AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054414

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054414.t1 MTR_7g112330 95.455 44 2 0 1 44 1 44 2.20e-27 95.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 16 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCTCTCCAAAGTGGTGTTT+TGG 0.317787 7.4:+4320999 None:intergenic
AATGATACCTTGGGTCCATT+TGG 0.368205 7.4:+4320973 None:intergenic
AATGGGAATCATGGATCAAA+TGG 0.411033 7.4:-4321203 MS.gene054414:CDS
ATGTTGTTCATACGATGAAA+TGG 0.428480 7.4:-4321058 MS.gene054414:CDS
AATCATGGATCAAATGGATA+AGG 0.481862 7.4:-4321197 MS.gene054414:intron
CTTTGGAGAGGAGGACCAAA+TGG 0.503109 7.4:-4320988 MS.gene054414:CDS
TGTGAATCAAATGGGAATCA+TGG 0.514991 7.4:-4321212 None:intergenic
AAACCACCAAAACACCACTT+TGG 0.542523 7.4:-4321005 MS.gene054414:CDS
TGTTGTTCATACGATGAAAT+GGG 0.559954 7.4:-4321057 MS.gene054414:CDS
AATCAGGTACAGAAAGAGAA+GGG 0.588011 7.4:-4320687 MS.gene054414:intron
GAATCAGGTACAGAAAGAGA+AGG 0.619622 7.4:-4320688 MS.gene054414:intron
TTTGGTCCTCCTCTCCAAAG+TGG 0.621363 7.4:+4320991 None:intergenic
AAAACACCACTTTGGAGAGG+AGG 0.625709 7.4:-4320997 MS.gene054414:CDS
AGGAGGACCAAATGGACCCA+AGG 0.633971 7.4:-4320980 MS.gene054414:intron
ACCAAAACACCACTTTGGAG+AGG 0.669357 7.4:-4321000 MS.gene054414:CDS
ATCAGGTACAGAAAGAGAAG+GGG 0.680743 7.4:-4320686 MS.gene054414:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGTTTATTAATTTGATTAA+AGG - chr7.4:4321084-4321103 MS.gene054414:intron 10.0%
!!! TGTTTATTAATTTGATTAAA+GGG - chr7.4:4321085-4321104 MS.gene054414:intron 10.0%
!! AAAAAAAAAAAATGATACCT+TGG + chr7.4:4320919-4320938 None:intergenic 15.0%
!! AAAAAAAAAAATGATACCTT+GGG + chr7.4:4320918-4320937 None:intergenic 15.0%
!! AAACAATAATCATATCAAAA+AGG + chr7.4:4321050-4321069 None:intergenic 15.0%
!! AAGTGAATAATATATCAAAT+TGG + chr7.4:4321021-4321040 None:intergenic 15.0%
!!! ATGATTTTTTTGTTTTTGTT+GGG - chr7.4:4321141-4321160 MS.gene054414:intron 15.0%
!!! GTTTTCAAATATAGATAAAA+TGG + chr7.4:4320993-4321012 None:intergenic 15.0%
!! AAGTTACAAAATGATGAAAT+GGG + chr7.4:4320944-4320963 None:intergenic 20.0%
!! TAAGTTACAAAATGATGAAA+TGG + chr7.4:4320945-4320964 None:intergenic 20.0%
!! TGAATAATATATCAAATTGG+TGG + chr7.4:4321018-4321037 None:intergenic 20.0%
!!! GATGATTTTTTTGTTTTTGT+TGG - chr7.4:4321140-4321159 MS.gene054414:intron 20.0%
! AGATAAAATGGAAGTGAAAA+AGG + chr7.4:4320981-4321000 None:intergenic 25.0%
! CTTCTTTCTATTTGTTTAAC+AGG - chr7.4:4320797-4320816 MS.gene054414:intron 25.0%
AATCATGGATCAAATGGATA+AGG - chr7.4:4320682-4320701 MS.gene054414:CDS 30.0%
ATGTTGTTCATACGATGAAA+TGG - chr7.4:4320821-4320840 MS.gene054414:intron 30.0%
TGTTGTTCATACGATGAAAT+GGG - chr7.4:4320822-4320841 MS.gene054414:intron 30.0%
AATCAGGTACAGAAAGAGAA+GGG - chr7.4:4321192-4321211 MS.gene054414:intron 35.0%
TTTCTTTGAGCTAACTAGCT+AGG - chr7.4:4320719-4320738 MS.gene054414:intron 35.0%
AAACCACCAAAACACCACTT+TGG - chr7.4:4320874-4320893 MS.gene054414:intron 40.0%
AATGATACCTTGGGTCCATT+TGG + chr7.4:4320909-4320928 None:intergenic 40.0%
ATCAGGTACAGAAAGAGAAG+GGG - chr7.4:4321193-4321212 MS.gene054414:intron 40.0%
GAATCAGGTACAGAAAGAGA+AGG - chr7.4:4321191-4321210 MS.gene054414:intron 40.0%
! AAAACACCACTTTGGAGAGG+AGG - chr7.4:4320882-4320901 MS.gene054414:intron 45.0%
! ACCAAAACACCACTTTGGAG+AGG - chr7.4:4320879-4320898 MS.gene054414:intron 45.0%
! TCCTCTCCAAAGTGGTGTTT+TGG + chr7.4:4320883-4320902 None:intergenic 45.0%
!! TCTCCAAAGTGGTGTTTTGG+TGG + chr7.4:4320880-4320899 None:intergenic 45.0%
TAGACGTTGTGCAACGCTTG+TGG - chr7.4:4321169-4321188 MS.gene054414:intron 50.0%
TGTGCAACGCTTGTGGAATC+AGG - chr7.4:4321176-4321195 MS.gene054414:intron 50.0%
TTTGGTCCTCCTCTCCAAAG+TGG + chr7.4:4320891-4320910 None:intergenic 50.0%
! CTTTGGAGAGGAGGACCAAA+TGG - chr7.4:4320891-4320910 MS.gene054414:intron 50.0%
AGGAGGACCAAATGGACCCA+AGG - chr7.4:4320899-4320918 MS.gene054414:intron 55.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 4320677 4321224 4320677 ID=MS.gene054414
chr7.4 mRNA 4320677 4321224 4320677 ID=MS.gene054414.t1;Parent=MS.gene054414
chr7.4 exon 4321198 4321224 4321198 ID=MS.gene054414.t1.exon1;Parent=MS.gene054414.t1
chr7.4 CDS 4321198 4321224 4321198 ID=cds.MS.gene054414.t1;Parent=MS.gene054414.t1
chr7.4 exon 4320981 4321082 4320981 ID=MS.gene054414.t1.exon2;Parent=MS.gene054414.t1
chr7.4 CDS 4320981 4321082 4320981 ID=cds.MS.gene054414.t1;Parent=MS.gene054414.t1
chr7.4 exon 4320677 4320703 4320677 ID=MS.gene054414.t1.exon3;Parent=MS.gene054414.t1
chr7.4 CDS 4320677 4320703 4320677 ID=cds.MS.gene054414.t1;Parent=MS.gene054414.t1
Gene Sequence

