AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene84017

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene84017.t1 MTR_1g050502 86.473 207 12 2 1 207 1 191 1.13e-124 351
MS.gene84017.t1 MTR_1g050502 88.384 198 7 2 1 198 1 182 2.86e-122 347
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene84017.t1 AT1G42990 56.250 64 27 1 136 198 155 218 2.06e-14 70.9

Find 51 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGAGATTCGAAATCGATTT+GGG 0.252626 1.3:-32178541 None:intergenic
AGAGAGATTCGAAATCGATT+TGG 0.334822 1.3:-32178542 None:intergenic
GAAGGCTCTTGAGGAGTTAC+TGG 0.356888 1.3:-32178807 None:intergenic
GGAGTCTGCTGTGCTCTTGT+TGG 0.367032 1.3:+32179325 MS.gene84017:CDS
GGAACCTCTTGAGGAGTTAC+TGG 0.381189 1.3:-32178852 None:intergenic
TTGCAATCGCGTGGTGGCTT+TGG 0.414223 1.3:+32179284 MS.gene84017:CDS
CCTCGACCCGATCCCTCAAT+CGG 0.430109 1.3:+32178743 MS.gene84017:CDS
GAGTCTGCTGTGCTCTTGTT+GGG 0.447976 1.3:+32179326 MS.gene84017:CDS
TGATCATCCGATTGAGGGAT+CGG 0.459847 1.3:-32178750 None:intergenic
AGCCTTCTTCTGATGAAGCC+AGG 0.459858 1.3:+32178823 MS.gene84017:CDS
TGAAGGGGAATGCAGAAGAC+TGG 0.491226 1.3:+32179211 MS.gene84017:CDS
GGGAATTGCGTCGTCATCAT+CGG 0.491346 1.3:+32178686 MS.gene84017:CDS
AGCAGACTCCTGCATGGTCA+TGG 0.499805 1.3:-32179312 None:intergenic
AACCTTGATCATCCGATTGA+GGG 0.507174 1.3:-32178755 None:intergenic
CAGCTTGTTTGTAGCAGCCA+AGG 0.508536 1.3:-32179796 None:intergenic
ATGCTGAGAACCATGCTTTG+CGG 0.510527 1.3:+32179255 MS.gene84017:CDS
AAACCTTGATCATCCGATTG+AGG 0.512112 1.3:-32178756 None:intergenic
CCGATTGAGGGATCGGGTCG+AGG 0.513783 1.3:-32178743 None:intergenic
TCAATCTCTGAGAGAGGAGA+GGG 0.520952 1.3:-32178639 None:intergenic
CTCAATCTCTGAGAGAGGAG+AGG 0.521491 1.3:-32178640 None:intergenic
TGGTGCTCCCATGACCATGC+AGG 0.523079 1.3:+32179304 MS.gene84017:CDS
TCATCAGAAGAAGGCTCTTG+AGG 0.530695 1.3:-32178816 None:intergenic
GCCTTCTTCTGATGAAGCCA+GGG 0.533209 1.3:+32178824 MS.gene84017:CDS
TCTTCTCATGTCTGATGCCG+AGG 0.542387 1.3:+32178665 MS.gene84017:CDS
AGGAGTTACTGGATCAACTC+TGG 0.544068 1.3:-32178796 None:intergenic
ATCCCTCAATCGGATGATCA+AGG 0.545906 1.3:+32178753 MS.gene84017:CDS
TTCGAGAAACTTATGATAGT+CGG 0.546362 1.3:-32178712 None:intergenic
TCAACTCTGGCTTCATCAGA+AGG 0.547608 1.3:-32178783 None:intergenic
