AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0343850


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0343850 MtrunA17_Chr4g0068751 96.703 182 6 0 1 182 1 182 2.84e-130 362
Msa0343850 MtrunA17_Chr4g0068711 48.352 182 85 2 1 182 1 173 1.34e-55 173
Msa0343850 MtrunA17_Chr4g0068791 43.716 183 94 3 1 182 1 175 4.52e-47 152
Msa0343850 MtrunA17_Chr4g0068731 43.713 167 87 3 15 177 8 171 6.52e-42 138
Msa0343850 MtrunA17_Chr4g0001591 50.926 108 51 2 77 182 1 108 6.18e-27 98.6
Msa0343850 MtrunA17_Chr2g0294121 31.429 175 107 3 12 182 11 176 1.39e-19 81.3
Msa0343850 MtrunA17_Chr4g0068651 28.649 185 117 7 5 182 3 179 3.27e-18 78.2
Msa0343850 MtrunA17_Chr4g0068701 30.939 181 116 4 5 182 3 177 3.29e-16 72.4
Msa0343850 MtrunA17_Chr2g0294161 29.480 173 103 5 22 181 20 186 2.33e-12 62.8
Msa0343850 MtrunA17_Chr4g0068681 27.397 146 102 2 41 182 40 185 3.03e-12 63.9
Msa0343850 MtrunA17_Chr4g0068681 27.778 144 101 2 41 182 231 373 1.14e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0343850 AT1G47960.2 46.154 143 77 0 40 182 24 166 2.71e-40 134
Msa0343850 AT1G47960.1 44.928 138 76 0 40 177 24 161 9.24e-37 127
Msa0343850 AT3G17140.1 36.842 95 58 2 89 182 19 112 7.92e-14 65.1
Msa0343850 AT3G17150.1 26.573 143 103 1 42 182 39 181 3.24e-11 59.7

