AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene31376

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31376.t1 MTR_2g091190 97.976 247 5 0 1 247 1 247 4.89e-179 491
MS.gene31376.t1 MTR_4g079760 72.266 256 62 3 1 247 1 256 1.56e-121 346
MS.gene31376.t1 MTR_2g015890 50.732 205 95 3 23 225 29 229 3.47e-62 196
MS.gene31376.t1 MTR_4g087920 44.672 244 124 6 2 235 13 255 7.80e-51 167
MS.gene31376.t1 MTR_2g015890 50.667 150 69 2 23 170 29 175 4.19e-44 148
MS.gene31376.t1 MTR_3g096568 88.158 76 9 0 127 202 236 311 1.23e-43 150
MS.gene31376.t1 MTR_2g015890 51.111 135 62 2 91 225 1 131 3.28e-38 131
MS.gene31376.t1 MTR_8g032210 87.059 85 10 1 1 85 12 95 3.71e-36 124
MS.gene31376.t1 MTR_1g093750 40.594 202 109 3 45 242 144 338 2.55e-34 126
MS.gene31376.t1 MTR_3g070970 33.333 201 115 5 46 234 60 253 2.71e-30 114
MS.gene31376.t1 MTR_5g066080 40.606 165 72 2 49 188 27 190 6.41e-25 99.4
MS.gene31376.t1 MTR_5g032375 36.000 150 75 4 54 188 40 183 1.68e-20 86.7
MS.gene31376.t1 MTR_2g015890 51.250 80 36 1 91 170 1 77 2.96e-20 83.6
MS.gene31376.t1 MTR_1g018820 87.179 39 5 0 90 128 58 96 2.74e-16 72.4
MS.gene31376.t1 MTR_5g030430 40.244 82 49 0 28 109 459 540 4.39e-12 65.9
MS.gene31376.t1 MTR_8g067280 39.506 81 49 0 29 109 429 509 1.03e-11 64.7
MS.gene31376.t1 MTR_2g081040 26.582 158 75 3 66 186 181 334 1.29e-11 63.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31376.t1 AT1G68810 41.327 196 107 5 45 236 160 351 2.01e-33 124
MS.gene31376.t1 AT3G25710 46.622 148 70 2 45 188 118 260 9.09e-32 119
MS.gene31376.t1 AT3G56770 38.857 175 98 4 51 223 37 204 1.49e-30 113
MS.gene31376.t1 AT2G40200 39.634 164 89 3 61 219 65 223 1.60e-29 111
MS.gene31376.t1 AT2G41130 40.571 175 96 3 51 223 59 227 3.98e-27 105
MS.gene31376.t1 AT4G38070 36.154 130 76 2 59 188 92 214 1.14e-17 80.1
MS.gene31376.t1 AT5G46760 44.156 77 42 1 39 114 391 467 2.16e-11 63.9
MS.gene31376.t1 AT4G17880 40.789 76 45 0 39 114 393 468 2.26e-11 63.5
MS.gene31376.t1 AT1G32640 36.634 101 61 2 33 130 421 521 3.48e-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 2.4:+9147357 MS.gene31376:CDS
CACTTCATCTTATGATAATA+AGG 0.194458 2.4:+9148611 MS.gene31376:CDS
AATGATGCTCTAATTGAATA+AGG 0.233216 2.4:-9148535 None:intergenic
CTTATCTCATCACTGTCTTT+TGG 0.234136 2.4:-9148478 None:intergenic
ATATTCAGTTCTTCATCTTT+AGG 0.245592 2.4:+9148826 MS.gene31376:CDS
TCACAAGAAGGTGGATTAAA+TGG 0.279597 2.4:+9148508 MS.gene31376:CDS