ACCCTGGCTTCATCAGAAGA+AGG 0.549174 1.3:-32178825 None:intergenic
CTTTGTTTGCAATCGCGTGG+TGG 0.550397 1.3:+32179278 MS.gene84017:CDS
TGGTGTAGCGGAGTGGCCCT+TGG 0.560767 1.3:+32179779 MS.gene84017:intron
GCAGACTCCTGCATGGTCAT+GGG 0.561161 1.3:-32179311 None:intergenic
TTGGGGTTCTAAAGTGTCCA+TGG 0.561259 1.3:-32178523 None:intergenic
AGCTTGTTTGTAGCAGCCAA+GGG 0.564734 1.3:-32179795 None:intergenic
GCAAACAAAGCCGCAAAGCA+TGG 0.573484 1.3:-32179265 None:intergenic
TGATGACGACGCAATTCCCT+CGG 0.574197 1.3:-32178682 None:intergenic
GATCATCCGATTGAGGGATC+GGG 0.580413 1.3:-32178749 None:intergenic
AGGAGAGGGAGTGTCTGCGA+CGG 0.585460 1.3:-32178625 None:intergenic
GGTTCAGGAGGAACCTCTTG+AGG 0.589392 1.3:-32178861 None:intergenic
CTGCTGTGAAGTCAAGAGAG+AGG 0.599823 1.3:+32179144 MS.gene84017:CDS
AGGAGTTACTGGATCAACCC+TGG 0.607536 1.3:-32178841 None:intergenic
CGGCTTTGTTTGCAATCGCG+TGG 0.608761 1.3:+32179275 MS.gene84017:CDS
GTGTCTGCGACGGAAACAGA+AGG 0.621465 1.3:-32178615 None:intergenic
CTTCTCATGTCTGATGCCGA+GGG 0.622387 1.3:+32178666 MS.gene84017:CDS
AGATTCTCAATCTCTGAGAG+AGG 0.623970 1.3:-32178645 None:intergenic
AAAATCTTGAGACGAAGAGT+AGG 0.630085 1.3:+32179183 MS.gene84017:CDS
TGATCCAGTAACTCCTCAAG+AGG 0.636811 1.3:+32178848 MS.gene84017:CDS
AGAGATTCGAAATCGATTTG+GGG 0.646761 1.3:-32178540 None:intergenic
TTTCAGGCAGATGAGGAACA+GGG 0.660559 1.3:+32179118 MS.gene84017:intron
TGAATAGTGGTGTAGCGGAG+TGG 0.665903 1.3:+32179772 MS.gene84017:intron
GAGCACAGCAGACTCCTGCA+TGG 0.688063 1.3:-32179318 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGTTTCAATTTCATATAT+TGG + chr1.3:32179571-32179590 MS.gene84017:intron 15.0%
!!! TGTCATTATCATTTTATTTT+AGG + chr1.3:32179395-32179414 MS.gene84017:intron 15.0%
!! AGTAAGCAAAAAAAATTGTT+AGG - chr1.3:32179518-32179537 None:intergenic 20.0%
!!! TAATTTGTAATTTGTATTCG+AGG + chr1.3:32179029-32179048 MS.gene84017:intron 20.0%
! AACTATATAGCATTAGCAAA+AGG - chr1.3:32179557-32179576 None:intergenic 25.0%
! AGAGATTAAGGTTACAATTT+GGG - chr1.3:32179611-32179630 None:intergenic 25.0%
! TAGAGATTAAGGTTACAATT+TGG - chr1.3:32179612-32179631 None:intergenic 25.0%
! TTTAACAGTGTTATGAATAG+TGG + chr1.3:32179759-32179778 MS.gene84017:intron 25.0%
!! CTAAAAGTATAACCATATGA+AGG + chr1.3:32179434-32179453 MS.gene84017:intron 25.0%
!! TTTTTGCTTACTTTCTTGAA+TGG + chr1.3:32179526-32179545 MS.gene84017:intron 25.0%
