AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene77509

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene77509.t1 MTR_3g083880 97.000 200 6 0 1 200 1 200 3.43e-141 392
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene77509.t1 AT1G55300 62.621 206 68 4 1 200 1 203 9.01e-84 247
MS.gene77509.t1 AT1G55300 73.826 149 38 1 1 149 1 148 8.20e-77 230

Find 48 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACTTATGATGATAACTCTT+TGG 0.299738 3.2:+72405669 MS.gene77509:CDS
GTTATCATCATAAGTCTTGT+AGG 0.342174 3.2:-72405662 None:intergenic
GATCTTCTCAAAATCATTGC+TGG 0.365224 3.2:+72406079 MS.gene77509:CDS
GAAGCGGTACGTTTGTGATT+GGG 0.368830 3.2:+72405590 MS.gene77509:CDS
ATGATTATGGTGAGGGAATC+TGG 0.375382 3.2:+72405820 MS.gene77509:CDS
TCAATCCGCTCCGCAACATT+AGG 0.383671 3.2:-72405493 None:intergenic
ATCCAATTAACAGATGATTA+TGG 0.395551 3.2:+72405807 MS.gene77509:intron
TCTGCGGAATCTACGCTTAC+GGG 0.407200 3.2:-72405902 None:intergenic
GGAAGGTCCAGCAGAGAAGC+TGG 0.408243 3.2:-72405625 None:intergenic
AGAAGCGGTACGTTTGTGAT+TGG 0.414235 3.2:+72405589 MS.gene77509:CDS
CCAGCATTTGTATGAGTCTC+TGG 0.415981 3.2:-72406498 None:intergenic
TTGGTTAAGACTGCTGATAT+TGG 0.419842 3.2:+72405688 MS.gene77509:CDS
GATTTGCAATTTAGCGATGA+TGG 0.420289 3.2:+72405565 MS.gene77509:CDS
CGCTTACGGGCATCTCTCAT+GGG 0.466049 3.2:-72405889 None:intergenic
CTCTGCGGAATCTACGCTTA+CGG 0.471366 3.2:-72405903 None:intergenic
ACGCTTACGGGCATCTCTCA+TGG 0.476622 3.2:-72405890 None:intergenic
TGTCGACACTCAATTACATC+TGG 0.485186 3.2:-72405853 None:intergenic
CATCTCTCATGGGAGGGGTG+AGG 0.487949 3.2:-72405879 None:intergenic
TTTGATGTGGATGTAGCTGC+TGG 0.491171 3.2:-72406465 None:intergenic
GCATTACCCAGCTTCTCTGC+TGG 0.493380 3.2:+72405618 MS.gene77509:CDS
TGGAACATCATTCTTTGATG+TGG 0.505743 3.2:-72406478 None:intergenic
AAGCGGTACGTTTGTGATTG+GGG 0.509827 3.2:+72405591 MS.gene77509:CDS
TAAGACTGCTGATATTGGTC+AGG 0.517098 3.2:+72405693 MS.gene77509:CDS
CCAGAGACTCATACAAATGC+TGG 0.519889 3.2:+72406498 MS.gene77509:CDS
TACGGGCATCTCTCATGGGA+GGG 0.526533 3.2:-72405885 None:intergenic
TTGTAGGATTCAACGACAGC+AGG 0.536746 3.2:-72405646 None:intergenic
GAATATATTACATTAAGGTC+AGG 0.539111 3.2:-72405928 None:intergenic
TCAACACGGGAGACAAGCTC+AGG 0.549986 3.2:-72406052 None:intergenic
TTACGGGCATCTCTCATGGG+AGG 0.551219 3.2:-72405886 None:intergenic
ACGGGCATCTCTCATGGGAG+GGG 0.554455 3.2:-72405884 None:intergenic
CAAAATCATTGCTGGAGGAA+CGG 0.557535 3.2:+72406087 MS.gene77509:CDS
ATCCGCTCCGCAACATTAGG+TGG 0.567255 3.2:-72405490 None:intergenic
GAGAAGATCTTTCTCAACAC+GGG 0.572853 3.2:-72406065 None:intergenic
TTAACAGATGATTATGGTGA+GGG 0.581913 3.2:+72405813 MS.gene77509:intron
CTTGAAACAAACAAGATGAA+AGG 0.591470 3.2:-72406126 None:intergenic
GAAGGTCCAGCAGAGAAGCT+GGG 0.594836 3.2:-72405624 None:intergenic
