AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene06617


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06617.t1 MTR_3g092600 99.091 110 1 0 1 110 1 110 3.12e-74 215
MS.gene06617.t1 MTR_2g066750 98.182 110 2 0 1 110 1 110 1.07e-73 214
MS.gene06617.t1 MTR_8g024350 64.545 110 37 2 1 110 1 108 1.42e-33 112
MS.gene06617.t1 MTR_7g118060 62.712 59 22 0 1 59 1 59 1.00e-20 80.5
MS.gene06617.t1 MTR_7g005740 66.129 62 2 1 1 62 1 43 1.52e-19 79.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06617.t1 AT5G24510 57.391 115 40 4 1 110 1 111 4.14e-36 119
MS.gene06617.t1 AT5G47700 57.658 111 45 1 2 110 3 113 7.99e-29 100
MS.gene06617.t1 AT5G47700 57.658 111 45 1 2 110 3 113 7.99e-29 100
MS.gene06617.t1 AT1G01100 60.185 108 42 1 4 110 5 112 4.26e-28 99.0
MS.gene06617.t1 AT1G01100 60.185 108 42 1 4 110 5 112 4.26e-28 99.0
MS.gene06617.t1 AT1G01100 60.185 108 42 1 4 110 5 112 4.26e-28 99.0
MS.gene06617.t1 AT1G01100 50.459 109 39 1 2 110 3 96 2.14e-27 96.7
MS.gene06617.t1 AT4G00810 54.955 111 48 1 2 110 3 113 2.87e-27 97.1
MS.gene06617.t1 AT4G00810 54.955 111 48 1 2 110 3 113 2.87e-27 97.1

Find 32 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAAATGAGTTCCGGCGAAT+TGG 0.294649 3.3:-77305222 None:intergenic
GTCATCGTCACTTTCTTCCT+TGG 0.329724 3.3:+77303886 None:intergenic
GATAATAGACTTACGGTGAT+TGG 0.337914 3.3:+77305158 None:intergenic
ACGTCACCGTTGAATCTTAC+TGG 0.348075 3.3:-77305016 MS.gene06617:CDS
AAAATGAGTTCCGGCGAATT+GGG 0.368280 3.3:-77305221 MS.gene06617:CDS
TCTGAGCAAGCTTAGCGAAT+AGG 0.392998 3.3:+77304988 None:intergenic
GCCGTATCTGCACCCGCTGC+TGG 0.401410 3.3:-77304909 MS.gene06617:CDS
TCTGCACCCGCTGCTGGTGG+TGG 0.439771 3.3:-77304903 MS.gene06617:CDS
ATAATAGACTTACGGTGATT+GGG 0.445449 3.3:+77305159 None:intergenic
GCGGCTCCACCACCAGCAGC+GGG 0.451994 3.3:+77304897 None:intergenic
GAAGATCGGTACTTTGTTGA+AGG 0.461021 3.3:-77305045 MS.gene06617:CDS
ACCTGCCGCCGTTGAAAAGA+AGG 0.476631 3.3:-77304862 MS.gene06617:intron
TGCGGCTCCACCACCAGCAG+CGG 0.489051 3.3:+77304896 None:intergenic
TTGAACTCCGGCGCTGTTGG+TGG 0.510539 3.3:-77304942 MS.gene06617:CDS
ACAATTCACAAAATGAGTTC+CGG 0.522809 3.3:-77305230 None:intergenic
GGAAGAAAGTGACGATGACA+TGG 0.523361 3.3:-77303882 MS.gene06617:CDS
AGCGGCACCACCAACAGCGC+CGG 0.527844 3.3:+77304935 None:intergenic
ACCAGCAGCGGGTGCAGATA+CGG 0.530473 3.3:+77304908 None:intergenic
