AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0059890


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0059890 MtrunA17_Chr1g0159571 95.528 246 6 2 1 244 1 243 1.30e-171 473
Msa0059890 MtrunA17_Chr3g0125561 38.679 212 98 8 1 199 31 223 2.12e-23 95.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0059890 AT1G76980.1 40.609 197 88 9 26 204 13 198 1.10e-29 112
Msa0059890 AT1G76980.2 40.609 197 88 9 26 204 13 198 2.17e-29 111
Msa0059890 AT1G21390.1 41.176 170 76 5 47 197 26 190 5.01e-27 105

Find 42 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTATGTGTTCACCACCTTTA+TGG 0.137469 1_2:-17401440 Msa0059890:CDS
TTAGATGATCCCAAAGAAAT+TGG 0.202956 1_2:+17401126 None:intergenic
TGATAAGAAGAAAGAGTTAT+TGG 0.226827 1_2:-17401097 Msa0059890:CDS
AAGAGGTCAAAGAGAGTTAA+TGG 0.266398 1_2:-17401352 Msa0059890:CDS
ATGGCTTGTGTCTTTGATTC+AGG 0.274722 1_2:+17401378 None:intergenic
GTAAGTTCATAGCTTGATTC+TGG 0.277190 1_2:+17401312 None:intergenic
AATTAGGGCTAGTAGAAATA+TGG 0.334807 1_2:-17401196 Msa0059890:CDS
TTATTCTTTGTTGTCCATAA+AGG 0.353698 1_2:+17401426 None:intergenic
TGTATTCTATCATCAGAAAC+TGG 0.389778 1_2:+17401540 None:intergenic
CTCTCTTTGACCTCTTTCAA+TGG 0.402619 1_2:+17401359 None:intergenic
TCAAAGAGAGTTAATGGAAA+TGG 0.417465 1_2:-17401346 Msa0059890:CDS
TTCTGATGGATCTGTTAGTA+AGG 0.426899 1_2:-17401025 Msa0059890:CDS
GGATTGGTGGAAGAAGAAAC+TGG 0.436996 1_2:-17401004 Msa0059890:CDS
AATGGTAGCATCAAAAGATA+TGG 0.453475 1_2:-17400922 Msa0059890:CDS
CAACATGTTGAAGATGAATC+TGG 0.475461 1_2:-17401462 Msa0059890:CDS
AAGAAATTGTGGGTTGGTAA+TGG 0.479830 1_2:+17401565 None:intergenic
CCAAGAGCATCTGTTTCTGA+TGG 0.489074 1_2:-17401039 Msa0059890:CDS
GAACTAGTAGTTGCAGCAGC+AGG 0.491364 1_2:-17400891 Msa0059890:CDS
AGAAACTGGAAAAGAAATTG+TGG 0.502575 1_2:+17401554 None:intergenic
GATCTGTTAGTAAGGATTGG+TGG 0.520890 1_2:-17401017 Msa0059890:CDS
TAAAAGTAGTAGTAATTCAA+AGG 0.523482 1_2:-17401067 Msa0059890:CDS
AGTGGTGTATCTAGCATGAA+TGG 0.524163 1_2:-17400940 Msa0059890:CDS
GAAACTGGAAAAGAAATTGT+GGG 0.525639 1_2:+17401555 None:intergenic
TTCTTTGTTGTCCATAAAGG+TGG 0.536559 1_2:+17401429 None:intergenic
AAGACACAAGCCATTGAAAG+AGG 0.538043 1_2:-17401369 Msa0059890:CDS
CCATCAGAAACAGATGCTCT+TGG 0.545084 1_2:+17401039 None:intergenic
GGGAGTAGTGGTTCAGAATG+TGG 0.556003 1_2:-17400982 Msa0059890:CDS
AAAATAACAAGGTAAAAGAG+AGG 0.570398 1_2:-17401254 Msa0059890:CDS
GCAGCAGCAGGAGTAATAGC+AGG 0.570433 1_2:-17400879 Msa0059890:CDS
CTGGAAAAGAAATTGTGGGT+TGG 0.579799 1_2:+17401559 None:intergenic
AGAAGAATATTGACAGTGGA+GGG 0.588979 1_2:-17401170 Msa0059890:CDS
ATGGATCTGTTAGTAAGGAT+TGG 0.591287 1_2:-17401020 Msa0059890:CDS
GGTTGGTAATGGTATCTTCG+TGG 0.594866 1_2:+17401576 None:intergenic
AAGAAGAAACTGGGGAGTAG+TGG 0.594902 1_2:-17400994 Msa0059890:CDS
GATTGGTGGAAGAAGAAACT+GGG 0.596215 1_2:-17401003 Msa0059890:CDS
AAGAAGAATATTGACAGTGG+AGG 0.610321 1_2:-17401171 Msa0059890:CDS
GATAAGAAGAATATTGACAG+TGG 0.625867 1_2:-17401174 Msa0059890:CDS
TACTTTGAAAGATCTTGTTG+AGG 0.634719 1_2:-17401292 Msa0059890:CDS
ATTGGTGGAAGAAGAAACTG+GGG 0.670609 1_2:-17401002 Msa0059890:CDS
AGTAGTGGTTCAGAATGTGG+AGG 0.678513 1_2:-17400979 Msa0059890:CDS
TCATGTTGAAGAAAATAACA+AGG 0.690119 1_2:-17401265 Msa0059890:CDS
GGTGATCAAAGTGATCATAG+TGG 0.721338 1_2:-17400958 Msa0059890:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATGATTTTTCCAATTTCTT+TGG - chr1_2:17401316-17401335 Msa0059890:CDS 20.0%
!!! ATGATTTTTCCAATTTCTTT+GGG - chr1_2:17401317-17401336 Msa0059890:CDS 20.0%
!! TAAAAGTAGTAGTAATTCAA+AGG - chr1_2:17401385-17401404 Msa0059890:CDS 20.0%
!! TTATTCTTTGTTGTCCATAA+AGG + chr1_2:17401029-17401048 None:intergenic 25.0%
