AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1408190


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1408190 MtrunA17_Chr7g0275981 93.913 230 9 1 1 230 1 225 3.82e-155 429
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1408190 AT4G00895.1 40.945 127 61 3 65 187 75 191 3.27e-19 82.4
Msa1408190 AT4G09650.1 29.333 150 99 3 87 230 52 200 5.44e-14 69.3

Find 55 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGGAAGAGAAATGAGATTT+TGG 0.211304 tig0023376:+42167 None:intergenic
ACTGAGTTTCTGCACACTTT+TGG 0.309140 tig0023376:+41683 None:intergenic
TCAGTGGTGCAGTGAGGGTT+AGG 0.341774 tig0023376:-41665 Msa1408190:CDS
ATGTGGAACTCAAGTTGTTT+TGG 0.349249 tig0023376:-41751 Msa1408190:CDS
ATGGTTTGTGTTTGAGAGGT+TGG 0.358792 tig0023376:+42078 None:intergenic
ATTGGTGAAGATGAAATGTT+TGG 0.381129 tig0023376:-41711 Msa1408190:CDS
TGGTTTGTGTTTGAGAGGTT+GGG 0.403119 tig0023376:+42079 None:intergenic
TTTGAGAGGTTGGGTCTTTG+AGG 0.403625 tig0023376:+42088 None:intergenic
GCAGCAGCATAGCCAGTAGC+AGG 0.415721 tig0023376:+42029 None:intergenic
TGAAGGGCATGTGGTTGGTT+TGG 0.422427 tig0023376:-41853 Msa1408190:CDS
TGTTGGTGTTGACCCTTCAT+TGG 0.430284 tig0023376:-41904 Msa1408190:CDS
TTGAGAGGTTGGGTCTTTGA+GGG 0.430753 tig0023376:+42089 None:intergenic
ACCACCTTCCTCACCAATGA+AGG 0.445507 tig0023376:+41891 None:intergenic
TTGTGAAGTGATAGAATTCA+CGG 0.447151 tig0023376:+42231 None:intergenic
CACCCTTCCCTCGGTTCAAA+GGG 0.453751 tig0023376:-41979 Msa1408190:CDS
TTCCATCACAAGCCTGCTAC+TGG 0.468777 tig0023376:-42041 Msa1408190:CDS
TTGGTTGTTGAGGATGAGAA+GGG 0.471694 tig0023376:+42186 None:intergenic
TTTGGTTGTTGAGGATGAGA+AGG 0.473648 tig0023376:+42185 None:intergenic
ACACCCTTCCCTCGGTTCAA+AGG 0.483662 tig0023376:-41980 Msa1408190:CDS
TAGAATTCACGGTTGGTTGT+TGG 0.484183 tig0023376:+42242 None:intergenic
TTGGTGAAGATGAAATGTTT+GGG 0.494512 tig0023376:-41710 Msa1408190:CDS
CAGTGGTGCAGTGAGGGTTA+GGG 0.506987 tig0023376:-41664 Msa1408190:CDS
TTGAACCGAGGGAAGGGTGT+TGG 0.514330 tig0023376:+41983 None:intergenic
TGGGTCTTTGAGGGTAGTGA+AGG 0.516568 tig0023376:+42098 None:intergenic
AATTCACGGTTGGTTGTTGG+TGG 0.518266 tig0023376:+42245 None:intergenic
AGCCAGTAGCAGGCTTGTGA+TGG 0.522904 tig0023376:+42039 None:intergenic
AGGATTTATGATGAATTATG+TGG 0.523605 tig0023376:-41768 Msa1408190:CDS
GAAGATGGTTTGTGTTTGAG+AGG 0.530277 tig0023376:+42074 None:intergenic
TGGAATACTTGAGAAGAAGA+TGG 0.533703 tig0023376:+42059 None:intergenic
AAATTTGAAGGGCATGTGGT+TGG 0.536206 tig0023376:-41858 Msa1408190:CDS
AAGTGTTGGAAGAGTTCATG+AGG 0.536714 tig0023376:-41788 Msa1408190:CDS
TGACCCTTCATTGGTGAGGA+AGG 0.538931 tig0023376:-41895 Msa1408190:CDS
GTGGAGCAGAGAAAATTTGA+AGG 0.540648 tig0023376:-41870 Msa1408190:CDS
GGGAATTGTTGAGGAAGTGT+TGG 0.544791 tig0023376:-41802 Msa1408190:CDS
ATCCCTTTGAACCGAGGGAA+GGG 0.545984 tig0023376:+41977 None:intergenic
GCTGATGAAGAAGAACAAGC+TGG 0.546081 tig0023376:-41823 Msa1408190:CDS
AAATTTCAATCAGTTGATGT+TGG 0.559351 tig0023376:-41921 Msa1408190:CDS
GAAACTCAGTGGTGCAGTGA+GGG 0.562635 tig0023376:-41670 Msa1408190:CDS
AGAGCTTGAGAAAGCATCCA+TGG 0.563193 tig0023376:+42286 None:intergenic
ATTCACGGTTGGTTGTTGGT+GGG 0.565174 tig0023376:+42246 None:intergenic
