AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene053452

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053452.t1 MTR_1g045040 85.821 134 19 0 1 134 1 134 2.88e-76 222
MS.gene053452.t1 MTR_1g089830 74.809 131 26 2 1 130 1 125 3.75e-67 200
MS.gene053452.t1 MTR_8g089170 38.776 147 64 3 6 127 7 152 2.21e-22 86.7
MS.gene053452.t1 MTR_8g089130 35.762 151 71 3 6 130 7 157 3.90e-21 83.6
MS.gene053452.t1 MTR_8g039350 78.378 37 8 0 8 44 19 55 6.26e-17 70.1
MS.gene053452.t1 MTR_4g028990 39.583 96 48 4 43 130 3 96 1.73e-11 57.0
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:+29340101 MS.gene053452:CDS
CGCTTGTGGGCTACATTTCA+AGG 0.378248 1.4:+29339504 MS.gene053452:CDS
CAATACTATGTAACGCTTGT+GGG 0.416623 1.4:+29339491 MS.gene053452:CDS
CCACAAGCGTTACATAGTAT+TGG 0.447482 1.4:-29339490 None:intergenic
TGGAGATTGGTTTGAAAGCT+CGG 0.447768 1.4:-29339617 None:intergenic
TGTATACCAAGCAATGAGAT+AGG 0.462534 1.4:+29340190 MS.gene053452:CDS
ATCAGACCTTGACGTTGAAA+AGG 0.465983 1.4:+29339579 MS.gene053452:CDS
GAAACTAAACTTTGGCGTAA+AGG 0.477501 1.4:+29339454 MS.gene053452:CDS
TCTTCGGAAGATAGTTATCA+AGG 0.478433 1.4:-29339537 None:intergenic
CATAGTATTGGCTTCTCATA+CGG 0.490978 1.4:-29339478 None:intergenic
ATCGATTGTGAAGAATCAAA+TGG 0.491491 1.4:+29340069 MS.gene053452:CDS
GGGCTACATTTCAAGGCTAA+AGG 0.492067 1.4:+29339511 MS.gene053452:CDS
GGAGATTGGTTTGAAAGCTC+GGG 0.493147 1.4:-29339616 None:intergenic
CCAAGCAATGAGATAGGCAT+TGG 0.496933 1.4:+29340196 MS.gene053452:CDS
ATTTGATTCTTCACAATCGA+TGG 0.523804 1.4:-29340067 None:intergenic
CCAATACTATGTAACGCTTG+TGG 0.549603 1.4:+29339490 MS.gene053452:CDS
ACAAAAGCTTCAAAGTCTAT+GGG 0.556384 1.4:+29340102 MS.gene053452:CDS
CCAATGCCTATCTCATTGCT+TGG 0.566560 1.4:-29340196 None:intergenic
GAGCTTTCAAACCAATCTCC+AGG 0.568278 1.4:+29339619 MS.gene053452:CDS
CTTCGGAAGATAGTTATCAA+GGG 0.629882 1.4:-29339536 None:intergenic
GATTGTGAAGAATCAAATGG+AGG 0.680011 1.4:+29340072 MS.gene053452:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTAATTTTTTTTGTAGAA+AGG + chr1.4:29340041-29340060 MS.gene053452:intron 10.0%
!!! CTTTATATTTGTTGAAAAAT+GGG - chr1.4:29339680-29339699 None:intergenic 15.0%
!!! TTTATATTTGTTGAAAAATG+GGG - chr1.4:29339679-29339698 None:intergenic 15.0%
!! AACACTACTATTTATATATG+AGG + chr1.4:29339785-29339804 MS.gene053452:intron 20.0%
!! TTATATGTATACATCATACA+CGG - chr1.4:29340019-29340038 None:intergenic 20.0%
!!! ATTGTAAGAATTTTCTTAAG+AGG + chr1.4:29339734-29339753 MS.gene053452:intron 20.0%
!!! GCTTTATATTTGTTGAAAAA+TGG - chr1.4:29339681-29339700 None:intergenic 20.0%
!!! TTATTGCATTTTTTATTACC+TGG - chr1.4:29339640-29339659 None:intergenic 20.0%
!!! TTTGAATGAATTGTATTGAT+GGG + chr1.4:29339879-29339898 MS.gene053452:intron 20.0%
!!! TTTTGAATGAATTGTATTGA+TGG + chr1.4:29339878-29339897 MS.gene053452:intron 20.0%
! ATTGACAATGAAAGGAATTA+GGG - chr1.4:29339825-29339844 None:intergenic 25.0%
! TATCCATAAATGTATGAATG+TGG - chr1.4:29339928-29339947 None:intergenic 25.0%
! TATTGACAATGAAAGGAATT+AGG - chr1.4:29339826-29339845 None:intergenic 25.0%
!! TTGAATGAATTGTATTGATG+GGG + chr1.4:29339880-29339899 MS.gene053452:intron 25.0%