! TCATGTTGAAGAAAATAACA+AGG - chr1_2:17401187-17401206 Msa0059890:CDS 25.0%
! AAAATAACAAGGTAAAAGAG+AGG - chr1_2:17401198-17401217 Msa0059890:CDS 25.0%
! TGATAAGAAGAAAGAGTTAT+TGG - chr1_2:17401355-17401374 Msa0059890:CDS 25.0%
GAAACTGGAAAAGAAATTGT+GGG + chr1_2:17400900-17400919 None:intergenic 30.0%
AGAAACTGGAAAAGAAATTG+TGG + chr1_2:17400901-17400920 None:intergenic 30.0%
TGTATTCTATCATCAGAAAC+TGG + chr1_2:17400915-17400934 None:intergenic 30.0%
TCAAAGAGAGTTAATGGAAA+TGG - chr1_2:17401106-17401125 Msa0059890:CDS 30.0%
! TACTTTGAAAGATCTTGTTG+AGG - chr1_2:17401160-17401179 Msa0059890:CDS 30.0%
AAAAACACACGAAAAAGAGA+AGG - chr1_2:17401233-17401252 Msa0059890:CDS 30.0%
ACGAAAAAGAGAAGGAATTA+GGG - chr1_2:17401241-17401260 Msa0059890:CDS 30.0%
! AATTAGGGCTAGTAGAAATA+TGG - chr1_2:17401256-17401275 Msa0059890:CDS 30.0%
GATAAGAAGAATATTGACAG+TGG - chr1_2:17401278-17401297 Msa0059890:CDS 30.0%
TTAGATGATCCCAAAGAAAT+TGG + chr1_2:17401329-17401348 None:intergenic 30.0%
AATGGTAGCATCAAAAGATA+TGG - chr1_2:17401530-17401549 Msa0059890:CDS 30.0%
!! AAGAAATTGTGGGTTGGTAA+TGG + chr1_2:17400890-17400909 None:intergenic 35.0%
CAACATGTTGAAGATGAATC+TGG - chr1_2:17400990-17401009 Msa0059890:CDS 35.0%
! TTCTTTGTTGTCCATAAAGG+TGG + chr1_2:17401026-17401045 None:intergenic 35.0%
AAGAGGTCAAAGAGAGTTAA+TGG - chr1_2:17401100-17401119 Msa0059890:CDS 35.0%
GTAAGTTCATAGCTTGATTC+TGG + chr1_2:17401143-17401162 None:intergenic 35.0%
CACGAAAAAGAGAAGGAATT+AGG - chr1_2:17401240-17401259 Msa0059890:CDS 35.0%
AAGAAGAATATTGACAGTGG+AGG - chr1_2:17401281-17401300 Msa0059890:CDS 35.0%
AGAAGAATATTGACAGTGGA+GGG - chr1_2:17401282-17401301 Msa0059890:CDS 35.0%
! TTCTGATGGATCTGTTAGTA+AGG - chr1_2:17401427-17401446 Msa0059890:CDS 35.0%
ATGGATCTGTTAGTAAGGAT+TGG - chr1_2:17401432-17401451 Msa0059890:CDS 35.0%
CTGGAAAAGAAATTGTGGGT+TGG + chr1_2:17400896-17400915 None:intergenic 40.0%
GTATGTGTTCACCACCTTTA+TGG - chr1_2:17401012-17401031 Msa0059890:CDS 40.0%
! ATGGCTTGTGTCTTTGATTC+AGG + chr1_2:17401077-17401096 None:intergenic 40.0%
AAGACACAAGCCATTGAAAG+AGG - chr1_2:17401083-17401102 Msa0059890:CDS 40.0%
CTCTCTTTGACCTCTTTCAA+TGG + chr1_2:17401096-17401115 None:intergenic 40.0%
GATCTGTTAGTAAGGATTGG+TGG - chr1_2:17401435-17401454 Msa0059890:CDS 40.0%
GATTGGTGGAAGAAGAAACT+GGG - chr1_2:17401449-17401468 Msa0059890:CDS 40.0%
ATTGGTGGAAGAAGAAACTG+GGG - chr1_2:17401450-17401469 Msa0059890:CDS 40.0%
GGTGATCAAAGTGATCATAG+TGG - chr1_2:17401494-17401513 Msa0059890:CDS 40.0%
AGTGGTGTATCTAGCATGAA+TGG - chr1_2:17401512-17401531 Msa0059890:CDS 40.0%
!! GGTTGGTAATGGTATCTTCG+TGG + chr1_2:17400879-17400898 None:intergenic 45.0%
CCATCAGAAACAGATGCTCT+TGG + chr1_2:17401416-17401435 None:intergenic 45.0%
!! CCAAGAGCATCTGTTTCTGA+TGG - chr1_2:17401413-17401432 Msa0059890:CDS 45.0%
! GGATTGGTGGAAGAAGAAAC+TGG - chr1_2:17401448-17401467 Msa0059890:CDS 45.0%
AAGAAGAAACTGGGGAGTAG+TGG - chr1_2:17401458-17401477 Msa0059890:CDS 45.0%
AGTAGTGGTTCAGAATGTGG+AGG - chr1_2:17401473-17401492 Msa0059890:CDS 45.0%
GGGAGTAGTGGTTCAGAATG+TGG - chr1_2:17401470-17401489 Msa0059890:CDS 50.0%
GAACTAGTAGTTGCAGCAGC+AGG - chr1_2:17401561-17401580 Msa0059890:CDS 50.0%
GCAGCAGCAGGAGTAATAGC+AGG - chr1_2:17401573-17401592 Msa0059890:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 17400867 17401607 17400867 ID=Msa0059890;Name=Msa0059890
chr1_2 mRNA 17400867 17401607 17400867 ID=Msa0059890-mRNA-1;Parent=Msa0059890;Name=Msa0059890-mRNA-1;_AED=0.22;_eAED=0.22;_QI=0|-1|0|1|-1|1|1|0|246
chr1_2 exon 17400867 17401607 17400867 ID=Msa0059890-mRNA-1:exon:6764;Parent=Msa0059890-mRNA-1
chr1_2 CDS 17400867 17401607 17400867 ID=Msa0059890-mRNA-1:cds;Parent=Msa0059890-mRNA-1
Gene Sequence

