AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene57249


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene57249.t1 MTR_1g016170 95.133 226 10 1 1 225 80 305 2.39e-135 382
MS.gene57249.t1 MTR_3g050550 79.787 94 18 1 18 110 1 94 1.09e-44 145
MS.gene57249.t1 MTR_3g050610 75.833 120 23 3 4 120 31 147 4.59e-42 140
MS.gene57249.t1 MTR_2g038720 45.985 137 46 5 105 223 162 288 2.44e-16 76.6
MS.gene57249.t1 MTR_4g121110 62.500 48 18 0 104 151 27 74 4.60e-16 72.8
MS.gene57249.t1 MTR_4g126350 40.741 108 44 3 29 136 128 215 1.21e-15 74.7
MS.gene57249.t1 MTR_7g112330 69.444 36 11 0 107 142 22 57 3.41e-13 64.7
MS.gene57249.t1 MTR_5g020230 50.000 66 27 1 84 143 93 158 1.68e-12 65.1
MS.gene57249.t1 MTR_1g094930 56.098 41 18 0 102 142 142 182 2.73e-11 61.6
MS.gene57249.t1 MTR_1g094930 56.098 41 18 0 102 142 237 277 4.29e-11 62.0
MS.gene57249.t1 MTR_8g077510 63.158 38 14 0 106 143 124 161 5.56e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene57249.t1 AT5G56860 41.538 130 50 6 29 140 142 263 8.68e-19 84.3
MS.gene57249.t1 AT5G49300 66.667 45 15 0 103 147 32 76 2.14e-17 76.3
MS.gene57249.t1 AT5G26930 66.667 42 14 0 103 144 22 63 3.74e-16 72.4
MS.gene57249.t1 AT4G26150 40.179 112 37 3 29 138 147 230 7.21e-16 75.9
MS.gene57249.t1 AT3G06740 66.667 42 14 0 104 145 38 79 9.62e-15 69.3
MS.gene57249.t1 AT4G16141 68.293 41 13 0 104 144 34 74 1.56e-14 70.1
MS.gene57249.t1 AT3G16870 57.143 56 20 1 104 159 39 90 2.97e-14 68.9
MS.gene57249.t1 AT4G36620 58.333 48 20 0 103 150 71 118 1.43e-12 64.7
MS.gene57249.t1 AT2G18380 68.293 41 12 1 107 146 92 132 3.28e-12 63.9
MS.gene57249.t1 AT5G25830 55.556 45 20 0 98 142 210 254 1.53e-11 63.2
MS.gene57249.t1 AT3G50870 33.058 121 68 4 106 223 151 261 2.16e-11 62.4
MS.gene57249.t1 AT1G08010 56.000 50 21 1 93 142 207 255 3.63e-11 62.0
MS.gene57249.t1 AT1G08010 56.000 50 21 1 93 142 207 255 3.63e-11 62.0
MS.gene57249.t1 AT1G08010 56.000 50 21 1 93 142 207 255 3.63e-11 62.0

Find 52 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTTGTTTGGTCTCATTAT+TGG 0.223553 1.4:-6191684 None:intergenic
TGTTACTACTAGGGCTTGTT+TGG 0.323214 1.4:-6191806 None:intergenic
ATGATGAGACCTAGTAATTA+TGG 0.329839 1.4:+6191750 MS.gene57249:CDS
TTGTTACCGCTGTTACTACT+AGG 0.336848 1.4:-6191816 None:intergenic
