AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene007496

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene007496.t1 MTR_7g100880 92.857 84 6 0 1 84 1 84 1.31e-29 100
MS.gene007496.t1 MTR_7g100905 89.474 76 3 1 9 84 3 73 2.02e-16 67.4
MS.gene007496.t1 MTR_7g100905 94.030 67 4 0 18 84 2 68 5.59e-15 63.5
MS.gene007496.t1 MTR_7g100890 82.716 81 10 2 8 84 417 497 1.04e-13 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene007496.t1 AT2G37120 78.689 61 13 0 24 84 16 76 5.80e-15 63.5
MS.gene007496.t1 AT3G53370 80.000 60 12 0 25 84 17 76 7.23e-13 58.2

Find 25 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAATAGTTCTCCTGGTTAT+TGG 0.281375 7.4:+9521089 MS.gene007496:CDS
GTTTAGAAAGCTGGATCTCT+AGG 0.416187 7.4:+9521053 MS.gene007496:intron
TGGGGAAATGTTTAGAAAGC+TGG 0.417081 7.4:+9521044 MS.gene007496:intron
GTCTCTGCACCTGGAGAGTA+GGG 0.431630 7.4:+9521239 MS.gene007496:CDS
GTCCATTGCCCCTACTCTCC+AGG 0.446840 7.4:-9521248 None:intergenic
ATGGCCGATGACTTTGAATT+CGG 0.448197 7.4:+9520691 MS.gene007496:CDS
ACCAGGAGAACTATTAAGCC+TGG 0.450176 7.4:-9521083 None:intergenic
TTGCTGTTGACATTCCTCAT+AGG 0.463310 7.4:+9521116 MS.gene007496:CDS
CCCAGGCTTAATAGTTCTCC+TGG 0.470539 7.4:+9521082 MS.gene007496:CDS
ATAGTTCTCCTGGTTATTGG+TGG 0.478741 7.4:+9521092 MS.gene007496:CDS
TCCTCCTTCCTTTGATCGCA+TGG 0.481901 7.4:+9520723 MS.gene007496:CDS
TAGTTCTCCTGGTTATTGGT+GGG 0.495632 7.4:+9521093 MS.gene007496:CDS
AAGCAAGGAGTCTCTGCACC+TGG 0.523372 7.4:+9521230 MS.gene007496:CDS
AGTCTCTGCACCTGGAGAGT+AGG 0.526480 7.4:+9521238 MS.gene007496:CDS
GAAGAGTACCATGCGATCAA+AGG 0.548062 7.4:-9520731 None:intergenic
TTTAGAAAGCTGGATCTCTA+GGG 0.566106 7.4:+9521054 MS.gene007496:intron
GAATTCAAAGTCATCGGCCA+TGG 0.568004 7.4:-9520689 None:intergenic
AGAGTGCATAATTTCCTATG+AGG 0.578802 7.4:-9521130 None:intergenic
ATCACCGAATTCAAAGTCAT+CGG 0.579370 7.4:-9520695 None:intergenic
CCAGGAGAACTATTAAGCCT+GGG 0.597197 7.4:-9521082 None:intergenic
ACAGCAACCCACCAATAACC+AGG 0.598951 7.4:-9521100 None:intergenic
AGTACCATGCGATCAAAGGA+AGG 0.619049 7.4:-9520727 None:intergenic
GGATCTCTAGGGTTCAACCC+AGG 0.683092 7.4:+9521065 MS.gene007496:CDS
ACCATGCGATCAAAGGAAGG+AGG 0.683503 7.4:-9520724 None:intergenic
TCTCTGCACCTGGAGAGTAG+GGG 0.689358 7.4:+9521240 MS.gene007496:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGATAAAAAACTTGATTA+AGG - chr7.4:9521012-9521031 None:intergenic 15.0%
!! TTAAGTTTAACTATATGTGT+TGG - chr7.4:9520876-9520895 None:intergenic 20.0%
! ATAACACAGAGCAATTAAAT+CGG - chr7.4:9520980-9520999 None:intergenic 25.0%
! ATGAGATGTAAGAAAAGAAA+AGG - chr7.4:9520756-9520775 None:intergenic 25.0%
! CTCAAAAAAGAAGATGAAAA+AGG + chr7.4:9521199-9521218 MS.gene007496:CDS 25.0%
! TTCAAATTATTATGCTAGCT+CGG + chr7.4:9520908-9520927 MS.gene007496:intron 25.0%
TCTTTAGATTAGACATGTCT+TGG + chr7.4:9520824-9520843 MS.gene007496:intron 30.0%
TTAATAGTTCTCCTGGTTAT+TGG + chr7.4:9521089-9521108 MS.gene007496:CDS 30.0%
! TTAACTATATGTGTTGGTGT+CGG - chr7.4:9520870-9520889 None:intergenic 30.0%
!!! TATCTTTTGTTGTTGCTCTT+GGG + chr7.4:9521025-9521044 MS.gene007496:intron 30.0%
!!! TTATCTTTTGTTGTTGCTCT+TGG + chr7.4:9521024-9521043 MS.gene007496:intron 30.0%
!!! TTCATCTTCTTTTTTGAGAC+TGG - chr7.4:9521197-9521216 None:intergenic 30.0%
AGAGTGCATAATTTCCTATG+AGG - chr7.4:9521133-9521152 None:intergenic 35.0%
ATCACCGAATTCAAAGTCAT+CGG - chr7.4:9520698-9520717 None:intergenic 35.0%
TTTAGAAAGCTGGATCTCTA+GGG + chr7.4:9521054-9521073 MS.gene007496:intron 35.0%
!!! ATCTTTTGTTGTTGCTCTTG+GGG + chr7.4:9521026-9521045 MS.gene007496:intron 35.0%
AAAAAGGAGAGACTGAAGCA+AGG + chr7.4:9521215-9521234 MS.gene007496:CDS 40.0%
ATAGTTCTCCTGGTTATTGG+TGG + chr7.4:9521092-9521111 MS.gene007496:CDS 40.0%
ATGGCCGATGACTTTGAATT+CGG + chr7.4:9520691-9520710 MS.gene007496:CDS 40.0%
GTTTAGAAAGCTGGATCTCT+AGG + chr7.4:9521053-9521072 MS.gene007496:intron 40.0%
TAGTTCTCCTGGTTATTGGT+GGG + chr7.4:9521093-9521112 MS.gene007496:CDS 40.0%
TGGGGAAATGTTTAGAAAGC+TGG + chr7.4:9521044-9521063 MS.gene007496:intron 40.0%
! ATTATTATGCTAGCTCGGTG+TGG + chr7.4:9520913-9520932 MS.gene007496:intron 40.0%
! GATTAGACATGTCTTGGTGT+AGG + chr7.4:9520830-9520849 MS.gene007496:intron 40.0%
! TTGCTGTTGACATTCCTCAT+AGG + chr7.4:9521116-9521135 MS.gene007496:CDS 40.0%
!!! ACTGGCTTCTTTTTTCTAGG+AGG - chr7.4:9521179-9521198 None:intergenic 40.0%
!!! CTGGCTTCTTTTTTCTAGGA+GGG - chr7.4:9521178-9521197 None:intergenic 40.0%
!!! CTTCTTTTTTCTAGGAGGGA+GGG - chr7.4:9521174-9521193 None:intergenic 40.0%
!!! GAGACTGGCTTCTTTTTTCT+AGG - chr7.4:9521182-9521201 None:intergenic 40.0%
ACCAGGAGAACTATTAAGCC+TGG - chr7.4:9521086-9521105 None:intergenic 45.0%
AGTACCATGCGATCAAAGGA+AGG - chr7.4:9520730-9520749 None:intergenic 45.0%
CCAGGAGAACTATTAAGCCT+GGG - chr7.4:9521085-9521104 None:intergenic 45.0%
!! CTATATGTGTTGGTGTCGGA+CGG - chr7.4:9520866-9520885 None:intergenic 45.0%
!! GAAGAGTACCATGCGATCAA+AGG - chr7.4:9520734-9520753 None:intergenic 45.0%
!!! GCTTCTTTTTTCTAGGAGGG+AGG - chr7.4:9521175-9521194 None:intergenic 45.0%
ACAGCAACCCACCAATAACC+AGG - chr7.4:9521103-9521122 None:intergenic 50.0%
ACCATGCGATCAAAGGAAGG+AGG - chr7.4:9520727-9520746 None:intergenic 50.0%
CCCAGGCTTAATAGTTCTCC+TGG + chr7.4:9521082-9521101 MS.gene007496:CDS 50.0%
TCCTCCTTCCTTTGATCGCA+TGG + chr7.4:9520723-9520742 MS.gene007496:CDS 50.0%
!! AAGAGTGTCTGCGTGTGAGA+TGG - chr7.4:9520808-9520827 None:intergenic 50.0%
AAGCAAGGAGTCTCTGCACC+TGG + chr7.4:9521230-9521249 MS.gene007496:CDS 55.0%
!! GGATCTCTAGGGTTCAACCC+AGG + chr7.4:9521065-9521084 MS.gene007496:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.4 gene 9520691 9521259 9520691 ID=MS.gene007496
chr7.4 mRNA 9520691 9521259 9520691 ID=MS.gene007496.t1;Parent=MS.gene007496
chr7.4 exon 9520691 9520744 9520691 ID=MS.gene007496.t1.exon1;Parent=MS.gene007496.t1
chr7.4 CDS 9520691 9520744 9520691 ID=cds.MS.gene007496.t1;Parent=MS.gene007496.t1
chr7.4 exon 9521059 9521259 9521059 ID=MS.gene007496.t1.exon2;Parent=MS.gene007496.t1
chr7.4 CDS 9521059 9521259 9521059 ID=cds.MS.gene007496.t1;Parent=MS.gene007496.t1
Gene Sequence

