AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0380430


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0380430 MtrunA17_Chr3g0146001 98.649 74 1 0 17 90 320 393 2.76e-47 154
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0380430 AT4G35250.1 83.784 74 12 0 17 90 322 395 1.28e-39 135

Find 21 sgRNAs with CRISPR-Local

Find 134 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTAATGTAATTATATCTT+TGG 0.230175 3_1:+82096175 None:intergenic
ATAAATTAACCAATGTGTTT+TGG 0.250609 3_1:+82095935 None:intergenic
CTGACGAGTGAGTCTTAAAA+TGG 0.323717 3_1:+82096789 None:intergenic
CACTTCTCACTATGTACATT+TGG 0.339648 3_1:+82095870 None:intergenic
TTATTCTTAAATACGCTTGC+CGG 0.341313 3_1:-82096017 Msa0380430:three_prime_UTR
TACATTAGAGAAGTATTTGC+AGG 0.361917 3_1:-82096162 Msa0380430:CDS
TTCTTACGTGGGCTTACAAT+TGG 0.375224 3_1:-82095976 Msa0380430:three_prime_UTR
AAATATCTGATTGTTTCGAC+TGG 0.443973 3_1:+82096096 None:intergenic
TGCATACGAGGTAATGTTGT+GGG 0.476275 3_1:-82096050 Msa0380430:three_prime_UTR
TATTTATGAATTGTGTCAGT+TGG 0.477239 3_1:-82095720 Msa0380430:three_prime_UTR
GAACATATTGAAGAAGTTGA+AGG 0.506295 3_1:-82096129 Msa0380430:CDS
AAATGATGTTGCTGACAGAT+TGG 0.529217 3_1:-82096744 Msa0380430:CDS
AGGTTGTATGTCTCCGCCAT+TGG 0.538477 3_1:+82096212 None:intergenic
GTGAGTCTTAAAATGGAGAC+AGG 0.552942 3_1:+82096796 None:intergenic
GACACAATTCATAAATACTT+AGG 0.556487 3_1:+82095726 None:intergenic
GCGGAGACATACAACCTACT+TGG 0.567860 3_1:-82096206 Msa0380430:CDS
AATATCTGATTGTTTCGACT+GGG 0.571429 3_1:+82096097 None:intergenic
CTTTGGTATCGACACCAAGT+AGG 0.582966 3_1:+82096192 None:intergenic
TGTATTCATCCAAAACACAT+TGG 0.600129 3_1:-82095944 Msa0380430:three_prime_UTR
TTGCATACGAGGTAATGTTG+TGG 0.612997 3_1:-82096051 Msa0380430:three_prime_UTR
ATGATTTGTAATTGCATACG+AGG 0.645440 3_1:-82096062 Msa0380430:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTTCTCTTTCATTTTAA+TGG - chr3_1:82096164-82096183 Msa0380430:CDS 15.0%
!! AATAAAAAAACAATATACAC+CGG + chr3_1:82096478-82096497 None:intergenic 15.0%
!!! TATTTTCTCTTTCATTTTAA+TGG - chr3_1:82096164-82096183 Msa0380430:CDS 15.0%
!! AATAAAAAAACAATATACAC+CGG + chr3_1:82096478-82096497 None:intergenic 15.0%
!! ATACAAAAAAAAGAAGAAGA+AGG + chr3_1:82095831-82095850 None:intergenic 20.0%
!! CTCTAATGTAATTATATCTT+TGG + chr3_1:82096301-82096320 None:intergenic 20.0%
!!! TTGTTTTTTTATTTCTTACG+TGG - chr3_1:82096485-82096504 Msa0380430:intron 20.0%
!!! TGTTTTTTTATTTCTTACGT+GGG - chr3_1:82096486-82096505 Msa0380430:intron 20.0%
!!! ATAAATTAACCAATGTGTTT+TGG + chr3_1:82096541-82096560 None:intergenic 20.0%
!! ATACAAAAAAAAGAAGAAGA+AGG + chr3_1:82095831-82095850 None:intergenic 20.0%
!! CTCTAATGTAATTATATCTT+TGG + chr3_1:82096301-82096320 None:intergenic 20.0%
