AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene06633


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06633.t1 MTR_5g004830 41.429 140 71 3 6 142 11 142 3.49e-33 115
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 44 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTTCAAACTCGCAGTTATA+CGG 0.304728 3.3:-77112279 None:intergenic
TGGGAGGTGCTGATTCATTC+TGG 0.307310 3.3:+77110762 MS.gene06633:CDS
CTTCTCTGCATCAACCTTAC+TGG 0.321088 3.3:-77110619 None:intergenic
GTTTAAGATGGACAGTAATC+CGG 0.386700 3.3:+77111111 MS.gene06633:CDS
TACATTTGTTGAAGCGAGTA+AGG 0.420870 3.3:+77111066 MS.gene06633:CDS
AGACATGGAGGAACCGGTAT+TGG 0.457153 3.3:-77110720 None:intergenic
TGAATGTTCGAACAAATTCA+TGG 0.458298 3.3:+77110742 MS.gene06633:CDS
CGAATTCCATTCCACATCAA+TGG 0.458515 3.3:+77110902 MS.gene06633:CDS
GCAGGTTCTACATCAATTTG+AGG 0.461169 3.3:-77110681 None:intergenic
TGACAGATTGTTGTTTAAGA+TGG 0.463808 3.3:+77111099 MS.gene06633:CDS
ACATTCAGACATGGAGGAAC+CGG 0.479236 3.3:-77110726 None:intergenic
AATGTCAGAGTCTCTTTCCC+AGG 0.481300 3.3:-77110938 None:intergenic
TTTAAGATGGACAGTAATCC+GGG 0.497303 3.3:+77111112 MS.gene06633:CDS
AAAGATCCATTGATGTGGAA+TGG 0.510519 3.3:-77110908 None:intergenic
TATGTGCAGAAGAAATTCAT+AGG 0.511115 3.3:+77111031 MS.gene06633:CDS
TTCGACGGTGTTGCCTCCAC+CGG 0.514992 3.3:-77112253 None:intergenic
ATGCAATATTCGAATGAAGA+AGG 0.515264 3.3:+77110642 MS.gene06633:CDS
GGCTCACGGTAATCATCTGC+AGG 0.521858 3.3:-77110699 None:intergenic
AAGATGCAGTTGATGCGATC+TGG 0.525388 3.3:+77110981 MS.gene06633:CDS
TGCAGAAGAAATTCATAGGA+AGG 0.530136 3.3:+77111035 MS.gene06633:CDS
TAGATTACCAGCTTATGAGT+TGG 0.531267 3.3:-77110795 None:intergenic
GTAATCAATAACGCCGGTGG+AGG 0.535659 3.3:+77112240 MS.gene06633:CDS
TTCTTCTGCACATAATCACC+AGG 0.548008 3.3:-77111022 None:intergenic
TTTACGTCCAACTCATAAGC+TGG 0.553121 3.3:+77110788 MS.gene06633:CDS
CAGAAGAAATTCATAGGAAG+GGG 0.562018 3.3:+77111037 MS.gene06633:CDS
TGATTACCGTGAGCCAATAC+CGG 0.564459 3.3:+77110707 MS.gene06633:CDS
AGAAATTCATAGGAAGGGGT+TGG 0.574152 3.3:+77111041 MS.gene06633:CDS
GAAGCGAGTAAGGTGAAAGT+TGG 0.578483 3.3:+77111076 MS.gene06633:CDS
GCAGAAGAAATTCATAGGAA+GGG 0.580030 3.3:+77111036 MS.gene06633:CDS
GAATGTTCGAACAAATTCAT+GGG 0.580892 3.3:+77110743 MS.gene06633:CDS
AGAGACTCTGACATTGACAT+TGG 0.584037 3.3:+77110946 MS.gene06633:CDS