TAGAGTTCCACCTAATGTTG+CGG 0.600957 3.2:+72405483 MS.gene77509:CDS
ATTAACAGATGATTATGGTG+AGG 0.615154 3.2:+72405812 MS.gene77509:intron
CTTCTCAAAATCATTGCTGG+AGG 0.618086 3.2:+72406082 MS.gene77509:CDS
GATGTAATTGAGTGTCGACA+TGG 0.622447 3.2:+72405856 MS.gene77509:CDS
GTGGAAGTAGCTGAGCAAGA+AGG 0.629194 3.2:+72406411 MS.gene77509:intron
TTTAGCGATGATGGAAGAAG+CGG 0.638453 3.2:+72405574 MS.gene77509:CDS
TGAGAAGATCTTTCTCAACA+CGG 0.645887 3.2:-72406066 None:intergenic
AGGATTCAACGACAGCAGGA+AGG 0.676349 3.2:-72405642 None:intergenic
GAAGTAGCTGAGCAAGAAGG+CGG 0.683444 3.2:+72406414 MS.gene77509:intron
GAAGGCGGTGAGAATGCTCG+AGG 0.701876 3.2:+72406429 MS.gene77509:CDS
TTCCACCTAATGTTGCGGAG+CGG 0.701947 3.2:+72405488 MS.gene77509:CDS
CATTAAGGTCAGGCTCTCTG+CGG 0.708159 3.2:-72405918 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAAAAAAAATCTTTGAAA+TGG + chr3.2:72406199-72406218 MS.gene77509:intron 10.0%
!! AAATAGAGAAATGAGTTATA+AGG - chr3.2:72406264-72406283 None:intergenic 20.0%
!! AATAGAGAAATGAGTTATAA+GGG - chr3.2:72406263-72406282 None:intergenic 20.0%
!! CGAATGAATATATTACATTA+AGG - chr3.2:72405936-72405955 None:intergenic 20.0%
!! TTAGTAAACATTCTAAATCT+TGG + chr3.2:72406156-72406175 MS.gene77509:intron 20.0%
!!! AAAAAAAATCTTTGAAATGG+AGG + chr3.2:72406202-72406221 MS.gene77509:intron 20.0%
! AAACGAAGAATGAAAACATA+CGG - chr3.2:72406027-72406046 None:intergenic 25.0%
! ATCCAATTAACAGATGATTA+TGG + chr3.2:72405807-72405826 MS.gene77509:intron 25.0%
! GAATATATTACATTAAGGTC+AGG - chr3.2:72405931-72405950 None:intergenic 25.0%
! GTTAATTGGATTCATTAAGA+AGG - chr3.2:72405798-72405817 None:intergenic 25.0%
! TTATTTAATCATCCGAATCT+AGG - chr3.2:72405768-72405787 None:intergenic 25.0%
ACTCATTTCTCTATTTGAAC+TGG + chr3.2:72406268-72406287 MS.gene77509:intron 30.0%
ATTAACAGATGATTATGGTG+AGG + chr3.2:72405812-72405831 MS.gene77509:intron 30.0%
CACCATAATCATCTGTTAAT+TGG - chr3.2:72405812-72405831 None:intergenic 30.0%
CTCATTTCTCTATTTGAACT+GGG + chr3.2:72406269-72406288 MS.gene77509:intron 30.0%
CTTAATCATACACCTAGATT+CGG + chr3.2:72405753-72405772 MS.gene77509:intron 30.0%
CTTGAAACAAACAAGATGAA+AGG - chr3.2:72406129-72406148 None:intergenic 30.0%
GACTTATGATGATAACTCTT+TGG + chr3.2:72405669-72405688 MS.gene77509:CDS 30.0%
TCATTTCTCTATTTGAACTG+GGG + chr3.2:72406270-72406289 MS.gene77509:intron 30.0%
TTAACAGATGATTATGGTGA+GGG + chr3.2:72405813-72405832 MS.gene77509:intron 30.0%
! GTTATCATCATAAGTCTTGT+AGG - chr3.2:72405665-72405684 None:intergenic 30.0%
ACAGATAATAGAGCAGTATC+AGG - chr3.2:72405981-72406000 None:intergenic 35.0%
GATCTTCTCAAAATCATTGC+TGG + chr3.2:72406079-72406098 MS.gene77509:CDS 35.0%
GATTTGCAATTTAGCGATGA+TGG + chr3.2:72405565-72405584 MS.gene77509:CDS 35.0%
TCAGTCAAGAAAATAGCCAA+AGG - chr3.2:72406382-72406401 None:intergenic 35.0%
