AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene053454

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053454.t1 MTR_1g045040 86.567 134 18 0 1 134 1 134 3.74e-77 224
MS.gene053454.t1 MTR_1g089830 75.573 131 25 2 1 130 1 125 4.62e-68 202
MS.gene053454.t1 MTR_8g089170 39.456 147 63 3 6 127 7 152 2.81e-23 89.0
MS.gene053454.t1 MTR_8g089130 36.424 151 70 3 6 130 7 157 5.73e-22 85.9
MS.gene053454.t1 MTR_8g039350 78.378 37 8 0 8 44 19 55 6.06e-17 70.5
MS.gene053454.t1 MTR_4g028990 40.625 96 47 4 43 130 3 96 1.88e-12 59.7
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 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAAAAGCTTCAAAGTCTA+TGG 0.184389 1.4:+29375059 MS.gene053454:CDS
CGCTTGTGGGCTACATTTCA+AGG 0.378248 1.4:+29374464 MS.gene053454:CDS
CAATACTATGTAACGCTTGT+GGG 0.416623 1.4:+29374451 MS.gene053454:CDS
CCACAAGCGTTACATAGTAT+TGG 0.447482 1.4:-29374450 None:intergenic
TGGAGATTGGTTTGAAAGCT+CGG 0.447768 1.4:-29374577 None:intergenic
ATCAGACCTTGACGTTGAAA+AGG 0.465983 1.4:+29374539 MS.gene053454:CDS
GAAACTAAACTTTGGCGTAA+AGG 0.477501 1.4:+29374414 MS.gene053454:CDS
TCTTCGGAAGATAGTTATCA+AGG 0.478433 1.4:-29374497 None:intergenic
TGTATACCAAGCAATGAGAT+AGG 0.478624 1.4:+29375148 MS.gene053454:CDS
CATAGTATTGGCTTCTCATA+CGG 0.490978 1.4:-29374438 None:intergenic
ATCGATTGTGAAGAATCAAA+TGG 0.491491 1.4:+29375027 MS.gene053454:CDS
GGGCTACATTTCAAGGCTAA+AGG 0.492067 1.4:+29374471 MS.gene053454:CDS
GGAGATTGGTTTGAAAGCTC+GGG 0.493147 1.4:-29374576 None:intergenic
CCAAGCAATGAGATAGGCAT+TGG 0.496933 1.4:+29375154 MS.gene053454:CDS
ATTTGATTCTTCACAATCGA+TGG 0.523804 1.4:-29375025 None:intergenic
CCAATACTATGTAACGCTTG+TGG 0.549603 1.4:+29374450 MS.gene053454:CDS
ACAAAAGCTTCAAAGTCTAT+GGG 0.556384 1.4:+29375060 MS.gene053454:CDS
CCAATGCCTATCTCATTGCT+TGG 0.566560 1.4:-29375154 None:intergenic
GAGCTTTCAAACCAATCTCC+AGG 0.568278 1.4:+29374579 MS.gene053454:CDS
CTTCGGAAGATAGTTATCAA+GGG 0.629882 1.4:-29374496 None:intergenic
GATTGTGAAGAATCAAATGG+AGG 0.680011 1.4:+29375030 MS.gene053454:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ACTTTTAATTTTTTGTAGAA+AGG + chr1.4:29374999-29375018 MS.gene053454:intron 15.0%
!!! CTTTATATTTGTTGAAAAAT+GGG - chr1.4:29374640-29374659 None:intergenic 15.0%
!!! TTTATATTTGTTGAAAAATG+GGG - chr1.4:29374639-29374658 None:intergenic 15.0%
!! AACACTACTATTTATATATG+AGG + chr1.4:29374745-29374764 MS.gene053454:intron 20.0%
!! TTATATGTATACATCATACA+CGG - chr1.4:29374979-29374998 None:intergenic 20.0%
!!! ATTGTAAGAATTTTCTTAAG+AGG + chr1.4:29374694-29374713 MS.gene053454:intron 20.0%
!!! GCTTTATATTTGTTGAAAAA+TGG - chr1.4:29374641-29374660 None:intergenic 20.0%
!!! TTATTGCATTTTTTATTACC+TGG - chr1.4:29374600-29374619 None:intergenic 20.0%
!!! TTTGAATGAATTGTATTGAT+GGG + chr1.4:29374839-29374858 MS.gene053454:intron 20.0%
!!! TTTTGAATGAATTGTATTGA+TGG + chr1.4:29374838-29374857 MS.gene053454:intron 20.0%
! ATTGACAATGAAAGGAATTA+GGG - chr1.4:29374785-29374804 None:intergenic 25.0%
! TATCCATAAATGTATGAATG+TGG - chr1.4:29374888-29374907 None:intergenic 25.0%
! TATTGACAATGAAAGGAATT+AGG - chr1.4:29374786-29374805 None:intergenic 25.0%
!! TTGAATGAATTGTATTGATG+GGG + chr1.4:29374840-29374859 MS.gene053454:intron 25.0%
