AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene043507

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043507.t1 MTR_2g091190 98.785 247 3 0 1 247 1 247 2.37e-180 494
MS.gene043507.t1 MTR_4g079760 72.266 256 62 3 1 247 1 256 1.50e-121 346
MS.gene043507.t1 MTR_2g015890 50.732 205 95 3 23 225 29 229 2.34e-61 193
MS.gene043507.t1 MTR_4g087920 44.262 244 125 6 2 235 13 255 4.87e-50 165
MS.gene043507.t1 MTR_3g096568 88.158 76 9 0 127 202 236 311 1.23e-43 150
MS.gene043507.t1 MTR_2g015890 50.667 150 69 2 23 170 29 175 3.01e-43 146
MS.gene043507.t1 MTR_2g015890 51.111 135 62 2 91 225 1 131 2.07e-37 129
MS.gene043507.t1 MTR_8g032210 90.123 81 7 1 5 85 16 95 4.70e-36 124
MS.gene043507.t1 MTR_1g093750 40.594 202 109 3 45 242 144 338 3.75e-34 125
MS.gene043507.t1 MTR_3g070970 33.333 201 115 5 46 234 60 253 1.83e-30 114
MS.gene043507.t1 MTR_5g066080 40.606 165 72 2 49 188 27 190 1.96e-24 98.2
MS.gene043507.t1 MTR_5g032375 36.000 150 75 4 54 188 40 183 1.04e-20 87.4
MS.gene043507.t1 MTR_2g015890 51.250 80 36 1 91 170 1 77 1.75e-19 81.6
MS.gene043507.t1 MTR_1g018820 89.744 39 4 0 90 128 58 96 7.65e-17 73.9
MS.gene043507.t1 MTR_5g030430 40.244 82 49 0 28 109 459 540 4.11e-12 65.9
MS.gene043507.t1 MTR_8g067280 39.506 81 49 0 29 109 429 509 1.12e-11 64.7
MS.gene043507.t1 MTR_2g081040 25.949 158 76 3 66 186 181 334 8.00e-11 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene043507.t1 AT1G68810 41.327 196 107 5 45 236 160 351 2.86e-33 124
MS.gene043507.t1 AT3G25710 46.622 148 70 2 45 188 118 260 4.52e-31 117
MS.gene043507.t1 AT3G56770 38.857 175 98 4 51 223 37 204 1.79e-30 113
MS.gene043507.t1 AT2G40200 39.634 164 89 3 61 219 65 223 1.33e-29 112
MS.gene043507.t1 AT2G41130 40.571 175 96 3 51 223 59 227 4.75e-27 105
MS.gene043507.t1 AT4G38070 36.154 130 76 2 59 188 92 214 1.04e-17 80.1
MS.gene043507.t1 AT1G32640 37.624 101 60 2 33 130 421 521 1.17e-11 64.7
MS.gene043507.t1 AT5G46760 44.156 77 42 1 39 114 391 467 2.19e-11 63.5
MS.gene043507.t1 AT4G17880 40.789 76 45 0 39 114 393 468 2.24e-11 63.5

Find 37 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCATCTTCTTCACTGGTTT+TGG 0.180837 2.2:+8219136 MS.gene043507:CDS
CACTTCATCTTATGATAATA+AGG 0.194458 2.2:+8220403 MS.gene043507:CDS
AATGATGCTCTAATTGAATA+AGG 0.233216 2.2:-8220327 None:intergenic
CTTATCTCATCACTGTCTTT+TGG 0.234136 2.2:-8220270 None:intergenic
ATATTCAGTTCTTCATCTTT+AGG 0.245592 2.2:+8220618 MS.gene043507:CDS
TCACAAGAAGGTGGATTAAA+TGG 0.279597 2.2:+8220300 MS.gene043507:CDS
