AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene85949


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene85949.t1 MTR_2g104810 88.119 101 12 0 41 141 19 119 2.56e-62 190
MS.gene85949.t1 MTR_4g116860 49.451 91 35 1 108 198 1542 1621 3.55e-18 82.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene85949.t1 AT1G80650 45.652 92 40 1 104 195 111 192 2.33e-18 79.7
MS.gene85949.t1 AT4G00420 44.330 97 43 3 104 200 59 144 2.11e-16 73.6
MS.gene85949.t1 AT4G00420 44.330 97 43 3 104 200 80 165 3.16e-16 73.6
MS.gene85949.t1 AT4G00420 44.330 97 43 3 104 200 81 166 3.22e-16 73.6
MS.gene85949.t1 AT4G00420 44.330 97 43 3 104 200 81 166 3.22e-16 73.6
MS.gene85949.t1 AT4G00420 44.330 97 43 3 104 200 81 166 3.22e-16 73.6
MS.gene85949.t1 AT5G20320 39.823 113 57 1 86 198 1586 1687 7.57e-15 72.8
MS.gene85949.t1 AT5G20320 39.823 113 57 1 86 198 1600 1701 7.73e-15 72.8
MS.gene85949.t1 AT5G20320 39.823 113 57 1 86 198 1375 1476 8.00e-15 72.8
MS.gene85949.t1 AT1G80650 39.130 92 36 1 104 195 111 182 7.77e-12 62.0

Find 24 sgRNAs with CRISPR-Local

Find 109 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCTAAAATGACACTCTCTT+TGG 0.292490 2.1:-1122218 None:intergenic
CTTGAATAATCAAATGAAAA+TGG 0.300650 2.1:+1122120 MS.gene85949:CDS
ATTCAAGGTTATTGTTGAAA+TGG 0.336999 2.1:+1123428 MS.gene85949:CDS
TTCATTTGATTATTCAAGTT+GGG 0.380029 2.1:-1122115 None:intergenic
TTCTTCTCACTCCACCTTCA+AGG 0.388623 2.1:+1121946 MS.gene85949:CDS
TGTTTGTTAGGTATGAAGAA+AGG 0.445413 2.1:+1122366 MS.gene85949:intron
TTGTGGTACTTAAAGCATAT+AGG 0.446945 2.1:+1123570 MS.gene85949:CDS
GTTTGTTAGGTATGAAGAAA+GGG 0.447288 2.1:+1122367 MS.gene85949:intron
TTTCATTTGATTATTCAAGT+TGG 0.449161 2.1:-1122116 None:intergenic
TGGAAGATGAAACTGAAGAT+TGG 0.449737 2.1:-1122198 None:intergenic
GTTATTGTTGAAATGGAGAC+AGG 0.475716 2.1:+1123435 MS.gene85949:CDS
AGACATGTGCTGTAAATCAT+TGG 0.504933 2.1:+1122412 MS.gene85949:CDS
GGCAGCAGACAATGCAGCCG+AGG 0.547846 2.1:+1123542 MS.gene85949:CDS
TAAGTACCACAATGCACCCT+CGG 0.553491 2.1:-1123559 None:intergenic
AAGACAACAACTTCAGATGA+AGG 0.557587 2.1:+1122241 MS.gene85949:CDS
TTAGGTATGAAGAAAGGGTG+TGG 0.557962 2.1:+1122372 MS.gene85949:intron
TGTGTTTGAGTGTTGTAAAG+AGG 0.558213 2.1:+1122443 MS.gene85949:CDS
GCAGCAGACAATGCAGCCGA+GGG 0.565055 2.1:+1123543 MS.gene85949:CDS
