AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene057606


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene057606.t1 MTR_5g037950 99.213 127 1 0 1 127 1 127 9.54e-91 258
MS.gene057606.t1 MTR_5g037930 72.441 127 34 1 1 126 1 127 1.45e-54 167
MS.gene057606.t1 MTR_5g037890 66.667 126 41 1 1 126 1 125 6.50e-53 162
MS.gene057606.t1 MTR_7g009070 60.577 104 41 0 23 126 30 133 7.25e-45 142
MS.gene057606.t1 MTR_3g112410 49.550 111 56 0 15 125 2 112 4.79e-38 125
MS.gene057606.t1 MTR_1g023140 43.750 112 63 0 15 126 2 113 1.37e-34 116
MS.gene057606.t1 MTR_5g021180 44.144 111 62 0 15 125 4 114 6.89e-34 114
MS.gene057606.t1 MTR_8g107460 43.137 102 58 0 21 122 256 357 2.50e-27 103
MS.gene057606.t1 MTR_4g081380 44.340 106 57 2 19 123 10 114 7.97e-26 94.4
MS.gene057606.t1 MTR_2g010750 40.952 105 62 0 19 123 9 113 2.39e-25 93.2
MS.gene057606.t1 MTR_2g082590 39.604 101 59 1 23 123 29 127 2.24e-23 88.6
MS.gene057606.t1 MTR_2g082590 35.238 105 68 0 19 123 10 114 3.36e-23 87.4
MS.gene057606.t1 MTR_8g005320 38.710 93 57 0 30 122 37 129 4.66e-23 87.8
MS.gene057606.t1 MTR_7g073680 39.560 91 55 0 30 120 35 125 4.82e-23 87.8
MS.gene057606.t1 MTR_8g006685 38.710 93 57 0 30 122 106 198 1.95e-22 87.8
MS.gene057606.t1 MTR_8g006560 38.710 93 57 0 30 122 106 198 1.95e-22 87.8
MS.gene057606.t1 MTR_1g098660 38.372 86 50 2 40 124 77 160 2.58e-19 79.0
MS.gene057606.t1 MTR_4g094690 39.024 82 48 1 45 124 85 166 9.95e-19 77.4
MS.gene057606.t1 MTR_7g080250 41.379 87 50 1 41 126 94 180 5.42e-16 70.5
MS.gene057606.t1 MTR_3g089065 37.349 83 50 2 44 124 89 171 4.50e-15 68.2
MS.gene057606.t1 MTR_2g079420 38.554 83 49 2 44 124 89 171 4.01e-14 65.5
MS.gene057606.t1 MTR_8g059015 36.145 83 51 2 44 124 92 174 2.04e-13 63.5
MS.gene057606.t1 MTR_1g114290 34.615 78 47 2 40 116 85 159 7.07e-13 62.4
MS.gene057606.t1 MTR_4g088905 32.500 80 54 0 45 124 25 104 1.22e-11 60.8
MS.gene057606.t1 MTR_4g081380 36.905 84 51 2 13 95 4 86 1.38e-11 57.0
MS.gene057606.t1 MTR_4g085880 31.579 76 51 1 44 118 84 159 6.77e-11 57.0
MS.gene057606.t1 MTR_2g079340 36.620 71 44 1 43 112 54 124 8.72e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene057606.t1 AT5G39950 52.252 111 53 0 16 126 22 132 1.79e-44 142
MS.gene057606.t1 AT1G59730 43.077 130 70 2 1 127 1 129 1.16e-37 124
MS.gene057606.t1 AT3G51030 44.144 111 62 0 15 125 2 112 6.05e-34 114
MS.gene057606.t1 AT5G42980 48.113 106 55 0 21 126 7 112 3.14e-33 112
MS.gene057606.t1 AT1G69880 48.077 104 54 0 21 124 39 142 2.72e-32 111
MS.gene057606.t1 AT1G19730 45.536 112 60 1 15 125 2 113 4.15e-31 107
MS.gene057606.t1 AT1G45145 41.905 105 61 0 21 125 7 111 2.03e-30 105