GTTGGACAAAGCATCCTTAC+TGG 0.310877 2.2:+8220179 MS.gene043507:intron
TTTCAAGGTGTAAATGGAAA+TGG 0.359014 2.2:+8219107 MS.gene043507:CDS
TGTGGAGGCAGCTGTGAAAT+TGG 0.360925 2.2:+8219178 MS.gene043507:CDS
TGTTATCCCAGGTGCTAATA+AGG 0.365921 2.2:+8219310 MS.gene043507:CDS
AAGGGCAGAGATTGCAACTT+TGG 0.372459 2.2:+8220422 MS.gene043507:CDS
GAGTATCGACAGTTTCTTGC+TGG 0.401116 2.2:+8220507 MS.gene043507:CDS
AGGGCAGAGATTGCAACTTT+GGG 0.424505 2.2:+8220423 MS.gene043507:CDS
TCTTATATCAGACAATAAAC+CGG 0.424693 2.2:-8220367 None:intergenic
GGTGTAAATGGAAATGGATA+TGG 0.430429 2.2:+8219113 MS.gene043507:CDS
TGTAATAACTTCAGCCAGTA+AGG 0.442964 2.2:-8220193 None:intergenic
ATGATGCTCTAATTGAATAA+GGG 0.448376 2.2:-8220326 None:intergenic
ATATGGTTCATCTTCTTCAC+TGG 0.451383 2.2:+8219130 MS.gene043507:CDS
ACTTCATCTTATGATAATAA+GGG 0.489015 2.2:+8220404 MS.gene043507:CDS
TCGACAGTTTCTTGCTGGAT+CGG 0.489881 2.2:+8220512 MS.gene043507:CDS
AAAGCTTCAATACTTCTCTC+AGG 0.498631 2.2:-8219218 None:intergenic
CTTATATCAGACAATAAACC+GGG 0.504302 2.2:-8220366 None:intergenic
GAACTAACCTTATTAGCACC+TGG 0.521161 2.2:-8219317 None:intergenic
AGCAAGAAACTGTCGATACT+CGG 0.542573 2.2:-8220505 None:intergenic
TTATGTTGTGAATACAAACC+CGG 0.569012 2.2:+8220348 MS.gene043507:CDS
AACTAACCTTATTAGCACCT+GGG 0.573545 2.2:-8219316 None:intergenic
GCTTCAAGTAGAATGAATGA+TGG 0.589941 2.2:+8219080 MS.gene043507:CDS
GCAGAGATTGCAACTTTGGG+AGG 0.592208 2.2:+8220426 MS.gene043507:CDS
ATCATAGTGAAGCAGAGAGG+AGG 0.603979 2.2:+8219246 MS.gene043507:CDS
TCTTAGAAACTAGAAAGAGA+AGG 0.613686 2.2:+8220586 MS.gene043507:CDS
TAGAAACTAGAAAGAGAAGG+AGG 0.614835 2.2:+8220589 MS.gene043507:CDS
ATAAGAGTTGAATCACAAGA+AGG 0.621854 2.2:+8220288 MS.gene043507:CDS
ACACTTCGTAGTGTTATCCC+AGG 0.622939 2.2:+8219299 MS.gene043507:CDS
AGAGTTGAATCACAAGAAGG+TGG 0.624818 2.2:+8220291 MS.gene043507:CDS
AATGCAGCACAAGCAAGTGA+AGG 0.627293 2.2:+8220237 MS.gene043507:CDS
GCTGTGAAATTGGAACGCAA+AGG 0.704659 2.2:+8219188 MS.gene043507:CDS
AGAATCATAGTGAAGCAGAG+AGG 0.708784 2.2:+8219243 MS.gene043507:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GGAATAGAATAATTTAATTT+TGG + chr2.2:8219983-8220002 MS.gene043507:intron 15.0%
!! ACTTCATCTTATGATAATAA+GGG + chr2.2:8220404-8220423 MS.gene043507:CDS 20.0%
!!! AATTTTCTTTCCTAAAAGAA+GGG + chr2.2:8219962-8219981 MS.gene043507:intron 20.0%
! AACTTAGTTATGCTTATACT+TGG + chr2.2:8220065-8220084 MS.gene043507:intron 25.0%
! AAGTATAAGCATAACTAAGT+TGG - chr2.2:8220066-8220085 None:intergenic 25.0%
! AATGATGCTCTAATTGAATA+AGG - chr2.2:8220330-8220349 None:intergenic 25.0%
