AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene64006


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64006.t1 MTR_1g024840 96.835 158 4 1 1 158 1 157 4.69e-110 310
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64006.t1 AT1G75690 75.497 151 34 3 8 158 7 154 2.51e-78 229

Find 33 sgRNAs with CRISPR-Local

Find 94 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGCTGCGTGTTATCTCTTT+TGG 0.263030 1.4:-811744 None:intergenic
TGCTTCCCATGCAATGGTTC+TGG 0.280691 1.4:+811767 MS.gene64006:CDS
CGTGGATAAAATGTGGGTTT+TGG 0.374056 1.4:-811406 None:intergenic
TTGAGTGTGGCTGTTGGAAT+TGG 0.393770 1.4:+811576 MS.gene64006:CDS
AGAACCATTGCATGGGAAGC+AGG 0.424768 1.4:-811765 None:intergenic
AAGTTCAACAGTCACATTAC+CGG 0.426738 1.4:-812735 None:intergenic
CAGGTAGTTGCTATAACTGT+TGG 0.428401 1.4:+811549 MS.gene64006:intron
TTTAAGAGGAGAAGAAAGAA+AGG 0.455802 1.4:-811341 None:intergenic
GTAGTAGATAAGGATTTAAG+AGG 0.469567 1.4:-811355 None:intergenic
TGTACAACTTGTCAAGGATC+TGG 0.478203 1.4:+812818 MS.gene64006:CDS
TTTAATACGTGGATAAAATG+TGG 0.513316 1.4:-811413 None:intergenic
AGAAAGGTGGAATGTAATTG+AGG 0.514748 1.4:-811325 None:intergenic
TAATTGTGTAGTAGTAGATA+AGG 0.518803 1.4:-811365 None:intergenic
TTAATACGTGGATAAAATGT+GGG 0.525605 1.4:-811412 None:intergenic
AAGAGGAGAAGAAAGAAAGG+TGG 0.539027 1.4:-811338 None:intergenic
CAGCCCTGCTTCCCATGCAA+TGG 0.546625 1.4:+811761 MS.gene64006:CDS
GAACACCGTACCTACGATCA+AGG 0.554130 1.4:-812856 None:intergenic
GGTAATGTGACTGTTGAACT+TGG 0.571939 1.4:+812737 MS.gene64006:CDS
GAACCATTGCATGGGAAGCA+GGG 0.571952 1.4:-811764 None:intergenic
TGAACTTGGTGGAGCTGAGA+CGG 0.581832 1.4:+812751 MS.gene64006:CDS
CTGCATAAATTGTGATGGTG+CGG 0.586364 1.4:+812784 MS.gene64006:CDS
TGCATAAATTGTGATGGTGC+GGG 0.591712 1.4:+812785 MS.gene64006:CDS
CGAGCTCCAGAACCATTGCA+TGG 0.592093 1.4:-811773 None:intergenic
TCTCGCTGCATAAATTGTGA+TGG 0.600927 1.4:+812779 MS.gene64006:CDS
CTGACATGTACAACTTGTCA+AGG 0.612986 1.4:+812812 MS.gene64006:CDS
ATTTGCGATTCATAAAACAC+TGG 0.613193 1.4:-811603 None:intergenic
ACTTGGTGGAGCTGAGACGG+AGG 0.632275 1.4:+812754 MS.gene64006:CDS
AGTTCAAGAGCTTTAATACG+TGG 0.639758 1.4:-811424 None:intergenic
AACCTCGTTACCTTGATCGT+AGG 0.640316 1.4:+812846 MS.gene64006:CDS
GAGCTCCAGAACCATTGCAT+GGG 0.645320 1.4:-811772 None:intergenic
AATGTGACTGTTGAACTTGG+TGG 0.646977 1.4:+812740 MS.gene64006:CDS
TCTTGAACTTGATCAAAACA+CGG 0.674004 1.4:+811438 MS.gene64006:CDS
