AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene54903


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54903.t1 MTR_4g037750 92.920 113 8 0 1 113 1 113 9.28e-77 223
MS.gene54903.t1 MTR_6g004540 97.333 75 2 0 1 75 1 75 3.90e-51 157
MS.gene54903.t1 MTR_7g020830 41.176 51 30 0 28 78 9 59 6.81e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54903.t1 AT3G52090 83.036 112 19 0 1 112 1 112 1.33e-69 205
MS.gene54903.t1 AT3G52090 65.035 143 20 1 1 113 1 143 1.31e-62 188
MS.gene54903.t1 AT2G29540 47.059 51 27 0 28 78 9 59 8.55e-11 55.8
MS.gene54903.t1 AT2G29540 47.059 51 27 0 28 78 9 59 8.55e-11 55.8

Find 30 sgRNAs with CRISPR-Local

Find 111 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTAACGCAGTAAGTCGTTC+TGG 0.318460 4.4:-65944096 MS.gene54903:CDS
TATCCAGCGAATAACACATT+AGG 0.348978 4.4:+65945598 None:intergenic
ATGAATCCATTGGCATGCTT+TGG 0.379732 4.4:-65944119 MS.gene54903:CDS
TTCAGTACAAAATTATCATC+AGG 0.382359 4.4:-65945558 MS.gene54903:CDS
TACCTCAAAACCACTCTTCA+AGG 0.393375 4.4:+65944643 None:intergenic
TAACCAGTCTATTAATGATC+TGG 0.435786 4.4:-65944681 MS.gene54903:CDS
ATCCAGCGAATAACACATTA+GGG 0.445494 4.4:+65945599 None:intergenic
AGTGTGATCTTCTCTTTCAA+TGG 0.460602 4.4:+65945762 None:intergenic
GACCCTAATGTGTTATTCGC+TGG 0.469437 4.4:-65945601 MS.gene54903:CDS
CAGCCAGTCTTCACCAATGC+AGG 0.497359 4.4:-65944708 MS.gene54903:CDS
TGTCCAGATCATTAATAGAC+TGG 0.498287 4.4:+65944678 None:intergenic
TTGGTTGAAGGTAAAATCAA+AGG 0.502993 4.4:-65944169 MS.gene54903:intron
TGGTTGAAGGTAAAATCAAA+GGG 0.515508 4.4:-65944168 MS.gene54903:intron
TTAACGCAGTAAGTCGTTCT+GGG 0.516655 4.4:-65944095 MS.gene54903:CDS
GACGAAACGCTCGTAACGAT+CGG 0.522382 4.4:+65945946 None:intergenic
TTTAAAGGGTTTCGTACGAG+AGG 0.523969 4.4:-65945816 MS.gene54903:intron
ACGAAACGCTCGTAACGATC+GGG 0.531962 4.4:+65945947 None:intergenic
CTGCATTGGTGAAGACTGGC+TGG 0.534907 4.4:+65944709 None:intergenic
ATGCCTGCATTGGTGAAGAC+TGG 0.541956 4.4:+65944705 None:intergenic
GAGCGTTTCGTCGTCCCCGA+AGG 0.569274 4.4:-65945935 MS.gene54903:CDS
TCAGTACAAAATTATCATCA+GGG 0.570840 4.4:-65945557 MS.gene54903:intron
TTAAAGGGTTTCGTACGAGA+GGG 0.578031 4.4:-65945815 MS.gene54903:intron
GAACTTGATACCTTGAAGAG+TGG 0.588358 4.4:-65944653 MS.gene54903:CDS
GAAAGAGAAGATCACACTAT+CGG 0.589235 4.4:-65945757 MS.gene54903:CDS
GGATTCATGCTCGTGTGAAG+TGG 0.589758 4.4:+65944134 None:intergenic
TCACACGAGCATGAATCCAT+TGG 0.598773 4.4:-65944129 MS.gene54903:CDS
