AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene059688


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059688.t1 MTR_8g091410 88.636 132 12 1 1 129 82 213 1.70e-78 231
MS.gene059688.t1 MTR_4g094785 49.593 123 57 2 2 120 116 237 1.92e-32 114
MS.gene059688.t1 MTR_8g012380 36.364 110 56 3 23 129 46 144 1.22e-12 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene059688.t1 AT4G39710 70.455 132 36 1 1 129 86 217 1.90e-61 187
MS.gene059688.t1 AT4G39710 70.455 132 36 1 1 129 86 217 1.90e-61 187
MS.gene059688.t1 AT5G45680 50.407 123 58 1 2 121 84 206 3.51e-34 118
MS.gene059688.t1 AT4G39710 65.432 81 25 1 1 78 86 166 5.04e-29 104
MS.gene059688.t1 AT5G48580 34.951 103 53 3 23 122 48 139 5.85e-11 57.0

Find 37 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGATTGGATCAGGGAATTT+TGG 0.124572 4.3:+9838118 MS.gene059688:CDS
TAAATTTGTTGGTCTTTATT+CGG 0.242676 4.3:+9838813 MS.gene059688:CDS
TGCGATTATGTTGAGGGTTT+TGG 0.282156 4.3:+9837787 MS.gene059688:CDS
GGTAATTAGGGGATTGGATC+AGG 0.291509 4.3:+9838109 MS.gene059688:intron
GAGCTTAATTATGTTAAATC+TGG 0.297049 4.3:+9837754 MS.gene059688:CDS
AAATTTGTTGGTCTTTATTC+GGG 0.311128 4.3:+9838814 MS.gene059688:CDS
CTGTATGATATTAAATTTGT+TGG 0.318710 4.3:+9838802 MS.gene059688:CDS
GAACCTGCAGGCTGCTTCTC+AGG 0.336346 4.3:+9838294 MS.gene059688:CDS
TTTGGTGATGAAGCTCCTTT+AGG 0.338411 4.3:+9837805 MS.gene059688:CDS
GAGAAGCAGCCTGCAGGTTC+AGG 0.345343 4.3:-9838291 None:intergenic
AATTATGTTAAATCTGGGCT+TGG 0.422396 4.3:+9837760 MS.gene059688:CDS
ATTTCAGGTAATTAGGGGAT+TGG 0.431931 4.3:+9838103 MS.gene059688:intron
GGTTATTGCGATTATGTTGA+GGG 0.433499 4.3:+9837781 MS.gene059688:CDS
AGCTTAATTATGTTAAATCT+GGG 0.462974 4.3:+9837755 MS.gene059688:CDS
AATAGGTGACTGCAATATAC+CGG 0.483379 4.3:+9838765 MS.gene059688:intron
GATAGTAGTTATAACGTGCT+AGG 0.505469 4.3:+9837970 MS.gene059688:CDS
TGGTTATTGCGATTATGTTG+AGG 0.512709 4.3:+9837780 MS.gene059688:CDS
AATTTAATACCTATCCGCAT+TGG 0.515893 4.3:-9838158 None:intergenic
ATTCCTCCATTGTTAGCGTA+TGG 0.515896 4.3:+9838267 MS.gene059688:CDS
AAACCTGAGAAGCAGCCTGC+AGG 0.532161 4.3:-9838297 None:intergenic
TTAATACCTATCCGCATTGG+AGG 0.539094 4.3:-9838155 None:intergenic
TACAGAAGAGTTGCATTGCC+CGG 0.539306 4.3:-9838784 None:intergenic
AGGCCACTCACTATGCGTAT+TGG 0.545910 4.3:+9837990 MS.gene059688:CDS
ACATCAATAAGCTCTCCTAA+AGG 0.553954 4.3:-9837820 None:intergenic
GCGTATGGTCCTGAACCTGC+AGG 0.559980 4.3:+9838282 MS.gene059688:CDS
CTCACTATGCGTATTGGTGT+TGG 0.565060 4.3:+9837996 MS.gene059688:CDS
GTAATTAGGGGATTGGATCA+GGG 0.593610 4.3:+9838110 MS.gene059688:intron
ACTATCAAATACTATTCCAT+CGG 0.594477 4.3:-9837953 None:intergenic
TATGCGTATTGGTGTTGGCA+AGG 0.622438 4.3:+9838001 MS.gene059688:CDS
ACATAATTAAGCTCACACAT+TGG 0.625130 4.3:-9837745 None:intergenic
GGCGTACCTCCAATGCGGAT+AGG 0.639198 4.3:+9838149 MS.gene059688:CDS
ATAGGTGACTGCAATATACC+GGG 0.650180 4.3:+9838766 MS.gene059688:intron
TCAGGACCATACGCTAACAA+TGG 0.656714 4.3:-9838273 None:intergenic
GGACCATACGCTAACAATGG+AGG 0.666829 4.3:-9838270 None:intergenic
ACACCAATACGCATAGTGAG+TGG 0.668322 4.3:-9837993 None:intergenic
TATACTGCTAGATTCGCCGA+TGG 0.684653 4.3:+9837937 MS.gene059688:CDS
GTGAAGGCGTACCTCCAATG+CGG 0.724987 4.3:+9838144 MS.gene059688:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTATTTACTATTTTACTT+AGG + chr4.3:9838225-9838244 MS.gene059688:intron 10.0%