TACCTACGATCAAGGTAACG+AGG 0.728545 1.4:-812848 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATGATATAGTAATAAATAAA+TGG - chr1.4:811653-811672 None:intergenic 10.0%
!! ATTATTAAATTATTACAAAG+GGG - chr1.4:812893-812912 None:intergenic 10.0%
!! CATTATTAAATTATTACAAA+GGG - chr1.4:812894-812913 None:intergenic 10.0%
!! TCATTATTAAATTATTACAA+AGG - chr1.4:812895-812914 None:intergenic 10.0%
!!! TAAAATACTGATTAATAATA+TGG - chr1.4:812478-812497 None:intergenic 10.0%
!! AAGTTAAATTATATAACTTC+TGG + chr1.4:812248-812267 MS.gene64006:intron 15.0%
!! TATACCAAGAATAATAAAAT+AGG + chr1.4:812520-812539 MS.gene64006:intron 15.0%
!! TATATCATATAATAATGTGT+TGG + chr1.4:811665-811684 MS.gene64006:intron 15.0%
!!! ATAACCTATTTTATTATTCT+TGG - chr1.4:812527-812546 None:intergenic 15.0%
!! ATTTGTAAAAGATTGCTTAT+AGG + chr1.4:812211-812230 MS.gene64006:intron 20.0%
!! CAAAAAGTTTATATGCTTAT+AGG + chr1.4:812033-812052 MS.gene64006:intron 20.0%
!! CTGCAACAAATTAAAAAAAA+AGG - chr1.4:811723-811742 None:intergenic 20.0%
!! TGAATGAATGAATAAGAAAT+AGG - chr1.4:811480-811499 None:intergenic 20.0%
!!! AACATTTTCAAAGATAAGAT+TGG - chr1.4:812678-812697 None:intergenic 20.0%
!!! AAGTTTTTTTTTATAGGTAG+TGG + chr1.4:812070-812089 MS.gene64006:intron 20.0%
!!! CTATAAGCATATAAACTTTT+TGG - chr1.4:812035-812054 None:intergenic 20.0%
!!! CTTTTTTTTTAATTTGTTGC+AGG + chr1.4:811721-811740 MS.gene64006:intron 20.0%
!!! GTGGATAAGTTTTTTTTTAT+AGG + chr1.4:812064-812083 MS.gene64006:intron 20.0%
! ATGAATGAATAAGAAATAGG+AGG - chr1.4:811477-811496 None:intergenic 25.0%
! CTCACAAGTTATTGTTAATT+TGG + chr1.4:811872-811891 MS.gene64006:intron 25.0%
! TAATTGTGTAGTAGTAGATA+AGG - chr1.4:811368-811387 None:intergenic 25.0%
! TTAATACGTGGATAAAATGT+GGG - chr1.4:811415-811434 None:intergenic 25.0%
! TTTAATACGTGGATAAAATG+TGG - chr1.4:811416-811435 None:intergenic 25.0%
!! AATAGTGTTAGCAATTTTCA+TGG - chr1.4:812978-812997 None:intergenic 25.0%
!! ACACTTCATACTTTTATGAA+TGG + chr1.4:811830-811849 MS.gene64006:intron 25.0%
!! TACCATGATAATTTGTCATT+TGG + chr1.4:812935-812954 MS.gene64006:intron 25.0%
!!! TGAATTAGCTTTTAGTTCAT+TGG + chr1.4:811969-811988 MS.gene64006:intron 25.0%
AAACAAAATCTGCATTTCTC+TGG - chr1.4:812710-812729 None:intergenic 30.0%
AAGAAATTAGCAACCTGATA+TGG - chr1.4:812653-812672 None:intergenic 30.0%
ATTTGCGATTCATAAAACAC+TGG - chr1.4:811606-811625 None:intergenic 30.0%
GTAGTAGATAAGGATTTAAG+AGG - chr1.4:811358-811377 None:intergenic 30.0%
TCTTGAACTTGATCAAAACA+CGG + chr1.4:811438-811457 MS.gene64006:CDS 30.0%
TTGCTTATAGGTAGTGTTTA+TGG + chr1.4:812223-812242 MS.gene64006:intron 30.0%
