AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0829570


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0829570 MtrunA17_Chr2g0281101 95.714 140 6 0 1 140 1 140 1.26e-99 281
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0829570 AT4G21445.1 77.778 90 20 0 51 140 65 154 2.74e-49 155

Find 43 sgRNAs with CRISPR-Local

Find 130 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAACTTCATCAACAGAAAA+AGG 0.207487 5_4:-2582126 Msa0829570:three_prime_UTR
TTATCTTCCTTTGTGCTATC+AGG 0.247231 5_4:+2582787 None:intergenic
TGTTTGAAGACATGATTTAT+AGG 0.337289 5_4:+2582866 None:intergenic
TTTAACTTAATGTGAGAGAT+TGG 0.338033 5_4:+2582966 None:intergenic
AATTGTACTTTCTCATGAAT+CGG 0.359210 5_4:-2582164 Msa0829570:three_prime_UTR
AAATTTGTAAAGAAATGATA+TGG 0.389251 5_4:+2582081 None:intergenic
TGTTCTTCAGTGGGATGATT+CGG 0.397395 5_4:-2582373 Msa0829570:CDS
TCCTAAAAGACAAGCTCAAA+AGG 0.401395 5_4:-2582416 Msa0829570:CDS
GCTGGTTTGGTTGAGATGTC+TGG 0.414517 5_4:-2582687 Msa0829570:CDS
GACACTGGAAGAAGCTGGTT+TGG 0.416136 5_4:-2582700 Msa0829570:CDS
GAAAATTGATCAGCAATAGA+AGG 0.425165 5_4:+2582254 None:intergenic
GTTTGAAGACATGATTTATA+GGG 0.432921 5_4:+2582867 None:intergenic
ATTGTACTTTCTCATGAATC+GGG 0.441787 5_4:-2582163 Msa0829570:three_prime_UTR
TGATTTGTAACAAGGTTTGA+AGG 0.448700 5_4:+2582828 None:intergenic
CCAGCATTGAGCTCCTCTAC+TGG 0.451355 5_4:+2582456 None:intergenic
CTTTGTGTGGAGGAGGGTGA+TGG 0.454412 5_4:+2583015 None:intergenic
CTCTTGTGTTATTCTAAACA+AGG 0.466068 5_4:+2582201 None:intergenic
CTGTTAGCTTTGTGTGGAGG+AGG 0.467927 5_4:+2583008 None:intergenic
CCTTATCTGTTAGCTTTGTG+TGG 0.479941 5_4:+2583002 None:intergenic
TGATTCTGCTGTTCTTCAGT+GGG 0.485721 5_4:-2582382 Msa0829570:CDS
CCAGTAGAGGAGCTCAATGC+TGG 0.486468 5_4:-2582456 Msa0829570:CDS
TTCAATTATAACTATGTAGT+GGG 0.505484 5_4:+2582300 None:intergenic
GATTTGTAACAAGGTTTGAA+GGG 0.518410 5_4:+2582829 None:intergenic
CAGAAGAGAAGAAGAGTGAG+AGG 0.523957 5_4:-2582734 Msa0829570:CDS
TGAGAGATTGGAATGGGTTG+AGG 0.528179 5_4:+2582978 None:intergenic
TTGATTCTGCTGTTCTTCAG+TGG 0.529384 5_4:-2582383 Msa0829570:CDS
CCACACAAAGCTAACAGATA+AGG 0.541206 5_4:-2583002 Msa0829570:five_prime_UTR
TTTGTGTGGAGGAGGGTGAT+GGG 0.541825 5_4:+2583016 None:intergenic
AAGAAATGATATGGAGAACA+TGG 0.543069 5_4:+2582090 None:intergenic
TATCTGTTAGCTTTGTGTGG+AGG 0.550231 5_4:+2583005 None:intergenic
ATTCAATTATAACTATGTAG+TGG 0.555175 5_4:+2582299 None:intergenic
