AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene020507

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene020507.t1 MTR_8g105110 100.000 154 0 0 1 154 1 154 4.92e-111 312
MS.gene020507.t1 MTR_1g070450 95.455 154 5 1 1 154 1 152 4.61e-104 294
MS.gene020507.t1 MTR_4g075450 92.857 154 9 1 1 154 1 152 4.90e-92 264
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene020507.t1 AT5G09500 87.662 154 15 1 1 154 1 150 1.07e-93 268
MS.gene020507.t1 AT5G09510 91.558 154 11 1 1 154 1 152 3.57e-92 264
MS.gene020507.t1 AT1G04270 91.558 154 11 1 1 154 1 152 4.12e-92 264
MS.gene020507.t1 AT1G04270 90.909 154 11 2 1 154 1 151 1.39e-89 258
MS.gene020507.t1 AT5G09490 81.818 154 26 1 1 154 1 152 9.71e-89 255
MS.gene020507.t1 AT5G43640 85.906 149 21 0 6 154 1 149 1.10e-82 240
MS.gene020507.t1 AT5G09510 94.915 118 6 0 37 154 1 118 2.08e-71 210
MS.gene020507.t1 AT5G63070 62.500 160 54 2 1 154 1 160 3.08e-64 194
MS.gene020507.t1 AT1G33850 83.607 61 10 0 12 72 7 67 1.12e-19 78.2

Find 43 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGATTTCAACTTGGTTAA+AGG 0.236449 4.4:-2237826 None:intergenic
GAGATGATTGGGAGCATTAT+TGG 0.247005 4.4:+2237786 MS.gene020507:CDS
CAGTTTCAGAGGAGTTGATT+TGG 0.292075 4.4:+2236552 MS.gene020507:CDS
CCAGGTCTACCATGCTTAAC+AGG 0.341486 4.4:-2237897 None:intergenic
TCAGTGCTCGTGCTCGTAGA+AGG 0.367007 4.4:+2236617 MS.gene020507:CDS
TTCTTGAATGTTCTCTTCTT+CGG 0.377124 4.4:-2236526 None:intergenic
AGATGGGTCCTAACAGGTTC+GGG 0.405557 4.4:-2237741 None:intergenic
GTGAGAAGCCCGAACCTGTT+AGG 0.409377 4.4:+2237733 MS.gene020507:CDS
GATGCAGCAGCCGCCGCCGC+GGG 0.422266 4.4:+2236499 MS.gene020507:CDS
TTACGAAGATGGGTCCTAAC+AGG 0.435557 4.4:-2237747 None:intergenic
AAGATGGGTCCTAACAGGTT+CGG 0.450751 4.4:-2237742 None:intergenic
CAATGATCATGTTACGAAGA+TGG 0.465315 4.4:-2237758 None:intergenic
ATCATTGTACCTGAGATGAT+TGG 0.468347 4.4:+2237774 MS.gene020507:CDS
TTCAAGAAGTTCAGTTTCAG+AGG 0.481387 4.4:+2236541 MS.gene020507:CDS
AGGTAATGACCGATCATCTC+AGG 0.492365 4.4:-2237849 None:intergenic
CCTGTTAAGCATGGTAGACC+TGG 0.509940 4.4:+2237897 MS.gene020507:CDS
AATGATCATGTTACGAAGAT+GGG 0.516658 4.4:-2237757 None:intergenic
GCATTATTGGAGTGTACAAT+GGG 0.517140 4.4:+2237799 MS.gene020507:CDS
ACAGGTTCGGGCTTCTCACC+AGG 0.517899 4.4:-2237729 None:intergenic
CTTCGGTACTCCCGCGGCGG+CGG 0.518043 4.4:-2236509 None:intergenic
TTGGTGCTACTCACTCCTCC+AGG 0.521787 4.4:+2237922 MS.gene020507:CDS
