AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene54856

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene54856.t1 MTR_2g091190 98.381 247 4 0 1 247 1 247 9.13e-180 493
MS.gene54856.t1 MTR_4g079760 71.875 256 63 3 1 247 1 256 8.17e-121 344
MS.gene54856.t1 MTR_2g015890 50.732 205 95 3 23 225 29 229 3.91e-62 196
MS.gene54856.t1 MTR_4g087920 44.672 244 124 6 2 235 13 255 5.77e-51 167
MS.gene54856.t1 MTR_2g015890 50.667 150 69 2 23 170 29 175 4.92e-44 148
MS.gene54856.t1 MTR_3g096568 88.158 76 9 0 127 202 236 311 1.29e-43 150
MS.gene54856.t1 MTR_2g015890 51.111 135 62 2 91 225 1 131 3.31e-38 131
MS.gene54856.t1 MTR_8g032210 85.882 85 11 1 1 85 12 95 4.96e-36 124
MS.gene54856.t1 MTR_1g093750 40.594 202 109 3 45 242 144 338 2.77e-34 126
MS.gene54856.t1 MTR_3g070970 33.333 201 115 5 46 234 60 253 2.57e-30 114
MS.gene54856.t1 MTR_5g066080 40.606 165 72 2 49 188 27 190 6.08e-25 99.4
MS.gene54856.t1 MTR_5g032375 36.000 150 75 4 54 188 40 183 1.62e-20 87.0
MS.gene54856.t1 MTR_2g015890 51.250 80 36 1 91 170 1 77 2.96e-20 83.6
MS.gene54856.t1 MTR_1g018820 87.179 39 5 0 90 128 58 96 2.98e-16 72.4
MS.gene54856.t1 MTR_5g030430 40.244 82 49 0 28 109 459 540 4.15e-12 65.9
MS.gene54856.t1 MTR_8g067280 39.506 81 49 0 29 109 429 509 1.08e-11 64.7
MS.gene54856.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.gene54856.t1 AT1G68810 41.327 196 107 5 45 236 160 351 2.21e-33 124
MS.gene54856.t1 AT3G25710 46.622 148 70 2 45 188 118 260 9.78e-32 119
MS.gene54856.t1 AT3G56770 38.857 175 98 4 51 223 37 204 1.56e-30 113
MS.gene54856.t1 AT2G40200 39.634 164 89 3 61 219 65 223 1.94e-29 111
MS.gene54856.t1 AT2G41130 40.571 175 96 3 51 223 59 227 4.19e-27 105
MS.gene54856.t1 AT4G38070 36.154 130 76 2 59 188 92 214 1.26e-17 80.1
MS.gene54856.t1 AT4G17880 40.789 76 45 0 39 114 393 468 2.20e-11 63.5
MS.gene54856.t1 AT5G46760 44.156 77 42 1 39 114 391 467 2.25e-11 63.5
MS.gene54856.t1 AT1G32640 36.634 101 61 2 33 130 421 521 3.58e-11 63.2

Find 37 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCATCTTCTTCACTGGTTT+TGG 0.180837 2.1:+9740731 MS.gene54856:CDS
CACTTCATCTTATGATAATA+AGG 0.194458 2.1:+9741994 MS.gene54856:CDS
AATGATGCTCTAATTGAATA+AGG 0.233216 2.1:-9741918 None:intergenic
CTTATCTCATCACTGTCTTT+TGG 0.234136 2.1:-9741861 None:intergenic
ATATTCAGTTCTTCATCTTT+AGG 0.245592 2.1:+9742209 MS.gene54856:CDS
TCACAAGAAGGTGGATTAAA+TGG 0.279597 2.1:+9741891 MS.gene54856:CDS
