AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene63249

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63249.t1 MTR_5g039180 82.051 78 13 1 16 92 16 93 2.23e-39 126
MS.gene63249.t1 MTR_7g010120 75.532 94 21 2 1 93 1 93 2.63e-38 123
MS.gene63249.t1 MTR_6g011670 74.359 78 19 1 17 93 15 92 3.99e-32 107
MS.gene63249.t1 MTR_3g438070 71.795 78 19 2 17 93 17 92 6.03e-31 104
MS.gene63249.t1 MTR_7g059260 50.617 81 34 3 1 80 1 76 5.69e-13 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63249.t1 AT3G47710 69.474 95 24 3 1 93 1 92 6.29e-37 120
MS.gene63249.t1 AT3G28857 65.957 94 28 2 1 92 1 92 7.92e-36 117
MS.gene63249.t1 AT1G26945 78.378 74 15 1 19 91 19 92 1.26e-33 111
MS.gene63249.t1 AT5G15160 68.000 75 22 1 19 91 18 92 1.48e-31 106
MS.gene63249.t1 AT1G74500 73.418 79 17 2 17 93 17 93 1.87e-31 106
MS.gene63249.t1 AT5G39860 66.667 78 24 1 17 92 15 92 8.04e-31 104

Find 14 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGACCGATTGTCACAACTTT+TGG 0.247784 8.4:+42375840 MS.gene63249:CDS
TTGAGCACTGTTAGGGTCTA+TGG 0.329793 8.4:-42375866 None:intergenic
ATAGCTGCTTGAGCACTGTT+AGG 0.352323 8.4:-42375874 None:intergenic
TGGGAACGCCTTGAGAGTTC+AGG 0.406573 8.4:-42374750 None:intergenic
AGAAAATTATTATACCTTAT+GGG 0.418461 8.4:-42374769 None:intergenic
GTGCTCAAGCAGCTATCATT+AGG 0.423047 8.4:+42375881 MS.gene63249:CDS
ATTGTAGGTTTCAGCTGCTA+AGG 0.479345 8.4:+42375759 MS.gene63249:intron
AGATCTCGTTCAAGACAATC+TGG 0.480776 8.4:+42374663 MS.gene63249:CDS
AGGTACAAGTTGTTGTAACT+TGG 0.482816 8.4:-42374730 None:intergenic
ACTCTCAAGGCGTTCCCATA+AGG 0.483554 8.4:+42374755 MS.gene63249:CDS
TAGCTGCTTGAGCACTGTTA+GGG 0.522205 8.4:-42375873 None:intergenic
TGTCCAAAAGTTGTGACAAT+CGG 0.545364 8.4:-42375843 None:intergenic
AACTTGTACCTGAACTCTCA+AGG 0.607839 8.4:+42374742 MS.gene63249:CDS
TTGAGCATCAGAGATCTCAG+TGG 0.738554 8.4:-42374691 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGAAAATTATTATACCTTA+TGG - chr8.4:42374773-42374792 None:intergenic 15.0%
!! AGAAAATTATTATACCTTAT+GGG - chr8.4:42374772-42374791 None:intergenic 15.0%
!! TATAATGTTTATTGTATTGT+AGG + chr8.4:42375744-42375763 MS.gene63249:intron 15.0%
!! TTTATTTCATTCAAAATCAA+TGG + chr8.4:42375086-42375105 MS.gene63249:intron 15.0%
!!! AAATCAATTTTATGTGTTTA+GGG - chr8.4:42374873-42374892 None:intergenic 15.0%
!!! AAATGATCTTTAATTTTTTC+TGG + chr8.4:42375203-42375222 MS.gene63249:intron 15.0%
!!! AAATTGATTTCTAAATGATA+TGG + chr8.4:42374883-42374902 MS.gene63249:intron 15.0%
!!! TAAAAACATATCTTCAATTT+TGG + chr8.4:42375325-42375344 MS.gene63249:intron 15.0%
!!! TTTTGAATGAAATAAATTTG+AGG - chr8.4:42375082-42375101 None:intergenic 15.0%
!!! GAAATCAATTTTATGTGTTT+AGG - chr8.4:42374874-42374893 None:intergenic 20.0%
! TAAAAGAGAGAATACAGAAA+AGG - chr8.4:42374797-42374816 None:intergenic 25.0%
!!! AAATTTGTTGTGTTCAAGAA+AGG + chr8.4:42375450-42375469 MS.gene63249:intron 25.0%
!!! AATTTGTTGTGTTCAAGAAA+GGG + chr8.4:42375451-42375470 MS.gene63249:intron 25.0%
AGTTCTTGAAATTGTTACGT+AGG - chr8.4:42375231-42375250 None:intergenic 30.0%