TGAGAAGATCTTTCTCAACA+CGG - chr3.2:72406069-72406088 None:intergenic 35.0%
TGGAACATCATTCTTTGATG+TGG - chr3.2:72406481-72406500 None:intergenic 35.0%
TGTTAAGTGTGAACAACCTT+TGG + chr3.2:72406363-72406382 MS.gene77509:intron 35.0%
TTGGTTAAGACTGCTGATAT+TGG + chr3.2:72405688-72405707 MS.gene77509:CDS 35.0%
ATGATTATGGTGAGGGAATC+TGG + chr3.2:72405820-72405839 MS.gene77509:CDS 40.0%
CAAAATCATTGCTGGAGGAA+CGG + chr3.2:72406087-72406106 MS.gene77509:CDS 40.0%
CTTCTCAAAATCATTGCTGG+AGG + chr3.2:72406082-72406101 MS.gene77509:CDS 40.0%
GAGAAGATCTTTCTCAACAC+GGG - chr3.2:72406068-72406087 None:intergenic 40.0%
TAAGACTGCTGATATTGGTC+AGG + chr3.2:72405693-72405712 MS.gene77509:CDS 40.0%
TAGAGTTCCACCTAATGTTG+CGG + chr3.2:72405483-72405502 MS.gene77509:CDS 40.0%
TCTATTTGAACTGGGGTTCA+TGG + chr3.2:72406277-72406296 MS.gene77509:intron 40.0%
TCTTGACTGAGATTCACATG+TGG + chr3.2:72406392-72406411 MS.gene77509:intron 40.0%
TGTCGACACTCAATTACATC+TGG - chr3.2:72405856-72405875 None:intergenic 40.0%
!! GATGTAATTGAGTGTCGACA+TGG + chr3.2:72405856-72405875 MS.gene77509:CDS 40.0%
!! TTTAGCGATGATGGAAGAAG+CGG + chr3.2:72405574-72405593 MS.gene77509:CDS 40.0%
AAGCGGTACGTTTGTGATTG+GGG + chr3.2:72405591-72405610 MS.gene77509:CDS 45.0%
AGAAGCGGTACGTTTGTGAT+TGG + chr3.2:72405589-72405608 MS.gene77509:CDS 45.0%
CCAGAGACTCATACAAATGC+TGG + chr3.2:72406498-72406517 MS.gene77509:CDS 45.0%
CCAGCATTTGTATGAGTCTC+TGG - chr3.2:72406501-72406520 None:intergenic 45.0%
GAAGCGGTACGTTTGTGATT+GGG + chr3.2:72405590-72405609 MS.gene77509:CDS 45.0%
TTGTAGGATTCAACGACAGC+AGG - chr3.2:72405649-72405668 None:intergenic 45.0%
TTTGATGTGGATGTAGCTGC+TGG - chr3.2:72406468-72406487 None:intergenic 45.0%
AGGATTCAACGACAGCAGGA+AGG - chr3.2:72405645-72405664 None:intergenic 50.0%
CATTAAGGTCAGGCTCTCTG+CGG - chr3.2:72405921-72405940 None:intergenic 50.0%
CTCTGCGGAATCTACGCTTA+CGG - chr3.2:72405906-72405925 None:intergenic 50.0%
CTGCTGATATTGGTCAGGTC+AGG + chr3.2:72405698-72405717 MS.gene77509:intron 50.0%
GAAGTAGCTGAGCAAGAAGG+CGG + chr3.2:72406414-72406433 MS.gene77509:intron 50.0%
GTGGAAGTAGCTGAGCAAGA+AGG + chr3.2:72406411-72406430 MS.gene77509:intron 50.0%
TCAATCCGCTCCGCAACATT+AGG - chr3.2:72405496-72405515 None:intergenic 50.0%
TCTGCGGAATCTACGCTTAC+GGG - chr3.2:72405905-72405924 None:intergenic 50.0%
TTCCACCTAATGTTGCGGAG+CGG + chr3.2:72405488-72405507 MS.gene77509:CDS 50.0%
ACGCTTACGGGCATCTCTCA+TGG - chr3.2:72405893-72405912 None:intergenic 55.0%
ATCCGCTCCGCAACATTAGG+TGG - chr3.2:72405493-72405512 None:intergenic 55.0%
CGCTTACGGGCATCTCTCAT+GGG - chr3.2:72405892-72405911 None:intergenic 55.0%
GAAGGTCCAGCAGAGAAGCT+GGG - chr3.2:72405627-72405646 None:intergenic 55.0%
GCATTACCCAGCTTCTCTGC+TGG + chr3.2:72405618-72405637 MS.gene77509:CDS 55.0%
TACGGGCATCTCTCATGGGA+GGG - chr3.2:72405888-72405907 None:intergenic 55.0%