!!! TTGTTTTTTTATTTCTTACG+TGG - chr3_1:82096485-82096504 Msa0380430:intron 20.0%
!!! TGTTTTTTTATTTCTTACGT+GGG - chr3_1:82096486-82096505 Msa0380430:intron 20.0%
!!! ATAAATTAACCAATGTGTTT+TGG + chr3_1:82096541-82096560 None:intergenic 20.0%
! TGCAACAAGTATAATGATTT+AGG + chr3_1:82095789-82095808 None:intergenic 25.0%
!! AATCATTATACTTGTTGCAT+TGG - chr3_1:82095790-82095809 Msa0380430:three_prime_UTR 25.0%
!! TTTTTGTTACATTGCTTGAA+TGG - chr3_1:82095873-82095892 Msa0380430:three_prime_UTR 25.0%
! GAAATAAACCTGTAAGAATA+GGG + chr3_1:82096054-82096073 None:intergenic 25.0%
!!! TATCAAATAATAGTGTTGGT+CGG + chr3_1:82096089-82096108 None:intergenic 25.0%
! GATGTATCAAATAATAGTGT+TGG + chr3_1:82096093-82096112 None:intergenic 25.0%
! GAGAAAATATTATATGCACT+AGG + chr3_1:82096153-82096172 None:intergenic 25.0%
!!! TTTCTCTTTCATTTTAATGG+TGG - chr3_1:82096167-82096186 Msa0380430:CDS 25.0%
! GACACAATTCATAAATACTT+AGG + chr3_1:82096750-82096769 None:intergenic 25.0%
! TATTTATGAATTGTGTCAGT+TGG - chr3_1:82096753-82096772 Msa0380430:CDS 25.0%
! TGCAACAAGTATAATGATTT+AGG + chr3_1:82095789-82095808 None:intergenic 25.0%
!! AATCATTATACTTGTTGCAT+TGG - chr3_1:82095790-82095809 Msa0380430:three_prime_UTR 25.0%
!! TTTTTGTTACATTGCTTGAA+TGG - chr3_1:82095873-82095892 Msa0380430:three_prime_UTR 25.0%
! GAAATAAACCTGTAAGAATA+GGG + chr3_1:82096054-82096073 None:intergenic 25.0%
!!! TATCAAATAATAGTGTTGGT+CGG + chr3_1:82096089-82096108 None:intergenic 25.0%
! GATGTATCAAATAATAGTGT+TGG + chr3_1:82096093-82096112 None:intergenic 25.0%
! GAGAAAATATTATATGCACT+AGG + chr3_1:82096153-82096172 None:intergenic 25.0%
!!! TTTCTCTTTCATTTTAATGG+TGG - chr3_1:82096167-82096186 Msa0380430:CDS 25.0%
! GACACAATTCATAAATACTT+AGG + chr3_1:82096750-82096769 None:intergenic 25.0%
! TATTTATGAATTGTGTCAGT+TGG - chr3_1:82096753-82096772 Msa0380430:CDS 25.0%
AAAAAGAAGAAGAAGGACTT+GGG + chr3_1:82095824-82095843 None:intergenic 30.0%
AAAAAAGAAGAAGAAGGACT+TGG + chr3_1:82095825-82095844 None:intergenic 30.0%
TGCATTACTACATTTCCATT+GGG - chr3_1:82095942-82095961 Msa0380430:three_prime_UTR 30.0%
GGAAATAAACCTGTAAGAAT+AGG + chr3_1:82096055-82096074 None:intergenic 30.0%
CAGGTTTATTTCCATTCTAT+TGG - chr3_1:82096062-82096081 Msa0380430:three_prime_UTR 30.0%
CATGCCTATAGTTGATTATA+CGG - chr3_1:82096195-82096214 Msa0380430:CDS 30.0%
ATGCCTATAGTTGATTATAC+GGG - chr3_1:82096196-82096215 Msa0380430:CDS 30.0%
TTTCCCGTATAATCAACTAT+AGG + chr3_1:82096202-82096221 None:intergenic 30.0%
ATTATACGGGAAATATTTGC+AGG - chr3_1:82096209-82096228 Msa0380430:CDS 30.0%
!! TACATTAGAGAAGTATTTGC+AGG - chr3_1:82096311-82096330 Msa0380430:intron 30.0%
GAACATATTGAAGAAGTTGA+AGG - chr3_1:82096344-82096363 Msa0380430:intron 30.0%
AATATCTGATTGTTTCGACT+GGG + chr3_1:82096379-82096398 None:intergenic 30.0%
