AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene049171


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049171.t1 MTR_3g098520 95.597 159 6 1 1 158 1 159 9.07e-111 311
MS.gene049171.t1 MTR_3g098520 94.681 94 4 1 1 93 1 94 2.61e-60 182
MS.gene049171.t1 MTR_5g008050 50.000 60 24 2 55 110 181 238 2.76e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049171.t1 AT5G51010 60.377 159 55 4 1 157 1 153 9.33e-61 185
MS.gene049171.t1 AT5G17170 41.584 101 33 5 55 150 180 259 6.78e-13 64.7

Find 48 sgRNAs with CRISPR-Local

Find 87 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCCAATTGCTTCATCTCTT+TGG 0.237136 3.3:+81017005 None:intergenic
GTTGATTAGGATGAAGTAAA+AGG 0.290725 3.3:+81017925 None:intergenic
AATCAACTACAAGTTTCTTA+TGG 0.292009 3.3:-81017909 MS.gene049171:CDS
TAAGAAACTTGTAGTTGATT+AGG 0.306861 3.3:+81017912 None:intergenic
CCAGGGCAGAAGTATTTATC+AGG 0.317364 3.3:+81017699 None:intergenic
AAAGATGTCTTGAGAGTAGA+TGG 0.349045 3.3:+81017966 None:intergenic
TAGGATGAAGTAAAAGGTTA+AGG 0.356489 3.3:+81017931 None:intergenic
ACGACAGATATAAGCTTGTT+TGG 0.361476 3.3:+81017857 None:intergenic
GTGGGAGTTGTAGTTCTTGC+AGG 0.375454 3.3:-81016859 MS.gene049171:CDS
CTCCAAAGAGATGAAGCAAT+TGG 0.389726 3.3:-81017007 MS.gene049171:CDS
ACTCCCACGGCAACTGCAAT+AGG 0.395621 3.3:+81016874 None:intergenic
ATAGGGCTTAAACCTTCGTT+TGG 0.408207 3.3:+81017090 None:intergenic
AGCTACACGCATGGTAAACC+TGG 0.428236 3.3:+81017881 None:intergenic
TTTGTTGACATCTGTTGCAT+AGG 0.431914 3.3:+81017072 None:intergenic
TTGTTGACATCTGTTGCATA+GGG 0.437509 3.3:+81017073 None:intergenic
TGTCTTGAGAGTAGATGGAT+TGG 0.449903 3.3:+81017971 None:intergenic
TTGGAGAGTGGTCGGAGGGT+AGG 0.455499 3.3:+81017990 None:intergenic
AGGATGAAGTAAAAGGTTAA+GGG 0.468286 3.3:+81017932 None:intergenic
TAGGGCTTAAACCTTCGTTT+GGG 0.473259 3.3:+81017091 None:intergenic
TTATCAGGCAATTTATCAAA+GGG 0.481492 3.3:+81017714 None:intergenic
GTGATAATCTTGTAGTGTGA+AGG 0.484953 3.3:+81018024 None:intergenic
TCCAAAGAGATGAAGCAATT+GGG 0.489224 3.3:-81017006 MS.gene049171:intron
TAGATGGATTGGAGAGTGGT+CGG 0.491971 3.3:+81017982 None:intergenic
TGATAATCTTGTAGTGTGAA+GGG 0.498122 3.3:+81018025 None:intergenic
CTTATATCTGTCGTGACTGC+GGG 0.498593 3.3:-81017848 MS.gene049171:intron
TTTATCAGGCAATTTATCAA+AGG 0.502560 3.3:+81017713 None:intergenic
CAAAATGGCCTTGCAAGTGC+AGG 0.518248 3.3:-81018051 None:intergenic
AAATGAAACAGATGTTAGAA+AGG 0.526185 3.3:-81017044 MS.gene049171:CDS
TGGATTGGAGAGTGGTCGGA+GGG 0.526512 3.3:+81017986 None:intergenic
ACTTCCTATTGCAGTTGCCG+TGG 0.541016 3.3:-81016878 MS.gene049171:CDS