!! AGCTTAATTATGTTAAATCT+GGG + chr4.3:9837755-9837774 MS.gene059688:CDS 20.0%
!! ATTATTATCAGAAGAAGAAA+AGG + chr4.3:9838697-9838716 MS.gene059688:intron 20.0%
!! CTGTATGATATTAAATTTGT+TGG + chr4.3:9838802-9838821 MS.gene059688:CDS 20.0%
!! TGAAACATTAATCATGTATT+TGG + chr4.3:9838428-9838447 MS.gene059688:intron 20.0%
!!! ATTTACTATTTTACTTAGGT+GGG + chr4.3:9838229-9838248 MS.gene059688:intron 20.0%
!!! TAAATTTGTTGGTCTTTATT+CGG + chr4.3:9838813-9838832 MS.gene059688:CDS 20.0%
!!! TATTTACTATTTTACTTAGG+TGG + chr4.3:9838228-9838247 MS.gene059688:intron 20.0%
! ACTATCAAATACTATTCCAT+CGG - chr4.3:9837956-9837975 None:intergenic 25.0%
! GAGCTTAATTATGTTAAATC+TGG + chr4.3:9837754-9837773 MS.gene059688:CDS 25.0%
! TACATTGGTAGAAAATATAC+CGG - chr4.3:9838479-9838498 None:intergenic 25.0%
!! AAAAGACCATGGATTTTATT+AGG + chr4.3:9838649-9838668 MS.gene059688:intron 25.0%
!! AATGTGAATTTCAGGTAATT+AGG + chr4.3:9838096-9838115 MS.gene059688:intron 25.0%
!! ATGTGAATTTCAGGTAATTA+GGG + chr4.3:9838097-9838116 MS.gene059688:intron 25.0%
!!! AAATTTGTTGGTCTTTATTC+GGG + chr4.3:9838814-9838833 MS.gene059688:CDS 25.0%
!!! AGTTTTGTCATTGATTCAAT+AGG + chr4.3:9838748-9838767 MS.gene059688:intron 25.0%
!!! TTTCTTGTTTTTGTTGAGTT+TGG + chr4.3:9838060-9838079 MS.gene059688:intron 25.0%
AATTATGTTAAATCTGGGCT+TGG + chr4.3:9837760-9837779 MS.gene059688:CDS 30.0%
AATTTAATACCTATCCGCAT+TGG - chr4.3:9838161-9838180 None:intergenic 30.0%
ACATTGGTAGAAAATATACC+GGG - chr4.3:9838478-9838497 None:intergenic 30.0%
ATCTACAATTGAAAAGACCA+TGG + chr4.3:9838638-9838657 MS.gene059688:intron 30.0%
CTAACATATTTGATGCAGAT+AGG + chr4.3:9838185-9838204 MS.gene059688:intron 30.0%
TAAAAAATGTAGCAGACACT+TGG + chr4.3:9838396-9838415 MS.gene059688:intron 30.0%
TGTTGAGTTTGGACTTATAA+GGG + chr4.3:9838071-9838090 MS.gene059688:intron 30.0%
TTGTTGAGTTTGGACTTATA+AGG + chr4.3:9838070-9838089 MS.gene059688:intron 30.0%
! GTCTTTTCAATTGTAGATTG+CGG - chr4.3:9838636-9838655 None:intergenic 30.0%
! TGTGAATTTCAGGTAATTAG+GGG + chr4.3:9838098-9838117 MS.gene059688:intron 30.0%
!! ATGTGATTTGCTACTAAACA+TGG + chr4.3:9838347-9838366 MS.gene059688:intron 30.0%
AATAGGTGACTGCAATATAC+CGG + chr4.3:9838765-9838784 MS.gene059688:intron 35.0%
ACATCAATAAGCTCTCCTAA+AGG - chr4.3:9837823-9837842 None:intergenic 35.0%
ATTGGTAGAAAATATACCGG+GGG - chr4.3:9838476-9838495 None:intergenic 35.0%
CATTGGTAGAAAATATACCG+GGG - chr4.3:9838477-9838496 None:intergenic 35.0%
GATAGTAGTTATAACGTGCT+AGG + chr4.3:9837970-9837989 MS.gene059688:CDS 35.0%
GGTTATTGCGATTATGTTGA+GGG + chr4.3:9837781-9837800 MS.gene059688:CDS 35.0%
TAAGGGTGAATGTGAATTTC+AGG + chr4.3:9838088-9838107 MS.gene059688:intron 35.0%
TGGTTATTGCGATTATGTTG+AGG + chr4.3:9837780-9837799 MS.gene059688:CDS 35.0%
! ACCATGGATTTTATTAGGCT+GGG + chr4.3:9838654-9838673 MS.gene059688:intron 35.0%
! ATTTCAGGTAATTAGGGGAT+TGG + chr4.3:9838103-9838122 MS.gene059688:intron 35.0%
!!! TGTAGCTGCTTGTTTTACAT+TGG - chr4.3:9838494-9838513 None:intergenic 35.0%
ATAGGTGACTGCAATATACC+GGG + chr4.3:9838766-9838785 MS.gene059688:intron 40.0%
ATTCCTCCATTGTTAGCGTA+TGG + chr4.3:9838267-9838286 MS.gene059688:CDS 40.0%
GTAATTAGGGGATTGGATCA+GGG + chr4.3:9838110-9838129 MS.gene059688:intron 40.0%
TCCCAGCCTAATAAAATCCA+TGG - chr4.3:9838658-9838677 None:intergenic 40.0%
