AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene95929


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene95929.t1 MTR_1g037520 94.924 197 10 0 1 197 58 254 2.31e-128 361
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene95929.t1 AT5G08240 48.235 85 39 2 112 195 176 256 1.11e-23 94.7
MS.gene95929.t1 AT5G23160 32.642 193 85 7 22 195 104 270 5.70e-21 87.8

Find 44 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCTAGTGATAATGATATTT+TGG 0.090980 1.3:-21238742 MS.gene95929:CDS
ATCATTCTTTGACATTATTT+TGG 0.171434 1.3:+21238625 None:intergenic
ACCTGCGTTGGTGTATAATA+AGG 0.229088 1.3:+21239798 None:intergenic
AGCTTCAAGCGGCACCGTTT+TGG 0.297229 1.3:+21239944 None:intergenic
GTGATTATGGAAGGACTTCT+TGG 0.303559 1.3:-21238569 MS.gene95929:CDS
CACTAGGGTCACACCTAGTA+TGG 0.331968 1.3:+21238757 None:intergenic
CCTGCGTTGGTGTATAATAA+GGG 0.377190 1.3:+21239799 None:intergenic
CGGAATTGACGGTGGAGAAT+TGG 0.382165 1.3:+21239848 None:intergenic
AGCCTTCGTTCTTGTCGTTT+AGG 0.393219 1.3:+21238860 None:intergenic
TCTGTAATAATGTCATCAAT+TGG 0.442337 1.3:+21238920 None:intergenic
ACCGTCAATTCCGCCGTCTA+CGG 0.455743 1.3:-21239838 MS.gene95929:CDS
AGTATGGACATTCCAACTAT+AGG 0.463810 1.3:+21238773 None:intergenic
CCGTCTACGGTGGTGCTCCC+CGG 0.471029 1.3:-21239825 MS.gene95929:CDS
AGTTCGTATGATCCTATAGT+TGG 0.471500 1.3:-21238785 MS.gene95929:CDS
CCATTCTATGTACTTCAGCT+TGG 0.478889 1.3:-21238706 MS.gene95929:CDS
ACCGTAGACGGCGGAATTGA+CGG 0.482737 1.3:+21239837 None:intergenic
TGATTATGGAAGGACTTCTT+GGG 0.486920 1.3:-21238568 MS.gene95929:CDS
TAGTGGTGTTGGAAATTATG+AGG 0.517184 1.3:-21238657 MS.gene95929:CDS
TCTTGTCGTTTAGGTCGTGT+TGG 0.522518 1.3:+21238869 None:intergenic
GGTGTATAATAAGGGGTGCC+GGG 0.528463 1.3:+21239807 None:intergenic
TGGTGTATAATAAGGGGTGC+CGG 0.530445 1.3:+21239806 None:intergenic
CCCAAAATATCATTATCACT+AGG 0.532345 1.3:+21238741 None:intergenic
ATAGTTGGAATGTCCATACT+AGG 0.535327 1.3:-21238770 MS.gene95929:CDS
CCAAGCTGAAGTACATAGAA+TGG 0.538851 1.3:+21238706 None:intergenic
CCGGGGAGCACCACCGTAGA+CGG 0.542653 1.3:+21239825 None:intergenic
TGTTTGGTTCAGACAAGGCA+TGG 0.557886 1.3:-21238944 MS.gene95929:intron
AATGAAGTCAACGTCCAAAA+CGG 0.561793 1.3:-21239958 MS.gene95929:CDS
CCAAAATATCATTATCACTA+GGG 0.576254 1.3:+21238742 None:intergenic
TCTCTCATTATTCAAAGTCA+CGG 0.583059 1.3:-21239917 MS.gene95929:CDS
AATAATGTCAAAGAATGATG+TGG 0.595806 1.3:-21238621 MS.gene95929:CDS