TCTTTACAACACTCAAACAC+AGG 0.578805 2.1:-1122441 None:intergenic
ATCATACACAATACAAAACA+TGG 0.634806 2.1:+1121910 MS.gene85949:CDS
TTTGAGTGTTGTAAAGAGGA+AGG 0.648639 2.1:+1122447 MS.gene85949:CDS
TTACAACACTCAAACACAGG+AGG 0.658087 2.1:-1122438 None:intergenic
ACTTACATTATGCAATGACA+TGG 0.673466 2.1:-1122471 None:intergenic
ATGCAGCCGAGGGTGCATTG+TGG 0.682343 2.1:+1123553 MS.gene85949:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTAATTAAAATAAATAATT+GGG + chr2.1:1121993-1122012 MS.gene85949:intron 0.0%
!!! TTTTAATTAAAATAAATAAT+TGG + chr2.1:1121992-1122011 MS.gene85949:intron 0.0%
!!! TTTTATTTATGAAAAATGAA+GGG + chr2.1:1122496-1122515 MS.gene85949:intron 10.0%
!!! TTTTTATTTATGAAAAATGA+AGG + chr2.1:1122495-1122514 MS.gene85949:intron 10.0%
!! AAAAAAAATTATTACCTTGA+AGG - chr2.1:1121963-1121982 None:intergenic 15.0%
!! TTTATTTATGAAAAATGAAG+GGG + chr2.1:1122497-1122516 MS.gene85949:intron 15.0%
!!! ACAAAAAAAATGAACTTTTT+TGG - chr2.1:1122296-1122315 None:intergenic 15.0%
!! ATATAAACAACTTACAACTT+AGG + chr2.1:1122785-1122804 MS.gene85949:intron 20.0%
!! CTTGAATAATCAAATGAAAA+TGG + chr2.1:1122120-1122139 MS.gene85949:CDS 20.0%
!! TCATTATGAATTGTAGAAAA+GGG - chr2.1:1123338-1123357 None:intergenic 20.0%
!! TTCATTATGAATTGTAGAAA+AGG - chr2.1:1123339-1123358 None:intergenic 20.0%
!! TTTCATTTGATTATTCAAGT+TGG - chr2.1:1122119-1122138 None:intergenic 20.0%
!!! AATGAGAAAAATGAGTATTT+TGG + chr2.1:1122337-1122356 MS.gene85949:intron 20.0%
!!! GAAATGAAATTTTCTATAAG+TGG + chr2.1:1122544-1122563 MS.gene85949:intron 20.0%
!!! TTCATTTGATTATTCAAGTT+GGG - chr2.1:1122118-1122137 None:intergenic 20.0%
!!! TTTTGGTATTATTGTTTGTT+AGG + chr2.1:1122354-1122373 MS.gene85949:intron 20.0%
! AAAAACATTGTAGAGGTTTA+TGG + chr2.1:1123495-1123514 MS.gene85949:CDS 25.0%
! AAAAATTATTACCTTGAAGG+TGG - chr2.1:1121960-1121979 None:intergenic 25.0%
! AAAAGTTTATGCTGCAAAAA+TGG + chr2.1:1122087-1122106 MS.gene85949:CDS 25.0%
! AAAGGGAAGCAAAATATAAT+AGG - chr2.1:1123321-1123340 None:intergenic 25.0%
! AATATTGCAAAAGATTTAGC+TGG - chr2.1:1123211-1123230 None:intergenic 25.0%
! ATCATACACAATACAAAACA+TGG + chr2.1:1121910-1121929 MS.gene85949:CDS 25.0%
! ATTCAAGGTTATTGTTGAAA+TGG + chr2.1:1123428-1123447 MS.gene85949:CDS 25.0%
! GGAAAACATGCAATAATTAA+TGG - chr2.1:1122275-1122294 None:intergenic 25.0%
! TCATGCAATAAGACAAATAT+TGG - chr2.1:1123294-1123313 None:intergenic 25.0%