TTTAAGAGGAGAAGAAAGAA+AGG - chr1.4:811344-811363 None:intergenic 30.0%
! AGAGAAATGCAGATTTTGTT+TGG + chr1.4:812709-812728 MS.gene64006:intron 30.0%
! CTTCATACTTTTATGAATGG+AGG + chr1.4:811833-811852 MS.gene64006:intron 30.0%
!! GAGAAATGCAGATTTTGTTT+GGG + chr1.4:812710-812729 MS.gene64006:intron 30.0%
!!! ATGTGAGTGTTTGTTTTTTC+AGG + chr1.4:811530-811549 MS.gene64006:intron 30.0%
AAGTTCAACAGTCACATTAC+CGG - chr1.4:812738-812757 None:intergenic 35.0%
AATCAGTTCAAGTCCATATC+AGG + chr1.4:812637-812656 MS.gene64006:intron 35.0%
AGAAAGGTGGAATGTAATTG+AGG - chr1.4:811328-811347 None:intergenic 35.0%
ATCATTGGTCAGACTTTACT+TGG - chr1.4:812178-812197 None:intergenic 35.0%
CGCCAAATGACAAATTATCA+TGG - chr1.4:812940-812959 None:intergenic 35.0%
CTAAAAGCTAATTCAAACGC+TGG - chr1.4:811964-811983 None:intergenic 35.0%
! AGTTCAAGAGCTTTAATACG+TGG - chr1.4:811427-811446 None:intergenic 35.0%
! ATGCTAGCTTGAACAATCAT+TGG - chr1.4:812193-812212 None:intergenic 35.0%
!! TTATGAATGGAGGAGCATTA+TGG + chr1.4:811843-811862 MS.gene64006:intron 35.0%
!! TTGTTGAGCTCTAAGTCAAA+GGG + chr1.4:812384-812403 MS.gene64006:intron 35.0%
!! TTTGTTGAGCTCTAAGTCAA+AGG + chr1.4:812383-812402 MS.gene64006:intron 35.0%
AAGAGGAGAAGAAAGAAAGG+TGG - chr1.4:811341-811360 None:intergenic 40.0%
AATGTGACTGTTGAACTTGG+TGG + chr1.4:812740-812759 MS.gene64006:CDS 40.0%
ACAACCTAGTGTCTAGTAAC+CGG - chr1.4:812611-812630 None:intergenic 40.0%
ATGCTTATAGGCAGTGTTTG+TGG + chr1.4:812045-812064 MS.gene64006:intron 40.0%
CAGGTAGTTGCTATAACTGT+TGG + chr1.4:811549-811568 MS.gene64006:intron 40.0%
CTGACATGTACAACTTGTCA+AGG + chr1.4:812812-812831 MS.gene64006:CDS 40.0%
CTGTTGTAGTGTAATGTGCA+AGG + chr1.4:811938-811957 MS.gene64006:intron 40.0%
GACTCTGGTAATATGGAGTT+CGG + chr1.4:812138-812157 MS.gene64006:intron 40.0%
GCGATGCTTATGATTGTGTT+TGG + chr1.4:812575-812594 MS.gene64006:intron 40.0%
GGAAAGAGACTCTGGTAATA+TGG + chr1.4:812131-812150 MS.gene64006:intron 40.0%
GGTAATGTGACTGTTGAACT+TGG + chr1.4:812737-812756 MS.gene64006:CDS 40.0%
TCTCGCTGCATAAATTGTGA+TGG + chr1.4:812779-812798 MS.gene64006:CDS 40.0%
TGGTAATATGGAGTTCGGTT+GGG + chr1.4:812143-812162 MS.gene64006:intron 40.0%
TGTACAACTTGTCAAGGATC+TGG + chr1.4:812818-812837 MS.gene64006:CDS 40.0%
! CGTGGATAAAATGTGGGTTT+TGG - chr1.4:811409-811428 None:intergenic 40.0%
! CTGCATAAATTGTGATGGTG+CGG + chr1.4:812784-812803 MS.gene64006:CDS 40.0%
! TGCATAAATTGTGATGGTGC+GGG + chr1.4:812785-812804 MS.gene64006:CDS 40.0%
!! AACTGTTGGTGTTTTGAGTG+TGG + chr1.4:811563-811582 MS.gene64006:CDS 40.0%
