AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene93356


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene93356.t1 MTR_3g435550 88.265 196 19 2 94 289 1 192 1.14e-124 354
MS.gene93356.t1 MTR_3g091700 50.467 107 47 1 159 265 159 259 4.42e-30 114
MS.gene93356.t1 MTR_0140s0010 40.805 174 78 7 87 250 61 219 2.59e-27 106
MS.gene93356.t1 MTR_5g024070 36.719 128 73 2 140 260 188 314 1.90e-21 92.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene93356.t1 AT1G18790 62.500 128 41 2 141 261 112 239 8.20e-50 166
MS.gene93356.t1 AT1G74480 61.207 116 40 2 147 257 127 242 6.75e-42 146
MS.gene93356.t1 AT5G66990 51.128 133 58 2 135 262 142 272 1.30e-40 142
MS.gene93356.t1 AT5G53040 53.704 108 44 2 154 261 148 249 1.12e-30 116
MS.gene93356.t1 AT4G35590 37.313 134 72 2 154 280 192 320 6.70e-19 85.5
MS.gene93356.t1 AT4G35590 38.060 134 71 3 154 280 242 370 9.28e-19 85.9

Find 52 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTACTTGTACATTCTTTATA+AGG 0.172964 3.2:+26832604 None:intergenic
GATTATCATACGTAGAAAAT+TGG 0.202707 3.2:+26833311 None:intergenic
TTCAATGATTGGTCACATTA+TGG 0.214480 3.2:-26833145 MS.gene93356:CDS
TGATAACCTTCTATGCTTAA+TGG 0.225802 3.2:+26833025 None:intergenic
AGAGTTTCATTTCGAAATTC+AGG 0.227635 3.2:+26833073 None:intergenic
TTCCATGAAAGGATCAAAAT+TGG 0.229603 3.2:+26833105 None:intergenic
TCTCTAGCAGCTTGAGATAT+TGG 0.323623 3.2:+26832717 None:intergenic
AAGAAAAGGTGTAGGGATCT+TGG 0.330015 3.2:-26832669 MS.gene93356:CDS
TCAATGACAGACTATGGTTA+TGG 0.334072 3.2:-26832936 MS.gene93356:intron
GCTCATGGTTATGAGGTTAA+TGG 0.347444 3.2:-26831867 MS.gene93356:CDS
TACTTGTACATTCTTTATAA+GGG 0.359802 3.2:+26832605 None:intergenic
AGTTGATGCTGGATATTATT+CGG 0.383233 3.2:-26832880 MS.gene93356:CDS
GGTGCAGGTACAAGTAATTC+AGG 0.392094 3.2:+26833046 None:intergenic
CCTGCACCATTAAGCATAGA+AGG 0.395032 3.2:-26833031 MS.gene93356:intron
GGCTTACACATTTGAAGAAA+AGG 0.415724 3.2:-26832683 MS.gene93356:CDS
CAATGACAGACTATGGTTAT+GGG 0.417103 3.2:-26832935 MS.gene93356:intron
CATTCTTTATAAGGGTTTGA+AGG 0.417292 3.2:+26832613 None:intergenic
TATGAGGTTAATGGAACAAC+AGG 0.443913 3.2:-26831858 MS.gene93356:CDS
ATCAAAATTGGTATCTTGCA+TGG 0.445144 3.2:+26833117 None:intergenic
CTGCTAGAGACCTTAATGTT+GGG 0.489436 3.2:-26832704 MS.gene93356:CDS
GAAAGAAATGAAGAAGGTAG+AGG 0.489935 3.2:-26831969 MS.gene93356:CDS
ATGAATGTGATGAGAAGATA+AGG 0.493501 3.2:-26832012 MS.gene93356:CDS
