AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0158330

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 36 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTTCAGGTCTTGAATAATT+TGG 0.148201 1_4:+27282612 Msa0158330:five_prime_UTR
CATTGTTTATAATTGTATAT+AGG 0.251213 1_4:+27282806 Msa0158330:five_prime_UTR
ACATTGAGCAAGCTTTAAAA+TGG 0.306011 1_4:+27282976 Msa0158330:CDS
ATTGTTTATAATTGTATATA+GGG 0.318157 1_4:+27282807 Msa0158330:five_prime_UTR
TTTAAAGCTTGCTCAATGTT+TGG 0.324866 1_4:-27282972 None:intergenic
GCATGGCTGATGGGAGTTCT+TGG 0.340243 1_4:+27282676 Msa0158330:five_prime_UTR
AAATGGGATAGGAACCCTTT+TGG 0.349341 1_4:+27283122 Msa0158330:CDS
TAAAGAAAGTTGTCTGATAT+TGG 0.364580 1_4:+27283318 Msa0158330:three_prime_UTR
AATAGAAGTATAATATCAAC+TGG 0.365951 1_4:-27283152 None:intergenic
TGTTGCTCAATGTAAGAGAT+AGG 0.373738 1_4:+27283346 Msa0158330:three_prime_UTR
TGACACTATCAGCAGTTCTT+AGG 0.383062 1_4:-27283202 None:intergenic
GCATATTTGCAATTATTGAT+TGG 0.415200 1_4:+27282698 Msa0158330:five_prime_UTR
AAAAGGGTTCCTATCCCATT+TGG 0.423193 1_4:-27283120 None:intergenic
TATGACAAACAACAATGTTC+AGG 0.429636 1_4:+27282597 Msa0158330:five_prime_UTR
GTATTAGTTTATCCTTAGAA+TGG 0.441788 1_4:+27282880 Msa0158330:CDS
GTAATGTGTCGGCTCTTTGT+TGG 0.450714 1_4:+27282742 Msa0158330:five_prime_UTR
CTATCTCTAATTATTCAAAA+AGG 0.452282 1_4:+27282546 Msa0158330:five_prime_UTR
TAATGTGTCGGCTCTTTGTT+GGG 0.460399 1_4:+27282743 Msa0158330:five_prime_UTR
AGCCCGGATATTACCACCTT+CGG 0.469144 1_4:-27283012 None:intergenic
AAAGCTTGCTCAATGTTTGG+AGG 0.482572 1_4:-27282969 None:intergenic
TCAACTGGGTCATTCCCAAA+AGG 0.485241 1_4:-27283137 None:intergenic
TTGTAGGTGCCAAATGGGAT+AGG 0.506945 1_4:+27283111 Msa0158330:intron
CACTTCTGCTGAAAAGATGA+AGG 0.515069 1_4:+27283235 Msa0158330:three_prime_UTR
CAACTGGGTCATTCCCAAAA+GGG 0.525279 1_4:-27283136 None:intergenic
AGTTTATCCTTAGAATGGAA+TGG 0.543581 1_4:+27282885 Msa0158330:CDS
GAAAATGATTGCATGGCTGA+TGG 0.559798 1_4:+27282666 Msa0158330:five_prime_UTR
ACAACTTTCTTTACGCGCCA+CGG 0.560682 1_4:-27283308 None:intergenic
AAAATGATTGCATGGCTGAT+GGG 0.581276 1_4:+27282667 Msa0158330:five_prime_UTR
CTATATACAATTATAAACAA+TGG 0.600047 1_4:-27282805 None:intergenic
TTGTATAAAGCTTCCGAAGG+TGG 0.604312 1_4:+27282999 Msa0158330:CDS
GAAAACTGAAAATGATTGCA+TGG 0.604677 1_4:+27282659 Msa0158330:five_prime_UTR
ATAGATGCATTGTAATGTGT+CGG 0.612151 1_4:+27282731 Msa0158330:five_prime_UTR
GAGGCTCAACTGCATAGCAT+AGG 0.621630 1_4:-27282950 None:intergenic
TGGTTGTATAAAGCTTCCGA+AGG 0.667521 1_4:+27282996 Msa0158330:CDS
TGATAGTTTATGTCTAACAA+AGG 0.675453 1_4:+27282923 Msa0158330:CDS