!!! ACGTCTTTAGGTTTTTTATT+GGG + chr1.3:32179697-32179716 MS.gene84017:intron 25.0%
!!! CCTAATTTGCTTTTTTGAAA+CGG - chr1.3:32178886-32178905 None:intergenic 25.0%
!!! CTAATTTGCTTTTTTGAAAC+GGG - chr1.3:32178885-32178904 None:intergenic 25.0%
!!! TTTTTTTTTTTTCAACCTGC+TGG + chr1.3:32179004-32179023 MS.gene84017:intron 25.0%
AAATTACAAATTACTCCAGC+AGG - chr1.3:32179022-32179041 None:intergenic 30.0%
ACAGTAGTCATTAGAGATTA+AGG - chr1.3:32179623-32179642 None:intergenic 30.0%
ATAACAGCAAGAAGAAAACA+TGG - chr1.3:32179659-32179678 None:intergenic 30.0%
CCGTTTCAAAAAAGCAAATT+AGG + chr1.3:32178883-32178902 MS.gene84017:CDS 30.0%
GGTTTCATTATTGCATTCTT+TGG + chr1.3:32179484-32179503 MS.gene84017:intron 30.0%
TATTGCATTCTTTGGTTGTT+TGG + chr1.3:32179492-32179511 MS.gene84017:intron 30.0%
TTCGAGAAACTTATGATAGT+CGG - chr1.3:32178715-32178734 None:intergenic 30.0%
!!! GACGTCTTTAGGTTTTTTAT+TGG + chr1.3:32179696-32179715 MS.gene84017:intron 30.0%
!!! TGTTTTGGTATCTGATTTTC+AGG + chr1.3:32179102-32179121 MS.gene84017:intron 30.0%
AAAATCTTGAGACGAAGAGT+AGG + chr1.3:32179183-32179202 MS.gene84017:CDS 35.0%
AGAGAGATTCGAAATCGATT+TGG - chr1.3:32178545-32178564 None:intergenic 35.0%
CCTAAAGACGTCTTTAACAT+CGG - chr1.3:32179688-32179707 None:intergenic 35.0%
TGCTTACTTTCTTGAATGGA+TGG + chr1.3:32179530-32179549 MS.gene84017:intron 35.0%
TGTTATGAATAGTGGTGTAG+CGG + chr1.3:32179767-32179786 MS.gene84017:intron 35.0%
! GAGAGATTCGAAATCGATTT+GGG - chr1.3:32178544-32178563 None:intergenic 35.0%
!! ACGAAGAGTAGGTATTTTGA+AGG + chr1.3:32179194-32179213 MS.gene84017:CDS 35.0%
!! AGAGATTCGAAATCGATTTG+GGG - chr1.3:32178543-32178562 None:intergenic 35.0%
!! CGAAGAGTAGGTATTTTGAA+GGG + chr1.3:32179195-32179214 MS.gene84017:CDS 35.0%
!! GAAGAGTAGGTATTTTGAAG+GGG + chr1.3:32179196-32179215 MS.gene84017:CDS 35.0%
!!! GGTTCTAATGAGAAGTGTTT+TGG + chr1.3:32179087-32179106 MS.gene84017:intron 35.0%
AAACCTTGATCATCCGATTG+AGG - chr1.3:32178759-32178778 None:intergenic 40.0%
AACCTTGATCATCCGATTGA+GGG - chr1.3:32178758-32178777 None:intergenic 40.0%
CCATAAGACCCCATCAAATT+CGG - chr1.3:32179058-32179077 None:intergenic 40.0%
CCGATGTTAAAGACGTCTTT+AGG + chr1.3:32179685-32179704 MS.gene84017:intron 40.0%
CTCATCCTCCTGCAAAAAAT+CGG - chr1.3:32178586-32178605 None:intergenic 40.0%