GTCAACAAAAAACTTTAGCT+TGG - chr8.4:42375403-42375422 None:intergenic 30.0%
! ACATATTTTATGTGTGGCTT+TGG + chr8.4:42375537-42375556 MS.gene63249:intron 30.0%
! CAACAAATTTTCAGTTGCTA+TGG - chr8.4:42375690-42375709 None:intergenic 30.0%
! CAACACACATATTTTATGTG+TGG + chr8.4:42375531-42375550 MS.gene63249:intron 30.0%
AATGATGTATGCTTTGCAAG+TGG - chr8.4:42375653-42375672 None:intergenic 35.0%
AGGTACAAGTTGTTGTAACT+TGG - chr8.4:42374733-42374752 None:intergenic 35.0%
ATGATGTATGCTTTGCAAGT+GGG - chr8.4:42375652-42375671 None:intergenic 35.0%
CATCAAAAACTTGCATAGAG+AGG + chr8.4:42375804-42375823 MS.gene63249:CDS 35.0%
GTAAACGAGTTAAGGATTCA+GGG - chr8.4:42375595-42375614 None:intergenic 35.0%
TGTCCAAAAGTTGTGACAAT+CGG - chr8.4:42375846-42375865 None:intergenic 35.0%
!!! ATTTTATGTGTGGCTTTGGT+TGG + chr8.4:42375541-42375560 MS.gene63249:intron 35.0%
AACTTGTACCTGAACTCTCA+AGG + chr8.4:42374742-42374761 MS.gene63249:CDS 40.0%
AGATCTCGTTCAAGACAATC+TGG + chr8.4:42374663-42374682 MS.gene63249:CDS 40.0%
ATTGTAGGTTTCAGCTGCTA+AGG + chr8.4:42375759-42375778 MS.gene63249:intron 40.0%
CGTTTACCCACAAACTTGTA+GGG + chr8.4:42375608-42375627 MS.gene63249:intron 40.0%
GGTAAACGAGTTAAGGATTC+AGG - chr8.4:42375596-42375615 None:intergenic 40.0%
GTTTGTGGGTAAACGAGTTA+AGG - chr8.4:42375603-42375622 None:intergenic 40.0%
TAGTGTGTGTTCGTTCTACA+TGG - chr8.4:42375116-42375135 None:intergenic 40.0%
TCGTTTACCCACAAACTTGT+AGG + chr8.4:42375607-42375626 MS.gene63249:intron 40.0%
! TGACCGATTGTCACAACTTT+TGG + chr8.4:42375840-42375859 MS.gene63249:CDS 40.0%
ACTTGTAGGGCTGTGGAATT+CGG + chr8.4:42375621-42375640 MS.gene63249:intron 45.0%
GTGCTCAAGCAGCTATCATT+AGG + chr8.4:42375881-42375900 MS.gene63249:CDS 45.0%
TTGAGCATCAGAGATCTCAG+TGG - chr8.4:42374694-42374713 None:intergenic 45.0%
! ATAGCTGCTTGAGCACTGTT+AGG - chr8.4:42375877-42375896 None:intergenic 45.0%
! TAGCTGCTTGAGCACTGTTA+GGG - chr8.4:42375876-42375895 None:intergenic 45.0%
! TTGAGCACTGTTAGGGTCTA+TGG - chr8.4:42375869-42375888 None:intergenic 45.0%
!! TTAAAATTTAATTAATTCTA+AGG - chr8.4:42375184-42375203 None:intergenic 5.0%
CCACAGCCCTACAAGTTTGT+GGG - chr8.4:42375617-42375636 None:intergenic 50.0%
TCCACAGCCCTACAAGTTTG+TGG - chr8.4:42375618-42375637 None:intergenic 50.0%
! ACTCTCAAGGCGTTCCCATA+AGG + chr8.4:42374755-42374774 MS.gene63249:CDS 50.0%
CCCACAAACTTGTAGGGCTG+TGG + chr8.4:42375614-42375633 MS.gene63249:intron 55.0%
TGGGAACGCCTTGAGAGTTC+AGG - chr8.4:42374753-42374772 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr8.4 gene 42374651 42375921 42374651 ID=MS.gene63249
chr8.4 mRNA 42374651 42375921 42374651 ID=MS.gene63249.t1;Parent=MS.gene63249
chr8.4 exon 42374651 42374776 42374651 ID=MS.gene63249.t1.exon1;Parent=MS.gene63249.t1
chr8.4 CDS 42374651 42374776 42374651 ID=cds.MS.gene63249.t1;Parent=MS.gene63249.t1
chr8.4 exon 42375766 42375921 42375766 ID=MS.gene63249.t1.exon2;Parent=MS.gene63249.t1
chr8.4 CDS 42375766 42375921 42375766 ID=cds.MS.gene63249.t1;Parent=MS.gene63249.t1
Gene Sequence