GACTGGTTATATGCCTGCAT+TGG 0.605258 4.4:+65944695 None:intergenic
TCGGTAGTGCATACATGCGA+AGG 0.622957 4.4:+65945728 None:intergenic
GTCTATTAATGATCTGGACA+AGG 0.664690 4.4:-65944675 MS.gene54903:CDS
GTTAAGCCAAAGCATGCCAA+TGG 0.667524 4.4:+65944113 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAAAACAACATACAT+AGG + chr4.4:65945209-65945228 None:intergenic 15.0%
!!! ACATTTTATACGAAAATAAT+TGG + chr4.4:65944637-65944656 None:intergenic 15.0%
!! AAGATAAAAAAAGATCCATT+TGG + chr4.4:65944909-65944928 None:intergenic 20.0%
!! AGAACATAAAGTTAATAGTT+TGG - chr4.4:65945778-65945797 MS.gene54903:CDS 20.0%
!! ATAAAGTTAATAGTTTGGAT+TGG - chr4.4:65945783-65945802 MS.gene54903:CDS 20.0%
!! ATAGATTTATTTGGAGAAAA+TGG - chr4.4:65944811-65944830 MS.gene54903:intron 20.0%
!! ATGAGAAAAAAAAAGAGAAT+AGG + chr4.4:65944201-65944220 None:intergenic 20.0%
!! GAATATAAACTGAAAACTTA+TGG + chr4.4:65945029-65945048 None:intergenic 20.0%
!! TGAGAAAAAAAAAGAGAATA+GGG + chr4.4:65944200-65944219 None:intergenic 20.0%
!!! CATTGTTTTTAAATTACTAC+CGG + chr4.4:65944564-65944583 None:intergenic 20.0%
!!! TTCTTTTCTTTTCTTAAAGT+AGG - chr4.4:65945228-65945247 MS.gene54903:intron 20.0%
!!! TTTGAATGTTTAAACTTTTC+AGG - chr4.4:65944412-65944431 MS.gene54903:intron 20.0%
! AAACAGGCTATAGATTTATT+TGG - chr4.4:65944802-65944821 MS.gene54903:intron 25.0%
! AAATAAATCTATAGCCTGTT+TGG + chr4.4:65944803-65944822 None:intergenic 25.0%
! ACTTTCTTATAGCAATGAAT+TGG - chr4.4:65944937-65944956 MS.gene54903:intron 25.0%
! ATTTATTTACTCTCCTTTCT+TGG - chr4.4:65945495-65945514 MS.gene54903:intron 25.0%
! GAAAGGAGAGTAAATAAATA+TGG + chr4.4:65945494-65945513 None:intergenic 25.0%
! TCAGTACAAAATTATCATCA+GGG - chr4.4:65944491-65944510 MS.gene54903:intron 25.0%
! TTCAGTACAAAATTATCATC+AGG - chr4.4:65944490-65944509 MS.gene54903:intron 25.0%
!! ATGATAATTTTGTACTGAAG+AGG + chr4.4:65944489-65944508 None:intergenic 25.0%
!! ATTTTTATCTGTATGCGAAT+TGG - chr4.4:65945269-65945288 MS.gene54903:intron 25.0%
!! TAAATGAACTGAATTGGTTT+CGG - chr4.4:65944882-65944901 MS.gene54903:intron 25.0%
!! TTTTTATCTGTATGCGAATT+GGG - chr4.4:65945270-65945289 MS.gene54903:intron 25.0%
!!! GCTATTTTTATAAGCTATCT+TGG - chr4.4:65944659-65944678 MS.gene54903:CDS 25.0%
!!! TTTTGATTCAAACAAAGAGA+GGG + chr4.4:65944350-65944369 None:intergenic 25.0%
AAAAAGAGAATAGGGAAAGA+TGG + chr4.4:65944192-65944211 None:intergenic 30.0%
AAATAAGCTGAAAACAGCTT+AGG - chr4.4:65944694-65944713 MS.gene54903:CDS 30.0%