GAAACCAAATCATTCGTGCA+AGG - chr1.3:32179470-32179489 None:intergenic 40.0%
GGTCACTGTAAACCTTCATA+TGG - chr1.3:32179449-32179468 None:intergenic 40.0%
TCGAGGTTACCGAATTTGAT+GGG + chr1.3:32179046-32179065 MS.gene84017:intron 40.0%
TTCGAGGTTACCGAATTTGA+TGG + chr1.3:32179045-32179064 MS.gene84017:intron 40.0%
! AGATTCTCAATCTCTGAGAG+AGG - chr1.3:32178648-32178667 None:intergenic 40.0%
! CGAATTTGATGGGGTCTTAT+GGG + chr1.3:32179056-32179075 MS.gene84017:intron 40.0%
!! ATCTGATTTTCAGGCAGATG+AGG + chr1.3:32179111-32179130 MS.gene84017:intron 40.0%
!!! TGCTTTTTTGAAACGGGTTC+AGG - chr1.3:32178879-32178898 None:intergenic 40.0%
!!! TTTTTTGAAACGGGTTCAGG+AGG - chr1.3:32178876-32178895 None:intergenic 40.0%
AGGAGTTACTGGATCAACTC+TGG - chr1.3:32178799-32178818 None:intergenic 45.0%
ATCCCTCAATCGGATGATCA+AGG + chr1.3:32178753-32178772 MS.gene84017:CDS 45.0%
ATGCTGAGAACCATGCTTTG+CGG + chr1.3:32179255-32179274 MS.gene84017:CDS 45.0%
CCGAATTTGATGGGGTCTTA+TGG + chr1.3:32179055-32179074 MS.gene84017:intron 45.0%
CGAGGTTACCGAATTTGATG+GGG + chr1.3:32179047-32179066 MS.gene84017:intron 45.0%
GTGACCTTGCACGAATGATT+TGG + chr1.3:32179463-32179482 MS.gene84017:intron 45.0%
TCATCAGAAGAAGGCTCTTG+AGG - chr1.3:32178819-32178838 None:intergenic 45.0%
TGATCATCCGATTGAGGGAT+CGG - chr1.3:32178753-32178772 None:intergenic 45.0%
TGATCCAGTAACTCCTCAAG+AGG + chr1.3:32178803-32178822 MS.gene84017:CDS 45.0%
TTTCAGGCAGATGAGGAACA+GGG + chr1.3:32179118-32179137 MS.gene84017:intron 45.0%
! AGCTTGTTTGTAGCAGCCAA+GGG - chr1.3:32179798-32179817 None:intergenic 45.0%
! GGGGTCTTATGGGATGATTA+TGG + chr1.3:32179066-32179085 MS.gene84017:intron 45.0%
! TCAACTCTGGCTTCATCAGA+AGG - chr1.3:32178786-32178805 None:intergenic 45.0%
! TCAATCTCTGAGAGAGGAGA+GGG - chr1.3:32178642-32178661 None:intergenic 45.0%
!! TTTTCAGGCAGATGAGGAAC+AGG + chr1.3:32179117-32179136 MS.gene84017:intron 45.0%
!!! CGATTTTTTGCAGGAGGATG+AGG + chr1.3:32178584-32178603 MS.gene84017:CDS 45.0%
ACCCTGGCTTCATCAGAAGA+AGG - chr1.3:32178828-32178847 None:intergenic 50.0%
AGCCTTCTTCTGATGAAGCC+AGG + chr1.3:32178823-32178842 MS.gene84017:CDS 50.0%
AGGAGTTACTGGATCAACCC+TGG - chr1.3:32178844-32178863 None:intergenic 50.0%
CTGCTGTGAAGTCAAGAGAG+AGG + chr1.3:32179144-32179163 MS.gene84017:CDS 50.0%
CTTCTCATGTCTGATGCCGA+GGG + chr1.3:32178666-32178685 MS.gene84017:CDS 50.0%
