AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004569

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004569.t1 MTR_2g436800 100.000 81 0 0 1 81 1 81 4.97e-58 172
MS.gene004569.t1 MTR_7g076530 93.827 81 5 0 1 81 1 81 1.73e-55 166
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004569.t1 AT5G27700 85.185 81 12 0 1 81 1 81 9.02e-51 154
MS.gene004569.t1 AT3G53890 80.247 81 16 0 1 81 1 81 1.61e-48 148
MS.gene004569.t1 AT3G53890 80.247 81 16 0 1 81 1 81 1.61e-48 148

Find 18 sgRNAs with CRISPR-Local

Find 91 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAGCTGAACATAGGTCATT+TGG 0.363523 2.2:-52399788 MS.gene004569:CDS
GTTTCAGTTCTGCTACAAAC+AGG 0.431981 2.2:-52399840 MS.gene004569:intron
CTGTGGCTTCACCCGTGCTC+AGG 0.453938 2.2:-52399722 MS.gene004569:intron
AAAAGTTCATACCACTTCCT+AGG 0.458041 2.2:+52399937 None:intergenic
TCACCGAGCTCTACATTCCT+AGG 0.480407 2.2:-52399954 MS.gene004569:CDS
GAAGCCACAGAGAGCAAAAG+TGG 0.501571 2.2:+52399735 None:intergenic
CTAAAGATGCAGAACGAAGA+AGG 0.519629 2.2:-52399982 None:intergenic
ACAGTGGAATTGATCGCCTA+TGG 0.527769 2.2:-52398290 MS.gene004569:CDS
AGCTCTACATTCCTAGGAAG+TGG 0.545691 2.2:-52399948 MS.gene004569:intron
TTGTGTCTACTGCTTAAGCT+CGG 0.551699 2.2:+52398254 None:intergenic
AAACAGGCTTATTACTGCTA+AGG 0.565079 2.2:-52399824 MS.gene004569:CDS
GCATCAGTTCAGCTGAACAT+AGG 0.573016 2.2:-52399796 MS.gene004569:CDS
GATGAGAGCGGTGTTTACAA+TGG 0.604206 2.2:-52399766 MS.gene004569:CDS
ACAAATGGATACCTGAGCAC+GGG 0.612936 2.2:+52399711 None:intergenic
TTTCAGGGAGATGCTGACAG+TGG 0.628229 2.2:-52398306 MS.gene004569:intron
CTTCCTAGGAATGTAGAGCT+CGG 0.633169 2.2:+52399951 None:intergenic
AACAAATGGATACCTGAGCA+CGG 0.637714 2.2:+52399710 None:intergenic
ATAGGTCATTTGGATGAGAG+CGG 0.690184 2.2:-52399778 MS.gene004569:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTAAGAAATTATGTTATAT+TGG + chr2.2:52398935-52398954 None:intergenic 10.0%
!!! AAAATAAGTTTTTAATAAAC+AGG + chr2.2:52399300-52399319 None:intergenic 10.0%
!!! GTTTATTAAAAACTTATTTT+GGG - chr2.2:52399300-52399319 MS.gene004569:intron 10.0%
!!! TGTTTATTAAAAACTTATTT+TGG - chr2.2:52399299-52399318 MS.gene004569:intron 10.0%
!! GAATTAAGAGTAAATAATTA+GGG - chr2.2:52398596-52398615 MS.gene004569:intron 15.0%
!! TATACCAATATAAGATATAT+TGG + chr2.2:52399271-52399290 None:intergenic 15.0%