TCCATCGTCGTGGAGGATCA+AGG 0.532980 3.3:+77305184 None:intergenic
GCAAGCTTAGCGAATAGGCT+TGG 0.542190 3.3:+77304993 None:intergenic
TTTGTTTAGGCGGAGAAGAT+CGG 0.543289 3.3:-77305059 MS.gene06617:intron
GGCAGGTTCGGCAGCTGCTG+CGG 0.548908 3.3:+77304878 None:intergenic
GTAAATGCAGCCCAATTCGC+CGG 0.571217 3.3:+77305211 None:intergenic
ACCTTGATCCTCCACGACGA+TGG 0.573503 3.3:-77305185 MS.gene06617:CDS
GTATCTGCACCCGCTGCTGG+TGG 0.603091 3.3:-77304906 MS.gene06617:CDS
GCTTGGCCAGTAAGATTCAA+CGG 0.629260 3.3:+77305010 None:intergenic
TTGGGATTCCATCGTCGTGG+AGG 0.650788 3.3:+77305177 None:intergenic
GTGTTTGTAGGAGGAAGCCA+AGG 0.654949 3.3:-77303903 MS.gene06617:intron
TGATTGGGATTCCATCGTCG+TGG 0.662981 3.3:+77305174 None:intergenic
GGGTGCAGATACGGCAACAG+CGG 0.665524 3.3:+77304917 None:intergenic
GAAGAAAGTGACGATGACAT+GGG 0.678372 3.3:-77303881 MS.gene06617:CDS
ATCGTCGTGGAGGATCAAGG+TGG 0.743990 3.3:+77305187 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTATATGTTTTTATCTTT+AGG + chr3.3:77304418-77304437 None:intergenic 10.0%
!! AATTGTATTGAAATTAGAAA+CGG - chr3.3:77304319-77304338 MS.gene06617:intron 15.0%
!!! TTTTCATGCAAAATAATTTT+TGG + chr3.3:77304636-77304655 None:intergenic 15.0%
!! AAAGTAAAAAATGTGGATAT+AGG + chr3.3:77305005-77305024 None:intergenic 20.0%
!! AAGTAAAAAATGTGGATATA+GGG + chr3.3:77305004-77305023 None:intergenic 20.0%
!!! AATTGTTGTTTTTCTTCATT+GGG - chr3.3:77304715-77304734 MS.gene06617:intron 20.0%
!!! ATATCCACATTTTTTACTTT+TGG - chr3.3:77305005-77305024 MS.gene06617:CDS 20.0%
!!! ATGAAAACATGTAGTTATTT+TGG - chr3.3:77304673-77304692 MS.gene06617:intron 20.0%
!!! ATTTTTCTTTTGTTACTGTT+TGG - chr3.3:77303991-77304010 MS.gene06617:intron 20.0%
!!! TAATTGTTGTTTTTCTTCAT+TGG - chr3.3:77304714-77304733 MS.gene06617:intron 20.0%
!!! TATCCACATTTTTTACTTTT+GGG - chr3.3:77305006-77305025 MS.gene06617:CDS 20.0%
!!! TTTTTCTTTTGTTACTGTTT+GGG - chr3.3:77303992-77304011 MS.gene06617:intron 20.0%
! GACAACTCTGAATATAATTA+TGG - chr3.3:77304765-77304784 MS.gene06617:intron 25.0%
! TTAAATAAGCCAATCATAAC+TGG - chr3.3:77304978-77304997 MS.gene06617:CDS 25.0%
!! AAACAATACCTTCTTTTCAA+CGG + chr3.3:77304229-77304248 None:intergenic 25.0%
!!! ATAAAGTTAACTTGTTATCC+TGG - chr3.3:77304895-77304914 MS.gene06617:CDS 25.0%
!!! TAAAGTTAACTTGTTATCCT+GGG - chr3.3:77304896-77304915 MS.gene06617:CDS 25.0%
AATGTAAGCTTATGCATAAG+TGG + chr3.3:77304850-77304869 None:intergenic 30.0%