>MS.gene63249

ATGTCTAGCAGAAGATCTCGTTCAAGACAATCTGGTGTTTCCACTGAGATCTCTGATGCTCAAATTAATGATCTCGTCACCAAGTTACAACAACTTGTACCTGAACTCTCAAGGCGTTCCCATAAGGTATAATAATTTTCTTTCCTTTTCTGTATTCTCTCTTTTACACATAAATGTGAAAGACATCATCATATATATGTGTTTTTAATTGTGCTGATACCCTAAACACATAAAATTGATTTCTAAATGATATGGATTAACATTTGTAGTTTTTTTTTTATTTCAAACATAATTTTTACAATAAATTTATTGTTCAACTGAATTTATGTAAACATATTCAAATATAAATAACTTACATTCAACTCATTTTTAATTAATTTCTTCAACAACAAAAAAAATCTCATTTTTTAATTAATCAAAATCTAATTCCTCAAATTTATTTCATTCAAAATCAATGGTTATCCATGTAGAACGAACACACACTACATCATTAATTTTAGACTTTAAACTGTAACTATTGTCATTTTCATCCTTAGAATTAATTAAATTTTAAAATGATCTTTAATTTTTTCTGGTTCCTACGTAACAATTTCAAGAACTCAATAGACTTATCTATTTAATCAAAAATAATTTAACTTTTCAAAGTAATTTTACAATATTTATGTTGTAGAAACTAAAAACATATCTTCAATTTTGGTTGATAAACATATATTTATTATGTGATGCAAACAACTAATCTAGATATTTTACCAAGCTAAAGTTTTTTGTTGACAAGATCTAATCTAACTTAAAGTATCTTAAATTTGTTGTGTTCAAGAAAGGGTGTTTATCAAAGAATTAATTATACAAAGTAGTCACATGCATGCACATGACACACACACAACACACATATTTTATGTGTGGCTTTGGTTGGATTTGCTAGATAAGTCATCACGCTTGTGCCCTGAATCCTTAACTCGTTTACCCACAAACTTGTAGGGCTGTGGAATTCGGACATTCCCACTTGCAAAGCATACATCATTGTCGAGTATAATATCCATAGCAACTGAAAATTTGTTGAAAATGACATTAAATTCTATTAACATTTATTTATTATAATGTTTATTGTATTGTAGGTTTCAGCTGCTAAGGTATTGCAAGAGACTTGCAATTACATCAAAAACTTGCATAGAGAGGTCGATGATCTTAGTGACCGATTGTCACAACTTTTGGACACCATAGACCCTAACAGTGCTCAAGCAGCTATCATTAGGAGCTTACTTATGCAATAG
Protein sequence

>MS.gene63249.t1

MSSRRSRSRQSGVSTEISDAQINDLVTKLQQLVPELSRRSHKVSAAKVLQETCNYIKNLHREVDDLSDRLSQLLDTIDPNSAQAAIIRSLLMQ