CTTAATGTGAGAGATTGGAA+TGG 0.560459 5_4:+2582971 None:intergenic
TGTTAGCTTTGTGTGGAGGA+GGG 0.565168 5_4:+2583009 None:intergenic
CCTAAAAGACAAGCTCAAAA+GGG 0.568726 5_4:-2582415 Msa0829570:CDS
TTAATGTGAGAGATTGGAAT+GGG 0.577438 5_4:+2582972 None:intergenic
GAGAGATTGGAATGGGTTGA+GGG 0.578878 5_4:+2582979 None:intergenic
ACAAGAAGGGTGTCCAGTAG+AGG 0.582601 5_4:-2582469 Msa0829570:CDS
ATGCTGGAAAGGTATGTGAT+TGG 0.593475 5_4:-2582440 Msa0829570:CDS
AAGTGATATCAGAACAAGAA+GGG 0.598781 5_4:-2582482 Msa0829570:CDS
AGAGGAGCTCAATGCTGGAA+AGG 0.602474 5_4:-2582451 Msa0829570:CDS
AAAGTGATATCAGAACAAGA+AGG 0.604912 5_4:-2582483 Msa0829570:CDS
TGTGTCTATGATTTGTAACA+AGG 0.620077 5_4:+2582820 None:intergenic
AAACAAGCCTGATAGCACAA+AGG 0.711054 5_4:-2582794 Msa0829570:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTACAACTTTATATTTTA+GGG - chr5_4:2582754-2582773 Msa0829570:CDS 10.0%
!!! AATTACAACTTTATATTTTA+GGG - chr5_4:2582754-2582773 Msa0829570:CDS 10.0%
!! AGAAGAAAAAGAATTAAAAT+TGG + chr5_4:2582690-2582709 None:intergenic 15.0%
!!! GAATTACAACTTTATATTTT+AGG - chr5_4:2582753-2582772 Msa0829570:CDS 15.0%
!!! ATTACAACTTTATATTTTAG+GGG - chr5_4:2582755-2582774 Msa0829570:CDS 15.0%
!! AAATTTGTAAAGAAATGATA+TGG + chr5_4:2582955-2582974 None:intergenic 15.0%
!! AGAAGAAAAAGAATTAAAAT+TGG + chr5_4:2582690-2582709 None:intergenic 15.0%
!!! GAATTACAACTTTATATTTT+AGG - chr5_4:2582753-2582772 Msa0829570:CDS 15.0%
!!! ATTACAACTTTATATTTTAG+GGG - chr5_4:2582755-2582774 Msa0829570:CDS 15.0%
!! AAATTTGTAAAGAAATGATA+TGG + chr5_4:2582955-2582974 None:intergenic 15.0%
!! CACAAACAATATGAAAATTT+AGG + chr5_4:2582502-2582521 None:intergenic 20.0%
!! TTCAATTATAACTATGTAGT+GGG + chr5_4:2582736-2582755 None:intergenic 20.0%
!! ATTCAATTATAACTATGTAG+TGG + chr5_4:2582737-2582756 None:intergenic 20.0%
!!! TTACAACTTTATATTTTAGG+GGG - chr5_4:2582756-2582775 Msa0829570:CDS 20.0%
!!! TTATTCTAAACAAGGATTTT+TGG + chr5_4:2582827-2582846 None:intergenic 20.0%
!! CACAAACAATATGAAAATTT+AGG + chr5_4:2582502-2582521 None:intergenic 20.0%
!! TTCAATTATAACTATGTAGT+GGG + chr5_4:2582736-2582755 None:intergenic 20.0%
!! ATTCAATTATAACTATGTAG+TGG + chr5_4:2582737-2582756 None:intergenic 20.0%
!!! TTACAACTTTATATTTTAGG+GGG - chr5_4:2582756-2582775 Msa0829570:CDS 20.0%
!!! TTATTCTAAACAAGGATTTT+TGG + chr5_4:2582827-2582846 None:intergenic 20.0%
!! TTTAACTTAATGTGAGAGAT+TGG + chr5_4:2582070-2582089 None:intergenic 25.0%