!! TGCAGATTTTGTTTGGGAAC+CGG + chr1.4:812716-812735 MS.gene64006:CDS 40.0%
AACCTCGTTACCTTGATCGT+AGG + chr1.4:812846-812865 MS.gene64006:CDS 45.0%
CGTTACCTTGATCGTAGGTA+CGG + chr1.4:812851-812870 MS.gene64006:intron 45.0%
CTGGTAATATGGAGTTCGGT+TGG + chr1.4:812142-812161 MS.gene64006:intron 45.0%
TACCTACGATCAAGGTAACG+AGG - chr1.4:812851-812870 None:intergenic 45.0%
TCTTTCCCTCGAGAACATGA+CGG - chr1.4:812118-812137 None:intergenic 45.0%
TTGAGTGTGGCTGTTGGAAT+TGG + chr1.4:811576-811595 MS.gene64006:CDS 45.0%
! TGTGTTTGGTTGCTTTGTGC+CGG + chr1.4:812589-812608 MS.gene64006:intron 45.0%
!! TGAATGGAGGAGCATTATGG+AGG + chr1.4:811846-811865 MS.gene64006:intron 45.0%
!!! TTATTATTTTAACTTTTTAT+CGG + chr1.4:812320-812339 MS.gene64006:intron 5.0%
AGAACCATTGCATGGGAAGC+AGG - chr1.4:811768-811787 None:intergenic 50.0%
CTTGACCGTCATGTTCTCGA+GGG + chr1.4:812110-812129 MS.gene64006:intron 50.0%
GAACACCGTACCTACGATCA+AGG - chr1.4:812859-812878 None:intergenic 50.0%
GAACCATTGCATGGGAAGCA+GGG - chr1.4:811767-811786 None:intergenic 50.0%
GAGCTCCAGAACCATTGCAT+GGG - chr1.4:811775-811794 None:intergenic 50.0%
TCTTGACCGTCATGTTCTCG+AGG + chr1.4:812109-812128 MS.gene64006:intron 50.0%
TGCTTCCCATGCAATGGTTC+TGG + chr1.4:811767-811786 MS.gene64006:CDS 50.0%
TTCTCGAGGGAAAGAGACTC+TGG + chr1.4:812123-812142 MS.gene64006:intron 50.0%
! CTAAGTCAAAGGGAGTGTGG+AGG + chr1.4:812394-812413 MS.gene64006:intron 50.0%
! GCTCTAAGTCAAAGGGAGTG+TGG + chr1.4:812391-812410 MS.gene64006:intron 50.0%
! GGGCTGCGTGTTATCTCTTT+TGG - chr1.4:811747-811766 None:intergenic 50.0%
! TGAACTTGGTGGAGCTGAGA+CGG + chr1.4:812751-812770 MS.gene64006:CDS 50.0%
!! GGTGTTTTGAGTGTGGCTGT+TGG + chr1.4:811570-811589 MS.gene64006:CDS 50.0%
!! TGTGCCGGTTACTAGACACT+AGG + chr1.4:812604-812623 MS.gene64006:intron 50.0%
CGAGCTCCAGAACCATTGCA+TGG - chr1.4:811776-811795 None:intergenic 55.0%
CAGCCCTGCTTCCCATGCAA+TGG + chr1.4:811761-811780 MS.gene64006:CDS 60.0%
! ACTTGGTGGAGCTGAGACGG+AGG + chr1.4:812754-812773 MS.gene64006:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 811298 813040 811298 ID=MS.gene64006
chr1.4 mRNA 811298 813040 811298 ID=MS.gene64006.t1;Parent=MS.gene64006
chr1.4 exon 811298 811459 811298 ID=MS.gene64006.t1.exon1;Parent=MS.gene64006.t1
chr1.4 CDS 811298 811459 811298 ID=cds.MS.gene64006.t1;Parent=MS.gene64006.t1
chr1.4 exon 811552 811635 811552 ID=MS.gene64006.t1.exon2;Parent=MS.gene64006.t1
chr1.4 CDS 811552 811635 811552 ID=cds.MS.gene64006.t1;Parent=MS.gene64006.t1