TCAACACGGGAGACAAGCTC+AGG - chr3.2:72406055-72406074 None:intergenic 55.0%
TTACGGGCATCTCTCATGGG+AGG - chr3.2:72405889-72405908 None:intergenic 55.0%
ACGGGCATCTCTCATGGGAG+GGG - chr3.2:72405887-72405906 None:intergenic 60.0%
CATCTCTCATGGGAGGGGTG+AGG - chr3.2:72405882-72405901 None:intergenic 60.0%
GAAGGCGGTGAGAATGCTCG+AGG + chr3.2:72406429-72406448 MS.gene77509:CDS 60.0%
GGAAGGTCCAGCAGAGAAGC+TGG - chr3.2:72405628-72405647 None:intergenic 60.0%
CACGGGAGACAAGCTCAGGC+TGG - chr3.2:72406051-72406070 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 72405463 72406566 72405463 ID=MS.gene77509
chr3.2 mRNA 72405463 72406566 72405463 ID=MS.gene77509.t1;Parent=MS.gene77509
chr3.2 exon 72405463 72405714 72405463 ID=MS.gene77509.t1.exon1;Parent=MS.gene77509.t1
chr3.2 CDS 72405463 72405714 72405463 ID=cds.MS.gene77509.t1;Parent=MS.gene77509.t1
chr3.2 exon 72405820 72405939 72405820 ID=MS.gene77509.t1.exon2;Parent=MS.gene77509.t1
chr3.2 CDS 72405820 72405939 72405820 ID=cds.MS.gene77509.t1;Parent=MS.gene77509.t1
chr3.2 exon 72406052 72406136 72406052 ID=MS.gene77509.t1.exon3;Parent=MS.gene77509.t1
chr3.2 CDS 72406052 72406136 72406052 ID=cds.MS.gene77509.t1;Parent=MS.gene77509.t1
chr3.2 exon 72406421 72406566 72406421 ID=MS.gene77509.t1.exon4;Parent=MS.gene77509.t1
chr3.2 CDS 72406421 72406566 72406421 ID=cds.MS.gene77509.t1;Parent=MS.gene77509.t1
Gene Sequence

>MS.gene77509

ATGGAGGAGCAATTCATACTTAGAGTTCCACCTAATGTTGCGGAGCGGATTGAGCTACTTTTGAATGAAAACAATGCTTCTTCATCTGAAGACAAGTCGCTAGATTTGCAATTTAGCGATGATGGAAGAAGCGGTACGTTTGTGATTGGGGATGAGCATTACCCAGCTTCTCTGCTGGACCTTCCTGCTGTCGTTGAATCCTACAAGACTTATGATGATAACTCTTTGGTTAAGACTGCTGATATTGGTCAGGTCAGGTATCTATCGTTAATTCATATTATTTGTTTATTCTTAATCATACACCTAGATTCGGATGATTAAATAACTGATTGCCTTCTTAATGAATCCAATTAACAGATGATTATGGTGAGGGAATCTGGTGATGCTGCTCCAGATGTAATTGAGTGTCGACATGGCCTCACCCCTCCCATGAGAGATGCCCGTAAGCGTAGATTCCGCAGAGAGCCTGACCTTAATGTAATATATTCATTCGTGCATTATATTATCTAAGCATACCTGATACTGCTCTATTATCTGTGCGTTTGTGTGCTCTCTTACTTACCGTATGTTTTCATTCTTCGTTTTCCAGCCTGAGCTTGTCTCCCGTGTTGAGAAAGATCTTCTCAAAATCATTGCTGGAGGAACGGCTGAAAATATTGATATCCTTTCATCTTGTTTGTTTCAAGCAGTAGTTTAGTAAACATTCTAAATCTTGGATACAAATGTATGATTTCACTTTAAAAAAAATCTTTGAAATGGAGGTCTGTTGAGATCTTTTTTGTTGATTACTTTCTTTGCCCTTATAACTCATTTCTCTATTTGAACTGGGGTTCATGGAATGAGTAGCATCTATTTGCATTTGCATCAATGACAAAAGCAAGTTTTTCGCTTTCATTATATTGTTAAGTGTGAACAACCTTTGGCTATTTTCTTGACTGAGATTCACATGTGGAAGTAGCTGAGCAAGAAGGCGGTGAGAATGCTCGAGGTTCTAATAAAAAACCAGCAGCTACATCCACATCAAAGAATGATGTTCCAGAGACTCATACAAATGCTGGTGATGCTGACAGAAGTGACTCTGATGAATCTGATGACTCAGTTTGA
Protein sequence

>MS.gene77509.t1

MEEQFILRVPPNVAERIELLLNENNASSSEDKSLDLQFSDDGRSGTFVIGDEHYPASLLDLPAVVESYKTYDDNSLVKTADIGQMIMVRESGDAAPDVIECRHGLTPPMRDARKRRFRREPDLNPELVSRVEKDLLKIIAGGTAENIDILSSSEQEGGENARGSNKKPAATSTSKNDVPETHTNAGDADRSDSDESDDSV