AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53532

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53532.t1 MTR_1g045040 87.313 134 17 0 1 134 1 134 8.24e-78 226
MS.gene53532.t1 MTR_1g089830 76.336 131 24 2 1 130 1 125 1.24e-68 203
MS.gene53532.t1 MTR_8g089170 39.456 147 63 3 6 127 7 152 2.69e-23 89.0
MS.gene53532.t1 MTR_8g089130 36.424 151 70 3 6 130 7 157 5.67e-22 85.9
MS.gene53532.t1 MTR_8g039350 73.171 41 11 0 4 44 15 55 3.68e-17 70.9
MS.gene53532.t1 MTR_4g028990 40.625 96 47 4 43 130 3 96 1.84e-12 59.7
MS.gene53532.t1 MTR_5g013370 51.852 54 25 1 3 56 12 64 3.22e-11 59.7
MS.gene53532.t1 MTR_5g013370 51.852 54 25 1 3 56 12 64 4.83e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAAAAGCTTCAAAGTCTA+TGG 0.184389 1.2:+27931405 MS.gene53532:CDS
CCACAAGCATTACATAGTAT+TGG 0.433061 1.2:-27930795 None:intergenic
TGGAGATTGGTTTGAAAGCT+CGG 0.447768 1.2:-27930922 None:intergenic
GAAACTAAACTTTGGCGTAA+AGG 0.456777 1.2:+27930759 MS.gene53532:CDS
TGCTTGTGGACTACATTTCA+AGG 0.461822 1.2:+27930809 MS.gene53532:CDS
ATCAGACCTTGACGTTGAAA+AGG 0.465983 1.2:+27930884 MS.gene53532:CDS
GGACTACATTTCAAGGCTAA+AGG 0.474721 1.2:+27930816 MS.gene53532:CDS
TCTTCGGAAGATAGTTATCA+AGG 0.478433 1.2:-27930842 None:intergenic
TGTATACCAAGCAATGAGAT+AGG 0.478624 1.2:+27931494 MS.gene53532:CDS
ATCGATTGTGAAGAATCAAA+TGG 0.491491 1.2:+27931373 MS.gene53532:CDS
CATAGTATTGGCTTCTCATA+CGG 0.492997 1.2:-27930783 None:intergenic
GGAGATTGGTTTGAAAGCTC+GGG 0.493147 1.2:-27930921 None:intergenic
CCAAGCAATGAGATAGGCAT+TGG 0.496933 1.2:+27931500 MS.gene53532:CDS
ATTTGATTCTTCACAATCGA+TGG 0.523804 1.2:-27931371 None:intergenic
ACAAAAGCTTCAAAGTCTAT+GGG 0.556384 1.2:+27931406 MS.gene53532:CDS
CCAATGCCTATCTCATTGCT+TGG 0.566560 1.2:-27931500 None:intergenic
GAGCTTTCAAACCAATCTCC+AGG 0.568278 1.2:+27930924 MS.gene53532:CDS
CCAATACTATGTAATGCTTG+TGG 0.579274 1.2:+27930795 MS.gene53532:CDS
CTTCGGAAGATAGTTATCAA+GGG 0.629882 1.2:-27930841 None:intergenic
GATTGTGAAGAATCAAATGG+AGG 0.680011 1.2:+27931376 MS.gene53532:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACTTTTAATTTTTTGTAGAA+AGG + chr1.2:27931345-27931364 MS.gene53532:intron 15.0%
!!! CTTTATATTTGTTGAAAAAT+GGG - chr1.2:27930985-27931004 None:intergenic 15.0%
!!! TTTATATTTGTTGAAAAATG+GGG - chr1.2:27930984-27931003 None:intergenic 15.0%
!! AACACTACTATTTATATATG+AGG + chr1.2:27931090-27931109 MS.gene53532:intron 20.0%
!! TTATATGTATACATCATACA+CGG - chr1.2:27931325-27931344 None:intergenic 20.0%
!!! ATTGTAAGAATTTTCTTAAG+AGG + chr1.2:27931039-27931058 MS.gene53532:intron 20.0%
!!! GCTTTATATTTGTTGAAAAA+TGG - chr1.2:27930986-27931005 None:intergenic 20.0%
!!! TTATTGCATTTTTTATTACC+TGG - chr1.2:27930945-27930964 None:intergenic 20.0%
!!! TTTGAATGAATTGTATTGAT+GGG + chr1.2:27931184-27931203 MS.gene53532:intron 20.0%
!!! TTTTGAATGAATTGTATTGA+TGG + chr1.2:27931183-27931202 MS.gene53532:intron 20.0%
! ATTCATTCAAAACCTAATAC+CGG - chr1.2:27931175-27931194 None:intergenic 25.0%
! ATTGACAATGAAAGGAATTA+GGG - chr1.2:27931130-27931149 None:intergenic 25.0%
! TATCCATAAATGTATGAATG+TGG - chr1.2:27931233-27931252 None:intergenic 25.0%
! TATTGACAATGAAAGGAATT+AGG - chr1.2:27931131-27931150 None:intergenic 25.0%