!! TTTCTTAAGAGGTACAATTT+AGG + chr1.4:29339745-29339764 MS.gene053452:intron 25.0%
!!! ATTTTTTATTACCTGGAGAT+TGG - chr1.4:29339633-29339652 None:intergenic 25.0%
AACAAAAGCTTCAAAGTCTA+TGG + chr1.4:29340101-29340120 MS.gene053452:CDS 30.0%
ACAAAAGCTTCAAAGTCTAT+GGG + chr1.4:29340102-29340121 MS.gene053452:CDS 30.0%
ACTCCACATTCATACATTTA+TGG + chr1.4:29339922-29339941 MS.gene053452:intron 30.0%
ATCGATTGTGAAGAATCAAA+TGG + chr1.4:29340069-29340088 MS.gene053452:CDS 30.0%
ATGCTCTTATTGACAATGAA+AGG - chr1.4:29339833-29339852 None:intergenic 30.0%
ATTTGATTCTTCACAATCGA+TGG - chr1.4:29340070-29340089 None:intergenic 30.0%
! TTTTGGCAGAAACTAAACTT+TGG + chr1.4:29339446-29339465 MS.gene053452:CDS 30.0%
AGCATTCATTTGAGTAGACA+CGG + chr1.4:29339848-29339867 MS.gene053452:intron 35.0%
ATTTGAGTAGACACGGTATT+AGG + chr1.4:29339855-29339874 MS.gene053452:intron 35.0%
CAATACTATGTAACGCTTGT+GGG + chr1.4:29339491-29339510 MS.gene053452:CDS 35.0%
CTTCGGAAGATAGTTATCAA+GGG - chr1.4:29339539-29339558 None:intergenic 35.0%
GAAACTAAACTTTGGCGTAA+AGG + chr1.4:29339454-29339473 MS.gene053452:CDS 35.0%
GATTGTGAAGAATCAAATGG+AGG + chr1.4:29340072-29340091 MS.gene053452:CDS 35.0%
TCATACACGGTACATATCAA+TGG - chr1.4:29340006-29340025 None:intergenic 35.0%
TCTTCGGAAGATAGTTATCA+AGG - chr1.4:29339540-29339559 None:intergenic 35.0%
TGTATACCAAGCAATGAGAT+AGG + chr1.4:29340190-29340209 MS.gene053452:CDS 35.0%
! GAATTGTATTGATGGGGATT+AGG + chr1.4:29339886-29339905 MS.gene053452:intron 35.0%
!! CATAGTATTGGCTTCTCATA+CGG - chr1.4:29339481-29339500 None:intergenic 35.0%
!! GTCTGATAACTGATTTTGCT+GGG - chr1.4:29339566-29339585 None:intergenic 35.0%
ATCAGACCTTGACGTTGAAA+AGG + chr1.4:29339579-29339598 MS.gene053452:CDS 40.0%
CCAATACTATGTAACGCTTG+TGG + chr1.4:29339490-29339509 MS.gene053452:CDS 40.0%
CCACAAGCGTTACATAGTAT+TGG - chr1.4:29339493-29339512 None:intergenic 40.0%
! CAGATTCCTTTTCAACGTCA+AGG - chr1.4:29339588-29339607 None:intergenic 40.0%
! TGATTTTGCTGGGATGTCTT+CGG - chr1.4:29339556-29339575 None:intergenic 40.0%
!! GGTCTGATAACTGATTTTGC+TGG - chr1.4:29339567-29339586 None:intergenic 40.0%
!! TGGAGATTGGTTTGAAAGCT+CGG - chr1.4:29339620-29339639 None:intergenic 40.0%
CCAAGCAATGAGATAGGCAT+TGG + chr1.4:29340196-29340215 MS.gene053452:CDS 45.0%
CCAATGCCTATCTCATTGCT+TGG - chr1.4:29340199-29340218 None:intergenic 45.0%
GAGCTTTCAAACCAATCTCC+AGG + chr1.4:29339619-29339638 MS.gene053452:CDS 45.0%
GGGCTACATTTCAAGGCTAA+AGG + chr1.4:29339511-29339530 MS.gene053452:CDS 45.0%
!! GGAGATTGGTTTGAAAGCTC+GGG - chr1.4:29339619-29339638 None:intergenic 45.0%
! CGCTTGTGGGCTACATTTCA+AGG + chr1.4:29339504-29339523 MS.gene053452:CDS 50.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 29339442 29340264 29339442 ID=MS.gene053452
chr1.4 mRNA 29339442 29340264 29339442 ID=MS.gene053452.t1;Parent=MS.gene053452
chr1.4 exon 29339442 29339640 29339442 ID=MS.gene053452.t1.exon1;Parent=MS.gene053452.t1
chr1.4 CDS 29339442 29339640 29339442 ID=cds.MS.gene053452.t1;Parent=MS.gene053452.t1
chr1.4 exon 29340059 29340264 29340059 ID=MS.gene053452.t1.exon2;Parent=MS.gene053452.t1
chr1.4 CDS 29340059 29340264 29340059 ID=cds.MS.gene053452.t1;Parent=MS.gene053452.t1
Gene Sequence

