AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene045382

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene045382.t1 MTR_3g083880 97.000 200 6 0 1 200 1 200 5.48e-142 394
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene045382.t1 AT1G55300 62.621 206 68 4 1 200 1 203 1.50e-84 249
MS.gene045382.t1 AT1G55300 73.826 149 38 1 1 149 1 148 9.24e-78 233

Find 49 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACTTATGATGATAACTCTT+TGG 0.299738 3.4:+78726032 MS.gene045382:CDS
GTTATCATCATAAGTCTTGT+AGG 0.342174 3.4:-78726025 None:intergenic
GATCTTCTCAAAATCATTGC+TGG 0.365224 3.4:+78726442 MS.gene045382:CDS
GAAGCGGTACGTTTGTGATT+GGG 0.368830 3.4:+78725953 MS.gene045382:CDS
ATGATTATGGTGAGGGAATC+TGG 0.375382 3.4:+78726183 MS.gene045382:CDS
GATTTGCAATTTACCGATGA+TGG 0.382947 3.4:+78725928 MS.gene045382:CDS
TCAATCCGCTCCGCAACATT+AGG 0.383040 3.4:-78725856 None:intergenic
ATCCAATTAACAGATGATTA+TGG 0.395551 3.4:+78726170 MS.gene045382:intron
TCTGCGGAATCTACGCTTAC+GGG 0.407200 3.4:-78726265 None:intergenic
GGAAGGTCCAGCAGAGAAGC+TGG 0.408243 3.4:-78725988 None:intergenic
AGAAGCGGTACGTTTGTGAT+TGG 0.414235 3.4:+78725952 MS.gene045382:CDS
CCAGCATTTGTATGAGTCTC+TGG 0.415981 3.4:-78726861 None:intergenic
TTGGTTAAGACTGCTGATAT+TGG 0.419842 3.4:+78726051 MS.gene045382:CDS
CGCTTACGGGCATCTCTCAT+GGG 0.466049 3.4:-78726252 None:intergenic
CTCTGCGGAATCTACGCTTA+CGG 0.471366 3.4:-78726266 None:intergenic
ACGCTTACGGGCATCTCTCA+TGG 0.476622 3.4:-78726253 None:intergenic
TGTCGACACTCAATTACATC+TGG 0.485186 3.4:-78726216 None:intergenic
CATCTCTCATGGGAGGGGTG+AGG 0.487949 3.4:-78726242 None:intergenic
GCATTACCCAGCTTCTCTGC+TGG 0.493380 3.4:+78725981 MS.gene045382:CDS
TGGAACATCATTCTTTGATG+TGG 0.505743 3.4:-78726841 None:intergenic
AAGCGGTACGTTTGTGATTG+GGG 0.509827 3.4:+78725954 MS.gene045382:CDS
TAAGACTGCTGATATTGGTC+AGG 0.517098 3.4:+78726056 MS.gene045382:CDS
CCAGAGACTCATACAAATGC+TGG 0.519889 3.4:+78726861 MS.gene045382:CDS
TACGGGCATCTCTCATGGGA+GGG 0.526533 3.4:-78726248 None:intergenic
TTTGATGTGGATGTAGCTGC+AGG 0.533860 3.4:-78726828 None:intergenic
TTGTAGGATTCAACGACAGC+AGG 0.536746 3.4:-78726009 None:intergenic
GAATGTATTACATTAAGGTC+AGG 0.543174 3.4:-78726291 None:intergenic
TCAACACGGGAGACAAGCTC+AGG 0.549986 3.4:-78726415 None:intergenic
TTACGGGCATCTCTCATGGG+AGG 0.551219 3.4:-78726249 None:intergenic
ACGGGCATCTCTCATGGGAG+GGG 0.554455 3.4:-78726247 None:intergenic
CAAAATCATTGCTGGAGGAA+CGG 0.557535 3.4:+78726450 MS.gene045382:CDS
ATCCGCTCCGCAACATTAGG+TGG 0.567255 3.4:-78725853 None:intergenic
GAGAAGATCTTTCTCAACAC+GGG 0.572853 3.4:-78726428 None:intergenic
TTAACAGATGATTATGGTGA+GGG 0.581913 3.4:+78726176 MS.gene045382:intron
CTTGAAACAAACAAGATGAA+AGG 0.591470 3.4:-78726489 None:intergenic
GAAGGTCCAGCAGAGAAGCT+GGG 0.594836 3.4:-78725987 None:intergenic
TAGAGTTCCACCTAATGTTG+CGG 0.600957 3.4:+78725846 MS.gene045382:CDS