TTCATTGGTGAGGAAGGTGG+TGG 0.567833 tig0023376:-41889 Msa1408190:CDS
CATCCCTTTGAACCGAGGGA+AGG 0.585509 tig0023376:+41976 None:intergenic
CCCTTCATTGGTGAGGAAGG+TGG 0.586166 tig0023376:-41892 Msa1408190:CDS
CTGATGAAGAAGAACAAGCT+GGG 0.589597 tig0023376:-41822 Msa1408190:CDS
GAGAAAATTTGAAGGGCATG+TGG 0.597790 tig0023376:-41862 Msa1408190:CDS
TGAACATCCCTTTGAACCGA+GGG 0.602693 tig0023376:+41972 None:intergenic
GTGTTGACCCTTCATTGGTG+AGG 0.604863 tig0023376:-41899 Msa1408190:CDS
TTGAACATCCCTTTGAACCG+AGG 0.616637 tig0023376:+41971 None:intergenic
GAAGGGTTTGCAGTTGCATG+AGG 0.616977 tig0023376:+42203 None:intergenic
GAACAAGCTGGGAATTGTTG+AGG 0.625515 tig0023376:-41811 Msa1408190:CDS
CCACCTTCCTCACCAATGAA+GGG 0.627070 tig0023376:+41892 None:intergenic
GAAGTGATAGAATTCACGGT+TGG 0.666630 tig0023376:+42235 None:intergenic
TGGAGCAGAGAAAATTTGAA+GGG 0.672649 tig0023376:-41869 Msa1408190:CDS
AGAAACTCAGTGGTGCAGTG+AGG 0.695602 tig0023376:-41671 Msa1408190:CDS
AAAAGTGTGCAGAAACTCAG+TGG 0.740335 tig0023376:-41681 Msa1408190:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAGAAAGTTTTTGTTTTTT+GGG + tig0023376:41765-41784 None:intergenic 20.0%
!!! GTGAGAAAGTTTTTGTTTTT+TGG + tig0023376:41766-41785 None:intergenic 25.0%
!!! ATTGAAATTTCAGTTTTTGG+AGG + tig0023376:41967-41986 None:intergenic 25.0%
!! CTGATTGAAATTTCAGTTTT+TGG + tig0023376:41970-41989 None:intergenic 25.0%
!! AAATTTCAATCAGTTGATGT+TGG - tig0023376:41977-41996 Msa1408190:CDS 25.0%
! AGGATTTATGATGAATTATG+TGG - tig0023376:42130-42149 Msa1408190:CDS 25.0%
! GTTTCATCAAAAAGAGAAAT+TGG - tig0023376:42169-42188 Msa1408190:CDS 25.0%
TTGTGAAGTGATAGAATTCA+CGG + tig0023376:41670-41689 None:intergenic 30.0%
!!! AAATGAGATTTTGGTTGTTG+AGG + tig0023376:41725-41744 None:intergenic 30.0%
! TTGGAAGAGAAATGAGATTT+TGG + tig0023376:41734-41753 None:intergenic 30.0%
ATTGGTGAAGATGAAATGTT+TGG - tig0023376:42187-42206 Msa1408190:CDS 30.0%
TTGGTGAAGATGAAATGTTT+GGG - tig0023376:42188-42207 Msa1408190:CDS 30.0%
!!! TGTTTTTTGGGTGACTAAGT+TGG + tig0023376:41753-41772 None:intergenic 35.0%
TGGAATACTTGAGAAGAAGA+TGG + tig0023376:41842-41861 None:intergenic 35.0%
TGGAGCAGAGAAAATTTGAA+GGG - tig0023376:42029-42048 Msa1408190:CDS 35.0%
!! ATGTGGAACTCAAGTTGTTT+TGG - tig0023376:42147-42166 Msa1408190:CDS 35.0%
GAGGGTTAGGGTTAAAAATT+TGG - tig0023376:42246-42265 Msa1408190:CDS 35.0%
! TAGAATTCACGGTTGGTTGT+TGG + tig0023376:41659-41678 None:intergenic 40.0%
GAAGTGATAGAATTCACGGT+TGG + tig0023376:41666-41685 None:intergenic 40.0%
TTGGTTGTTGAGGATGAGAA+GGG + tig0023376:41715-41734 None:intergenic 40.0%
TTTGGTTGTTGAGGATGAGA+AGG + tig0023376:41716-41735 None:intergenic 40.0%
! TGGTTTGTGTTTGAGAGGTT+GGG + tig0023376:41822-41841 None:intergenic 40.0%
! ATGGTTTGTGTTTGAGAGGT+TGG + tig0023376:41823-41842 None:intergenic 40.0%
! GAAGATGGTTTGTGTTTGAG+AGG + tig0023376:41827-41846 None:intergenic 40.0%
GTGGAGCAGAGAAAATTTGA+AGG - tig0023376:42028-42047 Msa1408190:CDS 40.0%
! GAGAAAATTTGAAGGGCATG+TGG - tig0023376:42036-42055 Msa1408190:CDS 40.0%
! AAATTTGAAGGGCATGTGGT+TGG - tig0023376:42040-42059 Msa1408190:CDS 40.0%
CTGATGAAGAAGAACAAGCT+GGG - tig0023376:42076-42095 Msa1408190:CDS 40.0%
