AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene051594


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051594.t1 MTR_5g010330 93.671 79 5 0 6 84 241 319 1.54e-48 157
MS.gene051594.t1 MTR_8g098390 62.025 79 28 2 5 83 272 348 7.08e-23 90.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 21 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATCAAAACTATACAGCTTC+TGG 0.279195 1.3:-6168836 MS.gene051594:CDS
TGATTAGGTGGCTCACTTCC+TGG 0.283204 1.3:+6168854 None:intergenic
AAAACTGTATTAGATGGTTA+AGG 0.301473 1.3:-6168621 None:intergenic
CCCCAAAACAAATGAGACTT+TGG 0.364990 1.3:-6169000 None:intergenic
AAACTGTATTAGATGGTTAA+GGG 0.378396 1.3:-6168620 None:intergenic
AACTATACAGCTTCTGGAAC+AGG 0.388590 1.3:-6168830 MS.gene051594:CDS
TCAGAAAACAATGGAGCAAA+TGG 0.434254 1.3:-6168659 MS.gene051594:intron
AGAGAGATACCTTGGTATCA+AGG 0.477477 1.3:+6168745 None:intergenic
AGTGACAAATTAGCTTCTCC+AGG 0.534618 1.3:-6168872 MS.gene051594:CDS
GCACAATGTGGCATGGATCA+AGG 0.545853 1.3:-6168808 MS.gene051594:CDS
GTAGTTTGCAGCTTTGTGTA+CGG 0.556100 1.3:-6168965 MS.gene051594:CDS
AATGAGACTTTGGTTGCTGC+AGG 0.562965 1.3:-6168990 MS.gene051594:CDS
GAAAACAATGGAGCAAATGG+TGG 0.588829 1.3:-6168656 MS.gene051594:CDS
GGAACAGGCACAATGTGGCA+TGG 0.608270 1.3:-6168815 MS.gene051594:CDS
CTGGTATCTCCTTGATACCA+AGG 0.620045 1.3:-6168754 MS.gene051594:intron
GTTTGCAGCTTTGTGTACGG+TGG 0.633716 1.3:-6168962 MS.gene051594:CDS
AAAAGTACACAACCACACAC+TGG 0.665666 1.3:-6168773 MS.gene051594:CDS
GAGACTTTGGTTGCTGCAGG+TGG 0.669900 1.3:-6168987 MS.gene051594:CDS
GCTAATTTGTCACTACTCTG+AGG 0.677251 1.3:+6168881 None:intergenic
CTTCTGGAACAGGCACAATG+TGG 0.706254 1.3:-6168820 MS.gene051594:CDS
ATCAAGGAGATACCAGTGTG+TGG 0.744996 1.3:+6168761 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGGTGTTATTAAAGTTTATA+CGG - chr1.3:6168914-6168933 MS.gene051594:CDS 20.0%
!!! TTCTTATTTTCAGAAAACAA+TGG - chr1.3:6168944-6168963 MS.gene051594:CDS 20.0%
! GACTTAAAAACTGTATTAGA+TGG - chr1.3:6168985-6169004 MS.gene051594:CDS 25.0%
!! GTGTTATTAAAGTTTATACG+GGG - chr1.3:6168916-6168935 MS.gene051594:CDS 25.0%
!! TTTATTGTCTAACTGAGTTT+TGG - chr1.3:6168894-6168913 MS.gene051594:CDS 25.0%
!!! GGTGTTATTAAAGTTTATAC+GGG - chr1.3:6168915-6168934 MS.gene051594:CDS 25.0%
AATCAAAACTATACAGCTTC+TGG - chr1.3:6168776-6168795 MS.gene051594:CDS 30.0%
TAAATATGAGAGAGATACCT+TGG + chr1.3:6168878-6168897 None:intergenic 30.0%
!!! GAAGCTGTATAGTTTTGATT+AGG + chr1.3:6168776-6168795 None:intergenic 30.0%
