AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene068738

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068738.t1 MTR_2g079120 98.936 94 1 0 6 99 153 246 9.11e-60 183
MS.gene068738.t1 MTR_2g013950 59.596 99 27 3 8 94 155 252 4.82e-25 94.7
MS.gene068738.t1 MTR_4g088695 56.044 91 28 3 16 94 143 233 1.20e-23 90.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene068738.t1 AT5G53830 69.663 89 20 4 11 92 151 239 1.90e-32 113
MS.gene068738.t1 AT1G28280 68.132 91 24 2 8 95 151 239 1.69e-31 110
MS.gene068738.t1 AT1G28280 67.778 90 24 2 8 94 151 238 6.10e-31 109
MS.gene068738.t1 AT3G15300 65.591 93 18 4 11 95 130 216 4.85e-30 106
MS.gene068738.t1 AT2G33780 48.780 82 30 2 19 90 113 192 1.51e-17 73.9

Find 20 sgRNAs with CRISPR-Local

Find 53 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATAAATCTTCACCTTCATT+AGG 0.311360 2.3:+18817184 MS.gene068738:CDS
GCATCTCTTGGTGTAGTAAT+AGG 0.315866 2.3:-18817265 None:intergenic
GAAGGTGAAGATTTATCAAA+AGG 0.403207 2.3:-18817178 None:intergenic
TCATCATTCAATGGTGTGAC+AGG 0.420771 2.3:-18817154 None:intergenic
TCTGATGAGTTTCCTAATGA+AGG 0.454202 2.3:-18817196 None:intergenic
GAAGGAAAATCAAGCAAGCT+TGG 0.463885 2.3:-18817118 None:intergenic
AGTTGTGGCTCTGCATCTCT+TGG 0.480249 2.3:-18817277 None:intergenic
TCAAAAGGGTCATCATTCAA+TGG 0.482624 2.3:-18817163 None:intergenic
GACAAAGCAATTGCTGAAAG+AGG 0.510604 2.3:+18817223 MS.gene068738:CDS
CTTGGTGTAGTAATAGGAGA+GGG 0.527748 2.3:-18817259 None:intergenic
AAGGTGAAGATTTATCAAAA+GGG 0.535615 2.3:-18817177 None:intergenic
GAATTTGATTGTGAAACTCT+AGG 0.540707 2.3:-18817325 None:intergenic
GGTGAAGAAAGAGGAAACAA+AGG 0.573082 2.3:-18817304 None:intergenic
GGAAACAAAGGAAGAAGTTG+TGG 0.576455 2.3:-18817292 None:intergenic
GAAACTCTAGGTGAAGAAAG+AGG 0.626680 2.3:-18817313 None:intergenic
CATCATTCAATGGTGTGACA+GGG 0.632245 2.3:-18817153 None:intergenic
TCTTGGTGTAGTAATAGGAG+AGG 0.640047 2.3:-18817260 None:intergenic
ACAGGGCTAAGAGCAAGAGA+AGG 0.663065 2.3:-18817136 None:intergenic
TTCATTAGGAAACTCATCAG+AGG 0.664188 2.3:+18817198 MS.gene068738:CDS
TTGGTGTAGTAATAGGAGAG+GGG 0.712277 2.3:-18817258 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAGGTGAAGATTTATCAAAA+GGG - chr2.3:18817180-18817199 None:intergenic 25.0%
! TTGGAATTCTGTGAAAAATT+TGG - chr2.3:18817061-18817080 None:intergenic 25.0%
!! AATTTGAAACCTTGTTTCTT+TGG - chr2.3:18816983-18817002 None:intergenic 25.0%
!! TTAAAGTTTCTTGTTTGTTG+AGG - chr2.3:18816938-18816957 None:intergenic 25.0%
!!! ATTTCTTGTTGTTGTTTTCT+TGG - chr2.3:18817091-18817110 None:intergenic 25.0%
ATAAGGATTTGAATCAGATC+TGG - chr2.3:18816780-18816799 None:intergenic 30.0%
CAAGTAGTTCAAATGTTAAC+TGG + chr2.3:18816839-18816858 MS.gene068738:intron 30.0%
GAAGGTGAAGATTTATCAAA+AGG - chr2.3:18817181-18817200 None:intergenic 30.0%
GAATTTGATTGTGAAACTCT+AGG - chr2.3:18817328-18817347 None:intergenic 30.0%
GATAAATCTTCACCTTCATT+AGG + chr2.3:18817184-18817203 MS.gene068738:CDS 30.0%
TAAGGATTTGAATCAGATCT+GGG - chr2.3:18816779-18816798 None:intergenic 30.0%
TTGAACTACTTGTTTGAAAG+TGG - chr2.3:18816831-18816850 None:intergenic 30.0%
! TTGTTTTCTTGGTGAGAAAT+TGG - chr2.3:18817080-18817099 None:intergenic 30.0%
AAAACAGCACCAAAGAAACA+AGG + chr2.3:18816971-18816990 MS.gene068738:intron 35.0%
AAGGATTTGAATCAGATCTG+GGG - chr2.3:18816778-18816797 None:intergenic 35.0%
AATTTGGATTCCATTGCTGT+TGG - chr2.3:18816726-18816745 None:intergenic 35.0%
