AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1388690


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1388690 MtrunA17_Chr7g0273661 97.436 156 4 0 1 156 1 156 3.25e-112 316
Msa1388690 MtrunA17_Chr7g0223361 58.523 176 72 1 1 176 1 175 3.21e-71 213
Msa1388690 MtrunA17_Chr7g0223351 60.920 174 66 2 1 174 1 172 3.23e-67 203
Msa1388690 MtrunA17_Chr1g0204971 46.784 171 86 2 4 171 19 187 5.09e-48 154
Msa1388690 MtrunA17_Chr1g0204951 45.614 171 88 2 4 171 19 187 5.57e-47 152
Msa1388690 MtrunA17_Chr5g0394621 42.442 172 96 1 3 171 16 187 1.15e-46 151
Msa1388690 MtrunA17_Chr5g0394631 43.030 165 91 1 4 165 17 181 7.54e-43 147
Msa1388690 MtrunA17_Chr5g0394631 43.429 175 90 5 4 171 226 398 2.80e-39 138
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1388690 AT3G22560.1 55.422 166 72 1 8 171 7 172 1.01e-63 194
Msa1388690 AT2G32030.1 47.305 167 84 2 8 173 24 187 4.95e-57 178
Msa1388690 AT2G32020.1 47.701 174 87 2 1 173 12 182 1.22e-56 177