GTCAATTCCGCCGTCTACGG+TGG 0.605008 1.3:-21239835 MS.gene95929:CDS
CTGCGTTGGTGTATAATAAG+GGG 0.614541 1.3:+21239800 None:intergenic
ATTGACGGTGGAGAATTGGT+TGG 0.618047 1.3:+21239852 None:intergenic
GTTGGAAATTATGAGGAAGA+TGG 0.618802 1.3:-21238650 MS.gene95929:CDS
GACCTAAACGACAAGAACGA+AGG 0.630389 1.3:-21238862 MS.gene95929:CDS
GTGTATAATAAGGGGTGCCG+GGG 0.641424 1.3:+21239808 None:intergenic
TGAGAGAATGAAGCTTCAAG+CGG 0.647573 1.3:+21239933 None:intergenic
ACAGAAGACACACATGAACA+AGG 0.659785 1.3:-21238902 MS.gene95929:CDS
ATATAGATACATACCTGCGT+TGG 0.660530 1.3:+21239786 None:intergenic
GGGAGCACCACCGTAGACGG+CGG 0.676555 1.3:+21239828 None:intergenic
CCCTTATTATACACCAACGC+AGG 0.682151 1.3:-21239799 MS.gene95929:intron
ACACCACTATTTCTAAAACG+TGG 0.710690 1.3:+21238671 None:intergenic
GTAGACGGCGGAATTGACGG+TGG 0.731544 1.3:+21239840 None:intergenic
CTTCTTGGGAGAAATAATCG+AGG 0.735972 1.3:-21238554 MS.gene95929:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTAAAAGTAATTAAACAA+AGG + chr1.3:21239341-21239360 None:intergenic 10.0%
!! TAAAAAAAATTATGTTAACA+TGG - chr1.3:21238836-21238855 MS.gene95929:CDS 10.0%
!!! AAGTATAATTTTTTTTTTGA+AGG - chr1.3:21239261-21239280 MS.gene95929:intron 10.0%
!!! TTTTAAAAAAATGAATTTCT+TGG + chr1.3:21239208-21239227 None:intergenic 10.0%
!!! TTTTATGAAAAAAATCAAAA+TGG + chr1.3:21239395-21239414 None:intergenic 10.0%
!! ATTATTAAATTGACTACAAT+GGG - chr1.3:21238946-21238965 MS.gene95929:intron 15.0%
!! TATTATTAAATTGACTACAA+TGG - chr1.3:21238945-21238964 MS.gene95929:intron 15.0%
!!! TTATTTTGTTTGTTAATGTT+TGG - chr1.3:21239538-21239557 MS.gene95929:intron 15.0%
!!! TTTTTTTTTTCTTTTTCTGA+TGG + chr1.3:21239132-21239151 None:intergenic 15.0%
!! GTATAAGAAAAAAGTGATTA+TGG - chr1.3:21239916-21239935 MS.gene95929:CDS 20.0%
!!! AAAATCATGAACTTGTTAAT+AGG + chr1.3:21238752-21238771 None:intergenic 20.0%
!!! ATCATTCTTTGACATTATTT+TGG + chr1.3:21239876-21239895 None:intergenic 20.0%
!!! TAACAAGTTCATGATTTTTA+GGG - chr1.3:21238754-21238773 MS.gene95929:CDS 20.0%
!!! TCAACTATACTTTCTTTTTT+TGG - chr1.3:21239046-21239065 MS.gene95929:intron 20.0%
!!! TTAACAAGTTCATGATTTTT+AGG - chr1.3:21238753-21238772 MS.gene95929:CDS 20.0%
! AAAATTTACTACTTCAAGTG+TGG + chr1.3:21238919-21238938 None:intergenic 25.0%
! AAGAAAAAAGTGATTATGGA+AGG - chr1.3:21239920-21239939 MS.gene95929:CDS 25.0%
! AATAATGTCAAAGAATGATG+TGG - chr1.3:21239877-21239896 MS.gene95929:CDS 25.0%