>MS.gene053452

ATGGTTTTGGCAGAAACTAAACTTTGGCGTAAAGGACCGTATGAGAAGCCAATACTATGTAACGCTTGTGGGCTACATTTCAAGGCTAAAGGAACCCTTGATAACTATCTTCCGAAGACATCCCAGCAAAATCAGTTATCAGACCTTGACGTTGAAAAGGAATCTGAAAGTGATCCCGAGCTTTCAAACCAATCTCCAGGTAATAAAAAATGCAATAAGTTAATTAACTATTCACCCCATTTTTCAACAAATATAAAGCACAATTTATACAAGAAGAGTGAGCGAGAAAGTTATTGTAAGAATTTTCTTAAGAGGTACAATTTAGGAGTATTGTTATGATATAAACACTACTATTTATATATGAGGTGTAACATTGTCAACCCTAATTCCTTTCATTGTCAATAAGAGCATTCATTTGAGTAGACACGGTATTAGGTTTTGAATGAATTGTATTGATGGGGATTAGGTGACATACATACAACTCCACATTCATACATTTATGGATATATTTTTTTCAAATAATAGCATATATTTTTTCAAATAATACATATAAATGATTATCCATTGATATGTACCGTGTATGATGTATACATATAAACTTTTAATTTTTTTTGTAGAAAGGACACCATCGATTGTGAAGAATCAAATGGAGGAGTTTCAACAAAAGCTTCAAAGTCTATGGGAATCTGAGAAAGAATCAAATGAATCATCTGCAGACAATATTTTGTTGTTTGATAATATGAACAAATGTATACCAAGCAATGAGATAGGCATTGGATGCACTCTACTGAAGACAGATGTTACTTCTAAAAAATCTGCATGA
Protein sequence

>MS.gene053452.t1

MVLAETKLWRKGPYEKPILCNACGLHFKAKGTLDNYLPKTSQQNQLSDLDVEKESESDPELSNQSPERTPSIVKNQMEEFQQKLQSLWESEKESNESSADNILLFDNMNKCIPSNEIGIGCTLLKTDVTSKKSA