AAATATCTGATTGTTTCGAC+TGG + chr3_1:82096380-82096399 None:intergenic 30.0%
! ATGATTTGTAATTGCATACG+AGG - chr3_1:82096411-82096430 Msa0380430:intron 30.0%
TTATTCTTAAATACGCTTGC+CGG - chr3_1:82096456-82096475 Msa0380430:intron 30.0%
TGTATTCATCCAAAACACAT+TGG - chr3_1:82096529-82096548 Msa0380430:intron 30.0%
AAAAAGAAGAAGAAGGACTT+GGG + chr3_1:82095824-82095843 None:intergenic 30.0%
AAAAAAGAAGAAGAAGGACT+TGG + chr3_1:82095825-82095844 None:intergenic 30.0%
TGCATTACTACATTTCCATT+GGG - chr3_1:82095942-82095961 Msa0380430:three_prime_UTR 30.0%
GGAAATAAACCTGTAAGAAT+AGG + chr3_1:82096055-82096074 None:intergenic 30.0%
CAGGTTTATTTCCATTCTAT+TGG - chr3_1:82096062-82096081 Msa0380430:three_prime_UTR 30.0%
CATGCCTATAGTTGATTATA+CGG - chr3_1:82096195-82096214 Msa0380430:CDS 30.0%
ATGCCTATAGTTGATTATAC+GGG - chr3_1:82096196-82096215 Msa0380430:CDS 30.0%
TTTCCCGTATAATCAACTAT+AGG + chr3_1:82096202-82096221 None:intergenic 30.0%
ATTATACGGGAAATATTTGC+AGG - chr3_1:82096209-82096228 Msa0380430:CDS 30.0%
!! TACATTAGAGAAGTATTTGC+AGG - chr3_1:82096311-82096330 Msa0380430:intron 30.0%
GAACATATTGAAGAAGTTGA+AGG - chr3_1:82096344-82096363 Msa0380430:intron 30.0%
AATATCTGATTGTTTCGACT+GGG + chr3_1:82096379-82096398 None:intergenic 30.0%
AAATATCTGATTGTTTCGAC+TGG + chr3_1:82096380-82096399 None:intergenic 30.0%
! ATGATTTGTAATTGCATACG+AGG - chr3_1:82096411-82096430 Msa0380430:intron 30.0%
TTATTCTTAAATACGCTTGC+CGG - chr3_1:82096456-82096475 Msa0380430:intron 30.0%
TGTATTCATCCAAAACACAT+TGG - chr3_1:82096529-82096548 Msa0380430:intron 30.0%
TCATTTGTCCACTCAAAAAG+CGG + chr3_1:82095715-82095734 None:intergenic 35.0%
AAATGATGTTGCTGACAGAT+TGG - chr3_1:82095729-82095748 Msa0380430:three_prime_UTR 35.0%
TTGTTACATTGCTTGAATGG+TGG - chr3_1:82095876-82095895 Msa0380430:three_prime_UTR 35.0%
CTGCATTACTACATTTCCAT+TGG - chr3_1:82095941-82095960 Msa0380430:three_prime_UTR 35.0%
GCATTACTACATTTCCATTG+GGG - chr3_1:82095943-82095962 Msa0380430:three_prime_UTR 35.0%
! CTGTAAGAATAGGGTTTGTT+TGG + chr3_1:82096045-82096064 None:intergenic 35.0%
CAAACAAACCCTATTCTTAC+AGG - chr3_1:82096043-82096062 Msa0380430:three_prime_UTR 35.0%
ATATGCACTAGGAATCTGTT+TGG + chr3_1:82096142-82096161 None:intergenic 35.0%
CACTTCTCACTATGTACATT+TGG + chr3_1:82096606-82096625 None:intergenic 35.0%
TCATTTGTCCACTCAAAAAG+CGG + chr3_1:82095715-82095734 None:intergenic 35.0%
AAATGATGTTGCTGACAGAT+TGG - chr3_1:82095729-82095748 Msa0380430:three_prime_UTR 35.0%
TTGTTACATTGCTTGAATGG+TGG - chr3_1:82095876-82095895 Msa0380430:three_prime_UTR 35.0%
CTGCATTACTACATTTCCAT+TGG - chr3_1:82095941-82095960 Msa0380430:three_prime_UTR 35.0%
GCATTACTACATTTCCATTG+GGG - chr3_1:82095943-82095962 Msa0380430:three_prime_UTR 35.0%
! CTGTAAGAATAGGGTTTGTT+TGG + chr3_1:82096045-82096064 None:intergenic 35.0%