GAAGGCTCTTGAGGAGTTAC+TGG - chr1.3:32178810-32178829 None:intergenic 50.0%
GAGTCTGCTGTGCTCTTGTT+GGG + chr1.3:32179326-32179345 MS.gene84017:CDS 50.0%
GATCATCCGATTGAGGGATC+GGG - chr1.3:32178752-32178771 None:intergenic 50.0%
GCAAACAAAGCCGCAAAGCA+TGG - chr1.3:32179268-32179287 None:intergenic 50.0%
GCCTTCTTCTGATGAAGCCA+GGG + chr1.3:32178824-32178843 MS.gene84017:CDS 50.0%
GGAACCTCTTGAGGAGTTAC+TGG - chr1.3:32178855-32178874 None:intergenic 50.0%
GGGAATTGCGTCGTCATCAT+CGG + chr1.3:32178686-32178705 MS.gene84017:CDS 50.0%
TCTTCTCATGTCTGATGCCG+AGG + chr1.3:32178665-32178684 MS.gene84017:CDS 50.0%
TGAAGGGGAATGCAGAAGAC+TGG + chr1.3:32179211-32179230 MS.gene84017:CDS 50.0%
TGCTGTGCTCTTGTTGGGTA+AGG + chr1.3:32179331-32179350 MS.gene84017:intron 50.0%
! CAGCTTGTTTGTAGCAGCCA+AGG - chr1.3:32179799-32179818 None:intergenic 50.0%
! CTCAATCTCTGAGAGAGGAG+AGG - chr1.3:32178643-32178662 None:intergenic 50.0%
! CTTTGTTTGCAATCGCGTGG+TGG + chr1.3:32179278-32179297 MS.gene84017:CDS 50.0%
! TGAATAGTGGTGTAGCGGAG+TGG + chr1.3:32179772-32179791 MS.gene84017:intron 50.0%
! TGATGACGACGCAATTCCCT+CGG - chr1.3:32178685-32178704 None:intergenic 50.0%
!!! AGTCGCCGATTTTTTGCAGG+AGG + chr1.3:32178578-32178597 MS.gene84017:CDS 50.0%
!!! CGAAGTCGCCGATTTTTTGC+AGG + chr1.3:32178575-32178594 MS.gene84017:CDS 50.0%
AGCAGACTCCTGCATGGTCA+TGG - chr1.3:32179315-32179334 None:intergenic 55.0%
GCAGACTCCTGCATGGTCAT+GGG - chr1.3:32179314-32179333 None:intergenic 55.0%
GGAGTCTGCTGTGCTCTTGT+TGG + chr1.3:32179325-32179344 MS.gene84017:CDS 55.0%
GGTTCAGGAGGAACCTCTTG+AGG - chr1.3:32178864-32178883 None:intergenic 55.0%
GTGTCTGCGACGGAAACAGA+AGG - chr1.3:32178618-32178637 None:intergenic 55.0%
TTGCAATCGCGTGGTGGCTT+TGG + chr1.3:32179284-32179303 MS.gene84017:CDS 55.0%
!! CGGCTTTGTTTGCAATCGCG+TGG + chr1.3:32179275-32179294 MS.gene84017:CDS 55.0%
CCTCGACCCGATCCCTCAAT+CGG + chr1.3:32178743-32178762 MS.gene84017:CDS 60.0%
GAGCACAGCAGACTCCTGCA+TGG - chr1.3:32179321-32179340 None:intergenic 60.0%
TGGTGCTCCCATGACCATGC+AGG + chr1.3:32179304-32179323 MS.gene84017:CDS 60.0%
!! AGGAGAGGGAGTGTCTGCGA+CGG - chr1.3:32178628-32178647 None:intergenic 60.0%
CCGATTGAGGGATCGGGTCG+AGG - chr1.3:32178746-32178765 None:intergenic 65.0%