AGATGCAAGTTCTACAAAAT+AGG + chr3.3:77304518-77304537 None:intergenic 30.0%
ATAATAGACTTACGGTGATT+GGG + chr3.3:77303924-77303943 None:intergenic 30.0%
ATGTAAGCTTATGCATAAGT+GGG + chr3.3:77304849-77304868 None:intergenic 30.0%
GAAGAGAGATAATAGACTTA+CGG + chr3.3:77303932-77303951 None:intergenic 30.0%
TATTCAGAGTTGTCTTGAAA+AGG + chr3.3:77304759-77304778 None:intergenic 30.0%
TGTTAAATGAATGCTAGTTC+TGG - chr3.3:77304367-77304386 MS.gene06617:intron 30.0%
TTTGTTTAGTGACACTGTTT+GGG + chr3.3:77304951-77304970 None:intergenic 30.0%
! ATTTTGTAGAACTTGCATCT+AGG - chr3.3:77304518-77304537 MS.gene06617:intron 30.0%
! CGATTTGGAGATTATAGAAA+TGG + chr3.3:77303959-77303978 None:intergenic 30.0%
AATGAGATCTATGAGCGATT+TGG + chr3.3:77303974-77303993 None:intergenic 35.0%
CTTCATTGGGATTTGAGAAT+TGG - chr3.3:77304728-77304747 MS.gene06617:intron 35.0%
GATAATAGACTTACGGTGAT+TGG + chr3.3:77303925-77303944 None:intergenic 35.0%
GTTTGTTTAGTGACACTGTT+TGG + chr3.3:77304952-77304971 None:intergenic 35.0%
TCATTCCATACTGTGTTTGT+AGG - chr3.3:77305165-77305184 MS.gene06617:intron 35.0%
TCGCCCAAAAGTAAAAAATG+TGG + chr3.3:77305012-77305031 None:intergenic 35.0%
TGTAATGACGAGTTACTGAT+TGG - chr3.3:77304290-77304309 MS.gene06617:intron 35.0%
! ATTTTGTGCTGTGATCAAGT+TGG - chr3.3:77304485-77304504 MS.gene06617:intron 35.0%
! TCTTTTGTTACTGTTTGGGT+TGG - chr3.3:77303996-77304015 MS.gene06617:intron 35.0%
! TTTTGTGCTGTGATCAAGTT+GGG - chr3.3:77304486-77304505 MS.gene06617:intron 35.0%
!!! GTTTGGGTTGGTTTTTGTTT+AGG - chr3.3:77304008-77304027 MS.gene06617:intron 35.0%
GAAGAAAGTGACGATGACAT+GGG - chr3.3:77305199-77305218 MS.gene06617:CDS 40.0%
GAAGATCGGTACTTTGTTGA+AGG - chr3.3:77304035-77304054 MS.gene06617:intron 40.0%
GATATAGGGCCAGTTATGAT+TGG + chr3.3:77304990-77305009 None:intergenic 40.0%
TTCCATACTGTGTTTGTAGG+AGG - chr3.3:77305168-77305187 MS.gene06617:intron 40.0%
TTCCTCCTACAAACACAGTA+TGG + chr3.3:77305173-77305192 None:intergenic 40.0%
TTTGTTTAGGCGGAGAAGAT+CGG - chr3.3:77304021-77304040 MS.gene06617:intron 40.0%
! CAATACCTTCTTTTCAACGG+CGG + chr3.3:77304226-77304245 None:intergenic 40.0%
! TTTGTGCTGTGATCAAGTTG+GGG - chr3.3:77304487-77304506 MS.gene06617:intron 40.0%
!! GATGATCTCGTTTTGAACTC+CGG - chr3.3:77304126-77304145 MS.gene06617:intron 40.0%
!!! TGGGTTGGTTTTTGTTTAGG+CGG - chr3.3:77304011-77304030 MS.gene06617:intron 40.0%
AATCCCCTTCGAGGAAAATG+AGG + chr3.3:77304576-77304595 None:intergenic 45.0%