!! AAGTGTTGGAAGAGTTCATG+AGG - tig0023376:42110-42129 Msa1408190:CDS 40.0%
! ACTGAGTTTCTGCACACTTT+TGG + tig0023376:42218-42237 None:intergenic 40.0%
! AAAAGTGTGCAGAAACTCAG+TGG - tig0023376:42217-42236 Msa1408190:CDS 40.0%
!! GGTTGTTGGTGGGATTTTGA+GGG + tig0023376:41645-41664 None:intergenic 45.0%
!! TGGTTGTTGGTGGGATTTTG+AGG + tig0023376:41646-41665 None:intergenic 45.0%
! ATTCACGGTTGGTTGTTGGT+GGG + tig0023376:41655-41674 None:intergenic 45.0%
! AATTCACGGTTGGTTGTTGG+TGG + tig0023376:41656-41675 None:intergenic 45.0%
TTGAGAGGTTGGGTCTTTGA+GGG + tig0023376:41812-41831 None:intergenic 45.0%
TTTGAGAGGTTGGGTCTTTG+AGG + tig0023376:41813-41832 None:intergenic 45.0%
AAAAACCAACACCCTTCCCT+CGG - tig0023376:41910-41929 Msa1408190:CDS 45.0%
TGAACATCCCTTTGAACCGA+GGG + tig0023376:41929-41948 None:intergenic 45.0%
TTGAACATCCCTTTGAACCG+AGG + tig0023376:41930-41949 None:intergenic 45.0%
!! TGTTGGTGTTGACCCTTCAT+TGG - tig0023376:41994-42013 Msa1408190:CDS 45.0%
GCTGATGAAGAAGAACAAGC+TGG - tig0023376:42075-42094 Msa1408190:CDS 45.0%
GAACAAGCTGGGAATTGTTG+AGG - tig0023376:42087-42106 Msa1408190:CDS 45.0%
! GGGAATTGTTGAGGAAGTGT+TGG - tig0023376:42096-42115 Msa1408190:CDS 45.0%
GAAGGGTTTGCAGTTGCATG+AGG + tig0023376:41698-41717 None:intergenic 50.0%
! TGGGTCTTTGAGGGTAGTGA+AGG + tig0023376:41803-41822 None:intergenic 50.0%
TTCCATCACAAGCCTGCTAC+TGG - tig0023376:41857-41876 Msa1408190:CDS 50.0%
ATCCCTTTGAACCGAGGGAA+GGG + tig0023376:41924-41943 None:intergenic 50.0%
! GTGTTGACCCTTCATTGGTG+AGG - tig0023376:41999-42018 Msa1408190:CDS 50.0%
TGACCCTTCATTGGTGAGGA+AGG - tig0023376:42003-42022 Msa1408190:CDS 50.0%
CCACCTTCCTCACCAATGAA+GGG + tig0023376:42009-42028 None:intergenic 50.0%
ACCACCTTCCTCACCAATGA+AGG + tig0023376:42010-42029 None:intergenic 50.0%
TTCATTGGTGAGGAAGGTGG+TGG - tig0023376:42009-42028 Msa1408190:CDS 50.0%
! TGAAGGGCATGTGGTTGGTT+TGG - tig0023376:42045-42064 Msa1408190:CDS 50.0%
AGAAACTCAGTGGTGCAGTG+AGG - tig0023376:42227-42246 Msa1408190:CDS 50.0%
GAAACTCAGTGGTGCAGTGA+GGG - tig0023376:42228-42247 Msa1408190:CDS 50.0%
AGCCAGTAGCAGGCTTGTGA+TGG + tig0023376:41862-41881 None:intergenic 55.0%
! TTGAACCGAGGGAAGGGTGT+TGG + tig0023376:41918-41937 None:intergenic 55.0%
ACACCCTTCCCTCGGTTCAA+AGG - tig0023376:41918-41937 Msa1408190:CDS 55.0%
CACCCTTCCCTCGGTTCAAA+GGG - tig0023376:41919-41938 Msa1408190:CDS 55.0%
CATCCCTTTGAACCGAGGGA+AGG + tig0023376:41925-41944 None:intergenic 55.0%
CCCTTCATTGGTGAGGAAGG+TGG - tig0023376:42006-42025 Msa1408190:CDS 55.0%
TCAGTGGTGCAGTGAGGGTT+AGG - tig0023376:42233-42252 Msa1408190:CDS 55.0%
CAGTGGTGCAGTGAGGGTTA+GGG - tig0023376:42234-42253 Msa1408190:CDS 55.0%
GCAGCAGCATAGCCAGTAGC+AGG + tig0023376:41872-41891 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
tig0023376 gene 41614 42306 41614 ID=Msa1408190;Name=Msa1408190
tig0023376 mRNA 41614 42306 41614 ID=Msa1408190-mRNA-1;Parent=Msa1408190;Name=Msa1408190-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|230
tig0023376 exon 41614 42306 41614 ID=Msa1408190-mRNA-1:exon:25499;Parent=Msa1408190-mRNA-1
tig0023376 CDS 41614 42306 41614 ID=Msa1408190-mRNA-1:cds;Parent=Msa1408190-mRNA-1
Gene Sequence