! CTAAAAAAAAGAAGATAGCA+AGG - chr5_4:2582090-2582109 Msa0829570:three_prime_UTR 25.0%
!! TATTTTCAATCTCTTTCTCT+GGG + chr5_4:2582126-2582145 None:intergenic 25.0%
!! TTATTTTCAATCTCTTTCTC+TGG + chr5_4:2582127-2582146 None:intergenic 25.0%
! GTTTGAAGACATGATTTATA+GGG + chr5_4:2582169-2582188 None:intergenic 25.0%
! TGTTTGAAGACATGATTTAT+AGG + chr5_4:2582170-2582189 None:intergenic 25.0%
!! GAAAATTTAGGACATATACT+AGG + chr5_4:2582490-2582509 None:intergenic 25.0%
! AATTGTACTTTCTCATGAAT+CGG - chr5_4:2582869-2582888 Msa0829570:CDS 25.0%
!! TTTAACTTAATGTGAGAGAT+TGG + chr5_4:2582070-2582089 None:intergenic 25.0%
! CTAAAAAAAAGAAGATAGCA+AGG - chr5_4:2582090-2582109 Msa0829570:three_prime_UTR 25.0%
!! TATTTTCAATCTCTTTCTCT+GGG + chr5_4:2582126-2582145 None:intergenic 25.0%
!! TTATTTTCAATCTCTTTCTC+TGG + chr5_4:2582127-2582146 None:intergenic 25.0%
! GTTTGAAGACATGATTTATA+GGG + chr5_4:2582169-2582188 None:intergenic 25.0%
! TGTTTGAAGACATGATTTAT+AGG + chr5_4:2582170-2582189 None:intergenic 25.0%
!! GAAAATTTAGGACATATACT+AGG + chr5_4:2582490-2582509 None:intergenic 25.0%
! AATTGTACTTTCTCATGAAT+CGG - chr5_4:2582869-2582888 Msa0829570:CDS 25.0%
TTAATGTGAGAGATTGGAAT+GGG + chr5_4:2582064-2582083 None:intergenic 30.0%
GATTTGTAACAAGGTTTGAA+GGG + chr5_4:2582207-2582226 None:intergenic 30.0%
! TGATTTGTAACAAGGTTTGA+AGG + chr5_4:2582208-2582227 None:intergenic 30.0%
! TGTGTCTATGATTTGTAACA+AGG + chr5_4:2582216-2582235 None:intergenic 30.0%
CAATGAAGAAACAAAATCCT+AGG + chr5_4:2582448-2582467 None:intergenic 30.0%
!! CTAGGATTTTGTTTCTTCAT+TGG - chr5_4:2582446-2582465 Msa0829570:CDS 30.0%
AAAGTGATATCAGAACAAGA+AGG - chr5_4:2582550-2582569 Msa0829570:intron 30.0%
AAGTGATATCAGAACAAGAA+GGG - chr5_4:2582551-2582570 Msa0829570:intron 30.0%
GAAAATTGATCAGCAATAGA+AGG + chr5_4:2582782-2582801 None:intergenic 30.0%
!!! TTCCTTTTTTGTGCAAAATG+TGG - chr5_4:2582799-2582818 Msa0829570:CDS 30.0%
! CTCTTGTGTTATTCTAAACA+AGG + chr5_4:2582835-2582854 None:intergenic 30.0%
ATTGTACTTTCTCATGAATC+GGG - chr5_4:2582870-2582889 Msa0829570:CDS 30.0%
TGAACTTCATCAACAGAAAA+AGG - chr5_4:2582907-2582926 Msa0829570:five_prime_UTR 30.0%
AAGAAATGATATGGAGAACA+TGG + chr5_4:2582946-2582965 None:intergenic 30.0%
TTAATGTGAGAGATTGGAAT+GGG + chr5_4:2582064-2582083 None:intergenic 30.0%
GATTTGTAACAAGGTTTGAA+GGG + chr5_4:2582207-2582226 None:intergenic 30.0%
! TGATTTGTAACAAGGTTTGA+AGG + chr5_4:2582208-2582227 None:intergenic 30.0%
! TGTGTCTATGATTTGTAACA+AGG + chr5_4:2582216-2582235 None:intergenic 30.0%