!! TTTCTTAAGAGGTACAATTT+AGG + chr1.4:29374705-29374724 MS.gene053454:intron 25.0%
!!! ATTTTTTATTACCTGGAGAT+TGG - chr1.4:29374593-29374612 None:intergenic 25.0%
AACAAAAGCTTCAAAGTCTA+TGG + chr1.4:29375059-29375078 MS.gene053454:CDS 30.0%
ACAAAAGCTTCAAAGTCTAT+GGG + chr1.4:29375060-29375079 MS.gene053454:CDS 30.0%
ACTCCACATTCATACATTTA+TGG + chr1.4:29374882-29374901 MS.gene053454:intron 30.0%
ATCGATTGTGAAGAATCAAA+TGG + chr1.4:29375027-29375046 MS.gene053454:CDS 30.0%
ATGCTCTTATTGACAATGAA+AGG - chr1.4:29374793-29374812 None:intergenic 30.0%
ATTTGATTCTTCACAATCGA+TGG - chr1.4:29375028-29375047 None:intergenic 30.0%
! TTTTGGCAGAAACTAAACTT+TGG + chr1.4:29374406-29374425 MS.gene053454:CDS 30.0%
AGCATTCATTTGAGTAGACA+CGG + chr1.4:29374808-29374827 MS.gene053454:intron 35.0%
ATTTGAGTAGACACGGTATT+AGG + chr1.4:29374815-29374834 MS.gene053454:intron 35.0%
CAATACTATGTAACGCTTGT+GGG + chr1.4:29374451-29374470 MS.gene053454:CDS 35.0%
CTTCGGAAGATAGTTATCAA+GGG - chr1.4:29374499-29374518 None:intergenic 35.0%
GAAACTAAACTTTGGCGTAA+AGG + chr1.4:29374414-29374433 MS.gene053454:CDS 35.0%
GATTGTGAAGAATCAAATGG+AGG + chr1.4:29375030-29375049 MS.gene053454:CDS 35.0%
TCATACACGGTACATATCAA+TGG - chr1.4:29374966-29374985 None:intergenic 35.0%
TCTTCGGAAGATAGTTATCA+AGG - chr1.4:29374500-29374519 None:intergenic 35.0%
TGTATACCAAGCAATGAGAT+AGG + chr1.4:29375148-29375167 MS.gene053454:CDS 35.0%
! GAATTGTATTGATGGGGATT+AGG + chr1.4:29374846-29374865 MS.gene053454:intron 35.0%
!! CATAGTATTGGCTTCTCATA+CGG - chr1.4:29374441-29374460 None:intergenic 35.0%
!! GTCTGATAACTGATTTTGCT+GGG - chr1.4:29374526-29374545 None:intergenic 35.0%
ATCAGACCTTGACGTTGAAA+AGG + chr1.4:29374539-29374558 MS.gene053454:CDS 40.0%
CCAATACTATGTAACGCTTG+TGG + chr1.4:29374450-29374469 MS.gene053454:CDS 40.0%
CCACAAGCGTTACATAGTAT+TGG - chr1.4:29374453-29374472 None:intergenic 40.0%
! CAGATTCCTTTTCAACGTCA+AGG - chr1.4:29374548-29374567 None:intergenic 40.0%
! TGATTTTGCTGGGATGTCTT+CGG - chr1.4:29374516-29374535 None:intergenic 40.0%
!! GGTCTGATAACTGATTTTGC+TGG - chr1.4:29374527-29374546 None:intergenic 40.0%
!! TGGAGATTGGTTTGAAAGCT+CGG - chr1.4:29374580-29374599 None:intergenic 40.0%
CCAAGCAATGAGATAGGCAT+TGG + chr1.4:29375154-29375173 MS.gene053454:CDS 45.0%
CCAATGCCTATCTCATTGCT+TGG - chr1.4:29375157-29375176 None:intergenic 45.0%
GAGCTTTCAAACCAATCTCC+AGG + chr1.4:29374579-29374598 MS.gene053454:CDS 45.0%
GGGCTACATTTCAAGGCTAA+AGG + chr1.4:29374471-29374490 MS.gene053454:CDS 45.0%
!! GGAGATTGGTTTGAAAGCTC+GGG - chr1.4:29374579-29374598 None:intergenic 45.0%
! CGCTTGTGGGCTACATTTCA+AGG + chr1.4:29374464-29374483 MS.gene053454:CDS 50.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 29374402 29375222 29374402 ID=MS.gene053454
chr1.4 mRNA 29374402 29375222 29374402 ID=MS.gene053454.t1;Parent=MS.gene053454
chr1.4 exon 29374402 29374600 29374402 ID=MS.gene053454.t1.exon1;Parent=MS.gene053454.t1
chr1.4 CDS 29374402 29374600 29374402 ID=cds.MS.gene053454.t1;Parent=MS.gene053454.t1
chr1.4 exon 29375017 29375222 29375017 ID=MS.gene053454.t1.exon2;Parent=MS.gene053454.t1
chr1.4 CDS 29375017 29375222 29375017 ID=cds.MS.gene053454.t1;Parent=MS.gene053454.t1
Gene Sequence