AATTGGAATGGAGGTTGCAA+TGG 0.509497 3.2:+26833328 None:intergenic
GCTTAGACAAGCATGTTTCA+AGG 0.510842 3.2:-26831909 MS.gene93356:CDS
CCTTCTATGCTTAATGGTGC+AGG 0.511925 3.2:+26833031 None:intergenic
ATTGCAGAAAGAAATGAAGA+AGG 0.517898 3.2:-26831975 MS.gene93356:CDS
AGAGAAGGCTCATGGTTATG+AGG 0.522137 3.2:-26831874 MS.gene93356:CDS
GCTGCTAGAGACCTTAATGT+TGG 0.523622 3.2:-26832705 MS.gene93356:CDS
AATGTGTAAGCCCAACATTA+AGG 0.530566 3.2:+26832694 None:intergenic
CACATTTGAAGAAAAGGTGT+AGG 0.540159 3.2:-26832677 MS.gene93356:CDS
GAATTCAAAGGTGGCCACAT+AGG 0.544869 3.2:-26832647 MS.gene93356:CDS
TCAAAATTGGTATCTTGCAT+GGG 0.545683 3.2:+26833118 None:intergenic
ATGTGGAATGAAGTTGATGC+TGG 0.550987 3.2:-26832891 MS.gene93356:CDS
TACTGGAGAAAATGTTGCAA+AGG 0.556786 3.2:-26832829 MS.gene93356:CDS
AGGCTAATTACAAGAAGAGA+AGG 0.568624 3.2:-26831889 MS.gene93356:CDS
AGGCTCATTAGTTTCCTATG+TGG 0.571114 3.2:+26832633 None:intergenic
TGTTGCAAAGGAAATTGTGA+AGG 0.572064 3.2:-26832817 MS.gene93356:CDS
ACATTTGAAGAAAAGGTGTA+GGG 0.575896 3.2:-26832676 MS.gene93356:CDS
TTATTGGTGGTGCAGGAGCA+AGG 0.586794 3.2:-26832037 MS.gene93356:intron
TCATATTTCAAAACCGTGAG+TGG 0.589090 3.2:+26833379 None:intergenic
AACTTGATGAAAACACAAAG+AGG 0.589787 3.2:-26831931 MS.gene93356:CDS
TTACAAGAAGAGAAGGCTCA+TGG 0.590126 3.2:-26831882 MS.gene93356:CDS
GTAGGGATCTTGGAATTCAA+AGG 0.603743 3.2:-26832659 MS.gene93356:CDS
TACGTAGAAAATTGGAATGG+AGG 0.603829 3.2:+26833319 None:intergenic
AATGACAGACTATGGTTATG+GGG 0.605489 3.2:-26832934 MS.gene93356:intron
TCATACGTAGAAAATTGGAA+TGG 0.613632 3.2:+26833316 None:intergenic
GTTGCAAAGGAAATTGTGAA+GGG 0.628143 3.2:-26832816 MS.gene93356:CDS
GCATCAACTTCATTCCACAT+TGG 0.632538 3.2:+26832894 None:intergenic
GGAGAATGTTGATCCACTCA+CGG 0.640251 3.2:-26833392 MS.gene93356:CDS
TGAGAAGATAAGGAATGCTG+TGG 0.656309 3.2:-26832002 MS.gene93356:CDS
GCAGGTACAAGTAATTCAGG+TGG 0.663503 3.2:+26833049 None:intergenic
GGGATCTTGGAATTCAAAGG+TGG 0.676630 3.2:-26832656 MS.gene93356:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTATTTTTATTTTTTTA+CGG - chr3.2:26833005-26833024 MS.gene93356:intron 0.0%
!! AAAGTAAAAAAAATACAAAA+AGG + chr3.2:26831969-26831988 None:intergenic 10.0%
!! CTGTAAAAAAAATAAAAAAT+AGG + chr3.2:26832015-26832034 None:intergenic 10.0%
!!! AATTTATTTATTTTGTTAAC+GGG - chr3.2:26832206-26832225 MS.gene93356:intron 10.0%
!!! AATTTTTAAAGATAATTTCA+TGG + chr3.2:26831992-26832011 None:intergenic 10.0%