! TCCTCATCAAAAAAAGAAAA+TGG + chr2.1:1123521-1123540 MS.gene85949:CDS 25.0%
! TCTACAATTCATAATGAAAC+TGG + chr2.1:1123341-1123360 MS.gene85949:intron 25.0%
! TCTCAAATTATTAACAGTGT+CGG + chr2.1:1122974-1122993 MS.gene85949:intron 25.0%
!! ATAAACCTCTACAATGTTTT+TGG - chr2.1:1123496-1123515 None:intergenic 25.0%
!! ATTTTCAACCAAGTGATTAT+AGG + chr2.1:1122708-1122727 MS.gene85949:intron 25.0%
!! TTTTCAACCAAGTGATTATA+GGG + chr2.1:1122709-1122728 MS.gene85949:intron 25.0%
AACCTGTGAAAAACATCAAT+TGG - chr2.1:1123405-1123424 None:intergenic 30.0%
AAGATTATTCCATTGCATGT+TGG + chr2.1:1123182-1123201 MS.gene85949:intron 30.0%
AATGAAGGGGAAAAAAACTA+TGG + chr2.1:1122510-1122529 MS.gene85949:intron 30.0%
ACAATTCATAATGAAACTGG+AGG + chr2.1:1123344-1123363 MS.gene85949:intron 30.0%
ACTTACATTATGCAATGACA+TGG - chr2.1:1122474-1122493 None:intergenic 30.0%
AGTAACCAAAAACATTGTAG+AGG + chr2.1:1123488-1123507 MS.gene85949:CDS 30.0%
TTAGAAGATGCATAGATTTG+TGG + chr2.1:1122819-1122838 MS.gene85949:intron 30.0%
TTGTGGTACTTAAAGCATAT+AGG + chr2.1:1123570-1123589 MS.gene85949:CDS 30.0%
! AAGTGGTATATTTTGTGTGT+TGG + chr2.1:1122561-1122580 MS.gene85949:intron 30.0%
! GACAAATATTGGTTGATATC+TGG - chr2.1:1123283-1123302 None:intergenic 30.0%
! GTTTGTTAGGTATGAAGAAA+GGG + chr2.1:1122367-1122386 MS.gene85949:intron 30.0%
! TGTTTGTTAGGTATGAAGAA+AGG + chr2.1:1122366-1122385 MS.gene85949:intron 30.0%
! TTGCAGCATAAACTTTTGTT+CGG - chr2.1:1122084-1122103 None:intergenic 30.0%
! TTTTCACAGGTTTACATTCA+AGG + chr2.1:1123413-1123432 MS.gene85949:intron 30.0%
!!! GCCATTTTCTTTTTTTGATG+AGG - chr2.1:1123525-1123544 None:intergenic 30.0%
AAGACAACAACTTCAGATGA+AGG + chr2.1:1122241-1122260 MS.gene85949:CDS 35.0%
AGACATGTGCTGTAAATCAT+TGG + chr2.1:1122412-1122431 MS.gene85949:CDS 35.0%
GTTATTGTTGAAATGGAGAC+AGG + chr2.1:1123435-1123454 MS.gene85949:CDS 35.0%
TCAGCTGTAGATTTCAAATC+AGG + chr2.1:1122755-1122774 MS.gene85949:intron 35.0%
TCTTTACAACACTCAAACAC+AGG - chr2.1:1122444-1122463 None:intergenic 35.0%
TGGAAGATGAAACTGAAGAT+TGG - chr2.1:1122201-1122220 None:intergenic 35.0%
TTATCGAACTTAAGTCACCA+AGG + chr2.1:1122674-1122693 MS.gene85949:intron 35.0%
! GAAAATTTGCTCTTCAACCT+TGG - chr2.1:1122694-1122713 None:intergenic 35.0%
! GACCAATTGATGTTTTTCAC+AGG + chr2.1:1123400-1123419 MS.gene85949:intron 35.0%
