AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene044060

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene044060.t1 MTR_1g047060 60.204 98 32 2 56 153 3 93 1.51e-33 114
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACCGGATTCTGGAGGAAAA+AGG 0.330121 1.2:-4320083 MS.gene044060:CDS
GACACTGCAAGACCGGATTC+TGG 0.388814 1.2:-4320093 MS.gene044060:CDS
ATGGATCTGGATGCTGAGTT+TGG 0.391512 1.2:-4319770 MS.gene044060:CDS
TCAGCATCCAGATCCATCTT+TGG 0.442178 1.2:+4319776 None:intergenic
GTTAGTTCTGATAGCAGTGT+TGG 0.458231 1.2:+4319979 None:intergenic
TTAGTTCTGATAGCAGTGTT+GGG 0.461166 1.2:+4319980 None:intergenic
CTGCCCACCAAAGATGGATC+TGG 0.482322 1.2:-4319783 MS.gene044060:CDS
ACACTGCTATCAGAACTAAC+TGG 0.486063 1.2:-4319976 MS.gene044060:CDS
TGGAGTTACTCAGAAACCTA+TGG 0.490884 1.2:-4319687 MS.gene044060:CDS
TGGTGCTGGTAATGTTGTGT+TGG 0.499495 1.2:-4320041 MS.gene044060:CDS
AAAACACGACAAATGACAAA+AGG 0.501966 1.2:+4319809 None:intergenic
GAGAGAAGACACTGCAAGAC+CGG 0.507192 1.2:-4320100 MS.gene044060:CDS
GATAATGTATGAGCATGCTT+TGG 0.511387 1.2:-4319954 MS.gene044060:CDS
GGTGCTGGTAATGTTGTGTT+GGG 0.514976 1.2:-4320040 MS.gene044060:CDS
GACTCTGCTGACAAGATGAA+TGG 0.517567 1.2:-4319707 MS.gene044060:CDS
TGCTTTGGCTGACAAGCCTC+AGG 0.528648 1.2:-4319939 MS.gene044060:intron
GCATCCAGATCCATCTTTGG+TGG 0.546474 1.2:+4319779 None:intergenic
ACCATCACCTTCATCAACCT+TGG 0.550147 1.2:+4319739 None:intergenic
GTTCAAGACATCACTGGTGC+TGG 0.556036 1.2:-4320055 MS.gene044060:CDS
GCGTTATCCAAGGTTGATGA+AGG 0.556534 1.2:-4319746 MS.gene044060:CDS
GGAGTTACTCAGAAACCTAT+GGG 0.559803 1.2:-4319686 MS.gene044060:CDS
ACTAGTGTTGCTGCTGAGCA+AGG 0.563406 1.2:-4319644 MS.gene044060:CDS
TAGTTCTGATAGCAGTGTTG+GGG 0.568976 1.2:+4319981 None:intergenic
CATCCAGATCCATCTTTGGT+GGG 0.591585 1.2:+4319780 None:intergenic
GGAGCTGTTCAAGACATCAC+TGG 0.599122 1.2:-4320061 MS.gene044060:CDS
TGAGTTTGGAGCGTTATCCA+AGG 0.615415 1.2:-4319756 MS.gene044060:CDS
AGTTCTGATAGCAGTGTTGG+GGG 0.663335 1.2:+4319982 None:intergenic
TCCAAGGTTGATGAAGGTGA+TGG 0.681651 1.2:-4319740 MS.gene044060:CDS
ACTGCAAGACCGGATTCTGG+AGG 0.686245 1.2:-4320090 MS.gene044060:CDS
GAGTTACTCAGAAACCTATG+GGG 0.687052 1.2:-4319685 MS.gene044060:CDS
AGTGTTGCTGCTGAGCAAGG+CGG 0.699580 1.2:-4319641 MS.gene044060:CDS
AGTTACTCAGAAACCTATGG+GGG 0.734801 1.2:-4319684 MS.gene044060:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAAATTTTAAAATATTAA+TGG - chr1.2:4319765-4319784 MS.gene044060:CDS 0.0%
!! AATAATAGTAATTGTAAAAT+AGG - chr1.2:4319926-4319945 MS.gene044060:intron 10.0%
!! AATTAATCATCAATGATTTA+AGG + chr1.2:4319333-4319352 None:intergenic 15.0%
!! TAATGGAAATTATTGATATA+TGG - chr1.2:4319782-4319801 MS.gene044060:CDS 15.0%