CCTGATAAATACTTCTGCCC+TGG 0.541318 3.3:-81017699 MS.gene049171:intron
AAGTTTCTTATGGACCTCCC+AGG 0.547146 3.3:-81017899 MS.gene049171:CDS
CTTCCTATTGCAGTTGCCGT+GGG 0.547663 3.3:-81016877 MS.gene049171:CDS
GAGTGGTCGGAGGGTAGGAG+TGG 0.553144 3.3:+81017995 None:intergenic
ATCAGGCAATTTATCAAAGG+GGG 0.560795 3.3:+81017716 None:intergenic
AAGGGAGGCCTGCACTTGCA+AGG 0.564120 3.3:+81018043 None:intergenic
GCAGGTATATTTACAATGAG+AGG 0.564968 3.3:-81017740 MS.gene049171:intron
GCTTATATCTGTCGTGACTG+CGG 0.577229 3.3:-81017849 MS.gene049171:CDS
CGGAGGGTAGGAGTGGCAGT+AGG 0.598226 3.3:+81018002 None:intergenic
ATGGATTGGAGAGTGGTCGG+AGG 0.602826 3.3:+81017985 None:intergenic
TTGTTTGGAAGCTACACGCA+TGG 0.631363 3.3:+81017872 None:intergenic
TTTGTGGTGCTCCCAAACGA+AGG 0.633347 3.3:-81017102 MS.gene049171:CDS
TGCAAGAACTACAACTCCCA+CGG 0.635141 3.3:+81016861 None:intergenic
AGAGTAGATGGATTGGAGAG+TGG 0.641832 3.3:+81017978 None:intergenic
TATCAGGCAATTTATCAAAG+GGG 0.660862 3.3:+81017715 None:intergenic
GCTACACGCATGGTAAACCT+GGG 0.677062 3.3:+81017882 None:intergenic
TAATCTTGTAGTGTGAAGGG+AGG 0.698956 3.3:+81018028 None:intergenic
ACACGCATGGTAAACCTGGG+AGG 0.732150 3.3:+81017885 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAAATATATATCTTATTATT+TGG - chr3.3:81017093-81017112 MS.gene049171:CDS 10.0%
!! AATATTTATCAAATTCTTGT+TGG - chr3.3:81017303-81017322 MS.gene049171:intron 15.0%
!! ATGTCAAAAACAAAAATAAT+GGG + chr3.3:81017947-81017966 None:intergenic 15.0%
!! CATATCTATTATCTATATAT+AGG - chr3.3:81017435-81017454 MS.gene049171:intron 15.0%
!! GAATTTGATAAATATTCATA+TGG + chr3.3:81017299-81017318 None:intergenic 15.0%
!! TAATATTATACTGATAAGAA+AGG - chr3.3:81017668-81017687 MS.gene049171:intron 15.0%
!! TATGTCAAAAACAAAAATAA+TGG + chr3.3:81017948-81017967 None:intergenic 15.0%
!! AAAAAGTAATGAAATTACCA+GGG + chr3.3:81017196-81017215 None:intergenic 20.0%
!! TAAAAAGTAATGAAATTACC+AGG + chr3.3:81017197-81017216 None:intergenic 20.0%
!! TTATCTATATATAGGATGTA+TGG - chr3.3:81017443-81017462 MS.gene049171:intron 20.0%
!! TTTAAGAAGCAAAAGAAATA+CGG - chr3.3:81017705-81017724 MS.gene049171:CDS 20.0%
!!! TAACAATTTCTATTGACTTA+AGG - chr3.3:81017367-81017386 MS.gene049171:intron 20.0%
!!! TTTTTCAACCAAGTTTATTA+AGG - chr3.3:81017636-81017655 MS.gene049171:intron 20.0%
! AAAAGAGAATGATCAAAGAA+AGG + chr3.3:81017059-81017078 None:intergenic 25.0%
! AAATGAAACAGATGTTAGAA+AGG - chr3.3:81017831-81017850 MS.gene049171:intron 25.0%
! AATCAACTACAAGTTTCTTA+TGG - chr3.3:81016966-81016985 MS.gene049171:intron 25.0%
! ACTGATAAGAAAGGAAAAAT+AGG - chr3.3:81017677-81017696 MS.gene049171:intron 25.0%