!!! ATTTTTTTTACTAATTTTTG+TGG - chr3.2:26832942-26832961 MS.gene93356:intron 10.0%
!! ATTGCAAACTAAAAAAATAT+TGG + chr3.2:26832606-26832625 None:intergenic 15.0%
!!! AGTAAGAATGAAAAATATTT+TGG + chr3.2:26832789-26832808 None:intergenic 15.0%
!!! ATTTATTTATTTTGTTAACG+GGG - chr3.2:26832207-26832226 MS.gene93356:intron 15.0%
!!! TTGAAACGTTTTATTATTAT+TGG - chr3.2:26833128-26833147 MS.gene93356:CDS 15.0%
!! TACTTGTACATTCTTTATAA+GGG + chr3.2:26832579-26832598 None:intergenic 20.0%
!! TTACTTGTACATTCTTTATA+AGG + chr3.2:26832580-26832599 None:intergenic 20.0%
!!! AAACGTTTTATTATTATTGG+TGG - chr3.2:26833131-26833150 MS.gene93356:CDS 20.0%
!!! TTCATTCTTACTTATTTTTG+TGG - chr3.2:26832797-26832816 MS.gene93356:CDS 20.0%
!!! TTTTTTACAGATTCAATGAT+TGG - chr3.2:26832025-26832044 MS.gene93356:CDS 20.0%
! AAAATACAAAAAGGAACTAG+TGG + chr3.2:26831960-26831979 None:intergenic 25.0%
! AATTATTCAATGACAGACTA+TGG - chr3.2:26832239-26832258 MS.gene93356:intron 25.0%
! GATTATCATACGTAGAAAAT+TGG + chr3.2:26831873-26831892 None:intergenic 25.0%
!! AATTCCATCACTAAATTTTG+CGG - chr3.2:26832718-26832737 MS.gene93356:CDS 25.0%
!! GGATAATAATTTTCCATGAA+AGG + chr3.2:26832090-26832109 None:intergenic 25.0%
!! TTAGTGATGGAATTAAAGAT+CGG + chr3.2:26832712-26832731 None:intergenic 25.0%
!!! AATGTGGATTACTTTTTTTG+TGG - chr3.2:26832860-26832879 MS.gene93356:CDS 25.0%
!!! GAATGAAAAATATTTTGGCA+AGG + chr3.2:26832784-26832803 None:intergenic 25.0%
!!! TGTAGTGAATTGTTTTAATG+TGG - chr3.2:26832844-26832863 MS.gene93356:CDS 25.0%
!!! TTACTTTTTTTGTGGCTTTT+TGG - chr3.2:26832868-26832887 MS.gene93356:CDS 25.0%
AACTTGATGAAAACACAAAG+AGG - chr3.2:26833250-26833269 MS.gene93356:intron 30.0%
AGAGTTTCATTTCGAAATTC+AGG + chr3.2:26832111-26832130 None:intergenic 30.0%
ATCAAAATTGGTATCTTGCA+TGG + chr3.2:26832067-26832086 None:intergenic 30.0%
ATGAATGTGATGAGAAGATA+AGG - chr3.2:26833169-26833188 MS.gene93356:intron 30.0%
ATTGCAGAAAGAAATGAAGA+AGG - chr3.2:26833206-26833225 MS.gene93356:intron 30.0%
CATTCTTTATAAGGGTTTGA+AGG + chr3.2:26832571-26832590 None:intergenic 30.0%
TCAAAATTGGTATCTTGCAT+GGG + chr3.2:26832066-26832085 None:intergenic 30.0%
TCATACGTAGAAAATTGGAA+TGG + chr3.2:26831868-26831887 None:intergenic 30.0%
TGATAACCTTCTATGCTTAA+TGG + chr3.2:26832159-26832178 None:intergenic 30.0%
TTCCATGAAAGGATCAAAAT+TGG + chr3.2:26832079-26832098 None:intergenic 30.0%