TTTCAAGGTGTAAATGGAAA+TGG 0.359014 2.1:+9740702 MS.gene54856:CDS
TGTGGAGGCAGCTGTGAAAT+TGG 0.360925 2.1:+9740773 MS.gene54856:CDS
TGTTATCCCAGGTGCTAATA+AGG 0.365921 2.1:+9740905 MS.gene54856:CDS
TGTAATAACTTCAGCTAGTA+AGG 0.369694 2.1:-9741784 None:intergenic
AAGGGCAGAGATTGCAACTT+TGG 0.372459 2.1:+9742013 MS.gene54856:CDS
GAGTATCGACAGTTTCTTGC+TGG 0.401116 2.1:+9742098 MS.gene54856:CDS
CAAAGCTTCAATACTTCTCT+CGG 0.423960 2.1:-9740814 None:intergenic
AGGGCAGAGATTGCAACTTT+GGG 0.424505 2.1:+9742014 MS.gene54856:CDS
TCTTATATCAGACAATAAAC+CGG 0.424693 2.1:-9741958 None:intergenic
GGTGTAAATGGAAATGGATA+TGG 0.430429 2.1:+9740708 MS.gene54856:CDS
ATGATGCTCTAATTGAATAA+GGG 0.448376 2.1:-9741917 None:intergenic
ATATGGTTCATCTTCTTCAC+TGG 0.451383 2.1:+9740725 MS.gene54856:CDS
ACTTCATCTTATGATAATAA+GGG 0.489015 2.1:+9741995 MS.gene54856:CDS
TCGACAGTTTCTTGCTGGAT+CGG 0.489881 2.1:+9742103 MS.gene54856:CDS
CTTATATCAGACAATAAACC+GGG 0.504302 2.1:-9741957 None:intergenic
GAACTAACCTTATTAGCACC+TGG 0.521161 2.1:-9740912 None:intergenic
AAAGCTTCAATACTTCTCTC+GGG 0.540932 2.1:-9740813 None:intergenic
AGCAAGAAACTGTCGATACT+CGG 0.542573 2.1:-9742096 None:intergenic
TTATGTTGTGAATACAAACC+CGG 0.569012 2.1:+9741939 MS.gene54856:CDS
AACTAACCTTATTAGCACCT+GGG 0.573545 2.1:-9740911 None:intergenic
AATGCAGCACAAGCAAGTGA+AGG 0.583141 2.1:+9741828 MS.gene54856:CDS
GCTTCAAGTAGAATGAATGA+TGG 0.589941 2.1:+9740675 MS.gene54856:CDS
GCAGAGATTGCAACTTTGGG+AGG 0.592208 2.1:+9742017 MS.gene54856:CDS
ATGCAGCACAAGCAAGTGAA+GGG 0.603381 2.1:+9741829 MS.gene54856:CDS
TCTTAGAAACTAGAAAGAGA+AGG 0.613686 2.1:+9742177 MS.gene54856:CDS
TAGAAACTAGAAAGAGAAGG+AGG 0.614835 2.1:+9742180 MS.gene54856:CDS
ATAAGAGTTGAATCACAAGA+AGG 0.621854 2.1:+9741879 MS.gene54856:CDS
ACACTTCGTAGTGTTATCCC+AGG 0.622939 2.1:+9740894 MS.gene54856:CDS
AGAGTTGAATCACAAGAAGG+TGG 0.624818 2.1:+9741882 MS.gene54856:CDS
GCTGTGAAATTGGAACGCAA+AGG 0.704659 2.1:+9740783 MS.gene54856:CDS
AGAATCATAGTGAAGCAGAG+AGG 0.708784 2.1:+9740838 MS.gene54856:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GGAATAGAATAATTTAATTT+TGG + chr2.1:9741574-9741593 MS.gene54856:intron 15.0%
!! ACTTCATCTTATGATAATAA+GGG + chr2.1:9741995-9742014 MS.gene54856:CDS 20.0%
!! ATTAACTCCAAATATTTGAA+GGG + chr2.1:9741032-9741051 MS.gene54856:intron 20.0%
!!! AATTTTCTTTCCTAAAAGAA+GGG + chr2.1:9741553-9741572 MS.gene54856:intron 20.0%
! AACATAGTTATGCTTATACT+TGG + chr2.1:9741656-9741675 MS.gene54856:intron 25.0%