GTCCAAGAAGTCAAAATATA+AGG 0.340331 1.4:+6191778 MS.gene57249:CDS
TTTGCAATGCTTGTGGAATC+AGG 0.357272 1.4:+6192494 MS.gene57249:CDS
TCATCATAATCATAATCTAA+TGG 0.373491 1.4:-6192706 None:intergenic
CACTCCTCCAAAGTGGGGTA+TGG 0.383367 1.4:-6191872 None:intergenic
CACAAATTTATCATCATCCT+TGG 0.395360 1.4:+6191554 MS.gene57249:CDS
AGCAACGGCGGCACGACTTC+TGG 0.401059 1.4:+6192732 MS.gene57249:CDS
GTGGCTGCAATATTGTTGTT+TGG 0.421269 1.4:-6191696 None:intergenic
GGCTGAAGCTGCCAATGGTT+TGG 0.422143 1.4:+6192540 MS.gene57249:CDS
CTTTGGAGGAGTGGCCCTAT+GGG 0.439971 1.4:+6191882 MS.gene57249:CDS
ACTTTGGAGGAGTGGCCCTA+TGG 0.441269 1.4:+6191881 MS.gene57249:CDS
CGAATTACCTTTGGACCCAT+AGG 0.444966 1.4:-6191897 None:intergenic
TGAGTCACGGGTCTGAGAAA+TGG 0.451328 1.4:+6191601 MS.gene57249:CDS
CTTCTGGTGGATATATCTTC+TGG 0.451597 1.4:+6192748 MS.gene57249:CDS
ACAGCGGTAACAACACCGTT+AGG 0.456940 1.4:+6191826 MS.gene57249:CDS
TTTATCATCATCCTTGGAGC+TGG 0.479939 1.4:+6191560 MS.gene57249:CDS
CTTGATAGCTTTGTCAGTAG+TGG 0.482210 1.4:-6191715 None:intergenic
ACTCCTCCAAAGTGGGGTAT+GGG 0.495268 1.4:-6191871 None:intergenic
TTCTTAGTCTTGAATTGTGT+AGG 0.495944 1.4:-6192601 None:intergenic
TAATTACTAGGTCTCATCAT+TGG 0.503467 1.4:-6191747 None:intergenic
GCTGCTATCTTCCAGCTCCA+AGG 0.513483 1.4:-6191571 None:intergenic
TGGTCTCATTATTGGAGTTG+TGG 0.515285 1.4:-6191676 None:intergenic
TCAGGCAGAGAAAGGCAAGA+AGG 0.520139 1.4:+6192512 MS.gene57249:CDS
ACAACTTCAACTACTTCTGC+TGG 0.524955 1.4:+6192646 MS.gene57249:CDS
CAGGCAGAGAAAGGCAAGAA+GGG 0.526577 1.4:+6192513 MS.gene57249:CDS
GAATTACCTTTGGACCCATA+GGG 0.528192 1.4:-6191896 None:intergenic
AGGGGATGTAGCCAAACCAT+TGG 0.539225 1.4:-6192551 None:intergenic
CAGTCACTTTGCAATGCTTG+TGG 0.543553 1.4:+6192487 MS.gene57249:intron
CAGCGGTAACAACACCGTTA+GGG 0.546032 1.4:+6191827 MS.gene57249:CDS
ACCATTGGCAGCTTCAGCCA+TGG 0.551217 1.4:-6192536 None:intergenic
TTGTGGAATCAGGCAGAGAA+AGG 0.551715 1.4:+6192504 MS.gene57249:CDS
GTACATCCCATACCCCACTT+TGG 0.556830 1.4:+6191865 MS.gene57249:CDS
TGTTACCGCTGTTACTACTA+GGG 0.563428 1.4:-6191815 None:intergenic
TAGGGCCACTCCTCCAAAGT+GGG 0.565226 1.4:-6191878 None:intergenic
GGACTAGTACCATAATTACT+AGG 0.573336 1.4:-6191759 None:intergenic