ATAATGCTCCCAATCATCTC+AGG 0.528225 4.4:-2237783 None:intergenic
TCATTGTACCTGAGATGATT+GGG 0.539509 4.4:+2237775 MS.gene020507:CDS
GCTTACGAGTGAGACCTCTC+TGG 0.541580 4.4:-2236642 None:intergenic
TCTCAGGTTTGATTTCAACT+TGG 0.546765 4.4:-2237833 None:intergenic
AGCATTATTGGAGTGTACAA+TGG 0.558872 4.4:+2237798 MS.gene020507:CDS
TAGAAAAGGGAGGCACCACC+TGG 0.561975 4.4:+2237711 MS.gene020507:intron
TCACTTGAGAGGAATGAACC+TGG 0.566509 4.4:-2237940 None:intergenic
AGATGCAGCAGCCGCCGCCG+CGG 0.579389 4.4:+2236498 MS.gene020507:CDS
GAGTGAGTAGCACCAATACC+AGG 0.584094 4.4:-2237915 None:intergenic
GAAATCAAACCTGAGATGAT+CGG 0.585387 4.4:+2237840 MS.gene020507:CDS
AAGCATGGTAGACCTGGTAT+TGG 0.586812 4.4:+2237903 MS.gene020507:CDS
TCATACAAGCCTGTTAAGCA+TGG 0.604339 4.4:+2237888 MS.gene020507:CDS
GAGCTTAACAAGCTCATCAG+TGG 0.607114 4.4:-2236593 None:intergenic
AGGTCTCACTCGTAAGCCCA+TGG 0.623580 4.4:+2236648 MS.gene020507:CDS
AACAAGGTGATTCACTTGAG+AGG 0.631770 4.4:-2237951 None:intergenic
ATGAGATCGAGAATTCAGCT+AGG 0.682732 4.4:-2237869 None:intergenic
GGTTCGGGCTTCTCACCAGG+TGG 0.683492 4.4:-2237726 None:intergenic
TCTCTTCTTCGGTACTCCCG+CGG 0.697626 4.4:-2236515 None:intergenic
CTTCTTCGGTACTCCCGCGG+CGG 0.700206 4.4:-2236512 None:intergenic
GAATTGGTTGTAGAAAAGGG+AGG 0.733330 4.4:+2237701 MS.gene020507:intron
CTTGAGAGGAATGAACCTGG+AGG 0.737810 4.4:-2237937 None:intergenic
GCTCGTAGAAGGTTCCAGAG+AGG 0.763484 4.4:+2236628 MS.gene020507:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTACTATTTTACAAATTTA+AGG - chr4.4:2236834-2236853 None:intergenic 10.0%
!! ATTACTATTATGCAAATTTA+AGG - chr4.4:2237149-2237168 None:intergenic 15.0%
!!! AAAAAAAAGTGTTCAATTTA+AGG - chr4.4:2237178-2237197 None:intergenic 15.0%
!!! AAAAAAAGTGTTCAATTTAA+GGG - chr4.4:2237177-2237196 None:intergenic 15.0%
!!! ATTGTTATAATTTTGTGAAT+TGG + chr4.4:2237685-2237704 MS.gene020507:intron 15.0%
!!! GAACACTTTTTTTTTTTTTT+TGG + chr4.4:2237184-2237203 MS.gene020507:intron 15.0%
!!! TTTGTTATTCTTTTATTTAG+TGG + chr4.4:2237321-2237340 MS.gene020507:intron 15.0%
!!! TTTGTTATTTTGTTAATTTG+AGG + chr4.4:2237083-2237102 MS.gene020507:intron 15.0%
!! AAGGAACTAAATTGATATAT+TGG - chr4.4:2237130-2237149 None:intergenic 20.0%
!! ATATGCAAAATACTAACAAT+TGG + chr4.4:2236805-2236824 MS.gene020507:intron 20.0%
!! ATTCCAAATTCAAATTCAAT+CGG - chr4.4:2236452-2236471 None:intergenic 20.0%