TTGATTTAGCTAGCAAATCA+TGG + chr3.2:26833043-26833062 None:intergenic 30.0%
! ACATTTGAAGAAAAGGTGTA+GGG - chr3.2:26832505-26832524 MS.gene93356:intron 30.0%
! AGTTGATGCTGGATATTATT+CGG - chr3.2:26832301-26832320 MS.gene93356:intron 30.0%
! TGCAAGCAAATCATGATTTT+AGG + chr3.2:26832910-26832929 None:intergenic 30.0%
! TTCAATGATTGGTCACATTA+TGG - chr3.2:26832036-26832055 MS.gene93356:intron 30.0%
! TTTTCGATTAGCAACATTAC+TGG - chr3.2:26832335-26832354 MS.gene93356:intron 30.0%
!! TACCAATTTTGATCCTTTCA+TGG - chr3.2:26832074-26832093 MS.gene93356:intron 30.0%
!! TGGAATTAAAGATCGGTTTT+AGG + chr3.2:26832705-26832724 None:intergenic 30.0%
!! TTTATTATTATTGGTGGTGC+AGG - chr3.2:26833137-26833156 MS.gene93356:CDS 30.0%
!! TTTTCATCAAGTTGCAAATC+TGG + chr3.2:26833243-26833262 None:intergenic 30.0%
AATGACAGACTATGGTTATG+GGG - chr3.2:26832247-26832266 MS.gene93356:intron 35.0%
AATGTGTAAGCCCAACATTA+AGG + chr3.2:26832490-26832509 None:intergenic 35.0%
AGGCTAATTACAAGAAGAGA+AGG - chr3.2:26833292-26833311 MS.gene93356:CDS 35.0%
CAATGACAGACTATGGTTAT+GGG - chr3.2:26832246-26832265 MS.gene93356:intron 35.0%
CATAATCACATTGTGTAGTG+AGG - chr3.2:26832659-26832678 MS.gene93356:CDS 35.0%
CTAAAAATGTGGTTCCAATG+TGG - chr3.2:26832273-26832292 MS.gene93356:intron 35.0%
GAAAGAAATGAAGAAGGTAG+AGG - chr3.2:26833212-26833231 MS.gene93356:intron 35.0%
GGCTTACACATTTGAAGAAA+AGG - chr3.2:26832498-26832517 MS.gene93356:intron 35.0%
GTTGCAAAGGAAATTGTGAA+GGG - chr3.2:26832365-26832384 MS.gene93356:intron 35.0%
TACGTAGAAAATTGGAATGG+AGG + chr3.2:26831865-26831884 None:intergenic 35.0%
TACTGGAGAAAATGTTGCAA+AGG - chr3.2:26832352-26832371 MS.gene93356:intron 35.0%
TATGAGGTTAATGGAACAAC+AGG - chr3.2:26833323-26833342 MS.gene93356:CDS 35.0%
TCAATGACAGACTATGGTTA+TGG - chr3.2:26832245-26832264 MS.gene93356:intron 35.0%
TCATATTTCAAAACCGTGAG+TGG + chr3.2:26831805-26831824 None:intergenic 35.0%
TGTTGCAAAGGAAATTGTGA+AGG - chr3.2:26832364-26832383 MS.gene93356:intron 35.0%
TTATGGGGATGCTAAAAATG+TGG - chr3.2:26832262-26832281 MS.gene93356:intron 35.0%
! CACATTTGAAGAAAAGGTGT+AGG - chr3.2:26832504-26832523 MS.gene93356:intron 35.0%
! GGCAAGGAAATCATGATTTT+AGG + chr3.2:26832768-26832787 None:intergenic 35.0%
!! TTTTGTGGCTTTTTGGTAAG+CGG - chr3.2:26832875-26832894 MS.gene93356:CDS 35.0%
AATTGGAATGGAGGTTGCAA+TGG + chr3.2:26831856-26831875 None:intergenic 40.0%
CAAGCCGCAAAATTTAGTGA+TGG + chr3.2:26832725-26832744 None:intergenic 40.0%
