AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060292

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060292.t1 MTR_1g106955 99.061 213 2 0 1 213 1 213 7.28e-156 430
MS.gene060292.t1 MTR_8g076890 42.675 157 88 2 25 180 105 260 1.81e-38 134
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060292.t1 AT2G18990 77.885 208 45 1 6 213 5 211 1.36e-119 338
MS.gene060292.t1 AT3G25580 77.404 208 45 2 6 213 5 210 1.32e-118 336
MS.gene060292.t1 AT3G25580 77.073 205 45 2 9 213 3 205 1.25e-116 330
MS.gene060292.t1 AT5G66410 36.585 205 123 4 7 209 28 227 1.05e-38 133
MS.gene060292.t1 AT3G50960 42.000 150 85 2 23 171 40 188 3.95e-37 129
MS.gene060292.t1 AT3G50960 42.000 150 85 2 23 171 40 188 3.95e-37 129

Find 44 sgRNAs with CRISPR-Local

Find 78 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGACAAACATTTAAGTATTT+TGG 0.135807 1.2:+79658284 MS.gene060292:CDS
GTTGCAGCCTCCGTTCTCTT+AGG 0.233181 1.2:-79657620 None:intergenic
TGACTTTAGCACCGAGGTTT+TGG 0.292143 1.2:+79658597 MS.gene060292:CDS
GTCATTTCTTCCGCGAAAAT+TGG 0.299383 1.2:+79657763 MS.gene060292:CDS
GCTCTGCCGAACACTTCTTT+TGG 0.354451 1.2:-79658698 None:intergenic
AGAAATTGTGCGAACCTTGC+AGG 0.367889 1.2:-79657787 None:intergenic
TCAATACACCGTGCAAGGTC+CGG 0.394040 1.2:+79658667 MS.gene060292:CDS
TTGCAGCCTCCGTTCTCTTA+GGG 0.396133 1.2:-79657619 None:intergenic
GCTGCAACAAATGAAGAAAA+TGG 0.402598 1.2:+79657635 MS.gene060292:CDS
CTTGATTCTCGATCACCTCT+TGG 0.414878 1.2:-79657512 None:intergenic
CAATACACCGTGCAAGGTCC+GGG 0.431500 1.2:+79658668 MS.gene060292:CDS
TTTGCGCCCCGGACCTTGCA+CGG 0.490890 1.2:-79658675 None:intergenic
GTCTTTCTCTGACGGAATCT+CGG 0.495284 1.2:-79657703 None:intergenic
TTCTTTATGAGAGCAATAGT+TGG 0.506238 1.2:-79658393 None:intergenic
CGCAAACCAAAAGAAGTGTT+CGG 0.506657 1.2:+79658692 MS.gene060292:CDS
CGGTGTAATCTCCGTGTCCG+AGG 0.513907 1.2:-79657683 None:intergenic
CGTCATCGTCGAGACGTTCA+AGG 0.517999 1.2:-79657587 None:intergenic
CGAAGCAGCATATTGAGACT+CGG 0.534134 1.2:+79658307 MS.gene060292:CDS
GAAATTGTGCGAACCTTGCA+GGG 0.544550 1.2:-79657786 None:intergenic
GACGGTGGCGCAAGCAGTCG+AGG 0.556072 1.2:+79657539 MS.gene060292:CDS
CCGCGAAAATTGGCCCTGCA+AGG 0.557879 1.2:+79657773 MS.gene060292:CDS
TACCAAAGTGGATGATTATG+TGG 0.558275 1.2:+79658416 MS.gene060292:CDS
GTCATCGTCGAGACGTTCAA+GGG 0.565214 1.2:-79657586 None:intergenic
GAGAAGAAGTCTTTCTCTGA+CGG 0.577836 1.2:-79657711 None:intergenic