TGTGGAGGCAGCTGTGAAAT+TGG 0.360925 2.4:+9147399 MS.gene31376:CDS
TGTTATCCCAGGTGCTAATA+AGG 0.365921 2.4:+9147531 MS.gene31376:CDS
TGTAATAACTTCAGCTAGTA+AGG 0.369694 2.4:-9148401 None:intergenic
AAGGGCAGAGATTGCAACTT+TGG 0.372459 2.4:+9148630 MS.gene31376:CDS
GAGTATCGACAGTTTCTTGC+TGG 0.401116 2.4:+9148715 MS.gene31376:CDS
GGTGTAAATGGAAGTGGATA+TGG 0.413506 2.4:+9147334 MS.gene31376:CDS
CAAAGCTTCAATACTTCTCT+CGG 0.423960 2.4:-9147440 None:intergenic
AGGGCAGAGATTGCAACTTT+GGG 0.424505 2.4:+9148631 MS.gene31376:CDS
TCTTATATCAGACAATAAAC+CGG 0.424693 2.4:-9148575 None:intergenic
ATATGGTTCATCTTCTTCAC+TGG 0.433898 2.4:+9147351 MS.gene31376:CDS
ATGATGCTCTAATTGAATAA+GGG 0.448376 2.4:-9148534 None:intergenic
TTTCAAGGTGTAAATGGAAG+TGG 0.455677 2.4:+9147328 MS.gene31376:CDS
ACTTCATCTTATGATAATAA+GGG 0.489015 2.4:+9148612 MS.gene31376:CDS
TCGACAGTTTCTTGCTGGAT+CGG 0.489881 2.4:+9148720 MS.gene31376:CDS
CTTATATCAGACAATAAACC+GGG 0.504302 2.4:-9148574 None:intergenic
GAACTAACCTTATTAGCACC+TGG 0.521161 2.4:-9147538 None:intergenic
AAAGCTTCAATACTTCTCTC+GGG 0.540932 2.4:-9147439 None:intergenic
AGCAAGAAACTGTCGATACT+CGG 0.542573 2.4:-9148713 None:intergenic
TTATGTTGTGAATACAAACC+CGG 0.569012 2.4:+9148556 MS.gene31376:CDS
AACTAACCTTATTAGCACCT+GGG 0.573545 2.4:-9147537 None:intergenic
AATGCAGCACAAGCAAGTGA+AGG 0.583141 2.4:+9148445 MS.gene31376:CDS
GCTTCAAGTAGAATGAATGA+TGG 0.589941 2.4:+9147301 MS.gene31376:CDS
GCAGAGATTGCAACTTTGGG+AGG 0.592208 2.4:+9148634 MS.gene31376:CDS
ATGCAGCACAAGCAAGTGAA+GGG 0.603381 2.4:+9148446 MS.gene31376:CDS
TCTTAGAAACTAGAAAGAGA+AGG 0.613686 2.4:+9148794 MS.gene31376:CDS
TAGAAACTAGAAAGAGAAGG+AGG 0.614835 2.4:+9148797 MS.gene31376:CDS
ATAAGAGTTGAATCACAAGA+AGG 0.621854 2.4:+9148496 MS.gene31376:CDS
ACACTTCGTAGTGTTATCCC+AGG 0.622939 2.4:+9147520 MS.gene31376:CDS
AGAGTTGAATCACAAGAAGG+TGG 0.624818 2.4:+9148499 MS.gene31376:CDS
GCTGTGAAATTGGAACGCAA+AGG 0.704659 2.4:+9147409 MS.gene31376:CDS
AGAATCATAGTGAAGCAGAG+AGG 0.708784 2.4:+9147464 MS.gene31376:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GGAATAAAATAATTTAATTT+TGG + chr2.4:9148191-9148210 MS.gene31376:intron 10.0%
!! ACTTCATCTTATGATAATAA+GGG + chr2.4:9148612-9148631 MS.gene31376:CDS 20.0%
!! ATTAACTCCAAATATTTGAA+GGG + chr2.4:9147658-9147677 MS.gene31376:intron 20.0%
!!! AATTTTCTTTCCTAAAAGAA+GGG + chr2.4:9148170-9148189 MS.gene31376:intron 20.0%
!!! TTATTTTATTCCCTTCTTTT+AGG - chr2.4:9148183-9148202 None:intergenic 20.0%