! ACTTTAGACCTTAATAAACT+TGG + chr3.3:81017647-81017666 None:intergenic 25.0%
! TAAGAAACTTGTAGTTGATT+AGG + chr3.3:81016966-81016985 None:intergenic 25.0%
! TGATAAATATTCATATGGCA+TGG + chr3.3:81017294-81017313 None:intergenic 25.0%
! TTAAGAAGCAAAAGAAATAC+GGG - chr3.3:81017706-81017725 MS.gene049171:CDS 25.0%
! TTATCAGGCAATTTATCAAA+GGG + chr3.3:81017164-81017183 None:intergenic 25.0%
! TTTATCAGGCAATTTATCAA+AGG + chr3.3:81017165-81017184 None:intergenic 25.0%
! TTTATTATGCTAATGTCAAC+AGG - chr3.3:81017969-81017988 MS.gene049171:CDS 25.0%
!!! CAAAAACAAAAATAATGGGT+AGG + chr3.3:81017943-81017962 None:intergenic 25.0%
!!! TCTGCTTTAAGTTCTAAATT+TGG + chr3.3:81017581-81017600 None:intergenic 25.0%
!!! TTTGTTGATAATAATGTTGC+AGG - chr3.3:81017117-81017136 MS.gene049171:intron 25.0%
AAGTACAGAGAAAGAAAATC+AGG - chr3.3:81017412-81017431 MS.gene049171:intron 30.0%
AGGATGAAGTAAAAGGTTAA+GGG + chr3.3:81016946-81016965 None:intergenic 30.0%
AGGCAAAAAGAAAATGACTA+TGG + chr3.3:81017903-81017922 None:intergenic 30.0%
GCATTATGATTGTCTCAAAA+TGG - chr3.3:81017740-81017759 MS.gene049171:intron 30.0%
GTTGATTAGGATGAAGTAAA+AGG + chr3.3:81016953-81016972 None:intergenic 30.0%
TAGGATGAAGTAAAAGGTTA+AGG + chr3.3:81016947-81016966 None:intergenic 30.0%
TATCAGGCAATTTATCAAAG+GGG + chr3.3:81017163-81017182 None:intergenic 30.0%
TGATAATCTTGTAGTGTGAA+GGG + chr3.3:81016853-81016872 None:intergenic 30.0%
! TCTAAAATGTGTTGCCTATA+TGG + chr3.3:81017535-81017554 None:intergenic 30.0%
!! GCTTTAAGTTCTAAATTTGG+TGG + chr3.3:81017578-81017597 None:intergenic 30.0%
AAAATGTGTTGCCTATATGG+CGG + chr3.3:81017532-81017551 None:intergenic 35.0%
AAAGATGTCTTGAGAGTAGA+TGG + chr3.3:81016912-81016931 None:intergenic 35.0%
AGGAGTGAACATATTAAGCA+AGG + chr3.3:81017923-81017942 None:intergenic 35.0%
ATCAGGCAATTTATCAAAGG+GGG + chr3.3:81017162-81017181 None:intergenic 35.0%
GCAGGTATATTTACAATGAG+AGG - chr3.3:81017135-81017154 MS.gene049171:intron 35.0%
GTGATAATCTTGTAGTGTGA+AGG + chr3.3:81016854-81016873 None:intergenic 35.0%
GTTAGGTTCAGTGAATTTGA+CGG - chr3.3:81017479-81017498 MS.gene049171:intron 35.0%
TCCAAAGAGATGAAGCAATT+GGG - chr3.3:81017869-81017888 MS.gene049171:CDS 35.0%
TGTCCACTATTACTCATAGA+TGG - chr3.3:81017226-81017245 MS.gene049171:intron 35.0%
TTGTTGACATCTGTTGCATA+GGG + chr3.3:81017805-81017824 None:intergenic 35.0%
TTTGTTGACATCTGTTGCAT+AGG + chr3.3:81017806-81017825 None:intergenic 35.0%
! ACGACAGATATAAGCTTGTT+TGG + chr3.3:81017021-81017040 None:intergenic 35.0%
ACCCAATTGCTTCATCTCTT+TGG + chr3.3:81017873-81017892 None:intergenic 40.0%
ATAGGGCTTAAACCTTCGTT+TGG + chr3.3:81017788-81017807 None:intergenic 40.0%