! TGTGTTTGAGTGTTGTAAAG+AGG + chr2.1:1122443-1122462 MS.gene85949:CDS 35.0%
! TTTGAGTGTTGTAAAGAGGA+AGG + chr2.1:1122447-1122466 MS.gene85949:CDS 35.0%
!!! CCAAAGAGAGTGTCATTTTA+GGG + chr2.1:1122218-1122237 MS.gene85949:CDS 35.0%
!!! GCATCAATGTTTTTCAAGAC+TGG - chr2.1:1122175-1122194 None:intergenic 35.0%
!!! TCCAAAGAGAGTGTCATTTT+AGG + chr2.1:1122217-1122236 MS.gene85949:CDS 35.0%
CCAAGTGATTATAGGGAAAC+TGG + chr2.1:1122716-1122735 MS.gene85949:intron 40.0%
CCAGTTTCCCTATAATCACT+TGG - chr2.1:1122719-1122738 None:intergenic 40.0%
CCCTAAAATGACACTCTCTT+TGG - chr2.1:1122221-1122240 None:intergenic 40.0%
GATGTTAGAGCCTAGTGTTT+CGG - chr2.1:1123130-1123149 None:intergenic 40.0%
TATATGTGTCAGTGTCGTGT+CGG - chr2.1:1122932-1122951 None:intergenic 40.0%
TATGTGCTTGAGTGCTTCAT+AGG - chr2.1:1122860-1122879 None:intergenic 40.0%
TTACAACACTCAAACACAGG+AGG - chr2.1:1122441-1122460 None:intergenic 40.0%
TTAGGTATGAAGAAAGGGTG+TGG + chr2.1:1122372-1122391 MS.gene85949:intron 40.0%
! GACGTTTTATGCAGGTATCT+GGG - chr2.1:1123101-1123120 None:intergenic 40.0%
ACTCAAGCACATACACTCCT+CGG + chr2.1:1122867-1122886 MS.gene85949:intron 45.0%
AGCTGGATACCAACATGCAA+TGG - chr2.1:1123194-1123213 None:intergenic 45.0%
TAAGTACCACAATGCACCCT+CGG - chr2.1:1123562-1123581 None:intergenic 45.0%
TGAGTGCTTCATAGGTGTGT+GGG - chr2.1:1122852-1122871 None:intergenic 45.0%
TTCATAGCCACACACAGACA+CGG + chr2.1:1123044-1123063 MS.gene85949:intron 45.0%
TTCTTCTCACTCCACCTTCA+AGG + chr2.1:1121946-1121965 MS.gene85949:CDS 45.0%
TTGAGTGCTTCATAGGTGTG+TGG - chr2.1:1122853-1122872 None:intergenic 45.0%
! GGACGTTTTATGCAGGTATC+TGG - chr2.1:1123102-1123121 None:intergenic 45.0%
!!! AATTGTTTTTTTTTTAAAAT+TGG + chr2.1:1122025-1122044 MS.gene85949:intron 5.0%
ATGAAGCGCGGATATGGACA+CGG - chr2.1:1123029-1123048 None:intergenic 50.0%
GCACATACACTCCTCGGATT+AGG + chr2.1:1122873-1122892 MS.gene85949:intron 50.0%
TTCATAGGTGTGTGGGCACT+AGG - chr2.1:1122845-1122864 None:intergenic 50.0%
! GGAGTGTGGACGTTTTATGC+AGG - chr2.1:1123109-1123128 None:intergenic 50.0%
AGGTATCTGGGCTTGATCCC+AGG - chr2.1:1123089-1123108 None:intergenic 55.0%
CGTCCACACTCCGAAACACT+AGG + chr2.1:1123117-1123136 MS.gene85949:intron 55.0%
CTGTGTGTGGCTATGAAGCG+CGG - chr2.1:1123041-1123060 None:intergenic 55.0%
GAGCCTAGTGTTTCGGAGTG+TGG - chr2.1:1123123-1123142 None:intergenic 55.0%
