AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene028814

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028814.t1 MTR_2g091190 98.381 247 4 0 1 247 1 247 9.13e-180 493
MS.gene028814.t1 MTR_4g079760 71.875 256 63 3 1 247 1 256 8.17e-121 344
MS.gene028814.t1 MTR_2g015890 50.732 205 95 3 23 225 29 229 3.91e-62 196
MS.gene028814.t1 MTR_4g087920 44.672 244 124 6 2 235 13 255 5.77e-51 167
MS.gene028814.t1 MTR_2g015890 50.667 150 69 2 23 170 29 175 4.92e-44 148
MS.gene028814.t1 MTR_3g096568 88.158 76 9 0 127 202 236 311 1.29e-43 150
MS.gene028814.t1 MTR_2g015890 51.111 135 62 2 91 225 1 131 3.31e-38 131
MS.gene028814.t1 MTR_8g032210 85.882 85 11 1 1 85 12 95 4.96e-36 124
MS.gene028814.t1 MTR_1g093750 40.594 202 109 3 45 242 144 338 2.77e-34 126
MS.gene028814.t1 MTR_3g070970 33.333 201 115 5 46 234 60 253 2.57e-30 114
MS.gene028814.t1 MTR_5g066080 40.606 165 72 2 49 188 27 190 6.08e-25 99.4
MS.gene028814.t1 MTR_5g032375 36.000 150 75 4 54 188 40 183 1.62e-20 87.0
MS.gene028814.t1 MTR_2g015890 51.250 80 36 1 91 170 1 77 2.96e-20 83.6
MS.gene028814.t1 MTR_1g018820 87.179 39 5 0 90 128 58 96 2.98e-16 72.4
MS.gene028814.t1 MTR_5g030430 40.244 82 49 0 28 109 459 540 4.15e-12 65.9
MS.gene028814.t1 MTR_8g067280 39.506 81 49 0 29 109 429 509 1.08e-11 64.7
MS.gene028814.t1 MTR_2g081040 26.582 158 75 3 66 186 181 334 1.10e-11 64.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028814.t1 AT1G68810 41.327 196 107 5 45 236 160 351 2.21e-33 124
MS.gene028814.t1 AT3G25710 46.622 148 70 2 45 188 118 260 9.78e-32 119
MS.gene028814.t1 AT3G56770 38.857 175 98 4 51 223 37 204 1.56e-30 113
MS.gene028814.t1 AT2G40200 39.634 164 89 3 61 219 65 223 1.94e-29 111
MS.gene028814.t1 AT2G41130 40.571 175 96 3 51 223 59 227 4.19e-27 105
MS.gene028814.t1 AT4G38070 36.154 130 76 2 59 188 92 214 1.26e-17 80.1
MS.gene028814.t1 AT4G17880 40.789 76 45 0 39 114 393 468 2.20e-11 63.5
MS.gene028814.t1 AT5G46760 44.156 77 42 1 39 114 391 467 2.25e-11 63.5
MS.gene028814.t1 AT1G32640 36.634 101 61 2 33 130 421 521 3.58e-11 63.2

Find 38 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCATCTTCTTCACTGGTTT+TGG 0.180837 2.3:+9069104 MS.gene028814:CDS
CACTTCATCTTATGATAATA+AGG 0.194458 2.3:+9070369 MS.gene028814:CDS
AATGATGCTCTAATTGAATA+AGG 0.233216 2.3:-9070293 None:intergenic
CTTATCTCATCACTGTCTTT+TGG 0.234136 2.3:-9070236 None:intergenic
ATATTCAGTTCTTCATCTTT+AGG 0.245592 2.3:+9070584 MS.gene028814:CDS
TCACAAGAAGGTGGATTAAA+TGG 0.279597 2.3:+9070266 MS.gene028814:CDS
GTTGGACAAAGCATCCTTAC+TGG 0.310877 2.3:+9070145 MS.gene028814:intron