MS.gene057606.t1 AT3G17880 39.474 114 65 1 13 122 253 366 1.54e-25 99.0
MS.gene057606.t1 AT3G17880 39.474 114 65 1 13 122 260 373 1.61e-25 99.4
MS.gene057606.t1 AT1G11530 39.806 103 62 0 21 123 4 106 7.44e-24 89.4
MS.gene057606.t1 AT3G08710 41.758 91 53 0 30 120 34 124 2.45e-23 88.6
MS.gene057606.t1 AT3G08710 41.758 91 53 0 30 120 34 124 2.45e-23 88.6
MS.gene057606.t1 AT3G08710 41.758 91 53 0 30 120 34 124 2.45e-23 88.6
MS.gene057606.t1 AT3G56420 38.043 92 57 0 29 120 50 141 4.44e-23 88.2
MS.gene057606.t1 AT3G56420 38.043 92 57 0 29 120 50 141 4.44e-23 88.2
MS.gene057606.t1 AT3G56420 38.043 92 57 0 29 120 50 141 4.44e-23 88.2
MS.gene057606.t1 AT2G40790 39.130 92 56 0 29 120 50 141 1.72e-19 79.0
MS.gene057606.t1 AT2G40790 39.130 92 56 0 29 120 50 141 1.72e-19 79.0
MS.gene057606.t1 AT1G43560 41.379 87 49 2 40 124 75 161 4.76e-19 78.2
MS.gene057606.t1 AT1G76760 38.372 86 51 2 40 123 80 165 2.28e-18 76.6
MS.gene057606.t1 AT5G16400 42.529 87 49 1 41 126 97 183 1.71e-17 74.7
MS.gene057606.t1 AT2G35010 40.244 82 47 1 45 124 110 191 6.68e-17 73.2
MS.gene057606.t1 AT2G35010 40.244 82 47 1 45 124 110 191 6.68e-17 73.2
MS.gene057606.t1 AT3G02730 43.023 86 48 1 42 126 88 173 8.91e-17 72.4
MS.gene057606.t1 AT3G15360 32.673 101 63 3 26 124 92 189 6.05e-15 68.2
MS.gene057606.t1 AT1G31020 39.024 82 48 1 45 124 75 156 7.98e-15 67.0
MS.gene057606.t1 AT1G03680 38.272 81 48 2 46 124 97 177 1.43e-14 67.0
MS.gene057606.t1 AT4G03520 33.735 83 53 2 44 124 101 183 1.13e-13 64.7
MS.gene057606.t1 AT1G52990 34.066 91 58 2 35 124 222 311 1.73e-13 65.9
MS.gene057606.t1 AT1G50320 39.189 74 41 2 44 116 90 160 3.80e-13 63.2
MS.gene057606.t1 AT4G04950 29.787 94 66 0 31 124 11 104 9.42e-12 61.2
MS.gene057606.t1 AT4G32580 30.864 81 56 0 44 124 24 104 9.86e-12 58.9
MS.gene057606.t1 AT1G07700 36.364 99 55 2 34 124 100 198 1.72e-11 59.3
MS.gene057606.t1 AT1G07700 36.364 99 55 2 34 124 100 198 1.72e-11 59.3
MS.gene057606.t1 AT1G07700 36.364 99 55 2 34 124 100 198 1.72e-11 59.3
MS.gene057606.t1 AT1G07700 36.364 99 55 2 34 124 113 211 3.61e-11 58.5

Find 25 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAGCTAATTCTTTGATAAT+TGG 0.122091 5.4:+27240188 None:intergenic
GGAGGTGGCAAGTGCATTTC+AGG 0.225705 5.4:-27240019 MS.gene057606:CDS
CTCAACAACAGACTCTAAAT+TGG 0.230357 5.4:+27240895 None:intergenic
GATTGACGTGGATGAGTTAA+TGG 0.268688 5.4:-27240138 MS.gene057606:intron
CCTTCCACTCAACTGCTAAA+TGG 0.287365 5.4:-27240844 MS.gene057606:CDS
CAGCTAATTCTTTGATAATT+GGG 0.312442 5.4:+27240189 None:intergenic
TACCAGCTTGTTTGTTACTT+TGG 0.383274 5.4:+27240802 None:intergenic