GCGGATATGGACACGGAAAC+CGG - chr2.1:1123022-1123041 None:intergenic 55.0%
GTCAGTATGCGTGTCGTGTC+CGG + chr2.1:1123000-1123019 MS.gene85949:intron 55.0%
GTGGCTATGAAGCGCGGATA+TGG - chr2.1:1123035-1123054 None:intergenic 55.0%
! TGTCAGTGTCGTGTCGGTGT+TGG - chr2.1:1122926-1122945 None:intergenic 55.0%
ACACGACACCTGTCCGACAC+CGG - chr2.1:1122903-1122922 None:intergenic 60.0%
ACAGACACGGAGAGGGGGAA+GGG + chr2.1:1123057-1123076 MS.gene85949:intron 60.0%
AGCCACACACAGACACGGAG+AGG + chr2.1:1123049-1123068 MS.gene85949:intron 60.0%
AGGGGGAAGGGTGGAAACCT+GGG + chr2.1:1123069-1123088 MS.gene85949:intron 60.0%
CACACACAGACACGGAGAGG+GGG + chr2.1:1123052-1123071 MS.gene85949:intron 60.0%
CCACACACAGACACGGAGAG+GGG + chr2.1:1123051-1123070 MS.gene85949:intron 60.0%
GCAGCAGACAATGCAGCCGA+GGG + chr2.1:1123543-1123562 MS.gene85949:CDS 60.0%
GCCACACACAGACACGGAGA+GGG + chr2.1:1123050-1123069 MS.gene85949:intron 60.0%
! ACTCCTCGGATTAGGCGTCC+CGG + chr2.1:1122881-1122900 MS.gene85949:intron 60.0%
! ATGCAGCCGAGGGTGCATTG+TGG + chr2.1:1123553-1123572 MS.gene85949:CDS 60.0%
ACACCGGGACGCCTAATCCG+AGG - chr2.1:1122887-1122906 None:intergenic 65.0%
CACAGACACGGAGAGGGGGA+AGG + chr2.1:1123056-1123075 MS.gene85949:intron 65.0%
CACGACACCTGTCCGACACC+GGG - chr2.1:1122902-1122921 None:intergenic 65.0%
CCCCTCTCCGTGTCTGTGTG+TGG - chr2.1:1123054-1123073 None:intergenic 65.0%
GAGGGGGAAGGGTGGAAACC+TGG + chr2.1:1123068-1123087 MS.gene85949:intron 65.0%
GGCAGCAGACAATGCAGCCG+AGG + chr2.1:1123542-1123561 MS.gene85949:CDS 65.0%
! CGGATTAGGCGTCCCGGTGT+CGG + chr2.1:1122887-1122906 MS.gene85949:intron 65.0%
GACACGGAGAGGGGGAAGGG+TGG + chr2.1:1123060-1123079 MS.gene85949:intron 70.0%
! TAGGCGTCCCGGTGTCGGAC+AGG + chr2.1:1122892-1122911 MS.gene85949:intron 70.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 1121852 1123614 1121852 ID=MS.gene85949
chr2.1 mRNA 1121852 1123614 1121852 ID=MS.gene85949.t1;Parent=MS.gene85949
chr2.1 exon 1121852 1121967 1121852 ID=MS.gene85949.t1.exon1;Parent=MS.gene85949.t1
chr2.1 CDS 1121852 1121967 1121852 ID=cds.MS.gene85949.t1;Parent=MS.gene85949.t1
chr2.1 exon 1122075 1122262 1122075 ID=MS.gene85949.t1.exon2;Parent=MS.gene85949.t1
chr2.1 CDS 1122075 1122262 1122075 ID=cds.MS.gene85949.t1;Parent=MS.gene85949.t1
chr2.1 exon 1122376 1122487 1122376 ID=MS.gene85949.t1.exon3;Parent=MS.gene85949.t1