TTTCAAGGTGTAAATGGAAA+TGG 0.359014 2.3:+9069075 MS.gene028814:CDS
TGTGGAGGCAGCTGTGAAAT+TGG 0.360925 2.3:+9069146 MS.gene028814:CDS
TGTTATCCCAGGTGCTAATA+AGG 0.365921 2.3:+9069278 MS.gene028814:CDS
AAGGGCAGAGATTGCAACTT+TGG 0.372459 2.3:+9070388 MS.gene028814:CDS
GAGTATCGACAGTTTCTTGC+TGG 0.401116 2.3:+9070473 MS.gene028814:CDS
AGGGCAGAGATTGCAACTTT+GGG 0.424505 2.3:+9070389 MS.gene028814:CDS
TCTTATATCAGACAATAAAC+CGG 0.424693 2.3:-9070333 None:intergenic
GGTGTAAATGGAAATGGATA+TGG 0.430429 2.3:+9069081 MS.gene028814:CDS
TGTAATAACTTCAGCCAGTA+AGG 0.442964 2.3:-9070159 None:intergenic
ATGATGCTCTAATTGAATAA+GGG 0.448376 2.3:-9070292 None:intergenic
ATATGGTTCATCTTCTTCAC+TGG 0.451383 2.3:+9069098 MS.gene028814:CDS
ACTTCATCTTATGATAATAA+GGG 0.489015 2.3:+9070370 MS.gene028814:CDS
TCGACAGTTTCTTGCTGGAT+CGG 0.489881 2.3:+9070478 MS.gene028814:CDS
AAAGCTTCAATACTTCTCTC+AGG 0.498631 2.3:-9069186 None:intergenic
CTTATATCAGACAATAAACC+GGG 0.504302 2.3:-9070332 None:intergenic
GAACTAACCTTATTAGCACC+TGG 0.521161 2.3:-9069285 None:intergenic
AGCAAGAAACTGTCGATACT+CGG 0.542573 2.3:-9070471 None:intergenic
TTATGTTGTGAATACAAACC+CGG 0.569012 2.3:+9070314 MS.gene028814:CDS
AACTAACCTTATTAGCACCT+GGG 0.573545 2.3:-9069284 None:intergenic
AATGCAGCACAAGCAAGTGA+AGG 0.583141 2.3:+9070203 MS.gene028814:CDS
GCTTCAAGTAGAATGAATGA+TGG 0.589941 2.3:+9069048 MS.gene028814:CDS
GCAGAGATTGCAACTTTGGG+AGG 0.592208 2.3:+9070392 MS.gene028814:CDS
ATGCAGCACAAGCAAGTGAA+GGG 0.603381 2.3:+9070204 MS.gene028814:CDS
ATCATAGTGAAGCAGAGAGG+AGG 0.603979 2.3:+9069214 MS.gene028814:CDS
TCTTAGAAACTAGAAAGAGA+AGG 0.613686 2.3:+9070552 MS.gene028814:CDS
TAGAAACTAGAAAGAGAAGG+AGG 0.614835 2.3:+9070555 MS.gene028814:CDS
ATAAGAGTTGAATCACAAGA+AGG 0.621854 2.3:+9070254 MS.gene028814:CDS
ACACTTCGTAGTGTTATCCC+AGG 0.622939 2.3:+9069267 MS.gene028814:CDS
AGAGTTGAATCACAAGAAGG+TGG 0.624818 2.3:+9070257 MS.gene028814:CDS
GCTGTGAAATTGGAACGCAA+AGG 0.704659 2.3:+9069156 MS.gene028814:CDS
AGAATCATAGTGAAGCAGAG+AGG 0.708784 2.3:+9069211 MS.gene028814:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCAAAATAAACAACAAAAA+AGG - chr2.3:9069336-9069355 None:intergenic 15.0%
!! ACTTCATCTTATGATAATAA+GGG + chr2.3:9070370-9070389 MS.gene028814:CDS 20.0%
!!! AATTTTCTTTCCTAAAAGAA+GGG + chr2.3:9069928-9069947 MS.gene028814:intron 20.0%
!!! GGAATCGAATAATTTAATTT+TGG + chr2.3:9069949-9069968 MS.gene028814:intron 20.0%
! AACTTAGTTATGCTTATACT+TGG + chr2.3:9070031-9070050 MS.gene028814:intron 25.0%
! AAGTATAAGCATAACTAAGT+TGG - chr2.3:9070032-9070051 None:intergenic 25.0%