AGAAGTAGTTGAAGTTGTAG+AGG 0.579757 1.4:-6192641 None:intergenic
GAGAAAGGCAAGAAGGGCCA+TGG 0.585866 1.4:+6192519 MS.gene57249:CDS
GAGTGGCCCTATGGGTCCAA+AGG 0.590272 1.4:+6191890 MS.gene57249:CDS
CATCCCATACCCCACTTTGG+AGG 0.595750 1.4:+6191868 MS.gene57249:CDS
TGATTATGATGAAGCAGCAA+CGG 0.614524 1.4:+6192717 MS.gene57249:CDS
CATACCCCACTTTGGAGGAG+TGG 0.615240 1.4:+6191873 MS.gene57249:CDS
GCCATGGCTGAAGCTGCCAA+TGG 0.619219 1.4:+6192535 MS.gene57249:CDS
AACGGCGGCACGACTTCTGG+TGG 0.640817 1.4:+6192735 MS.gene57249:CDS
ACAATCAGAACAAACCCTAA+CGG 0.645452 1.4:-6191841 None:intergenic
ATAGGGCCACTCCTCCAAAG+TGG 0.665162 1.4:-6191879 None:intergenic
ACAATTCAAGACTAAGAACA+AGG 0.668290 1.4:+6192606 MS.gene57249:CDS
AGGGCCACTCCTCCAAAGTG+GGG 0.692599 1.4:-6191877 None:intergenic
TTATGATGAAGCAGCAACGG+CGG 0.694941 1.4:+6192720 MS.gene57249:CDS
ACAAGCCCTAGTAGTAACAG+CGG 0.724459 1.4:+6191810 MS.gene57249:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATCAAATTAAGTTTAATTA+TGG - chr1.4:6192415-6192434 None:intergenic 10.0%
!! TAATTAAAAAGATAAAATAG+AGG - chr1.4:6192249-6192268 None:intergenic 10.0%
!! TGATAAAATATTTGTATTAA+AGG - chr1.4:6192152-6192171 None:intergenic 10.0%
!!! AATATCAATATATTTTTTTG+AGG - chr1.4:6192051-6192070 None:intergenic 10.0%
!!! ATATCAATATATTTTTTTGA+GGG - chr1.4:6192050-6192069 None:intergenic 10.0%
!! ATTGATATTTATTGTTCATA+AGG + chr1.4:6192062-6192081 MS.gene57249:intron 15.0%
!! TTGATATTTATTGTTCATAA+GGG + chr1.4:6192063-6192082 MS.gene57249:intron 15.0%
!!! GATATTAATAATTTTTGTGA+TGG - chr1.4:6192024-6192043 None:intergenic 15.0%
!!! TATCAATATATTTTTTTGAG+GGG - chr1.4:6192049-6192068 None:intergenic 15.0%
!!! TGTTTTTGTAAGAATTTTTA+TGG - chr1.4:6192118-6192137 None:intergenic 15.0%
!! ATTTGTATTAAAGGAAGTAA+AGG - chr1.4:6192143-6192162 None:intergenic 20.0%
!! TCATCATAATCATAATCTAA+TGG - chr1.4:6192709-6192728 None:intergenic 20.0%
! TAAAAAGATAAAATAGAGGC+AGG - chr1.4:6192245-6192264 None:intergenic 25.0%
! TAGTTAACATGAAAACATGT+TGG + chr1.4:6192462-6192481 MS.gene57249:intron 25.0%
!! CGATAAACGTTAAATTTTAG+TGG - chr1.4:6191990-6192009 None:intergenic 25.0%
!!! ATCTTAAGCACTTTAGTTTT+AGG - chr1.4:6192574-6192593 None:intergenic 25.0%
!!! TACCTTATATTTTGACTTCT+TGG - chr1.4:6191783-6191802 None:intergenic 25.0%
