AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene90729

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene90729.t1 MTR_1g023140 97.753 89 2 0 9 97 31 119 2.43e-58 175
MS.gene90729.t1 MTR_3g112410 84.146 82 13 0 9 90 31 112 6.50e-47 146
MS.gene90729.t1 MTR_5g021180 70.732 82 24 0 9 90 33 114 1.55e-39 127
MS.gene90729.t1 MTR_7g009070 57.831 83 35 0 9 91 51 133 9.98e-34 113
MS.gene90729.t1 MTR_8g107460 56.098 82 36 0 9 90 279 360 7.82e-28 103
MS.gene90729.t1 MTR_8g005320 45.570 79 43 0 9 87 51 129 1.16e-26 95.9
MS.gene90729.t1 MTR_8g006685 45.570 79 43 0 9 87 120 198 2.36e-26 96.7
MS.gene90729.t1 MTR_8g006560 45.570 79 43 0 9 87 120 198 2.36e-26 96.7
MS.gene90729.t1 MTR_7g073680 45.570 79 43 0 9 87 49 127 5.82e-25 91.3
MS.gene90729.t1 MTR_5g037930 53.571 84 39 0 9 92 45 128 4.09e-24 89.0
MS.gene90729.t1 MTR_5g037950 52.273 88 42 0 4 91 39 126 4.98e-23 86.3
MS.gene90729.t1 MTR_2g010750 48.315 89 46 0 9 97 34 122 6.60e-23 85.9
MS.gene90729.t1 MTR_5g037890 50.000 84 42 0 9 92 43 126 6.71e-21 80.5
MS.gene90729.t1 MTR_4g094690 43.836 73 39 1 8 78 83 155 6.21e-20 79.3
MS.gene90729.t1 MTR_2g082590 43.038 79 45 0 9 87 35 113 3.81e-19 76.3
MS.gene90729.t1 MTR_2g082590 39.560 91 55 0 4 94 43 133 3.96e-19 76.3
MS.gene90729.t1 MTR_4g081380 43.038 79 45 0 9 87 35 113 2.93e-18 73.9
MS.gene90729.t1 MTR_1g098660 40.845 71 41 1 9 78 81 151 5.74e-18 74.3
MS.gene90729.t1 MTR_3g089065 40.230 87 50 2 9 93 89 175 2.21e-17 72.8
MS.gene90729.t1 MTR_7g080250 41.463 82 47 1 7 87 95 176 3.05e-16 70.1
MS.gene90729.t1 MTR_3g112400 70.732 41 12 0 40 80 41 81 1.16e-15 66.2
MS.gene90729.t1 MTR_2g079420 42.254 71 40 1 9 78 89 159 3.29e-15 67.4
MS.gene90729.t1 MTR_7g102130 33.333 81 52 1 10 90 49 127 1.52e-14 64.3
MS.gene90729.t1 MTR_8g059015 38.554 83 49 2 9 89 92 174 2.92e-14 64.7
MS.gene90729.t1 MTR_1g114290 38.462 91 44 4 9 93 89 173 6.22e-14 63.9
MS.gene90729.t1 MTR_6g092700 35.165 91 56 2 9 96 98 188 2.34e-13 63.2
MS.gene90729.t1 MTR_4g088905 36.250 80 51 0 10 89 25 104 1.51e-12 62.0
MS.gene90729.t1 MTR_3g435370 33.333 87 55 2 9 92 110 196 3.65e-12 60.5
MS.gene90729.t1 MTR_3g435370 33.333 87 55 2 9 92 110 196 4.43e-12 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene90729.t1 AT3G51030 70.732 82 24 0 9 90 31 112 3.70e-42 134
MS.gene90729.t1 AT1G45145 60.976 82 32 0 9 90 30 111 7.45e-35 115
MS.gene90729.t1 AT1G19730 60.674 89 34 1 9 96 31 119 4.44e-33 111
MS.gene90729.t1 AT5G42980 57.955 88 37 0 9 96 30 117 1.71e-32 109
MS.gene90729.t1 AT5G39950 51.852 81 39 0 9 89 50 130 2.22e-28 100
MS.gene90729.t1 AT3G17880 48.235 85 44 0 9 93 288 372 6.86e-26 99.0
MS.gene90729.t1 AT3G17880 48.235 85 44 0 9 93 295 379 8.18e-26 98.6