TTACTGCAGTGAGTCCAGTA+AGG 0.589344 3.3:+77110605 MS.gene06633:intron
CACGAAAAGATCCATTGATG+TGG 0.608405 3.3:-77110913 None:intergenic
TTTGTTCGAACATTCAGACA+TGG 0.613761 3.3:-77110735 None:intergenic
TGAGAATGGCAACATTGAAG+AGG 0.623240 3.3:+77110508 None:intergenic
GAGGAACCGGTATTGGCTCA+CGG 0.632876 3.3:-77110713 None:intergenic
CAATATTCGAATGAAGAAGG+AGG 0.651295 3.3:+77110645 MS.gene06633:CDS
ATTGTAATCAATAACGCCGG+TGG 0.653478 3.3:+77112237 MS.gene06633:CDS
TGTGATATTGATGTTGAACC+TGG 0.654348 3.3:+77111004 MS.gene06633:CDS
GCAGTTATACGGTGGTTCGA+CGG 0.660300 3.3:-77112268 None:intergenic
GTTCGAACATTCAGACATGG+AGG 0.688432 3.3:-77110732 None:intergenic
TGTTCGAACAAATTCATGGG+AGG 0.689256 3.3:+77110746 MS.gene06633:CDS
GCAATTGTAATCAATAACGC+CGG 0.690508 3.3:+77112234 MS.gene06633:CDS
TCAAACTCGCAGTTATACGG+TGG 0.708422 3.3:-77112276 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTTATATATAATAAATA+AGG + chr3.3:77111381-77111400 MS.gene06633:intron 0.0%
!!! TATTTTCATCTTTTAAAATA+AGG - chr3.3:77112047-77112066 None:intergenic 10.0%
!! ATAAAACTAACATAAAGTAA+GGG - chr3.3:77110829-77110848 None:intergenic 15.0%
!! TATAAAACTAACATAAAGTA+AGG - chr3.3:77110830-77110849 None:intergenic 15.0%
!! TTAAAAGATGAAAATAGAAA+GGG + chr3.3:77112051-77112070 MS.gene06633:intron 15.0%
!! TTTAAAAGATGAAAATAGAA+AGG + chr3.3:77112050-77112069 MS.gene06633:intron 15.0%
!!! AAAAGCTAAAAAAATGTTTT+TGG + chr3.3:77111642-77111661 MS.gene06633:intron 15.0%
!!! AAAGTTGATTATTAATGAAA+TGG + chr3.3:77111450-77111469 MS.gene06633:intron 15.0%
!!! TATTTTAAACTTTGTAGTAA+TGG + chr3.3:77111283-77111302 MS.gene06633:intron 15.0%
!!! TTTTCTAATTTATTAATTCC+AGG - chr3.3:77111845-77111864 None:intergenic 15.0%
!! ACGAAAAGACTTAAATATAT+AGG + chr3.3:77111513-77111532 MS.gene06633:intron 20.0%
!! TAAAAGATGAAAATAGAAAG+GGG + chr3.3:77112052-77112071 MS.gene06633:intron 20.0%
!! TAATTGCTATGTTAAATTTC+TGG + chr3.3:77111135-77111154 MS.gene06633:intron 20.0%
!! TATTATGAATAAGAATAGCA+TGG + chr3.3:77111405-77111424 MS.gene06633:intron 20.0%
!! TTGATTATTAATGAAATGGT+TGG + chr3.3:77111454-77111473 MS.gene06633:intron 20.0%
! AAAAAGAATAAGAAGATGAG+AGG - chr3.3:77112150-77112169 None:intergenic 25.0%
! AAAAGATGAAAATAGAAAGG+GGG + chr3.3:77112053-77112072 MS.gene06633:intron 25.0%
! AAGACTTAAATATATAGGAG+TGG + chr3.3:77111518-77111537 MS.gene06633:intron 25.0%