!!! TCTTAAGCACTTTAGTTTTA+GGG - chr1.4:6192573-6192592 None:intergenic 25.0%
ACAATTCAAGACTAAGAACA+AGG + chr1.4:6192606-6192625 MS.gene57249:CDS 30.0%
ACTATTCGTCCATATTAAAG+TGG + chr1.4:6191941-6191960 MS.gene57249:intron 30.0%
AGAGTTTAACGAATTACCTT+TGG - chr1.4:6191909-6191928 None:intergenic 30.0%
ATATGGACGAATAGTGAATA+AGG - chr1.4:6191936-6191955 None:intergenic 30.0%
ATGATGAGACCTAGTAATTA+TGG + chr1.4:6191750-6191769 MS.gene57249:CDS 30.0%
CACAAATTTATCATCATCCT+TGG + chr1.4:6191554-6191573 MS.gene57249:CDS 30.0%
CTATTCGTCCATATTAAAGT+GGG + chr1.4:6191942-6191961 MS.gene57249:intron 30.0%
GTCCAAGAAGTCAAAATATA+AGG + chr1.4:6191778-6191797 MS.gene57249:CDS 30.0%
TAATTACTAGGTCTCATCAT+TGG - chr1.4:6191750-6191769 None:intergenic 30.0%
TATGGACGAATAGTGAATAA+GGG - chr1.4:6191935-6191954 None:intergenic 30.0%
!! TTCTTAGTCTTGAATTGTGT+AGG - chr1.4:6192604-6192623 None:intergenic 30.0%
!! TTGTTGTTTGGTCTCATTAT+TGG - chr1.4:6191687-6191706 None:intergenic 30.0%
!!! CTTAAGCACTTTAGTTTTAG+GGG - chr1.4:6192572-6192591 None:intergenic 30.0%
ACAATCAGAACAAACCCTAA+CGG - chr1.4:6191844-6191863 None:intergenic 35.0%
AGAAGTAGTTGAAGTTGTAG+AGG - chr1.4:6192644-6192663 None:intergenic 35.0%
TGATTATGATGAAGCAGCAA+CGG + chr1.4:6192717-6192736 MS.gene57249:CDS 35.0%
! GGACTAGTACCATAATTACT+AGG - chr1.4:6191762-6191781 None:intergenic 35.0%
ACAACTTCAACTACTTCTGC+TGG + chr1.4:6192646-6192665 MS.gene57249:CDS 40.0%
AGCAGCAAAAAGATGAGTCA+CGG + chr1.4:6191588-6191607 MS.gene57249:CDS 40.0%
GAATTACCTTTGGACCCATA+GGG - chr1.4:6191899-6191918 None:intergenic 40.0%
TCCATATTAAAGTGGGAGAG+TGG + chr1.4:6191949-6191968 MS.gene57249:intron 40.0%
TGGTCTCATTATTGGAGTTG+TGG - chr1.4:6191679-6191698 None:intergenic 40.0%
TGTTACCGCTGTTACTACTA+GGG - chr1.4:6191818-6191837 None:intergenic 40.0%
TTGTTACCGCTGTTACTACT+AGG - chr1.4:6191819-6191838 None:intergenic 40.0%
TTTATCATCATCCTTGGAGC+TGG + chr1.4:6191560-6191579 MS.gene57249:CDS 40.0%
TTTGCAATGCTTGTGGAATC+AGG + chr1.4:6192494-6192513 MS.gene57249:CDS 40.0%
! CTTCTGGTGGATATATCTTC+TGG + chr1.4:6192748-6192767 MS.gene57249:CDS 40.0%
! GTGGCTGCAATATTGTTGTT+TGG - chr1.4:6191699-6191718 None:intergenic 40.0%
! TGTTACTACTAGGGCTTGTT+TGG - chr1.4:6191809-6191828 None:intergenic 40.0%