ACGTCACCGTTGAATCTTAC+TGG - chr3.3:77304064-77304083 MS.gene06617:intron 45.0%
ATCAACAAGACGATCTTCCC+AGG + chr3.3:77304916-77304935 None:intergenic 45.0%
GCTTGGCCAGTAAGATTCAA+CGG + chr3.3:77304073-77304092 None:intergenic 45.0%
GGAAGAAAGTGACGATGACA+TGG - chr3.3:77305198-77305217 MS.gene06617:CDS 45.0%
TCTGAGCAAGCTTAGCGAAT+AGG + chr3.3:77304095-77304114 None:intergenic 45.0%
! GTCATCGTCACTTTCTTCCT+TGG + chr3.3:77305197-77305216 None:intergenic 45.0%
! TGTGCCTCATTTTCCTCGAA+GGG - chr3.3:77304569-77304588 MS.gene06617:intron 45.0%
CCAATACAGAATCCCCTTCG+AGG + chr3.3:77304585-77304604 None:intergenic 50.0%
CCTCGAAGGGGATTCTGTAT+TGG - chr3.3:77304582-77304601 MS.gene06617:intron 50.0%
GCAAGCTTAGCGAATAGGCT+TGG + chr3.3:77304090-77304109 None:intergenic 50.0%
GTAAATGCAGCCCAATTCGC+CGG + chr3.3:77303872-77303891 None:intergenic 50.0%
GTGTTTGTAGGAGGAAGCCA+AGG - chr3.3:77305177-77305196 MS.gene06617:CDS 50.0%
TGATTGGGATTCCATCGTCG+TGG + chr3.3:77303909-77303928 None:intergenic 50.0%
! CTGTGCCTCATTTTCCTCGA+AGG - chr3.3:77304568-77304587 MS.gene06617:intron 50.0%
! GTGCCTCATTTTCCTCGAAG+GGG - chr3.3:77304570-77304589 MS.gene06617:intron 50.0%
ACCTGCCGCCGTTGAAAAGA+AGG - chr3.3:77304218-77304237 MS.gene06617:intron 55.0%
ACCTTGATCCTCCACGACGA+TGG - chr3.3:77303895-77303914 MS.gene06617:CDS 55.0%
ATCGTCGTGGAGGATCAAGG+TGG + chr3.3:77303896-77303915 None:intergenic 55.0%
TCCATCGTCGTGGAGGATCA+AGG + chr3.3:77303899-77303918 None:intergenic 55.0%
TTGGGATTCCATCGTCGTGG+AGG + chr3.3:77303906-77303925 None:intergenic 55.0%
! ACCTTCTTTTCAACGGCGGC+AGG + chr3.3:77304222-77304241 None:intergenic 55.0%
! CTTTTCAACGGCGGCAGGTT+CGG + chr3.3:77304217-77304236 None:intergenic 55.0%
!! GTTTTGAACTCCGGCGCTGT+TGG - chr3.3:77304135-77304154 MS.gene06617:intron 55.0%
ACCAGCAGCGGGTGCAGATA+CGG + chr3.3:77304175-77304194 None:intergenic 60.0%
GGGTGCAGATACGGCAACAG+CGG + chr3.3:77304166-77304185 None:intergenic 60.0%
TTGAACTCCGGCGCTGTTGG+TGG - chr3.3:77304138-77304157 MS.gene06617:intron 60.0%
GTATCTGCACCCGCTGCTGG+TGG - chr3.3:77304174-77304193 MS.gene06617:intron 65.0%
AGCGGCACCACCAACAGCGC+CGG + chr3.3:77304148-77304167 None:intergenic 70.0%
GCCGTATCTGCACCCGCTGC+TGG - chr3.3:77304171-77304190 MS.gene06617:intron 70.0%
GGCAGGTTCGGCAGCTGCTG+CGG + chr3.3:77304205-77304224 None:intergenic 70.0%
TCTGCACCCGCTGCTGGTGG+TGG - chr3.3:77304177-77304196 MS.gene06617:intron 70.0%