!! TATGCAAAATACTAACAATT+GGG + chr4.4:2236806-2236825 MS.gene020507:intron 20.0%
!! TTTAGTACTTAAGATAGTAA+GGG - chr4.4:2237653-2237672 None:intergenic 20.0%
!!! GAAGTTTTTATTGATTTTGT+TGG + chr4.4:2237257-2237276 MS.gene020507:intron 20.0%
!!! GTTAGTATTTTGCATATTAA+AGG - chr4.4:2236802-2236821 None:intergenic 20.0%
!!! TGGTGGTTTTTTAAATTTAA+AGG + chr4.4:2237584-2237603 MS.gene020507:intron 20.0%
!!! TTGTTAATTTGTGAATTTGA+GGG + chr4.4:2237613-2237632 MS.gene020507:intron 20.0%
!!! TTTGTTAATTTGTGAATTTG+AGG + chr4.4:2237612-2237631 MS.gene020507:intron 20.0%
!!! TTTTAGTACTTAAGATAGTA+AGG - chr4.4:2237654-2237673 None:intergenic 20.0%
! AAATCCATGTTAGATTCTAT+CGG - chr4.4:2236429-2236448 None:intergenic 25.0%
! AACATGAAACCATTAAAATG+GGG - chr4.4:2236925-2236944 None:intergenic 25.0%
! AATAGCGATATTTAGGTATA+GGG + chr4.4:2237550-2237569 MS.gene020507:intron 25.0%
! AGTAATTGCATACCAAAAAT+TGG + chr4.4:2236848-2236867 MS.gene020507:intron 25.0%
! ATTTAACACTACCATTCTAA+AGG + chr4.4:2237448-2237467 MS.gene020507:intron 25.0%
! GAACATGAAACCATTAAAAT+GGG - chr4.4:2236926-2236945 None:intergenic 25.0%
! TGAACATGAAACCATTAAAA+TGG - chr4.4:2236927-2236946 None:intergenic 25.0%
! TTTCCGATTGAATTTGAATT+TGG + chr4.4:2236446-2236465 MS.gene020507:intron 25.0%
!! AAACAACAATCTTAGCATTT+TGG + chr4.4:2236759-2236778 MS.gene020507:intron 25.0%
!! AACAACAATCTTAGCATTTT+GGG + chr4.4:2236760-2236779 MS.gene020507:intron 25.0%
!! AGGACTAACATCAAAATTTT+TGG - chr4.4:2237359-2237378 None:intergenic 25.0%
!! ATATGACATTGTCCAATTTT+TGG - chr4.4:2236863-2236882 None:intergenic 25.0%
!! CTGAAGATATATTTTCATTG+AGG + chr4.4:2237029-2237048 MS.gene020507:intron 25.0%
!! GTGCTAATTTGCAAATATAA+AGG - chr4.4:2237379-2237398 None:intergenic 25.0%
!! TTTGATTTCAACTTGGTTAA+AGG - chr4.4:2237829-2237848 None:intergenic 25.0%
!!! AATTTGGAATTGAATTTTGC+AGG + chr4.4:2236462-2236481 MS.gene020507:intron 25.0%
!!! CTCTTGTTGATTATTGATTT+TGG + chr4.4:2236996-2237015 MS.gene020507:intron 25.0%
!!! GAAATTGATTGCTGTTTTTA+GGG + chr4.4:2237055-2237074 MS.gene020507:intron 25.0%
!!! TGTTGATTATTGATTTTGGT+GGG + chr4.4:2237000-2237019 MS.gene020507:intron 25.0%
!!! TTGTTGATTATTGATTTTGG+TGG + chr4.4:2236999-2237018 MS.gene020507:intron 25.0%
AAGGCATATAACCTTCAAAA+TGG - chr4.4:2237223-2237242 None:intergenic 30.0%
AATGATCATGTTACGAAGAT+GGG - chr4.4:2237760-2237779 None:intergenic 30.0%
ACTTCCATGTAAACTTGAAA+AGG - chr4.4:2237242-2237261 None:intergenic 30.0%