Find 32 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAAGGCAAACATTGTAATT+TGG 0.270319 3_1:+2268499 None:intergenic
CAGTCTTTGAAGGCATATTC+TGG 0.284723 3_1:-2268478 Msa0343850:CDS
ACCTCTGCTGGTGATGTAAC+AGG 0.308788 3_1:-2268454 Msa0343850:CDS
GTACTTCTGCTTTGGATTGT+TGG 0.314380 3_1:+2268580 None:intergenic
GGAAATTAGTACTTCTGCTT+TGG 0.322491 3_1:+2268572 None:intergenic
ACCTCAAGCTATTGAAGCTT+TGG 0.326895 3_1:-2268284 Msa0343850:CDS
CACCATCTTCTGCAAACTTA+GGG 0.376121 3_1:+2268251 None:intergenic
GCACCATCTTCTGCAAACTT+AGG 0.382996 3_1:+2268250 None:intergenic
TTCTCAACCTTTGTAGCTGG+TGG 0.401916 3_1:+2268371 None:intergenic
GCTATTGAAGCTTTGGAGAA+AGG 0.407146 3_1:-2268277 Msa0343850:CDS
CATTTCTCAACCTTTGTAGC+TGG 0.408972 3_1:+2268368 None:intergenic
CTATTGAAGCTTTGGAGAAA+GGG 0.422212 3_1:-2268276 Msa0343850:CDS
TGTTTGCCTTCAGTCTTTGA+AGG 0.426146 3_1:-2268488 Msa0343850:CDS
AGGAATAAGCAAAGAGTTTG+AGG 0.444609 3_1:+2268631 None:intergenic
ATTGTGAGAGTGAGTTCAAT+GGG 0.471484 3_1:-2268201 Msa0343850:CDS
GCATATTCTGGTACCTCTGC+TGG 0.484173 3_1:-2268466 Msa0343850:CDS
CAGCTACAAAGGTTGAGAAA+TGG 0.491946 3_1:-2268367 Msa0343850:CDS
TTATGATAACAATAGCTTGA+AGG 0.497754 3_1:+2268611 None:intergenic
GACCCTAAGTTTGCAGAAGA+TGG 0.509313 3_1:-2268253 Msa0343850:CDS
AAGTACTAATTTCCATTCAA+AGG 0.510612 3_1:-2268563 Msa0343850:CDS
TATTGTGAGAGTGAGTTCAA+TGG 0.517229 3_1:-2268202 Msa0343850:CDS
AGGAAAGCTTTGAGTTCTTG+TGG 0.532829 3_1:-2268340 Msa0343850:CDS
TCCAAAGCTTCAATAGCTTG+AGG 0.539762 3_1:+2268283 None:intergenic
AAAGGTTGAGAAATGGAGCT+AGG 0.556772 3_1:-2268360 Msa0343850:CDS
TGCAAATGATGCTGCTAATG+AGG 0.560849 3_1:-2268230 Msa0343850:CDS
AACAGGGCTAGCACAAATCA+TGG 0.565524 3_1:-2268437 Msa0343850:CDS
ATAGAATCCACCAGCTACAA+AGG 0.567634 3_1:-2268378 Msa0343850:CDS
TATTGAAGCTTTGGAGAAAG+GGG 0.591796 3_1:-2268275 Msa0343850:CDS
CCCTGTTACATCACCAGCAG+AGG 0.602085 3_1:+2268453 None:intergenic
CCTCTGCTGGTGATGTAACA+GGG 0.604777 3_1:-2268453 Msa0343850:CDS
AATATGCCTTCAAAGACTGA+AGG 0.626365 3_1:+2268482 None:intergenic
ATGAAAGCAAAAGCAAACGA+TGG 0.653893 3_1:-2268406 Msa0343850:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTATGATAACAATAGCTTGA+AGG + chr3_1:2268158-2268177 None:intergenic 25.0%
! AAGTACTAATTTCCATTCAA+AGG - chr3_1:2268203-2268222 Msa0343850:CDS 25.0%
!! ATAGTTTTTCATCCTTTGAA+TGG + chr3_1:2268218-2268237 None:intergenic 25.0%
TGAAGGCAAACATTGTAATT+TGG + chr3_1:2268270-2268289 None:intergenic 30.0%
AGGAATAAGCAAAGAGTTTG+AGG + chr3_1:2268138-2268157 None:intergenic 35.0%
GGAAATTAGTACTTCTGCTT+TGG + chr3_1:2268197-2268216 None:intergenic 35.0%
AATATGCCTTCAAAGACTGA+AGG + chr3_1:2268287-2268306 None:intergenic 35.0%
ATGAAAGCAAAAGCAAACGA+TGG - chr3_1:2268360-2268379 Msa0343850:CDS 35.0%
!! CTATTGAAGCTTTGGAGAAA+GGG - chr3_1:2268490-2268509 Msa0343850:CDS 35.0%
!! TATTGAAGCTTTGGAGAAAG+GGG - chr3_1:2268491-2268510 Msa0343850:CDS 35.0%
TATTGTGAGAGTGAGTTCAA+TGG - chr3_1:2268564-2268583 Msa0343850:CDS 35.0%
ATTGTGAGAGTGAGTTCAAT+GGG - chr3_1:2268565-2268584 Msa0343850:CDS 35.0%
! GTACTTCTGCTTTGGATTGT+TGG + chr3_1:2268189-2268208 None:intergenic 40.0%
TGTTTGCCTTCAGTCTTTGA+AGG - chr3_1:2268278-2268297 Msa0343850:CDS 40.0%
! CAGTCTTTGAAGGCATATTC+TGG - chr3_1:2268288-2268307 Msa0343850:CDS 40.0%
ATAGAATCCACCAGCTACAA+AGG - chr3_1:2268388-2268407 Msa0343850:CDS 40.0%
CATTTCTCAACCTTTGTAGC+TGG + chr3_1:2268401-2268420 None:intergenic 40.0%
CAGCTACAAAGGTTGAGAAA+TGG - chr3_1:2268399-2268418 Msa0343850:CDS 40.0%
AAAGGTTGAGAAATGGAGCT+AGG - chr3_1:2268406-2268425 Msa0343850:CDS 40.0%
!! AGGAAAGCTTTGAGTTCTTG+TGG - chr3_1:2268426-2268445 Msa0343850:CDS 40.0%
ACCTCAAGCTATTGAAGCTT+TGG - chr3_1:2268482-2268501 Msa0343850:CDS 40.0%
TCCAAAGCTTCAATAGCTTG+AGG + chr3_1:2268486-2268505 None:intergenic 40.0%
!! GCTATTGAAGCTTTGGAGAA+AGG - chr3_1:2268489-2268508 Msa0343850:CDS 40.0%
CACCATCTTCTGCAAACTTA+GGG + chr3_1:2268518-2268537 None:intergenic 40.0%
TGCAAATGATGCTGCTAATG+AGG - chr3_1:2268536-2268555 Msa0343850:CDS 40.0%
! GCATTGTTCTGTTTTGTGAG+TGG + chr3_1:2268597-2268616 None:intergenic 40.0%
! AACAGGGCTAGCACAAATCA+TGG - chr3_1:2268329-2268348 Msa0343850:CDS 45.0%
TTCTCAACCTTTGTAGCTGG+TGG + chr3_1:2268398-2268417 None:intergenic 45.0%
GACCCTAAGTTTGCAGAAGA+TGG - chr3_1:2268513-2268532 Msa0343850:CDS 45.0%
GCACCATCTTCTGCAAACTT+AGG + chr3_1:2268519-2268538 None:intergenic 45.0%
GCATATTCTGGTACCTCTGC+TGG - chr3_1:2268300-2268319 Msa0343850:CDS 50.0%
! ACCTCTGCTGGTGATGTAAC+AGG - chr3_1:2268312-2268331 Msa0343850:CDS 50.0%
! CCTCTGCTGGTGATGTAACA+GGG - chr3_1:2268313-2268332 Msa0343850:CDS 50.0%
CCCTGTTACATCACCAGCAG+AGG + chr3_1:2268316-2268335 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 2268120 2268668 2268120 ID=Msa0343850;Name=Msa0343850
chr3_1 mRNA 2268120 2268668 2268120 ID=Msa0343850-mRNA-1;Parent=Msa0343850;Name=Msa0343850-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|182
chr3_1 exon 2268120 2268668 2268120 ID=Msa0343850-mRNA-1:exon:691;Parent=Msa0343850-mRNA-1
chr3_1 CDS 2268120 2268668 2268120 ID=Msa0343850-mRNA-1:cds;Parent=Msa0343850-mRNA-1
Gene Sequence