ATAGAAGTATAATATCAACT+GGG 0.754814 1_4:-27283151 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTGTTTATAATTGTATATA+GGG + chr1_4:27282807-27282826 Msa0158330:five_prime_UTR 10.0%
!!! ATATTTTGTATTAAGATTTT+TGG + chr1_4:27283274-27283293 Msa0158330:three_prime_UTR 10.0%
!! ATTGTTTATAATTGTATATA+GGG + chr1_4:27282807-27282826 Msa0158330:five_prime_UTR 10.0%
!!! ATATTTTGTATTAAGATTTT+TGG + chr1_4:27283274-27283293 Msa0158330:three_prime_UTR 10.0%
!!! ACTACTAATTAATTTTTAAC+AGG + chr1_4:27282520-27282539 Msa0158330:five_prime_UTR 15.0%
!!! AAACATTCAAATTTTTCATT+AGG + chr1_4:27282635-27282654 Msa0158330:five_prime_UTR 15.0%
!! CTATATACAATTATAAACAA+TGG - chr1_4:27282808-27282827 None:intergenic 15.0%
!! CATTGTTTATAATTGTATAT+AGG + chr1_4:27282806-27282825 Msa0158330:five_prime_UTR 15.0%
!!! ACTACTAATTAATTTTTAAC+AGG + chr1_4:27282520-27282539 Msa0158330:five_prime_UTR 15.0%
!!! AAACATTCAAATTTTTCATT+AGG + chr1_4:27282635-27282654 Msa0158330:five_prime_UTR 15.0%
!! CTATATACAATTATAAACAA+TGG - chr1_4:27282808-27282827 None:intergenic 15.0%
!! CATTGTTTATAATTGTATAT+AGG + chr1_4:27282806-27282825 Msa0158330:five_prime_UTR 15.0%
!! CTATCTCTAATTATTCAAAA+AGG + chr1_4:27282546-27282565 Msa0158330:five_prime_UTR 20.0%
!!! ATAGAAGTATAATATCAACT+GGG - chr1_4:27283154-27283173 None:intergenic 20.0%
!!! AATAGAAGTATAATATCAAC+TGG - chr1_4:27283155-27283174 None:intergenic 20.0%
!! CTATCTCTAATTATTCAAAA+AGG + chr1_4:27282546-27282565 Msa0158330:five_prime_UTR 20.0%
!!! ATAGAAGTATAATATCAACT+GGG - chr1_4:27283154-27283173 None:intergenic 20.0%
!!! AATAGAAGTATAATATCAAC+TGG - chr1_4:27283155-27283174 None:intergenic 20.0%
! AGAGCTTAATGTCAAAAAAT+GGG - chr1_4:27282573-27282592 None:intergenic 25.0%
! AAGAGCTTAATGTCAAAAAA+TGG - chr1_4:27282574-27282593 None:intergenic 25.0%
! GCATATTTGCAATTATTGAT+TGG + chr1_4:27282698-27282717 Msa0158330:five_prime_UTR 25.0%
!! GTATTAGTTTATCCTTAGAA+TGG + chr1_4:27282880-27282899 Msa0158330:CDS 25.0%
! TGATAGTTTATGTCTAACAA+AGG + chr1_4:27282923-27282942 Msa0158330:CDS 25.0%
!!! TTAAGATTTTTGGTCTTTCA+CGG + chr1_4:27283284-27283303 Msa0158330:three_prime_UTR 25.0%
! TAAAGAAAGTTGTCTGATAT+TGG + chr1_4:27283318-27283337 Msa0158330:three_prime_UTR 25.0%
! AGAGCTTAATGTCAAAAAAT+GGG - chr1_4:27282573-27282592 None:intergenic 25.0%
! AAGAGCTTAATGTCAAAAAA+TGG - chr1_4:27282574-27282593 None:intergenic 25.0%
! GCATATTTGCAATTATTGAT+TGG + chr1_4:27282698-27282717 Msa0158330:five_prime_UTR 25.0%
!! GTATTAGTTTATCCTTAGAA+TGG + chr1_4:27282880-27282899 Msa0158330:CDS 25.0%