!! TATACCAATATATCTTATAT+TGG - chr2.2:52399264-52399283 MS.gene004569:intron 15.0%
!! TGAATTAAGAGTAAATAATT+AGG - chr2.2:52398595-52398614 MS.gene004569:intron 15.0%
!! TGATTCTATATATCTTATAT+TGG - chr2.2:52399205-52399224 MS.gene004569:intron 15.0%
!! TTTCATAAGCTAAAAAAATA+AGG - chr2.2:52398980-52398999 MS.gene004569:intron 15.0%
!! AAGTTTACATATTATCAGTA+TGG - chr2.2:52399544-52399563 MS.gene004569:intron 20.0%
!! ACTTAAAATTTATACTTCCT+CGG - chr2.2:52399378-52399397 MS.gene004569:intron 20.0%
!! TACTGATAATATGTAAACTT+AGG + chr2.2:52399544-52399563 None:intergenic 20.0%
!!! ACCATTTGTTTCTTATAAAA+AGG + chr2.2:52399406-52399425 None:intergenic 20.0%
!!! TCCTTTTTATAAGAAACAAA+TGG - chr2.2:52399402-52399421 MS.gene004569:intron 20.0%
! AACCAAATACATCAACTTTA+TGG - chr2.2:52399460-52399479 MS.gene004569:intron 25.0%
! AGCTAAAAAAATAAGGCAAA+CGG - chr2.2:52398987-52399006 MS.gene004569:intron 25.0%
! ATAATATGTAAACTTAGGCA+AGG + chr2.2:52399539-52399558 None:intergenic 25.0%
! CTTAAAATTTATACTTCCTC+GGG - chr2.2:52399379-52399398 MS.gene004569:intron 25.0%
! GAAAACCTTTATATCTATGT+TGG - chr2.2:52399837-52399856 MS.gene004569:intron 25.0%
! TATGTCCAACATAGATATAA+AGG + chr2.2:52399845-52399864 None:intergenic 25.0%
!! ACGAGTAGTTTTTAATAAAC+AGG + chr2.2:52399237-52399256 None:intergenic 25.0%
!!! GGTTTCTATCTTTGTTATTT+TGG - chr2.2:52398562-52398581 MS.gene004569:intron 25.0%
!!! TGATGCTTGTTTTATTTTCA+GGG - chr2.2:52399915-52399934 MS.gene004569:intron 25.0%
!!! TTGATGCTTGTTTTATTTTC+AGG - chr2.2:52399914-52399933 MS.gene004569:intron 25.0%
!!! TTTGAACTGTTTTTGTTTTG+TGG - chr2.2:52398369-52398388 MS.gene004569:intron 25.0%
AAAAGAGTGAAGACTCAATT+TGG + chr2.2:52399128-52399147 None:intergenic 30.0%
AGAAACACACTGAAATAAGT+AGG - chr2.2:52399805-52399824 MS.gene004569:CDS 30.0%
ATCAACTTTATGGTCAACTA+AGG - chr2.2:52399470-52399489 MS.gene004569:intron 30.0%
CATTTGTTCCACTCTAATTT+CGG - chr2.2:52398541-52398560 MS.gene004569:intron 30.0%
GAAACACACTGAAATAAGTA+GGG - chr2.2:52399806-52399825 MS.gene004569:CDS 30.0%
GTATTATTCATAAGCTTGTC+AGG - chr2.2:52398880-52398899 MS.gene004569:intron 30.0%
TAAGAAACAAATGGTTCAAC+AGG - chr2.2:52399411-52399430 MS.gene004569:intron 30.0%
TATTAATTCATGTCATGCCT+TGG - chr2.2:52399872-52399891 MS.gene004569:intron 30.0%
TCAAATTTCTCAGCTTACAT+TGG + chr2.2:52399604-52399623 None:intergenic 30.0%