ATTAACAGATGATTATGGTG+AGG 0.615154 3.4:+78726175 MS.gene045382:intron
CTTCTCAAAATCATTGCTGG+AGG 0.618086 3.4:+78726445 MS.gene045382:CDS
GATGTAATTGAGTGTCGACA+TGG 0.622447 3.4:+78726219 MS.gene045382:CDS
GTGGAAGTAGCTGAGCAAGA+AGG 0.629194 3.4:+78726774 MS.gene045382:intron
TGAGAAGATCTTTCTCAACA+CGG 0.645887 3.4:-78726429 None:intergenic
CGTACCGCTTCTTCCATCAT+CGG 0.650430 3.4:-78725941 None:intergenic
TTTACCGATGATGGAAGAAG+CGG 0.653044 3.4:+78725937 MS.gene045382:CDS
AGGATTCAACGACAGCAGGA+AGG 0.676349 3.4:-78726005 None:intergenic
GAAGTAGCTGAGCAAGAAGG+CGG 0.683444 3.4:+78726777 MS.gene045382:intron
GAAGGCGGTGAGAATGCTCG+AGG 0.701876 3.4:+78726792 MS.gene045382:CDS
TTCCACCTAATGTTGCGGAG+CGG 0.701947 3.4:+78725851 MS.gene045382:CDS
CATTAAGGTCAGGCTCTCTG+CGG 0.708159 3.4:-78726281 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAAAAAAAATCTTTGAAA+TGG + chr3.4:78726562-78726581 MS.gene045382:intron 10.0%
!! AAATAGAGAAATGAGTTATA+AGG - chr3.4:78726627-78726646 None:intergenic 20.0%
!! AATAGAGAAATGAGTTATAA+GGG - chr3.4:78726626-78726645 None:intergenic 20.0%
!! TTACTAAACATTCTAAATCT+TGG + chr3.4:78726519-78726538 MS.gene045382:intron 20.0%
!!! AAAAAAAATCTTTGAAATGG+AGG + chr3.4:78726565-78726584 MS.gene045382:intron 20.0%
! AAACGAAGAATGAAAACATA+CGG - chr3.4:78726390-78726409 None:intergenic 25.0%
! ATCCAATTAACAGATGATTA+TGG + chr3.4:78726170-78726189 MS.gene045382:intron 25.0%
! CGAATGAATGTATTACATTA+AGG - chr3.4:78726299-78726318 None:intergenic 25.0%
! GTTAATTGGATTCATTAAGA+AGG - chr3.4:78726161-78726180 None:intergenic 25.0%
! TTATTTAATCATCCGAATCT+AGG - chr3.4:78726131-78726150 None:intergenic 25.0%
ACTCATTTCTCTATTTGAAC+TGG + chr3.4:78726631-78726650 MS.gene045382:intron 30.0%
ATTAACAGATGATTATGGTG+AGG + chr3.4:78726175-78726194 MS.gene045382:intron 30.0%
CACCATAATCATCTGTTAAT+TGG - chr3.4:78726175-78726194 None:intergenic 30.0%
CTCATTTCTCTATTTGAACT+GGG + chr3.4:78726632-78726651 MS.gene045382:intron 30.0%
CTTAATCATACACCTAGATT+CGG + chr3.4:78726116-78726135 MS.gene045382:intron 30.0%
CTTGAAACAAACAAGATGAA+AGG - chr3.4:78726492-78726511 None:intergenic 30.0%
GAATGTATTACATTAAGGTC+AGG - chr3.4:78726294-78726313 None:intergenic 30.0%
GACTTATGATGATAACTCTT+TGG + chr3.4:78726032-78726051 MS.gene045382:CDS 30.0%
TCATTTCTCTATTTGAACTG+GGG + chr3.4:78726633-78726652 MS.gene045382:intron 30.0%
TTAACAGATGATTATGGTGA+GGG + chr3.4:78726176-78726195 MS.gene045382:intron 30.0%
! GTTATCATCATAAGTCTTGT+AGG - chr3.4:78726028-78726047 None:intergenic 30.0%
ACAGATAATAGAGCAGTATC+AGG - chr3.4:78726344-78726363 None:intergenic 35.0%
GATCTTCTCAAAATCATTGC+TGG + chr3.4:78726442-78726461 MS.gene045382:CDS 35.0%
GATTTGCAATTTACCGATGA+TGG + chr3.4:78725928-78725947 MS.gene045382:CDS 35.0%
TCAGTCAAGAAAATAGCCAA+AGG - chr3.4:78726745-78726764 None:intergenic 35.0%