AGACTCTAAATTGGAAAAGT+TGG 0.412160 5.4:+27240904 None:intergenic
AAAGATGGTCATTGATTTCA+CGG 0.422756 5.4:-27240243 MS.gene057606:intron
TAAATGGAAGGCTCACTTTG+AGG 0.488391 5.4:-27240828 MS.gene057606:CDS
TCATTGATTTCACGGCTACT+TGG 0.488401 5.4:-27240235 MS.gene057606:CDS
CCATTTAGCAGTTGAGTGGA+AGG 0.494217 5.4:+27240844 None:intergenic
TTCTTCAATAGTATAAATGT+TGG 0.495545 5.4:+27239985 None:intergenic
GATTTCACGGCTACTTGGTG+TGG 0.515795 5.4:-27240230 MS.gene057606:CDS
ACATTTATACTATTGAAGAA+AGG 0.532669 5.4:-27239982 MS.gene057606:CDS
GTGTGGACCTTGCAAATACA+TGG 0.544731 5.4:-27240213 MS.gene057606:CDS
TTCCAAAGTAACAAACAAGC+TGG 0.568571 5.4:-27240804 MS.gene057606:intron
GAAACTGATTGAGAAACGTA+GGG 0.577131 5.4:-27239914 MS.gene057606:CDS
CCTTCCATTTAGCAGTTGAG+TGG 0.582577 5.4:+27240840 None:intergenic
AGAAACTGATTGAGAAACGT+AGG 0.583938 5.4:-27239915 MS.gene057606:CDS
ATTGGGTCCATGTATTTGCA+AGG 0.586486 5.4:+27240206 None:intergenic
CCACTCAACTGCTAAATGGA+AGG 0.588835 5.4:-27240840 MS.gene057606:CDS
TAGCAGTTGAGTGGAAGGTG+AGG 0.659322 5.4:+27240849 None:intergenic
TGAGTTCATTAAGATTGACG+TGG 0.684888 5.4:-27240150 MS.gene057606:CDS
TGGAAGGTGAGGATGAGCGA+TGG 0.701264 5.4:+27240860 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTCTTAATTATTTTTAAAGA+TGG - chr5.4:27240562-27240581 MS.gene057606:intron 10.0%
!! TAATCAAATATATGTCATAT+AGG + chr5.4:27240425-27240444 None:intergenic 15.0%
!! TATAGATATAAGATATCAAA+AGG + chr5.4:27240739-27240758 None:intergenic 15.0%
!!! AGTTTTCATTTTTTTTTTGT+TGG + chr5.4:27240248-27240267 None:intergenic 15.0%
!!! GCTAAAATTTTCTTATTATT+TGG - chr5.4:27240502-27240521 MS.gene057606:intron 15.0%
!!! GTTAAATAATTTTTCTTAGA+GGG - chr5.4:27240166-27240185 MS.gene057606:CDS 15.0%
!!! TGTTAAATAATTTTTCTTAG+AGG - chr5.4:27240165-27240184 MS.gene057606:CDS 15.0%
!!! TTGTTGGTAAATTAATTATA+TGG + chr5.4:27240232-27240251 None:intergenic 15.0%
!! ACATTTATACTATTGAAGAA+AGG - chr5.4:27240838-27240857 MS.gene057606:CDS 20.0%
!! GATATCAAAAGGTAATTAAA+AGG + chr5.4:27240728-27240747 None:intergenic 20.0%
!! TTCTTCAATAGTATAAATGT+TGG + chr5.4:27240838-27240857 None:intergenic 20.0%
!!! TAATAAGAAAATTTTAGCCA+AGG + chr5.4:27240500-27240519 None:intergenic 20.0%
!!! TTAAAATCGTTTGTTTTATG+AGG - chr5.4:27240526-27240545 MS.gene057606:intron 20.0%
!!! TTTTTAGATACTTTGAAGTT+TGG + chr5.4:27240205-27240224 None:intergenic 20.0%
! AAAACCAAGGTTTCAAAAAA+CGG - chr5.4:27240329-27240348 MS.gene057606:intron 25.0%
! ATGACAACAATAACAATCAT+GGG + chr5.4:27240355-27240374 None:intergenic 25.0%
!! AAATTTTGTGACGAGAAAAA+CGG + chr5.4:27240275-27240294 None:intergenic 25.0%
!! CAGCTAATTCTTTGATAATT+GGG + chr5.4:27240634-27240653 None:intergenic 25.0%