! AATGATGCTCTAATTGAATA+AGG - chr2.3:9070296-9070315 None:intergenic 25.0%
! ATATTCAGTTCTTCATCTTT+AGG + chr2.3:9070584-9070603 MS.gene028814:CDS 25.0%
! ATGATGCTCTAATTGAATAA+GGG - chr2.3:9070295-9070314 None:intergenic 25.0%
! ATTAACTCCAAATATTTGAG+GGG + chr2.3:9069405-9069424 MS.gene028814:intron 25.0%
! ATTCAAATGACCATAAAAGA+GGG - chr2.3:9069652-9069671 None:intergenic 25.0%
! CACTTCATCTTATGATAATA+AGG + chr2.3:9070369-9070388 MS.gene028814:CDS 25.0%
! GATTAACTCCAAATATTTGA+GGG + chr2.3:9069404-9069423 MS.gene028814:intron 25.0%
! TCTTATATCAGACAATAAAC+CGG - chr2.3:9070336-9070355 None:intergenic 25.0%
! TGATTAACTCCAAATATTTG+AGG + chr2.3:9069403-9069422 MS.gene028814:intron 25.0%
! TTAGGAAAGAAAATTGAACT+TGG - chr2.3:9069923-9069942 None:intergenic 25.0%
! TTTGAATTACTAGTTAGTAC+TGG + chr2.3:9069350-9069369 MS.gene028814:intron 25.0%
!! CAAAATGTAGTGAGTATTTT+TGG + chr2.3:9069758-9069777 MS.gene028814:intron 25.0%
!! CAATTTTCTTTCCTAAAAGA+AGG + chr2.3:9069927-9069946 MS.gene028814:intron 25.0%
!!! ATGTAGCTTTTAGTTTTCAA+TGG + chr2.3:9069896-9069915 MS.gene028814:intron 25.0%
!!! GTGTACTTTTTTAACTTAGT+TGG + chr2.3:9070127-9070146 MS.gene028814:intron 25.0%
AGTTAAATTGAGACAGTGAA+TGG + chr2.3:9069797-9069816 MS.gene028814:intron 30.0%
ATAAGAGTTGAATCACAAGA+AGG + chr2.3:9070254-9070273 MS.gene028814:CDS 30.0%
ATTCTTTCCCCTCAAATATT+TGG - chr2.3:9069415-9069434 None:intergenic 30.0%
CATTCAAATGACCATAAAAG+AGG - chr2.3:9069653-9069672 None:intergenic 30.0%
CTTATATCAGACAATAAACC+GGG - chr2.3:9070335-9070354 None:intergenic 30.0%
GACTTCAAAAGTAAGCAAAA+TGG - chr2.3:9069855-9069874 None:intergenic 30.0%
TCTTAGAAACTAGAAAGAGA+AGG + chr2.3:9070552-9070571 MS.gene028814:CDS 30.0%
TTATGTTGTGAATACAAACC+CGG + chr2.3:9070314-9070333 MS.gene028814:CDS 30.0%
TTGTGTAGACATGAATTTCA+TGG - chr2.3:9070059-9070078 None:intergenic 30.0%
TTTCAAGGTGTAAATGGAAA+TGG + chr2.3:9069075-9069094 MS.gene028814:CDS 30.0%
! AATGGCTTTACTCACATATA+TGG - chr2.3:9069837-9069856 None:intergenic 30.0%
! ACAGTGAATGGCAAAATTTT+GGG + chr2.3:9069809-9069828 MS.gene028814:intron 30.0%
! TTATTCGATTCCCTTCTTTT+AGG - chr2.3:9069941-9069960 None:intergenic 30.0%
!! ATGAATGATGGTTGTTTTCA+AGG + chr2.3:9069060-9069079 MS.gene028814:CDS 30.0%
!!! GTCTAGTTTTTGTACTTCAT+AGG - chr2.3:9069517-9069536 None:intergenic 30.0%
AAAGCTTCAATACTTCTCTC+AGG - chr2.3:9069189-9069208 None:intergenic 35.0%
AACTAACCTTATTAGCACCT+GGG - chr2.3:9069287-9069306 None:intergenic 35.0%
AAGACTCACACACTTTAACA+GGG + chr2.3:9069613-9069632 MS.gene028814:intron 35.0%