AAGAAGAAGAGTTGAAAGAA+TGG + chr4.4:65944154-65944173 None:intergenic 30.0%
ATGGACAATGTAAATAGAAG+CGG + chr4.4:65945475-65945494 None:intergenic 30.0%
ATGTGTTTGGATGATTTAGA+AGG - chr4.4:65945806-65945825 MS.gene54903:CDS 30.0%
CAATTCAGTTCATTTACACA+TGG + chr4.4:65944878-65944897 None:intergenic 30.0%
CATGTGTAAATGAACTGAAT+TGG - chr4.4:65944876-65944895 MS.gene54903:intron 30.0%
TAACCAGTCTATTAATGATC+TGG - chr4.4:65945367-65945386 MS.gene54903:intron 30.0%
TGAACGAATAGAGAGATTAA+TGG - chr4.4:65944611-65944630 MS.gene54903:intron 30.0%
TGGTTGAAGGTAAAATCAAA+GGG - chr4.4:65945880-65945899 MS.gene54903:intron 30.0%
TGTATAAGAATTGCCAAGAA+AGG + chr4.4:65945511-65945530 None:intergenic 30.0%
TTCATTGCTATAAGAAAGTG+TGG + chr4.4:65944936-65944955 None:intergenic 30.0%
TTGGTTGAAGGTAAAATCAA+AGG - chr4.4:65945879-65945898 MS.gene54903:intron 30.0%
!! AAGTAAGAAGTTGATATCTG+TGG - chr4.4:65945851-65945870 MS.gene54903:intron 30.0%
!! CATTGAGCTTTATTAATCCT+TGG - chr4.4:65944838-65944857 MS.gene54903:intron 30.0%
!!! AATTACTTTTTTGTGCCTTC+GGG + chr4.4:65944131-65944150 None:intergenic 30.0%
!!! GAATTACTTTTTTGTGCCTT+CGG + chr4.4:65944132-65944151 None:intergenic 30.0%
!!! GTTTTGATTCAAACAAAGAG+AGG + chr4.4:65944351-65944370 None:intergenic 30.0%
!!! TGTTCTGTTGTTATTTTTCC+AGG - chr4.4:65945307-65945326 MS.gene54903:intron 30.0%
AAATCTATAGCCTGTTTGGA+TGG + chr4.4:65944799-65944818 None:intergenic 35.0%
AAGTGGTTATGCTAGTTGAT+AGG - chr4.4:65944762-65944781 MS.gene54903:intron 35.0%
AGCTATCTTGGAAAGCTTTA+TGG - chr4.4:65944671-65944690 MS.gene54903:CDS 35.0%
AGTGTGATCTTCTCTTTCAA+TGG + chr4.4:65944289-65944308 None:intergenic 35.0%
ATCCAGCGAATAACACATTA+GGG + chr4.4:65944452-65944471 None:intergenic 35.0%
ATGCATTTGGGAATAGTTTG+TGG - chr4.4:65945741-65945760 MS.gene54903:intron 35.0%
CAACATACATAGGTCATGTT+TGG + chr4.4:65945199-65945218 None:intergenic 35.0%
CTAGTGGTCATGGAAAAATT+TGG - chr4.4:65945662-65945681 MS.gene54903:intron 35.0%
GAAAGAGAAGATCACACTAT+CGG - chr4.4:65944291-65944310 MS.gene54903:intron 35.0%
GTCTATTAATGATCTGGACA+AGG - chr4.4:65945373-65945392 MS.gene54903:intron 35.0%
TATCCAGCGAATAACACATT+AGG + chr4.4:65944453-65944472 None:intergenic 35.0%
TCAAATATGTCCATCCAAAC+AGG - chr4.4:65944786-65944805 MS.gene54903:intron 35.0%
TGGTTTATCTGTCTTATCCA+AGG + chr4.4:65944858-65944877 None:intergenic 35.0%
TGTAAATAGAAGCGGTATTG+AGG + chr4.4:65945467-65945486 None:intergenic 35.0%