! AATTTAACATAGCAATTACC+CGG - chr3.3:77111133-77111152 None:intergenic 25.0%
! ACCTGTAAATATAGTGAATT+TGG + chr3.3:77111666-77111685 MS.gene06633:intron 25.0%
! AGTATCAAGTCAACATAAAA+TGG - chr3.3:77110576-77110595 None:intergenic 25.0%
! CCTGTAAATATAGTGAATTT+GGG + chr3.3:77111667-77111686 MS.gene06633:intron 25.0%
! GTATTAAGTACTAAAAGATC+AGG + chr3.3:77111233-77111252 MS.gene06633:intron 25.0%
! TACAGGAAGAAGAATAATAA+TGG - chr3.3:77112101-77112120 None:intergenic 25.0%
! TGAAGAGGTAATAAAGTTTA+TGG + chr3.3:77110523-77110542 MS.gene06633:intron 25.0%
! TGATATATAAAACTGGTAAG+TGG + chr3.3:77111162-77111181 MS.gene06633:intron 25.0%
! TGGAAAGTGATATATAAAAC+TGG + chr3.3:77111155-77111174 MS.gene06633:intron 25.0%
!!! TTGATGATTCAACACATTTT+CGG + chr3.3:77111773-77111792 MS.gene06633:intron 25.0%
!!! TTGTTTTTTAAAATAGCCTC+TGG + chr3.3:77111740-77111759 MS.gene06633:intron 25.0%
ATGCAATATTCGAATGAAGA+AGG + chr3.3:77110642-77110661 MS.gene06633:CDS 30.0%
CCCAAATTCACTATATTTAC+AGG - chr3.3:77111670-77111689 None:intergenic 30.0%
GAATGTTCGAACAAATTCAT+GGG + chr3.3:77110743-77110762 MS.gene06633:CDS 30.0%
TATGTGCAGAAGAAATTCAT+AGG + chr3.3:77111031-77111050 MS.gene06633:CDS 30.0%
TGAATGTTCGAACAAATTCA+TGG + chr3.3:77110742-77110761 MS.gene06633:CDS 30.0%
TTTCTTCTTATTCACAATCC+TGG + chr3.3:77112167-77112186 MS.gene06633:intron 30.0%
!! AATATAGTGAATTTGGGTTG+TGG + chr3.3:77111673-77111692 MS.gene06633:intron 30.0%
!! TGACAGATTGTTGTTTAAGA+TGG + chr3.3:77111099-77111118 MS.gene06633:CDS 30.0%
AAAGATCCATTGATGTGGAA+TGG - chr3.3:77110911-77110930 None:intergenic 35.0%
AAAGGGGGAGATTAAAAATG+AGG + chr3.3:77112068-77112087 MS.gene06633:intron 35.0%
AACCAATCAAGATTGTGTTG+TGG + chr3.3:77112197-77112216 MS.gene06633:intron 35.0%
AAGGGGGAGATTAAAAATGA+GGG + chr3.3:77112069-77112088 MS.gene06633:intron 35.0%
ACTTCAAACTCGCAGTTATA+CGG - chr3.3:77112282-77112301 None:intergenic 35.0%
CAATATTCGAATGAAGAAGG+AGG + chr3.3:77110645-77110664 MS.gene06633:CDS 35.0%
CAGAAGAAATTCATAGGAAG+GGG + chr3.3:77111037-77111056 MS.gene06633:CDS 35.0%
CCACTCATAAAGAAAAGAGA+TGG + chr3.3:77111604-77111623 MS.gene06633:intron 35.0%
GATTGTACAAAACTGTCAAG+TGG + chr3.3:77111950-77111969 MS.gene06633:intron 35.0%
GCAATTGTAATCAATAACGC+CGG + chr3.3:77112234-77112253 MS.gene06633:CDS 35.0%
GCAGAAGAAATTCATAGGAA+GGG + chr3.3:77111036-77111055 MS.gene06633:CDS 35.0%