!! CTTGATAGCTTTGTCAGTAG+TGG - chr1.4:6191718-6191737 None:intergenic 40.0%
ACAAGCCCTAGTAGTAACAG+CGG + chr1.4:6191810-6191829 MS.gene57249:CDS 45.0%
CGAATTACCTTTGGACCCAT+AGG - chr1.4:6191900-6191919 None:intergenic 45.0%
GCAGCAAAAAGATGAGTCAC+GGG + chr1.4:6191589-6191608 MS.gene57249:CDS 45.0%
GCCACTCTCCCACTTTAATA+TGG - chr1.4:6191953-6191972 None:intergenic 45.0%
TTATGATGAAGCAGCAACGG+CGG + chr1.4:6192720-6192739 MS.gene57249:CDS 45.0%
TTGTGGAATCAGGCAGAGAA+AGG + chr1.4:6192504-6192523 MS.gene57249:CDS 45.0%
! CAGTCACTTTGCAATGCTTG+TGG + chr1.4:6192487-6192506 MS.gene57249:intron 45.0%
!!! TAATTTTTATTATTATATCA+CGG + chr1.4:6192335-6192354 MS.gene57249:intron 5.0%
ACAGCGGTAACAACACCGTT+AGG + chr1.4:6191826-6191845 MS.gene57249:CDS 50.0%
ACTCCTCCAAAGTGGGGTAT+GGG - chr1.4:6191874-6191893 None:intergenic 50.0%
AGGGGATGTAGCCAAACCAT+TGG - chr1.4:6192554-6192573 None:intergenic 50.0%
CAGCGGTAACAACACCGTTA+GGG + chr1.4:6191827-6191846 MS.gene57249:CDS 50.0%
CAGGCAGAGAAAGGCAAGAA+GGG + chr1.4:6192513-6192532 MS.gene57249:CDS 50.0%
GTACATCCCATACCCCACTT+TGG + chr1.4:6191865-6191884 MS.gene57249:CDS 50.0%
TCAGGCAGAGAAAGGCAAGA+AGG + chr1.4:6192512-6192531 MS.gene57249:CDS 50.0%
TGAGTCACGGGTCTGAGAAA+TGG + chr1.4:6191601-6191620 MS.gene57249:CDS 50.0%
ACCATTGGCAGCTTCAGCCA+TGG - chr1.4:6192539-6192558 None:intergenic 55.0%
ATAGGGCCACTCCTCCAAAG+TGG - chr1.4:6191882-6191901 None:intergenic 55.0%
CACTCCTCCAAAGTGGGGTA+TGG - chr1.4:6191875-6191894 None:intergenic 55.0%
CATCCCATACCCCACTTTGG+AGG + chr1.4:6191868-6191887 MS.gene57249:CDS 55.0%
GAGAAAGGCAAGAAGGGCCA+TGG + chr1.4:6192519-6192538 MS.gene57249:CDS 55.0%
GCTGCTATCTTCCAGCTCCA+AGG - chr1.4:6191574-6191593 None:intergenic 55.0%
GGCTGAAGCTGCCAATGGTT+TGG + chr1.4:6192540-6192559 MS.gene57249:CDS 55.0%
TAGGGCCACTCCTCCAAAGT+GGG - chr1.4:6191881-6191900 None:intergenic 55.0%
! ACTTTGGAGGAGTGGCCCTA+TGG + chr1.4:6191881-6191900 MS.gene57249:CDS 55.0%
! CATACCCCACTTTGGAGGAG+TGG + chr1.4:6191873-6191892 MS.gene57249:CDS 55.0%
! CTTTGGAGGAGTGGCCCTAT+GGG + chr1.4:6191882-6191901 MS.gene57249:CDS 55.0%
AGGGCCACTCCTCCAAAGTG+GGG - chr1.4:6191880-6191899 None:intergenic 60.0%
GAGTGGCCCTATGGGTCCAA+AGG + chr1.4:6191890-6191909 MS.gene57249:CDS 60.0%
GCCATGGCTGAAGCTGCCAA+TGG + chr1.4:6192535-6192554 MS.gene57249:CDS 60.0%