>MS.gene054414

ATGGGAATCATGGATCAAATGGATAAGGTATATTCAACTTTTTTTCTTTGAGCTAACTAGCTAGGTAGCTGCTTCTACTAACGTTGTTGTTGTTGTTGAAATGTTGAACATGTTCATTTTCTTCTTTCTATTTGTTTAACAGGAATGTTGTTCATACGATGAAATGGGTGTGATCAAGAAATTTTGTTCTGATTGCAAAACCACCAAAACACCACTTTGGAGAGGAGGACCAAATGGACCCAAGGTATCATTTTTTTTTTTTTACCCATTTCATCATTTTGTAACTTATAATTTTTAATTTCCTTTTTCACTTCCATTTTATCTATATTTGAAAACAACCACCAATTTGATATATTATTCACTTTCTTAGCCTTTTTGATATGATTATTGTTTTATTTTATTTTTTCATGTTTATTAATTTGATTAAAGGGTTTTTTGATTTTACTATGAATAGATTTGTTTTGATGATTTTTTTGTTTTTGTTGGGTGATGTAGACGTTGTGCAACGCTTGTGGAATCAGGTACAGAAAGAGAAGGGGTTGTTGTAG
Protein sequence

>MS.gene054414.t1

MGIMDQMDKECCSYDEMGVIKKFCSDCKTTKTPLWRGGPNGPKVQKEKGLL