CAATGAAGAAACAAAATCCT+AGG + chr5_4:2582448-2582467 None:intergenic 30.0%
!! CTAGGATTTTGTTTCTTCAT+TGG - chr5_4:2582446-2582465 Msa0829570:CDS 30.0%
AAAGTGATATCAGAACAAGA+AGG - chr5_4:2582550-2582569 Msa0829570:intron 30.0%
AAGTGATATCAGAACAAGAA+GGG - chr5_4:2582551-2582570 Msa0829570:intron 30.0%
GAAAATTGATCAGCAATAGA+AGG + chr5_4:2582782-2582801 None:intergenic 30.0%
!!! TTCCTTTTTTGTGCAAAATG+TGG - chr5_4:2582799-2582818 Msa0829570:CDS 30.0%
! CTCTTGTGTTATTCTAAACA+AGG + chr5_4:2582835-2582854 None:intergenic 30.0%
ATTGTACTTTCTCATGAATC+GGG - chr5_4:2582870-2582889 Msa0829570:CDS 30.0%
TGAACTTCATCAACAGAAAA+AGG - chr5_4:2582907-2582926 Msa0829570:five_prime_UTR 30.0%
AAGAAATGATATGGAGAACA+TGG + chr5_4:2582946-2582965 None:intergenic 30.0%
CTTAATGTGAGAGATTGGAA+TGG + chr5_4:2582065-2582084 None:intergenic 35.0%
TTATCTTCCTTTGTGCTATC+AGG + chr5_4:2582249-2582268 None:intergenic 35.0%
TCCTAAAAGACAAGCTCAAA+AGG - chr5_4:2582617-2582636 Msa0829570:intron 35.0%
CCTAAAAGACAAGCTCAAAA+GGG - chr5_4:2582618-2582637 Msa0829570:intron 35.0%
! AGCCACATTTTGCACAAAAA+AGG + chr5_4:2582804-2582823 None:intergenic 35.0%
CTTAATGTGAGAGATTGGAA+TGG + chr5_4:2582065-2582084 None:intergenic 35.0%
TTATCTTCCTTTGTGCTATC+AGG + chr5_4:2582249-2582268 None:intergenic 35.0%
TCCTAAAAGACAAGCTCAAA+AGG - chr5_4:2582617-2582636 Msa0829570:intron 35.0%
CCTAAAAGACAAGCTCAAAA+GGG - chr5_4:2582618-2582637 Msa0829570:intron 35.0%
! AGCCACATTTTGCACAAAAA+AGG + chr5_4:2582804-2582823 None:intergenic 35.0%
!! TATCTGTTAGCTTTGTGTGG+AGG + chr5_4:2582031-2582050 None:intergenic 40.0%
!! CCTTATCTGTTAGCTTTGTG+TGG + chr5_4:2582034-2582053 None:intergenic 40.0%
CCACACAAAGCTAACAGATA+AGG - chr5_4:2582031-2582050 Msa0829570:three_prime_UTR 40.0%
AAACAAGCCTGATAGCACAA+AGG - chr5_4:2582239-2582258 Msa0829570:three_prime_UTR 40.0%
! GAGGAAAACGTTTTTGACAC+TGG - chr5_4:2582318-2582337 Msa0829570:three_prime_UTR 40.0%
! TTTTTGACACTGGAAGAAGC+TGG - chr5_4:2582328-2582347 Msa0829570:three_prime_UTR 40.0%
! GCGTTTTCTATGTCGTCTAA+CGG - chr5_4:2582384-2582403 Msa0829570:CDS 40.0%
CCTTAACTCTGTTGTCTTGT+CGG - chr5_4:2582413-2582432 Msa0829570:CDS 40.0%
! ATGCTGGAAAGGTATGTGAT+TGG - chr5_4:2582593-2582612 Msa0829570:intron 40.0%
! CCCTTTTGAGCTTGTCTTTT+AGG + chr5_4:2582621-2582640 None:intergenic 40.0%
TTGATTCTGCTGTTCTTCAG+TGG - chr5_4:2582650-2582669 Msa0829570:CDS 40.0%
TGATTCTGCTGTTCTTCAGT+GGG - chr5_4:2582651-2582670 Msa0829570:CDS 40.0%