CTGCTAGAGACCTTAATGTT+GGG - chr3.2:26832477-26832496 MS.gene93356:intron 40.0%
GCATCAACTTCATTCCACAT+TGG + chr3.2:26832290-26832309 None:intergenic 40.0%
GCTCATGGTTATGAGGTTAA+TGG - chr3.2:26833314-26833333 MS.gene93356:CDS 40.0%
GCTTAGACAAGCATGTTTCA+AGG - chr3.2:26833272-26833291 MS.gene93356:CDS 40.0%
GTAGGGATCTTGGAATTCAA+AGG - chr3.2:26832522-26832541 MS.gene93356:intron 40.0%
TCTCTAGCAGCTTGAGATAT+TGG + chr3.2:26832467-26832486 None:intergenic 40.0%
TGAGAAGATAAGGAATGCTG+TGG - chr3.2:26833179-26833198 MS.gene93356:intron 40.0%
TTACAAGAAGAGAAGGCTCA+TGG - chr3.2:26833299-26833318 MS.gene93356:CDS 40.0%
! AAGAAAAGGTGTAGGGATCT+TGG - chr3.2:26832512-26832531 MS.gene93356:intron 40.0%
! AGGCTCATTAGTTTCCTATG+TGG + chr3.2:26832551-26832570 None:intergenic 40.0%
! CATCACTAAATTTTGCGGCT+TGG - chr3.2:26832723-26832742 MS.gene93356:CDS 40.0%
!! ATGTGGAATGAAGTTGATGC+TGG - chr3.2:26832290-26832309 MS.gene93356:intron 40.0%
AGAGAAGGCTCATGGTTATG+AGG - chr3.2:26833307-26833326 MS.gene93356:CDS 45.0%
CCTGCACCATTAAGCATAGA+AGG - chr3.2:26832150-26832169 MS.gene93356:intron 45.0%
CCTTCTATGCTTAATGGTGC+AGG + chr3.2:26832153-26832172 None:intergenic 45.0%
GAATTCAAAGGTGGCCACAT+AGG - chr3.2:26832534-26832553 MS.gene93356:intron 45.0%
GCAGGTACAAGTAATTCAGG+TGG + chr3.2:26832135-26832154 None:intergenic 45.0%
GCTGCTAGAGACCTTAATGT+TGG - chr3.2:26832476-26832495 MS.gene93356:intron 45.0%
GGAGAATGTTGATCCACTCA+CGG - chr3.2:26831789-26831808 MS.gene93356:CDS 45.0%
GGGATCTTGGAATTCAAAGG+TGG - chr3.2:26832525-26832544 MS.gene93356:intron 45.0%
GGTGCAGGTACAAGTAATTC+AGG + chr3.2:26832138-26832157 None:intergenic 45.0%
!! CACTAAATTTTGCGGCTTGG+TGG - chr3.2:26832726-26832745 MS.gene93356:CDS 45.0%
!!! TAATTTATTTATTTTGTTAA+CGG - chr3.2:26832205-26832224 MS.gene93356:intron 5.0%
!! TTATTGGTGGTGCAGGAGCA+AGG - chr3.2:26833144-26833163 MS.gene93356:CDS 50.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 26831787 26833416 26831787 ID=MS.gene93356
chr3.2 mRNA 26831787 26833416 26831787 ID=MS.gene93356.t1;Parent=MS.gene93356
chr3.2 exon 26833268 26833416 26833268 ID=MS.gene93356.t1.exon1;Parent=MS.gene93356.t1
chr3.2 CDS 26833268 26833416 26833268 ID=cds.MS.gene93356.t1;Parent=MS.gene93356.t1
chr3.2 exon 26833032 26833168 26833032 ID=MS.gene93356.t1.exon2;Parent=MS.gene93356.t1
chr3.2 CDS 26833032 26833168 26833032 ID=cds.MS.gene93356.t1;Parent=MS.gene93356.t1