! AACATAGTTATGCTTATACT+TGG + chr2.4:9148273-9148292 MS.gene31376:intron 25.0%
! AAGTATAAGCATAACTATGT+TGG - chr2.4:9148274-9148293 None:intergenic 25.0%
! AATGATGCTCTAATTGAATA+AGG - chr2.4:9148538-9148557 None:intergenic 25.0%
! ACACTTTAATAGGGAATATA+AGG + chr2.4:9147864-9147883 MS.gene31376:intron 25.0%
! ATATTCAGTTCTTCATCTTT+AGG + chr2.4:9148826-9148845 MS.gene31376:CDS 25.0%
! ATGATGCTCTAATTGAATAA+GGG - chr2.4:9148537-9148556 None:intergenic 25.0%
! ATTCAAATGACCATAAAAGA+GGG - chr2.4:9147894-9147913 None:intergenic 25.0%
! ATTCTTTCCCTTCAAATATT+TGG - chr2.4:9147668-9147687 None:intergenic 25.0%
! CACTTCATCTTATGATAATA+AGG + chr2.4:9148611-9148630 MS.gene31376:CDS 25.0%
! GATTAACTCCAAATATTTGA+AGG + chr2.4:9147657-9147676 MS.gene31376:intron 25.0%
! TCTTATATCAGACAATAAAC+CGG - chr2.4:9148578-9148597 None:intergenic 25.0%
! TTAGGAAAGAAAATTGAACT+TGG - chr2.4:9148165-9148184 None:intergenic 25.0%
! TTTGAATTACTAGTTAGTAC+TGG + chr2.4:9147603-9147622 MS.gene31376:intron 25.0%
!! CAAAATGTAGTGAGTATTTT+TGG + chr2.4:9148000-9148019 MS.gene31376:intron 25.0%
!! CAATTTTCTTTCCTAAAAGA+AGG + chr2.4:9148169-9148188 MS.gene31376:intron 25.0%
!!! ATGTAGCTTTTAGTTTTCAA+TGG + chr2.4:9148138-9148157 MS.gene31376:intron 25.0%
AGTTAAATTGAGACAGTGAA+TGG + chr2.4:9148039-9148058 MS.gene31376:intron 30.0%
ATAAGAGTTGAATCACAAGA+AGG + chr2.4:9148496-9148515 MS.gene31376:CDS 30.0%
CATTCAAATGACCATAAAAG+AGG - chr2.4:9147895-9147914 None:intergenic 30.0%
CTTATATCAGACAATAAACC+GGG - chr2.4:9148577-9148596 None:intergenic 30.0%
GACTTCAAAAGTAAGCAAAA+TGG - chr2.4:9148097-9148116 None:intergenic 30.0%
TCTTAGAAACTAGAAAGAGA+AGG + chr2.4:9148794-9148813 MS.gene31376:CDS 30.0%
TGAAGACTCACACTTTAATA+GGG + chr2.4:9147855-9147874 MS.gene31376:intron 30.0%
TGTAATAACTTCAGCTAGTA+AGG - chr2.4:9148404-9148423 None:intergenic 30.0%
TTATGTTGTGAATACAAACC+CGG + chr2.4:9148556-9148575 MS.gene31376:CDS 30.0%
! AATGGCTTTACTCACATATA+TGG - chr2.4:9148079-9148098 None:intergenic 30.0%
! ACAGTGAATGGCAAAATTTT+GGG + chr2.4:9148051-9148070 MS.gene31376:intron 30.0%
!! ATGAATGATGGTTGTTTTCA+AGG + chr2.4:9147313-9147332 MS.gene31376:CDS 30.0%
!! GTGTACTTTTTGAACTTAGT+TGG + chr2.4:9148369-9148388 MS.gene31376:intron 30.0%
AAAGCTTCAATACTTCTCTC+GGG - chr2.4:9147442-9147461 None:intergenic 35.0%
AACTAACCTTATTAGCACCT+GGG - chr2.4:9147540-9147559 None:intergenic 35.0%
ATATGGTTCATCTTCTTCAC+TGG + chr2.4:9147351-9147370 MS.gene31376:CDS 35.0%