TGTCCAGATCATTAATAGAC+TGG + chr4.4:65945373-65945392 None:intergenic 35.0%
! AGATTTGTCATTTGACCTAG+TGG - chr4.4:65945646-65945665 MS.gene54903:intron 35.0%
! ATTTTGTACTGAAGAGGATG+AGG + chr4.4:65944483-65944502 None:intergenic 35.0%
! CAAATTTTTCCATGACCACT+AGG + chr4.4:65945664-65945683 None:intergenic 35.0%
! TAGTTTGGATTGGATGTGTT+TGG - chr4.4:65945793-65945812 MS.gene54903:CDS 35.0%
!! TAAGAAGTTGATATCTGTGG+AGG - chr4.4:65945854-65945873 MS.gene54903:intron 35.0%
!!! ATTACTTTTTTGTGCCTTCG+GGG + chr4.4:65944130-65944149 None:intergenic 35.0%
AAGCGTTCTTTGCATGCATT+TGG - chr4.4:65945728-65945747 MS.gene54903:intron 40.0%
AGCGTTCTTTGCATGCATTT+GGG - chr4.4:65945729-65945748 MS.gene54903:intron 40.0%
ATGAATCCATTGGCATGCTT+TGG - chr4.4:65945929-65945948 MS.gene54903:CDS 40.0%
CAAACAAAGAGAGGGAAAGT+CGG + chr4.4:65944342-65944361 None:intergenic 40.0%
GAACTTGATACCTTGAAGAG+TGG - chr4.4:65945395-65945414 MS.gene54903:intron 40.0%
GAGTTATATACGCTGAACCT+CGG + chr4.4:65945694-65945713 None:intergenic 40.0%
GCTGAAAACAGCTTAGGAAA+AGG - chr4.4:65944700-65944719 MS.gene54903:CDS 40.0%
GTATTAGCGCTATTACTGTC+AGG - chr4.4:65945542-65945561 MS.gene54903:intron 40.0%
GTTGATATCTGTGGAGGAAT+TGG - chr4.4:65945860-65945879 MS.gene54903:intron 40.0%
GTTGTATGCATAAGCTACTC+TGG + chr4.4:65945057-65945076 None:intergenic 40.0%
TAACCACTTGTGACACTGTT+TGG + chr4.4:65944751-65944770 None:intergenic 40.0%
TACCTCAAAACCACTCTTCA+AGG + chr4.4:65945408-65945427 None:intergenic 40.0%
TTAAAGGGTTTCGTACGAGA+GGG - chr4.4:65944233-65944252 MS.gene54903:intron 40.0%
TTAACGCAGTAAGTCGTTCT+GGG - chr4.4:65945953-65945972 MS.gene54903:CDS 40.0%
TTTAAAGGGTTTCGTACGAG+AGG - chr4.4:65944232-65944251 MS.gene54903:intron 40.0%
! CATTTGGGAATAGTTTGTGG+AGG - chr4.4:65945744-65945763 MS.gene54903:CDS 40.0%
! GAAAAATTTGGAGTTGACCG+AGG - chr4.4:65945674-65945693 MS.gene54903:intron 40.0%
! GTTACTTCCCATTTGAAGCA+CGG - chr4.4:65944521-65944540 MS.gene54903:intron 40.0%
! TGAATTGGTTTCGGTCCAAA+TGG - chr4.4:65944891-65944910 MS.gene54903:intron 40.0%
!! TACCTTGAAGAGTGGTTTTG+AGG - chr4.4:65945403-65945422 MS.gene54903:intron 40.0%
CTTAACGCAGTAAGTCGTTC+TGG - chr4.4:65945952-65945971 MS.gene54903:CDS 45.0%
CTTCCAAACAGTGTCACAAG+TGG - chr4.4:65944745-65944764 MS.gene54903:intron 45.0%
GTCATTTGACCTAGTGGTCA+TGG - chr4.4:65945652-65945671 MS.gene54903:intron 45.0%
GTTAAGCCAAAGCATGCCAA+TGG + chr4.4:65945938-65945957 None:intergenic 45.0%