! ATATTCAGTTCTTCATCTTT+AGG + chr2.2:8220618-8220637 MS.gene043507:CDS 25.0%
! ATGATGCTCTAATTGAATAA+GGG - chr2.2:8220329-8220348 None:intergenic 25.0%
! ATTAACTCCAAATATTTGAG+GGG + chr2.2:8219437-8219456 MS.gene043507:intron 25.0%
! ATTCAAATGACCATAAAAGA+GGG - chr2.2:8219684-8219703 None:intergenic 25.0%
! CACTTCATCTTATGATAATA+AGG + chr2.2:8220403-8220422 MS.gene043507:CDS 25.0%
! GATTAACTCCAAATATTTGA+GGG + chr2.2:8219436-8219455 MS.gene043507:intron 25.0%
! TCTTATATCAGACAATAAAC+CGG - chr2.2:8220370-8220389 None:intergenic 25.0%
! TGATTAACTCCAAATATTTG+AGG + chr2.2:8219435-8219454 MS.gene043507:intron 25.0%
! TTAGGAAAGAAAATTGAACT+TGG - chr2.2:8219957-8219976 None:intergenic 25.0%
! TTTGAATTACTAGTTAGTAC+TGG + chr2.2:8219382-8219401 MS.gene043507:intron 25.0%
!! CAATTTTCTTTCCTAAAAGA+AGG + chr2.2:8219961-8219980 MS.gene043507:intron 25.0%
!! TTATTCTATTCCCTTCTTTT+AGG - chr2.2:8219975-8219994 None:intergenic 25.0%
!!! ATGTAGCTTTTAGTTTTCAA+TGG + chr2.2:8219930-8219949 MS.gene043507:intron 25.0%
!!! GTGTACTTTTTTAACTTAGT+TGG + chr2.2:8220161-8220180 MS.gene043507:intron 25.0%
ACACTTTAACAGGGAATATA+AGG + chr2.2:8219654-8219673 MS.gene043507:intron 30.0%
AGTTAAATTGAGACAGTGAA+TGG + chr2.2:8219831-8219850 MS.gene043507:intron 30.0%
ATAAGAGTTGAATCACAAGA+AGG + chr2.2:8220288-8220307 MS.gene043507:CDS 30.0%
ATTCTTTCCCCTCAAATATT+TGG - chr2.2:8219447-8219466 None:intergenic 30.0%
CATTCAAATGACCATAAAAG+AGG - chr2.2:8219685-8219704 None:intergenic 30.0%
CTTATATCAGACAATAAACC+GGG - chr2.2:8220369-8220388 None:intergenic 30.0%
GACTTCAAAAGTAAGCAAAA+TGG - chr2.2:8219889-8219908 None:intergenic 30.0%
TATAAGTCTTGAGCTATGAA+TGG + chr2.2:8219764-8219783 MS.gene043507:intron 30.0%
TCTTAGAAACTAGAAAGAGA+AGG + chr2.2:8220586-8220605 MS.gene043507:CDS 30.0%
TTATGTTGTGAATACAAACC+CGG + chr2.2:8220348-8220367 MS.gene043507:CDS 30.0%
TTGTGTAGACATGAATTTCA+TGG - chr2.2:8220093-8220112 None:intergenic 30.0%
TTTCAAGGTGTAAATGGAAA+TGG + chr2.2:8219107-8219126 MS.gene043507:CDS 30.0%
! AATGGCTTTACTCACATATA+TGG - chr2.2:8219871-8219890 None:intergenic 30.0%
! ACAGTGAATGGCAAAATTTT+GGG + chr2.2:8219843-8219862 MS.gene043507:intron 30.0%
! CAAAATGCAGTGAGTATTTT+TGG + chr2.2:8219792-8219811 MS.gene043507:intron 30.0%
!! ATGAATGATGGTTGTTTTCA+AGG + chr2.2:8219092-8219111 MS.gene043507:CDS 30.0%
!!! GTCTAGTTTTTGTACTTCAT+AGG - chr2.2:8219549-8219568 None:intergenic 30.0%
AAAGCTTCAATACTTCTCTC+AGG - chr2.2:8219221-8219240 None:intergenic 35.0%
AACTAACCTTATTAGCACCT+GGG - chr2.2:8219319-8219338 None:intergenic 35.0%