CAAACAAACCCTATTCTTAC+AGG - chr3_1:82096043-82096062 Msa0380430:three_prime_UTR 35.0%
ATATGCACTAGGAATCTGTT+TGG + chr3_1:82096142-82096161 None:intergenic 35.0%
CACTTCTCACTATGTACATT+TGG + chr3_1:82096606-82096625 None:intergenic 35.0%
GTGAGTCTTAAAATGGAGAC+AGG + chr3_1:82095680-82095699 None:intergenic 40.0%
CTGACGAGTGAGTCTTAAAA+TGG + chr3_1:82095687-82095706 None:intergenic 40.0%
CATTTGTCCACTCAAAAAGC+GGG + chr3_1:82095714-82095733 None:intergenic 40.0%
! TGACAGATTGGCATTTTCAG+AGG - chr3_1:82095741-82095760 Msa0380430:three_prime_UTR 40.0%
! ACTACTAGAGCAGCTGATTT+GGG + chr3_1:82095908-82095927 None:intergenic 40.0%
TGGATTTGGGTAAAAGCCAA+TGG + chr3_1:82095977-82095996 None:intergenic 40.0%
! CACAGTTTTCTCTGTTCCAA+TGG - chr3_1:82096245-82096264 Msa0380430:CDS 40.0%
! AGTTTTCTCTGTTCCAATGG+CGG - chr3_1:82096248-82096267 Msa0380430:intron 40.0%
TTGCATACGAGGTAATGTTG+TGG - chr3_1:82096422-82096441 Msa0380430:intron 40.0%
TGCATACGAGGTAATGTTGT+GGG - chr3_1:82096423-82096442 Msa0380430:intron 40.0%
TTCTTACGTGGGCTTACAAT+TGG - chr3_1:82096497-82096516 Msa0380430:intron 40.0%
!!! GGGCTTACAATTGGTTTTGT+TGG - chr3_1:82096506-82096525 Msa0380430:intron 40.0%
! GTCTTTTAAGCATGCGATAC+AGG + chr3_1:82096728-82096747 None:intergenic 40.0%
GTGAGTCTTAAAATGGAGAC+AGG + chr3_1:82095680-82095699 None:intergenic 40.0%
CTGACGAGTGAGTCTTAAAA+TGG + chr3_1:82095687-82095706 None:intergenic 40.0%
CATTTGTCCACTCAAAAAGC+GGG + chr3_1:82095714-82095733 None:intergenic 40.0%
! TGACAGATTGGCATTTTCAG+AGG - chr3_1:82095741-82095760 Msa0380430:three_prime_UTR 40.0%
! ACTACTAGAGCAGCTGATTT+GGG + chr3_1:82095908-82095927 None:intergenic 40.0%
TGGATTTGGGTAAAAGCCAA+TGG + chr3_1:82095977-82095996 None:intergenic 40.0%
! CACAGTTTTCTCTGTTCCAA+TGG - chr3_1:82096245-82096264 Msa0380430:CDS 40.0%
! AGTTTTCTCTGTTCCAATGG+CGG - chr3_1:82096248-82096267 Msa0380430:intron 40.0%
TTGCATACGAGGTAATGTTG+TGG - chr3_1:82096422-82096441 Msa0380430:intron 40.0%
TGCATACGAGGTAATGTTGT+GGG - chr3_1:82096423-82096442 Msa0380430:intron 40.0%
TTCTTACGTGGGCTTACAAT+TGG - chr3_1:82096497-82096516 Msa0380430:intron 40.0%
!!! GGGCTTACAATTGGTTTTGT+TGG - chr3_1:82096506-82096525 Msa0380430:intron 40.0%
! GTCTTTTAAGCATGCGATAC+AGG + chr3_1:82096728-82096747 None:intergenic 40.0%
!!! CAGTTAACCCGCTTTTTGAG+TGG - chr3_1:82095704-82095723 Msa0380430:three_prime_UTR 45.0%
GACTACTAGAGCAGCTGATT+TGG + chr3_1:82095909-82095928 None:intergenic 45.0%
GGGTAAAAGCCAATGGCAAT+AGG + chr3_1:82095970-82095989 None:intergenic 45.0%
! GCATCGACATGAGTGGATTT+GGG + chr3_1:82095990-82096009 None:intergenic 45.0%
! TGCATCGACATGAGTGGATT+TGG + chr3_1:82095991-82096010 None:intergenic 45.0%
! TTGATGTGCATCGACATGAG+TGG + chr3_1:82095997-82096016 None:intergenic 45.0%