ATATGGTTCATCTTCTTCAC+TGG + chr2.3:9069098-9069117 MS.gene028814:CDS 35.0%
ATGAATGTGCATTTACACTG+AGG + chr2.3:9069694-9069713 MS.gene028814:intron 35.0%
GCTTCAAGTAGAATGAATGA+TGG + chr2.3:9069048-9069067 MS.gene028814:CDS 35.0%
GGTGTAAATGGAAATGGATA+TGG + chr2.3:9069081-9069100 MS.gene028814:CDS 35.0%
TAGAAACTAGAAAGAGAAGG+AGG + chr2.3:9070555-9070574 MS.gene028814:CDS 35.0%
TGTAATAACTTCAGCCAGTA+AGG - chr2.3:9070162-9070181 None:intergenic 35.0%
! ATAATGACGACCCTCTTTTA+TGG + chr2.3:9069639-9069658 MS.gene028814:intron 35.0%
! CTTATCTCATCACTGTCTTT+TGG - chr2.3:9070239-9070258 None:intergenic 35.0%
! GACAGTGAATGGCAAAATTT+TGG + chr2.3:9069808-9069827 MS.gene028814:intron 35.0%
!! GGTTGTTTTCAAGGTGTAAA+TGG + chr2.3:9069069-9069088 MS.gene028814:CDS 35.0%
!! TCACAAGAAGGTGGATTAAA+TGG + chr2.3:9070266-9070285 MS.gene028814:CDS 35.0%
!!! CTGGTTTTGGATAGAGAAAA+AGG + chr2.3:9069117-9069136 MS.gene028814:CDS 35.0%
!!! TTCATCTTCTTCACTGGTTT+TGG + chr2.3:9069104-9069123 MS.gene028814:CDS 35.0%
AGAATCATAGTGAAGCAGAG+AGG + chr2.3:9069211-9069230 MS.gene028814:CDS 40.0%
AGAGTTGAATCACAAGAAGG+TGG + chr2.3:9070257-9070276 MS.gene028814:CDS 40.0%
AGCAAGAAACTGTCGATACT+CGG - chr2.3:9070474-9070493 None:intergenic 40.0%
CAAGAGCTCAATGAGTTTGA+TGG + chr2.3:9069977-9069996 MS.gene028814:intron 40.0%
GAACTAACCTTATTAGCACC+TGG - chr2.3:9069288-9069307 None:intergenic 40.0%
GAAGACTCACACACTTTAAC+AGG + chr2.3:9069612-9069631 MS.gene028814:intron 40.0%
TAAAGTGTGTGAGTCTTCAC+AGG - chr2.3:9069610-9069629 None:intergenic 40.0%
TAGAGAAAAAGGAGAGCTTG+TGG + chr2.3:9069128-9069147 MS.gene028814:CDS 40.0%
TGTTATCCCAGGTGCTAATA+AGG + chr2.3:9069278-9069297 MS.gene028814:CDS 40.0%
AAGGGCAGAGATTGCAACTT+TGG + chr2.3:9070388-9070407 MS.gene028814:CDS 45.0%
AATGCAGCACAAGCAAGTGA+AGG + chr2.3:9070203-9070222 MS.gene028814:CDS 45.0%
ACACTTCGTAGTGTTATCCC+AGG + chr2.3:9069267-9069286 MS.gene028814:CDS 45.0%
AGAAAAAGGAGAGCTTGTGG+AGG + chr2.3:9069131-9069150 MS.gene028814:CDS 45.0%
AGGGCAGAGATTGCAACTTT+GGG + chr2.3:9070389-9070408 MS.gene028814:CDS 45.0%
ATCATAGTGAAGCAGAGAGG+AGG + chr2.3:9069214-9069233 MS.gene028814:CDS 45.0%
ATGCAGCACAAGCAAGTGAA+GGG + chr2.3:9070204-9070223 MS.gene028814:CDS 45.0%
GCTGTGAAATTGGAACGCAA+AGG + chr2.3:9069156-9069175 MS.gene028814:CDS 45.0%
TCGACAGTTTCTTGCTGGAT+CGG + chr2.3:9070478-9070497 MS.gene028814:CDS 45.0%
! GTTGGACAAAGCATCCTTAC+TGG + chr2.3:9070145-9070164 MS.gene028814:intron 45.0%
!! GAGTATCGACAGTTTCTTGC+TGG + chr2.3:9070473-9070492 MS.gene028814:CDS 45.0%
GCAGAGATTGCAACTTTGGG+AGG + chr2.3:9070392-9070411 MS.gene028814:CDS 50.0%