ATATGGTTCATCTTCTTCAC+TGG + chr2.2:8219130-8219149 MS.gene043507:CDS 35.0%
GCTTCAAGTAGAATGAATGA+TGG + chr2.2:8219080-8219099 MS.gene043507:CDS 35.0%
GGTGTAAATGGAAATGGATA+TGG + chr2.2:8219113-8219132 MS.gene043507:CDS 35.0%
TAGAAACTAGAAAGAGAAGG+AGG + chr2.2:8220589-8220608 MS.gene043507:CDS 35.0%
TGTAATAACTTCAGCCAGTA+AGG - chr2.2:8220196-8220215 None:intergenic 35.0%
! CTTATCTCATCACTGTCTTT+TGG - chr2.2:8220273-8220292 None:intergenic 35.0%
! GACAGTGAATGGCAAAATTT+TGG + chr2.2:8219842-8219861 MS.gene043507:intron 35.0%
!! GGTTGTTTTCAAGGTGTAAA+TGG + chr2.2:8219101-8219120 MS.gene043507:CDS 35.0%
!! TCACAAGAAGGTGGATTAAA+TGG + chr2.2:8220300-8220319 MS.gene043507:CDS 35.0%
!!! CTGGTTTTGGATAGAGAAAA+AGG + chr2.2:8219149-8219168 MS.gene043507:CDS 35.0%
!!! TTCATCTTCTTCACTGGTTT+TGG + chr2.2:8219136-8219155 MS.gene043507:CDS 35.0%
AAGAGTCGCACACTTTAACA+GGG + chr2.2:8219645-8219664 MS.gene043507:intron 40.0%
AGAATCATAGTGAAGCAGAG+AGG + chr2.2:8219243-8219262 MS.gene043507:CDS 40.0%
AGAGTTGAATCACAAGAAGG+TGG + chr2.2:8220291-8220310 MS.gene043507:CDS 40.0%
AGCAAGAAACTGTCGATACT+CGG - chr2.2:8220508-8220527 None:intergenic 40.0%
CAAGAGCTCAATGAGTTTGA+TGG + chr2.2:8220011-8220030 MS.gene043507:intron 40.0%
GAACTAACCTTATTAGCACC+TGG - chr2.2:8219320-8219339 None:intergenic 40.0%
TAGAGAAAAAGGAGAGCTTG+TGG + chr2.2:8219160-8219179 MS.gene043507:CDS 40.0%
TGTTATCCCAGGTGCTAATA+AGG + chr2.2:8219310-8219329 MS.gene043507:CDS 40.0%
! ATAAGGACGACCCTCTTTTA+TGG + chr2.2:8219671-8219690 MS.gene043507:intron 40.0%
AAGGGCAGAGATTGCAACTT+TGG + chr2.2:8220422-8220441 MS.gene043507:CDS 45.0%
AATGCAGCACAAGCAAGTGA+AGG + chr2.2:8220237-8220256 MS.gene043507:CDS 45.0%
ACACTTCGTAGTGTTATCCC+AGG + chr2.2:8219299-8219318 MS.gene043507:CDS 45.0%
AGAAAAAGGAGAGCTTGTGG+AGG + chr2.2:8219163-8219182 MS.gene043507:CDS 45.0%
AGGGCAGAGATTGCAACTTT+GGG + chr2.2:8220423-8220442 MS.gene043507:CDS 45.0%
ATCATAGTGAAGCAGAGAGG+AGG + chr2.2:8219246-8219265 MS.gene043507:CDS 45.0%
GAAGAGTCGCACACTTTAAC+AGG + chr2.2:8219644-8219663 MS.gene043507:intron 45.0%
GCTGTGAAATTGGAACGCAA+AGG + chr2.2:8219188-8219207 MS.gene043507:CDS 45.0%
TAAAGTGTGCGACTCTTCAC+AGG - chr2.2:8219642-8219661 None:intergenic 45.0%
TCGACAGTTTCTTGCTGGAT+CGG + chr2.2:8220512-8220531 MS.gene043507:CDS 45.0%
! GTTGGACAAAGCATCCTTAC+TGG + chr2.2:8220179-8220198 MS.gene043507:intron 45.0%
!! GAGTATCGACAGTTTCTTGC+TGG + chr2.2:8220507-8220526 MS.gene043507:CDS 45.0%
GCAGAGATTGCAACTTTGGG+AGG + chr2.2:8220426-8220445 MS.gene043507:CDS 50.0%