TGCGGCTCCACCACCAGCAG+CGG + chr3.3:77304187-77304206 None:intergenic 70.0%
GCGGCTCCACCACCAGCAGC+GGG + chr3.3:77304186-77304205 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 77303862 77305240 77303862 ID=MS.gene06617
chr3.3 mRNA 77303862 77305240 77303862 ID=MS.gene06617.t1;Parent=MS.gene06617
chr3.3 exon 77305172 77305240 77305172 ID=MS.gene06617.t1.exon1;Parent=MS.gene06617.t1
chr3.3 CDS 77305172 77305240 77305172 ID=cds.MS.gene06617.t1;Parent=MS.gene06617.t1
chr3.3 exon 77304863 77305072 77304863 ID=MS.gene06617.t1.exon2;Parent=MS.gene06617.t1
chr3.3 CDS 77304863 77305072 77304863 ID=cds.MS.gene06617.t1;Parent=MS.gene06617.t1
chr3.3 exon 77303862 77303915 77303862 ID=MS.gene06617.t1.exon3;Parent=MS.gene06617.t1
chr3.3 CDS 77303862 77303915 77303862 ID=cds.MS.gene06617.t1;Parent=MS.gene06617.t1
Gene Sequence

>MS.gene06617

ATGAGTTCCGGCGAATTGGGCTGCATTTACGCCACCTTGATCCTCCACGACGATGGAATCCCAATCACCGTAAGTCTATTATCTCTCTTCAATTCCATTTCTATAATCTCCAAATCGCTCATAGATCTCATTTTTCTTTTGTTACTGTTTGGGTTGGTTTTTGTTTAGGCGGAGAAGATCGGTACTTTGTTGAAGGCTGCTAACGTCACCGTTGAATCTTACTGGCCAAGCCTATTCGCTAAGCTTGCTCAGAGCAAGAACGTTGATGATCTCGTTTTGAACTCCGGCGCTGTTGGTGGTGCCGCTGTTGCCGTATCTGCACCCGCTGCTGGTGGTGGAGCCGCAGCAGCTGCCGAACCTGCCGCCGTTGAAAAGAAGGTATTGTTTTTAATTCTTTTTTTTATGATTATGATTTTTGTATGAAATTGTGTAATGACGAGTTACTGATTGGTGAACTAATTGTATTGAAATTAGAAACGGATTTTGATAAATCGTTCATCTGTAGTGTTAAATGAATGCTAGTTCTGGAATTGTACAATAGTATTGCAATTTTCCTAAAGATAAAAACATATAATTGATTTTCTTACATTGTTTGTTCTGTTGAATTTGCTTGCAAATTGATGATTTTGTGCTGTGATCAAGTTGGGGTTATACCTATTTTGTAGAACTTGCATCTAGGTATAAAAGATATAATTTTTCTACACTTCTGTGCCTCATTTTCCTCGAAGGGGATTCTGTATTGGATAAATACTGTCATTTGCTGCAATTACTCCAAAAATTATTTTGCATGAAAACATTCACTATAAGTTTTATGAAAACATGTAGTTATTTTGGTTTTTTGAAGAAATAGTATAATTGTTGTTTTTCTTCATTGGGATTTGAGAATTGGACTATCCTTTTCAAGACAACTCTGAATATAATTATGGTACTCTTTTGATTTGCAACTTATGTACAGCTTATTGCTCAAGCGCTTCTCTTGATATGCCCACTTATGCATAAGCTTACATTTTCTATTTTCTATAGAAAAGATAAAATAAAGTTAACTTGTTATCCTGGGAAGATCGTCTTGTTGATTTCATTAGTTCTCCCAAACAGTGTCACTAAACAAACATAGCTTTAAATAAGCCAATCATAACTGGCCCTATATCCACATTTTTTACTTTTGGGCGAGTTTTTACTCTTTCACAATAATTTAATGTTTAATGTTGTATTATAGCTTTGATGCAGTCAATTATGAGCAATGCACAGACATAGCTTATTACTTCAATTTGTTTTGATTATGTTGTATATAGCAAAACTTAATTCATTCCATACTGTGTTTGTAGGAGGAAGCCAAGGAAGAAAGTGACGATGACATGGGCTTTAGTTTGTTTGATTAA

Protein sequence

>MS.gene06617.t1

MSSGELGCIYATLILHDDGIPITAEKIGTLLKAANVTVESYWPSLFAKLAQSKNVDDLVLNSGAVGGAAVAVSAPAAGGGAAAAAEPAAVEKKEEAKEESDDDMGFSLFD