ATTTCCGATAGAATCTAACA+TGG + chr4.4:2236422-2236441 MS.gene020507:intron 30.0%
CTTACTGAATAGCGATATTT+AGG + chr4.4:2237543-2237562 MS.gene020507:intron 30.0%
GAATAGCGATATTTAGGTAT+AGG + chr4.4:2237549-2237568 MS.gene020507:intron 30.0%
TGTGAATTGGTTGTAGAAAA+GGG + chr4.4:2237698-2237717 MS.gene020507:intron 30.0%
TTCTTGAATGTTCTCTTCTT+CGG - chr4.4:2236529-2236548 None:intergenic 30.0%
TTGTGAATTGGTTGTAGAAA+AGG + chr4.4:2237697-2237716 MS.gene020507:intron 30.0%
! ACTTTAGTACCCCATTTTAA+TGG + chr4.4:2236913-2236932 MS.gene020507:intron 30.0%
! TTAAAATGGGGTACTAAAGT+CGG - chr4.4:2236913-2236932 None:intergenic 30.0%
!!! CGAAATTGATTGCTGTTTTT+AGG + chr4.4:2237054-2237073 MS.gene020507:intron 30.0%
!!! TATGCCTTTTCAAGTTTACA+TGG + chr4.4:2237235-2237254 MS.gene020507:intron 30.0%
AGCATTATTGGAGTGTACAA+TGG + chr4.4:2237798-2237817 MS.gene020507:CDS 35.0%
ATAGGGACTAAATTGATTGG+TGG + chr4.4:2237567-2237586 MS.gene020507:intron 35.0%
ATCATTGTACCTGAGATGAT+TGG + chr4.4:2237774-2237793 MS.gene020507:CDS 35.0%
ATCGGAAATCAAGTTTCAGA+AGG - chr4.4:2236411-2236430 None:intergenic 35.0%
CAATGATCATGTTACGAAGA+TGG - chr4.4:2237761-2237780 None:intergenic 35.0%
GAAATCAAACCTGAGATGAT+CGG + chr4.4:2237840-2237859 MS.gene020507:CDS 35.0%
GCATATAACCTTCAAAATGG+TGG - chr4.4:2237220-2237239 None:intergenic 35.0%
GCATTATTGGAGTGTACAAT+GGG + chr4.4:2237799-2237818 MS.gene020507:CDS 35.0%
GGTATAGGGACTAAATTGAT+TGG + chr4.4:2237564-2237583 MS.gene020507:intron 35.0%
GTGACTCAGTGTTCAAATTA+AGG - chr4.4:2237409-2237428 None:intergenic 35.0%
TCATTGTACCTGAGATGATT+GGG + chr4.4:2237775-2237794 MS.gene020507:CDS 35.0%
TTCAAGAAGTTCAGTTTCAG+AGG + chr4.4:2236541-2236560 MS.gene020507:CDS 35.0%
! ACGCATGTAAACCTTTAGAA+TGG - chr4.4:2237462-2237481 None:intergenic 35.0%
! CAAAGTTACCACCATTTTGA+AGG + chr4.4:2237209-2237228 MS.gene020507:intron 35.0%
! TCTCAGGTTTGATTTCAACT+TGG - chr4.4:2237836-2237855 None:intergenic 35.0%
ATAATGCTCCCAATCATCTC+AGG - chr4.4:2237786-2237805 None:intergenic 40.0%
ATGAGATCGAGAATTCAGCT+AGG - chr4.4:2237872-2237891 None:intergenic 40.0%
CATCAAAAAGCTTCGCAAAG+CGG + chr4.4:2236675-2236694 MS.gene020507:CDS 40.0%
GAATTGGTTGTAGAAAAGGG+AGG + chr4.4:2237701-2237720 MS.gene020507:intron 40.0%
TCATACAAGCCTGTTAAGCA+TGG + chr4.4:2237888-2237907 MS.gene020507:CDS 40.0%
! AAGCTTTTTGATGAGAGCCA+TGG - chr4.4:2236668-2236687 None:intergenic 40.0%