TAGATTACCAGCTTATGAGT+TGG - chr3.3:77110798-77110817 None:intergenic 35.0%
TGCAGAAGAAATTCATAGGA+AGG + chr3.3:77111035-77111054 MS.gene06633:CDS 35.0%
TGTGATATTGATGTTGAACC+TGG + chr3.3:77111004-77111023 MS.gene06633:CDS 35.0%
TTTGTTCGAACATTCAGACA+TGG - chr3.3:77110738-77110757 None:intergenic 35.0%
! CCATCTCTTTTCTTTATGAG+TGG - chr3.3:77111607-77111626 None:intergenic 35.0%
! GATCAGGTTGCTTAAGATAA+TGG + chr3.3:77111249-77111268 MS.gene06633:intron 35.0%
! GTTTAAGATGGACAGTAATC+CGG + chr3.3:77111111-77111130 MS.gene06633:CDS 35.0%
! TACATTTGTTGAAGCGAGTA+AGG + chr3.3:77111066-77111085 MS.gene06633:CDS 35.0%
! TTTAAGATGGACAGTAATCC+GGG + chr3.3:77111112-77111131 MS.gene06633:CDS 35.0%
!!! CTTGATTGGTTTTGATTTCC+AGG - chr3.3:77112188-77112207 None:intergenic 35.0%
ACTGGTAAGTGGTGTTTGTT+TGG + chr3.3:77111173-77111192 MS.gene06633:intron 40.0%
ACTGTCAAGTGGCATTTACT+TGG + chr3.3:77111961-77111980 MS.gene06633:intron 40.0%
AGAAATTCATAGGAAGGGGT+TGG + chr3.3:77111041-77111060 MS.gene06633:CDS 40.0%
AGAAGATGAGAGGAGAAACA+AGG - chr3.3:77112140-77112159 None:intergenic 40.0%
AGAGACTCTGACATTGACAT+TGG + chr3.3:77110946-77110965 MS.gene06633:CDS 40.0%
ATAGGAGTGGATGATGAATG+TGG + chr3.3:77111531-77111550 MS.gene06633:intron 40.0%
ATTGGACAAAACTGTCAACG+TGG + chr3.3:77111813-77111832 MS.gene06633:intron 40.0%
ATTGTAATCAATAACGCCGG+TGG + chr3.3:77112237-77112256 MS.gene06633:CDS 40.0%
CACGAAAAGATCCATTGATG+TGG - chr3.3:77110916-77110935 None:intergenic 40.0%
CGAATTCCATTCCACATCAA+TGG + chr3.3:77110902-77110921 MS.gene06633:CDS 40.0%
GAGGAAGAGAAAACGATTAC+AGG - chr3.3:77112118-77112137 None:intergenic 40.0%
GCAGGTTCTACATCAATTTG+AGG - chr3.3:77110684-77110703 None:intergenic 40.0%
GTCCACAACACAATCTTGAT+TGG - chr3.3:77112202-77112221 None:intergenic 40.0%
TGTTCGAACAAATTCATGGG+AGG + chr3.3:77110746-77110765 MS.gene06633:CDS 40.0%
TTCTTCTGCACATAATCACC+AGG - chr3.3:77111025-77111044 None:intergenic 40.0%
TTTACGTCCAACTCATAAGC+TGG + chr3.3:77110788-77110807 MS.gene06633:CDS 40.0%
TTTGTTTGGAGACAGTGTGT+TGG + chr3.3:77111187-77111206 MS.gene06633:intron 40.0%
! AATGGATCTTTTCGTGAACC+TGG + chr3.3:77110920-77110939 MS.gene06633:CDS 40.0%
! ATGGATCTTTTCGTGAACCT+GGG + chr3.3:77110921-77110940 MS.gene06633:CDS 40.0%
AATGTCAGAGTCTCTTTCCC+AGG - chr3.3:77110941-77110960 None:intergenic 45.0%
ACATTCAGACATGGAGGAAC+CGG - chr3.3:77110729-77110748 None:intergenic 45.0%