!!! TTTTCTTTCAATTATTTTGT+AGG - chr1.2:4319376-4319395 MS.gene044060:intron 15.0%
!! ATTTATTACTAGAGAAAAGA+CGG + chr1.2:4319909-4319928 None:intergenic 20.0%
!! TGCAAGATAAAAAATAAACA+GGG + chr1.2:4319204-4319223 None:intergenic 20.0%
!! TTAATAAAGAGAGATCAAAA+TGG + chr1.2:4319644-4319663 None:intergenic 20.0%
!! TTGCAAGATAAAAAATAAAC+AGG + chr1.2:4319205-4319224 None:intergenic 20.0%
! ATCAATGATTTAAGGAATCA+AGG + chr1.2:4319325-4319344 None:intergenic 25.0%
! TCAATGATTTAAGGAATCAA+GGG + chr1.2:4319324-4319343 None:intergenic 25.0%
! TTTATTACTAGAGAAAAGAC+GGG + chr1.2:4319908-4319927 None:intergenic 25.0%
!! TCAAATTTCACAGATTTTGA+AGG - chr1.2:4319596-4319615 MS.gene044060:intron 25.0%
!! TTTTCAAATACACACTTTCA+AGG + chr1.2:4320040-4320059 None:intergenic 25.0%
AAAACACGACAAATGACAAA+AGG + chr1.2:4319404-4319423 None:intergenic 30.0%
AAACTGCGGAAATAAAACAA+AGG + chr1.2:4320139-4320158 None:intergenic 30.0%
ATTAGAAAGAGAGAACAAAC+GGG + chr1.2:4319689-4319708 None:intergenic 30.0%
CATAGCTGTGAAAATTTGAT+TGG - chr1.2:4320063-4320082 MS.gene044060:CDS 30.0%
CATTAGAAAGAGAGAACAAA+CGG + chr1.2:4319690-4319709 None:intergenic 30.0%
GACGAGAAAATTATAAACTG+CGG + chr1.2:4320153-4320172 None:intergenic 30.0%
GTACGATCAACAACATTAAT+TGG + chr1.2:4319667-4319686 None:intergenic 30.0%
TTTATCACTAACCAAGTGTT+GGG - chr1.2:4319971-4319990 MS.gene044060:CDS 30.0%
! ATGGAATATATTTTACCTGC+AGG + chr1.2:4319625-4319644 None:intergenic 30.0%
! GAAAGAGATAATTTTGCGTT+TGG + chr1.2:4319082-4319101 None:intergenic 30.0%
! TGGAATATATTTTACCTGCA+GGG + chr1.2:4319624-4319643 None:intergenic 30.0%
! TTTTATCACTAACCAAGTGT+TGG - chr1.2:4319970-4319989 MS.gene044060:CDS 30.0%
AATAAAAAGAGCGGAAAGAC+GGG - chr1.2:4319872-4319891 MS.gene044060:intron 35.0%
CAATAAAAAGAGCGGAAAGA+CGG - chr1.2:4319871-4319890 MS.gene044060:intron 35.0%
CGTTAGTGCAATAAAAAGAG+CGG - chr1.2:4319863-4319882 MS.gene044060:intron 35.0%
GATAATGTATGAGCATGCTT+TGG - chr1.2:4319256-4319275 MS.gene044060:intron 35.0%
GATTTAAGGAATCAAGGGAA+TGG + chr1.2:4319319-4319338 None:intergenic 35.0%
TACATTAATGACCCAACACT+TGG + chr1.2:4319985-4320004 None:intergenic 35.0%
! AAAATTTGATTGGCCACGTT+TGG - chr1.2:4320073-4320092 MS.gene044060:CDS 35.0%
! AGTGTTGGGTCATTAATGTA+TGG - chr1.2:4319985-4320004 MS.gene044060:CDS 35.0%
! TGATTTTGCTTCGTTGTCAT+GGG - chr1.2:4320012-4320031 MS.gene044060:CDS 35.0%
! TTGATTTTGCTTCGTTGTCA+TGG - chr1.2:4320011-4320030 MS.gene044060:CDS 35.0%
!! TTAGTTCTGATAGCAGTGTT+GGG + chr1.2:4319233-4319252 None:intergenic 35.0%
ACACTGCTATCAGAACTAAC+TGG - chr1.2:4319234-4319253 MS.gene044060:intron 40.0%
AGTTACTCAGAAACCTATGG+GGG - chr1.2:4319526-4319545 MS.gene044060:intron 40.0%
GAGTTACTCAGAAACCTATG+GGG - chr1.2:4319525-4319544 MS.gene044060:intron 40.0%
