AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene93487

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene93487.t1 MTR_3g025510 88.961 154 16 1 1 153 1 154 1.04e-97 278
MS.gene93487.t1 MTR_3g025380 48.701 154 63 5 1 151 1 141 1.81e-31 110
MS.gene93487.t1 MTR_3g025550 74.468 47 12 0 100 146 13 59 2.16e-21 82.0
MS.gene93487.t1 MTR_3g025620 67.857 56 18 0 97 152 1 56 2.48e-21 81.6
MS.gene93487.t1 MTR_7g074170 39.785 93 52 2 57 145 294 386 7.79e-17 76.6
MS.gene93487.t1 MTR_6g079660 32.039 103 66 2 47 145 174 276 1.29e-16 75.5
MS.gene93487.t1 MTR_2g058360 47.500 80 36 4 74 149 64 141 1.82e-14 66.6
MS.gene93487.t1 MTR_3g088080 48.214 56 25 1 90 145 28 79 4.19e-14 64.3
MS.gene93487.t1 MTR_1g114320 30.097 103 68 2 47 145 133 235 6.70e-14 67.8
MS.gene93487.t1 MTR_3g072630 36.559 93 58 1 57 148 173 265 5.83e-13 65.1
MS.gene93487.t1 MTR_3g072630 36.559 93 58 1 57 148 173 265 7.53e-13 65.1
MS.gene93487.t1 MTR_1g114620 35.484 93 54 2 57 145 215 305 7.72e-13 64.7
MS.gene93487.t1 MTR_3g083480 32.632 95 56 2 57 148 192 281 3.06e-12 63.2
MS.gene93487.t1 MTR_2g097620 38.462 65 38 2 82 145 167 230 4.34e-12 62.8
MS.gene93487.t1 MTR_4g064570 43.077 65 35 2 82 145 159 222 6.34e-12 62.4
MS.gene93487.t1 MTR_0067s0100 30.693 101 70 0 45 145 131 231 1.17e-11 61.2
MS.gene93487.t1 MTR_2g007340 39.394 66 40 0 88 153 185 250 1.80e-11 60.8
MS.gene93487.t1 MTR_5g080350 40.984 61 36 0 88 148 177 237 1.99e-11 60.8
MS.gene93487.t1 MTR_4g108830 42.188 64 36 1 86 148 128 191 3.42e-11 58.9
MS.gene93487.t1 MTR_4g108830 42.188 64 36 1 86 148 156 219 4.47e-11 58.9
MS.gene93487.t1 MTR_0186s0090 48.980 49 22 1 103 148 115 163 7.50e-11 57.4
MS.gene93487.t1 MTR_4g110100 44.262 61 33 1 86 145 341 401 8.14e-11 59.3
MS.gene93487.t1 MTR_5g058530 46.939 49 26 0 97 145 217 265 8.15e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene93487.t1 AT3G02340 41.758 91 48 3 60 145 286 376 5.17e-15 71.2
MS.gene93487.t1 AT3G02340 41.758 91 48 3 60 145 286 376 5.17e-15 71.2
MS.gene93487.t1 AT5G15820 37.895 95 52 3 58 145 238 332 1.04e-14 70.1
MS.gene93487.t1 AT4G26400 34.951 103 59 2 46 145 185 282 2.38e-14 69.3
MS.gene93487.t1 AT4G26400 34.951 103 59 2 46 145 185 282 2.38e-14 69.3
MS.gene93487.t1 AT1G14200 38.667 75 46 0 71 145 76 150 2.79e-14 67.0
MS.gene93487.t1 AT5G01980 36.957 92 55 1 57 145 300 391 1.04e-13 67.8
MS.gene93487.t1 AT3G19950 30.108 93 61 2 57 145 165 257 1.07e-13 67.4
MS.gene93487.t1 AT3G19950 30.108 93 61 2 57 145 223 315 1.20e-13 67.4
MS.gene93487.t1 AT3G19950 30.108 93 61 2 57 145 223 315 1.20e-13 67.4
MS.gene93487.t1 AT5G08139 44.615 65 35 1 82 145 286 350 1.43e-13 67.0
MS.gene93487.t1 AT5G54990 55.556 45 20 0 101 145 171 215 4.04e-13 64.7
MS.gene93487.t1 AT2G40830 30.275 109 71 3 49 153 132 239 7.97e-13 64.7
MS.gene93487.t1 AT2G40830 30.275 109 71 3 49 153 132 239 7.97e-13 64.7
MS.gene93487.t1 AT2G40830 30.275 109 71 3 49 153 132 239 7.97e-13 64.7
MS.gene93487.t1 AT2G40830 30.275 109 71 3 49 153 132 239 7.97e-13 64.7
MS.gene93487.t1 AT1G60360 39.130 69 41 1 86 153 205 273 1.05e-12 64.3
MS.gene93487.t1 AT4G05350 39.437 71 40 1 81 148 134 204 4.85e-12 61.6
MS.gene93487.t1 AT1G18770 43.750 48 27 0 103 150 58 105 6.36e-12 58.9
MS.gene93487.t1 AT3G30460 39.744 78 45 1 73 148 64 141 6.70e-12 60.1
MS.gene93487.t1 AT3G30460 46.032 63 32 1 88 148 115 177 7.02e-12 60.5
MS.gene93487.t1 AT3G60080 38.806 67 33 1 87 145 144 210 1.45e-11 61.2
MS.gene93487.t1 AT5G56340 32.609 92 54 2 57 145 214 300 1.65e-11 61.2
MS.gene93487.t1 AT4G12190 41.935 62 33 1 90 148 8 69 2.55e-11 56.6
MS.gene93487.t1 AT3G10815 46.667 45 24 0 104 148 121 165 4.61e-11 58.5
MS.gene93487.t1 AT4G12210 36.486 74 44 1 78 148 127 200 4.95e-11 58.5
MS.gene93487.t1 AT3G46620 40.000 65 37 2 82 145 193 256 6.61e-11 59.7
MS.gene93487.t1 AT2G29840 47.826 46 24 0 100 145 240 285 7.43e-11 58.9
MS.gene93487.t1 AT2G44330 48.000 50 26 0 104 153 96 145 7.65e-11 57.8
MS.gene93487.t1 AT1G55530 28.431 102 61 3 49 145 170 264 9.60e-11 58.9
MS.gene93487.t1 AT1G55530 28.431 102 61 3 49 145 170 264 9.60e-11 58.9