MS.gene90729.t1 AT3G08710 43.750 80 45 0 9 88 48 127 3.22e-25 92.0
MS.gene90729.t1 AT3G08710 43.750 80 45 0 9 88 48 127 3.22e-25 92.0
MS.gene90729.t1 AT3G08710 43.750 80 45 0 9 88 48 127 3.22e-25 92.0
MS.gene90729.t1 AT1G59730 44.578 83 46 0 9 91 46 128 5.66e-24 88.6
MS.gene90729.t1 AT3G56420 46.053 76 41 0 9 84 65 140 4.47e-23 87.0
MS.gene90729.t1 AT3G56420 46.053 76 41 0 9 84 65 140 4.47e-23 87.0
MS.gene90729.t1 AT3G56420 46.053 76 41 0 9 84 65 140 4.47e-23 87.0
MS.gene90729.t1 AT1G69880 42.353 85 49 0 9 93 62 146 9.33e-22 83.6
MS.gene90729.t1 AT1G11530 48.101 79 41 0 9 87 27 105 1.43e-20 79.7
MS.gene90729.t1 AT2G40790 43.421 76 43 0 9 84 65 140 9.20e-20 78.6
MS.gene90729.t1 AT2G40790 43.421 76 43 0 9 84 65 140 9.20e-20 78.6
MS.gene90729.t1 AT2G35010 44.872 78 41 1 10 85 110 187 8.50e-19 77.0
MS.gene90729.t1 AT2G35010 44.872 78 41 1 10 85 110 187 8.50e-19 77.0
MS.gene90729.t1 AT1G43560 37.647 85 47 2 9 87 79 163 2.65e-17 72.4
MS.gene90729.t1 AT1G76760 39.437 71 42 1 9 78 84 154 7.45e-17 71.6
MS.gene90729.t1 AT5G16400 41.250 80 46 1 9 87 100 179 4.79e-16 69.7
MS.gene90729.t1 AT1G31020 44.286 70 37 1 10 77 75 144 2.41e-15 67.4
MS.gene90729.t1 AT3G02730 37.209 86 53 1 9 93 90 175 5.04e-15 67.0
MS.gene90729.t1 AT4G26160 37.209 86 51 2 9 91 116 201 7.93e-15 67.0
MS.gene90729.t1 AT3G15360 36.145 83 51 2 9 89 107 189 5.14e-14 64.7
MS.gene90729.t1 AT1G03680 36.145 83 51 2 9 89 95 177 8.03e-14 63.9
MS.gene90729.t1 AT1G50320 36.047 86 48 3 7 91 88 167 6.78e-13 61.2
MS.gene90729.t1 AT4G03520 35.211 71 45 1 9 78 101 171 8.02e-13 61.2
MS.gene90729.t1 AT4G32580 33.333 81 54 0 9 89 24 104 4.58e-12 58.9
MS.gene90729.t1 AT4G04950 34.568 81 53 0 9 89 24 104 5.77e-12 60.5
MS.gene90729.t1 AT3G53220 30.864 81 54 1 10 90 47 125 9.10e-12 57.4

Find 24 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAGCAATCTCAGCTAGAAT+TGG 0.355652 1.4:-1541808 None:intergenic
AGAAGGTAAGGAAGTGGATA+AGG 0.412033 1.4:+1542265 MS.gene90729:CDS
CTTATTCTTGAAAGAAGGTA+AGG 0.442943 1.4:+1542253 MS.gene90729:CDS
ACCTTCTTATTCTTGAAAGA+AGG 0.451509 1.4:+1542248 MS.gene90729:CDS
ACCTTGAGGAAGATGACTTC+AGG 0.453976 1.4:-1541838 None:intergenic
AAATGCAATCACCAAGCATA+AGG 0.465102 1.4:+1542316 MS.gene90729:CDS
TAAGGTAGTTGGTGCTAGGA+AGG 0.479587 1.4:+1542283 MS.gene90729:CDS
TGGATAAGGTAGTTGGTGCT+AGG 0.488936 1.4:+1542279 MS.gene90729:CDS
AAGGAAGTGGATAAGGTAGT+TGG 0.491604 1.4:+1542272 MS.gene90729:CDS
AACAGTTGCATCCTTATGCT+TGG 0.492616 1.4:-1542327 None:intergenic
ACCTTCTTTCAAGAATAAGA+AGG 0.495256 1.4:-1542249 None:intergenic
TTCAGAGTGTTGCTGAGGAA+TGG 0.506641 1.4:+1542207 MS.gene90729:intron