! TGATAGTTTATGTCTAACAA+AGG + chr1_4:27282923-27282942 Msa0158330:CDS 25.0%
!!! TTAAGATTTTTGGTCTTTCA+CGG + chr1_4:27283284-27283303 Msa0158330:three_prime_UTR 25.0%
! TAAAGAAAGTTGTCTGATAT+TGG + chr1_4:27283318-27283337 Msa0158330:three_prime_UTR 25.0%
TATGACAAACAACAATGTTC+AGG + chr1_4:27282597-27282616 Msa0158330:five_prime_UTR 30.0%
TGTTCAGGTCTTGAATAATT+TGG + chr1_4:27282612-27282631 Msa0158330:five_prime_UTR 30.0%
GAAAACTGAAAATGATTGCA+TGG + chr1_4:27282659-27282678 Msa0158330:five_prime_UTR 30.0%
ATAGATGCATTGTAATGTGT+CGG + chr1_4:27282731-27282750 Msa0158330:five_prime_UTR 30.0%
AGTTTATCCTTAGAATGGAA+TGG + chr1_4:27282885-27282904 Msa0158330:CDS 30.0%
! TTCTTTTCCATTCCATTCTA+AGG - chr1_4:27282895-27282914 None:intergenic 30.0%
! TTTAAAGCTTGCTCAATGTT+TGG - chr1_4:27282975-27282994 None:intergenic 30.0%
!! ACATTGAGCAAGCTTTAAAA+TGG + chr1_4:27282976-27282995 Msa0158330:CDS 30.0%
TATGACAAACAACAATGTTC+AGG + chr1_4:27282597-27282616 Msa0158330:five_prime_UTR 30.0%
TGTTCAGGTCTTGAATAATT+TGG + chr1_4:27282612-27282631 Msa0158330:five_prime_UTR 30.0%
GAAAACTGAAAATGATTGCA+TGG + chr1_4:27282659-27282678 Msa0158330:five_prime_UTR 30.0%
ATAGATGCATTGTAATGTGT+CGG + chr1_4:27282731-27282750 Msa0158330:five_prime_UTR 30.0%
AGTTTATCCTTAGAATGGAA+TGG + chr1_4:27282885-27282904 Msa0158330:CDS 30.0%
! TTCTTTTCCATTCCATTCTA+AGG - chr1_4:27282895-27282914 None:intergenic 30.0%
! TTTAAAGCTTGCTCAATGTT+TGG - chr1_4:27282975-27282994 None:intergenic 30.0%
!! ACATTGAGCAAGCTTTAAAA+TGG + chr1_4:27282976-27282995 Msa0158330:CDS 30.0%
AAAATGATTGCATGGCTGAT+GGG + chr1_4:27282667-27282686 Msa0158330:five_prime_UTR 35.0%
GATGCACAATTCAGACAAAT+GGG - chr1_4:27283080-27283099 None:intergenic 35.0%
AGATGCACAATTCAGACAAA+TGG - chr1_4:27283081-27283100 None:intergenic 35.0%
! TTGATTTTGTAGGTGCCAAA+TGG + chr1_4:27283105-27283124 Msa0158330:intron 35.0%
! TGATTTTGTAGGTGCCAAAT+GGG + chr1_4:27283106-27283125 Msa0158330:intron 35.0%
TGTTGCTCAATGTAAGAGAT+AGG + chr1_4:27283346-27283365 Msa0158330:three_prime_UTR 35.0%
AAAATGATTGCATGGCTGAT+GGG + chr1_4:27282667-27282686 Msa0158330:five_prime_UTR 35.0%
GATGCACAATTCAGACAAAT+GGG - chr1_4:27283080-27283099 None:intergenic 35.0%
AGATGCACAATTCAGACAAA+TGG - chr1_4:27283081-27283100 None:intergenic 35.0%
! TTGATTTTGTAGGTGCCAAA+TGG + chr1_4:27283105-27283124 Msa0158330:intron 35.0%
! TGATTTTGTAGGTGCCAAAT+GGG + chr1_4:27283106-27283125 Msa0158330:intron 35.0%
TGTTGCTCAATGTAAGAGAT+AGG + chr1_4:27283346-27283365 Msa0158330:three_prime_UTR 35.0%
GAAAATGATTGCATGGCTGA+TGG + chr1_4:27282666-27282685 Msa0158330:five_prime_UTR 40.0%