TGTTCTTCAGTGGGATGATT+CGG - chr5_4:2582660-2582679 Msa0829570:CDS 40.0%
!! TATCTGTTAGCTTTGTGTGG+AGG + chr5_4:2582031-2582050 None:intergenic 40.0%
!! CCTTATCTGTTAGCTTTGTG+TGG + chr5_4:2582034-2582053 None:intergenic 40.0%
CCACACAAAGCTAACAGATA+AGG - chr5_4:2582031-2582050 Msa0829570:three_prime_UTR 40.0%
AAACAAGCCTGATAGCACAA+AGG - chr5_4:2582239-2582258 Msa0829570:three_prime_UTR 40.0%
! GAGGAAAACGTTTTTGACAC+TGG - chr5_4:2582318-2582337 Msa0829570:three_prime_UTR 40.0%
! TTTTTGACACTGGAAGAAGC+TGG - chr5_4:2582328-2582347 Msa0829570:three_prime_UTR 40.0%
! GCGTTTTCTATGTCGTCTAA+CGG - chr5_4:2582384-2582403 Msa0829570:CDS 40.0%
CCTTAACTCTGTTGTCTTGT+CGG - chr5_4:2582413-2582432 Msa0829570:CDS 40.0%
! ATGCTGGAAAGGTATGTGAT+TGG - chr5_4:2582593-2582612 Msa0829570:intron 40.0%
! CCCTTTTGAGCTTGTCTTTT+AGG + chr5_4:2582621-2582640 None:intergenic 40.0%
TTGATTCTGCTGTTCTTCAG+TGG - chr5_4:2582650-2582669 Msa0829570:CDS 40.0%
TGATTCTGCTGTTCTTCAGT+GGG - chr5_4:2582651-2582670 Msa0829570:CDS 40.0%
TGTTCTTCAGTGGGATGATT+CGG - chr5_4:2582660-2582679 Msa0829570:CDS 40.0%
!! TGTTAGCTTTGTGTGGAGGA+GGG + chr5_4:2582027-2582046 None:intergenic 45.0%
!! GAGAGATTGGAATGGGTTGA+GGG + chr5_4:2582057-2582076 None:intergenic 45.0%
!! TGAGAGATTGGAATGGGTTG+AGG + chr5_4:2582058-2582077 None:intergenic 45.0%
CAGAAGAGAAGAAGAGTGAG+AGG - chr5_4:2582299-2582318 Msa0829570:three_prime_UTR 45.0%
CCGACAAGACAACAGAGTTA+AGG + chr5_4:2582416-2582435 None:intergenic 45.0%
CTTGTCGGATGATATGTCCT+AGG - chr5_4:2582428-2582447 Msa0829570:CDS 45.0%
!! TGTTAGCTTTGTGTGGAGGA+GGG + chr5_4:2582027-2582046 None:intergenic 45.0%
!! GAGAGATTGGAATGGGTTGA+GGG + chr5_4:2582057-2582076 None:intergenic 45.0%
!! TGAGAGATTGGAATGGGTTG+AGG + chr5_4:2582058-2582077 None:intergenic 45.0%
CAGAAGAGAAGAAGAGTGAG+AGG - chr5_4:2582299-2582318 Msa0829570:three_prime_UTR 45.0%
CCGACAAGACAACAGAGTTA+AGG + chr5_4:2582416-2582435 None:intergenic 45.0%
CTTGTCGGATGATATGTCCT+AGG - chr5_4:2582428-2582447 Msa0829570:CDS 45.0%
TTTGTGTGGAGGAGGGTGAT+GGG + chr5_4:2582020-2582039 None:intergenic 50.0%
!! CTGTTAGCTTTGTGTGGAGG+AGG + chr5_4:2582028-2582047 None:intergenic 50.0%
GACACTGGAAGAAGCTGGTT+TGG - chr5_4:2582333-2582352 Msa0829570:three_prime_UTR 50.0%
!! GCTGGTTTGGTTGAGATGTC+TGG - chr5_4:2582346-2582365 Msa0829570:exon 50.0%
!! ACAAGAAGGGTGTCCAGTAG+AGG - chr5_4:2582564-2582583 Msa0829570:intron 50.0%