ATGGCTTCTAAGTGCATGTT+AGG - chr3.3:81017462-81017481 MS.gene049171:intron 40.0%
CCACTATTACTCATAGATGG+AGG - chr3.3:81017229-81017248 MS.gene049171:intron 40.0%
CCTCCATCTATGAGTAATAG+TGG + chr3.3:81017232-81017251 None:intergenic 40.0%
CGGTGAATTTGACAGAATCA+CGG - chr3.3:81017499-81017518 MS.gene049171:intron 40.0%
CTCCAAAGAGATGAAGCAAT+TGG - chr3.3:81017868-81017887 MS.gene049171:CDS 40.0%
TAATCTTGTAGTGTGAAGGG+AGG + chr3.3:81016850-81016869 None:intergenic 40.0%
TAGGGCTTAAACCTTCGTTT+GGG + chr3.3:81017787-81017806 None:intergenic 40.0%
TGAATTTGACAGAATCACGG+TGG - chr3.3:81017502-81017521 MS.gene049171:intron 40.0%
TGTCTTGAGAGTAGATGGAT+TGG + chr3.3:81016907-81016926 None:intergenic 40.0%
! AAATGGCGTTTTGCAGTTTG+TGG - chr3.3:81017757-81017776 MS.gene049171:intron 40.0%
AAGTTTCTTATGGACCTCCC+AGG - chr3.3:81016976-81016995 MS.gene049171:intron 45.0%
ATGAGACCAGTCTTTGTGAG+TGG + chr3.3:81017613-81017632 None:intergenic 45.0%
CCTGATAAATACTTCTGCCC+TGG - chr3.3:81017176-81017195 MS.gene049171:intron 45.0%
CTTATATCTGTCGTGACTGC+GGG - chr3.3:81017027-81017046 MS.gene049171:CDS 45.0%
GCTTATATCTGTCGTGACTG+CGG - chr3.3:81017026-81017045 MS.gene049171:CDS 45.0%
TGCAAGAACTACAACTCCCA+CGG + chr3.3:81018017-81018036 None:intergenic 45.0%
TTGTTTGGAAGCTACACGCA+TGG + chr3.3:81017006-81017025 None:intergenic 45.0%
!! AGAGTAGATGGATTGGAGAG+TGG + chr3.3:81016900-81016919 None:intergenic 45.0%
!! CCAGGGCAGAAGTATTTATC+AGG + chr3.3:81017179-81017198 None:intergenic 45.0%
!! TAGATGGATTGGAGAGTGGT+CGG + chr3.3:81016896-81016915 None:intergenic 45.0%
ACTTCCTATTGCAGTTGCCG+TGG - chr3.3:81017997-81018016 MS.gene049171:CDS 50.0%
AGCTACACGCATGGTAAACC+TGG + chr3.3:81016997-81017016 None:intergenic 50.0%
CTTCCTATTGCAGTTGCCGT+GGG - chr3.3:81017998-81018017 MS.gene049171:CDS 50.0%
GCTACACGCATGGTAAACCT+GGG + chr3.3:81016996-81017015 None:intergenic 50.0%
GTGGGAGTTGTAGTTCTTGC+AGG - chr3.3:81018016-81018035 MS.gene049171:CDS 50.0%
TCACTGCCACTCACAAAGAC+TGG - chr3.3:81017604-81017623 MS.gene049171:intron 50.0%
TTTGTGGTGCTCCCAAACGA+AGG - chr3.3:81017773-81017792 MS.gene049171:intron 50.0%
!! ACGGTGGATTACCGCCATAT+AGG - chr3.3:81017518-81017537 MS.gene049171:intron 50.0%
ACACGCATGGTAAACCTGGG+AGG + chr3.3:81016993-81017012 None:intergenic 55.0%
ACTCCCACGGCAACTGCAAT+AGG + chr3.3:81018004-81018023 None:intergenic 55.0%
! TGGATTGGAGAGTGGTCGGA+GGG + chr3.3:81016892-81016911 None:intergenic 55.0%
!! ATGGATTGGAGAGTGGTCGG+AGG + chr3.3:81016893-81016912 None:intergenic 55.0%
AAGGGAGGCCTGCACTTGCA+AGG + chr3.3:81016835-81016854 None:intergenic 60.0%
