AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0180005525.01

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180005525.01.T01 MTR_1g102380 93.333 60 4 0 1 60 1 60 2.73e-33 115
MsG0180005525.01.T01 MTR_1g102380 89.286 56 6 0 61 116 136 191 2.29e-30 107
MsG0180005525.01.T01 MTR_0007s0330 57.778 45 19 0 17 61 4 48 5.99e-13 62.0
MsG0180005525.01.T01 MTR_0007s0330 57.778 45 19 0 17 61 16 60 1.32e-12 61.6
MsG0180005525.01.T01 MTR_0007s0380 54.545 44 20 0 18 61 70 113 1.07e-11 59.7
MsG0180005525.01.T01 MTR_1g102370 60.000 45 18 0 17 61 73 117 1.19e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0180005525.01.T01 AT5G51780 57.143 49 21 0 13 61 19 67 4.29e-12 60.5

Find 18 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCACGTTTATCAGATTTAA+TGG 0.200332 1:-92879093 MsG0180005525.01.T01:intron
TTTGCAGCTGAGCAAGATTA+AGG 0.301232 1:+92878806 None:intergenic
TGCTCAGCTGCAAAATAAAC+TGG 0.330890 1:-92878797 MsG0180005525.01.T01:CDS
TGTGTTACCAACCAAGTAAA+TGG 0.368730 1:-92879035 MsG0180005525.01.T01:CDS
AAGACCTTGATGAGCTCAAA+AGG 0.412689 1:+92879460 None:intergenic
GAAATATCTTGCCATTTACT+TGG 0.419250 1:+92879024 None:intergenic
TATCTTGCCATTTACTTGGT+TGG 0.419948 1:+92879028 None:intergenic
TTTATGCTGATTCAGATCTT+CGG 0.455944 1:+92879591 None:intergenic
ATGGAAATAATACTTCAAGA+AGG 0.552508 1:-92879074 MsG0180005525.01.T01:CDS
AGACCTTGATGAGCTCAAAA+GGG 0.578199 1:+92879461 None:intergenic
GCATAAAATATTAACTACAT+CGG 0.611900 1:-92879575 MsG0180005525.01.T01:CDS
ATTTCATACTGTTAAATCTG+AGG 0.612912 1:-92879006 MsG0180005525.01.T01:intron
GCTCAAAAGGGAGTGAAGAA+CGG 0.633531 1:+92879473 None:intergenic
GTAGGGAAGTTGAAAAGCAA+AGG 0.634358 1:-92879528 MsG0180005525.01.T01:CDS
AAAAGGGAGTGAAGAACGGA+GGG 0.640895 1:+92879477 None:intergenic
CGTTCAGTATCAGATCACAT+AGG 0.655166 1:-92879324 MsG0180005525.01.T01:intron
CAAAAGGGAGTGAAGAACGG+AGG 0.674543 1:+92879476 None:intergenic
GGGAAGTTGAAAAGCAAAGG+AGG 0.678696 1:-92879525 MsG0180005525.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACTTAATAATTAATTAGCT+AGG + Chr1:92879388-92879407 None:intergenic 15.0%
!!! ATTATTGTTGTTGAATATAT+AGG - Chr1:92879521-92879540 MsG0180005525.01.T01:CDS 15.0%
!! GCATAAAATATTAACTACAT+CGG - Chr1:92878791-92878810 MsG0180005525.01.T01:CDS 20.0%
!!! TAATTTTCTGCTTCAAAATT+TGG + Chr1:92879086-92879105 None:intergenic 20.0%
!!! TCATGTTGATAAATAATAAG+AGG + Chr1:92878953-92878972 None:intergenic 20.0%