TCAACAGGAGTTAATGTATT+TGG - chr2.2:52399426-52399445 MS.gene004569:intron 30.0%
!! GACCATAAAGTTGATGTATT+TGG + chr2.2:52399465-52399484 None:intergenic 30.0%
AAAAGTTCATACCACTTCCT+AGG + chr2.2:52398302-52398321 None:intergenic 35.0%
AAACAGGCTTATTACTGCTA+AGG - chr2.2:52398412-52398431 MS.gene004569:intron 35.0%
AAGACAAGCAAAGAAACACA+AGG + chr2.2:52399332-52399351 None:intergenic 35.0%
AGAGACCAAAACAAGTAGTT+CGG + chr2.2:52399041-52399060 None:intergenic 35.0%
CGAAATTAGAGTGGAACAAA+TGG + chr2.2:52398543-52398562 None:intergenic 35.0%
GATAGAAACCGAAATTAGAG+TGG + chr2.2:52398552-52398571 None:intergenic 35.0%
TTTCTTATAAAAAGGACCCG+AGG + chr2.2:52399398-52399417 None:intergenic 35.0%
! GTTCGGGTTTAATTCTTTGT+CGG + chr2.2:52399024-52399043 None:intergenic 35.0%
! TAAACCCGAACTACTTGTTT+TGG - chr2.2:52399033-52399052 MS.gene004569:intron 35.0%
! TTCGGGTTTAATTCTTTGTC+GGG + chr2.2:52399023-52399042 None:intergenic 35.0%
!! ACTCGTCAAAGTATTTTCCA+AGG + chr2.2:52399892-52399911 None:intergenic 35.0%
AAACCCAGAACATGTGTGTA+TGG + chr2.2:52398695-52398714 None:intergenic 40.0%
AACAAATGGATACCTGAGCA+CGG + chr2.2:52398529-52398548 None:intergenic 40.0%
ATAGGTCATTTGGATGAGAG+CGG - chr2.2:52398458-52398477 MS.gene004569:intron 40.0%
CACTGAAATAAGTAGGGAAG+TGG - chr2.2:52399812-52399831 MS.gene004569:CDS 40.0%
CGATGTCATTGTGTTATCTC+TGG - chr2.2:52399150-52399169 MS.gene004569:intron 40.0%
GAGACCAAAACAAGTAGTTC+GGG + chr2.2:52399040-52399059 None:intergenic 40.0%
GTTTCAGTTCTGCTACAAAC+AGG - chr2.2:52398396-52398415 MS.gene004569:intron 40.0%
TACATCACTGATGTCTCTAG+TGG - chr2.2:52399666-52399685 MS.gene004569:intron 40.0%
TCAGCTGAACATAGGTCATT+TGG - chr2.2:52398448-52398467 MS.gene004569:intron 40.0%
ACAAATGGATACCTGAGCAC+GGG + chr2.2:52398528-52398547 None:intergenic 45.0%
ACAGTGGAATTGATCGCCTA+TGG - chr2.2:52399946-52399965 MS.gene004569:intron 45.0%
AGAATAAGCCCATCCAAACC+AGG + chr2.2:52398811-52398830 None:intergenic 45.0%
AGCACCATACACACATGTTC+TGG - chr2.2:52398688-52398707 MS.gene004569:intron 45.0%
AGCTCTACATTCCTAGGAAG+TGG - chr2.2:52398288-52398307 MS.gene004569:CDS 45.0%
CTTCCTAGGAATGTAGAGCT+CGG + chr2.2:52398288-52398307 None:intergenic 45.0%
GATGAGAGCGGTGTTTACAA+TGG - chr2.2:52398470-52398489 MS.gene004569:intron 45.0%
GCACCATACACACATGTTCT+GGG - chr2.2:52398689-52398708 MS.gene004569:intron 45.0%