ATTAAAGTGTGAGTCTTCAC+AGG - chr2.4:9147854-9147873 None:intergenic 35.0%
CAAAGCTTCAATACTTCTCT+CGG - chr2.4:9147443-9147462 None:intergenic 35.0%
GCTTCAAGTAGAATGAATGA+TGG + chr2.4:9147301-9147320 MS.gene31376:CDS 35.0%
GTGAAGACTCACACTTTAAT+AGG + chr2.4:9147854-9147873 MS.gene31376:intron 35.0%
TAGAAACTAGAAAGAGAAGG+AGG + chr2.4:9148797-9148816 MS.gene31376:CDS 35.0%
TTTCAAGGTGTAAATGGAAG+TGG + chr2.4:9147328-9147347 MS.gene31376:CDS 35.0%
! CTTATCTCATCACTGTCTTT+TGG - chr2.4:9148481-9148500 None:intergenic 35.0%
! GACAGTGAATGGCAAAATTT+TGG + chr2.4:9148050-9148069 MS.gene31376:intron 35.0%
!! GGTTGTTTTCAAGGTGTAAA+TGG + chr2.4:9147322-9147341 MS.gene31376:CDS 35.0%
!! TCACAAGAAGGTGGATTAAA+TGG + chr2.4:9148508-9148527 MS.gene31376:CDS 35.0%
!!! CTGGTTTTGGATAGAGAAAA+AGG + chr2.4:9147370-9147389 MS.gene31376:CDS 35.0%
!!! GTCTAGTTTTTGTACTTCGT+AGG - chr2.4:9147763-9147782 None:intergenic 35.0%
!!! TTCATCTTCTTCACTGGTTT+TGG + chr2.4:9147357-9147376 MS.gene31376:CDS 35.0%
AGAATCATAGTGAAGCAGAG+AGG + chr2.4:9147464-9147483 MS.gene31376:CDS 40.0%
AGAGTTGAATCACAAGAAGG+TGG + chr2.4:9148499-9148518 MS.gene31376:CDS 40.0%
AGCAAGAAACTGTCGATACT+CGG - chr2.4:9148716-9148735 None:intergenic 40.0%
CAAGAGCTCAATGAGTTTGA+TGG + chr2.4:9148219-9148238 MS.gene31376:intron 40.0%
GAACTAACCTTATTAGCACC+TGG - chr2.4:9147541-9147560 None:intergenic 40.0%
GGTGTAAATGGAAGTGGATA+TGG + chr2.4:9147334-9147353 MS.gene31376:CDS 40.0%
TAGAGAAAAAGGAGAGCTTG+TGG + chr2.4:9147381-9147400 MS.gene31376:CDS 40.0%
TGTTATCCCAGGTGCTAATA+AGG + chr2.4:9147531-9147550 MS.gene31376:CDS 40.0%
! ATAAGGACGACCCTCTTTTA+TGG + chr2.4:9147881-9147900 MS.gene31376:intron 40.0%
AAGGGCAGAGATTGCAACTT+TGG + chr2.4:9148630-9148649 MS.gene31376:CDS 45.0%
AATGCAGCACAAGCAAGTGA+AGG + chr2.4:9148445-9148464 MS.gene31376:CDS 45.0%
ACACTTCGTAGTGTTATCCC+AGG + chr2.4:9147520-9147539 MS.gene31376:CDS 45.0%
AGAAAAAGGAGAGCTTGTGG+AGG + chr2.4:9147384-9147403 MS.gene31376:CDS 45.0%
AGGGCAGAGATTGCAACTTT+GGG + chr2.4:9148631-9148650 MS.gene31376:CDS 45.0%
ATGCAGCACAAGCAAGTGAA+GGG + chr2.4:9148446-9148465 MS.gene31376:CDS 45.0%
GCTGTGAAATTGGAACGCAA+AGG + chr2.4:9147409-9147428 MS.gene31376:CDS 45.0%
TCGACAGTTTCTTGCTGGAT+CGG + chr2.4:9148720-9148739 MS.gene31376:CDS 45.0%
!! GAGTATCGACAGTTTCTTGC+TGG + chr2.4:9148715-9148734 MS.gene31376:CDS 45.0%
GCAGAGATTGCAACTTTGGG+AGG + chr2.4:9148634-9148653 MS.gene31376:CDS 50.0%