>MS.gene053454

ATGGTTTTGGCAGAAACTAAACTTTGGCGTAAAGGACCGTATGAGAAGCCAATACTATGTAACGCTTGTGGGCTACATTTCAAGGCTAAAGGAACCCTTGATAACTATCTTCCGAAGACATCCCAGCAAAATCAGTTATCAGACCTTGACGTTGAAAAGGAATCTGAAAGTGATCCCGAGCTTTCAAACCAATCTCCAGGTAATAAAAAATGCAATAAGTTAATTAACTATTCACCCCATTTTTCAACAAATATAAAGCACAATTTATACAAGAAGAGTGAGCGAGAAAGTTATTGTAAGAATTTTCTTAAGAGGTACAATTTAGGAGTATTGTTATGATATAAACACTACTATTTATATATGAGGTGTAACATTGTCAACCCTAATTCCTTTCATTGTCAATAAGAGCATTCATTTGAGTAGACACGGTATTAGGTTTTGAATGAATTGTATTGATGGGGATTAGGTGACATACATACAACTCCACATTCATACATTTATGGATATATTTTTTTCAAATAATAGCATATATTTTTTCAAATAATACATATAAATGATTATCCATTGATATGTACCGTGTATGATGTATACATATAAACTTTTAATTTTTTGTAGAAAGGACACCATCGATTGTGAAGAATCAAATGGAGGAGTTTCAACAAAAGCTTCAAAGTCTATGGGAATCTGAGAAAGAATCAAATGAATCATCTGCAGACAATATTTTGTTGTTTGATAATATGAACAACTGTATACCAAGCAATGAGATAGGCATTGGATGCACTCTACTAAAGACAGATGTTACTTCTAAAAAATCTGCATGA
Protein sequence

>MS.gene053454.t1

MVLAETKLWRKGPYEKPILCNACGLHFKAKGTLDNYLPKTSQQNQLSDLDVEKESESDPELSNQSPERTPSIVKNQMEEFQQKLQSLWESEKESNESSADNILLFDNMNNCIPSNEIGIGCTLLKTDVTSKKSA