GGAGTTACTCAGAAACCTAT+GGG - chr1.2:4319524-4319543 MS.gene044060:intron 40.0%
TAAGGAATCAAGGGAATGGT+GGG + chr1.2:4319315-4319334 None:intergenic 40.0%
TGGAGTTACTCAGAAACCTA+TGG - chr1.2:4319523-4319542 MS.gene044060:intron 40.0%
TTAAGGAATCAAGGGAATGG+TGG + chr1.2:4319316-4319335 None:intergenic 40.0%
TTCAAAAAGTCCCATACCTG+AGG + chr1.2:4319290-4319309 None:intergenic 40.0%
!! GTTAGTTCTGATAGCAGTGT+TGG + chr1.2:4319234-4319253 None:intergenic 40.0%
!! TAGTTCTGATAGCAGTGTTG+GGG + chr1.2:4319232-4319251 None:intergenic 40.0%
ACCATCACCTTCATCAACCT+TGG + chr1.2:4319474-4319493 None:intergenic 45.0%
ATGGATCTGGATGCTGAGTT+TGG - chr1.2:4319440-4319459 MS.gene044060:intron 45.0%
CATCCAGATCCATCTTTGGT+GGG + chr1.2:4319433-4319452 None:intergenic 45.0%
GACTCTGCTGACAAGATGAA+TGG - chr1.2:4319503-4319522 MS.gene044060:intron 45.0%
TCAGCATCCAGATCCATCTT+TGG + chr1.2:4319437-4319456 None:intergenic 45.0%
TGATATCGTTGAGCCAAACG+TGG + chr1.2:4320089-4320108 None:intergenic 45.0%
! ACCGGATTCTGGAGGAAAAA+GGG - chr1.2:4319128-4319147 MS.gene044060:intron 45.0%
! AGTTCTGATAGCAGTGTTGG+GGG + chr1.2:4319231-4319250 None:intergenic 45.0%
! TCCCTTTTTCCTCCAGAATC+CGG + chr1.2:4319132-4319151 None:intergenic 45.0%
! TGAGTTTGGAGCGTTATCCA+AGG - chr1.2:4319454-4319473 MS.gene044060:intron 45.0%
!! GCGTTATCCAAGGTTGATGA+AGG - chr1.2:4319464-4319483 MS.gene044060:intron 45.0%
!! GGTGCTGGTAATGTTGTGTT+GGG - chr1.2:4319170-4319189 MS.gene044060:intron 45.0%
!! TCCAAGGTTGATGAAGGTGA+TGG - chr1.2:4319470-4319489 MS.gene044060:intron 45.0%
!! TGGTGCTGGTAATGTTGTGT+TGG - chr1.2:4319169-4319188 MS.gene044060:intron 45.0%
!! TTTTGACTGCCCACCAAAGA+TGG - chr1.2:4319421-4319440 MS.gene044060:intron 45.0%
GAGAGAAGACACTGCAAGAC+CGG - chr1.2:4319110-4319129 MS.gene044060:intron 50.0%
GCATCCAGATCCATCTTTGG+TGG + chr1.2:4319434-4319453 None:intergenic 50.0%
GGAGCTGTTCAAGACATCAC+TGG - chr1.2:4319149-4319168 MS.gene044060:intron 50.0%
GTTCAAGACATCACTGGTGC+TGG - chr1.2:4319155-4319174 MS.gene044060:intron 50.0%
! ACTAGTGTTGCTGCTGAGCA+AGG - chr1.2:4319566-4319585 MS.gene044060:intron 50.0%
! GACCGGATTCTGGAGGAAAA+AGG - chr1.2:4319127-4319146 MS.gene044060:intron 50.0%
!!! AGATTTTGAAGGCACCCTGC+AGG - chr1.2:4319607-4319626 MS.gene044060:CDS 50.0%
ACTCAGAAACCTATGGGGGC+TGG - chr1.2:4319530-4319549 MS.gene044060:intron 55.0%
ACTGCAAGACCGGATTCTGG+AGG - chr1.2:4319120-4319139 MS.gene044060:intron 55.0%
CTCAGAAACCTATGGGGGCT+GGG - chr1.2:4319531-4319550 MS.gene044060:intron 55.0%
CTGCCCACCAAAGATGGATC+TGG - chr1.2:4319427-4319446 MS.gene044060:intron 55.0%
GACACTGCAAGACCGGATTC+TGG - chr1.2:4319117-4319136 MS.gene044060:intron 55.0%
GGCTGACAAGCCTCAGGTAT+GGG - chr1.2:4319277-4319296 MS.gene044060:intron 55.0%