Find 27 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAACGACTCGGTTATGATTT+TGG 0.133349 3.4:+17838257 MS.gene93487:CDS
GATTTGTTTGGTGGAGCTTT+CGG 0.379375 3.4:+17838527 MS.gene93487:CDS
TCTTCTACAATTTCGACTCT+TGG 0.408499 3.4:-17838477 None:intergenic
TTTGATGTGTTCGATTTGTT+TGG 0.422388 3.4:+17838515 MS.gene93487:CDS
ACGACTACTCCATATGTTGA+TGG 0.440424 3.4:+17838369 MS.gene93487:CDS
CGGTTGGGTTGAAAGCAATT+CGG 0.442494 3.4:+17838547 MS.gene93487:CDS
ACGATGAATGTATCATGAAA+TGG 0.447486 3.4:+17838592 MS.gene93487:CDS
TGTTTGGTGGAGCTTTCGGT+TGG 0.460170 3.4:+17838531 MS.gene93487:CDS
ATATAGTGGCCATCAACATA+TGG 0.473428 3.4:-17838378 None:intergenic
TAAGAGTGTGATAATGAGGA+GGG 0.483867 3.4:-17838299 None:intergenic
GATGTGTTCGATTTGTTTGG+TGG 0.485259 3.4:+17838518 MS.gene93487:CDS
AGAGTGTGATAATGAGGAGG+GGG 0.485557 3.4:-17838297 None:intergenic
TGGAGCAACATCGTCGTTCA+AGG 0.491831 3.4:+17838214 MS.gene93487:CDS
CTAGTAAGAGTGTGATAATG+AGG 0.496331 3.4:-17838303 None:intergenic
TTACTAGAAATTCATCAAGA+AGG 0.507286 3.4:+17838319 MS.gene93487:CDS
GTTTGGTGGAGCTTTCGGTT+GGG 0.522058 3.4:+17838532 MS.gene93487:CDS
TGATGACATGTAAAATATAG+TGG 0.527734 3.4:-17838392 None:intergenic
GATACACTCTGACGACACAT+AGG 0.555715 3.4:-17838636 None:intergenic
GTAAGAGTGTGATAATGAGG+AGG 0.560718 3.4:-17838300 None:intergenic
AACCGAGTCGTTGTCTTCAG+CGG 0.564335 3.4:-17838247 None:intergenic
TGAACGACGATGTTGCTCCA+TGG 0.567207 3.4:-17838211 None:intergenic
TAGTATGATTCTCGTTGATG+TGG 0.592252 3.4:-17838416 None:intergenic
ATACACTCTGACGACACATA+GGG 0.607340 3.4:-17838635 None:intergenic
TCGTGGTAGATATGCGAGCA+AGG 0.609523 3.4:-17838573 None:intergenic
AAGAGTGTGATAATGAGGAG+GGG 0.625865 3.4:-17838298 None:intergenic
GTCCGCTGAAGACAACGACT+CGG 0.678762 3.4:+17838245 MS.gene93487:CDS
ATTTCATGATACATTCATCG+TGG 0.701379 3.4:-17838590 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGATGACATGTAAAATATAG+TGG - chr3.4:17838395-17838414 None:intergenic 25.0%
! TTACTAGAAATTCATCAAGA+AGG + chr3.4:17838319-17838338 MS.gene93487:CDS 25.0%
ACGATGAATGTATCATGAAA+TGG + chr3.4:17838592-17838611 MS.gene93487:CDS 30.0%
ATTTCATGATACATTCATCG+TGG - chr3.4:17838593-17838612 None:intergenic 30.0%
! TTTGATGTGTTCGATTTGTT+TGG + chr3.4:17838515-17838534 MS.gene93487:CDS 30.0%
ATATAGTGGCCATCAACATA+TGG - chr3.4:17838381-17838400 None:intergenic 35.0%
TAGTATGATTCTCGTTGATG+TGG - chr3.4:17838419-17838438 None:intergenic 35.0%
TCTTCTACAATTTCGACTCT+TGG - chr3.4:17838480-17838499 None:intergenic 35.0%
! CTAGTAAGAGTGTGATAATG+AGG - chr3.4:17838306-17838325 None:intergenic 35.0%
! TAAGAGTGTGATAATGAGGA+GGG - chr3.4:17838302-17838321 None:intergenic 35.0%
ACGACTACTCCATATGTTGA+TGG + chr3.4:17838369-17838388 MS.gene93487:CDS 40.0%
ATACACTCTGACGACACATA+GGG - chr3.4:17838638-17838657 None:intergenic 40.0%
! AAGAGTGTGATAATGAGGAG+GGG - chr3.4:17838301-17838320 None:intergenic 40.0%
! GATGTGTTCGATTTGTTTGG+TGG + chr3.4:17838518-17838537 MS.gene93487:CDS 40.0%
! GATTTGTTTGGTGGAGCTTT+CGG + chr3.4:17838527-17838546 MS.gene93487:CDS 40.0%
! GTAAGAGTGTGATAATGAGG+AGG - chr3.4:17838303-17838322 None:intergenic 40.0%
!!! CAACGACTCGGTTATGATTT+TGG + chr3.4:17838257-17838276 MS.gene93487:CDS 40.0%
GATACACTCTGACGACACAT+AGG - chr3.4:17838639-17838658 None:intergenic 45.0%
! AGAGTGTGATAATGAGGAGG+GGG - chr3.4:17838300-17838319 None:intergenic 45.0%
!! CGGTTGGGTTGAAAGCAATT+CGG + chr3.4:17838547-17838566 MS.gene93487:CDS 45.0%
AACCGAGTCGTTGTCTTCAG+CGG - chr3.4:17838250-17838269 None:intergenic 50.0%
TCGTGGTAGATATGCGAGCA+AGG - chr3.4:17838576-17838595 None:intergenic 50.0%
TGGAGCAACATCGTCGTTCA+AGG + chr3.4:17838214-17838233 MS.gene93487:CDS 50.0%
! GTTTGGTGGAGCTTTCGGTT+GGG + chr3.4:17838532-17838551 MS.gene93487:CDS 50.0%
! TGTTTGGTGGAGCTTTCGGT+TGG + chr3.4:17838531-17838550 MS.gene93487:CDS 50.0%
GTCCGCTGAAGACAACGACT+CGG + chr3.4:17838245-17838264 MS.gene93487:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 17838213 17838674 17838213 ID=MS.gene93487
chr3.4 mRNA 17838213 17838674 17838213 ID=MS.gene93487.t1;Parent=MS.gene93487
chr3.4 exon 17838213 17838674 17838213 ID=MS.gene93487.t1.exon1;Parent=MS.gene93487.t1
chr3.4 CDS 17838213 17838674 17838213 ID=cds.MS.gene93487.t1;Parent=MS.gene93487.t1
Gene Sequence