>Msa0059890

ATGCTTGATCCACGAAGATACCATTACCAACCCACAATTTCTTTTCCAGTTTCTGATGATAGAATACAACAAAAAACTCACATCAACAATAACAAAAACTACAACAATTTTCATCATCATGATCAACATGTTGAAGATGAATCTGGTATGTGTTCACCACCTTTATGGACAACAAAGAATAAAAGCAACAACTATAGAAGTCTTTCACCTGAATCAAAGACACAAGCCATTGAAAGAGGTCAAAGAGAGTTAATGGAAATGGTTAAGAACATGCCAGAATCAAGCTATGAACTTACTTTGAAAGATCTTGTTGAGGAACATCATGTTGAAGAAAATAACAAGGTAAAAGAGAGGAATTTGAGCAACAAAAACACACGAAAAAGAGAAGGAATTAGGGCTAGTAGAAATATGGATAAGAAGAATATTGACAGTGGAGGGCTTTATTTGAAAATGATTTTTCCAATTTCTTTGGGATCATCTAAGAAACATGATAAGAAGAAAGAGTTATTGGTTAGTAATAAAAGTAGTAGTAATTCAAAGGTTTCACCAAGAGCATCTGTTTCTGATGGATCTGTTAGTAAGGATTGGTGGAAGAAGAAACTGGGGAGTAGTGGTTCAGAATGTGGAGGTGATCAAAGTGATCATAGTGGTGTATCTAGCATGAATGGTAGCATCAAAAGATATGGTAGTAGCAGAACTAGTAGTTGCAGCAGCAGGAGTAATAGCAGGTATGCTTCTTAA

Protein sequence

>Msa0059890

MLDPRRYHYQPTISFPVSDDRIQQKTHINNNKNYNNFHHHDQHVEDESGMCSPPLWTTKNKSNNYRSLSPESKTQAIERGQRELMEMVKNMPESSYELTLKDLVEEHHVEENNKVKERNLSNKNTRKREGIRASRNMDKKNIDSGGLYLKMIFPISLGSSKKHDKKKELLVSNKSSSNSKVSPRASVSDGSVSKDWWKKKLGSSGSECGGDQSDHSGVSSMNGSIKRYGSSRTSSCSSRSNSRYAS*