AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene89871

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene89871.t1 MTR_7g068140 63.030 165 61 0 17 181 59 223 5.92e-71 214
MS.gene89871.t1 MTR_7g068110 54.348 184 74 4 6 181 39 220 3.08e-57 179
MS.gene89871.t1 MTR_1g070500 96.667 60 2 0 115 174 12 71 5.23e-36 120
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 31 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGCAACTCTAGATTATAAA+TGG 0.267239 7.3:+37038458 None:intergenic
TCATACTTCTCTTGATATTT+CGG 0.276741 7.3:-37038675 MS.gene89871:CDS
TAATAAGAAGAAGAAAATTA+TGG 0.296429 7.3:-37038504 MS.gene89871:CDS
TGAAGAAGTCATCAAGTCTA+AGG 0.321607 7.3:+37038787 None:intergenic
TATAATAATCATCTTCATCT+TGG 0.339469 7.3:+37038630 None:intergenic
TTCATATAACTTGCGTGTTA+AGG 0.354616 7.3:+37038574 None:intergenic
TGAAAATAGAAGTAAGCATT+TGG 0.397068 7.3:-37038555 MS.gene89871:CDS
TTATAGACGTATTGTTGCCT+TGG 0.414115 7.3:-37038612 MS.gene89871:CDS
ATAATAATCATCTTCATCTT+GGG 0.417174 7.3:+37038631 None:intergenic
CCACCTCCAAGTTATGTACT+AGG 0.431047 7.3:-37038965 MS.gene89871:CDS
CTCGATGTTCTCAAGATGTA+TGG 0.444720 7.3:-37038743 MS.gene89871:CDS
GAAGAAAATTATGGACGAAA+GGG 0.475570 7.3:-37038495 MS.gene89871:CDS
ACGTATTGTTGCCTTGGATG+AGG 0.518522 7.3:-37038606 MS.gene89871:CDS
TGGCGAAATATTCATAAGCT+TGG 0.525315 7.3:+37038840 None:intergenic
TCAGAGCCTAGTACATAACT+TGG 0.527013 7.3:+37038959 None:intergenic
AGAAGAAAATTATGGACGAA+AGG 0.532177 7.3:-37038496 MS.gene89871:CDS
TGTGTATCTGTTCTGAAAGA+AGG 0.564953 7.3:+37038879 None:intergenic
GAGCCTAGTACATAACTTGG+AGG 0.566495 7.3:+37038962 None:intergenic
AGTACATAACTTGGAGGTGG+AGG 0.568062 7.3:+37038968 None:intergenic
CTCAAGATGTATGGCTTCAG+AGG 0.570430 7.3:-37038734 MS.gene89871:CDS
GACTAGAAGAAAACTCTATG+AGG 0.574559 7.3:+37038912 None:intergenic
AAATATCAAGAGAAGTATGA+TGG 0.576216 7.3:+37038678 None:intergenic
CCTAGTACATAACTTGGAGG+TGG 0.577199 7.3:+37038965 None:intergenic
ATGAGGAGCTGTGCATCTTG+CGG 0.587430 7.3:+37038929 None:intergenic
AAATTATGGACGAAAGGGCA+AGG 0.606306 7.3:-37038490 MS.gene89871:CDS
AGGAGCTGTGCATCTTGCGG+AGG 0.617586 7.3:+37038932 None:intergenic
TTTGGCTGAGAGAGAAGCTG+TGG 0.626193 7.3:-37038537 MS.gene89871:CDS
GGAGCTGTGCATCTTGCGGA+GGG 0.627195 7.3:+37038933 None:intergenic
GGCTGCGTACTCCTCATCCA+AGG 0.627531 7.3:+37038595 None:intergenic
TTTCAGAACAGATACACACA+TGG 0.688292 7.3:-37038874 MS.gene89871:CDS
TGTATGGCTTCAGAGGCGAA+TGG 0.695014 7.3:-37038727 MS.gene89871:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATTGGAAAAAAAAAATT+AGG + chr7.3:37038521-37038540 None:intergenic 10.0%
!! TTGACAAAAAATTTAAATAT+TGG + chr7.3:37038536-37038555 None:intergenic 10.0%
!! TAATAAGAAGAAGAAAATTA+TGG - chr7.3:37039093-37039112 MS.gene89871:intron 15.0%
!! ATAATAATCATCTTCATCTT+GGG + chr7.3:37038969-37038988 None:intergenic 20.0%
!! TATAATAATCATCTTCATCT+TGG + chr7.3:37038970-37038989 None:intergenic 20.0%
! AAAGAAAACATATCAAGTTC+AGG + chr7.3:37038603-37038622 None:intergenic 25.0%
! AACTCATGAAAGATTAAAAC+CGG - chr7.3:37038554-37038573 MS.gene89871:CDS 25.0%
! AAGAAAACATATCAAGTTCA+GGG + chr7.3:37038602-37038621 None:intergenic 25.0%