GCAGAGGACAAATTCGTCTA+TGG + chr2.2:52399077-52399096 None:intergenic 45.0%
GCATCAGTTCAGCTGAACAT+AGG - chr2.2:52398440-52398459 MS.gene004569:intron 45.0%
TCCTCTGCCAGGTCTAAATT+TGG - chr2.2:52399089-52399108 MS.gene004569:intron 45.0%
! CGGTTTTCTTCTTCTGCCAT+AGG + chr2.2:52399965-52399984 None:intergenic 45.0%
!! TTCTCCACTTTTGCTCTCTG+TGG - chr2.2:52398497-52398516 MS.gene004569:intron 45.0%
!!! TTTTTTTATTTTTTATCAAT+TGG - chr2.2:52399738-52399757 MS.gene004569:CDS 5.0%
AGACGAATTTGTCCTCTGCC+AGG - chr2.2:52399078-52399097 MS.gene004569:intron 50.0%
ATCCAAACCAGGCCTAGACT+GGG + chr2.2:52398800-52398819 None:intergenic 50.0%
GAAGCCACAGAGAGCAAAAG+TGG + chr2.2:52398504-52398523 None:intergenic 50.0%
GCCAAATTTAGACCTGGCAG+AGG + chr2.2:52399093-52399112 None:intergenic 50.0%
GCCAGGTCTAAATTTGGCCT+CGG - chr2.2:52399095-52399114 MS.gene004569:intron 50.0%
TCACCGAGCTCTACATTCCT+AGG - chr2.2:52398282-52398301 MS.gene004569:CDS 50.0%
TCTAAATTTGGCCTCGGCGA+GGG - chr2.2:52399101-52399120 MS.gene004569:intron 50.0%
TTTCAGGGAGATGCTGACAG+TGG - chr2.2:52399930-52399949 MS.gene004569:intron 50.0%
!! AGTCTAGGCCTGGTTTGGAT+GGG - chr2.2:52398800-52398819 MS.gene004569:intron 50.0%
AGTTTCCCTCTGCCCAGTCT+AGG - chr2.2:52398785-52398804 MS.gene004569:intron 55.0%
CATCCAAACCAGGCCTAGAC+TGG + chr2.2:52398801-52398820 None:intergenic 55.0%
GCCGAGGCCAAATTTAGACC+TGG + chr2.2:52399099-52399118 None:intergenic 55.0%
GTCTAAATTTGGCCTCGGCG+AGG - chr2.2:52399100-52399119 MS.gene004569:intron 55.0%
!! CAGTCTAGGCCTGGTTTGGA+TGG - chr2.2:52398799-52398818 MS.gene004569:intron 55.0%
CTCAATTTGGTCCCTCGCCG+AGG + chr2.2:52399115-52399134 None:intergenic 60.0%
TGCCCAGTCTAGGCCTGGTT+TGG - chr2.2:52398795-52398814 MS.gene004569:intron 60.0%
ACCAGGCCTAGACTGGGCAG+AGG + chr2.2:52398794-52398813 None:intergenic 65.0%
CCAGGCCTAGACTGGGCAGA+GGG + chr2.2:52398793-52398812 None:intergenic 65.0%
CTGTGGCTTCACCCGTGCTC+AGG - chr2.2:52398514-52398533 MS.gene004569:intron 65.0%
CCCTCTGCCCAGTCTAGGCC+TGG - chr2.2:52398790-52398809 MS.gene004569:intron 70.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 52398260 52399998 52398260 ID=MS.gene004569
chr2.2 mRNA 52398260 52399998 52398260 ID=MS.gene004569.t1;Parent=MS.gene004569
chr2.2 exon 52399949 52399998 52399949 ID=MS.gene004569.t1.exon1;Parent=MS.gene004569.t1