TGAGAAGATCTTTCTCAACA+CGG - chr3.4:78726432-78726451 None:intergenic 35.0%
TGGAACATCATTCTTTGATG+TGG - chr3.4:78726844-78726863 None:intergenic 35.0%
TGTTAAGTGTGAACAACCTT+TGG + chr3.4:78726726-78726745 MS.gene045382:intron 35.0%
TTGGTTAAGACTGCTGATAT+TGG + chr3.4:78726051-78726070 MS.gene045382:CDS 35.0%
ATGATTATGGTGAGGGAATC+TGG + chr3.4:78726183-78726202 MS.gene045382:CDS 40.0%
CAAAATCATTGCTGGAGGAA+CGG + chr3.4:78726450-78726469 MS.gene045382:CDS 40.0%
CTTCTCAAAATCATTGCTGG+AGG + chr3.4:78726445-78726464 MS.gene045382:CDS 40.0%
GAGAAGATCTTTCTCAACAC+GGG - chr3.4:78726431-78726450 None:intergenic 40.0%
TAAGACTGCTGATATTGGTC+AGG + chr3.4:78726056-78726075 MS.gene045382:CDS 40.0%
TAGAGTTCCACCTAATGTTG+CGG + chr3.4:78725846-78725865 MS.gene045382:CDS 40.0%
TCTATTTGAACTGGGGTTCA+TGG + chr3.4:78726640-78726659 MS.gene045382:intron 40.0%
TCTTGACTGAGATTCACATG+TGG + chr3.4:78726755-78726774 MS.gene045382:intron 40.0%
TGTCGACACTCAATTACATC+TGG - chr3.4:78726219-78726238 None:intergenic 40.0%
!! GATGTAATTGAGTGTCGACA+TGG + chr3.4:78726219-78726238 MS.gene045382:CDS 40.0%
!! TTTACCGATGATGGAAGAAG+CGG + chr3.4:78725937-78725956 MS.gene045382:CDS 40.0%
AAGCGGTACGTTTGTGATTG+GGG + chr3.4:78725954-78725973 MS.gene045382:CDS 45.0%
AGAAGCGGTACGTTTGTGAT+TGG + chr3.4:78725952-78725971 MS.gene045382:CDS 45.0%
CCAGAGACTCATACAAATGC+TGG + chr3.4:78726861-78726880 MS.gene045382:CDS 45.0%
CCAGCATTTGTATGAGTCTC+TGG - chr3.4:78726864-78726883 None:intergenic 45.0%
GAAGCGGTACGTTTGTGATT+GGG + chr3.4:78725953-78725972 MS.gene045382:CDS 45.0%
TTGTAGGATTCAACGACAGC+AGG - chr3.4:78726012-78726031 None:intergenic 45.0%
TTTGATGTGGATGTAGCTGC+AGG - chr3.4:78726831-78726850 None:intergenic 45.0%
AGGATTCAACGACAGCAGGA+AGG - chr3.4:78726008-78726027 None:intergenic 50.0%
CATTAAGGTCAGGCTCTCTG+CGG - chr3.4:78726284-78726303 None:intergenic 50.0%
CGTACCGCTTCTTCCATCAT+CGG - chr3.4:78725944-78725963 None:intergenic 50.0%
CTCTGCGGAATCTACGCTTA+CGG - chr3.4:78726269-78726288 None:intergenic 50.0%
CTGCTGATATTGGTCAGGTC+AGG + chr3.4:78726061-78726080 MS.gene045382:intron 50.0%
GAAGTAGCTGAGCAAGAAGG+CGG + chr3.4:78726777-78726796 MS.gene045382:intron 50.0%
GTGGAAGTAGCTGAGCAAGA+AGG + chr3.4:78726774-78726793 MS.gene045382:intron 50.0%
TCAATCCGCTCCGCAACATT+AGG - chr3.4:78725859-78725878 None:intergenic 50.0%
TCTGCGGAATCTACGCTTAC+GGG - chr3.4:78726268-78726287 None:intergenic 50.0%
TTCCACCTAATGTTGCGGAG+CGG + chr3.4:78725851-78725870 MS.gene045382:CDS 50.0%
ACGCTTACGGGCATCTCTCA+TGG - chr3.4:78726256-78726275 None:intergenic 55.0%
ATCCGCTCCGCAACATTAGG+TGG - chr3.4:78725856-78725875 None:intergenic 55.0%
CGCTTACGGGCATCTCTCAT+GGG - chr3.4:78726255-78726274 None:intergenic 55.0%
GAAGGTCCAGCAGAGAAGCT+GGG - chr3.4:78725990-78726009 None:intergenic 55.0%
GCATTACCCAGCTTCTCTGC+TGG + chr3.4:78725981-78726000 MS.gene045382:CDS 55.0%
