AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene63381

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63381.t1 MTR_6g081160 65.000 60 17 1 20 75 1 60 4.74e-17 78.2
MS.gene63381.t1 MTR_6g081160 57.812 64 22 2 114 172 1 64 2.15e-14 70.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 40 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATACAAGGTAGTTATAAT+AGG 0.224337 2.4:-21829197 MS.gene63381:CDS
AAATAATACTATGGCTAGTT+TGG 0.292025 2.4:-21828905 MS.gene63381:CDS
CATGATGAAGTTTCTGCTTA+AGG 0.329845 2.4:+21828965 None:intergenic
AATACAAGGAAATAATACTA+TGG 0.401260 2.4:-21828914 MS.gene63381:CDS
TTTAGCAATGGAAAAGCATT+GGG 0.422284 2.4:-21829291 MS.gene63381:CDS
TTTAGCAAAATAAAAGCATT+GGG 0.424274 2.4:-21829009 MS.gene63381:CDS
AATACAAGGTAGTTATAATA+GGG 0.431054 2.4:-21829196 MS.gene63381:CDS
ACACATCAATGCAATGTTTG+TGG 0.441710 2.4:-21829039 MS.gene63381:CDS
TTATTTCCTTGTATTGAGAA+AGG 0.466446 2.4:+21828922 None:intergenic
TATTTCCTTGTATTGAGAAA+GGG 0.470601 2.4:+21828923 None:intergenic
AGTCAGAAAAGAGGGTGAAA+AGG 0.473192 2.4:-21828843 MS.gene63381:CDS
ATTCTGAAAAGACGATGAAA+AGG 0.473955 2.4:-21829407 MS.gene63381:CDS
ACACATCAGTGCAATGTTTG+TGG 0.475496 2.4:-21829321 MS.gene63381:CDS
CACATCAGTGCAATGTTTGT+GGG 0.483344 2.4:-21829320 MS.gene63381:CDS
AGTCTGAAAAGAGGATAAAG+AGG 0.489348 2.4:-21829125 MS.gene63381:CDS
TTTGATAAAGATAGTAAGCA+TGG 0.491925 2.4:-21829168 MS.gene63381:CDS
GATACCCCTTTCTCAATACA+AGG 0.503509 2.4:-21828928 MS.gene63381:CDS
ACTTCATCATGATTCACAAA+AGG 0.507116 2.4:-21828953 MS.gene63381:CDS
AACTACCTTGTATTGAGAGA+GGG 0.509993 2.4:+21829205 None:intergenic
AATTAATCATCGTTCACAAA+AGG 0.518691 2.4:-21829235 MS.gene63381:CDS
GCTTAAGGAAGTGAGATCTT+CGG 0.523012 2.4:+21828980 None:intergenic
CAAACCCCTCTCTCAATACA+AGG 0.526964 2.4:-21829210 MS.gene63381:CDS
AGAATCTACACATCAGTGCT+AGG 0.545184 2.4:-21828764 None:intergenic
TCTTAAGAAAGTGAGATCTC+CGG 0.549197 2.4:+21829262 None:intergenic
CCCGTGAAGAGTCTGAAAAG+AGG 0.549764 2.4:-21829134 MS.gene63381:CDS
ATTTCCTTGTATTGAGAAAG+GGG 0.553284 2.4:+21828924 None:intergenic
GAAAAGCATTGGGTGGTCAC+CGG 0.556634 2.4:-21829281 MS.gene63381:CDS
CTATGAAGAGTCAGAAAAGA+GGG 0.570873 2.4:-21828851 MS.gene63381:CDS
CCTATGAAGAGTCAGAAAAG+AGG 0.578028 2.4:-21828852 MS.gene63381:CDS
AAGCGATGAAGATGATGCTA+AGG 0.582770 2.4:-21828803 MS.gene63381:CDS
TGAAGATGATGCTAAGGATG+AGG 0.590398 2.4:-21828797 MS.gene63381:CDS
ACTACCTTGTATTGAGAGAG+GGG 0.593179 2.4:+21829206 None:intergenic
TAACTACCTTGTATTGAGAG+AGG 0.601425 2.4:+21829204 None:intergenic
AGCAAAATAAAAGCATTGGG+TGG 0.607881 2.4:-21829006 MS.gene63381:CDS
TAGTGATGAAGATGATGCTA+AGG 0.613974 2.4:-21829367 MS.gene63381:CDS
AGCAATGGAAAAGCATTGGG+TGG 0.615604 2.4:-21829288 MS.gene63381:CDS
AAGTGATGAAGATGATGCTA+AGG 0.616457 2.4:-21829085 MS.gene63381:CDS
ATGGATAAAGATCATAAGCA+TGG 0.623190 2.4:-21829450 MS.gene63381:CDS
TGAAGATGATGCTAAGGATG+AGG 0.644459 2.4:-21829361 MS.gene63381:CDS
AGATCATAAGCATGATCACG+AGG 0.690275 2.4:-21828878 MS.gene63381:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATACAAGGAAATAATACTA+TGG - chr2.4:21829301-21829320 MS.gene63381:CDS 20.0%
!! AATACAAGGTAGTTATAATA+GGG - chr2.4:21829019-21829038 MS.gene63381:CDS 20.0%
!!! TTTAGCAAAATAAAAGCATT+GGG - chr2.4:21829206-21829225 MS.gene63381:CDS 20.0%
!!! TTTTAGCAAAATAAAAGCAT+TGG - chr2.4:21829205-21829224 MS.gene63381:CDS 20.0%
! AATTAATCATCGTTCACAAA+AGG - chr2.4:21828980-21828999 MS.gene63381:CDS 25.0%