! AGAAAGACATACATTTAAGA+AGG + chr1.3:21239025-21239044 None:intergenic 25.0%
! AGTATTGTGTAGCTTAATTA+AGG - chr1.3:21238782-21238801 MS.gene95929:CDS 25.0%
! CCAAAATATCATTATCACTA+GGG + chr1.3:21239759-21239778 None:intergenic 25.0%
! GAAAGACATACATTTAAGAA+GGG + chr1.3:21239024-21239043 None:intergenic 25.0%
! TCTGTAATAATGTCATCAAT+TGG + chr1.3:21239581-21239600 None:intergenic 25.0%
!! ATTTGTATTTTACCTAAGGA+AGG + chr1.3:21238997-21239016 None:intergenic 25.0%
!! TCGTATTTGTATTTTACCTA+AGG + chr1.3:21239001-21239020 None:intergenic 25.0%
!!! CCTAGTGATAATGATATTTT+GGG - chr1.3:21239757-21239776 MS.gene95929:intron 25.0%
!!! CTAGTGATAATGATATTTTG+GGG - chr1.3:21239758-21239777 MS.gene95929:intron 25.0%
CCCAAAATATCATTATCACT+AGG + chr1.3:21239760-21239779 None:intergenic 30.0%
TCTCTCATTATTCAAAGTCA+CGG - chr1.3:21238581-21238600 MS.gene95929:CDS 30.0%
! GTGTGGTAATTTGTGATAAA+TGG + chr1.3:21238902-21238921 None:intergenic 30.0%
! TATTTTACCTAAGGAAGGAA+GGG + chr1.3:21238992-21239011 None:intergenic 30.0%
!! CCCTAGTGATAATGATATTT+TGG - chr1.3:21239756-21239775 MS.gene95929:intron 30.0%
!! TCATGAACTTGTTAATAGGT+TGG + chr1.3:21238748-21238767 None:intergenic 30.0%
!! TTAGGTTTTTGATTGTCGTT+TGG + chr1.3:21239682-21239701 None:intergenic 30.0%
!!! ATACCACGTTTTAGAAATAG+TGG - chr1.3:21239824-21239843 MS.gene95929:CDS 30.0%
AGTATGGACATTCCAACTAT+AGG + chr1.3:21239728-21239747 None:intergenic 35.0%
AGTTCGTATGATCCTATAGT+TGG - chr1.3:21239713-21239732 MS.gene95929:intron 35.0%
ATAGTTGGAATGTCCATACT+AGG - chr1.3:21239728-21239747 MS.gene95929:intron 35.0%
ATATAGATACATACCTGCGT+TGG + chr1.3:21238715-21238734 None:intergenic 35.0%
ATGGTTCTCTCAAAAATGTG+TGG + chr1.3:21238883-21238902 None:intergenic 35.0%
GTTGGAAATTATGAGGAAGA+TGG - chr1.3:21239848-21239867 MS.gene95929:CDS 35.0%
TCTCAAAAATGTGTGGTAGT+TGG + chr1.3:21238876-21238895 None:intergenic 35.0%
TGATTATGGAAGGACTTCTT+GGG - chr1.3:21239930-21239949 MS.gene95929:CDS 35.0%
! GTATTTTACCTAAGGAAGGA+AGG + chr1.3:21238993-21239012 None:intergenic 35.0%
! GTTAATGTTTGGTTCAGACA+AGG - chr1.3:21239549-21239568 MS.gene95929:intron 35.0%
! TAGTGGTGTTGGAAATTATG+AGG - chr1.3:21239841-21239860 MS.gene95929:CDS 35.0%
!! ACACCACTATTTCTAAAACG+TGG + chr1.3:21239830-21239849 None:intergenic 35.0%
!!! ACGAACTTCGTACGTTTTTT+AGG + chr1.3:21239700-21239719 None:intergenic 35.0%