! ATGGAAATAATACTTCAAGA+AGG - Chr1:92879292-92879311 MsG0180005525.01.T01:intron 25.0%
! ATTTCATACTGTTAAATCTG+AGG - Chr1:92879360-92879379 MsG0180005525.01.T01:intron 25.0%
! TTCACGTTTATCAGATTTAA+TGG - Chr1:92879273-92879292 MsG0180005525.01.T01:intron 25.0%
!! ATTGTTGTTGAATATATAGG+TGG - Chr1:92879524-92879543 MsG0180005525.01.T01:CDS 25.0%
!!! TCATAACATCTTTGCTTTTA+GGG - Chr1:92879015-92879034 MsG0180005525.01.T01:CDS 25.0%
!!! TTCATAACATCTTTGCTTTT+AGG - Chr1:92879014-92879033 MsG0180005525.01.T01:CDS 25.0%
ATGAGAAAAAGATGATTCGT+AGG - Chr1:92878820-92878839 MsG0180005525.01.T01:CDS 30.0%
GAGAGATAAGATCAAAGAAA+TGG - Chr1:92879121-92879140 MsG0180005525.01.T01:intron 30.0%
GTGGAAATTGTTATATGTAG+TGG - Chr1:92879235-92879254 MsG0180005525.01.T01:intron 30.0%
TGAGAAAAAGATGATTCGTA+GGG - Chr1:92878821-92878840 MsG0180005525.01.T01:CDS 30.0%
! AAGAAATGGTTAGTTCAAGT+AGG - Chr1:92879135-92879154 MsG0180005525.01.T01:intron 30.0%
! AGAAATGGTTAGTTCAAGTA+GGG - Chr1:92879136-92879155 MsG0180005525.01.T01:intron 30.0%
! ATCACGCAATTTTATTGTCA+AGG - Chr1:92879592-92879611 MsG0180005525.01.T01:CDS 30.0%
! GAAATATCTTGCCATTTACT+TGG + Chr1:92879345-92879364 None:intergenic 30.0%
!! TTTATGCTGATTCAGATCTT+CGG + Chr1:92878778-92878797 None:intergenic 30.0%
AAGATTGATCTAATTCCAGG+AGG - Chr1:92879212-92879231 MsG0180005525.01.T01:intron 35.0%
AGATTGATCTAATTCCAGGA+GGG - Chr1:92879213-92879232 MsG0180005525.01.T01:intron 35.0%
GTCAAGATTGATCTAATTCC+AGG - Chr1:92879209-92879228 MsG0180005525.01.T01:intron 35.0%
TGTGTTACCAACCAAGTAAA+TGG - Chr1:92879331-92879350 MsG0180005525.01.T01:CDS 35.0%
TGTTATATGTAGTGGTTTCG+AGG - Chr1:92879243-92879262 MsG0180005525.01.T01:intron 35.0%
! TATCTTGCCATTTACTTGGT+TGG + Chr1:92879341-92879360 None:intergenic 35.0%
!! TCTAGGGTATTTCTGAGTTT+TGG - Chr1:92879460-92879479 MsG0180005525.01.T01:intron 35.0%
AAGACCTTGATGAGCTCAAA+AGG + Chr1:92878909-92878928 None:intergenic 40.0%
AGACCTTGATGAGCTCAAAA+GGG + Chr1:92878908-92878927 None:intergenic 40.0%
AGTATCAGATCACATAGGTG+AGG - Chr1:92879047-92879066 MsG0180005525.01.T01:CDS 40.0%
AGTTCAAGTAGGGTTGAAAC+TGG - Chr1:92879146-92879165 MsG0180005525.01.T01:intron 40.0%
CGTTCAGTATCAGATCACAT+AGG - Chr1:92879042-92879061 MsG0180005525.01.T01:CDS 40.0%
GTAGGGAAGTTGAAAAGCAA+AGG - Chr1:92878838-92878857 MsG0180005525.01.T01:intron 40.0%
TACGATCTAGCTAGAGTCTA+GGG - Chr1:92879444-92879463 MsG0180005525.01.T01:intron 40.0%
