AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene027757

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene027757.t1 MTR_5g032375 87.442 215 19 2 1 208 1 214 1.45e-134 376
MS.gene027757.t1 MTR_1g093750 35.928 167 89 3 43 198 156 315 2.44e-24 98.2
MS.gene027757.t1 MTR_5g066080 39.130 161 77 2 45 184 37 197 1.26e-23 94.7
MS.gene027757.t1 MTR_3g070970 35.928 167 91 3 45 198 73 236 3.02e-23 94.0
MS.gene027757.t1 MTR_2g015890 37.589 141 80 2 34 173 56 189 9.92e-22 89.7
MS.gene027757.t1 MTR_2g091190 34.270 178 100 4 6 177 22 188 4.86e-21 87.8
MS.gene027757.t1 MTR_4g079760 35.220 159 86 3 34 185 57 205 1.53e-18 81.3
MS.gene027757.t1 MTR_2g015890 40.000 120 64 2 34 152 56 168 2.81e-18 79.7
MS.gene027757.t1 MTR_4g087920 36.364 143 78 4 39 175 68 203 1.84e-12 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene027757.t1 AT4G38070 45.596 193 84 5 1 184 42 222 5.57e-46 152
MS.gene027757.t1 AT3G25710 42.029 138 70 3 43 177 130 260 4.73e-25 100
MS.gene027757.t1 AT1G68810 40.828 169 80 3 43 198 172 333 1.74e-24 99.4
MS.gene027757.t1 AT3G56770 33.333 174 93 6 40 200 39 202 2.17e-22 91.3
MS.gene027757.t1 AT2G41130 36.994 173 91 5 39 200 60 225 2.47e-20 86.3
MS.gene027757.t1 AT2G40200 37.500 136 67 4 46 172 64 190 8.02e-20 84.7

Find 53 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTGCTTCACTATGTTTCT+TGG 0.145261 5.2:-22412986 None:intergenic
TGGGGCGGACAAATTGAATT+TGG 0.240537 5.2:+22413439 MS.gene027757:CDS
TGTCCGCCCCACTAGGAAAC+TGG 0.364856 5.2:-22413427 None:intergenic
TTGGACCCATAACACACTTC+TGG 0.378699 5.2:-22413606 None:intergenic
GCACTAACTTTGATCAAGTT+GGG 0.385066 5.2:-22413063 None:intergenic
AGGTGTTGAAAATGAAGGTT+TGG 0.393224 5.2:+22413628 MS.gene027757:CDS
AATGAAAGCCAAAGTTGTTA+AGG 0.399548 5.2:+22413556 MS.gene027757:CDS
GAAGAACCAGAAGTGTGTTA+TGG 0.408049 5.2:+22413600 MS.gene027757:CDS
CATCTCAACCTTAACAACTT+TGG 0.408942 5.2:-22413564 None:intergenic
GGCACTAACTTTGATCAAGT+TGG 0.420765 5.2:-22413064 None:intergenic
AAGAACCAGAAGTGTGTTAT+GGG 0.427563 5.2:+22413601 MS.gene027757:CDS
CTATAACGCAGAAGCTCAAA+TGG 0.441129 5.2:+22412870 MS.gene027757:CDS
GATGAGGCGGTATACTCAAT+AGG 0.446628 5.2:+22413700 MS.gene027757:CDS
GGTGTTGAAAATGAAGGTTT+GGG 0.450241 5.2:+22413629 MS.gene027757:CDS
GATATAGATGACATTAATCC+TGG 0.453149 5.2:-22413518 None:intergenic
GATAGCCATGGTACCTCAAA+GGG 0.466904 5.2:+22413401 MS.gene027757:CDS
GTTTGCGAGATGAGTGAACT+TGG 0.483401 5.2:-22412907 None:intergenic
TACCGCCTCATCTTAAAGCT+TGG 0.493542 5.2:-22413689 None:intergenic
TTGAGTTGTGAGGATAGGCC+AGG 0.504463 5.2:+22413500 MS.gene027757:CDS
TTCAATTTGTCCGCCCCACT+AGG 0.507536 5.2:-22413434 None:intergenic
AGACGTAGAATGCGAATCAA+TGG 0.510341 5.2:+22413012 MS.gene027757:CDS
GGAGACTATCAAACAAGTGC+AGG 0.527796 5.2:+22413346 MS.gene027757:CDS