Find 42 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGTTGCTTCTAACTATT+GGG 0.152318 tig0021157:+69673 Msa1388690:CDS
TTCTGATTTGTTAAGGTTGC+AGG 0.201561 tig0021157:+69754 Msa1388690:CDS
ATGCTGTTGCTTCTAACTAT+TGG 0.211993 tig0021157:+69672 Msa1388690:CDS
CAAGGCTTCTCAAAGAGTTT+TGG 0.245031 tig0021157:+69796 Msa1388690:CDS
AGACATCTTTGATGAAAGTT+AGG 0.305845 tig0021157:-69541 None:intergenic
CAAAGGTACCATCATGGATT+TGG 0.335385 tig0021157:+69868 Msa1388690:CDS
AATAGATCATAAAGAGTAAC+AGG 0.344936 tig0021157:-69945 None:intergenic
CGTTGACGATTTCATGTTAT+GGG 0.361603 tig0021157:+69457 Msa1388690:CDS
TTCTAAGAACACCCTCTCTA+AGG 0.383141 tig0021157:-69832 None:intergenic
ACGTTGACGATTTCATGTTA+TGG 0.384226 tig0021157:+69456 Msa1388690:CDS
TCAACGTCTGTTAGCTTGAA+TGG 0.418956 tig0021157:-69440 None:intergenic
GTTTCTGTGTATCCTTGGTC+AGG 0.429314 tig0021157:+69620 Msa1388690:CDS
GACGATTTCATGTTATGGGC+AGG 0.454598 tig0021157:+69461 Msa1388690:CDS
GACATCTTTGATGAAAGTTA+GGG 0.457791 tig0021157:-69540 None:intergenic
CAGGAGACAAAATAATCAAC+AGG 0.459432 tig0021157:-69926 None:intergenic
TGGCAAAGGTGGATCTATCT+AGG 0.472926 tig0021157:+69405 Msa1388690:CDS
CGATTTCATGTTATGGGCAG+GGG 0.502678 tig0021157:+69463 Msa1388690:CDS
GCTTCTAACTATTGGGGTCA+AGG 0.506483 tig0021157:+69680 Msa1388690:CDS
ATCGAATGACGCCAAGGGTG+AGG 0.527528 tig0021157:-69569 None:intergenic
TGTCTCGACGACCGTTCCAT+CGG 0.528351 tig0021157:+69593 Msa1388690:CDS
GCTGTTGCTTCTAACTATTG+GGG 0.550437 tig0021157:+69674 Msa1388690:CDS
AGAAAGTATACTTATATCAA+AGG 0.562044 tig0021157:+69851 Msa1388690:CDS
CTTCTAACTATTGGGGTCAA+GGG 0.563961 tig0021157:+69681 Msa1388690:CDS
TTTGACCAACATGGCAAAGG+TGG 0.564105 tig0021157:+69394 None:intergenic
ATCCTTGGTCAGGTGATGAT+AGG 0.566062 tig0021157:+69630 Msa1388690:CDS
GATGGAAAACTTGCAATTCG+AGG 0.572925 tig0021157:+69510 Msa1388690:CDS
ACGATTTCATGTTATGGGCA+GGG 0.580454 tig0021157:+69462 Msa1388690:CDS
GATAGGTGCAAAGCTGACAT+AGG 0.586688 tig0021157:+69647 Msa1388690:CDS
ATGGAAAACTTGCAATTCGA+GGG 0.591968 tig0021157:+69511 Msa1388690:CDS
ATGTCTGCATACCTCACCCT+TGG 0.593939 tig0021157:+69558 Msa1388690:CDS
TTATATCAAAGGTACCATCA+TGG 0.596125 tig0021157:+69862 Msa1388690:CDS
AGACAGATCGAATGACGCCA+AGG 0.596639 tig0021157:-69575 None:intergenic
TCATTTGACCAACATGGCAA+AGG 0.601751 tig0021157:+69391 None:intergenic
AAAGGCTGGGTTCCTTAGAG+AGG 0.612674 tig0021157:+69820 Msa1388690:CDS
ATACACAGAAACAAAACCGA+TGG 0.615405 tig0021157:-69609 None:intergenic
AAAGACAGCCAAATCCATGA+TGG 0.623533 tig0021157:-69876 None:intergenic
GACAGATCGAATGACGCCAA+GGG 0.628805 tig0021157:-69574 None:intergenic
CAGAAACAAAACCGATGGAA+CGG 0.641063 tig0021157:-69604 None:intergenic
AAGGCTGGGTTCCTTAGAGA+GGG 0.646930 tig0021157:+69821 Msa1388690:CDS
GAGACAAAATAATCAACAGG+AGG 0.670315 tig0021157:-69923 None:intergenic
CACCTATCATCACCTGACCA+AGG 0.677858 tig0021157:-69632 None:intergenic
ATCTATCTAGGATATCTCTG+AGG 0.735761 tig0021157:+69417 Msa1388690:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGATTTTTCTGATTTGTTA+AGG + tig0021157:69747-69766 Msa1388690:CDS 20.0%
!!! AGAAAGTATACTTATATCAA+AGG + tig0021157:69851-69870 Msa1388690:CDS 20.0%
GACATCTTTGATGAAAGTTA+GGG - tig0021157:69543-69562 None:intergenic 30.0%
AGACATCTTTGATGAAAGTT+AGG - tig0021157:69544-69563 None:intergenic 30.0%
!!! AGCAATTTTGATTGCTTTTG+TGG - tig0021157:69711-69730 None:intergenic 30.0%
! TTTTACTTACGTGGATAACA+AGG + tig0021157:69778-69797 Msa1388690:CDS 30.0%
!!! TTCTCAAAGAGTTTTGGAAA+AGG + tig0021157:69802-69821 Msa1388690:CDS 30.0%
!! TTATATCAAAGGTACCATCA+TGG + tig0021157:69862-69881 Msa1388690:CDS 30.0%
! ATCTATCTAGGATATCTCTG+AGG + tig0021157:69417-69436 Msa1388690:CDS 35.0%
ACGTTGACGATTTCATGTTA+TGG + tig0021157:69456-69475 Msa1388690:CDS 35.0%
CGTTGACGATTTCATGTTAT+GGG + tig0021157:69457-69476 Msa1388690:CDS 35.0%
AAGTAACCAAAAACATCCGA+TGG + tig0021157:69492-69511 Msa1388690:CDS 35.0%
! AGTTTTCCATCGGATGTTTT+TGG - tig0021157:69501-69520 None:intergenic 35.0%
! TCGAATTGCAAGTTTTCCAT+CGG - tig0021157:69511-69530 None:intergenic 35.0%
ATGGAAAACTTGCAATTCGA+GGG + tig0021157:69511-69530 Msa1388690:CDS 35.0%
ATACACAGAAACAAAACCGA+TGG - tig0021157:69612-69631 None:intergenic 35.0%
!!! GTTTTGTTTCTGTGTATCCT+TGG + tig0021157:69615-69634 Msa1388690:CDS 35.0%
! ATGCTGTTGCTTCTAACTAT+TGG + tig0021157:69672-69691 Msa1388690:CDS 35.0%
! TGCTGTTGCTTCTAACTATT+GGG + tig0021157:69673-69692 Msa1388690:CDS 35.0%
!! TTCTGATTTGTTAAGGTTGC+AGG + tig0021157:69754-69773 Msa1388690:CDS 35.0%
!!! AAAGAGTTTTGGAAAAGGCT+GGG + tig0021157:69807-69826 Msa1388690:CDS 35.0%
GAGACAAAATAATCAACAGG+AGG - tig0021157:69926-69945 None:intergenic 35.0%
CAGGAGACAAAATAATCAAC+AGG - tig0021157:69929-69948 None:intergenic 35.0%
! TCAACGTCTGTTAGCTTGAA+TGG - tig0021157:69443-69462 None:intergenic 40.0%
ACGATTTCATGTTATGGGCA+GGG + tig0021157:69462-69481 Msa1388690:CDS 40.0%
GATGGAAAACTTGCAATTCG+AGG + tig0021157:69510-69529 Msa1388690:CDS 40.0%
CAGAAACAAAACCGATGGAA+CGG - tig0021157:69607-69626 None:intergenic 40.0%
! GCTGTTGCTTCTAACTATTG+GGG + tig0021157:69674-69693 Msa1388690:CDS 40.0%
CTTCTAACTATTGGGGTCAA+GGG + tig0021157:69681-69700 Msa1388690:CDS 40.0%
! CAAGGCTTCTCAAAGAGTTT+TGG + tig0021157:69796-69815 Msa1388690:CDS 40.0%
!!! CAAAGAGTTTTGGAAAAGGC+TGG + tig0021157:69806-69825 Msa1388690:CDS 40.0%
! TTCTAAGAACACCCTCTCTA+AGG - tig0021157:69835-69854 None:intergenic 40.0%
!! CAAAGGTACCATCATGGATT+TGG + tig0021157:69868-69887 Msa1388690:CDS 40.0%
AAAGACAGCCAAATCCATGA+TGG - tig0021157:69879-69898 None:intergenic 40.0%
TGGCAAAGGTGGATCTATCT+AGG + tig0021157:69405-69424 Msa1388690:CDS 45.0%
GACGATTTCATGTTATGGGC+AGG + tig0021157:69461-69480 Msa1388690:CDS 45.0%
CGATTTCATGTTATGGGCAG+GGG + tig0021157:69463-69482 Msa1388690:CDS 45.0%
GTTTCTGTGTATCCTTGGTC+AGG + tig0021157:69620-69639 Msa1388690:CDS 45.0%
ATCCTTGGTCAGGTGATGAT+AGG + tig0021157:69630-69649 Msa1388690:CDS 45.0%
GATAGGTGCAAAGCTGACAT+AGG + tig0021157:69647-69666 Msa1388690:CDS 45.0%
GCTTCTAACTATTGGGGTCA+AGG + tig0021157:69680-69699 Msa1388690:CDS 45.0%
! GTTGCAGGCTTTTACTTACG+TGG + tig0021157:69769-69788 Msa1388690:CDS 45.0%
ATGTCTGCATACCTCACCCT+TGG + tig0021157:69558-69577 Msa1388690:CDS 50.0%
GACAGATCGAATGACGCCAA+GGG - tig0021157:69577-69596 None:intergenic 50.0%
AGACAGATCGAATGACGCCA+AGG - tig0021157:69578-69597 None:intergenic 50.0%
CACCTATCATCACCTGACCA+AGG - tig0021157:69635-69654 None:intergenic 50.0%
AAAGGCTGGGTTCCTTAGAG+AGG + tig0021157:69820-69839 Msa1388690:CDS 50.0%
AAGGCTGGGTTCCTTAGAGA+GGG + tig0021157:69821-69840 Msa1388690:CDS 50.0%
ATCGAATGACGCCAAGGGTG+AGG - tig0021157:69572-69591 None:intergenic 55.0%
TGTCTCGACGACCGTTCCAT+CGG + tig0021157:69593-69612 Msa1388690:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0021157 gene 69404 69961 69404 ID=Msa1388690;Name=Msa1388690
tig0021157 mRNA 69404 69961 69404 ID=Msa1388690-mRNA-1;Parent=Msa1388690;Name=Msa1388690-mRNA-1;_AED=0.05;_eAED=0.05;_QI=0|-1|0|1|-1|1|1|0|185
tig0021157 exon 69404 69961 69404 ID=Msa1388690-mRNA-1:exon:11238;Parent=Msa1388690-mRNA-1
tig0021157 CDS 69404 69961 69404 ID=Msa1388690-mRNA-1:cds;Parent=Msa1388690-mRNA-1
Gene Sequence