TATAACAATTTCCACCCTCC+TGG + Chr1:92879230-92879249 None:intergenic 40.0%
TGCTCAGCTGCAAAATAAAC+TGG - Chr1:92879569-92879588 MsG0180005525.01.T01:CDS 40.0%
TTACGATCTAGCTAGAGTCT+AGG - Chr1:92879443-92879462 MsG0180005525.01.T01:intron 40.0%
TTTGCAGCTGAGCAAGATTA+AGG + Chr1:92879563-92879582 None:intergenic 40.0%
AAAAGGGAGTGAAGAACGGA+GGG + Chr1:92878892-92878911 None:intergenic 45.0%
GCTCAAAAGGGAGTGAAGAA+CGG + Chr1:92878896-92878915 None:intergenic 45.0%
GGGAAGTTGAAAAGCAAAGG+AGG - Chr1:92878841-92878860 MsG0180005525.01.T01:intron 45.0%
TTGATCTAATTCCAGGAGGG+TGG - Chr1:92879216-92879235 MsG0180005525.01.T01:intron 45.0%
! ACTCCCTTTTGAGCTCATCA+AGG - Chr1:92878902-92878921 MsG0180005525.01.T01:intron 45.0%
CAAAAGGGAGTGAAGAACGG+AGG + Chr1:92878893-92878912 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
Chr1 gene 92878771 92879617 92878771 ID=MsG0180005525.01;Name=MsG0180005525.01
Chr1 mRNA 92878771 92879617 92878771 ID=MsG0180005525.01.T01;Parent=MsG0180005525.01;Name=MsG0180005525.01.T01;_AED=0.44;_eAED=0.44;_QI=0|0|0|1|0|0|4|0|116
Chr1 exon 92879465 92879617 92879465 ID=MsG0180005525.01.T01:exon:49792;Parent=MsG0180005525.01.T01
Chr1 exon 92879325 92879352 92879325 ID=MsG0180005525.01.T01:exon:49791;Parent=MsG0180005525.01.T01
Chr1 exon 92879007 92879101 92879007 ID=MsG0180005525.01.T01:exon:49790;Parent=MsG0180005525.01.T01
Chr1 exon 92878771 92878845 92878771 ID=MsG0180005525.01.T01:exon:49789;Parent=MsG0180005525.01.T01
Chr1 CDS 92879465 92879617 92879465 ID=MsG0180005525.01.T01:cds;Parent=MsG0180005525.01.T01
Chr1 CDS 92879325 92879352 92879325 ID=MsG0180005525.01.T01:cds;Parent=MsG0180005525.01.T01
Chr1 CDS 92879007 92879101 92879007 ID=MsG0180005525.01.T01:cds;Parent=MsG0180005525.01.T01
Chr1 CDS 92878771 92878845 92878771 ID=MsG0180005525.01.T01:cds;Parent=MsG0180005525.01.T01
Gene Sequence

>MsG0180005525.01.T01

ATGGCCGAAGATCTGAATCAGCATAAAATATTAACTACATCGGACAATGATGAGAAAAAGATGATTCGTAGGGAAGTTGAAAAGCAAAGGAGGATGCAAATGTCTAGTCTATGTTCATCCCTCCGTTCTTCACTCCCTTTTGAGCTCATCAAGGGTAAGCGTTCAGTATCAGATCACATAGATTTAATGGAAATAATACTTCAAGAAGGATGTGATGTTGTTCATTGTGTTACCAACCAAGTAAATGGCAAGATATTTCATACTGTTAAATCTGAGGTGGAGAACTTGACACGCCTTAATCTTGCTCAGCTGCAAAATAAACTGGATCACGCAATTTTATTGTCAAGGTAA
Protein sequence

>MsG0180005525.01.T01

MAEDLNQHKILTTSDNDEKKMIRREVEKQRRMQMSSLCSSLRSSLPFELIKGKRSVSDHIDLMEIILQEGCDVVHCVTNQVNGKIFHTVKSEVENLTRLNLAQLQNKLDHAILLSR*