chr3.2 exon 26832608 26832948 26832608 ID=MS.gene93356.t1.exon3;Parent=MS.gene93356.t1
chr3.2 CDS 26832608 26832948 26832608 ID=cds.MS.gene93356.t1;Parent=MS.gene93356.t1
chr3.2 exon 26831787 26832044 26831787 ID=MS.gene93356.t1.exon4;Parent=MS.gene93356.t1
chr3.2 CDS 26831787 26832044 26831787 ID=cds.MS.gene93356.t1;Parent=MS.gene93356.t1
Gene Sequence

>MS.gene93356

ATGGAGAATGTTGATCCACTCACGGTTTTGAAATATGATCATCATGCAATACAAGATTATGATGATCCATTGCAACCTCCATTCCAATTTTCTACGTATGATAATCATAATTATAATTATAATTATAATTATAATAATAATCTTTACAAGTAAGTATCAAATTTCTTATACCACTAGTTCCTTTTTGTATTTTTTTTACTTTCCATGAAATTATCTTTAAAAATTCCTATTTTTTATTTTTTTTACAGATTCAATGATTGGTCACATTATGGATTTCCCATGCAAGATACCAATTTTGATCCTTTCATGGAAAATTATTATCCTGAATTTCGAAATGAAACTCTTCCACCTGAATTACTTGTACCTGCACCATTAAGCATAGAAGGTTATCATTTTACAAATATAACTCTACTATTATTAATTTATTTATTTTGTTAACGGGGTATTTTTAAAATTATTCAATGACAGACTATGGTTATGGGGATGCTAAAAATGTGGTTCCAATGTGGAATGAAGTTGATGCTGGATATTATTCGGATAAACATGTCTTTTCGATTAGCAACATTACTGGAGAAAATGTTGCAAAGGAAATTGTGAAGGGTAAGAGATGTAGAGAAGAGAATACTAATAGTGCAAGAATGCTAACAAAAGAAACAATTTCTGAGTACTTCTATGTGCCAATATCTCAAGCTGCTAGAGACCTTAATGTTGGGCTTACACATTTGAAGAAAAGGTGTAGGGATCTTGGAATTCAAAGGTGGCCACATAGGAAACTAATGAGCCTTCAAACCCTTATAAAGAATGTACAAGTAAGTTCCAATATTTTTTTAGTTTGCAATACATATACATAATATGTAATTTTTTTCTTTGTTCATAATCACATTGTGTAGTGAGGAGATTTAGAGAGAACAAAAACCTAAAACCGATCTTTAATTCCATCACTAAATTTTGCGGCTTGGTGGTAAGCAGACTTTAAAACCTAAAATCATGATTTCCTTGCCAAAATATTTTTCATTCTTACTTATTTTTGTGGCAAATATTTTTTTCTAGTAAATTTTGTAGTGAATTGTTTTAATGTGGATTACTTTTTTTGTGGCTTTTTGGTAAGCGGTCTTTAAAACCTAAAATCATGATTTGCTTGCACGAATATTTTTTATTTTTTTTACTAATTTTTGTGGCAAATATTTTTTTTCTAGTAAATTTTGTAGTGTATTGTTTTATTTATTTTTATTTTTTTACGGATACATCAAAAACCATGATTTGCTAGCTAAATCAAACATAATTTTTTTTTCTTTCAAAATTTTGATTTATGTTGTCATTTTACATATGCTAATCATAATATTGAAACGTTTTATTATTATTGGTGGTGCAGGAGCAAGGTAATGAATGTGATGAGAAGATAAGGAATGCTGTGGAAGTATTGCAGAAAGAAATGAAGAAGGTAGAGGAAAAGCCAGATTTGCAACTTGATGAAAACACAAAGAGGCTTAGACAAGCATGTTTCAAGGCTAATTACAAGAAGAGAAGGCTCATGGTTATGAGGTTAATGGAACAACAGGAGTCTTCTCTCAGTGAAAGTGCAAGTGTTGATGATCACAAAAAGTCAAATTTCTTCTTAACATCATGTTAA

Protein sequence

>MS.gene93356.t1

MENVDPLTVLKYDHHAIQDYDDPLQPPFQFSTYDNHNYNYNYNYNNNLYKFNDWSHYGFPMQDTNFDPFMENYYPEFRNETLPPELLVPAPLSIEDYGYGDAKNVVPMWNEVDAGYYSDKHVFSISNITGENVAKEIVKGKRCREENTNSARMLTKETISEYFYVPISQAARDLNVGLTHLKKRCRDLGIQRWPHRKLMSLQTLIKNVQEQGNECDEKIRNAVEVLQKEMKKVEEKPDLQLDENTKRLRQACFKANYKKRRLMVMRLMEQQESSLSESASVDDHKKSNFFLTSC