AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene87118

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 25 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGTTATACCATTCAAAGTT+TGG 0.348370 6.2:+43427953 MS.gene87118:CDS
TTACTTCCGTGGCCGCTTCA+AGG 0.381428 6.2:-43427892 None:intergenic
ATGTTGCTTTGTATTCTTGT+TGG 0.414709 6.2:-43427548 None:intergenic
GCATCACGTGCTGCAGGGTC+AGG 0.420816 6.2:-43427833 None:intergenic
GAAATCGAATTAAACACTTC+CGG 0.423423 6.2:+43427992 MS.gene87118:CDS
GGAGCTGAAAGGAAAATTAG+AGG 0.424898 6.2:+43427602 MS.gene87118:CDS
ATTTCTGCATCACGTGCTGC+AGG 0.436134 6.2:-43427839 None:intergenic
ATCAGACTGCAGTTCTACTT+TGG 0.440143 6.2:+43427807 MS.gene87118:intron
CATTAGGAAGTCGCTGGTTG+TGG 0.443829 6.2:+43427862 MS.gene87118:CDS
AACTTCATGCTCAACATAAA+CGG 0.449489 6.2:-43428050 None:intergenic
GATAAACGCCAAACTTTGAA+TGG 0.462297 6.2:-43427961 None:intergenic
CACGTGATGCAGAAATCATT+AGG 0.480060 6.2:+43427846 MS.gene87118:CDS
TTTAGATATTGTAGTTGGGA+TGG 0.486564 6.2:-43427929 None:intergenic
CAGAAGCCTTGAAGCGGCCA+CGG 0.489696 6.2:+43427886 MS.gene87118:CDS
TTTGTATTCTTGTTGGAGGT+AGG 0.504801 6.2:-43427541 None:intergenic
GCTATCGAAACGCTTAGTTT+CGG 0.507005 6.2:+43427581 MS.gene87118:CDS
TTGCTTTGTATTCTTGTTGG+AGG 0.507782 6.2:-43427545 None:intergenic
CGCTTAGTTTCGGAGCTGAA+AGG 0.547329 6.2:+43427591 MS.gene87118:CDS
CACTTCCGGAGATCATCAAA+AGG 0.568952 6.2:+43428006 MS.gene87118:CDS
AGAAATCATTAGGAAGTCGC+TGG 0.602316 6.2:+43427856 MS.gene87118:CDS
TGTGGACAGAAGCCTTGAAG+CGG 0.613077 6.2:+43427880 MS.gene87118:CDS
CCGGAGATCATCAAAAGGTG+AGG 0.620058 6.2:+43428011 MS.gene87118:CDS
ATACAAAGCAACATATTCTG+AGG 0.622438 6.2:+43427557 MS.gene87118:CDS
TTTCTGCATCACGTGCTGCA+GGG 0.638169 6.2:-43427838 None:intergenic
ACGCGAACATATTACTTCCG+TGG 0.638767 6.2:-43427903 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACTGTTTTAGATATTGTAGT+TGG - chr6.2:43427937-43427956 None:intergenic 25.0%
!!! CTGTTTTAGATATTGTAGTT+GGG - chr6.2:43427936-43427955 None:intergenic 25.0%
AACTTCATGCTCAACATAAA+CGG - chr6.2:43428053-43428072 None:intergenic 30.0%
ATACAAAGCAACATATTCTG+AGG + chr6.2:43427557-43427576 MS.gene87118:CDS 30.0%
CAGTTATACCATTCAAAGTT+TGG + chr6.2:43427953-43427972 MS.gene87118:CDS 30.0%
CGTTCAATTCAATGTTATGA+TGG - chr6.2:43427677-43427696 None:intergenic 30.0%
GAAATCGAATTAAACACTTC+CGG + chr6.2:43427992-43428011 MS.gene87118:CDS 30.0%
TTTAGATATTGTAGTTGGGA+TGG - chr6.2:43427932-43427951 None:intergenic 30.0%
!! ATGTTGCTTTGTATTCTTGT+TGG - chr6.2:43427551-43427570 None:intergenic 30.0%
GATAAACGCCAAACTTTGAA+TGG - chr6.2:43427964-43427983 None:intergenic 35.0%
TTGCTTTGTATTCTTGTTGG+AGG - chr6.2:43427548-43427567 None:intergenic 35.0%
TTTGTATTCTTGTTGGAGGT+AGG - chr6.2:43427544-43427563 None:intergenic 35.0%
AGAAATCATTAGGAAGTCGC+TGG + chr6.2:43427856-43427875 MS.gene87118:CDS 40.0%
ATCAGACTGCAGTTCTACTT+TGG + chr6.2:43427807-43427826 MS.gene87118:intron 40.0%
CACGTGATGCAGAAATCATT+AGG + chr6.2:43427846-43427865 MS.gene87118:CDS 40.0%
GCTATCGAAACGCTTAGTTT+CGG + chr6.2:43427581-43427600 MS.gene87118:CDS 40.0%
GGAGCTGAAAGGAAAATTAG+AGG + chr6.2:43427602-43427621 MS.gene87118:CDS 40.0%
ACGCGAACATATTACTTCCG+TGG - chr6.2:43427906-43427925 None:intergenic 45.0%
CACTTCCGGAGATCATCAAA+AGG + chr6.2:43428006-43428025 MS.gene87118:CDS 45.0%
!! CCTCACCTTTTGATGATCTC+CGG - chr6.2:43428014-43428033 None:intergenic 45.0%
ATTTCTGCATCACGTGCTGC+AGG - chr6.2:43427842-43427861 None:intergenic 50.0%
CCGGAGATCATCAAAAGGTG+AGG + chr6.2:43428011-43428030 MS.gene87118:CDS 50.0%
CGCTTAGTTTCGGAGCTGAA+AGG + chr6.2:43427591-43427610 MS.gene87118:CDS 50.0%
TGTGGACAGAAGCCTTGAAG+CGG + chr6.2:43427880-43427899 MS.gene87118:CDS 50.0%
TTTCTGCATCACGTGCTGCA+GGG - chr6.2:43427841-43427860 None:intergenic 50.0%
! CATTAGGAAGTCGCTGGTTG+TGG + chr6.2:43427862-43427881 MS.gene87118:CDS 50.0%
TTACTTCCGTGGCCGCTTCA+AGG - chr6.2:43427895-43427914 None:intergenic 55.0%
CAGAAGCCTTGAAGCGGCCA+CGG + chr6.2:43427886-43427905 MS.gene87118:CDS 60.0%
GCATCACGTGCTGCAGGGTC+AGG - chr6.2:43427836-43427855 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 43427478 43428078 43427478 ID=MS.gene87118
chr6.2 mRNA 43427478 43428078 43427478 ID=MS.gene87118.t1;Parent=MS.gene87118
chr6.2 exon 43427478 43427623 43427478 ID=MS.gene87118.t1.exon1;Parent=MS.gene87118.t1
chr6.2 CDS 43427478 43427623 43427478 ID=cds.MS.gene87118.t1;Parent=MS.gene87118.t1
chr6.2 exon 43427812 43428078 43427812 ID=MS.gene87118.t1.exon2;Parent=MS.gene87118.t1
chr6.2 CDS 43427812 43428078 43427812 ID=cds.MS.gene87118.t1;Parent=MS.gene87118.t1
Gene Sequence