AATCATCAATACACCGTGCA+AGG 0.579819 1.2:+79658662 MS.gene060292:CDS
CGTTGGATCTCCCTCGGACA+CGG 0.582223 1.2:+79657672 MS.gene060292:CDS
TACCACATAATCATCCACTT+TGG 0.582640 1.2:-79658418 None:intergenic
CGTAGCCGTTGGATCTCCCT+CGG 0.582964 1.2:+79657666 MS.gene060292:CDS
ATCTTGAAGCCCTAAGAGAA+CGG 0.587564 1.2:+79657610 MS.gene060292:CDS
TGGCGGAGAAGCGTAGCCGT+TGG 0.601854 1.2:+79657655 MS.gene060292:CDS
CAATCTTTCTTCCAAAACCT+CGG 0.602383 1.2:-79658608 None:intergenic
ACGATCACTTGCTTTAACGA+CGG 0.607682 1.2:-79657733 None:intergenic
GGTGTAATCTCCGTGTCCGA+GGG 0.608291 1.2:-79657682 None:intergenic
TACAAGTTACTCAGAATCTG+AGG 0.610014 1.2:-79658734 None:intergenic
CGTGTCCGAGGGAGATCCAA+CGG 0.633581 1.2:-79657671 None:intergenic
AATACACCGTGCAAGGTCCG+GGG 0.655774 1.2:+79658669 MS.gene060292:CDS
GATCGAGAATCAAGTACTGA+CGG 0.657827 1.2:+79657521 MS.gene060292:CDS
TCTCATAAAGAATACCAAAG+TGG 0.658073 1.2:+79658404 MS.gene060292:CDS
TTGAAGCCCTAAGAGAACGG+AGG 0.699926 1.2:+79657613 MS.gene060292:CDS
TACTGATGACTTTAGCACCG+AGG 0.705317 1.2:+79658591 MS.gene060292:CDS
GCAACAAATGAAGAAAATGG+CGG 0.709368 1.2:+79657638 MS.gene060292:CDS
AAGTGTTCGGCAGAGCACAA+CGG 0.717985 1.2:+79658705 MS.gene060292:CDS
GGACAAAGGAAAGATCCAAG+AGG 0.724397 1.2:+79657497 MS.gene060292:CDS
CGAGAATCAAGTACTGACGG+TGG 0.737424 1.2:+79657524 MS.gene060292:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAACTTTATAAAAATATTAT+TGG + chr1.2:79658039-79658058 MS.gene060292:intron 10.0%
!!! AAGAATTTTAATTTAAACGT+AGG + chr1.2:79658017-79658036 MS.gene060292:intron 15.0%
!! ACATGTGATTACATAATTAT+CGG + chr1.2:79657903-79657922 MS.gene060292:intron 20.0%
! AATTATGTAATCACATGTGT+AGG - chr1.2:79657901-79657920 None:intergenic 25.0%
! ATATAAAAACTGTAAGTCTG+CGG - chr1.2:79658208-79658227 None:intergenic 25.0%
! TACTAACATCAAGATGATAA+TGG + chr1.2:79658533-79658552 MS.gene060292:intron 25.0%
! TAGAATTCTCTGTTTATCAT+TGG + chr1.2:79658134-79658153 MS.gene060292:intron 25.0%
! TATTGACATGAATGCTATAT+TGG + chr1.2:79658480-79658499 MS.gene060292:intron 25.0%
!! GGACAAACATTTAAGTATTT+TGG + chr1.2:79658284-79658303 MS.gene060292:CDS 25.0%
!!! ATGATAATGGTATGTGTTTT+AGG + chr1.2:79658546-79658565 MS.gene060292:intron 25.0%
AATATTATTGGCAGTGCATA+CGG + chr1.2:79658051-79658070 MS.gene060292:intron 30.0%
AATTCTCTGTTTATCATTGG+AGG + chr1.2:79658137-79658156 MS.gene060292:intron 30.0%
ATTATGTGGTATGTGCTTAA+AGG + chr1.2:79658430-79658449 MS.gene060292:intron 30.0%