>MS.gene007496

ATGGCCGATGACTTTGAATTCGGTGATAAAGTTCCTCCTTCCTTTGATCGCATGGTACTCTTCCTTTTCTTTTCTTACATCTCATTATTTGTATCATTTCATTCTTTATAGCATCCATCTCACACGCAGACACTCTTTAGATTAGACATGTCTTGGTGTAGGACACGTGACACCGTCCGACACCAACACATATAGTTAAACTTAACTATGTGATCTTTTCAAATTATTATGCTAGCTCGGTGTGGTATCTGATGTATGTGTATGTATTCGTGTTTTGCTAACATGTCCGATTTAATTGCTCTGTGTTATCTGATATGACCTTAATCAAGTTTTTTATCTTTTGTTGTTGCTCTTGGGGAAATGTTTAGAAAGCTGGATCTCTAGGGTTCAACCCAGGCTTAATAGTTCTCCTGGTTATTGGTGGGTTGCTGTTGACATTCCTCATAGGAAATTATGCACTCTACGTTTATGCACAGAAGACCCTCCCTCCTAGAAAAAAGAAGCCAGTCTCAAAAAAGAAGATGAAAAAGGAGAGACTGAAGCAAGGAGTCTCTGCACCTGGAGAGTAG
Protein sequence

>MS.gene007496.t1

MADDFEFGDKVPPSFDRMKAGSLGFNPGLIVLLVIGGLLLTFLIGNYALYVYAQKTLPPRKKKPVSKKKMKKERLKQGVSAPGE