>MS.gene87118

GATTTGGGTGTGACACAACTGCTGTGATCAATATTCTTGCTCATAGAGACGCTACACAGCGTGCCTACCTCCAACAAGAATACAAAGCAACATATTCTGAGGAGCTATCGAAACGCTTAGTTTCGGAGCTGAAAGGAAAATTAGAGGTACTAATTTACTTATATAATAGCTTATAGTAAATGCAAAATCAATCATTCCATCATAACATTGAATTGAACGTTCTTACAATAGTAGATCAAGTTTTCAATAACTTTGAATTGTTTTCTATGAATTTTCTACTTATTGCTTTTCGTGTAATGTTTCATTGTTTATCTTACACTTTTCTATTTATCAGACTGCAGTTCTACTTTGGTTGCCTGACCCTGCAGCACGTGATGCAGAAATCATTAGGAAGTCGCTGGTTGTGGACAGAAGCCTTGAAGCGGCCACGGAAGTAATATGTTCGCGTACTCCATCCCAACTACAATATCTAAAACAGTTATACCATTCAAAGTTTGGCGTTTATCTTGAGCATGAAATCGAATTAAACACTTCCGGAGATCATCAAAAGGTGAGGTTTCTATGTGTAAATGCCGTTTATGTTGAGCATGAAGTTGAATGA
Protein sequence

>MS.gene87118.t1

DLGVTQLLUSIFLLIETLHSVPTSNKNTKQHILRSYRNAUFRSUKENURLQFYFGCLTLQHVMQKSLGSRWLWTEALKRPRKUYVRVLHPNYNIUNSYTIQSLAFILSMKSNUTLPEIIKRUGFYVUMPFMLSMKLN