GGTGGATATTGATGAAGTAA+AGG 0.509236 1.4:+1541858 MS.gene90729:CDS
CTAGAATTGGAGCAATAAAA+CGG 0.524722 1.4:-1541795 None:intergenic
CTTGAAAGAAGGTAAGGAAG+TGG 0.537499 1.4:+1542259 MS.gene90729:CDS
TGGTGCTAGGAAGGAAGAGC+TGG 0.539272 1.4:+1542292 MS.gene90729:CDS
TCTTTCAAGAATAAGAAGGT+TGG 0.555397 1.4:-1542245 None:intergenic
TCCTGAAGTCATCTTCCTCA+AGG 0.561588 1.4:+1541837 MS.gene90729:CDS
TGAATAATAATAGATTGTGG+TGG 0.608090 1.4:+1541744 MS.gene90729:intron
TGCTGAGGAATGGTCTGTTG+AGG 0.618156 1.4:+1542217 MS.gene90729:CDS
CTTCATCAATATCCACCTTG+AGG 0.619089 1.4:-1541852 None:intergenic
ATTGGAGCAATAAAACGGCA+TGG 0.627618 1.4:-1541790 None:intergenic
CCTATTTCAGAGTGTTGCTG+AGG 0.630806 1.4:+1542202 MS.gene90729:intron
TGAAGTCATCTTCCTCAAGG+TGG 0.658466 1.4:+1541840 MS.gene90729:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGTTTCTAATATTTTAAGA+TGG + chr1.4:1542114-1542133 MS.gene90729:intron 15.0%
!! ATAAAGGTGGTTATAAATTA+AGG - chr1.4:1541592-1541611 None:intergenic 20.0%
!! ATTAAACTTGAGAAAGAATA+AGG - chr1.4:1541909-1541928 None:intergenic 20.0%
!! CATTGAATAATAATAGATTG+TGG + chr1.4:1541741-1541760 MS.gene90729:intron 20.0%
! CAAAACAAATAAGCACATAA+AGG - chr1.4:1541608-1541627 None:intergenic 25.0%
! TGAATAATAATAGATTGTGG+TGG + chr1.4:1541744-1541763 MS.gene90729:intron 25.0%
!! CTTTATGTGCTTATTTGTTT+TGG + chr1.4:1541606-1541625 MS.gene90729:intron 25.0%
AACAAATAAGCACATAAAGG+TGG - chr1.4:1541605-1541624 None:intergenic 30.0%
ACCTTCTTATTCTTGAAAGA+AGG + chr1.4:1542248-1542267 MS.gene90729:CDS 30.0%
ACCTTCTTTCAAGAATAAGA+AGG - chr1.4:1542252-1542271 None:intergenic 30.0%
CTAGAATTGGAGCAATAAAA+CGG - chr1.4:1541798-1541817 None:intergenic 30.0%
CTTATTCTTGAAAGAAGGTA+AGG + chr1.4:1542253-1542272 MS.gene90729:CDS 30.0%
GATCATAAGATGACATAACA+TGG - chr1.4:1542069-1542088 None:intergenic 30.0%
TCTTTCAAGAATAAGAAGGT+TGG - chr1.4:1542248-1542267 None:intergenic 30.0%
! TGTAGTTTTTGTCAAAATCG+TGG + chr1.4:1541989-1542008 MS.gene90729:intron 30.0%
AAATGCAATCACCAAGCATA+AGG + chr1.4:1542316-1542335 MS.gene90729:CDS 35.0%
GGTGGATATTGATGAAGTAA+AGG + chr1.4:1541858-1541877 MS.gene90729:CDS 35.0%
TTAGCAATCTCAGCTAGAAT+TGG - chr1.4:1541811-1541830 None:intergenic 35.0%
!! AACTAGTCTTAAAGCCGATT+CGG + chr1.4:1542179-1542198 MS.gene90729:intron 35.0%
AACAGTTGCATCCTTATGCT+TGG - chr1.4:1542330-1542349 None:intergenic 40.0%
AAGGAAGTGGATAAGGTAGT+TGG + chr1.4:1542272-1542291 MS.gene90729:CDS 40.0%
AGAAGGTAAGGAAGTGGATA+AGG + chr1.4:1542265-1542284 MS.gene90729:CDS 40.0%
ATTGGAGCAATAAAACGGCA+TGG - chr1.4:1541793-1541812 None:intergenic 40.0%
CTTCATCAATATCCACCTTG+AGG - chr1.4:1541855-1541874 None:intergenic 40.0%
CTTGAAAGAAGGTAAGGAAG+TGG + chr1.4:1542259-1542278 MS.gene90729:CDS 40.0%