!!! CGTTTTAGAAATAGTGGTGT+TGG - chr1.3:21239830-21239849 MS.gene95929:CDS 35.0%
!!! TGATGTGGATTTTGATTCTG+AGG - chr1.3:21239892-21239911 MS.gene95929:CDS 35.0%
ACAGAAGACACACATGAACA+AGG - chr1.3:21239596-21239615 MS.gene95929:intron 40.0%
CCAAGCTGAAGTACATAGAA+TGG + chr1.3:21239795-21239814 None:intergenic 40.0%
CCATTCTATGTACTTCAGCT+TGG - chr1.3:21239792-21239811 MS.gene95929:intron 40.0%
CTTCTTGGGAGAAATAATCG+AGG - chr1.3:21239944-21239963 MS.gene95929:CDS 40.0%
GTGATTATGGAAGGACTTCT+TGG - chr1.3:21239929-21239948 MS.gene95929:CDS 40.0%
TGAGAGAATGAAGCTTCAAG+CGG + chr1.3:21238568-21238587 None:intergenic 40.0%
! ACCTGCGTTGGTGTATAATA+AGG + chr1.3:21238703-21238722 None:intergenic 40.0%
! CCTGCGTTGGTGTATAATAA+GGG + chr1.3:21238702-21238721 None:intergenic 40.0%
! CTGCGTTGGTGTATAATAAG+GGG + chr1.3:21238701-21238720 None:intergenic 40.0%
AATACGACCCTTCCTTCCTT+AGG - chr1.3:21238982-21239001 MS.gene95929:intron 45.0%
ATTGACGGTGGAGAATTGGT+TGG + chr1.3:21238649-21238668 None:intergenic 45.0%
CCCTTATTATACACCAACGC+AGG - chr1.3:21238699-21238718 MS.gene95929:CDS 45.0%
GACCTAAACGACAAGAACGA+AGG - chr1.3:21239636-21239655 MS.gene95929:intron 45.0%
! AGCCTTCGTTCTTGTCGTTT+AGG + chr1.3:21239641-21239660 None:intergenic 45.0%
! TCTTGTCGTTTAGGTCGTGT+TGG + chr1.3:21239632-21239651 None:intergenic 45.0%
! TGGTGTATAATAAGGGGTGC+CGG + chr1.3:21238695-21238714 None:intergenic 45.0%
! TGTTTGGTTCAGACAAGGCA+TGG - chr1.3:21239554-21239573 MS.gene95929:intron 45.0%
!!! AATAAATAATTTTTAAAACA+TGG + chr1.3:21239523-21239542 None:intergenic 5.0%
!!! ATTTTTTTTAATTATGTTAT+AGG + chr1.3:21238826-21238845 None:intergenic 5.0%
CACTAGGGTCACACCTAGTA+TGG + chr1.3:21239744-21239763 None:intergenic 50.0%
CGGAATTGACGGTGGAGAAT+TGG + chr1.3:21238653-21238672 None:intergenic 50.0%
!! GGTGTATAATAAGGGGTGCC+GGG + chr1.3:21238694-21238713 None:intergenic 50.0%
!! GTGTATAATAAGGGGTGCCG+GGG + chr1.3:21238693-21238712 None:intergenic 50.0%
ACCGTAGACGGCGGAATTGA+CGG + chr1.3:21238664-21238683 None:intergenic 55.0%
ACCGTCAATTCCGCCGTCTA+CGG - chr1.3:21238660-21238679 MS.gene95929:CDS 55.0%
! AGCTTCAAGCGGCACCGTTT+TGG + chr1.3:21238557-21238576 None:intergenic 55.0%
GTAGACGGCGGAATTGACGG+TGG + chr1.3:21238661-21238680 None:intergenic 60.0%
GTCAATTCCGCCGTCTACGG+TGG - chr1.3:21238663-21238682 MS.gene95929:CDS 60.0%
CCGTCTACGGTGGTGCTCCC+CGG - chr1.3:21238673-21238692 MS.gene95929:CDS 70.0%