! TATTAAAAAAAACGCACTGA+TGG + chr7.3:37038482-37038501 None:intergenic 25.0%
! TCATACTTCTCTTGATATTT+CGG - chr7.3:37038922-37038941 MS.gene89871:CDS 25.0%
! TGAAAATAGAAGTAAGCATT+TGG - chr7.3:37039042-37039061 MS.gene89871:intron 25.0%
!! AAATATCAAGAGAAGTATGA+TGG + chr7.3:37038922-37038941 None:intergenic 25.0%
!! ATTAAAAAAAACGCACTGAT+GGG + chr7.3:37038481-37038500 None:intergenic 25.0%
ACTCATGAAAGATTAAAACC+GGG - chr7.3:37038555-37038574 MS.gene89871:CDS 30.0%
AGAAGAAAATTATGGACGAA+AGG - chr7.3:37039101-37039120 MS.gene89871:intron 30.0%
GAAGAAAATTATGGACGAAA+GGG - chr7.3:37039102-37039121 MS.gene89871:intron 30.0%
! TTCATATAACTTGCGTGTTA+AGG + chr7.3:37039026-37039045 None:intergenic 30.0%
!! GGAATTCTAAAATAAGCAGT+AGG + chr7.3:37038581-37038600 None:intergenic 30.0%
GACTAGAAGAAAACTCTATG+AGG + chr7.3:37038688-37038707 None:intergenic 35.0%
TGAAGAAGTCATCAAGTCTA+AGG + chr7.3:37038813-37038832 None:intergenic 35.0%
TGGCGAAATATTCATAAGCT+TGG + chr7.3:37038760-37038779 None:intergenic 35.0%
TTATAGACGTATTGTTGCCT+TGG - chr7.3:37038985-37039004 MS.gene89871:intron 35.0%
TTTCAGAACAGATACACACA+TGG - chr7.3:37038723-37038742 MS.gene89871:CDS 35.0%
!! TGTGTATCTGTTCTGAAAGA+AGG + chr7.3:37038721-37038740 None:intergenic 35.0%
AAATTATGGACGAAAGGGCA+AGG - chr7.3:37039107-37039126 MS.gene89871:intron 40.0%
AGTGAGATCGCAAAAACTTG+AGG + chr7.3:37038787-37038806 None:intergenic 40.0%
CTCGATGTTCTCAAGATGTA+TGG - chr7.3:37038854-37038873 MS.gene89871:CDS 40.0%
TCAGAGCCTAGTACATAACT+TGG + chr7.3:37038641-37038660 None:intergenic 40.0%
TCGCAAAAACTTGAGGAAAG+TGG + chr7.3:37038780-37038799 None:intergenic 40.0%
! GAGTTTTCTTCTAGTCACGT+TGG - chr7.3:37038692-37038711 MS.gene89871:CDS 40.0%
! TCTAAAATAAGCAGTAGGCC+CGG + chr7.3:37038576-37038595 None:intergenic 40.0%
ACGTATTGTTGCCTTGGATG+AGG - chr7.3:37038991-37039010 MS.gene89871:intron 45.0%
AGTACATAACTTGGAGGTGG+AGG + chr7.3:37038632-37038651 None:intergenic 45.0%
CCACCTCCAAGTTATGTACT+AGG - chr7.3:37038632-37038651 MS.gene89871:CDS 45.0%
CCTAGTACATAACTTGGAGG+TGG + chr7.3:37038635-37038654 None:intergenic 45.0%
CTCAAGATGTATGGCTTCAG+AGG - chr7.3:37038863-37038882 MS.gene89871:CDS 45.0%
GAGCCTAGTACATAACTTGG+AGG + chr7.3:37038638-37038657 None:intergenic 45.0%
ATGAGGAGCTGTGCATCTTG+CGG + chr7.3:37038671-37038690 None:intergenic 50.0%
TGTATGGCTTCAGAGGCGAA+TGG - chr7.3:37038870-37038889 MS.gene89871:CDS 50.0%
TTTGGCTGAGAGAGAAGCTG+TGG - chr7.3:37039060-37039079 MS.gene89871:intron 50.0%
AGGAGCTGTGCATCTTGCGG+AGG + chr7.3:37038668-37038687 None:intergenic 60.0%
GGAGCTGTGCATCTTGCGGA+GGG + chr7.3:37038667-37038686 None:intergenic 60.0%
GGCTGCGTACTCCTCATCCA+AGG + chr7.3:37039005-37039024 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 37038466 37039153 37038466 ID=MS.gene89871
chr7.3 mRNA 37038466 37039153 37038466 ID=MS.gene89871.t1;Parent=MS.gene89871
chr7.3 exon 37039135 37039153 37039135 ID=MS.gene89871.t1.exon1;Parent=MS.gene89871.t1
chr7.3 CDS 37039135 37039153 37039135 ID=cds.MS.gene89871.t1;Parent=MS.gene89871.t1
chr7.3 exon 37038466 37038992 37038466 ID=MS.gene89871.t1.exon2;Parent=MS.gene89871.t1
chr7.3 CDS 37038466 37038992 37038466 ID=cds.MS.gene89871.t1;Parent=MS.gene89871.t1
Gene Sequence