! TGGTGTAGCGGAGTGGCCCT+TGG + chr1.3:32179779-32179798 MS.gene84017:intron 65.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 32178525 32179821 32178525 ID=MS.gene84017
chr1.3 mRNA 32178525 32179821 32178525 ID=MS.gene84017.t1;Parent=MS.gene84017
chr1.3 exon 32178525 32178904 32178525 ID=MS.gene84017.t1.exon1;Parent=MS.gene84017.t1
chr1.3 CDS 32178525 32178904 32178525 ID=cds.MS.gene84017.t1;Parent=MS.gene84017.t1
chr1.3 exon 32179124 32179347 32179124 ID=MS.gene84017.t1.exon2;Parent=MS.gene84017.t1
chr1.3 CDS 32179124 32179347 32179124 ID=cds.MS.gene84017.t1;Parent=MS.gene84017.t1
chr1.3 exon 32179787 32179821 32179787 ID=MS.gene84017.t1.exon3;Parent=MS.gene84017.t1
chr1.3 CDS 32179787 32179821 32179787 ID=cds.MS.gene84017.t1;Parent=MS.gene84017.t1
Gene Sequence

>MS.gene84017

ATGGACACTTTAGAACCCCAAATCGATTTCGAATCTCTCTTCGCAGAATACGAAGTCGCCGATTTTTTGCAGGAGGATGAGGATATCAATCCTTCTGTTTCCGTCGCAGACACTCCCTCTCCTCTCTCAGAGATTGAGAATCTTCTCATGTCTGATGCCGAGGGAATTGCGTCGTCATCATCGGATTCCGACTATCATAAGTTTCTCGAAGATATTCTCCTCGACCCGATCCCTCAATCGGATGATCAAGGTTTCGTTCCTTCTGATGAAGCCAGAGTTGATCCAGTAACTCCTCAAGAGCCTTCTTCTGATGAAGCCAGGGTTGATCCAGTAACTCCTCAAGAGGTTCCTCCTGAACCCGTTTCAAAAAAGCAAATTAGGTAAAACAAAATAATTTATAAGAATTGTCAATGTTGATCATATTCTGTAATTAAGACACATAAGTATTAATTAGTCTATAAGAATCATGATTTGTTTTTTTTTTTTTTTTTCAACCTGCTGGAGTAATTTGTAATTTGTATTCGAGGTTACCGAATTTGATGGGGTCTTATGGGATGATTATGGTTCTAATGAGAAGTGTTTTGGTATCTGATTTTCAGGCAGATGAGGAACAGGGATGCTGCTGTGAAGTCAAGAGAGAGGAAGAAGATGTACGTGAAAAATCTTGAGACGAAGAGTAGGTATTTTGAAGGGGAATGCAGAAGACTGGAGCATTTGCTTCAGTGCTGCTATGCTGAGAACCATGCTTTGCGGCTTTGTTTGCAATCGCGTGGTGGCTTTGGTGCTCCCATGACCATGCAGGAGTCTGCTGTGCTCTTGTTGGGTAAGGCTTGTGATTGCAAATCAGATTTGCTTTGCTTCTTTTTTTATTGTCATTATCATTTTATTTTAGGTATTGTAGTTTAACTTCTAAAAGTATAACCATATGAAGGTTTACAGTGACCTTGCACGAATGATTTGGTTTCATTATTGCATTCTTTGGTTGTTTGGCCTAACAATTTTTTTTGCTTACTTTCTTGAATGGATGGACCTTTTGCTAATGCTATATAGTTTCAATTTCATATATTGGACTTATCATAGTTTCCCAAATTGTAACCTTAATCTCTAATGACTACTGTAGATATATTTATGCCATGTTTTCTTCTTGCTGTTATGTAGATCCGATGTTAAAGACGTCTTTAGGTTTTTTATTGGGTTTTGTAGAACACAAAGTACTGTGTGAATGTATTTTATGTTTAACAGTGTTATGAATAGTGGTGTAGCGGAGTGGCCCTTGGCTGCTACAAACAAGCTGTAG
Protein sequence

>MS.gene84017.t1

MDTLEPQIDFESLFAEYEVADFLQEDEDINPSVSVADTPSPLSEIENLLMSDAEGIASSSSDSDYHKFLEDILLDPIPQSDDQGFVPSDEARVDPVTPQEPSSDEARVDPVTPQEVPPEPVSKKQIRQMRNRDAAVKSRERKKMYVKNLETKSRYFEGECRRLEHLLQCCYAENHALRLCLQSRGGFGAPMTMQESAVLLLAEWPLAATNKL