chr2.2 CDS 52399949 52399998 52399949 ID=cds.MS.gene004569.t1;Parent=MS.gene004569.t1
chr2.2 exon 52399723 52399855 52399723 ID=MS.gene004569.t1.exon2;Parent=MS.gene004569.t1
chr2.2 CDS 52399723 52399855 52399723 ID=cds.MS.gene004569.t1;Parent=MS.gene004569.t1
chr2.2 exon 52398260 52398322 52398260 ID=MS.gene004569.t1.exon3;Parent=MS.gene004569.t1
chr2.2 CDS 52398260 52398322 52398260 ID=cds.MS.gene004569.t1;Parent=MS.gene004569.t1
Gene Sequence

>MS.gene004569

ATGCAGAACGAAGAAGGACAAATCACCGAGCTCTACATTCCTAGGAAGTGGTATGAACTTTTATAATCGCTTTTTTTATTATAATTGTTTTGAAAAATCAGTGTTTGATTTTGAACTGTTTTTGTTTTGTGGATTTGTTTCAGTTCTGCTACAAACAGGCTTATTACTGCTAAGGATCATGCATCAGTTCAGCTGAACATAGGTCATTTGGATGAGAGCGGTGTTTACAATGGTCACTTCTCCACTTTTGCTCTCTGTGGCTTCACCCGTGCTCAGGTATCCATTTGTTCCACTCTAATTTCGGTTTCTATCTTTGTTATTTTGGTGATTTGCGTTGAATTAAGAGTAAATAATTAGGGTTTTGTCTGTTTTTTTTGCTTATTATGTTGATCTAATTGTAAATTTGTTTTGTTTTTAATTAAGCTATAAGCACCATACACACATGTTCTGGGTTTTTAAATCGAATTTAGAAATTATTGTGTATACTGTAAGAATTATGTATCATTTATTCAAGACAACAAACATAGTTTCCCTCTGCCCAGTCTAGGCCTGGTTTGGATGGGCTTATTCTTATTTTTGAGCTTGTACAAAACAGCTTATGCAAATAAATAAGCTTATATGTATTATTCATAAGCTTGTCAGGCAATTTATGAAAAACAGATTATGATGAGACCAATATAACATAATTTCTTAAAAGCTTATTTATTTGCATACGCTATGTTTCATAAGCTAAAAAAATAAGGCAAACGGTCTTTTAGTACCCGACAAAGAATTAAACCCGAACTACTTGTTTTGGTCTCTCTGCTATGATGAGCCATAGACGAATTTGTCCTCTGCCAGGTCTAAATTTGGCCTCGGCGAGGGACCAAATTGAGTCTTCACTCTTTTTTCGATGTCATTGTGTTATCTCTGGATATGATTTGAATTAAATCATGTTGAAAGTGTTGATTCTATATATCTTATATTGGTATTTGCCTGTTTATTAAAAACTACTCGTTTTCGCTTATACCAATATATCTTATATTGGTATAAGCGAGCCTGTTTATTAAAAACTTATTTTGGGTTTTTGCCTTGTGTTTCTTTGCTTGTCTTTTAGCAGTTTGCTTCGCATTGTTTTAACTTAAAATTTATACTTCCTCGGGTCCTTTTTATAAGAAACAAATGGTTCAACAGGAGTTAATGTATTTGGTCTATATTATGAACCAAATACATCAACTTTATGGTCAACTAAGGTTGAATGCAGAAAACATAGTGAAATTAACTAATTTGTCTATTTCCTTGCCTAAGTTTACATATTATCAGTATGGTTTCTTTTCAAATTTTGCAATTGTGTCAAACTGACCAATGTAAGCTGAGAAATTTGACAAATTTTCTGCATGAATTCTTCGCATATTATAACTACTCTATACATCACTGATGTCTCTAGTGGAGTATTTTTTGAATGCAGAAAACACAGTGAAATTAACTAATGTGTAACATTTTTTTATTTTTTATCAATTGGCACTCTGAAAAATGAAAAATGTCGCTAAAACTGTGATTGTTATTAGAAACACACTGAAATAAGTAGGGAAGTGGATGAAAACCTTTATATCTATGTTGGACATATTTTATGTATTAATTCATGTCATGCCTTGGAAAATACTTTGACGAGTTATTGATGCTTGTTTTATTTTCAGGGAGATGCTGACAGTGGAATTGATCGCCTATGGCAGAAGAAGAAAACCGAGCTTAAGCAGTAG
Protein sequence

>MS.gene004569.t1

MQNEEGQITELYIPRKCSATNRLITAKDHASVQLNIGHLDESGVYNGHFSTFALCGFTRAQGDADSGIDRLWQKKKTELKQ