CAAAGTTGTTAAGGTTGAGA+TGG 0.542500 5.2:+22413565 MS.gene027757:CDS
GTCCAAGGTGTTGAAAATGA+AGG 0.548376 5.2:+22413623 MS.gene027757:CDS
AGGAAACTGGATCCCCTTTG+AGG 0.550743 5.2:-22413414 None:intergenic
CTACATTGAGTTGTGAGGAT+AGG 0.570986 5.2:+22413495 MS.gene027757:CDS
GGAAAAGTGTAATGATGAGG+AGG 0.576454 5.2:+22413460 MS.gene027757:CDS
AGATAGCCATGGTACCTCAA+AGG 0.576593 5.2:+22413400 MS.gene027757:CDS
AGGGGATCCAGTTTCCTAGT+GGG 0.580878 5.2:+22413420 MS.gene027757:CDS
CACTAACTTTGATCAAGTTG+GGG 0.582031 5.2:-22413062 None:intergenic
AGAAGTGTGTTATGGGTCCA+AGG 0.587934 5.2:+22413608 MS.gene027757:CDS
TCAAGTTGGGGAGGATATTG+CGG 0.598694 5.2:-22413050 None:intergenic
GTTGAGATGGTGACAGTGGG+TGG 0.609342 5.2:+22413578 MS.gene027757:CDS
GAAAAGTGTAATGATGAGGA+GGG 0.610839 5.2:+22413461 MS.gene027757:CDS
TAACTTTGATCAAGTTGGGG+AGG 0.613215 5.2:-22413059 None:intergenic
TAAGGTTGAGATGGTGACAG+TGG 0.619246 5.2:+22413574 MS.gene027757:CDS
TTTCTCGAAGCAAAGATCAA+AGG 0.627837 5.2:+22412942 MS.gene027757:CDS
GGACAAGGCATCAATACTAG+TGG 0.628919 5.2:+22413325 MS.gene027757:CDS
GGATCCCCTTTGAGGTACCA+TGG 0.636586 5.2:-22413406 None:intergenic
GGGGATCCAGTTTCCTAGTG+GGG 0.644968 5.2:+22413421 MS.gene027757:CDS
AAGGTTGAGATGGTGACAGT+GGG 0.645311 5.2:+22413575 MS.gene027757:CDS
CTCGAAGCAAAGATCAAAGG+CGG 0.646476 5.2:+22412945 MS.gene027757:CDS
AAGGGGATCCAGTTTCCTAG+TGG 0.647720 5.2:+22413419 MS.gene027757:CDS
AGCCAAGCTTTAAGATGAGG+CGG 0.655183 5.2:+22413687 MS.gene027757:CDS
ATAAGCCAAGCTTTAAGATG+AGG 0.659617 5.2:+22413684 MS.gene027757:CDS
AAGCTAGAAGAAGATAGCCA+TGG 0.662475 5.2:+22413389 MS.gene027757:CDS
TATTGATTAACAGAAGGACA+AGG 0.666615 5.2:+22413310 MS.gene027757:intron
AGTTGGGGAGGATATTGCGG+AGG 0.667078 5.2:-22413047 None:intergenic
TTTGGAAAAGTGTAATGATG+AGG 0.678742 5.2:+22413457 MS.gene027757:CDS
GATCCAGTTTCCTAGTGGGG+CGG 0.686927 5.2:+22413424 MS.gene027757:CDS
GAAAGCTACATTGAGTTGTG+AGG 0.689461 5.2:+22413490 MS.gene027757:CDS
GTTGGGGAGGATATTGCGGA+GGG 0.697366 5.2:-22413046 None:intergenic
ATAGCCATGGTACCTCAAAG+GGG 0.750021 5.2:+22413402 MS.gene027757:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AACAGTTAAATATTTTGATA+TGG + chr5.2:22413197-22413216 MS.gene027757:intron 15.0%
!!! GAAATTTTGTTTTATAAAGT+TGG - chr5.2:22413107-22413126 None:intergenic 15.0%
!!! TTTGATATGGTTTTTAATTT+TGG + chr5.2:22413210-22413229 MS.gene027757:intron 15.0%
!!! ATTTGTTATTGATTAACAGA+AGG + chr5.2:22413304-22413323 MS.gene027757:intron 20.0%
!!! TTGGTTTAATTTTTCATGAA+TGG - chr5.2:22413088-22413107 None:intergenic 20.0%
!! TAAATTTAGCAAGCTTGTTT+AGG - chr5.2:22413282-22413301 None:intergenic 25.0%
AATGAAAGCCAAAGTTGTTA+AGG + chr5.2:22413556-22413575 MS.gene027757:CDS 30.0%
GATATAGATGACATTAATCC+TGG - chr5.2:22413521-22413540 None:intergenic 30.0%
! TATTGATTAACAGAAGGACA+AGG + chr5.2:22413310-22413329 MS.gene027757:intron 30.0%