! GATTTTACTGCTTCATGGTG+TGG + chr1.4:1541766-1541785 MS.gene90729:CDS 40.0%
!!! TGGTGGATTTTACTGCTTCA+TGG + chr1.4:1541761-1541780 MS.gene90729:CDS 40.0%
ACCTTGAGGAAGATGACTTC+AGG - chr1.4:1541841-1541860 None:intergenic 45.0%
TCCTGAAGTCATCTTCCTCA+AGG + chr1.4:1541837-1541856 MS.gene90729:CDS 45.0%
TGAAGTCATCTTCCTCAAGG+TGG + chr1.4:1541840-1541859 MS.gene90729:CDS 45.0%
! TGGATAAGGTAGTTGGTGCT+AGG + chr1.4:1542279-1542298 MS.gene90729:CDS 45.0%
!! CACTCTGAAATAGGCCGAAT+CGG - chr1.4:1542196-1542215 None:intergenic 45.0%
!! CCTATTTCAGAGTGTTGCTG+AGG + chr1.4:1542202-1542221 MS.gene90729:intron 45.0%
!! CCTCAGCAACACTCTGAAAT+AGG - chr1.4:1542205-1542224 None:intergenic 45.0%
!! TAAGGTAGTTGGTGCTAGGA+AGG + chr1.4:1542283-1542302 MS.gene90729:CDS 45.0%
!! TTCAGAGTGTTGCTGAGGAA+TGG + chr1.4:1542207-1542226 MS.gene90729:intron 45.0%
TGCTGAGGAATGGTCTGTTG+AGG + chr1.4:1542217-1542236 MS.gene90729:CDS 50.0%
! TGGTGCTAGGAAGGAAGAGC+TGG + chr1.4:1542292-1542311 MS.gene90729:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 1541549 1542361 1541549 ID=MS.gene90729
chr1.4 mRNA 1541549 1542361 1541549 ID=MS.gene90729.t1;Parent=MS.gene90729
chr1.4 exon 1541549 1541572 1541549 ID=MS.gene90729.t1.exon1;Parent=MS.gene90729.t1
chr1.4 CDS 1541549 1541572 1541549 ID=cds.MS.gene90729.t1;Parent=MS.gene90729.t1
chr1.4 exon 1541757 1541879 1541757 ID=MS.gene90729.t1.exon2;Parent=MS.gene90729.t1
chr1.4 CDS 1541757 1541879 1541757 ID=cds.MS.gene90729.t1;Parent=MS.gene90729.t1
chr1.4 exon 1542212 1542361 1542212 ID=MS.gene90729.t1.exon3;Parent=MS.gene90729.t1
chr1.4 CDS 1542212 1542361 1542212 ID=cds.MS.gene90729.t1;Parent=MS.gene90729.t1
Gene Sequence

>MS.gene90729

ATGACAGTTGTGACATTTCAAAATGTCATTTTCATGTTTGCCTTAATTTATAACCACCTTTATGTGCTTATTTGTTTTGGAAACTTTATGCATTTAAATTATTTGAATATTTTTTGAGTTTAATTTTTTTTTTTTTGTTGCTGTTTAAGTTGATAATAGCATTATTCATAACACTTATAATGAATTGCATTTCATTGAATAATAATAGATTGTGGTGGATTTTACTGCTTCATGGTGTGGTCCATGCCGTTTTATTGCTCCAATTCTAGCTGAGATTGCTAAGAAGACTCCTGAAGTCATCTTCCTCAAGGTGGATATTGATGAAGTAAAGGTATAAGCATATCTTAATCTATATTACCTTATTCTTTCTCAAGTTTAATACATGTTTAGAATCACGTTGAGTTTGAAAAAATCACAACATGATTTTTGAAGCTCTATAGTGTAGTTTTTGTCAAAATCGTGGTAGCACGTAGTGATTCTTGATTCTGTCAAACTCAGATAACACAATCAAAGTTTACCATGTTATGTCATCTTATGATCATACTATAGAAACATTGTTTGAAACATGTTTCTAATATTTTAAGATGGTGACTGATTAATTACTATATAGTTAAACTTATTTTTACTTCAAACTAGTCTTAAAGCCGATTCGGCCTATTTCAGAGTGTTGCTGAGGAATGGTCTGTTGAGGCTATGCCAACCTTCTTATTCTTGAAAGAAGGTAAGGAAGTGGATAAGGTAGTTGGTGCTAGGAAGGAAGAGCTGGAAAATGCAATCACCAAGCATAAGGATGCAACTGTTGCTACTACTTGA
Protein sequence

>MS.gene90729.t1

MTVVTFQNIVVDFTASWCGPCRFIAPILAEIAKKTPEVIFLKVDIDEVKSVAEEWSVEAMPTFLFLKEGKEVDKVVGARKEELENAITKHKDATVATT