AACGGCGGCACGACTTCTGG+TGG + chr1.4:6192735-6192754 MS.gene57249:CDS 65.0%
AGCAACGGCGGCACGACTTC+TGG + chr1.4:6192732-6192751 MS.gene57249:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 6191528 6192783 6191528 ID=MS.gene57249
chr1.4 mRNA 6191528 6192783 6191528 ID=MS.gene57249.t1;Parent=MS.gene57249
chr1.4 exon 6191528 6191911 6191528 ID=MS.gene57249.t1.exon1;Parent=MS.gene57249.t1
chr1.4 CDS 6191528 6191911 6191528 ID=cds.MS.gene57249.t1;Parent=MS.gene57249.t1
chr1.4 exon 6192490 6192783 6192490 ID=MS.gene57249.t1.exon2;Parent=MS.gene57249.t1
chr1.4 CDS 6192490 6192783 6192490 ID=cds.MS.gene57249.t1;Parent=MS.gene57249.t1
Gene Sequence

>MS.gene57249

ATGGTTGATTCAAGCAGTGCACGTGACACAAATTTATCATCATCCTTGGAGCTGGAAGATAGCAGCAAAAAGATGAGTCACGGGTCTGAGAAATGGATGTCTTCAAAGATGAAGTTGATGAATATGATCAACACAACTGCTACTGTTGCCACAACTCCAATAATGAGACCAAACAACAATATTGCAGCCACTACTGACAAAGCTATCAAGACAACAACTCCAATGATGAGACCTAGTAATTATGGTACTAGTCCAAGAAGTCAAAATATAAGGTACAGCCAAACAAGCCCTAGTAGTAACAGCGGTAACAACACCGTTAGGGTTTGTTCTGATTGTAGTACATCCCATACCCCACTTTGGAGGAGTGGCCCTATGGGTCCAAAGGTAATTCGTTAAACTCTTCTCCCTTATTCACTATTCGTCCATATTAAAGTGGGAGAGTGGCATTGTTGTTACGATCCACTAAAATTTAACGTTTATCGTTTCAATTCGTCCATCACAAAAATTATTAATATCATCCCCTCAAAAAAATATATTGATATTTATTGTTCATAAGGGATGTGTCAAATATGAATATTTTATCAAGACCATAAAAATTCTTACAAAAACAATCCTTTACTTCCTTTAATACAAATATTTTATCAAAAAAATGTAGTATTCGTAGTAAAAATTGAATTCATAGAAACGTCAAAATTAGAGATCAATTTAATTTTTCCTGCCTCTATTTTATCTTTTTAATTACAATATTTATAGTTTTGATATTCAAACATAAATAAGATATCAAGCTATATACAAGATCAATTAAAATAATTTTTATTATTATATCACGGTTTTAATTAGTCGAATATTTCAATAGATGATAAATCATACAAGCAAGTATTATTCCATAATTAAACTTAATTTGATTGATATTTGAATCATATCTAGTTATATATAGTTAACATGAAAACATGTTGGTGCAGTCACTTTGCAATGCTTGTGGAATCAGGCAGAGAAAGGCAAGAAGGGCCATGGCTGAAGCTGCCAATGGTTTGGCTACATCCCCTAAAACTAAAGTGCTTAAGATAAAGAAGCCTACACAATTCAAGACTAAGAACAAGGCTTCTACTAGTACCTCTACAACTTCAACTACTTCTGCTGGCTCATCATCTCAAGATGTGAAGAAACTTGAATCTTTTCCATTAGATTATGATTATGATGAAGCAGCAACGGCGGCACGACTTCTGGTGGATATATCTTCTGGTGTTACTTACTGA

Protein sequence

>MS.gene57249.t1

MVDSSSARDTNLSSSLELEDSSKKMSHGSEKWMSSKMKLMNMINTTATVATTPIMRPNNNIAATTDKAIKTTTPMMRPSNYGTSPRSQNIRYSQTSPSSNSGNNTVRVCSDCSTSHTPLWRSGPMGPKSLCNACGIRQRKARRAMAEAANGLATSPKTKVLKIKKPTQFKTKNKASTSTSTTSTTSAGSSSQDVKKLESFPLDYDYDEAATAARLLVDISSGVTY