TGTGGAGGCAGCTGTGAAAT+TGG + chr2.2:8219178-8219197 MS.gene043507:CDS 50.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 8219062 8220653 8219062 ID=MS.gene043507
chr2.2 mRNA 8219062 8220653 8219062 ID=MS.gene043507.t1;Parent=MS.gene043507
chr2.2 exon 8219062 8219331 8219062 ID=MS.gene043507.t1.exon1;Parent=MS.gene043507.t1
chr2.2 CDS 8219062 8219331 8219062 ID=cds.MS.gene043507.t1;Parent=MS.gene043507.t1
chr2.2 exon 8220180 8220653 8220180 ID=MS.gene043507.t1.exon2;Parent=MS.gene043507.t1
chr2.2 CDS 8220180 8220653 8220180 ID=cds.MS.gene043507.t1;Parent=MS.gene043507.t1
Gene Sequence

>MS.gene043507

ATGGAAATGGATGATTTTGCTTCAAGTAGAATGAATGATGGTTGTTTTCAAGGTGTAAATGGAAATGGATATGGTTCATCTTCTTCACTGGTTTTGGATAGAGAAAAAGGAGAGCTTGTGGAGGCAGCTGTGAAATTGGAACGCAAAGGTGTGTCACCTGAGAGAAGTATTGAAGCTTTGAAGAATCATAGTGAAGCAGAGAGGAGGAGAAGAGCAAGAATTAATTCACATCTTGATACACTTCGTAGTGTTATCCCAGGTGCTAATAAGGTTAGTTCAATTTTATTCATTTATTTATTTTTACTTTTTTTGTTGTTTATTTTGAATTACTAGTTAGTACTGGTTTTGCTCATGTTGAGAACAATGTCTGTCATGATTAACTCCAAATATTTGAGGGGAAAGAATTATTTTTTATGTTTAATTAATGTAAAATTTACATATAATTTGTATTTTGTGTTGAATAACTTATGATTATTATTATTGACCTATGAAGTACAAAAACTAGACATCAATAATAATTTGAAAAAAAATAGAAGTAATTGTATATACACATATAAATAAAAGTGTCAGTATCGTGCCTGTGAAGAGTCGCACACTTTAACAGGGAATATAAGGACGACCCTCTTTTATGGTCATTTGAATGAAATAATAGCTTTTACTATATATGAATGTGCATATTACACTGAAGTTTTAAGTTTTAACTATAAGTCTTGAGCTATGAATGGCATTTCAAAATGCAGTGAGTATTTTTGGATGTTGAAACAATTGAAGTTAAATTGAGACAGTGAATGGCAAAATTTTGGGATCCATATATGTGAGTAAAGCCATTTTGCTTACTTTTGAAGTCTTGATTCTTCTTTTTTGTATAATGTAGCTTTTAGTTTTCAATGGACCAAGTTCAATTTTCTTTCCTAAAAGAAGGGAATAGAATAATTTAATTTTGGAGTAGCAAGAGCTCAATGAGTTTGATGGTATTAAAAAAAGATGTTAATATTAACTGTCCAACTTAGTTATGCTTATACTTGGAACCATGAAATTCATGTCTACACAAACAAATAAACATGATATATATGTTAATCTTTCAGAATCTAACATTTTTGTGTACTTTTTTAACTTAGTTGGACAAAGCATCCTTACTGGCTGAAGTTATTACACATTTGAAAGAGCTGAAAACAAATGCAGCACAAGCAAGTGAAGGATTAATTATTCCAAAAGACAGTGATGAGATAAGAGTTGAATCACAAGAAGGTGGATTAAATGGTTACCCTTATTCAATTAGAGCATCATTATGTTGTGAATACAAACCCGGTTTATTGTCTGATATAAGAAAAGCACTTGATGCACTTCATCTTATGATAATAAGGGCAGAGATTGCAACTTTGGGAGGTAGAATGAAGAATGTCTTTGTCATAATTAGCTGCAAAGAACAGAATTTTGAAGATGCCGAGTATCGACAGTTTCTTGCTGGATCGGTTCATCAAGCTCTTAGATCTGTACTTGATAGATTTTCTGTTTCACAAGATATCTTAGAAACTAGAAAGAGAAGGAGGATTTCTATATTCAGTTCTTCATCTTTAGGTGATTTCTTATAA
Protein sequence

>MS.gene043507.t1

MEMDDFASSRMNDGCFQGVNGNGYGSSSSLVLDREKGELVEAAVKLERKGVSPERSIEALKNHSEAERRRRARINSHLDTLRSVIPGANKLDKASLLAEVITHLKELKTNAAQASEGLIIPKDSDEIRVESQEGGLNGYPYSIRASLCCEYKPGLLSDIRKALDALHLMIIRAEIATLGGRMKNVFVIISCKEQNFEDAEYRQFLAGSVHQALRSVLDRFSVSQDILETRKRRRISIFSSSSLGDFL