ATTCTCTGTTTATCATTGGA+GGG + chr1.2:79658138-79658157 MS.gene060292:intron 30.0%
CGGAATTCAAATTCAAATTG+TGG - chr1.2:79658188-79658207 None:intergenic 30.0%
TCTCATAAAGAATACCAAAG+TGG + chr1.2:79658404-79658423 MS.gene060292:CDS 30.0%
TGATTACATAATTATCGGTG+TGG + chr1.2:79657908-79657927 MS.gene060292:intron 30.0%
TTCTTTATGAGAGCAATAGT+TGG - chr1.2:79658396-79658415 None:intergenic 30.0%
! TAAAGCTCAAGTCATCTTTT+TGG + chr1.2:79658633-79658652 MS.gene060292:CDS 30.0%
! TATTTTCTTTCGCTGAAATG+AGG + chr1.2:79658225-79658244 MS.gene060292:intron 30.0%
!! ATAATGGTATGTGTTTTAGG+TGG + chr1.2:79658549-79658568 MS.gene060292:intron 30.0%
!! TAATGGTATGTGTTTTAGGT+GGG + chr1.2:79658550-79658569 MS.gene060292:intron 30.0%
ACATGAATGCTATATTGGAC+AGG + chr1.2:79658485-79658504 MS.gene060292:intron 35.0%
ATATTATTGGCAGTGCATAC+GGG + chr1.2:79658052-79658071 MS.gene060292:intron 35.0%
CAATCTTTCTTCCAAAACCT+CGG - chr1.2:79658611-79658630 None:intergenic 35.0%
CATGAATGCTATATTGGACA+GGG + chr1.2:79658486-79658505 MS.gene060292:intron 35.0%
GCAACAAATGAAGAAAATGG+CGG + chr1.2:79657638-79657657 MS.gene060292:CDS 35.0%
GCTGCAACAAATGAAGAAAA+TGG + chr1.2:79657635-79657654 MS.gene060292:CDS 35.0%
TACCAAAGTGGATGATTATG+TGG + chr1.2:79658416-79658435 MS.gene060292:CDS 35.0%
TACCACATAATCATCCACTT+TGG - chr1.2:79658421-79658440 None:intergenic 35.0%
TTGAGCTTCTCAGCTAAAAA+TGG - chr1.2:79658360-79658379 None:intergenic 35.0%
AATCATCAATACACCGTGCA+AGG + chr1.2:79658662-79658681 MS.gene060292:CDS 40.0%
ACGATCACTTGCTTTAACGA+CGG - chr1.2:79657736-79657755 None:intergenic 40.0%
ATCTTGAAGCCCTAAGAGAA+CGG + chr1.2:79657610-79657629 MS.gene060292:CDS 40.0%
GAGAAGAAGTCTTTCTCTGA+CGG - chr1.2:79657714-79657733 None:intergenic 40.0%
GTAATCACATGTGTAGGTGT+CGG - chr1.2:79657895-79657914 None:intergenic 40.0%
GTCATTTCTTCCGCGAAAAT+TGG + chr1.2:79657763-79657782 MS.gene060292:CDS 40.0%
! AGCTCAAGTCATCTTTTTGG+AGG + chr1.2:79658636-79658655 MS.gene060292:CDS 40.0%
! GCTCAAGTCATCTTTTTGGA+GGG + chr1.2:79658637-79658656 MS.gene060292:CDS 40.0%
! TGCATTCAGTTTGCTTAGCT+TGG + chr1.2:79657989-79658008 MS.gene060292:intron 40.0%
!! CGCAAACCAAAAGAAGTGTT+CGG + chr1.2:79658692-79658711 MS.gene060292:CDS 40.0%
!! GATCGAGAATCAAGTACTGA+CGG + chr1.2:79657521-79657540 MS.gene060292:CDS 40.0%
!! TAGGTGGGTTTTGATGAACT+TGG + chr1.2:79658565-79658584 MS.gene060292:intron 40.0%
!!! CGAGGTTTTGGAAGAAAGAT+TGG + chr1.2:79658609-79658628 MS.gene060292:CDS 40.0%