!! CCGGGGAGCACCACCGTAGA+CGG + chr1.3:21238676-21238695 None:intergenic 70.0%
!! GGGAGCACCACCGTAGACGG+CGG + chr1.3:21238673-21238692 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 21238541 21239979 21238541 ID=MS.gene95929
chr1.3 mRNA 21238541 21239979 21238541 ID=MS.gene95929.t1;Parent=MS.gene95929
chr1.3 exon 21239800 21239979 21239800 ID=MS.gene95929.t1.exon1;Parent=MS.gene95929.t1
chr1.3 CDS 21239800 21239979 21239800 ID=cds.MS.gene95929.t1;Parent=MS.gene95929.t1
chr1.3 exon 21238541 21238954 21238541 ID=MS.gene95929.t1.exon2;Parent=MS.gene95929.t1
chr1.3 CDS 21238541 21238954 21238541 ID=cds.MS.gene95929.t1;Parent=MS.gene95929.t1
Gene Sequence

>MS.gene95929

ATGAAGTCAACGTCCAAAACGGTGCCGCTTGAAGCTTCATTCTCTCATTATTCAAAGTCACGGTCAAAGTTTTTAACTCTTCATCATAAATCTAAAAAAACTCTACCAACCAATTCTCCACCGTCAATTCCGCCGTCTACGGTGGTGCTCCCCGGCACCCCTTATTATACACCAACGCAGGTATGTATCTATATATAATCATCTCCAACCTATTAACAAGTTCATGATTTTTAGGGAGATTAGTATTGTGTAGCTTAATTAAGGATATATGTATATTTCATACCTATAACATAATTAAAAAAAATTATGTTAACATGGTAGCAAATTCATAACCAACTACCACACATTTTTGAGAGAACCATTTATCACAAATTACCACACTTGAAGTAGTAAATTTTAGTCGTTATTATTAAATTGACTACAATGGGATAATTAAGCTCTAATACGACCCTTCCTTCCTTAGGTAAAATACAAATACGACCCTTCTTAAATGTATGTCTTTCTCTCAACTATACTTTCTTTTTTTGGTTACACTCTCAACTATACTTTGATATTAAATTGTCTCAATACTATTTATTTCTGCAACTTCCATCAGAAAAAGAAAAAAAAAACTGTTTATTTCTGCAACTAGCTAGCTGTTTAATTAAGTCAATTATTTTATGTACCAAGAAATTCATTTTTTTAAAAAAGTTAATTAATATTAAAATTTTCAACAATATTAAGTATAATTTTTTTTTTGAAGGAACAATATTAAGTATAATTATTAAATATATAAATCATTTTTCTATTAAATTAAACCTTTGTTTAATTACTTTTAATTAAACTTTCAAGAATTTTATGATATCTCTTGTCCATTTTGATTTTTTTCATAAAATTAACATTTTGATATTTTTGTATATATGTTTTGTAATGATATCTTTGTTTTTCATCATGATTTTTTAATTAAATTATCATTTTGATAAATAAATTATTTTATTCACCATGTTTTAAAAATTATTTATTTTGTTTGTTAATGTTTGGTTCAGACAAGGCATGGTCCAATTGATGACATTATTACAGAAGACACACATGAACAAGGTAGAACTACTCCAACACGACCTAAACGACAAGAACGAAGGCTGTCGTCTACAACACAAAACCAAACGACAATCAAAAACCTAAAAAACGTACGAAGTTCGTATGATCCTATAGTTGGAATGTCCATACTAGGTGTGACCCTAGTGATAATGATATTTTGGGGTCGCTTTTGTGCCATTCTATGTACTTCAGCTTGGTTGTATTTTATACCACGTTTTAGAAATAGTGGTGTTGGAAATTATGAGGAAGATGGTGCCAAAATAATGTCAAAGAATGATGTGGATTTTGATTCTGAGGAGTATAAGAAAAAAGTGATTATGGAAGGACTTCTTGGGAGAAATAATCGAGGTAGTAACATATGA

Protein sequence

>MS.gene95929.t1

MKSTSKTVPLEASFSHYSKSRSKFLTLHHKSKKTLPTNSPPSIPPSTVVLPGTPYYTPTQTRHGPIDDIITEDTHEQGRTTPTRPKRQERRLSSTTQNQTTIKNLKNVRSSYDPIVGMSILGVTLVIMIFWGRFCAILCTSAWLYFIPRFRNSGVGNYEEDGAKIMSKNDVDFDSEEYKKKVIMEGLLGRNNRGSNI