chr1.4 exon 811743 811794 811743 ID=MS.gene64006.t1.exon3;Parent=MS.gene64006.t1
chr1.4 CDS 811743 811794 811743 ID=cds.MS.gene64006.t1;Parent=MS.gene64006.t1
chr1.4 exon 812711 812867 812711 ID=MS.gene64006.t1.exon4;Parent=MS.gene64006.t1
chr1.4 CDS 812711 812867 812711 ID=cds.MS.gene64006.t1;Parent=MS.gene64006.t1
chr1.4 exon 813019 813040 813019 ID=MS.gene64006.t1.exon5;Parent=MS.gene64006.t1
chr1.4 CDS 813019 813040 813019 ID=cds.MS.gene64006.t1;Parent=MS.gene64006.t1
Gene Sequence

>MS.gene64006

ATGACAATATCTTATTCACTTTCACTTCCTCAATTACATTCCACCTTTCTTTCTTCTCCTCTTAAATCCTTATCTACTACTACACAATTAGCTAGAAATAAATTTCAACCAAAACCCACATTTTATCCACGTATTAAAGCTCTTGAACTTGATCAAAACACGGTTGTTTATAATTTCCTCCTATTTCTTATTCATTCATTCAATGTTTTTTTGTTACATATTTATCTTAAATATGTGAGTGTTTGTTTTTTCAGGTAGTTGCTATAACTGTTGGTGTTTTGAGTGTGGCTGTTGGAATTGGCATACCAGTGTTTTATGAATCGCAAATTGATAATGCTGTAAAGTGTTTTTACCATTTATTTATTACTATATCATATAATAATGTGTTGGATTAAAATTTAGTTATATATGATATATACGTACCTTTTTTTTTAATTTGTTGCAGGCCAAAAGAGATAACACGCAGCCCTGCTTCCCATGCAATGGTTCTGGAGCTCGTAAGTATCATTTTTTTCTCTTCAATTTCATCATCACACTTCATACTTTTATGAATGGAGGAGCATTATGGAGGTAGCTCACAAGTTATTGTTAATTTGGAGTAGTTGTTAGTACATAACTAACTACTTATATAATATTGTTGCTGTTGTAGTGTAATGTGCAAGGCCAGCGTTTGAATTAGCTTTTAGTTCATTGGAATTTCTCGATTAAAATATGTCTATGATTCTTGACATACACCAAAAAGTTTATATGCTTATAGGCAGTGTTTGTGGATAAGTTTTTTTTTATAGGTAGTGGTATTTCTTGTCTTAACTCTTGACCGTCATGTTCTCGAGGGAAAGAGACTCTGGTAATATGGAGTTCGGTTGGGAGTTAACTGCCAAGTAAAGTCTGACCAATGATTGTTCAAGCTAGCATTTGTAAAAGATTGCTTATAGGTAGTGTTTATGGATAAGTTAAATTATATAACTTCTGGAAGAAAAATAATTTAAAATGCAGAATTTCATTCTAAATTAGACAAGAAGTTATTATTTTAACTTTTTATCGGTATTGTACGATTCTTTTAATAATTCTTTTTTTTAGAATTGTTTGTTGAGCTCTAAGTCAAAGGGAGTGTGGAGGTAGTACATATTTGCTTGCAAAGAAAATTATATTAATTGCTTCTCACTAACACTGTTTTCCATATTATTAATCAGTATTTTATTAAATCTGATTCATTTCTATCTATACCAAGAATAATAAAATAGGTTATTGCAATTTTGTTTTTATTGAAACTTTTTGCGATGCTTATGATTGTGTTTGGTTGCTTTGTGCCGGTTACTAGACACTAGGTTGTGAATGTAATCAGTTCAAGTCCATATCAGGTTGCTAATTTCTTTACCAATCTTATCTTTGAAAATGTTACACTTTTGCCAGAGAAATGCAGATTTTGTTTGGGAACCGGTAATGTGACTGTTGAACTTGGTGGAGCTGAGACGGAGGTCTCTCGCTGCATAAATTGTGATGGTGCGGGTTCACTGACATGTACAACTTGTCAAGGATCTGGAATTCAACCTCGTTACCTTGATCGTAGGTACGGTGTTCAATCTTATTTTCCCCTTTGTAATAATTTAATAATGAATAAGATTAGTCATTATGTATACCATGATAATTTGTCATTTGGCGCACGTTTTGCAATAACCATGAAAATTGCTAACACTATTTTGTGTTTAATATTTGATCAGAGAATTCAAAGATGATGACTGA

Protein sequence

>MS.gene64006.t1

MTISYSLSLPQLHSTFLSSPLKSLSTTTQLARNKFQPKPTFYPRIKALELDQNTVVAITVGVLSVAVGIGIPVFYESQIDNAAKRDNTQPCFPCNGSGAQKCRFCLGTGNVTVELGGAETEVSRCINCDGAGSLTCTTCQGSGIQPRYLDRREFKDDD