! AAGTATAAGCATAACTATGT+TGG - chr2.1:9741657-9741676 None:intergenic 25.0%
! AATGATGCTCTAATTGAATA+AGG - chr2.1:9741921-9741940 None:intergenic 25.0%
! ACACTTTAATAGGGAATATA+AGG + chr2.1:9741247-9741266 MS.gene54856:intron 25.0%
! ATATTCAGTTCTTCATCTTT+AGG + chr2.1:9742209-9742228 MS.gene54856:CDS 25.0%
! ATGATGCTCTAATTGAATAA+GGG - chr2.1:9741920-9741939 None:intergenic 25.0%
! ATTCAAATGACCATAAAAGA+GGG - chr2.1:9741277-9741296 None:intergenic 25.0%
! ATTCTTTCCCTTCAAATATT+TGG - chr2.1:9741042-9741061 None:intergenic 25.0%
! CACTTCATCTTATGATAATA+AGG + chr2.1:9741994-9742013 MS.gene54856:CDS 25.0%
! GATTAACTCCAAATATTTGA+AGG + chr2.1:9741031-9741050 MS.gene54856:intron 25.0%
! TCTTATATCAGACAATAAAC+CGG - chr2.1:9741961-9741980 None:intergenic 25.0%
! TTAGGAAAGAAAATTGAACT+TGG - chr2.1:9741548-9741567 None:intergenic 25.0%
! TTTGAATTACTAGTTAGTAC+TGG + chr2.1:9740977-9740996 MS.gene54856:intron 25.0%
!! CAAAATGTAGTGAGTATTTT+TGG + chr2.1:9741383-9741402 MS.gene54856:intron 25.0%
!! CAATTTTCTTTCCTAAAAGA+AGG + chr2.1:9741552-9741571 MS.gene54856:intron 25.0%
!! TTATTCTATTCCCTTCTTTT+AGG - chr2.1:9741566-9741585 None:intergenic 25.0%
!!! ATGTAGCTTTTAGTTTTCAA+TGG + chr2.1:9741521-9741540 MS.gene54856:intron 25.0%
AGTTAAATTGAGACAGTGAA+TGG + chr2.1:9741422-9741441 MS.gene54856:intron 30.0%
ATAAGAGTTGAATCACAAGA+AGG + chr2.1:9741879-9741898 MS.gene54856:CDS 30.0%
CATTCAAATGACCATAAAAG+AGG - chr2.1:9741278-9741297 None:intergenic 30.0%
CTTATATCAGACAATAAACC+GGG - chr2.1:9741960-9741979 None:intergenic 30.0%
GACTTCAAAAGTAAGCAAAA+TGG - chr2.1:9741480-9741499 None:intergenic 30.0%
TCTTAGAAACTAGAAAGAGA+AGG + chr2.1:9742177-9742196 MS.gene54856:CDS 30.0%
TGAAGACTCACACTTTAATA+GGG + chr2.1:9741238-9741257 MS.gene54856:intron 30.0%
TGTAATAACTTCAGCTAGTA+AGG - chr2.1:9741787-9741806 None:intergenic 30.0%
TTATGTTGTGAATACAAACC+CGG + chr2.1:9741939-9741958 MS.gene54856:CDS 30.0%
TTTCAAGGTGTAAATGGAAA+TGG + chr2.1:9740702-9740721 MS.gene54856:CDS 30.0%
! AATGGCTTTACTCACATATA+TGG - chr2.1:9741462-9741481 None:intergenic 30.0%
! ACAGTGAATGGCAAAATTTT+GGG + chr2.1:9741434-9741453 MS.gene54856:intron 30.0%
!! ATGAATGATGGTTGTTTTCA+AGG + chr2.1:9740687-9740706 MS.gene54856:CDS 30.0%
!! GTGTACTTTTTGAACTTAGT+TGG + chr2.1:9741752-9741771 MS.gene54856:intron 30.0%
AAAGCTTCAATACTTCTCTC+GGG - chr2.1:9740816-9740835 None:intergenic 35.0%
AACTAACCTTATTAGCACCT+GGG - chr2.1:9740914-9740933 None:intergenic 35.0%