TGTGGAGGCAGCTGTGAAAT+TGG + chr2.3:9069146-9069165 MS.gene028814:CDS 50.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 9069030 9070619 9069030 ID=MS.gene028814
chr2.3 mRNA 9069030 9070619 9069030 ID=MS.gene028814.t1;Parent=MS.gene028814
chr2.3 exon 9069030 9069299 9069030 ID=MS.gene028814.t1.exon1;Parent=MS.gene028814.t1
chr2.3 CDS 9069030 9069299 9069030 ID=cds.MS.gene028814.t1;Parent=MS.gene028814.t1
chr2.3 exon 9070146 9070619 9070146 ID=MS.gene028814.t1.exon2;Parent=MS.gene028814.t1
chr2.3 CDS 9070146 9070619 9070146 ID=cds.MS.gene028814.t1;Parent=MS.gene028814.t1
Gene Sequence

>MS.gene028814

ATGGAAATGGATGATTTTGCTTCAAGTAGAATGAATGATGGTTGTTTTCAAGGTGTAAATGGAAATGGATATGGTTCATCTTCTTCACTGGTTTTGGATAGAGAAAAAGGAGAGCTTGTGGAGGCAGCTGTGAAATTGGAACGCAAAGGTGTGTCACCTGAGAGAAGTATTGAAGCTTTGAAGAATCATAGTGAAGCAGAGAGGAGGAGAAGAGCAAGAATTAATTCACATCTTGATACACTTCGTAGTGTTATCCCAGGTGCTAATAAGGTTAGTTCAATTTTATTCATTTATTTATTTTTACCTTTTTTGTTGTTTATTTTGAATTACTAGTTAGTACTGGTTTTGCTCATGTTGAGAACAATTTCTGTCATGATTAACTCCAAATATTTGAGGGGAAAGAATTATTTTTTATGTTTAATTAATGTAAAATTTACATATAATTTGAATTTTGTGTTGAATAACTTATGATTATTATTATTGACCTATGAAGTACAAAAACTAGACATCAATAATAATTTGAAAAAAAATAGAAGTAATTGTATATATACATATAAATAAAAGTGTCAGTATCGTGCCTGTGAAGACTCACACACTTTAACAGGGAATATAATGACGACCCTCTTTTATGGTCATTTGAATGAAATAATAGCTTTTACTATATATGAATGTGCATTTACACTGAGGTTTTAAGTTTTAACTATAAGTCTTGAGCTATGAATGCATTTCAAAATGTAGTGAGTATTTTTGGATGTTGAAACAATTGAAGTTAAATTGAGACAGTGAATGGCAAAATTTTGGGATCCATATATGTGAGTAAAGCCATTTTGCTTACTTTTGAAGTCTTGATTCTTCTTTTTTGTATAATGTAGCTTTTAGTTTTCAATGGACCAAGTTCAATTTTCTTTCCTAAAAGAAGGGAATCGAATAATTTAATTTTGGAGTAGCAAGAGCTCAATGAGTTTGATGGTATTAAAAAAAGATGTTAATATTAACTATCCAACTTAGTTATGCTTATACTTGGAACCATGAAATTCATGTCTACACAAACAAATAAACATGATATATATGTTAATCTTTCAGAATCTAACATTTTTGTGTACTTTTTTAACTTAGTTGGACAAAGCATCCTTACTGGCTGAAGTTATTACACATTTGAAAGAGCTGAAAACAAATGCAGCACAAGCAAGTGAAGGGTTCATTATTCCAAAAGACAGTGATGAGATAAGAGTTGAATCACAAGAAGGTGGATTAAATGGTTACCCTTATTCAATTAGAGCATCATTATGTTGTGAATACAAACCCGGTTTATTGTCTGATATAAGAAAAGCACTTGATGCACTTCATCTTATGATAATAAGGGCAGAGATTGCAACTTTGGGAGGTAGAATGAAGAATGTCTTTGTCATAATTAGCTGCAAAGAACAGAATTTTGAAGATGCCGAGTATCGACAGTTTCTTGCTGGATCGGTTCATCAAGCTCTTAGATCTGTACTTGATAGATTTTCTGTTTCACAAGATATCTTAGAAACTAGAAAGAGAAGGAGGATTTCTATATTCAGTTCTTCATCTTTAGGTGATTTCTTATAA
Protein sequence

>MS.gene028814.t1

MEMDDFASSRMNDGCFQGVNGNGYGSSSSLVLDREKGELVEAAVKLERKGVSPERSIEALKNHSEAERRRRARINSHLDTLRSVIPGANKLDKASLLAEVITHLKELKTNAAQASEGFIIPKDSDEIRVESQEGGLNGYPYSIRASLCCEYKPGLLSDIRKALDALHLMIIRAEIATLGGRMKNVFVIISCKEQNFEDAEYRQFLAGSVHQALRSVLDRFSVSQDILETRKRRRISIFSSSSLGDFL