>MS.gene93487

ATGGAGCAACATCGTCGTTCAAGGAGAAGTGTGTCCGCTGAAGACAACGACTCGGTTATGATTTTGGATGCTATTGATCTAAATCCCCCTCCTCATTATCACACTCTTACTAGAAATTCATCAAGAAGGTTTGCAAGAAATTTTATAAGATCTTCAACGACTACTCCATATGTTGATGGCCACTATATTTTACATGTCATCAACCACATCAACGAGAATCATACTAGTAGAAGAAATAGAGTCAGACATGTTTATCACAATCTTCCAAGAGTCGAAATTGTAGAAGAAATGAAGTGTGAAGCTTTGATGTGTTCGATTTGTTTGGTGGAGCTTTCGGTTGGGTTGAAAGCAATTCGGTTGCCTTGCTCGCATATCTACCACGATGAATGTATCATGAAATGGTTAGATAGATCAAACACATGCCCTATGTGTCGTCAGAGTGTATCTCATGTTTCTTCATGA
Protein sequence

>MS.gene93487.t1

MEQHRRSRRSVSAEDNDSVMILDAIDLNPPPHYHTLTRNSSRRFARNFIRSSTTTPYVDGHYILHVINHINENHTSRRNRVRHVYHNLPRVEIVEEMKCEALMCSICLVELSVGLKAIRLPCSHIYHDECIMKWLDRSNTCPMCRQSVSHVSS