TTGGAGAGTGGTCGGAGGGT+AGG + chr3.3:81016888-81016907 None:intergenic 60.0%
CGGAGGGTAGGAGTGGCAGT+AGG + chr3.3:81016876-81016895 None:intergenic 65.0%
GAGTGGTCGGAGGGTAGGAG+TGG + chr3.3:81016883-81016902 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 81016828 81018069 81016828 ID=MS.gene049171
chr3.3 mRNA 81016828 81018069 81016828 ID=MS.gene049171.t1;Parent=MS.gene049171
chr3.3 exon 81017849 81018069 81017849 ID=MS.gene049171.t1.exon1;Parent=MS.gene049171.t1
chr3.3 CDS 81017849 81018069 81017849 ID=cds.MS.gene049171.t1;Parent=MS.gene049171.t1
chr3.3 exon 81017700 81017758 81017700 ID=MS.gene049171.t1.exon2;Parent=MS.gene049171.t1
chr3.3 CDS 81017700 81017758 81017700 ID=cds.MS.gene049171.t1;Parent=MS.gene049171.t1
chr3.3 exon 81017007 81017124 81017007 ID=MS.gene049171.t1.exon3;Parent=MS.gene049171.t1
chr3.3 CDS 81017007 81017124 81017007 ID=cds.MS.gene049171.t1;Parent=MS.gene049171.t1
chr3.3 exon 81016828 81016906 81016828 ID=MS.gene049171.t1.exon4;Parent=MS.gene049171.t1
chr3.3 CDS 81016828 81016906 81016828 ID=cds.MS.gene049171.t1;Parent=MS.gene049171.t1
Gene Sequence

>MS.gene049171

ATGGCCTTGCAAGTGCAGGCCTCCCTTCACACTACAAGATTATCACCTACTGCCACTCCTACCCTCCGACCACTCTCCAATCCATCTACTCTCAAGACATCTTTCTTCTCTCGTTCCCTTAACCTTTTACTTCATCCTAATCAACTACAAGTTTCTTATGGACCTCCCAGGTTTACCATGCGTGTAGCTTCCAAACAAGCTTATATCTGTCGTGACTGCGGGTTATTTCCTTTCTTTGATCATTCTCTTTTTAGTATATCTGAATGAAATATATATCTTATTATTTGGTTTTGTTGATAATAATGTTGCAGGTATATTTACAATGAGAGGACCCCCTTTGATAAATTGCCTGATAAATACTTCTGCCCTGGTAATTTCATTACTTTTTACTCATATAGTGTCCACTATTACTCATAGATGGAGGAACTTCATTTCAAAACTATAATATTTGCTTTTACGCTTTCCATGCCATATGAATATTTATCAAATTCTTGTTGGTTTAGTTGTCTAACAAAAAATAAACAATTTTATCATGATCATAACAATTTCTATTGACTTAAGGTATACTATTAAATTTCTCTTATAAGTACAGAGAAAGAAAATCAGGCATATCTATTATCTATATATAGGATGTATGGCTTCTAAGTGCATGTTAGGTTCAGTGAATTTGACGGTGAATTTGACAGAATCACGGTGGATTACCGCCATATAGGCAACACATTTTAGAGTTTCAAAAAAATCATAGTGCCACCAAATTTAGAACTTAAAGCAGAGCTTCACTGCCACTCACAAAGACTGGTCTCATTTGTTTTTCAACCAAGTTTATTAAGGTCTAAAGTCTAATATTATACTGATAAGAAAGGAAAAATAGGACTTTTTTAAGAAGCAAAAGAAATACGGGTCAATGAGACTGCATTATGATTGTCTCAAAATGGCGTTTTGCAGTTTGTGGTGCTCCCAAACGAAGGTTTAAGCCCTATGCAACAGATGTCAACAAAAAAGCAAATGAAACAGATGTTAGAAAGGCAAGAAAAGCTGAACTCCAAAGAGATGAAGCAATTGGGTGAGTGAGCCATAGTCATTTTCTTTTTGCCTTGCTTAATATGTTCACTCCTACCCATTATTTTTGTTTTTGACATAATTTATTATGCTAATGTCAACAGGAAAGCACTTCCTATTGCAGTTGCCGTGGGAGTTGTAGTTCTTGCAGGATTATACTTCTATCTCAACAACACATTTTAG

Protein sequence

>MS.gene049171.t1

MALQVQASLHTTRLSPTATPTLRPLSNPSTLKTSFFSRSLNLLLHPNQLQVSYGPPRFTMRVASKQAYICRDCGYIYNERTPFDKLPDKYFCPVCGAPKRRFKPYATDVNKKANETDVRKARKAELQRDEAIGKALPIAVAVGVVVLAGLYFYLNNTF