! CAATACAAGGTAGTTATAAT+AGG - chr2.4:21829018-21829037 MS.gene63381:CDS 25.0%
! TATTTCCTTGTATTGAGAAA+GGG + chr2.4:21829295-21829314 None:intergenic 25.0%
! TTATTTCCTTGTATTGAGAA+AGG + chr2.4:21829296-21829315 None:intergenic 25.0%
! TTTGATAAAGATAGTAAGCA+TGG - chr2.4:21829047-21829066 MS.gene63381:CDS 25.0%
!! AAATAATACTATGGCTAGTT+TGG - chr2.4:21829310-21829329 MS.gene63381:CDS 25.0%
ACTTCATCATGATTCACAAA+AGG - chr2.4:21829262-21829281 MS.gene63381:CDS 30.0%
ATGGATAAAGATCATAAGCA+TGG - chr2.4:21828765-21828784 MS.gene63381:CDS 30.0%
ATTTCCTTGTATTGAGAAAG+GGG + chr2.4:21829294-21829313 None:intergenic 30.0%
! ATTCTGAAAAGACGATGAAA+AGG - chr2.4:21828808-21828827 MS.gene63381:CDS 30.0%
!! TTTAGCAATGGAAAAGCATT+GGG - chr2.4:21828924-21828943 MS.gene63381:CDS 30.0%
!! TTTTAGCAATGGAAAAGCAT+TGG - chr2.4:21828923-21828942 MS.gene63381:CDS 30.0%
!!! TGTGGGAAAATTTTTAGCAA+TGG - chr2.4:21828912-21828931 MS.gene63381:CDS 30.0%
AACTACCTTGTATTGAGAGA+GGG + chr2.4:21829013-21829032 None:intergenic 35.0%
AAGTGATGAAGATGATGCTA+AGG - chr2.4:21829130-21829149 MS.gene63381:CDS 35.0%
ACACATCAATGCAATGTTTG+TGG - chr2.4:21829176-21829195 MS.gene63381:CDS 35.0%
AGTCTGAAAAGAGGATAAAG+AGG - chr2.4:21829090-21829109 MS.gene63381:CDS 35.0%
CATGATGAAGTTTCTGCTTA+AGG + chr2.4:21829253-21829272 None:intergenic 35.0%
CTATGAAGAGTCAGAAAAGA+GGG - chr2.4:21829364-21829383 MS.gene63381:CDS 35.0%
TAACTACCTTGTATTGAGAG+AGG + chr2.4:21829014-21829033 None:intergenic 35.0%
TAGTGATGAAGATGATGCTA+AGG - chr2.4:21828848-21828867 MS.gene63381:CDS 35.0%
TCTTAAGAAAGTGAGATCTC+CGG + chr2.4:21828956-21828975 None:intergenic 35.0%
! CGTCTTTTCAGAATCTTCAT+AGG + chr2.4:21828802-21828821 None:intergenic 35.0%
!! AGCAAAATAAAAGCATTGGG+TGG - chr2.4:21829209-21829228 MS.gene63381:CDS 35.0%
AAGCGATGAAGATGATGCTA+AGG - chr2.4:21829412-21829431 MS.gene63381:CDS 40.0%
ACACATCAGTGCAATGTTTG+TGG - chr2.4:21828894-21828913 MS.gene63381:CDS 40.0%
ACTACCTTGTATTGAGAGAG+GGG + chr2.4:21829012-21829031 None:intergenic 40.0%
AGATCATAAGCATGATCACG+AGG - chr2.4:21829337-21829356 MS.gene63381:CDS 40.0%
AGTCAGAAAAGAGGGTGAAA+AGG - chr2.4:21829372-21829391 MS.gene63381:CDS 40.0%
CACATCAGTGCAATGTTTGT+GGG - chr2.4:21828895-21828914 MS.gene63381:CDS 40.0%
CCTATGAAGAGTCAGAAAAG+AGG - chr2.4:21829363-21829382 MS.gene63381:CDS 40.0%
GATACCCCTTTCTCAATACA+AGG - chr2.4:21829287-21829306 MS.gene63381:CDS 40.0%
GCTTAAGGAAGTGAGATCTT+CGG + chr2.4:21829238-21829257 None:intergenic 40.0%
TGAAGATGATGCTAAGGATG+AGG - chr2.4:21828854-21828873 MS.gene63381:CDS 40.0%
! CCTCTTTTCTGACTCTTCAT+AGG + chr2.4:21829366-21829385 None:intergenic 40.0%
! TCCTCTTTTCAGACTCTTCA+CGG + chr2.4:21829085-21829104 None:intergenic 40.0%
CAAACCCCTCTCTCAATACA+AGG - chr2.4:21829005-21829024 MS.gene63381:CDS 45.0%
! CCTCTTTTCAGACTCTTCAC+GGG + chr2.4:21829084-21829103 None:intergenic 45.0%
!! AGCAATGGAAAAGCATTGGG+TGG - chr2.4:21828927-21828946 MS.gene63381:CDS 45.0%
CCCGTGAAGAGTCTGAAAAG+AGG - chr2.4:21829081-21829100 MS.gene63381:CDS 50.0%
!! GAAAAGCATTGGGTGGTCAC+CGG - chr2.4:21828934-21828953 MS.gene63381:CDS 50.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 21828765 21829472 21828765 ID=MS.gene63381
chr2.4 mRNA 21828765 21829472 21828765 ID=MS.gene63381.t1;Parent=MS.gene63381
chr2.4 exon 21828765 21829472 21828765 ID=MS.gene63381.t1.exon1;Parent=MS.gene63381.t1
chr2.4 CDS 21828765 21829472 21828765 ID=cds.MS.gene63381.t1;Parent=MS.gene63381.t1
Gene Sequence