>Msa0343850

ATGACAAATTTTAAGCCTCAAACTCTTTGCTTATTCCTTCAAGCTATTGTTATCATAATTTCAATACCAACAATCCAAAGCAGAAGTACTAATTTCCATTCAAAGGATGAAAAACTATCACTCATAGAAAACACTTGCAAAAAAACACCAAATTACAATGTTTGCCTTCAGTCTTTGAAGGCATATTCTGGTACCTCTGCTGGTGATGTAACAGGGCTAGCACAAATCATGGTGAAAGTGATGAAAGCAAAAGCAAACGATGGATTAAATAGAATCCACCAGCTACAAAGGTTGAGAAATGGAGCTAGGAAAGCTTTGAGTTCTTGTGGTGACAAATACAGAGCAATTTTGATAGCTGATATACCTCAAGCTATTGAAGCTTTGGAGAAAGGGGACCCTAAGTTTGCAGAAGATGGTGCAAATGATGCTGCTAATGAGGCTACTTATTGTGAGAGTGAGTTCAATGGGAAATCTCCACTCACAAAACAGAACAATGCTATGCATGATGTTTCAGCTGTTACATCATCTATTGTTAGACAATTACTCTAG

Protein sequence

>Msa0343850

MTNFKPQTLCLFLQAIVIIISIPTIQSRSTNFHSKDEKLSLIENTCKKTPNYNVCLQSLKAYSGTSAGDVTGLAQIMVKVMKAKANDGLNRIHQLQRLRNGARKALSSCGDKYRAILIADIPQAIEALEKGDPKFAEDGANDAANEATYCESEFNGKSPLTKQNNAMHDVSAVTSSIVRQLL*