TCACACGAGCATGAATCCAT+TGG - chr4.4:65945919-65945938 MS.gene54903:intron 45.0%
TCAGTGTCCGTGCTTCAAAT+GGG + chr4.4:65944531-65944550 None:intergenic 45.0%
TCTGTGGAGGAATTGGTTGA+AGG - chr4.4:65945867-65945886 MS.gene54903:intron 45.0%
! GACCCTAATGTGTTATTCGC+TGG - chr4.4:65944447-65944466 MS.gene54903:intron 45.0%
! GACTGGTTATATGCCTGCAT+TGG + chr4.4:65945356-65945375 None:intergenic 45.0%
!! AAATATAAAATAAAAAAGTT+AGG + chr4.4:65944374-65944393 None:intergenic 5.0%
!! AATATAAAATAAAAAAGTTA+GGG + chr4.4:65944373-65944392 None:intergenic 5.0%
!!! CATTTATTTTTATTTTTAAA+GGG - chr4.4:65944218-65944237 MS.gene54903:intron 5.0%
!!! TCATTTATTTTTATTTTTAA+AGG - chr4.4:65944217-65944236 MS.gene54903:intron 5.0%
ACGAAACGCTCGTAACGATC+GGG + chr4.4:65944104-65944123 None:intergenic 50.0%
AGCGCTATTACTGTCAGGCT+AGG - chr4.4:65945547-65945566 MS.gene54903:intron 50.0%
GACGAAACGCTCGTAACGAT+CGG + chr4.4:65944105-65944124 None:intergenic 50.0%
GGATTCATGCTCGTGTGAAG+TGG + chr4.4:65945917-65945936 None:intergenic 50.0%
GTCAGTGTCCGTGCTTCAAA+TGG + chr4.4:65944532-65944551 None:intergenic 50.0%
TCGGTAGTGCATACATGCGA+AGG + chr4.4:65944323-65944342 None:intergenic 50.0%
! ATGCCTGCATTGGTGAAGAC+TGG + chr4.4:65945346-65945365 None:intergenic 50.0%
! GGGAATAGTTTGTGGAGGAC+AGG - chr4.4:65945749-65945768 MS.gene54903:CDS 50.0%
CAGCCAGTCTTCACCAATGC+AGG - chr4.4:65945340-65945359 MS.gene54903:intron 55.0%
! CTGCATTGGTGAAGACTGGC+TGG + chr4.4:65945342-65945361 None:intergenic 55.0%
! ACTGGCTGGTCGTGTGTACC+TGG + chr4.4:65945328-65945347 None:intergenic 60.0%
GAGCGTTTCGTCGTCCCCGA+AGG - chr4.4:65944113-65944132 MS.gene54903:CDS 65.0%
! GGACACTGACGCGTCGACAC+CGG - chr4.4:65944542-65944561 MS.gene54903:intron 65.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 65944092 65945978 65944092 ID=MS.gene54903
chr4.4 mRNA 65944092 65945978 65944092 ID=MS.gene54903.t1;Parent=MS.gene54903
chr4.4 exon 65945926 65945978 65945926 ID=MS.gene54903.t1.exon1;Parent=MS.gene54903.t1
chr4.4 CDS 65945926 65945978 65945926 ID=cds.MS.gene54903.t1;Parent=MS.gene54903.t1
chr4.4 exon 65945742 65945831 65945742 ID=MS.gene54903.t1.exon2;Parent=MS.gene54903.t1
chr4.4 CDS 65945742 65945831 65945742 ID=cds.MS.gene54903.t1;Parent=MS.gene54903.t1
chr4.4 exon 65945558 65945636 65945558 ID=MS.gene54903.t1.exon3;Parent=MS.gene54903.t1
chr4.4 CDS 65945558 65945636 65945558 ID=cds.MS.gene54903.t1;Parent=MS.gene54903.t1
chr4.4 exon 65944646 65944741 65944646 ID=MS.gene54903.t1.exon4;Parent=MS.gene54903.t1