chr2.1 CDS 1122376 1122487 1122376 ID=cds.MS.gene85949.t1;Parent=MS.gene85949.t1
chr2.1 exon 1123422 1123614 1123422 ID=MS.gene85949.t1.exon4;Parent=MS.gene85949.t1
chr2.1 CDS 1123422 1123614 1123422 ID=cds.MS.gene85949.t1;Parent=MS.gene85949.t1
Gene Sequence

>MS.gene85949

ATGAAATTTCAACTATTTCATTCTGTTATTTGCACAGCTGAAGTCTGTTTACAGCAGCATCATACACAATACAAAACATGGACAAGAGCAATAATTCTTCTCACTCCACCTTCAAGGTAATAATTTTTTTTCTTCATTTTTTTTAATTAAAATAAATAATTGGGTATATGAAAAATTGTTTTTTTTTTAAAATTGGTTGAATTGAAATTCTTATCTTTTGCAGAGTAAACCGAACAAAAGTTTATGCTGCAAAAATGGTGAAACCCAACTTGAATAATCAAATGAAAATGGTTGAAACTGTTGAAAGCATTGTTCAAAATCCAGTCTTGAAAAACATTGATGCTGTCCAATCTTCAGTTTCATCTTCCAAAGAGAGTGTCATTTTAGGGAAGACAACAACTTCAGATGAAGGTAAACTAACCATTAATTATTGCATGTTTTCCAAAAAAGTTCATTTTTTTTGTATTTTTTTTCTTTCTTGTAAAAATGAGAAAAATGAGTATTTTGGTATTATTGTTTGTTAGGTATGAAGAAAGGGTGTGGTAGATCAAAGCTGTATGAGACATGTGCTGTAAATCATTGGAAGCCTCCTGTGTTTGAGTGTTGTAAAGAGGAAGGACCATGTCATTGCATAATGTAAGTCTTTTTATTTATGAAAAATGAAGGGGAAAAAAACTATGGTTATGATGATTGAAATGAAATTTTCTATAAGTGGTATATTTTGTGTGTTGGTAGCTGCAAGTTTATATAAATCAGAATCAATATAGCAAATAAGTGACATTTTCTATTTTGATTTATTCTTTTATTTTTTTCGCTGTGCGATTATCGAACTTAAGTCACCAAGGTTGAAGAGCAAATTTTCAACCAAGTGATTATAGGGAAACTGGCTTCTATGTTGATTTCTCAGCTGTAGATTTCAAATCAGGATTTTGTATATAAACAACTTACAACTTAGGTGCATAAGTTCTTAGAAGATGCATAGATTTGTGGCCTAGTGCCCACACACCTATGAAGCACTCAAGCACATACACTCCTCGGATTAGGCGTCCCGGTGTCGGACAGGTGTCGTGTCCAACACCGACACGACACTGACACATATAATTACACTAAATTATGTGATTTTCTCAAATTATTAACAGTGTCGGCATGTCAGTATGCGTGTCGTGTCCGGTTTCCGTGTCCATATCCGCGCTTCATAGCCACACACAGACACGGAGAGGGGGAAGGGTGGAAACCTGGGATCAAGCCCAGATACCTGCATAAAACGTCCACACTCCGAAACACTAGGCTCTAACATCTTGTAGATTTATTTCTGTTCATTCTTGTTCACAAGATTATTCCATTGCATGTTGGTATCCAGCTAAATCTTTTGCAATATTAGTCTTAATATAACGATTTATTGCTATGAAAAGTTGTTGAATTTCTTATCCAGATATCAACCAATATTTGTCTTATTGCATGACTTTCCTATTATATTTTGCTTCCCTTTTCTACAATTCATAATGAAACTGGAGGAAATACAGTCATAACTTTTTTCTTGTTCTCAGTGACCAATTGATGTTTTTCACAGGTTTACATTCAAGGTTATTGTTGAAATGGAGACAGGTAAAGCTTCTAAAAACATAAAGACAAGTGAAGTAACCAAAAACATTGTAGAGGTTTATGGTGCTCCTCATCAAAAAAAGAAAATGGCAGCAGACAATGCAGCCGAGGGTGCATTGTGGTACTTAAAGCATATAGGTTTTGTTTTGAAGAACAAATAA

Protein sequence

>MS.gene85949.t1

MKFQLFHSVICTAEVCLQQHHTQYKTWTRAIILLTPPSRVNRTKVYAAKMVKPNLNNQMKMVETVESIVQNPVLKNIDAVQSSVSSSKESVILGKTTTSDEGMKKGCGRSKLYETCAVNHWKPPVFECCKEEGPCHCIMFTFKVIVEMETGKASKNIKTSEVTKNIVEVYGAPHQKKKMAADNAAEGALWYLKHIGFVLKNK