!!! GTTTCTTGTTTTGTTGTCTT+TGG + chr1.3:6168683-6168702 None:intergenic 30.0%
TCAGAAAACAATGGAGCAAA+TGG - chr1.3:6168953-6168972 MS.gene051594:CDS 35.0%
!!! GCTGTATAGTTTTGATTAGG+TGG + chr1.3:6168773-6168792 None:intergenic 35.0%
AGAGAGATACCTTGGTATCA+AGG + chr1.3:6168870-6168889 None:intergenic 40.0%
GAAAACAATGGAGCAAATGG+TGG - chr1.3:6168956-6168975 MS.gene051594:CDS 40.0%
! AAAAGTACACAACCACACAC+TGG - chr1.3:6168839-6168858 MS.gene051594:CDS 40.0%
! AGTGACAAATTAGCTTCTCC+AGG - chr1.3:6168740-6168759 MS.gene051594:intron 40.0%
! GCTAATTTGTCACTACTCTG+AGG + chr1.3:6168734-6168753 None:intergenic 40.0%
! GTAGTTTGCAGCTTTGTGTA+CGG - chr1.3:6168647-6168666 MS.gene051594:CDS 40.0%
!! AACTATACAGCTTCTGGAAC+AGG - chr1.3:6168782-6168801 MS.gene051594:CDS 40.0%
ATCAAGGAGATACCAGTGTG+TGG + chr1.3:6168854-6168873 None:intergenic 45.0%
CTGGTATCTCCTTGATACCA+AGG - chr1.3:6168858-6168877 MS.gene051594:CDS 45.0%
GCACAATGTGGCATGGATCA+AGG - chr1.3:6168804-6168823 MS.gene051594:CDS 50.0%
TGATTAGGTGGCTCACTTCC+TGG + chr1.3:6168761-6168780 None:intergenic 50.0%
! GTTTGCAGCTTTGTGTACGG+TGG - chr1.3:6168650-6168669 MS.gene051594:CDS 50.0%
!! CTTCTGGAACAGGCACAATG+TGG - chr1.3:6168792-6168811 MS.gene051594:CDS 50.0%
GAGACTTTGGTTGCTGCAGG+TGG - chr1.3:6168625-6168644 MS.gene051594:CDS 55.0%
GGAACAGGCACAATGTGGCA+TGG - chr1.3:6168797-6168816 MS.gene051594:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 6168623 6169011 6168623 ID=MS.gene051594
chr1.3 mRNA 6168623 6169011 6168623 ID=MS.gene051594.t1;Parent=MS.gene051594
chr1.3 exon 6168755 6169011 6168755 ID=MS.gene051594.t1.exon1;Parent=MS.gene051594.t1
chr1.3 CDS 6168755 6169011 6168755 ID=cds.MS.gene051594.t1;Parent=MS.gene051594.t1
chr1.3 exon 6168623 6168677 6168623 ID=MS.gene051594.t1.exon2;Parent=MS.gene051594.t1
chr1.3 CDS 6168623 6168677 6168623 ID=cds.MS.gene051594.t1;Parent=MS.gene051594.t1
Gene Sequence

>MS.gene051594

ATGAGACTTTGGTTGCTGCAGGTGGTAGTTTGCAGCTTTGTGTACGGTGGTTCTAAGCCAAAGACAACAAAACAAGAAACTGCTGCAAAAGAAGATGATGATTCTGAGCCTCAGAGTAGTGACAAATTAGCTTCTCCAGGAAGTGAGCCACCTAATCAAAACTATACAGCTTCTGGAACAGGCACAATGTGGCATGGATCAAGGACAGTAGACGTGAAAAGTACACAACCACACACTGGTATCTCCTTGATACCAAGGTATCTCTCTCATATTTATTGTCTAACTGAGTTTTGGTGTTATTAAAGTTTATACGGGGTTGATTTCTTATTTTCAGAAAACAATGGAGCAAATGGTGGATAAGCGACTTAAAAACTGTATTAGATGGTTAA

Protein sequence

>MS.gene051594.t1

MRLWLLQVVVCSFVYGGSKPKTTKQETAAKEDDDSEPQSSDKLASPGSEPPNQNYTASGTGTMWHGSRTVDVKSTQPHTGISLIPRKQWSKWWISDLKTVLDG