CTGTGAAAAATTTGGCATCA+GGG - chr2.3:18817053-18817072 None:intergenic 35.0%
TCAAAAGGGTCATCATTCAA+TGG - chr2.3:18817166-18817185 None:intergenic 35.0%
TCTGATGAGTTTCCTAATGA+AGG - chr2.3:18817199-18817218 None:intergenic 35.0%
TCTGTGAAAAATTTGGCATC+AGG - chr2.3:18817054-18817073 None:intergenic 35.0%
TGAACAAAGGTTGTTGGATA+AGG - chr2.3:18816797-18816816 None:intergenic 35.0%
TTCATTAGGAAACTCATCAG+AGG + chr2.3:18817198-18817217 MS.gene068738:CDS 35.0%
!! CAGTTGCTTACATTGCTTTT+TGG - chr2.3:18816686-18816705 None:intergenic 35.0%
!!! GTTGTTGGTTTTGTTGTTGT+TGG - chr2.3:18816890-18816909 None:intergenic 35.0%
!!! TGTTGGTTTGGTTTTGTTGT+TGG - chr2.3:18816905-18816924 None:intergenic 35.0%
!!! TTCTTTGGTGCTGTTTTGAT+TGG - chr2.3:18816968-18816987 None:intergenic 35.0%
AGTAGCAATTCCAACAGCAA+TGG + chr2.3:18816713-18816732 MS.gene068738:intron 40.0%
CATCATTCAATGGTGTGACA+GGG - chr2.3:18817156-18817175 None:intergenic 40.0%
GAAACTCTAGGTGAAGAAAG+AGG - chr2.3:18817316-18817335 None:intergenic 40.0%
GAAGGAAAATCAAGCAAGCT+TGG - chr2.3:18817121-18817140 None:intergenic 40.0%
GACAAAGCAATTGCTGAAAG+AGG + chr2.3:18817223-18817242 MS.gene068738:CDS 40.0%
GGAAACAAAGGAAGAAGTTG+TGG - chr2.3:18817295-18817314 None:intergenic 40.0%
GGTGAAGAAAGAGGAAACAA+AGG - chr2.3:18817307-18817326 None:intergenic 40.0%
TCAGCTTGAACAAAGGTTGT+TGG - chr2.3:18816803-18816822 None:intergenic 40.0%
TCATCATTCAATGGTGTGAC+AGG - chr2.3:18817157-18817176 None:intergenic 40.0%
TTGGTGTAGTAATAGGAGAG+GGG - chr2.3:18817261-18817280 None:intergenic 40.0%
! CTTGGTGTAGTAATAGGAGA+GGG - chr2.3:18817262-18817281 None:intergenic 40.0%
! GCATCTCTTGGTGTAGTAAT+AGG - chr2.3:18817268-18817287 None:intergenic 40.0%
! GTTGAGGTAGATCTTGTTGT+TGG - chr2.3:18816922-18816941 None:intergenic 40.0%
! TCAGATCTGGGGATTGTTTT+TGG - chr2.3:18816767-18816786 None:intergenic 40.0%
! TCTTGGTGTAGTAATAGGAG+AGG - chr2.3:18817263-18817282 None:intergenic 40.0%
!! GGTAGATCTTGTTGTTGGTT+TGG - chr2.3:18816917-18816936 None:intergenic 40.0%
!! TGTTGTTGAGGTTGTTTCTG+AGG - chr2.3:18816867-18816886 None:intergenic 40.0%
!! TGTTGTTGTTGGTGTTGTTG+AGG - chr2.3:18816879-18816898 None:intergenic 40.0%
!!! ATTGTTTTTGGAGTGAGAGG+TGG - chr2.3:18816755-18816774 None:intergenic 40.0%
!!! TTGGTGCTGTTTTGATTGGT+GGG - chr2.3:18816964-18816983 None:intergenic 40.0%
!!! TTTGGTGCTGTTTTGATTGG+TGG - chr2.3:18816965-18816984 None:intergenic 40.0%
GGTTGTGTCAGCTTGAACAA+AGG - chr2.3:18816810-18816829 None:intergenic 45.0%
! TGAGAGGTGGTGTTGGAATT+TGG - chr2.3:18816742-18816761 None:intergenic 45.0%
!!! GGGATTGTTTTTGGAGTGAG+AGG - chr2.3:18816758-18816777 None:intergenic 45.0%
ACAGGGCTAAGAGCAAGAGA+AGG - chr2.3:18817139-18817158 None:intergenic 50.0%
! AGTTGTGGCTCTGCATCTCT+TGG - chr2.3:18817280-18817299 None:intergenic 50.0%
! TTTGGAGTGAGAGGTGGTGT+TGG - chr2.3:18816749-18816768 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 18816674 18817351 18816674 ID=MS.gene068738
chr2.3 mRNA 18816674 18817351 18816674 ID=MS.gene068738.t1;Parent=MS.gene068738
chr2.3 exon 18816674 18816694 18816674 ID=MS.gene068738.t1.exon1;Parent=MS.gene068738.t1
chr2.3 CDS 18816674 18816694 18816674 ID=cds.MS.gene068738.t1;Parent=MS.gene068738.t1
chr2.3 exon 18817073 18817351 18817073 ID=MS.gene068738.t1.exon2;Parent=MS.gene068738.t1
chr2.3 CDS 18817073 18817351 18817073 ID=cds.MS.gene068738.t1;Parent=MS.gene068738.t1
Gene Sequence