AGAGGAGCTCAATGCTGGAA+AGG - chr5_4:2582582-2582601 Msa0829570:intron 50.0%
TTTGTGTGGAGGAGGGTGAT+GGG + chr5_4:2582020-2582039 None:intergenic 50.0%
!! CTGTTAGCTTTGTGTGGAGG+AGG + chr5_4:2582028-2582047 None:intergenic 50.0%
GACACTGGAAGAAGCTGGTT+TGG - chr5_4:2582333-2582352 Msa0829570:three_prime_UTR 50.0%
!! GCTGGTTTGGTTGAGATGTC+TGG - chr5_4:2582346-2582365 Msa0829570:exon 50.0%
!! ACAAGAAGGGTGTCCAGTAG+AGG - chr5_4:2582564-2582583 Msa0829570:intron 50.0%
AGAGGAGCTCAATGCTGGAA+AGG - chr5_4:2582582-2582601 Msa0829570:intron 50.0%
CTTTGTGTGGAGGAGGGTGA+TGG + chr5_4:2582021-2582040 None:intergenic 55.0%
! CCAGCATTGAGCTCCTCTAC+TGG + chr5_4:2582580-2582599 None:intergenic 55.0%
CCAGTAGAGGAGCTCAATGC+TGG - chr5_4:2582577-2582596 Msa0829570:intron 55.0%
CTTTGTGTGGAGGAGGGTGA+TGG + chr5_4:2582021-2582040 None:intergenic 55.0%
! CCAGCATTGAGCTCCTCTAC+TGG + chr5_4:2582580-2582599 None:intergenic 55.0%
CCAGTAGAGGAGCTCAATGC+TGG - chr5_4:2582577-2582596 Msa0829570:intron 55.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 2582017 2583038 2582017 ID=Msa0829570;Name=Msa0829570
chr5_4 mRNA 2582017 2583038 2582017 ID=Msa0829570-mRNA-1;Parent=Msa0829570;Name=Msa0829570-mRNA-1;_AED=0.06;_eAED=0.06;_QI=134|1|1|1|1|1|2|342|140
chr5_4 exon 2582017 2582526 2582017 ID=Msa0829570-mRNA-1:exon:890;Parent=Msa0829570-mRNA-1
chr5_4 exon 2582650 2583038 2582650 ID=Msa0829570-mRNA-1:exon:889;Parent=Msa0829570-mRNA-1
chr5_4 five_prime_UTR 2582905 2583038 2582905 ID=Msa0829570-mRNA-1:five_prime_utr;Parent=Msa0829570-mRNA-1
chr5_4 CDS 2582650 2582904 2582650 ID=Msa0829570-mRNA-1:cds;Parent=Msa0829570-mRNA-1
chr5_4 CDS 2582359 2582526 2582359 ID=Msa0829570-mRNA-1:cds;Parent=Msa0829570-mRNA-1
chr5_4 three_prime_UTR 2582017 2582358 2582017 ID=Msa0829570-mRNA-1:three_prime_utr;Parent=Msa0829570-mRNA-1
Gene Sequence

>Msa0829570

ATGATTTGTCTACAACCCTATAAATCATGTCTTCAAACAACATTTGTATTCAGCCCTTCAAACCTTGTTACAAATCATAGACACACACAAACAAGCCTGATAGCACAAAGGAAGATAAAAGTACATAGAAGAAATGTCAAATGCAATGCAGAAGAGAAGAAGAGTGAGAGGAAAACGTTTTTGACACTGGAAGAAGCTGGTTTGGTTGAGATGTCTGGATTGAGCACTCATGAGCGTTTTCTATGTCGTCTAACGATATCTTCACTGAATTTACTAAAAGTGATATCAGAACAAGAAGGGTGTCCAGTAGAGGAGCTCAATGCTGGAAAGGTATGTGATTGGTTCCTAAAAGACAAGCTCAAAAGGGAGCAGAACATTGATTCTGCTGTTCTTCAGTGGGATGATTCGGATTTCCAATTTTAA

Protein sequence

>Msa0829570

MICLQPYKSCLQTTFVFSPSNLVTNHRHTQTSLIAQRKIKVHRRNVKCNAEEKKSERKTFLTLEEAGLVEMSGLSTHERFLCRLTISSLNLLKVISEQEGCPVEELNAGKVCDWFLKDKLKREQNIDSAVLQWDDSDFQF*