>MS.gene63381

ATGGATAAAGATCATAAGCATGGTTATGAGAAAACCTATGAAGATTCTGAAAAGACGATGAAAAGGTCTTCATGTTCACTATCTAGTGATGAAGATGATGCTAAGGATGAGGTTTCTGTTCAAGAATCTACACATCAGTGCAATGTTTGTGGGAAAATTTTTAGCAATGGAAAAGCATTGGGTGGTCACCGGAGATCTCACTTTCTTAAGAAGAAAATTAATCATCGTTCACAAAAGGTACAAACCCCTCTCTCAATACAAGGTAGTTATAATAGGGCTAGTTTTGATAAAGATAGTAAGCATGGTTTTGAGAACACCCGTGAAGAGTCTGAAAAGAGGATAAAGAGGTCTTTTAGTTCTCTATCAAGTGATGAAGATGATGCTAAGGATGAGCTTTCTATTCAAGAAACTACACATCAATGCAATGTTTGTGGAAAAACTTTTAGCAAAATAAAAGCATTGGGTGGTCACCGAAGATCTCACTTCCTTAAGCAGAAACTTCATCATGATTCACAAAAGGTTGATACCCCTTTCTCAATACAAGGAAATAATACTATGGCTAGTTTGGATAAAGATCATAAGCATGATCACGAGGATACCTATGAAGAGTCAGAAAAGAGGGTGAAAAGGTCAGCTTGTTCTCTATCAAGCGATGAAGATGATGCTAAGGATGAGGTTTCTGTTCAAGAATCTACACATCAGTGCTAG
Protein sequence

>MS.gene63381.t1

MDKDHKHGYEKTYEDSEKTMKRSSCSLSSDEDDAKDEVSVQESTHQCNVCGKIFSNGKALGGHRRSHFLKKKINHRSQKVQTPLSIQGSYNRASFDKDSKHGFENTREESEKRIKRSFSSLSSDEDDAKDELSIQETTHQCNVCGKTFSKIKALGGHRRSHFLKQKLHHDSQKVDTPFSIQGNNTMASLDKDHKHDHEDTYEESEKRVKRSACSLSSDEDDAKDEVSVQESTHQC