!!! TTTTTCATCGGTTAAAATCT+TGG + chr5.4:27240312-27240331 None:intergenic 25.0%
AAAAGTAGTTGAAAAAGTGG+TGG - chr5.4:27240861-27240880 MS.gene057606:CDS 30.0%
AAAGTAGTTGAAAAAGTGGT+GGG - chr5.4:27240862-27240881 MS.gene057606:CDS 30.0%
AGACTCTAAATTGGAAAAGT+TGG + chr5.4:27239919-27239938 None:intergenic 30.0%
AGGAAAAGTAGTTGAAAAAG+TGG - chr5.4:27240858-27240877 MS.gene057606:CDS 30.0%
CATGACAACAATAACAATCA+TGG + chr5.4:27240356-27240375 None:intergenic 30.0%
GATAATGCAAAATGTACCAA+TGG - chr5.4:27240773-27240792 MS.gene057606:intron 30.0%
TAACATTGAATGATTCGATG+AGG + chr5.4:27240108-27240127 None:intergenic 30.0%
TTTAACCGATGAAAAAACCA+AGG - chr5.4:27240316-27240335 MS.gene057606:intron 30.0%
! CTTAACATTTTCTTTGCACT+CGG - chr5.4:27240387-27240406 MS.gene057606:intron 30.0%
! GCAGCTAATTCTTTGATAAT+TGG + chr5.4:27240635-27240654 None:intergenic 30.0%
!! AAAGATGGTCATTGATTTCA+CGG - chr5.4:27240577-27240596 MS.gene057606:intron 30.0%
!!! TGAAACCTTGGTTTTTTCAT+CGG + chr5.4:27240324-27240343 None:intergenic 30.0%
!!! TTAGCCAAGGTTTTAAATCA+CGG + chr5.4:27240487-27240506 None:intergenic 30.0%
AGAAACTGATTGAGAAACGT+AGG - chr5.4:27240905-27240924 MS.gene057606:CDS 35.0%
CAAAATGTACCAATGGAAAC+AGG - chr5.4:27240780-27240799 MS.gene057606:intron 35.0%
CTCAACAACAGACTCTAAAT+TGG + chr5.4:27239928-27239947 None:intergenic 35.0%
GAAACTGATTGAGAAACGTA+GGG - chr5.4:27240906-27240925 MS.gene057606:CDS 35.0%
TGAGTTCATTAAGATTGACG+TGG - chr5.4:27240670-27240689 MS.gene057606:intron 35.0%
TTCCAAAGTAACAAACAAGC+TGG - chr5.4:27240016-27240035 MS.gene057606:CDS 35.0%
! TACCAGCTTGTTTGTTACTT+TGG + chr5.4:27240021-27240040 None:intergenic 35.0%
AATGTACCAATGGAAACAGG+AGG - chr5.4:27240783-27240802 MS.gene057606:intron 40.0%
ATTGGGTCCATGTATTTGCA+AGG + chr5.4:27240617-27240636 None:intergenic 40.0%
GATTGACGTGGATGAGTTAA+TGG - chr5.4:27240682-27240701 MS.gene057606:intron 40.0%
TAAATGGAAGGCTCACTTTG+AGG - chr5.4:27239992-27240011 MS.gene057606:CDS 40.0%
! AAAAGTGGTGGGAGCAAAAA+AGG - chr5.4:27240873-27240892 MS.gene057606:CDS 40.0%
! ACGACCGTGATTTAAAACCT+TGG - chr5.4:27240480-27240499 MS.gene057606:intron 40.0%
!! TCATTGATTTCACGGCTACT+TGG - chr5.4:27240585-27240604 MS.gene057606:intron 40.0%
!!! AAGGTTTTAAATCACGGTCG+TGG + chr5.4:27240481-27240500 None:intergenic 40.0%
ACAACGATGCTCACGTAGTT+TGG - chr5.4:27240069-27240088 MS.gene057606:intron 45.0%
CCACTCAACTGCTAAATGGA+AGG - chr5.4:27239980-27239999 MS.gene057606:CDS 45.0%
CCATTTAGCAGTTGAGTGGA+AGG + chr5.4:27239979-27239998 None:intergenic 45.0%
CCTTCCACTCAACTGCTAAA+TGG - chr5.4:27239976-27239995 MS.gene057606:CDS 45.0%