TCAGAAACCTATGGGGGCTG+GGG - chr1.2:4319532-4319551 MS.gene044060:intron 55.0%
TGCTTTGGCTGACAAGCCTC+AGG - chr1.2:4319271-4319290 MS.gene044060:intron 55.0%
TGGCTGACAAGCCTCAGGTA+TGG - chr1.2:4319276-4319295 MS.gene044060:intron 55.0%
! AGTGTTGCTGCTGAGCAAGG+CGG - chr1.2:4319569-4319588 MS.gene044060:intron 55.0%
AAACCTATGGGGGCTGGGGA+TGG - chr1.2:4319536-4319555 MS.gene044060:intron 60.0%
AACCTATGGGGGCTGGGGAT+GGG - chr1.2:4319537-4319556 MS.gene044060:intron 60.0%
ACCTATGGGGGCTGGGGATG+GGG - chr1.2:4319538-4319557 MS.gene044060:intron 65.0%
ATGGGGGCTGGGGATGGGGC+TGG - chr1.2:4319542-4319561 MS.gene044060:intron 75.0%
GCCCCATCCCCAGCCCCCAT+AGG + chr1.2:4319542-4319561 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 4319050 4320182 4319050 ID=MS.gene044060
chr1.2 mRNA 4319050 4320182 4319050 ID=MS.gene044060.t1;Parent=MS.gene044060
chr1.2 exon 4319940 4320182 4319940 ID=MS.gene044060.t1.exon1;Parent=MS.gene044060.t1
chr1.2 CDS 4319940 4320182 4319940 ID=cds.MS.gene044060.t1;Parent=MS.gene044060.t1
chr1.2 exon 4319604 4319834 4319604 ID=MS.gene044060.t1.exon2;Parent=MS.gene044060.t1
chr1.2 CDS 4319604 4319834 4319604 ID=cds.MS.gene044060.t1;Parent=MS.gene044060.t1
chr1.2 exon 4319050 4319076 4319050 ID=MS.gene044060.t1.exon3;Parent=MS.gene044060.t1
chr1.2 CDS 4319050 4319076 4319050 ID=cds.MS.gene044060.t1;Parent=MS.gene044060.t1
Gene Sequence

>MS.gene044060

ATGAAGGATGTTCATACTCAATCTCAATGCCAAACGCAAAATTATCTCTTTCAACACATTGAGAGAAGACACTGCAAGACCGGATTCTGGAGGAAAAAGGGAGCTGTTCAAGACATCACTGGTGCTGGTAATGTTGTGTTGGGCAAGAAGACCCTGTTTATTTTTTATCTTGCAAGTTCCCCCAACACTGCTATCAGAACTAACTGGATAATGTATGAGCATGCTTTGGCTGACAAGCCTCAGGTATGGGACTTTTTGAAAACCCACCATTCCCTTGATTCCTTAAATCATTGATGATTAATTAATGTATTCATAACTACTAACTATTTTCTTTCAATTATTTTGTAGGCTCCTTTTGTCATTTGTCGTGTTTTTGACTGCCCACCAAAGATGGATCTGGATGCTGAGTTTGGAGCGTTATCCAAGGTTGATGAAGGTGATGGTGCTAGAGATGACTCTGCTGACAAGATGAATGGAGTTACTCAGAAACCTATGGGGGCTGGGGATGGGGCTGGTACTAGTGTTGCTGCTGAGCAAGGCGGTGCTTCAAATTTCACAGATTTTGAAGGCACCCTGCAGGTAAAATATATTCCATTTTGATCTCTCTTTATTAACCAATTAATGTTGTTGATCGTACCCGTTTGTTCTCTCTTTCTAATGCGCTAACGCATGTGATTATTTTATTATGTTTGTTTGTATAATTTTGATTAAAACTTTTAAATTTTAAAATATTAATGGAAATTATTGATATATGGATTTATAAACAAAATATTGTCAAGACATATAACAATTATTTATGAACTCAACAATTAACGTTAGTGCAATAAAAAGAGCGGAAAGACGGGCACGTGAGTGCCCGTCTTTTCTCTAGTAATAAATAATAGTAATTGTAAAATAGGTGTAAAAGTATATAATTTTGTTTTTATCACTAACCAAGTGTTGGGTCATTAATGTATGGTAGTTGATTTTGCTTCGTTGTCATGGGTTCCTTGAAAGTGTGTATTTGAAAAATTCATAGCTGTGAAAATTTGATTGGCCACGTTTGGCTCAACGATATCATTAGTGCATGATATTTCAAGTTCATTTCCTTTGTTTTATTTCCGCAGTTTATAATTTTCTCGTCTTTGAAGTAG
Protein sequence

>MS.gene044060.t1

MKDVHTQSQCQTQNYLFQHIERRHCKTGFWRKKGAVQDITGAGNVVLGKKTLFIFYLASSPNTAIRTNWIMYEHALADKPQAPFVICRVFDCPPKMDLDAEFGALSKVDEGDGARDDSADKMNGVTQKPMGAGDGAGTSVAAEQGGASNFTDFEGTLQFIIFSSLK