!! TAATGTGTCGGCTCTTTGTT+GGG + chr1_4:27282743-27282762 Msa0158330:five_prime_UTR 40.0%
! AAAGCTTGCTCAATGTTTGG+AGG - chr1_4:27282972-27282991 None:intergenic 40.0%
TGGTTGTATAAAGCTTCCGA+AGG + chr1_4:27282996-27283015 Msa0158330:CDS 40.0%
TTGTATAAAGCTTCCGAAGG+TGG + chr1_4:27282999-27283018 Msa0158330:CDS 40.0%
! GCATCTCTGCTTGATTTTGT+AGG + chr1_4:27283095-27283114 Msa0158330:intron 40.0%
AAAAGGGTTCCTATCCCATT+TGG - chr1_4:27283123-27283142 None:intergenic 40.0%
! AAATGGGATAGGAACCCTTT+TGG + chr1_4:27283122-27283141 Msa0158330:CDS 40.0%
! AATGGGATAGGAACCCTTTT+GGG + chr1_4:27283123-27283142 Msa0158330:CDS 40.0%
TGACACTATCAGCAGTTCTT+AGG - chr1_4:27283205-27283224 None:intergenic 40.0%
CACTTCTGCTGAAAAGATGA+AGG + chr1_4:27283235-27283254 Msa0158330:three_prime_UTR 40.0%
GAAAATGATTGCATGGCTGA+TGG + chr1_4:27282666-27282685 Msa0158330:five_prime_UTR 40.0%
!! TAATGTGTCGGCTCTTTGTT+GGG + chr1_4:27282743-27282762 Msa0158330:five_prime_UTR 40.0%
! AAAGCTTGCTCAATGTTTGG+AGG - chr1_4:27282972-27282991 None:intergenic 40.0%
TGGTTGTATAAAGCTTCCGA+AGG + chr1_4:27282996-27283015 Msa0158330:CDS 40.0%
TTGTATAAAGCTTCCGAAGG+TGG + chr1_4:27282999-27283018 Msa0158330:CDS 40.0%
! GCATCTCTGCTTGATTTTGT+AGG + chr1_4:27283095-27283114 Msa0158330:intron 40.0%
AAAAGGGTTCCTATCCCATT+TGG - chr1_4:27283123-27283142 None:intergenic 40.0%
! AAATGGGATAGGAACCCTTT+TGG + chr1_4:27283122-27283141 Msa0158330:CDS 40.0%
! AATGGGATAGGAACCCTTTT+GGG + chr1_4:27283123-27283142 Msa0158330:CDS 40.0%
TGACACTATCAGCAGTTCTT+AGG - chr1_4:27283205-27283224 None:intergenic 40.0%
CACTTCTGCTGAAAAGATGA+AGG + chr1_4:27283235-27283254 Msa0158330:three_prime_UTR 40.0%
!! GTAATGTGTCGGCTCTTTGT+TGG + chr1_4:27282742-27282761 Msa0158330:five_prime_UTR 45.0%
CTTCCGAAGGTGGTAATATC+CGG + chr1_4:27283009-27283028 Msa0158330:intron 45.0%
TTCCGAAGGTGGTAATATCC+GGG + chr1_4:27283010-27283029 Msa0158330:intron 45.0%
TTGTAGGTGCCAAATGGGAT+AGG + chr1_4:27283111-27283130 Msa0158330:intron 45.0%
CAACTGGGTCATTCCCAAAA+GGG - chr1_4:27283139-27283158 None:intergenic 45.0%
TCAACTGGGTCATTCCCAAA+AGG - chr1_4:27283140-27283159 None:intergenic 45.0%
ACAACTTTCTTTACGCGCCA+CGG - chr1_4:27283311-27283330 None:intergenic 45.0%
!! GTAATGTGTCGGCTCTTTGT+TGG + chr1_4:27282742-27282761 Msa0158330:five_prime_UTR 45.0%
CTTCCGAAGGTGGTAATATC+CGG + chr1_4:27283009-27283028 Msa0158330:intron 45.0%
TTCCGAAGGTGGTAATATCC+GGG + chr1_4:27283010-27283029 Msa0158330:intron 45.0%
TTGTAGGTGCCAAATGGGAT+AGG + chr1_4:27283111-27283130 Msa0158330:intron 45.0%
CAACTGGGTCATTCCCAAAA+GGG - chr1_4:27283139-27283158 None:intergenic 45.0%