TGTTGGTCGGACCAATAGAA+TGG + chr3_1:82096076-82096095 None:intergenic 45.0%
!! CTTTGGTATCGACACCAAGT+AGG + chr3_1:82096284-82096303 None:intergenic 45.0%
!!! CAGTTAACCCGCTTTTTGAG+TGG - chr3_1:82095704-82095723 Msa0380430:three_prime_UTR 45.0%
GACTACTAGAGCAGCTGATT+TGG + chr3_1:82095909-82095928 None:intergenic 45.0%
GGGTAAAAGCCAATGGCAAT+AGG + chr3_1:82095970-82095989 None:intergenic 45.0%
! GCATCGACATGAGTGGATTT+GGG + chr3_1:82095990-82096009 None:intergenic 45.0%
! TGCATCGACATGAGTGGATT+TGG + chr3_1:82095991-82096010 None:intergenic 45.0%
! TTGATGTGCATCGACATGAG+TGG + chr3_1:82095997-82096016 None:intergenic 45.0%
TGTTGGTCGGACCAATAGAA+TGG + chr3_1:82096076-82096095 None:intergenic 45.0%
!! CTTTGGTATCGACACCAAGT+AGG + chr3_1:82096284-82096303 None:intergenic 45.0%
CAATGGCAATAGGTCCCCAA+TGG + chr3_1:82095960-82095979 None:intergenic 50.0%
CATTGGGGACCTATTGCCAT+TGG - chr3_1:82095958-82095977 Msa0380430:three_prime_UTR 50.0%
AGGTTGTATGTCTCCGCCAT+TGG + chr3_1:82096264-82096283 None:intergenic 50.0%
GCGGAGACATACAACCTACT+TGG - chr3_1:82096267-82096286 Msa0380430:intron 50.0%
CAATGGCAATAGGTCCCCAA+TGG + chr3_1:82095960-82095979 None:intergenic 50.0%
CATTGGGGACCTATTGCCAT+TGG - chr3_1:82095958-82095977 Msa0380430:three_prime_UTR 50.0%
AGGTTGTATGTCTCCGCCAT+TGG + chr3_1:82096264-82096283 None:intergenic 50.0%
GCGGAGACATACAACCTACT+TGG - chr3_1:82096267-82096286 Msa0380430:intron 50.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 82095657 82096838 82095657 ID=Msa0380430;Name=Msa0380430
chr3_1 mRNA 82095657 82096838 82095657 ID=Msa0380430-mRNA-1;Parent=Msa0380430;Name=Msa0380430-mRNA-1;_AED=0.10;_eAED=0.10;_QI=0|0.5|0.33|1|0.5|0.33|3|431|90
chr3_1 exon 82095657 82096264 82095657 ID=Msa0380430-mRNA-1:exon:20960;Parent=Msa0380430-mRNA-1
chr3_1 exon 82096733 82096820 82096733 ID=Msa0380430-mRNA-1:exon:20959;Parent=Msa0380430-mRNA-1
chr3_1 exon 82096831 82096838 82096831 ID=Msa0380430-mRNA-1:exon:20958;Parent=Msa0380430-mRNA-1
chr3_1 CDS 82096831 82096838 82096831 ID=Msa0380430-mRNA-1:cds;Parent=Msa0380430-mRNA-1
chr3_1 CDS 82096733 82096820 82096733 ID=Msa0380430-mRNA-1:cds;Parent=Msa0380430-mRNA-1
chr3_1 CDS 82096088 82096264 82096088 ID=Msa0380430-mRNA-1:cds;Parent=Msa0380430-mRNA-1
chr3_1 three_prime_UTR 82095657 82096087 82095657 ID=Msa0380430-mRNA-1:three_prime_utr;Parent=Msa0380430-mRNA-1
Gene Sequence

>Msa0380430

ATGCTAATTTCCTGTCTCCATTTTAAGACTCACTCGTCAGTTAACCCGCTTTTTGAGTGGACAAATGATGTTGCTGACAGATTGGCATTTTCAGAGGTGCTTACAAGTGACACAGTTTTCTCTGTTCCAATGGCGGAGACATACAACCTACTTGGTGTCGATACCAAAGATATAATTACATTAGAGAAGTATTTGCAGGACTACTTCACGAACATATTGAAGAAGTTGAAGGATCTCAAAGCCCAGTCGAAACAATCAGATATTTTCTTCTGA

Protein sequence

>Msa0380430

MLISCLHFKTHSSVNPLFEWTNDVADRLAFSEVLTSDTVFSVPMAETYNLLGVDTKDIITLEKYLQDYFTNILKKLKDLKAQSKQSDIFF*