! TTTGGAAAAGTGTAATGATG+AGG + chr5.2:22413457-22413476 MS.gene027757:CDS 30.0%
CAAAGTTGTTAAGGTTGAGA+TGG + chr5.2:22413565-22413584 MS.gene027757:CDS 35.0%
CATCTCAACCTTAACAACTT+TGG - chr5.2:22413567-22413586 None:intergenic 35.0%
GCACTAACTTTGATCAAGTT+GGG - chr5.2:22413066-22413085 None:intergenic 35.0%
TCGCGATCACTATTATTGTA+AGG + chr5.2:22413171-22413190 MS.gene027757:intron 35.0%
TTCTGCTTCACTATGTTTCT+TGG - chr5.2:22412989-22413008 None:intergenic 35.0%
TTTCTCGAAGCAAAGATCAA+AGG + chr5.2:22412942-22412961 MS.gene027757:CDS 35.0%
! AACCTTCATTTTCAACACCT+TGG - chr5.2:22413628-22413647 None:intergenic 35.0%
! AAGAACCAGAAGTGTGTTAT+GGG + chr5.2:22413601-22413620 MS.gene027757:CDS 35.0%
! CACTAACTTTGATCAAGTTG+GGG - chr5.2:22413065-22413084 None:intergenic 35.0%
! GAAAAGTGTAATGATGAGGA+GGG + chr5.2:22413461-22413480 MS.gene027757:CDS 35.0%
! GGTGTTGAAAATGAAGGTTT+GGG + chr5.2:22413629-22413648 MS.gene027757:CDS 35.0%
!! AGGTGTTGAAAATGAAGGTT+TGG + chr5.2:22413628-22413647 MS.gene027757:CDS 35.0%
!! ATAAGCCAAGCTTTAAGATG+AGG + chr5.2:22413684-22413703 MS.gene027757:CDS 35.0%
AAGCTAGAAGAAGATAGCCA+TGG + chr5.2:22413389-22413408 MS.gene027757:CDS 40.0%
AGACGTAGAATGCGAATCAA+TGG + chr5.2:22413012-22413031 MS.gene027757:CDS 40.0%
CTATAACGCAGAAGCTCAAA+TGG + chr5.2:22412870-22412889 MS.gene027757:CDS 40.0%
GGCACTAACTTTGATCAAGT+TGG - chr5.2:22413067-22413086 None:intergenic 40.0%
! CTACATTGAGTTGTGAGGAT+AGG + chr5.2:22413495-22413514 MS.gene027757:CDS 40.0%
! GAAAGCTACATTGAGTTGTG+AGG + chr5.2:22413490-22413509 MS.gene027757:CDS 40.0%
! GAAGAACCAGAAGTGTGTTA+TGG + chr5.2:22413600-22413619 MS.gene027757:CDS 40.0%
! GGAAAAGTGTAATGATGAGG+AGG + chr5.2:22413460-22413479 MS.gene027757:CDS 40.0%
!! GTCCAAGGTGTTGAAAATGA+AGG + chr5.2:22413623-22413642 MS.gene027757:CDS 40.0%
!! TAACTTTGATCAAGTTGGGG+AGG - chr5.2:22413062-22413081 None:intergenic 40.0%
AAGGTTGAGATGGTGACAGT+GGG + chr5.2:22413575-22413594 MS.gene027757:CDS 45.0%
AGATAGCCATGGTACCTCAA+AGG + chr5.2:22413400-22413419 MS.gene027757:CDS 45.0%
ATAGCCATGGTACCTCAAAG+GGG + chr5.2:22413402-22413421 MS.gene027757:CDS 45.0%
CTCGAAGCAAAGATCAAAGG+CGG + chr5.2:22412945-22412964 MS.gene027757:CDS 45.0%
GATAGCCATGGTACCTCAAA+GGG + chr5.2:22413401-22413420 MS.gene027757:CDS 45.0%
GGAGACTATCAAACAAGTGC+AGG + chr5.2:22413346-22413365 MS.gene027757:CDS 45.0%
GTTTGCGAGATGAGTGAACT+TGG - chr5.2:22412910-22412929 None:intergenic 45.0%
TAAGGTTGAGATGGTGACAG+TGG + chr5.2:22413574-22413593 MS.gene027757:CDS 45.0%
TACCGCCTCATCTTAAAGCT+TGG - chr5.2:22413692-22413711 None:intergenic 45.0%
TGGGGCGGACAAATTGAATT+TGG + chr5.2:22413439-22413458 MS.gene027757:CDS 45.0%
TTGGACCCATAACACACTTC+TGG - chr5.2:22413609-22413628 None:intergenic 45.0%
! AGAAGTGTGTTATGGGTCCA+AGG + chr5.2:22413608-22413627 MS.gene027757:CDS 45.0%