TTAATACCTATCCGCATTGG+AGG - chr4.3:9838158-9838177 None:intergenic 40.0%
TTGGTAGAAAATATACCGGG+GGG - chr4.3:9838475-9838494 None:intergenic 40.0%
! ATTGGATCAGGGAATTTTGG+GGG + chr4.3:9838121-9838140 MS.gene059688:CDS 40.0%
! GACCATGGATTTTATTAGGC+TGG + chr4.3:9838653-9838672 MS.gene059688:intron 40.0%
! GATTGGATCAGGGAATTTTG+GGG + chr4.3:9838120-9838139 MS.gene059688:CDS 40.0%
! GGATTGGATCAGGGAATTTT+GGG + chr4.3:9838119-9838138 MS.gene059688:CDS 40.0%
! TGCGATTATGTTGAGGGTTT+TGG + chr4.3:9837787-9837806 MS.gene059688:CDS 40.0%
!! TTTGGTGATGAAGCTCCTTT+AGG + chr4.3:9837805-9837824 MS.gene059688:CDS 40.0%
AACAAGCAGCTACAGTGCTA+TGG + chr4.3:9838500-9838519 MS.gene059688:intron 45.0%
ACACCAATACGCATAGTGAG+TGG - chr4.3:9837996-9838015 None:intergenic 45.0%
GGTAATTAGGGGATTGGATC+AGG + chr4.3:9838109-9838128 MS.gene059688:intron 45.0%
TACAGAAGAGTTGCATTGCC+CGG - chr4.3:9838787-9838806 None:intergenic 45.0%
TATACTGCTAGATTCGCCGA+TGG + chr4.3:9837937-9837956 MS.gene059688:CDS 45.0%
TCAGGACCATACGCTAACAA+TGG - chr4.3:9838276-9838295 None:intergenic 45.0%
TGGTAGAAAATATACCGGGG+GGG - chr4.3:9838474-9838493 None:intergenic 45.0%
! CTCACTATGCGTATTGGTGT+TGG + chr4.3:9837996-9838015 MS.gene059688:CDS 45.0%
! GGGATTGGATCAGGGAATTT+TGG + chr4.3:9838118-9838137 MS.gene059688:CDS 45.0%
! TTGGATCAGGGAATTTTGGG+GGG + chr4.3:9838122-9838141 MS.gene059688:CDS 45.0%
!! TATGCGTATTGGTGTTGGCA+AGG + chr4.3:9838001-9838020 MS.gene059688:CDS 45.0%
AGGCCACTCACTATGCGTAT+TGG + chr4.3:9837990-9838009 MS.gene059688:CDS 50.0%
GGACCATACGCTAACAATGG+AGG - chr4.3:9838273-9838292 None:intergenic 50.0%
AAACCTGAGAAGCAGCCTGC+AGG - chr4.3:9838300-9838319 None:intergenic 55.0%
! GTGAAGGCGTACCTCCAATG+CGG + chr4.3:9838144-9838163 MS.gene059688:CDS 55.0%
!! CAGGGAATTTTGGGGGGTGA+AGG + chr4.3:9838128-9838147 MS.gene059688:CDS 55.0%
GAACCTGCAGGCTGCTTCTC+AGG + chr4.3:9838294-9838313 MS.gene059688:CDS 60.0%
GAGAAGCAGCCTGCAGGTTC+AGG - chr4.3:9838294-9838313 None:intergenic 60.0%
GCGTATGGTCCTGAACCTGC+AGG + chr4.3:9838282-9838301 MS.gene059688:CDS 60.0%
GGCGTACCTCCAATGCGGAT+AGG + chr4.3:9838149-9838168 MS.gene059688:CDS 60.0%
CCATTGTGCGTACGCCCCCC+CGG + chr4.3:9838457-9838476 MS.gene059688:intron 70.0%
! CCGGGGGGGCGTACGCACAA+TGG - chr4.3:9838460-9838479 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 9837748 9838852 9837748 ID=MS.gene059688
chr4.3 mRNA 9837748 9838852 9837748 ID=MS.gene059688.t1;Parent=MS.gene059688
chr4.3 exon 9837748 9837840 9837748 ID=MS.gene059688.t1.exon1;Parent=MS.gene059688.t1
chr4.3 CDS 9837748 9837840 9837748 ID=cds.MS.gene059688.t1;Parent=MS.gene059688.t1
chr4.3 exon 9837931 9838022 9837931 ID=MS.gene059688.t1.exon2;Parent=MS.gene059688.t1
chr4.3 CDS 9837931 9838022 9837931 ID=cds.MS.gene059688.t1;Parent=MS.gene059688.t1
chr4.3 exon 9838118 9838170 9838118 ID=MS.gene059688.t1.exon3;Parent=MS.gene059688.t1
chr4.3 CDS 9838118 9838170 9838118 ID=cds.MS.gene059688.t1;Parent=MS.gene059688.t1
chr4.3 exon 9838247 9838315 9838247 ID=MS.gene059688.t1.exon4;Parent=MS.gene059688.t1
chr4.3 CDS 9838247 9838315 9838247 ID=cds.MS.gene059688.t1;Parent=MS.gene059688.t1
chr4.3 exon 9838770 9838852 9838770 ID=MS.gene059688.t1.exon5;Parent=MS.gene059688.t1
chr4.3 CDS 9838770 9838852 9838770 ID=cds.MS.gene059688.t1;Parent=MS.gene059688.t1
Gene Sequence