chr4.4 CDS 65944646 65944741 65944646 ID=cds.MS.gene54903.t1;Parent=MS.gene54903.t1
chr4.4 exon 65944092 65944181 65944092 ID=MS.gene54903.t1.exon5;Parent=MS.gene54903.t1
chr4.4 CDS 65944092 65944181 65944092 ID=cds.MS.gene54903.t1;Parent=MS.gene54903.t1
Gene Sequence

>MS.gene54903

ATGAATGCACCCGATCGTTACGAGCGTTTCGTCGTCCCCGAAGGCACAAAAAAGTAATTCCATTCTTTCAACTCTTCTTCTTCTTCTTCTTCTTTCACCATCTTTCCCTATTCTCTTTTTTTTTCTCATTTATTTTTATTTTTAAAGGGTTTCGTACGAGAGGGACACGAAGATCATCAACGCAGCATCTTTCACCATTGAAAGAGAAGATCACACTATCGGCAACATCCTTCGCATGTATGCACTACCGACTTTCCCTCTCTTTGTTTGAATCAAAACCCTAACTTTTTTATTTTATATTTTTTAATTTTAATTTTAATTTTGAATGTTTAAACTTTTCAGGCAGCTTCACAAAGACCCTAATGTGTTATTCGCTGGATACAAGCTTCCTCATCCTCTTCAGTACAAAATTATCATCAGGGTTAGTTTGTTACTTCCCATTTGAAGCACGGACACTGACGCGTCGACACCGGTAGTAATTTAAAAACAATGACATAATTAACTATAATCATGTATAATTGAACGAATAGAGAGATTAATGGCCAATTATTTTCGTATAAAATGTAAGCTATTTTTATAAGCTATCTTGGAAAGCTTTATGGAAATAAGCTGAAAACAGCTTAGGAAAAGGTTATAAGCTATTTTCGTAAATTCTTCCAAACAGTGTCACAAGTGGTTATGCTAGTTGATAGGCTCAAATATGTCCATCCAAACAGGCTATAGATTTATTTGGAGAAAATGGATTGCATTGAGCTTTATTAATCCTTGGATAAGACAGATAAACCATGTGTAAATGAACTGAATTGGTTTCGGTCCAAATGGATCTTTTTTTATCTTCTAACCACACTTTCTTATAGCAATGAATTGGATTTCTCTGAGATTATCTACTTACAAAAGCACTAGTGAGATGTTCAAGAGAGAGCTTATGACATGTCCATAAGTTTTCAGTTTATATTCACTCTCCAGAGTAGCTTATGCATACAACTTATAGCTTATATGAAAACAATTTGACTTCATTTTATCTTGTTATAGAGTTAGTTCATACATTAACACTTAAATGATATGCGATTATATTATAAGCGTTTTGTAAAGTTGTTTGTTTATCCAAACATGACCTATGTATGTTGTTTTTTTTTTTCTTTTCTTTTCTTAAAGTAGGAGTTAGAAGTGAATATTTATTTTTATCTGTATGCGAATTGGGAGCTCAGTATCAACTGTTCTGTTGTTATTTTTCCAGGTACACACGACCAGCCAGTCTTCACCAATGCAGGCATATAACCAGTCTATTAATGATCTGGACAAGGAACTTGATACCTTGAAGAGTGGTTTTGAGGTACAGTGTTTCTGCTTTTTTGTTCTTTGTGCGATGCGTCCTCAATACCGCTTCTATTTACATTGTCCATATTTATTTACTCTCCTTTCTTGGCAATTCTTATACATGTTAAATAAAGTATTAGCGCTATTACTGTCAGGCTAGGCTCGCTAGTCGTTACACTTGTCACTTTTCAATATCTTTAATATTCTTGAAAGCAGTAGCAGATTTTAACTACTATTAGATTTGTCATTTGACCTAGTGGTCATGGAAAAATTTGGAGTTGACCGAGGTTCAGCGTATATAACTCATTTTATTAATTAGAAGCGTTCTTTGCATGCATTTGGGAATAGTTTGTGGAGGACAGGTAGTTTAGAACATAAAGTTAATAGTTTGGATTGGATGTGTTTGGATGATTTAGAAGGAGAAGAATAGAAGAATATTACAAAGTAAGAAGTTGATATCTGTGGAGGAATTGGTTGAAGGTAAAATCAAAGGGATTTAACTGTTCCACTTCACACGAGCATGAATCCATTGGCATGCTTTGGCTTAACGCAGTAAGTCGTTCTGGGTAA

Protein sequence

>MS.gene54903.t1

MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREDHTIGNILRMQLHKDPNVLFAGYKLPHPLQYKIIIRVHTTSQSSPMQAYNQSINDLDKELDTLKSGFEVKSKGFNCSTSHEHESIGMLWLNAVSRSG