CCTTCCATTTAGCAGTTGAG+TGG + chr5.4:27239983-27240002 None:intergenic 45.0%
GTGTGGACCTTGCAAATACA+TGG - chr5.4:27240607-27240626 MS.gene057606:intron 45.0%
!!! TGGGCCGTTTTTTGAAACCT+TGG + chr5.4:27240336-27240355 None:intergenic 45.0%
GTACCAATGGAAACAGGAGG+TGG - chr5.4:27240786-27240805 MS.gene057606:intron 50.0%
TAGCAGTTGAGTGGAAGGTG+AGG + chr5.4:27239974-27239993 None:intergenic 50.0%
TTGCCACCTCCTGTTTCCAT+TGG + chr5.4:27240792-27240811 None:intergenic 50.0%
! GATTTCACGGCTACTTGGTG+TGG - chr5.4:27240590-27240609 MS.gene057606:intron 50.0%
GGAGGTGGCAAGTGCATTTC+AGG - chr5.4:27240801-27240820 MS.gene057606:intron 55.0%
TGGAAGGTGAGGATGAGCGA+TGG + chr5.4:27239963-27239982 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 27239909 27240933 27239909 ID=MS.gene057606
chr5.4 mRNA 27239909 27240933 27239909 ID=MS.gene057606.t1;Parent=MS.gene057606
chr5.4 exon 27240805 27240933 27240805 ID=MS.gene057606.t1.exon1;Parent=MS.gene057606.t1
chr5.4 CDS 27240805 27240933 27240805 ID=cds.MS.gene057606.t1;Parent=MS.gene057606.t1
chr5.4 exon 27240139 27240261 27240139 ID=MS.gene057606.t1.exon2;Parent=MS.gene057606.t1
chr5.4 CDS 27240139 27240261 27240139 ID=cds.MS.gene057606.t1;Parent=MS.gene057606.t1
chr5.4 exon 27239909 27240040 27239909 ID=MS.gene057606.t1.exon3;Parent=MS.gene057606.t1
chr5.4 CDS 27239909 27240040 27239909 ID=cds.MS.gene057606.t1;Parent=MS.gene057606.t1
Gene Sequence

>MS.gene057606

ATGGGAGCCAACTTTTCCAATTTAGAGTCTGTTGTTGAGAAATCATCACAGCCATCGCTCATCCTCACCTTCCACTCAACTGCTAAATGGAAGGCTCACTTTGAGGCTTCCAAAGTAACAAACAAGCTGGTATAAACTTCTGATATATAATTAGATCAACACAACGATGCTCACGTAGTTTGGTTGAATATATACTCCTCATCGAATCATTCAATGTTATCTTATATTTTCATATTAATTTATTTTAAACTTAAAATGTTAAATAATTTTTCTTAGAGGGTATCAGTATTCAACCAAACTTCAAAGTATCTAAAAATTTACCATATAATTAATTTACCAACAAAAAAAAAATGAAAACTTTCTCCGTTTTTCTCGTCACAAAATTTAGTGACATGCACAACCAAGATTTTAACCGATGAAAAAACCAAGGTTTCAAAAAACGGCCCATGATTGTTATTGTTGTCATGAAGTCAAGTTTCTTAACATTTTCTTTGCACTCGGTTTGTCATTGCGCCTATATGACATATATTTGATTACAATTTGTTGCAATATCAAAATTCACGATACAACCACGACCGTGATTTAAAACCTTGGCTAAAATTTTCTTATTATTTGGCTTAAAATCGTTTGTTTTATGAGGTGATTAATTTTGTTTCTTAATTATTTTTAAAGATGGTCATTGATTTCACGGCTACTTGGTGTGGACCTTGCAAATACATGGACCCAATTATCAAAGAATTAGCTGCAAAATACAAAGATGTTGAGTTCATTAAGATTGACGTGGATGAGTTAATGGTATGATACATATGATTAATTCCTTTTAATTACCTTTTGATATCTTATATCTATATATATAAACAATATGATAATGCAAAATGTACCAATGGAAACAGGAGGTGGCAAGTGCATTTCAGGTGCAAGCAATGCCAACATTTATACTATTGAAGAAAGGAAAAGTAGTTGAAAAAGTGGTGGGAGCAAAAAAGGAGCAATTACAGAAACTGATTGAGAAACGTAGGGTTTGA

Protein sequence

>MS.gene057606.t1

MGANFSNLESVVEKSSQPSLILTFHSTAKWKAHFEASKVTNKLMVIDFTATWCGPCKYMDPIIKELAAKYKDVEFIKIDVDELMEVASAFQVQAMPTFILLKKGKVVEKVVGAKKEQLQKLIEKRRV