!! TTGAATGAATTGTATTGATG+GGG + chr1.2:27931185-27931204 MS.gene53532:intron 25.0%
!! TTTCTTAAGAGGTACAATTT+AGG + chr1.2:27931050-27931069 MS.gene53532:intron 25.0%
!! TTTTGACAGAAACTAAACTT+TGG + chr1.2:27930751-27930770 MS.gene53532:CDS 25.0%
!!! ATTTTTTATTACCTGGAGAT+TGG - chr1.2:27930938-27930957 None:intergenic 25.0%
AACAAAAGCTTCAAAGTCTA+TGG + chr1.2:27931405-27931424 MS.gene53532:CDS 30.0%
ACAAAAGCTTCAAAGTCTAT+GGG + chr1.2:27931406-27931425 MS.gene53532:CDS 30.0%
ACTCCACATTCATACATTTA+TGG + chr1.2:27931227-27931246 MS.gene53532:intron 30.0%
ATCGATTGTGAAGAATCAAA+TGG + chr1.2:27931373-27931392 MS.gene53532:CDS 30.0%
ATGCTCTTATTGACAATGAA+AGG - chr1.2:27931138-27931157 None:intergenic 30.0%
ATTTGATTCTTCACAATCGA+TGG - chr1.2:27931374-27931393 None:intergenic 30.0%
TTCATTCAAAACCTAATACC+GGG - chr1.2:27931174-27931193 None:intergenic 30.0%
CCAATACTATGTAATGCTTG+TGG + chr1.2:27930795-27930814 MS.gene53532:CDS 35.0%
CCACAAGCATTACATAGTAT+TGG - chr1.2:27930798-27930817 None:intergenic 35.0%
CTTCGGAAGATAGTTATCAA+GGG - chr1.2:27930844-27930863 None:intergenic 35.0%
GAAACTAAACTTTGGCGTAA+AGG + chr1.2:27930759-27930778 MS.gene53532:CDS 35.0%
GATTGTGAAGAATCAAATGG+AGG + chr1.2:27931376-27931395 MS.gene53532:CDS 35.0%
TCATACACGGTACATATCAA+TGG - chr1.2:27931312-27931331 None:intergenic 35.0%
TCTTCGGAAGATAGTTATCA+AGG - chr1.2:27930845-27930864 None:intergenic 35.0%
TGTATACCAAGCAATGAGAT+AGG + chr1.2:27931494-27931513 MS.gene53532:CDS 35.0%
! GAATTGTATTGATGGGGATT+AGG + chr1.2:27931191-27931210 MS.gene53532:intron 35.0%
!! CATAGTATTGGCTTCTCATA+CGG - chr1.2:27930786-27930805 None:intergenic 35.0%
!! GTCTGATAACTGATTTTGCT+GGG - chr1.2:27930871-27930890 None:intergenic 35.0%
AGCATTCATTTGAGTAGACC+CGG + chr1.2:27931153-27931172 MS.gene53532:intron 40.0%
ATCAGACCTTGACGTTGAAA+AGG + chr1.2:27930884-27930903 MS.gene53532:CDS 40.0%
ATTTGAGTAGACCCGGTATT+AGG + chr1.2:27931160-27931179 MS.gene53532:intron 40.0%
GGACTACATTTCAAGGCTAA+AGG + chr1.2:27930816-27930835 MS.gene53532:CDS 40.0%
! CAGATTCCTTTTCAACGTCA+AGG - chr1.2:27930893-27930912 None:intergenic 40.0%
! TGATTTTGCTGGGATGTCTT+CGG - chr1.2:27930861-27930880 None:intergenic 40.0%
! TGCTTGTGGACTACATTTCA+AGG + chr1.2:27930809-27930828 MS.gene53532:CDS 40.0%
!! GGTCTGATAACTGATTTTGC+TGG - chr1.2:27930872-27930891 None:intergenic 40.0%
!! TGGAGATTGGTTTGAAAGCT+CGG - chr1.2:27930925-27930944 None:intergenic 40.0%
CCAAGCAATGAGATAGGCAT+TGG + chr1.2:27931500-27931519 MS.gene53532:CDS 45.0%
CCAATGCCTATCTCATTGCT+TGG - chr1.2:27931503-27931522 None:intergenic 45.0%
GAGCTTTCAAACCAATCTCC+AGG + chr1.2:27930924-27930943 MS.gene53532:CDS 45.0%
!! GGAGATTGGTTTGAAAGCTC+GGG - chr1.2:27930924-27930943 None:intergenic 45.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 27930747 27931568 27930747 ID=MS.gene53532
chr1.2 mRNA 27930747 27931568 27930747 ID=MS.gene53532.t1;Parent=MS.gene53532
chr1.2 exon 27930747 27930945 27930747 ID=MS.gene53532.t1.exon1;Parent=MS.gene53532.t1
chr1.2 CDS 27930747 27930945 27930747 ID=cds.MS.gene53532.t1;Parent=MS.gene53532.t1
chr1.2 exon 27931363 27931568 27931363 ID=MS.gene53532.t1.exon2;Parent=MS.gene53532.t1
chr1.2 CDS 27931363 27931568 27931363 ID=cds.MS.gene53532.t1;Parent=MS.gene53532.t1
Gene Sequence