! AGCTTTTTGATGAGAGCCAT+GGG - chr4.4:2236667-2236686 None:intergenic 40.0%
! CAGTTTCAGAGGAGTTGATT+TGG + chr4.4:2236552-2236571 MS.gene020507:CDS 40.0%
!! GAGATGATTGGGAGCATTAT+TGG + chr4.4:2237786-2237805 MS.gene020507:CDS 40.0%
AAGATGGGTCCTAACAGGTT+CGG - chr4.4:2237745-2237764 None:intergenic 45.0%
AAGCATGGTAGACCTGGTAT+TGG + chr4.4:2237903-2237922 MS.gene020507:CDS 45.0%
AGGTAATGACCGATCATCTC+AGG - chr4.4:2237852-2237871 None:intergenic 45.0%
GAGCTTAACAAGCTCATCAG+TGG - chr4.4:2236596-2236615 None:intergenic 45.0%
TCACTTGAGAGGAATGAACC+TGG - chr4.4:2237943-2237962 None:intergenic 45.0%
TTACGAAGATGGGTCCTAAC+AGG - chr4.4:2237750-2237769 None:intergenic 45.0%
! AATTTTGCAGGCAGACGTTG+AGG + chr4.4:2236474-2236493 MS.gene020507:intron 45.0%
!! ATAAATAAAAGAAATAAAAA+TGG - chr4.4:2236716-2236735 None:intergenic 5.0%
!! TAAATAAAAGAAATAAAAAT+GGG - chr4.4:2236715-2236734 None:intergenic 5.0%
AGATGGGTCCTAACAGGTTC+GGG - chr4.4:2237744-2237763 None:intergenic 50.0%
CCAGGTCTACCATGCTTAAC+AGG - chr4.4:2237900-2237919 None:intergenic 50.0%
CCTGTTAAGCATGGTAGACC+TGG + chr4.4:2237897-2237916 MS.gene020507:CDS 50.0%
CTTGAGAGGAATGAACCTGG+AGG - chr4.4:2237940-2237959 None:intergenic 50.0%
GAGTGAGTAGCACCAATACC+AGG - chr4.4:2237918-2237937 None:intergenic 50.0%
AGGTCTCACTCGTAAGCCCA+TGG + chr4.4:2236648-2236667 MS.gene020507:CDS 55.0%
GCTCGTAGAAGGTTCCAGAG+AGG + chr4.4:2236628-2236647 MS.gene020507:CDS 55.0%
GCTTACGAGTGAGACCTCTC+TGG - chr4.4:2236645-2236664 None:intergenic 55.0%
GTGAGAAGCCCGAACCTGTT+AGG + chr4.4:2237733-2237752 MS.gene020507:CDS 55.0%
TCAGTGCTCGTGCTCGTAGA+AGG + chr4.4:2236617-2236636 MS.gene020507:CDS 55.0%
TCTCTTCTTCGGTACTCCCG+CGG - chr4.4:2236518-2236537 None:intergenic 55.0%
!! TAGAAAAGGGAGGCACCACC+TGG + chr4.4:2237711-2237730 MS.gene020507:intron 55.0%
!! TTGGTGCTACTCACTCCTCC+AGG + chr4.4:2237922-2237941 MS.gene020507:CDS 55.0%
ACAGGTTCGGGCTTCTCACC+AGG - chr4.4:2237732-2237751 None:intergenic 60.0%
CTTCTTCGGTACTCCCGCGG+CGG - chr4.4:2236515-2236534 None:intergenic 65.0%
GGTTCGGGCTTCTCACCAGG+TGG - chr4.4:2237729-2237748 None:intergenic 65.0%
AGATGCAGCAGCCGCCGCCG+CGG + chr4.4:2236498-2236517 MS.gene020507:CDS 75.0%
CTTCGGTACTCCCGCGGCGG+CGG - chr4.4:2236512-2236531 None:intergenic 75.0%
! GATGCAGCAGCCGCCGCCGC+GGG + chr4.4:2236499-2236518 MS.gene020507:CDS 80.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 2236392 2237962 2236392 ID=MS.gene020507