>Msa1408190

ATGGATGCTTTCTCAAGCTCTGTTTCAACCCTCAAAATCCCACCAACAACCAACCGTGAATTCTATCACTTCACAAGAACTCCTCATGCAACTGCAAACCCTTCTCATCCTCAACAACCAAAATCTCATTTCTCTTCCAACTTAGTCACCCAAAAAACAAAAACTTTCTCACACAACAATCATTCTCCTTCACTACCCTCAAAGACCCAACCTCTCAAACACAAACCATCTTCTTCTCAAGTATTCCATCACAAGCCTGCTACTGGCTATGCTGCTGCAATCATAGATGTAGCTCAAAAAACCAACACCCTTCCCTCGGTTCAAAGGGATGTTCAAAGACTCTTGAAGTTCCTCCAAAAACTGAAATTTCAATCAGTTGATGTTGGTGTTGACCCTTCATTGGTGAGGAAGGTGGTGGAGCAGAGAAAATTTGAAGGGCATGTGGTTGGTTTGGTGAAGATGCTGATGAAGAAGAACAAGCTGGGAATTGTTGAGGAAGTGTTGGAAGAGTTCATGAGGATTTATGATGAATTATGTGGAACTCAAGTTGTTTTGGTTTCATCAAAAAGAGAAATTGGTGAAGATGAAATGTTTGGGATTGCCAAAAGTGTGCAGAAACTCAGTGGTGCAGTGAGGGTTAGGGTTAAAAATTTGGTTCAAGAAGAGAGTTTTCCTTCTTCTTTTGCAGTGTAA

Protein sequence

>Msa1408190

MDAFSSSVSTLKIPPTTNREFYHFTRTPHATANPSHPQQPKSHFSSNLVTQKTKTFSHNNHSPSLPSKTQPLKHKPSSSQVFHHKPATGYAAAIIDVAQKTNTLPSVQRDVQRLLKFLQKLKFQSVDVGVDPSLVRKVVEQRKFEGHVVGLVKMLMKKNKLGIVEEVLEEFMRIYDELCGTQVVLVSSKREIGEDEMFGIAKSVQKLSGAVRVRVKNLVQEESFPSSFAV*