>MS.gene059688

ATGTGTGAGCTTAATTATGTTAAATCTGGGCTTGGTTATTGCGATTATGTTGAGGGTTTTGGTGATGAAGCTCCTTTAGGAGAGCTTATTGATGTAAGTTGTTTATTACTCTTACTCGTTTTCTATATGCAAAAATTCAATTAGTGAATTAACAAGTGATATTTTTACTATTATACATTGCAGATTCACTATACTGCTAGATTCGCCGATGGAATAGTATTTGATAGTAGTTATAACGTGCTAGGCCACTCACTATGCGTATTGGTGTTGGCAAGGTAGATAAGTTTTACTTGCTGTTAATTCTTTTTGTTATTTCTTGTTTTTGTTGAGTTTGGACTTATAAGGGTGAATGTGAATTTCAGGTAATTAGGGGATTGGATCAGGGAATTTTGGGGGGTGAAGGCGTACCTCCAATGCGGATAGGTATTAAATTAAATCTAACATATTTGATGCAGATAGGTATATGACACTTGCTAAATTTATTTACTATTTTACTTAGGTGGGAAACGCAAACTCATGATTCCTCCATTGTTAGCGTATGGTCCTGAACCTGCAGGCTGCTTCTCAGGTTTCATTCATTATTAATTTACTGCATTATTATGTGATTTGCTACTAAACATGGATAACTACTTTAATCAAACGTAAAACTAAAAAATGTAGCAGACACTTGGATGAAGAAATGAAACATTAATCATGTATTTGGTCATATCCATTGTGCGTACGCCCCCCCGGTATATTTTCTACCAATGTAAAACAAGCAGCTACAGTGCTATGGAATTCAAATAAATTGCTATTGATTCATGATATGCTGTTTAGAACAAAGTGTTGTCAAATACTAGCTATGAAACAATGTAGCTTAGTAGAATTTGAGCAAACTGCTATATTCCGCAATCTACAATTGAAAAGACCATGGATTTTATTAGGCTGGGAAGATATTGAATGCAACATTATTATTATCAGAAGAAGAAAAGGAGAATCATTAAATATGTTAGATTTTGACAGTTTTGTCATTGATTCAATAGGTGACTGCAATATACCGGGCAATGCAACTCTTCTGTATGATATTAAATTTGTTGGTCTTTATTCGGGCAATCGAAGTCAATGA

Protein sequence

>MS.gene059688.t1

MCELNYVKSGLGYCDYVEGFGDEAPLGELIDIHYTARFADGIVFDSSYNVLGHSLCVLVLARGLDQGILGGEGVPPMRIGGKRKLMIPPLLAYGPEPAGCFSGDCNIPGNATLLYDIKFVGLYSGNRSQ