ATATGGTTCATCTTCTTCAC+TGG + chr2.1:9740725-9740744 MS.gene54856:CDS 35.0%
ATTAAAGTGTGAGTCTTCAC+AGG - chr2.1:9741237-9741256 None:intergenic 35.0%
CAAAGCTTCAATACTTCTCT+CGG - chr2.1:9740817-9740836 None:intergenic 35.0%
GCTTCAAGTAGAATGAATGA+TGG + chr2.1:9740675-9740694 MS.gene54856:CDS 35.0%
GGTGTAAATGGAAATGGATA+TGG + chr2.1:9740708-9740727 MS.gene54856:CDS 35.0%
GTGAAGACTCACACTTTAAT+AGG + chr2.1:9741237-9741256 MS.gene54856:intron 35.0%
TAGAAACTAGAAAGAGAAGG+AGG + chr2.1:9742180-9742199 MS.gene54856:CDS 35.0%
! CTTATCTCATCACTGTCTTT+TGG - chr2.1:9741864-9741883 None:intergenic 35.0%
! GACAGTGAATGGCAAAATTT+TGG + chr2.1:9741433-9741452 MS.gene54856:intron 35.0%
!! GGTTGTTTTCAAGGTGTAAA+TGG + chr2.1:9740696-9740715 MS.gene54856:CDS 35.0%
!! TCACAAGAAGGTGGATTAAA+TGG + chr2.1:9741891-9741910 MS.gene54856:CDS 35.0%
!!! CTGGTTTTGGATAGAGAAAA+AGG + chr2.1:9740744-9740763 MS.gene54856:CDS 35.0%
!!! GTCTAGTTTTTGTACTTCGT+AGG - chr2.1:9741137-9741156 None:intergenic 35.0%
!!! TTCATCTTCTTCACTGGTTT+TGG + chr2.1:9740731-9740750 MS.gene54856:CDS 35.0%
AGAATCATAGTGAAGCAGAG+AGG + chr2.1:9740838-9740857 MS.gene54856:CDS 40.0%
AGAGTTGAATCACAAGAAGG+TGG + chr2.1:9741882-9741901 MS.gene54856:CDS 40.0%
AGCAAGAAACTGTCGATACT+CGG - chr2.1:9742099-9742118 None:intergenic 40.0%
CAAGAGCTCAATGAGTTTGA+TGG + chr2.1:9741602-9741621 MS.gene54856:intron 40.0%
GAACTAACCTTATTAGCACC+TGG - chr2.1:9740915-9740934 None:intergenic 40.0%
TAGAGAAAAAGGAGAGCTTG+TGG + chr2.1:9740755-9740774 MS.gene54856:CDS 40.0%
TGTTATCCCAGGTGCTAATA+AGG + chr2.1:9740905-9740924 MS.gene54856:CDS 40.0%
! ATAAGGACGACCCTCTTTTA+TGG + chr2.1:9741264-9741283 MS.gene54856:intron 40.0%
AAGGGCAGAGATTGCAACTT+TGG + chr2.1:9742013-9742032 MS.gene54856:CDS 45.0%
AATGCAGCACAAGCAAGTGA+AGG + chr2.1:9741828-9741847 MS.gene54856:CDS 45.0%
ACACTTCGTAGTGTTATCCC+AGG + chr2.1:9740894-9740913 MS.gene54856:CDS 45.0%
AGAAAAAGGAGAGCTTGTGG+AGG + chr2.1:9740758-9740777 MS.gene54856:CDS 45.0%
AGGGCAGAGATTGCAACTTT+GGG + chr2.1:9742014-9742033 MS.gene54856:CDS 45.0%
ATGCAGCACAAGCAAGTGAA+GGG + chr2.1:9741829-9741848 MS.gene54856:CDS 45.0%
GCTGTGAAATTGGAACGCAA+AGG + chr2.1:9740783-9740802 MS.gene54856:CDS 45.0%
TCGACAGTTTCTTGCTGGAT+CGG + chr2.1:9742103-9742122 MS.gene54856:CDS 45.0%
!! GAGTATCGACAGTTTCTTGC+TGG + chr2.1:9742098-9742117 MS.gene54856:CDS 45.0%
GCAGAGATTGCAACTTTGGG+AGG + chr2.1:9742017-9742036 MS.gene54856:CDS 50.0%