chr4.4 mRNA 2236392 2237962 2236392 ID=MS.gene020507.t1;Parent=MS.gene020507
chr4.4 exon 2236392 2236394 2236392 ID=MS.gene020507.t1.exon1;Parent=MS.gene020507.t1
chr4.4 CDS 2236392 2236394 2236392 ID=cds.MS.gene020507.t1;Parent=MS.gene020507.t1
chr4.4 exon 2236484 2236696 2236484 ID=MS.gene020507.t1.exon2;Parent=MS.gene020507.t1
chr4.4 CDS 2236484 2236696 2236484 ID=cds.MS.gene020507.t1;Parent=MS.gene020507.t1
chr4.4 exon 2237714 2237962 2237714 ID=MS.gene020507.t1.exon3;Parent=MS.gene020507.t1
chr4.4 CDS 2237714 2237962 2237714 ID=cds.MS.gene020507.t1;Parent=MS.gene020507.t1
Gene Sequence

>MS.gene020507

ATGGTGAGTTAACAATCCTTCTGAAACTTGATTTCCGATAGAATCTAACATGGATTTCCGATTGAATTTGAATTTGGAATTGAATTTTGCAGGCAGACGTTGAGGTAGATGCAGCAGCCGCCGCCGCGGGAGTACCGAAGAAGAGAACATTCAAGAAGTTCAGTTTCAGAGGAGTTGATTTGGATGCACTTCTTGACATGTCCACTGATGAGCTTGTTAAGCTCTTCAGTGCTCGTGCTCGTAGAAGGTTCCAGAGAGGTCTCACTCGTAAGCCCATGGCTCTCATCAAAAAGCTTCGCAAAGCGGTACAATTTTATTTTCCCATTTTTATTTCTTTTATTTATCTGAAAATTAAATAGTAAAATTAAAACAACAATCTTAGCATTTTGGGCGTGCTCAATTTAGTTCCTTTAATATGCAAAATACTAACAATTGGGTTCCTTAAATTTGTAAAATAGTAATTGCATACCAAAAATTGGACAATGTCATATCAGTCATTAGTATTTTTGTGTTTTTGTCCGACTTTAGTACCCCATTTTAATGGTTTCATGTTCATTTTGATGCAATAATTGCTTCTAGAACATATTCAAGTTACTATTCAAGTCTCTTGTTGATTATTGATTTTGGTGGGTTTGTTCTGAAGATATATTTTCATTGAGGTGCGAAATTGATTGCTGTTTTTAGGGATTAATTTGTTATTTTGTTAATTTGAGGCATTAAATTGCTCAAACTTTACCAATATATCAATTTAGTTCCTTAAATTTGCATAATAGTAATTTAGTCCCTTAAATTGAACACTTTTTTTTTTTTTTTGGTGCAAAGTTACCACCATTTTGAAGGTTATATGCCTTTTCAAGTTTACATGGAAGTTTTTATTGATTTTGTTGGATCTTTACTAAAGTTATATTTTGCTTGAAGAACTTAGTTATTTTGTTATTCTTTTATTTAGTGGTTAATTGAATTTCCAAAAATTTTGATGTTAGTCCTTTATATTTGCAAATTAGCACTTTAGTACCTTAATTTGAACACTGAGTCACTTTTTTTTTTTTGCTTTAAATTTAACACTACCATTCTAAAGGTTTACATGCGTCAAATGCATCAAGAGACTAGTTAAGTTAATATTTAAACAATTTTATTGATTTTGATGAATGCTTACTGAATAGCGATATTTAGGTATAGGGACTAAATTGATTGGTGGTTTTTTAAATTTAAAGGACTACTTTGTTAATTTGTGAATTTGAGGGACTAAATTACTTGACCCTTACTATCTTAAGTACTAAAATGCTGATTCATATTGTTATAATTTTGTGAATTGGTTGTAGAAAAGGGAGGCACCACCTGGTGAGAAGCCCGAACCTGTTAGGACCCATCTTCGTAACATGATCATTGTACCTGAGATGATTGGGAGCATTATTGGAGTGTACAATGGGAAGACCTTTAACCAAGTTGAAATCAAACCTGAGATGATCGGTCATTACCTAGCTGAATTCTCGATCTCATACAAGCCTGTTAAGCATGGTAGACCTGGTATTGGTGCTACTCACTCCTCCAGGTTCATTCCTCTCAAGTGA
Protein sequence

>MS.gene020507.t1

MADVEVDAAAAAAGVPKKRTFKKFSFRGVDLDALLDMSTDELVKLFSARARRRFQRGLTRKPMALIKKLRKAKREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRPGIGATHSSRFIPLK