AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene063410


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 29 sgRNAs with CRISPR-Local

Find 107 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCCGACTGGCTTGGCTATC+TGG 0.093434 2.3:+26098738 MS.gene063410:CDS
CAGTCCTTTGGGTCGTAGAT+AGG 0.323072 2.3:-26098161 None:intergenic
CCGGTTGGAGACCAGTCCTT+TGG 0.338674 2.3:-26098173 None:intergenic
CGGTTGGAGACCAGTCCTTT+GGG 0.408090 2.3:-26098172 None:intergenic
CACCGTATTTGTCCACAAAC+TGG 0.410816 2.3:-26097723 None:intergenic
TCCGACTGGCTTGGCTATCT+GGG 0.439109 2.3:+26098739 MS.gene063410:CDS
AAAGGGTGTTTACCAGTTTG+TGG 0.454085 2.3:+26097711 MS.gene063410:CDS
GTGCTAATGTTGATGGATAC+AGG 0.463270 2.3:+26097743 MS.gene063410:CDS
AAATACGGTGCTAATGTTGA+TGG 0.464376 2.3:+26097736 MS.gene063410:CDS
TACCAGTTTGTGGACAAATA+CGG 0.473942 2.3:+26097721 MS.gene063410:CDS
TTATTAATTGCAGGTCCGAC+TGG 0.479017 2.3:+26098725 MS.gene063410:intron
ATCTGGGCAGTAACTCTAGC+TGG 0.496777 2.3:+26098755 MS.gene063410:CDS
CCAAAGGACTGGTCTCCAAC+CGG 0.502102 2.3:+26098173 MS.gene063410:CDS
ACTCTAGCTGGTCTTCTAGC+TGG 0.504630 2.3:+26098767 MS.gene063410:CDS
AGTCCTTTGGGTCGTAGATA+GGG 0.509259 2.3:-26098160 None:intergenic
AATTGCAGGTCCGACTGGCT+TGG 0.514526 2.3:+26098730 MS.gene063410:intron
ATGCTTCTGCAGGAAACAAA+AGG 0.521269 2.3:+26096839 MS.gene063410:CDS
TTTAGGAACTGGAGGTGGCA+TGG 0.542136 2.3:+26096798 None:intergenic
GATGGAAAAGATGCTTCTGC+AGG 0.556131 2.3:+26096829 MS.gene063410:CDS
CTAGCTGGTCTTCTAGCTGG+TGG 0.579831 2.3:+26098770 MS.gene063410:CDS
GGTGGCATGGCCTTGCCCGA+TGG 0.580943 2.3:+26096811 MS.gene063410:CDS
CTATCTACGACCCAAAGGAC+TGG 0.590400 2.3:+26098162 MS.gene063410:CDS
ACCTCCAGTGTAGACATCAC+CGG 0.624297 2.3:-26098192 None:intergenic
CAGCCCTATCTACGACCCAA+AGG 0.645785 2.3:+26098157 MS.gene063410:intron
CCAACCGGTGATGTCTACAC+TGG 0.647391 2.3:+26098188 MS.gene063410:CDS
AAGCACTTGTGTTGTAGACA+AGG 0.648013 2.3:-26098799 None:intergenic
GCCCAGATAGCCAAGCCAGT+CGG 0.648776 2.3:-26098740 None:intergenic
ACCGGTGATGTCTACACTGG+AGG 0.649993 2.3:+26098191 MS.gene063410:CDS
CCAGTGTAGACATCACCGGT+TGG 0.671824 2.3:-26098188 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTATTTATATTTTATTT+TGG + chr2.3:26096873-26096892 MS.gene063410:intron 0.0%
!! TATTTACTACCAATAAATAA+AGG - chr2.3:26097357-26097376 None:intergenic 15.0%
!!! AAATTACATTTTGAATAAGT+AGG - chr2.3:26098122-26098141 None:intergenic 15.0%
!!! ACTTAATAAACTTTTTTTTG+AGG + chr2.3:26096958-26096977 MS.gene063410:intron 15.0%
!!! CTTAATTTCAATTTTATTCA+GGG + chr2.3:26097688-26097707 MS.gene063410:intron 15.0%
!!! GAATTTTTATGTATTAACAT+AGG + chr2.3:26096910-26096929 MS.gene063410:intron 15.0%
!!! TAACAAATTTTATTAATTGC+AGG + chr2.3:26098716-26098735 MS.gene063410:intron 15.0%
!!! TCTTAATTTCAATTTTATTC+AGG + chr2.3:26097687-26097706 MS.gene063410:intron 15.0%
!!! TGTTTAAAACCTTTATTTAT+TGG + chr2.3:26097345-26097364 MS.gene063410:intron 15.0%
!! AATAATAGATAACAATGTTC+TGG - chr2.3:26097590-26097609 None:intergenic 20.0%
!! ACATGTTTAATAACATAGTT+AGG + chr2.3:26097810-26097829 MS.gene063410:intron 20.0%
!! ATTAAACATGTAAACAAAAC+TGG - chr2.3:26097801-26097820 None:intergenic 20.0%
!! ATTCAATTATTTACTTCAGA+GGG + chr2.3:26098501-26098520 MS.gene063410:intron 20.0%
!! GATCTAATGAAATACATTAA+AGG + chr2.3:26097486-26097505 MS.gene063410:intron 20.0%
!! TGAAATAATTATGTCATTAG+AGG + chr2.3:26097833-26097852 MS.gene063410:intron 20.0%
!!! AATTATCAAGATTTTTTCCA+TGG + chr2.3:26097065-26097084 MS.gene063410:intron 20.0%
!!! ATTATCAAGATTTTTTCCAT+GGG + chr2.3:26097066-26097085 MS.gene063410:intron 20.0%
!!! ATTTATTCAACTTTTAGCTT+TGG + chr2.3:26097133-26097152 MS.gene063410:intron 20.0%
!!! ATTTTTTTGTTTTAATCCTC+TGG - chr2.3:26097096-26097115 None:intergenic 20.0%
!!! TAAAGCAATGTTTTAAAAAC+TGG + chr2.3:26098303-26098322 MS.gene063410:intron 20.0%
!!! TTTCATTTTTTCTGAATTCT+AGG + chr2.3:26097774-26097793 MS.gene063410:intron 20.0%
!!! TTTTTAAAACATTGCTTTAG+AGG - chr2.3:26098302-26098321 None:intergenic 20.0%
! ATAAAATAGCATGAACTGTA+GGG + chr2.3:26098267-26098286 MS.gene063410:intron 25.0%
! CACATTATAACATCAACAAT+AGG - chr2.3:26098434-26098453 None:intergenic 25.0%
! CTCTTCTTATATGAAAAACT+TGG + chr2.3:26097189-26097208 MS.gene063410:intron 25.0%
! GATAACTAAAATCTGACTTA+TGG - chr2.3:26097029-26097048 None:intergenic 25.0%
! GATTCAATTATTTACTTCAG+AGG + chr2.3:26098500-26098519 MS.gene063410:intron 25.0%
! TTAAACAATCATGACATAAG+TGG + chr2.3:26097868-26097887 MS.gene063410:intron 25.0%
! TTTCAATCATATCTGAACTT+AGG - chr2.3:26097003-26097022 None:intergenic 25.0%
!! AGTTTTTCATATAAGAAGAG+AGG - chr2.3:26097189-26097208 None:intergenic 25.0%
!! GTTTTTCATATAAGAAGAGA+GGG - chr2.3:26097188-26097207 None:intergenic 25.0%
!! TTCAATTTTATTCAGGGAAA+GGG + chr2.3:26097694-26097713 MS.gene063410:intron 25.0%
!! TTTCAATTTTATTCAGGGAA+AGG + chr2.3:26097693-26097712 MS.gene063410:intron 25.0%
!! TTTGTTATCATACTATTGCT+AGG - chr2.3:26098703-26098722 None:intergenic 25.0%
!!! AAGTAAGGTGGATTTTATAT+AGG + chr2.3:26097464-26097483 MS.gene063410:intron 25.0%
!!! AGGTAAGAAACTTCTTTTTT+TGG + chr2.3:26098211-26098230 MS.gene063410:intron 25.0%
!!! GGTAAGAAACTTCTTTTTTT+GGG + chr2.3:26098212-26098231 MS.gene063410:intron 25.0%
!!! TATTTTGGTGCTTTATTTTG+TGG + chr2.3:26096888-26096907 MS.gene063410:intron 25.0%
AAATCTTTGTATAGCCAACA+CGG - chr2.3:26098643-26098662 None:intergenic 30.0%
AAGTAGAGAGTGATTCTTAA+GGG + chr2.3:26097304-26097323 MS.gene063410:intron 30.0%
AGAATAAATAGTAGACCAAG+AGG - chr2.3:26097159-26097178 None:intergenic 30.0%
CAGAAAGCCCAAAAATATAA+GGG - chr2.3:26097620-26097639 None:intergenic 30.0%
GATAAAATAGCATGAACTGT+AGG + chr2.3:26098266-26098285 MS.gene063410:intron 30.0%
GCTCGTACATATAAAAAAGT+TGG + chr2.3:26097985-26098004 MS.gene063410:intron 30.0%
GTTTCTCACAAGATAAAGTA+AGG + chr2.3:26097449-26097468 MS.gene063410:intron 30.0%
TAAGTAGAGAGTGATTCTTA+AGG + chr2.3:26097303-26097322 MS.gene063410:intron 30.0%
TATGTATTAACATAGGCTTG+TGG + chr2.3:26096917-26096936 MS.gene063410:intron 30.0%
TCAGAAAGCCCAAAAATATA+AGG - chr2.3:26097621-26097640 None:intergenic 30.0%
! GAAAAACTTGGTAGTTTCTA+AGG + chr2.3:26097201-26097220 MS.gene063410:intron 30.0%
! TTGATAATTCGTAGTTCGAT+CGG - chr2.3:26097054-26097073 None:intergenic 30.0%
!! AGAGTGTCCCTTATATTTTT+GGG + chr2.3:26097610-26097629 MS.gene063410:intron 30.0%
!! TAGAGAGTAGTGTTTAGTTT+TGG + chr2.3:26098536-26098555 MS.gene063410:intron 30.0%
!! TAGAGTGTCCCTTATATTTT+TGG + chr2.3:26097609-26097628 MS.gene063410:intron 30.0%
AACCACATAGGCTAATTGAA+AGG + chr2.3:26097260-26097279 MS.gene063410:intron 35.0%
ATAAGTTCAACTGGTCGAAT+TGG + chr2.3:26098335-26098354 MS.gene063410:intron 35.0%
ATAGGGCTGCATAATAAAAC+AGG - chr2.3:26098146-26098165 None:intergenic 35.0%
CAAGACTAATGTCTCATGTT+TGG + chr2.3:26097950-26097969 MS.gene063410:intron 35.0%
TAAGTTCAACTGGTCGAATT+GGG + chr2.3:26098336-26098355 MS.gene063410:intron 35.0%
TACCAGTTTGTGGACAAATA+CGG + chr2.3:26097721-26097740 MS.gene063410:CDS 35.0%
TCTCACAAGATAAAGTAAGG+TGG + chr2.3:26097452-26097471 MS.gene063410:intron 35.0%
! AAATACGGTGCTAATGTTGA+TGG + chr2.3:26097736-26097755 MS.gene063410:CDS 35.0%
! ATCCTTTCAATTAGCCTATG+TGG - chr2.3:26097265-26097284 None:intergenic 35.0%
! CATGAGCGAAGATAGTTTTT+AGG - chr2.3:26098567-26098586 None:intergenic 35.0%
! GACTAATGTCTCTCATGTTT+TGG + chr2.3:26098049-26098068 MS.gene063410:intron 35.0%
! TTTTGGGCTTTCTGAATTGT+TGG + chr2.3:26097626-26097645 MS.gene063410:intron 35.0%
AAGCACTTGTGTTGTAGACA+AGG - chr2.3:26098802-26098821 None:intergenic 40.0%
ATCGAGCTGATAAGTTCAAC+TGG + chr2.3:26098326-26098345 MS.gene063410:intron 40.0%
ATGCTTCTGCAGGAAACAAA+AGG + chr2.3:26096839-26096858 MS.gene063410:CDS 40.0%
CAACTATTTCAAGACCGTGT+TGG + chr2.3:26098626-26098645 MS.gene063410:intron 40.0%
CACAAGTGCTTTGTCACAAT+AGG + chr2.3:26098811-26098830 MS.gene063410:CDS 40.0%
CCTATGTGGTTGAGATGTTA+AGG - chr2.3:26097251-26097270 None:intergenic 40.0%
CCTTAACATCTCAACCACAT+AGG + chr2.3:26097248-26097267 MS.gene063410:intron 40.0%
GCATGAACTGTAGGGATTTA+TGG + chr2.3:26098275-26098294 MS.gene063410:intron 40.0%
TTATTAATTGCAGGTCCGAC+TGG + chr2.3:26098725-26098744 MS.gene063410:intron 40.0%
! GGCTTTCTGAATTGTTGGTT+TGG + chr2.3:26097631-26097650 MS.gene063410:intron 40.0%
! GTGCTAATGTTGATGGATAC+AGG + chr2.3:26097743-26097762 MS.gene063410:CDS 40.0%
!! AAAGGGTGTTTACCAGTTTG+TGG + chr2.3:26097711-26097730 MS.gene063410:CDS 40.0%
!! CTTGGTAGTTTCTAAGGTGT+TGG + chr2.3:26097207-26097226 MS.gene063410:intron 40.0%
!!! AACTTTTAGCTTTGGCCTCT+TGG + chr2.3:26097141-26097160 MS.gene063410:intron 40.0%
!!! TGCAGAAGCATCTTTTCCAT+CGG - chr2.3:26096830-26096849 None:intergenic 40.0%
AGTCCTTTGGGTCGTAGATA+GGG - chr2.3:26098163-26098182 None:intergenic 45.0%
CACCGTATTTGTCCACAAAC+TGG - chr2.3:26097726-26097745 None:intergenic 45.0%
GATGGAAAAGATGCTTCTGC+AGG + chr2.3:26096829-26096848 MS.gene063410:CDS 45.0%
TTAATCCTCTGGTGTTCCCA+TGG - chr2.3:26097085-26097104 None:intergenic 45.0%
TTGGGAATCGACTACTTCAC+CGG + chr2.3:26098354-26098373 MS.gene063410:intron 45.0%
! TTTTTCCATGGGAACACCAG+AGG + chr2.3:26097077-26097096 MS.gene063410:intron 45.0%
!! CGAATTGCTCAGTTCTGAAC+CGG - chr2.3:26098376-26098395 None:intergenic 45.0%
!!! GCAGAAGCATCTTTTCCATC+GGG - chr2.3:26096829-26096848 None:intergenic 45.0%
ACCTCCAGTGTAGACATCAC+CGG - chr2.3:26098195-26098214 None:intergenic 50.0%
ATCTGGGCAGTAACTCTAGC+TGG + chr2.3:26098755-26098774 MS.gene063410:CDS 50.0%
CAGTCCTTTGGGTCGTAGAT+AGG - chr2.3:26098164-26098183 None:intergenic 50.0%
CTATCTACGACCCAAAGGAC+TGG + chr2.3:26098162-26098181 MS.gene063410:CDS 50.0%
! AGCATCTTTTCCATCGGGCA+AGG - chr2.3:26096824-26096843 None:intergenic 50.0%
!! ACTCTAGCTGGTCTTCTAGC+TGG + chr2.3:26098767-26098786 MS.gene063410:CDS 50.0%
ACCGGTGATGTCTACACTGG+AGG + chr2.3:26098191-26098210 MS.gene063410:CDS 55.0%
CAGCCCTATCTACGACCCAA+AGG + chr2.3:26098157-26098176 MS.gene063410:intron 55.0%
CCAACCGGTGATGTCTACAC+TGG + chr2.3:26098188-26098207 MS.gene063410:CDS 55.0%
CCAGTGTAGACATCACCGGT+TGG - chr2.3:26098191-26098210 None:intergenic 55.0%
CGGTTGGAGACCAGTCCTTT+GGG - chr2.3:26098175-26098194 None:intergenic 55.0%
! AATTGCAGGTCCGACTGGCT+TGG + chr2.3:26098730-26098749 MS.gene063410:intron 55.0%
!! CCAAAGGACTGGTCTCCAAC+CGG + chr2.3:26098173-26098192 MS.gene063410:CDS 55.0%
!! CTAGCTGGTCTTCTAGCTGG+TGG + chr2.3:26098770-26098789 MS.gene063410:CDS 55.0%
!! TCCGACTGGCTTGGCTATCT+GGG + chr2.3:26098739-26098758 MS.gene063410:CDS 55.0%
CCGGTTGGAGACCAGTCCTT+TGG - chr2.3:26098176-26098195 None:intergenic 60.0%
GCCCAGATAGCCAAGCCAGT+CGG - chr2.3:26098743-26098762 None:intergenic 60.0%
!! GTCCGACTGGCTTGGCTATC+TGG + chr2.3:26098738-26098757 MS.gene063410:CDS 60.0%
! GGTGGCATGGCCTTGCCCGA+TGG + chr2.3:26096811-26096830 MS.gene063410:CDS 70.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 26096803 26098832 26096803 ID=MS.gene063410
chr2.3 mRNA 26096803 26098832 26096803 ID=MS.gene063410.t1;Parent=MS.gene063410
chr2.3 exon 26096803 26096864 26096803 ID=MS.gene063410.t1.exon1;Parent=MS.gene063410.t1
chr2.3 CDS 26096803 26096864 26096803 ID=cds.MS.gene063410.t1;Parent=MS.gene063410.t1
chr2.3 exon 26097709 26097764 26097709 ID=MS.gene063410.t1.exon2;Parent=MS.gene063410.t1
chr2.3 CDS 26097709 26097764 26097709 ID=cds.MS.gene063410.t1;Parent=MS.gene063410.t1
chr2.3 exon 26098160 26098212 26098160 ID=MS.gene063410.t1.exon3;Parent=MS.gene063410.t1
chr2.3 CDS 26098160 26098212 26098160 ID=cds.MS.gene063410.t1;Parent=MS.gene063410.t1
chr2.3 exon 26098738 26098832 26098738 ID=MS.gene063410.t1.exon4;Parent=MS.gene063410.t1
chr2.3 CDS 26098738 26098832 26098738 ID=cds.MS.gene063410.t1;Parent=MS.gene063410.t1
Gene Sequence

>MS.gene063410

GAACTGGAGGTGGCATGGCCTTGCCCGATGGAAAAGATGCTTCTGCAGGAAACAAAAGGTGTGTTTAATTTTTTTATTTATATTTTATTTTGGTGCTTTATTTTGTGGAATTTTTATGTATTAACATAGGCTTGTGGTTGAATTCAAAGTATTTAACTTAATAAACTTTTTTTTGAGGTTCAATTGTAACTAGAAATCCTAAGTTCAGATATGATTGAAATAACCATAAGTCAGATTTTAGTTATCTTCCGATCGAACTACGAATTATCAAGATTTTTTCCATGGGAACACCAGAGGATTAAAACAAAAAAATTATTAACTGATATAGTTATTTATTCAACTTTTAGCTTTGGCCTCTTGGTCTACTATTTATTCTTTATAACCCTCTCTTCTTATATGAAAAACTTGGTAGTTTCTAAGGTGTTGGAAAATATATCACTATAGTCCTTAACATCTCAACCACATAGGCTAATTGAAAGGATTTCACATGATTCAGAGATTAAGTAGAGAGTGATTCTTAAGGGATTAAGTTGAAGATTTATTGTTTAAAACCTTTATTTATTGGTAGTAAATACATCTTATGAATATGCATACTTTTTTTTTTTTTTACACAAATTATTTTTGTAGTGATATTCAAACATATAAAGTTTCTCACAAGATAAAGTAAGGTGGATTTTATATAGGATCTAATGAAATACATTAAAGGAAAAGAAAATATTAATTAACTTAACTTTCATGTTTATGATAACTAGAATATTGTTATCTTTTTTGTTTTTTGAACAAGCCAGAACATTGTTATCTATTATTAGAGTGTCCCTTATATTTTTGGGCTTTCTGAATTGTTGGTTTGGTTTATAGTTTTCATTTCATCTTATCTTCTAACTTCTTAATTTCAATTTTATTCAGGGAAAGGGTGTTTACCAGTTTGTGGACAAATACGGTGCTAATGTTGATGGATACAGGTAACTTACTTTCATTTTTTCTGAATTCTAGGTCCAGTTTTGTTTACATGTTTAATAACATAGTTAGGTGAAATAATTATGTCATTAGAGGAACTAATCTCAATTAAACAATCATGACATAAGTGGTTAAAATTATAATAAATTTAAATCAAACTATTATGATCATTCATGCATTATTATGTAATCAAGACTAATGTCTCATGTTTGGATTGATACTCTAGCTCGTACATATAAAAAAGTTGGAATAAGAGATCAAGTTCAATTTAATTAATTAATGTAATCAAGACTAATGTCTCTCATGTTTTGGATATTGATTTTAAATTAATTATTTTCATCAAATTATATAGACTTTGACCTACTTATTCAAAATGTAATTTTCCTGTTTTATTATGCAGCCCTATCTACGACCCAAAGGACTGGTCTCCAACCGGTGATGTCTACACTGGAGGTAAGAAACTTCTTTTTTTGGGCAACTTTGATGTCTTAAAATTGACTCTACAAGATAAAATAGCATGAACTGTAGGGATTTATGGTCCTCTAAAGCAATGTTTTAAAAACTGGATCGAGCTGATAAGTTCAACTGGTCGAATTGGGAATCGACTACTTCACCGGTTCAGAACTGAGCAATTCGTTTTAAACGATAAAATAAGTACACTGATCAACATACCTATTGTTGATGTTATAATGTGATCATGATTGTGTCAGAATATCAACTATTGATTTTTTTCATTAAATGATTCAATTATTTACTTCAGAGGGAAATCAAAATCTTAGAGAGTAGTGTTTAGTTTTGGTTCAACCTAAAAACTATCTTCGCTCATGAATGTGTTAGAATATCAACTGTTTTGAGAGTCATGTTATCAACTATTTCAAGACCGTGTTGGCTATACAAAGATTTTCTTGATCAAATTCAAATGTTAAAGAACAAATTTTTTCCTAGCAATAGTATGATAACAAATTTTATTAATTGCAGGTCCGACTGGCTTGGCTATCTGGGCAGTAACTCTAGCTGGTCTTCTAGCTGGTGGTGCACTCCTTGTCTACAACACAAGTGCTTTGTCACAATAG

Protein sequence

>MS.gene063410.t1

ELEVAWPCPMEKMLLQETKGVERVFTSLWTNTVLMLMDTALSTTQRTGLQPVMSTLEVRLAWLSGQULULVFULVVHSLSTTQVLCHN