGGGGTTAGGGTTC+CGG - chr2_3:11254147-11254166 Msa0278290:intron 60.0%
CTGAGGTTGCGGCGAGGACT+AGG - chr2_3:11254092-11254111 Msa0278290:intron 65.0%
TCCGATTAGGGGACGTGCCG+CGG - chr2_3:11254117-11254136 Msa0278290:intron 65.0%
ACCGCGGCACGTCCCCTAAT+CGG + chr2_3:11254121-11254140 None:intergenic 65.0%
! AGGGCGAAAGCGCGTTTGGG+AGG - chr2_3:11254179-11254198 Msa0278290:intron 65.0%
! GGGCGAAAGCGCGTTTGGGA+GGG - chr2_3:11254180-11254199 Msa0278290:intron 65.0%
!! TCGGGAAGGTGCCGTCGGCT+GGG - chr2_3:11254044-11254063 Msa0278290:intron 70.0%
CCTGCAATCGCCCCAGCCGA+CGG + chr2_3:11254058-11254077 None:intergenic 70.0%
! CGTCGGCTGGGGCGATTGCA+GGG - chr2_3:11254056-11254075 Msa0278290:intron 70.0%
GGGGGTTAGGGTTCCGGCTG+AGG - chr2_3:11254153-11254172 Msa0278290:intron 70.0%
!! GTCGGGAAGGTGCCGTCGGC+TGG - chr2_3:11254043-11254062 Msa0278290:intron 75.0%
!! CGGGAAGGTGCCGTCGGCTG+GGG - chr2_3:11254045-11254064 Msa0278290:intron 75.0%
! CCGTCGGCTGGGGCGATTGC+AGG - chr2_3:11254055-11254074 Msa0278290:intron 75.0%
CGGGGACTGAGGTTGCGGCG+AGG - chr2_3:11254086-11254105 Msa0278290:intron 75.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 11253615 11254348 11253615 ID=Msa0278290;Name=Msa0278290
chr2_3 mRNA 11253615 11254348 11253615 ID=Msa0278290-mRNA-1;Parent=Msa0278290;Name=Msa0278290-mRNA-1;_AED=0.22;_eAED=0.27;_QI=0|0|0|0.5|1|1|2|0|147
chr2_3 exon 11254331 11254348 11254331 ID=Msa0278290-mRNA-1:exon:5080;Parent=Msa0278290-mRNA-1
chr2_3 exon 11253615 11254040 11253615 ID=Msa0278290-mRNA-1:exon:5079;Parent=Msa0278290-mRNA-1
chr2_3 CDS 11254331 11254348 11254331 ID=Msa0278290-mRNA-1:cds;Parent=Msa0278290-mRNA-1
chr2_3 CDS 11253615 11254040 11253615 ID=Msa0278290-mRNA-1:cds;Parent=Msa0278290-mRNA-1
Gene Sequence

>Msa0278290

ATGTCGAAATCAAATCAGAAAACTCAGAGTTCGATTTTAGATGTTAAGGGTTATGCGTTTCCGCAAAACGGTGGCGTTTTGGGGAATGATGATACGAAATTTGAGTTTGTTGAATCTCCGGTGATTGGTGGGTTTAGTGTCGGGAAGGTGCCGTCGGCTGGGGCGATTGCAGGGTTGTTTTCGGGGACTGAGGTTGCGGCGAGGACTAGGGTTCCGATTAGGGGACGTGCCGCGGTGAATTTTAGGTGGGGGGTTAGGGTTCCGGCTGAGGTTAAGGGCGAAAGCGCGTTTGGGAGGGTTCTGTTTCTTGTGATGGATAAAATTGGGGTGGAACATTTGCCAGCGGAGTGTGGGGATTTAAAGAATTTGAAGAAAGGAAAGGTTGGTGCTGCTGGAGTTGGTGTTCCGACAAGTGCTGTGTTGCCGAGACGAGTTTTGCAGTGA

Protein sequence

>Msa0278290

MSKSNQKTQSSILDVKGYAFPQNGGVLGNDDTKFEFVESPVIGGFSVGKVPSAGAIAGLFSGTEVAARTRVPIRGRAAVNFRWGVRVPAEVKGESAFGRVLFLVMDKIGVEHLPAECGDLKNLKKGKVGAAGVGVPTSAVLPRRVLQ*