TACGGGCATCTCTCATGGGA+GGG - chr3.4:78726251-78726270 None:intergenic 55.0%
TCAACACGGGAGACAAGCTC+AGG - chr3.4:78726418-78726437 None:intergenic 55.0%
TTACGGGCATCTCTCATGGG+AGG - chr3.4:78726252-78726271 None:intergenic 55.0%
ACGGGCATCTCTCATGGGAG+GGG - chr3.4:78726250-78726269 None:intergenic 60.0%
CATCTCTCATGGGAGGGGTG+AGG - chr3.4:78726245-78726264 None:intergenic 60.0%
GAAGGCGGTGAGAATGCTCG+AGG + chr3.4:78726792-78726811 MS.gene045382:CDS 60.0%
GGAAGGTCCAGCAGAGAAGC+TGG - chr3.4:78725991-78726010 None:intergenic 60.0%
CACGGGAGACAAGCTCAGGC+TGG - chr3.4:78726414-78726433 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 78725826 78726929 78725826 ID=MS.gene045382
chr3.4 mRNA 78725826 78726929 78725826 ID=MS.gene045382.t1;Parent=MS.gene045382
chr3.4 exon 78725826 78726077 78725826 ID=MS.gene045382.t1.exon1;Parent=MS.gene045382.t1
chr3.4 CDS 78725826 78726077 78725826 ID=cds.MS.gene045382.t1;Parent=MS.gene045382.t1
chr3.4 exon 78726183 78726302 78726183 ID=MS.gene045382.t1.exon2;Parent=MS.gene045382.t1
chr3.4 CDS 78726183 78726302 78726183 ID=cds.MS.gene045382.t1;Parent=MS.gene045382.t1
chr3.4 exon 78726415 78726499 78726415 ID=MS.gene045382.t1.exon3;Parent=MS.gene045382.t1
chr3.4 CDS 78726415 78726499 78726415 ID=cds.MS.gene045382.t1;Parent=MS.gene045382.t1
chr3.4 exon 78726784 78726929 78726784 ID=MS.gene045382.t1.exon4;Parent=MS.gene045382.t1
chr3.4 CDS 78726784 78726929 78726784 ID=cds.MS.gene045382.t1;Parent=MS.gene045382.t1
Gene Sequence

>MS.gene045382

ATGGAGGAGCAATTCATACTTAGAGTTCCACCTAATGTTGCGGAGCGGATTGAGCGTCTTTTGAATGAAAACAATGCTTCTTCATCTGAAGACAAGTCGCTAGATTTGCAATTTACCGATGATGGAAGAAGCGGTACGTTTGTGATTGGGGATGAGCATTACCCAGCTTCTCTGCTGGACCTTCCTGCTGTCGTTGAATCCTACAAGACTTATGATGATAACTCTTTGGTTAAGACTGCTGATATTGGTCAGGTCAGGTATCTATCGTTAATTCATATTATTTGTTTATTCTTAATCATACACCTAGATTCGGATGATTAAATAACTGATTGCCTTCTTAATGAATCCAATTAACAGATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTGTCGACATGGCCTCACCCCTCCCATGAGAGATGCCCGTAAGCGTAGATTCCGCAGAGAGCCTGACCTTAATGTAATACATTCATTCGTGCATTATATTATCTAAGCATACCTGATACTGCTCTATTATCTGTGCGTTTGTGTGCTCTCTTACTTACCGTATGTTTTCATTCTTCGTTTTCCAGCCTGAGCTTGTCTCCCGTGTTGAGAAAGATCTTCTCAAAATCATTGCTGGAGGAACGGCTGAAAATATTGATATCCTTTCATCTTGTTTGTTTCAAGCAGTAGTTTACTAAACATTCTAAATCTTGGATACAAATTTATGATTTCACTTTAAAAAAAATCTTTGAAATGGAGGTCTGTTGAGATCTTTTTTGTTGATTACTTTCTTTGCCCTTATAACTCATTTCTCTATTTGAACTGGGGTTCATGGAATAAGTAGCATCTATTTGCATTTGCATCAATGACAAAAGCAAGTTTTTCGCTTTCATTATATTGTTAAGTGTGAACAACCTTTGGCTATTTTCTTGACTGAGATTCACATGTGGAAGTAGCTGAGCAAGAAGGCGGTGAGAATGCTCGAGGTTCTAATAAAAAACCTGCAGCTACATCCACATCAAAGAATGATGTTCCAGAGACTCATACAAATGCTGGTGATGCTGACAGAAGTGACTCTGATGAATCTGATGACTCAGTTTGA
Protein sequence

>MS.gene045382.t1

MEEQFILRVPPNVAERIERLLNENNASSSEDKSLDLQFTDDGRSGTFVIGDEHYPASLLDLPAVVESYKTYDDNSLVKTADIGQMIMVRESGDAAPDVIECRHGLTPPMRDARKRRFRREPDLNPELVSRVEKDLLKIIAGGTAENIDILSSSEQEGGENARGSNKKPAATSTSKNDVPETHTNAGDADRSDSDESDDSV