AGATGAGAGGAGAAACAAGG+AGG - chr3.3:77112137-77112156 None:intergenic 45.0%
CATCAAGAAAGTGAGTCCAG+AGG - chr3.3:77111759-77111778 None:intergenic 45.0%
CTTCTCTGCATCAACCTTAC+TGG - chr3.3:77110622-77110641 None:intergenic 45.0%
GAAGCGAGTAAGGTGAAAGT+TGG + chr3.3:77111076-77111095 MS.gene06633:CDS 45.0%
GTTCGAACATTCAGACATGG+AGG - chr3.3:77110735-77110754 None:intergenic 45.0%
TCAAACTCGCAGTTATACGG+TGG - chr3.3:77112279-77112298 None:intergenic 45.0%
TGATTACCGTGAGCCAATAC+CGG + chr3.3:77110707-77110726 MS.gene06633:CDS 45.0%
TTACTGCAGTGAGTCCAGTA+AGG + chr3.3:77110605-77110624 MS.gene06633:intron 45.0%
! AAGATGCAGTTGATGCGATC+TGG + chr3.3:77110981-77111000 MS.gene06633:CDS 45.0%
AGACATGGAGGAACCGGTAT+TGG - chr3.3:77110723-77110742 None:intergenic 50.0%
CTGTCAACGTGGCATTTACC+TGG + chr3.3:77111824-77111843 MS.gene06633:intron 50.0%
GCAGTTATACGGTGGTTCGA+CGG - chr3.3:77112271-77112290 None:intergenic 50.0%
GTAATCAATAACGCCGGTGG+AGG + chr3.3:77112240-77112259 MS.gene06633:CDS 50.0%
! TCAACACATTTTCGGCCACG+CGG + chr3.3:77111781-77111800 MS.gene06633:intron 50.0%
! TCAACACATTTTCGGCCACG+TGG + chr3.3:77111781-77111800 MS.gene06633:intron 50.0%
!! TGAATTTGGGTTGTGGCAGC+TGG + chr3.3:77111680-77111699 MS.gene06633:intron 50.0%
!! TGGGAGGTGCTGATTCATTC+TGG + chr3.3:77110762-77110781 MS.gene06633:CDS 50.0%
GGCTCACGGTAATCATCTGC+AGG - chr3.3:77110702-77110721 None:intergenic 55.0%
TCCAATCAGCAAGTGCCACG+TGG - chr3.3:77111799-77111818 None:intergenic 55.0%
! TACAATCAGCAAGTGCCGCG+TGG - chr3.3:77111937-77111956 None:intergenic 55.0%
!! GAGGAACCGGTATTGGCTCA+CGG - chr3.3:77110716-77110735 None:intergenic 55.0%
! GCCACGTGGCACTTGCTGAT+TGG + chr3.3:77111795-77111814 MS.gene06633:intron 60.0%
!! TTCGACGGTGTTGCCTCCAC+CGG - chr3.3:77112256-77112275 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 77110513 77112314 77110513 ID=MS.gene06633
chr3.3 mRNA 77110513 77112314 77110513 ID=MS.gene06633.t1;Parent=MS.gene06633
chr3.3 exon 77110513 77110529 77110513 ID=MS.gene06633.t1.exon1;Parent=MS.gene06633.t1
chr3.3 CDS 77110513 77110529 77110513 ID=cds.MS.gene06633.t1;Parent=MS.gene06633.t1
chr3.3 exon 77110614 77110809 77110614 ID=MS.gene06633.t1.exon2;Parent=MS.gene06633.t1
chr3.3 CDS 77110614 77110809 77110614 ID=cds.MS.gene06633.t1;Parent=MS.gene06633.t1
chr3.3 exon 77110902 77111133 77110902 ID=MS.gene06633.t1.exon3;Parent=MS.gene06633.t1