>MS.gene068738

ATGAACTCACCAAAAAGCAATGTAAGCAACTGCATGAGTAGTAGCAATTCCAACAGCAATGGAATCCAAATTCCAACACCACCTCTCACTCCAAAAACAATCCCCAGATCTGATTCAAATCCTTATCCAACAACCTTTGTTCAAGCTGACACAACCACTTTCAAACAAGTAGTTCAAATGTTAACTGGTTCCTCAGAAACAACCTCAACAACACCAACAACAACAAAACCAACAACAAAACCAAACCAACAACAAGATCTACCTCAACAAACAAGAAACTTTAACATCCCACCAATCAAAACAGCACCAAAGAAACAAGGTTTCAAATTATATGAAAGAAGAAACAGTCTCAAAAACAGTGTTCTTATGCTCAATACCCTGATGCCAAATTTTTCACAGAATTCCAATTTCTCACCAAGAAAACAACAACAAGAAATTCTCTCTCCAAGCTTGCTTGATTTTCCTTCTCTTGCTCTTAGCCCTGTCACACCATTGAATGATGACCCTTTTGATAAATCTTCACCTTCATTAGGAAACTCATCAGAGGAAGACAAAGCAATTGCTGAAAGAGGTTACTATTTGCACCCCTCTCCTATTACTACACCAAGAGATGCAGAGCCACAACTTCTTCCTTTGTTTCCTCTTTCTTCACCTAGAGTTTCACAATCAAATTCTTGA
Protein sequence

>MS.gene068738.t1

MNSPKSNNSNFSPRKQQQEILSPSLLDFPSLALSPVTPLNDDPFDKSSPSLGNSSEEDKAIAERGYYLHPSPITTPRDAEPQLLPLFPLSSPRVSQSNS