>MS.gene53532

ATGGTTTTGACAGAAACTAAACTTTGGCGTAAAGGACCGTATGAGAAGCCAATACTATGTAATGCTTGTGGACTACATTTCAAGGCTAAAGGAACCCTTGATAACTATCTTCCGAAGACATCCCAGCAAAATCAGTTATCAGACCTTGACGTTGAAAAGGAATCTGAAAGTGATCCCGAGCTTTCAAACCAATCTCCAGGTAATAAAAAATGCAATAAGTTAATTAACTATTCACCCCATTTTTCAACAAATATAAAGCACAATTTATACAAGAAGAGTGAGCGAGAAAGTTATTGTAAGAATTTTCTTAAGAGGTACAATTTAGGAGTATTGTTATGATATAAACACTACTATTTATATATGAGGTGTAACATTGTCAACCCTAATTCCTTTCATTGTCAATAAGAGCATTCATTTGAGTAGACCCGGTATTAGGTTTTGAATGAATTGTATTGATGGGGATTAGGTGACATACATACAACTCCACATTCATACATTTATGGATATATTTTTTTTCAAATAATAGCATATATTTTTTCAAATAATACATATAAATGATTATCCATTGATATGTACCGTGTATGATGTATACATATAAACTTTTAATTTTTTGTAGAAAGGACACCATCGATTGTGAAGAATCAAATGGAGGAGTTTCAACAAAAGCTTCAAAGTCTATGGGAATCTGAGAAAGAATCAAATGAATCATCTGCAGACAATATTTTGTTGTTTGATAATATGAACAACTGTATACCAAGCAATGAGATAGGCATTGGATGCACTCTACTGAAGACAGATGTTACTTCTAAAAAATCTGCATGA
Protein sequence

>MS.gene53532.t1

MVLTETKLWRKGPYEKPILCNACGLHFKAKGTLDNYLPKTSQQNQLSDLDVEKESESDPELSNQSPERTPSIVKNQMEEFQQKLQSLWESEKESNESSADNILLFDNMNNCIPSNEIGIGCTLLKTDVTSKKSA