TCAACTGGGTCATTCCCAAA+AGG - chr1_4:27283140-27283159 None:intergenic 45.0%
ACAACTTTCTTTACGCGCCA+CGG - chr1_4:27283311-27283330 None:intergenic 45.0%
GAGGCTCAACTGCATAGCAT+AGG - chr1_4:27282953-27282972 None:intergenic 50.0%
AGCCCGGATATTACCACCTT+CGG - chr1_4:27283015-27283034 None:intergenic 50.0%
GATGAAGACAGAGAGCAAGG+TGG - chr1_4:27283043-27283062 None:intergenic 50.0%
CTCGATGAAGACAGAGAGCA+AGG - chr1_4:27283046-27283065 None:intergenic 50.0%
!! TTTTGGTCTTTCACGGTCCG+TGG + chr1_4:27283291-27283310 Msa0158330:three_prime_UTR 50.0%
GAGGCTCAACTGCATAGCAT+AGG - chr1_4:27282953-27282972 None:intergenic 50.0%
AGCCCGGATATTACCACCTT+CGG - chr1_4:27283015-27283034 None:intergenic 50.0%
GATGAAGACAGAGAGCAAGG+TGG - chr1_4:27283043-27283062 None:intergenic 50.0%
CTCGATGAAGACAGAGAGCA+AGG - chr1_4:27283046-27283065 None:intergenic 50.0%
!! TTTTGGTCTTTCACGGTCCG+TGG + chr1_4:27283291-27283310 Msa0158330:three_prime_UTR 50.0%
GCATGGCTGATGGGAGTTCT+TGG + chr1_4:27282676-27282695 Msa0158330:five_prime_UTR 55.0%
GAGCAAGGTGGTACTAAGCC+CGG - chr1_4:27283031-27283050 None:intergenic 55.0%
GCTCTCTGTCTTCATCGAGC+TGG + chr1_4:27283047-27283066 Msa0158330:intron 55.0%
GCATGGCTGATGGGAGTTCT+TGG + chr1_4:27282676-27282695 Msa0158330:five_prime_UTR 55.0%
GAGCAAGGTGGTACTAAGCC+CGG - chr1_4:27283031-27283050 None:intergenic 55.0%
GCTCTCTGTCTTCATCGAGC+TGG + chr1_4:27283047-27283066 Msa0158330:intron 55.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 27282501 27283397 27282501 ID=Msa0158330;Name=Msa0158330
chr1_4 mRNA 27282501 27283397 27282501 ID=Msa0158330-mRNA-1;Parent=Msa0158330;Name=Msa0158330-mRNA-1;_AED=0.05;_eAED=0.06;_QI=375|0|0.5|1|1|1|2|219|68
chr1_4 exon 27282501 27283020 27282501 ID=Msa0158330-mRNA-1:exon:8963;Parent=Msa0158330-mRNA-1
chr1_4 exon 27283117 27283397 27283117 ID=Msa0158330-mRNA-1:exon:8964;Parent=Msa0158330-mRNA-1
chr1_4 five_prime_UTR 27282501 27282875 27282501 ID=Msa0158330-mRNA-1:five_prime_utr;Parent=Msa0158330-mRNA-1
chr1_4 CDS 27282876 27283020 27282876 ID=Msa0158330-mRNA-1:cds;Parent=Msa0158330-mRNA-1
chr1_4 CDS 27283117 27283178 27283117 ID=Msa0158330-mRNA-1:cds;Parent=Msa0158330-mRNA-1
chr1_4 three_prime_UTR 27283179 27283397 27283179 ID=Msa0158330-mRNA-1:three_prime_utr;Parent=Msa0158330-mRNA-1
Gene Sequence

>Msa0158330

ATGAGTATTAGTTTATCCTTAGAATGGAATGGAAAAGAAGATTATGATGATAGTTTATGTCTAACAAAGGTATACCTATGCTATGCAGTTGAGCCTCCAAACATTGAGCAAGCTTTAAAATGGTTGTATAAAGCTTCCGAAGGTGGTGCCAAATGGGATAGGAACCCTTTTGGGAATGACCCAGTTGATATTATACTTCTATTATGA
Protein sequence

>Msa0158330

MSISLSLEWNGKEDYDDSLCLTKVYLCYAVEPPNIEQALKWLYKASEGGAKWDRNPFGNDPVDIILLL*