TGTGGAGGCAGCTGTGAAAT+TGG + chr2.4:9147399-9147418 MS.gene31376:CDS 50.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 9147283 9148861 9147283 ID=MS.gene31376
chr2.4 mRNA 9147283 9148861 9147283 ID=MS.gene31376.t1;Parent=MS.gene31376
chr2.4 exon 9147283 9147552 9147283 ID=MS.gene31376.t1.exon1;Parent=MS.gene31376.t1
chr2.4 CDS 9147283 9147552 9147283 ID=cds.MS.gene31376.t1;Parent=MS.gene31376.t1
chr2.4 exon 9148388 9148861 9148388 ID=MS.gene31376.t1.exon2;Parent=MS.gene31376.t1
chr2.4 CDS 9148388 9148861 9148388 ID=cds.MS.gene31376.t1;Parent=MS.gene31376.t1
Gene Sequence

>MS.gene31376

ATGGAAATGGATGATTTTGCTTCAAGTAGAATGAATGATGGTTGTTTTCAAGGTGTAAATGGAAGTGGATATGGTTCATCTTCTTCACTGGTTTTGGATAGAGAAAAAGGAGAGCTTGTGGAGGCAGCTGTGAAATTGGAACGCAAAGGTGTGTCGCCCGAGAGAAGTATTGAAGCTTTGAAGAATCATAGTGAAGCAGAGAGGAGAAGAAGAGCAAGAATTAATTCACATCTTGATACACTTCGTAGTGTTATCCCAGGTGCTAATAAGGTTAGTTCAATTTTATTTATTTATTTATTTTTACTTTTTTTGTTGTTTATTTTGAATTACTAGTTAGTACTGGTTTTGCTCATGTTGAGAACAATTTCTGTCATGATTAACTCCAAATATTTGAAGGGAAAGAATTATTTTTTATGTTTAATTAATGTAAAATTTACATGTAATTTGTATTGAATAACTTATGATTATTATTATTGACCTACGAAGTACAAAAACTAGACATCAGTAATAATTTGAAGAAAAAAAATAGTACAAGTAATTGTATATAAATAAAAGTGTTAGTATCGTGCCTGTGAAGACTCACACTTTAATAGGGAATATAAGGACGACCCTCTTTTATGGTCATTTGAATGAAATAATAGCTTTTACTATATATGAATGTGCATTTACACTGAAGTTTTAAGTTTTAACTATAAGTCTTGAGCTATGAATGCATTTCAAAATGTAGTGAGTATTTTTGGATGTTGAAACAATTGAAGTTAAATTGAGACAGTGAATGGCAAAATTTTGGGATCCATATATGTGAGTAAAGCCATTTTGCTTACTTTTGAAGTCTTGATTCTTCTTTTTTGTATAATGTAGCTTTTAGTTTTCAATGGACCAAGTTCAATTTTCTTTCCTAAAAGAAGGGAATAAAATAATTTAATTTTGGAGTAGCAAGAGCTCAATGAGTTTGATGGTATTAAAAAAAGATGTTAATATTAACTGTCCAACATAGTTATGCTTATACTTGGAATCATGAAATTCATGTCTACACAAACATACAAACATGATATATATGTTAATCTTTCAGAATCTAACGTTTTTGTGTACTTTTTGAACTTAGTTGGACAAAGCATCCTTACTAGCTGAAGTTATTACACATTTGAAAGAGCTGAAAACAAATGCAGCACAAGCAAGTGAAGGGTTCATTATTCCAAAAGACAGTGATGAGATAAGAGTTGAATCACAAGAAGGTGGATTAAATGGTTACCCTTATTCAATTAGAGCATCATTATGTTGTGAATACAAACCCGGTTTATTGTCTGATATAAGAAAAGCACTTGATGCACTTCATCTTATGATAATAAGGGCAGAGATTGCAACTTTGGGAGGTAGAATGAAGAATGTCTTTGTCATAATTAGCTGCAAAGAACAGAATTTTGAAGATGCCGAGTATCGACAGTTTCTTGCTGGATCGGTTCATCAAGCTCTTAGATCTGTACTTGATAGATTTTCTGTTTCACAAGATATCTTAGAAACTAGAAAGAGAAGGAGGATTTCTATATTCAGTTCTTCATCTTTAGGTGATTTCTTATAA
Protein sequence

>MS.gene31376.t1

MEMDDFASSRMNDGCFQGVNGSGYGSSSSLVLDREKGELVEAAVKLERKGVSPERSIEALKNHSEAERRRRARINSHLDTLRSVIPGANKLDKASLLAEVITHLKELKTNAAQASEGFIIPKDSDEIRVESQEGGLNGYPYSIRASLCCEYKPGLLSDIRKALDALHLMIIRAEIATLGGRMKNVFVIISCKEQNFEDAEYRQFLAGSVHQALRSVLDRFSVSQDILETRKRRRISIFSSSSLGDFL