AGAAATTGTGCGAACCTTGC+AGG - chr1.2:79657790-79657809 None:intergenic 45.0%
CACAGTTCATTCACAGGTTG+TGG + chr1.2:79658263-79658282 MS.gene060292:intron 45.0%
CGAAGCAGCATATTGAGACT+CGG + chr1.2:79658307-79658326 MS.gene060292:CDS 45.0%
CTTGATTCTCGATCACCTCT+TGG - chr1.2:79657515-79657534 None:intergenic 45.0%
GAAATTGTGCGAACCTTGCA+GGG - chr1.2:79657789-79657808 None:intergenic 45.0%
GGACAAAGGAAAGATCCAAG+AGG + chr1.2:79657497-79657516 MS.gene060292:CDS 45.0%
GTCTTTCTCTGACGGAATCT+CGG - chr1.2:79657706-79657725 None:intergenic 45.0%
TACTGATGACTTTAGCACCG+AGG + chr1.2:79658591-79658610 MS.gene060292:CDS 45.0%
TGTGCTCACAGTTCATTCAC+AGG + chr1.2:79658257-79658276 MS.gene060292:intron 45.0%
!! GTGGGTTTTGATGAACTTGG+TGG + chr1.2:79658568-79658587 MS.gene060292:CDS 45.0%
!! TGACTTTAGCACCGAGGTTT+TGG + chr1.2:79658597-79658616 MS.gene060292:CDS 45.0%
AAGTGTTCGGCAGAGCACAA+CGG + chr1.2:79658705-79658724 MS.gene060292:CDS 50.0%
CGGTGTGGATGTGTAGTGTT+AGG + chr1.2:79657923-79657942 MS.gene060292:intron 50.0%
GTCATCGTCGAGACGTTCAA+GGG - chr1.2:79657589-79657608 None:intergenic 50.0%
TCAATACACCGTGCAAGGTC+CGG + chr1.2:79658667-79658686 MS.gene060292:CDS 50.0%
TTGAAGCCCTAAGAGAACGG+AGG + chr1.2:79657613-79657632 MS.gene060292:CDS 50.0%
TTGCAGCCTCCGTTCTCTTA+GGG - chr1.2:79657622-79657641 None:intergenic 50.0%
! GCTCTGCCGAACACTTCTTT+TGG - chr1.2:79658701-79658720 None:intergenic 50.0%
!! CGAGAATCAAGTACTGACGG+TGG + chr1.2:79657524-79657543 MS.gene060292:CDS 50.0%
!!! ACTTCTTTTGGTTTGCGCCC+CGG - chr1.2:79658689-79658708 None:intergenic 50.0%
AATACACCGTGCAAGGTCCG+GGG + chr1.2:79658669-79658688 MS.gene060292:CDS 55.0%
CAATACACCGTGCAAGGTCC+GGG + chr1.2:79658668-79658687 MS.gene060292:CDS 55.0%
CGTCATCGTCGAGACGTTCA+AGG - chr1.2:79657590-79657609 None:intergenic 55.0%
GGTGTAATCTCCGTGTCCGA+GGG - chr1.2:79657685-79657704 None:intergenic 55.0%
GTTGCAGCCTCCGTTCTCTT+AGG - chr1.2:79657623-79657642 None:intergenic 55.0%
! CCTTGCAGGGCCAATTTTCG+CGG - chr1.2:79657776-79657795 None:intergenic 55.0%
CCGCGAAAATTGGCCCTGCA+AGG + chr1.2:79657773-79657792 MS.gene060292:CDS 60.0%
CGGTGTAATCTCCGTGTCCG+AGG - chr1.2:79657686-79657705 None:intergenic 60.0%
CGTAGCCGTTGGATCTCCCT+CGG + chr1.2:79657666-79657685 MS.gene060292:CDS 60.0%
CGTGTCCGAGGGAGATCCAA+CGG - chr1.2:79657674-79657693 None:intergenic 60.0%
CGTTGGATCTCCCTCGGACA+CGG + chr1.2:79657672-79657691 MS.gene060292:CDS 60.0%
TTTGCGCCCCGGACCTTGCA+CGG - chr1.2:79658678-79658697 None:intergenic 65.0%