! GGACAAGGCATCAATACTAG+TGG + chr5.2:22413325-22413344 MS.gene027757:CDS 45.0%
!! AGCCAAGCTTTAAGATGAGG+CGG + chr5.2:22413687-22413706 MS.gene027757:CDS 45.0%
!! TCAAGTTGGGGAGGATATTG+CGG - chr5.2:22413053-22413072 None:intergenic 45.0%
AAGGGGATCCAGTTTCCTAG+TGG + chr5.2:22413419-22413438 MS.gene027757:CDS 50.0%
AGGAAACTGGATCCCCTTTG+AGG - chr5.2:22413417-22413436 None:intergenic 50.0%
AGGGGATCCAGTTTCCTAGT+GGG + chr5.2:22413420-22413439 MS.gene027757:CDS 50.0%
TTCAATTTGTCCGCCCCACT+AGG - chr5.2:22413437-22413456 None:intergenic 50.0%
! TTGAGTTGTGAGGATAGGCC+AGG + chr5.2:22413500-22413519 MS.gene027757:CDS 50.0%
AGTTGGGGAGGATATTGCGG+AGG - chr5.2:22413050-22413069 None:intergenic 55.0%
GATCCAGTTTCCTAGTGGGG+CGG + chr5.2:22413424-22413443 MS.gene027757:CDS 55.0%
GGGGATCCAGTTTCCTAGTG+GGG + chr5.2:22413421-22413440 MS.gene027757:CDS 55.0%
GTTGAGATGGTGACAGTGGG+TGG + chr5.2:22413578-22413597 MS.gene027757:CDS 55.0%
GTTGGGGAGGATATTGCGGA+GGG - chr5.2:22413049-22413068 None:intergenic 55.0%
!! GGATCCCCTTTGAGGTACCA+TGG - chr5.2:22413409-22413428 None:intergenic 55.0%
TGTCCGCCCCACTAGGAAAC+TGG - chr5.2:22413430-22413449 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 22412850 22413721 22412850 ID=MS.gene027757
chr5.2 mRNA 22412850 22413721 22412850 ID=MS.gene027757.t1;Parent=MS.gene027757
chr5.2 exon 22412850 22413077 22412850 ID=MS.gene027757.t1.exon1;Parent=MS.gene027757.t1
chr5.2 CDS 22412850 22413077 22412850 ID=cds.MS.gene027757.t1;Parent=MS.gene027757.t1
chr5.2 exon 22413323 22413721 22413323 ID=MS.gene027757.t1.exon2;Parent=MS.gene027757.t1
chr5.2 CDS 22413323 22413721 22413323 ID=cds.MS.gene027757.t1;Parent=MS.gene027757.t1
Gene Sequence

>MS.gene027757

ATGCAGCATGTTCGAAATTACTATAACGCAGAAGCTCAAATGGTAAGAAGCAACTTTCCAAGTTCACTCATCTCGCAAACATTCAAAAGCAGTTTCTCGAAGCAAAGATCAAAGGCGGAGAATAAATTACTAGCAGCCAAGAAACATAGTGAAGCAGAAAAGAGACGTAGAATGCGAATCAATGGTCAATATGACACCCTCCGCAATATCCTCCCCAACTTGATCAAAGTTAGTGCCATTCATGAAAAATTAAACCAACTTTATAAAACAAAATTTCTTATATTTTTGTGTTTATCACAAGTTTTTGAACTATTATCGTTTTCGCGATCACTATTATTGTAAGGAATAACAGTTAAATATTTTGATATGGTTTTTAATTTTGGCACTTTTTAAGTCGAGTTTTTAATGTTGTGTTCTCGTTGTGATTTTCCTAAACAAGCTTGCTAAATTTAGAATTTGTTATTGATTAACAGAAGGACAAGGCATCAATACTAGTGGAGACTATCAAACAAGTGCAGGAGTTGAAGAAAAAAGCATCAAAGCTAGAAGAAGATAGCCATGGTACCTCAAAGGGGATCCAGTTTCCTAGTGGGGCGGACAAATTGAATTTGGAAAAGTGTAATGATGAGGAGGGTCTAGTGAAAGCTACATTGAGTTGTGAGGATAGGCCAGGATTAATGTCATCTATATCAAGAGCACTATTGTCAATGAAAGCCAAAGTTGTTAAGGTTGAGATGGTGACAGTGGGTGGAAGAACCAGAAGTGTGTTATGGGTCCAAGGTGTTGAAAATGAAGGTTTGGGAATGCTCAAGAGTACTTTGAAAGTTGTTATGCATAAGCCAAGCTTTAAGATGAGGCGGTATACTCAATAG
Protein sequence

>MS.gene027757.t1

MQHVRNYYNAEAQMVRSNFPSSLISQTFKSSFSKQRSKAENKLLAAKKHSEAEKRRRMRINGQYDTLRNILPNLIKKDKASILVETIKQVQELKKKASKLEEDSHGTSKGIQFPSGADKLNLEKCNDEEGLVKATLSCEDRPGLMSSISRALLSMKAKVVKVEMVTVGGRTRSVLWVQGVENEGLGMLKSTLKVVMHKPSFKMRRYTQ