>MS.gene89871

ATGGGTTTAAGTCCCATCAGTGCGTTTTTTTTAATAATTTTCTTTTATAATGCCTAATTTTTTTTTTCCAATATTTAAATTTTTTGTCAACTCATGAAAGATTAAAACCGGGCCTACTGCTTATTTTAGAATTCCCTGAACTTGATATGTTTTCTTTACAGATCCTCCACCTCCAAGTTATGTACTAGGCTCTGATTTCCCTCCGCAAGATGCACAGCTCCTCATAGAGTTTTCTTCTAGTCACGTTGGCTTCCTTCTTTCAGAACAGATACACACATGGAACATGAGACGCCAAGCTTATGAATATTTCGCCACTTTCCTCAAGTTTTTGCGATCTCACTCTACCTTAGACTTGATGACTTCTTCAAAATCATCAATTTCTAATGATCTCGATGTTCTCAAGATGTATGGCTTCAGAGGCGAATGGTTTGATCGCTTAGTTCTTCGTCTCAACCATCATACTTCTCTTGATATTTCGGACAAAGAGATGCAAAATTTAACCCAAGATGAAGATGATTATTATAGACGTATTGTTGCCTTGGATGAGGAGTACGCAGCCTTAACACGCAAGTTATATGAAAATAGAAGTAAGCATTTGGCTGAGAGAGAAGCTGTGGAATACATTTCTAATAAGAAGAAGAAAATTATGGACGAAAGGGCAAGGTTAAACGTTCCATTTATAATCTAG
Protein sequence

>MS.gene89871.t1

MGLSPINPPPPSYVLGSDFPPQDAQLLIEFSSSHVGFLLSEQIHTWNMRRQAYEYFATFLKFLRSHSTLDLMTSSKSSISNDLDVLKMYGFRGEWFDRLVLRLNHHTSLDISDKEMQNLTQDEDDYYRRIVALDEEYAALTRKLYENRSKHLAEREAVEYISNKKKKIMDERARLNVPFII