! TGGCGGAGAAGCGTAGCCGT+TGG + chr1.2:79657655-79657674 MS.gene060292:CDS 65.0%
GACGGTGGCGCAAGCAGTCG+AGG + chr1.2:79657539-79657558 MS.gene060292:CDS 70.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 79657495 79658750 79657495 ID=MS.gene060292
chr1.2 mRNA 79657495 79658750 79657495 ID=MS.gene060292.t1;Parent=MS.gene060292
chr1.2 exon 79657495 79657794 79657495 ID=MS.gene060292.t1.exon1;Parent=MS.gene060292.t1
chr1.2 CDS 79657495 79657794 79657495 ID=cds.MS.gene060292.t1;Parent=MS.gene060292.t1
chr1.2 exon 79658279 79658437 79658279 ID=MS.gene060292.t1.exon2;Parent=MS.gene060292.t1
chr1.2 CDS 79658279 79658437 79658279 ID=cds.MS.gene060292.t1;Parent=MS.gene060292.t1
chr1.2 exon 79658568 79658750 79658568 ID=MS.gene060292.t1.exon3;Parent=MS.gene060292.t1
chr1.2 CDS 79658568 79658750 79658568 ID=cds.MS.gene060292.t1;Parent=MS.gene060292.t1
Gene Sequence

>MS.gene060292

ATGGACAAAGGAAAGATCCAAGAGGTGATCGAGAATCAAGTACTGACGGTGGCGCAAGCAGTCGAGGATAAGATCGACGAAGAGATTGCTGCCCTTGAACGTCTCGACGATGACGATCTTGAAGCCCTAAGAGAACGGAGGCTGCAACAAATGAAGAAAATGGCGGAGAAGCGTAGCCGTTGGATCTCCCTCGGACACGGAGATTACACCGAGATTCCGTCAGAGAAAGACTTCTTCTCCGTCGTTAAAGCAAGTGATCGTGTTGTTTGTCATTTCTTCCGCGAAAATTGGCCCTGCAAGGTTCGCACAATTTCTTGTTCATAATCATTTTATGTAGAAATTGAATGTTCAATCAACTTCGCAATTGTGAAATTAAATGTAAATTGCGACTCAGAGTCCGACACCTACACATGTGATTACATAATTATCGGTGTGGATGTGTAGTGTTAGGATATATTAGTGTCTGTCTGTGTTAGTGCTTCATAGAATTGCGATGCATTCAGTTTGCTTAGCTTGGCGATAAAGAATTTTAATTTAAACGTAGGAACTTTATAAAAATATTATTGGCAGTGCATACGGGTATGTTCATTGTTCTTATTGTCAATAATAACATAATGAACAATGTGCAGCTATTTCATTTAGAATTCTCTGTTTATCATTGGAGGGAAAGCAACTTAGACACTAGATGTACCACAATTTGAATTTGAATTCCGCAGACTTACAGTTTTTATATTTTCTTTCGCTGAAATGAGGTGAAACATCTGTGCTCACAGTTCATTCACAGGTTGTGGACAAACATTTAAGTATTTTGGCGAAGCAGCATATTGAGACTCGGTTTGTGAAAATAAATGCTGAAAAAAGTCCATTTTTAGCTGAGAAGCTCAAGATCATTGTTCTTCCAACTATTGCTCTCATAAAGAATACCAAAGTGGATGATTATGTGGTATGTGCTTAAAGGATTTTACTTATTCATAAAGTTGATAGATATTGACATGAATGCTATATTGGACAGGGTTTTTCTCTTTATTTAAGTAATTTTACTAACATCAAGATGATAATGGTATGTGTTTTAGGTGGGTTTTGATGAACTTGGTGGTACTGATGACTTTAGCACCGAGGTTTTGGAAGAAAGATTGGCTAAAGCTCAAGTCATCTTTTTGGAGGGTGAATCATCAATACACCGTGCAAGGTCCGGGGCGCAAACCAAAAGAAGTGTTCGGCAGAGCACAACGGCTGACTCCTCAGATTCTGAGTAA
Protein sequence

>MS.gene060292.t1

MDKGKIQEVIENQVLTVAQAVEDKIDEEIAALERLDDDDLEALRERRLQQMKKMAEKRSRWISLGHGDYTEIPSEKDFFSVVKASDRVVCHFFRENWPCKVVDKHLSILAKQHIETRFVKINAEKSPFLAEKLKIIVLPTIALIKNTKVDDYVVGFDELGGTDDFSTEVLEERLAKAQVIFLEGESSIHRARSGAQTKRSVRQSTTADSSDSE