TGTGGAGGCAGCTGTGAAAT+TGG + chr2.1:9740773-9740792 MS.gene54856:CDS 50.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 9740657 9742244 9740657 ID=MS.gene54856
chr2.1 mRNA 9740657 9742244 9740657 ID=MS.gene54856.t1;Parent=MS.gene54856
chr2.1 exon 9740657 9740926 9740657 ID=MS.gene54856.t1.exon1;Parent=MS.gene54856.t1
chr2.1 CDS 9740657 9740926 9740657 ID=cds.MS.gene54856.t1;Parent=MS.gene54856.t1
chr2.1 exon 9741771 9742244 9741771 ID=MS.gene54856.t1.exon2;Parent=MS.gene54856.t1
chr2.1 CDS 9741771 9742244 9741771 ID=cds.MS.gene54856.t1;Parent=MS.gene54856.t1
Gene Sequence

>MS.gene54856

ATGGAAATGGATGATTTTGCTTCAAGTAGAATGAATGATGGTTGTTTTCAAGGTGTAAATGGAAATGGATATGGTTCATCTTCTTCACTGGTTTTGGATAGAGAAAAAGGAGAGCTTGTGGAGGCAGCTGTGAAATTGGAACGCAAAGGTGTGTCGCCCGAGAGAAGTATTGAAGCTTTGAAGAATCATAGTGAAGCAGAGAGGAGAAGAAGAGCAAGAATTAATTCACATCTTGATACACTTCGTAGTGTTATCCCAGGTGCTAATAAGGTTAGTTCAATTTTATTTATTTATTTATTTTTACTTTTTTTGTTGTTTATTTTGAATTACTAGTTAGTACTGGTTTTGCTCATGTTGAGAACAATTTCTGTCATGATTAACTCCAAATATTTGAAGGGAAAGAATTATTTTTTATGTTTAATTAATGTAAAATTTACATGTAATTTGTATTGAATAACTTATGATTATTATTATTGACCTACGAAGTACAAAAACTAGACATCAGTAATAATTTGAAGAAAAAAAATAGTACAAGTAATTGTATATAAATTATATAAATAAAAGTGTTAGTATCGTGCCTGTGAAGACTCACACTTTAATAGGGAATATAAGGACGACCCTCTTTTATGGTCATTTGAATGAAATAATAGCTTTTACTATATATGAATGTGCATTTACACTGAAGTTTTAAGTTTTAACTATAAGTCTTGAGCTATGAATGCATTTCAAAATGTAGTGAGTATTTTTGGATGTTGAAACAATTGAAGTTAAATTGAGACAGTGAATGGCAAAATTTTGGGATCCATATATGTGAGTAAAGCCATTTTGCTTACTTTTGAAGTCTTGATTCTTCTTTTTTGTATAATGTAGCTTTTAGTTTTCAATGGACCAAGTTCAATTTTCTTTCCTAAAAGAAGGGAATAGAATAATTTAATTTTGGAGTAGCAAGAGCTCAATGAGTTTGATGGTATTAAAAAAAGATGTTAATATTAACTGTCCAACATAGTTATGCTTATACTTGGAATCATGAAATTCATGTCTACACAAACATACAAACATGATATATATGTTAATCTTTCAGAATCTAACGTTTTTGTGTACTTTTTGAACTTAGTTGGACAAAGCATCCTTACTAGCTGAAGTTATTACACATTTGAAAGAGCTGAAAACAAATGCAGCACAAGCAAGTGAAGGGTTCATTATTCCAAAAGACAGTGATGAGATAAGAGTTGAATCACAAGAAGGTGGATTAAATGGTTACCCTTATTCAATTAGAGCATCATTATGTTGTGAATACAAACCCGGTTTATTGTCTGATATAAGAAAAGCACTTGATGCACTTCATCTTATGATAATAAGGGCAGAGATTGCAACTTTGGGAGGTAGAATGAAGAATGTCTTTGTCATAATTAGCTGCAAAGAACAGAATTTTGAAGATGCCGAGTATCGACAGTTTCTTGCTGGATCGGTTCATCAAGCTCTTAGATCTGTACTTGATAGATTTTCTGTTTCACAAGATATCTTAGAAACTAGAAAGAGAAGGAGGATTTCTATATTCAGTTCTTCATCTTTAGGTGATTTCTTATAA
Protein sequence

>MS.gene54856.t1

MEMDDFASSRMNDGCFQGVNGNGYGSSSSLVLDREKGELVEAAVKLERKGVSPERSIEALKNHSEAERRRRARINSHLDTLRSVIPGANKLDKASLLAEVITHLKELKTNAAQASEGFIIPKDSDEIRVESQEGGLNGYPYSIRASLCCEYKPGLLSDIRKALDALHLMIIRAEIATLGGRMKNVFVIISCKEQNFEDAEYRQFLAGSVHQALRSVLDRFSVSQDILETRKRRRISIFSSSSLGDFL