chr3.3 CDS 77110902 77111133 77110902 ID=cds.MS.gene06633.t1;Parent=MS.gene06633.t1
chr3.3 exon 77112232 77112314 77112232 ID=MS.gene06633.t1.exon4;Parent=MS.gene06633.t1
chr3.3 CDS 77112232 77112314 77112232 ID=cds.MS.gene06633.t1;Parent=MS.gene06633.t1
Gene Sequence

>MS.gene06633

ATGGCAACATTGAAGAGGTAATAAAGTTTATGGTATGAAGTTAAGAAATCGTTGATTGAACCATTTTATGTTGACTTGATACTATGATTTAATTACTGCAGTGAGTCCAGTAAGGTTGATGCAGAGAAGATGCAATATTCGAATGAAGAAGGAGGAAGATCTGCAGAACCTCAAATTGATGTAGAACCTGCAGATGATTACCGTGAGCCAATACCGGTTCCTCCATGTCTGAATGTTCGAACAAATTCATGGGAGGTGCTGATTCATTCTGGTCATTTACGTCCAACTCATAAGCTGGTAATCTAAAGATATTCCCTTACTTTATGTTAGTTTTATAAGTAAACAAAGAATGTTTTTGAATTGACATATTTGTAATTGATATGATGTAGCGAATTCCATTCCACATCAATGGATCTTTTCGTGAACCTGGGAAAGAGACTCTGACATTGACATTGGTTGATTATGAAGAAGATGCAGTTGATGCGATCTGGTGTGATATTGATGTTGAACCTGGTGATTATGTGCAGAAGAAATTCATAGGAAGGGGTTGGCATACATTTGTTGAAGCGAGTAAGGTGAAAGTTGGTGACAGATTGTTGTTTAAGATGGACAGTAATCCGGGTAATTGCTATGTTAAATTTCTGGAAAGTGATATATAAAACTGGTAAGTGGTGTTTGTTTGGAGACAGTGTGTTGGTTGTACTATGTATTTGTTTAGTTGTATTAAGTACTAAAAGATCAGGTTGCTTAAGATAATGGTTTGTAATGTTTATTTTAAACTTTGTAGTAATGGTTGTTCTGAAGAATATCTACGTGTTTATTATGTTATGAAATTCGTTATTTTTATTGACAGCTGAATTATAAGTATAATTTTATATATAATAAATAAGGATATTATGAATAAGAATAGCATGGTACATGAGAAAAATATGAAGTGAAAGTTGATTATTAATGAAATGGTTGGCGAAAAATTCATTGTAAAATTGTTAAATATATATAAACGAAAAGACTTAAATATATAGGAGTGGATGATGAATGTGGCAATATTTTGTATTCATTTGTGTTACTGTAAAATGTAGAACTTGACTTGACCACTCATAAAGAAAAGAGATGGATTTAGTTAAAAAATAAAAGCTAAAAAAATGTTTTTGGTACCTGTAAATATAGTGAATTTGGGTTGTGGCAGCTGGTAAAAAAAACTTTTGAAACACGTCTATGTAAAATTTTTTGTTTTTTAAAATAGCCTCTGGACTCACTTTCTTGATGATTCAACACATTTTCGGCCACGTGGCACTTGCTGATTGGACAAAACTGTCAACGTGGCATTTACCTGGAATTAATAAATTAGAAAATAAAATAAAAAAACAGTTTTTTAAAATAGTCTCTAGACTCACTTTCTTGATGATTCAACACATTTTCGGCCACGCGGCACTTGCTGATTGTACAAAACTGTCAAGTGGCATTTACTTGGAATTAATAAATTAGAAAATAAAATAAAAAAACATAAAAAGATTTATTATTATTTTTATTTCCTTATTTTAAAAGATGAAAATAGAAAGGGGGAGATTAAAAATGAGGGTATATGCCATTATTATTCTTCTTCCTGTAATCGTTTTCTCTTCCTCCTTGTTTCTCCTCTCATCTTCTTATTCTTTTTCTTCTTATTCACAATCCTGGAAATCAAAACCAATCAAGATTGTGTTGTGGACAACAACTCAGATGCAATTGTAATCAATAACGCCGGTGGAGGCAACACCGTCGAACCACCGTATAACTGCGAGTTTGAAGTCGAGATTTGTTGA

Protein sequence

>MS.gene06633.t1

MATLKSESSKVDAEKMQYSNEEGGRSAEPQIDVEPADDYREPIPVPPCLNVRTNSWEVLIHSGHLRPTHKLRIPFHINGSFREPGKETLTLTLVDYEEDAVDAIWCDIDVEPGDYVQKKFIGRGWHTFVEASKVKVGDRLLFKMDSNPDAIVINNAGGGNTVEPPYNCEFEVEIC