>Msa1388690

ATGGCAAAGGTGGATCTATCTAGGATATCTCTGAGGCCATTCAAGCTAACAGACGTTGACGATTTCATGTTATGGGCAGGGGACGATGAAGTAACCAAAAACATCCGATGGAAAACTTGCAATTCGAGGGAAGAAGCCCTAACTTTCATCAAAGATGTCTGCATACCTCACCCTTGGCGTCATTCGATCTGTCTCGACGACCGTTCCATCGGTTTTGTTTCTGTGTATCCTTGGTCAGGTGATGATAGGTGCAAAGCTGACATAGGTTATGCTGTTGCTTCTAACTATTGGGGTCAAGGGATAGCCACAAAAGCAATCAAAATTGCTCTGTCTCAAGTGTTTAATGATTTTTCTGATTTGTTAAGGTTGCAGGCTTTTACTTACGTGGATAACAAGGCTTCTCAAAGAGTTTTGGAAAAGGCTGGGTTCCTTAGAGAGGGTGTTCTTAGAAAGTATACTTATATCAAAGGTACCATCATGGATTTGGCTGTCTTTAGTTTTTTGTCAACAGATGAAATTCCTCCTGTTGATTATTTTGTCTCCTGTTACTCTTTATGA

Protein sequence

>Msa1388690

MAKVDLSRISLRPFKLTDVDDFMLWAGDDEVTKNIRWKTCNSREEALTFIKDVCIPHPWRHSICLDDRSIGFVSVYPWSGDDRCKADIGYAVASNYWGQGIATKAIKIALSQVFNDFSDLLRLQAFTYVDNKASQRVLEKAGFLREGVLRKYTYIKGTIMDLAVFSFLSTDEIPPVDYFVSCYSL*