AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene74462

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene74462.t1 MTR_4g081120 98.649 148 2 0 1 148 29 176 4.55e-105 297
MS.gene74462.t1 MTR_4g081120 93.590 156 2 1 1 148 1 156 1.43e-101 288
MS.gene74462.t1 MTR_3g073140 48.462 130 67 0 8 137 23 152 2.42e-35 120
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene74462.t1 AT1G77750 44.118 136 73 1 4 139 7 139 4.03e-37 124
MS.gene74462.t1 AT5G14320 50.820 122 52 2 16 137 40 153 1.16e-34 119
MS.gene74462.t1 AT5G14320 49.398 83 34 2 16 98 40 114 4.76e-18 75.5

Find 43 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCGAAGGCAGGCAGCTATAT+TGG 0.250518 4.2:-28605308 None:intergenic
TACTCAAGCCGCTTGTTATC+TGG 0.260205 4.2:-28605600 None:intergenic
TTCAAGATGTTTGGCTCTGC+TGG 0.322981 4.2:+28605277 None:intergenic
GTACTTGATTGGAAATGATT+TGG 0.323882 4.2:+28605755 MS.gene74462:CDS
TTGCTTTCCAAGTACTTGAT+TGG 0.332620 4.2:+28605744 MS.gene74462:CDS
TATAAACATTGGAGGTGGTC+TGG 0.365430 4.2:+28605566 MS.gene74462:CDS
ATCATCCGATTCAAGATGTT+TGG 0.368876 4.2:+28605268 None:intergenic
TGCCGATAGTTTACCCTGTC+GGG 0.377868 4.2:+28605946 MS.gene74462:CDS
ATCATTTCCAATCAAGTACT+TGG 0.399433 4.2:-28605751 None:intergenic
TATGCTCTTCAGCGTATTCA+TGG 0.412168 4.2:+28605621 MS.gene74462:CDS
CCAATATAGCTGCCTGCCTT+CGG 0.417480 4.2:+28605308 MS.gene74462:CDS
ATGAGTTCGTTGTCCCCGAC+AGG 0.439732 4.2:-28605960 None:intergenic
CTTCAGCGTATTCATGGGAT+TGG 0.440182 4.2:+28605627 MS.gene74462:CDS
TCAGAGAGATGTGGGAAGGT+TGG 0.448954 4.2:+28605892 MS.gene74462:CDS
AAGTTAGTTCAGAGAGATGT+GGG 0.457319 4.2:+28605884 MS.gene74462:CDS
ATAAACATTGGAGGTGGTCT+GGG 0.459744 4.2:+28605567 MS.gene74462:CDS
GAGAGATGTGGGAAGGTTGG+TGG 0.493094 4.2:+28605895 MS.gene74462:CDS
TAGTTCAGAGAGATGTGGGA+AGG 0.493943 4.2:+28605888 MS.gene74462:CDS
CATCACATTGTGTGTGAGCT+TGG 0.494957 4.2:+28605663 MS.gene74462:CDS
TTCAATGCTACAGAGGGATC+AGG 0.509277 4.2:+28605921 MS.gene74462:CDS
AGGAGGACTATGCGTACTTA+CGG 0.516509 4.2:+28605998 MS.gene74462:CDS
AAAGTTAGTTCAGAGAGATG+TGG 0.539738 4.2:+28605883 MS.gene74462:CDS
AGAGATGTGGGAAGGTTGGT+GGG 0.544599 4.2:+28605896 MS.gene74462:CDS
CGTATTCATGGGATTGGCCG+TGG 0.544806 4.2:+28605633 MS.gene74462:CDS
ATGCTCTTCAGCGTATTCAT+GGG 0.565567 4.2:+28605622 MS.gene74462:CDS
TCCCCGACAGGGTAAACTAT+CGG 0.567861 4.2:-28605948 None:intergenic
CTCATACAAATGCCCGCACT+AGG 0.582313 4.2:+28605978 MS.gene74462:CDS
AGTTTCGCGGTGTGCAAGTG+CGG 0.582479 4.2:+28605541 MS.gene74462:intron
ATGCCGATAGTTTACCCTGT+CGG 0.584612 4.2:+28605945 MS.gene74462:CDS
GTGCGGAATATAAACATTGG+AGG 0.589196 4.2:+28605558 MS.gene74462:CDS
ACGCATAGTCCTCCTAGTGC+GGG 0.590149 4.2:-28605990 None:intergenic
CAAGTGCGGAATATAAACAT+TGG 0.595646 4.2:+28605555 MS.gene74462:CDS
CGGAATATAAACATTGGAGG+TGG 0.605864 4.2:+28605561 MS.gene74462:CDS
ATACAAATGCCCGCACTAGG+AGG 0.613577 4.2:+28605981 MS.gene74462:CDS
TACGCATAGTCCTCCTAGTG+CGG 0.618835 4.2:-28605991 None:intergenic
AACATTGGAGGTGGTCTGGG+AGG 0.637937 4.2:+28605570 MS.gene74462:CDS
GCCGATAGTTTACCCTGTCG+GGG 0.639544 4.2:+28605947 MS.gene74462:CDS
TGGGTATTCAATGCTACAGA+GGG 0.643857 4.2:+28605915 MS.gene74462:CDS
AGTTGAGAACAAATATGTGA+AGG 0.652674 4.2:+28605686 MS.gene74462:CDS
GTGAGATTCCAGATAACAAG+CGG 0.653241 4.2:+28605592 MS.gene74462:CDS
TGAGTTCGTTGTCCCCGACA+GGG 0.657819 4.2:-28605959 None:intergenic
GTGGGTATTCAATGCTACAG+AGG 0.707000 4.2:+28605914 MS.gene74462:CDS
AGGACTATGCGTACTTACGG+AGG 0.735045 4.2:+28606001 MS.gene74462:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGACATTATACATTATATTA+TGG - chr4.2:28605830-28605849 None:intergenic 15.0%
!!! ATAATGTTCTAAAACAAAAA+AGG - chr4.2:28605388-28605407 None:intergenic 15.0%
!!! TTTTCTCTTTTCATTATTAT+GGG + chr4.2:28605348-28605367 MS.gene74462:intron 15.0%
!! TTATGGAACAAAAATAGAAA+AGG - chr4.2:28605813-28605832 None:intergenic 20.0%
!!! GTTTTCTCTTTTCATTATTA+TGG + chr4.2:28605347-28605366 MS.gene74462:intron 20.0%
! TAATGAAAAGAGAAAACTCA+CGG - chr4.2:28605344-28605363 None:intergenic 25.0%
!! AATATAGTTCTCTTTTGCTT+AGG - chr4.2:28605713-28605732 None:intergenic 25.0%
!!! ATTTTTAATTGCAAAGCATG+CGG - chr4.2:28605491-28605510 None:intergenic 25.0%
AGTTGAGAACAAATATGTGA+AGG + chr4.2:28605686-28605705 MS.gene74462:CDS 30.0%
ATCATTTCCAATCAAGTACT+TGG - chr4.2:28605754-28605773 None:intergenic 30.0%
GTACTTGATTGGAAATGATT+TGG + chr4.2:28605755-28605774 MS.gene74462:CDS 30.0%
TCTTTCTTAGCTTCAACTTA+GGG + chr4.2:28605453-28605472 MS.gene74462:intron 30.0%
TTCTTTCTTAGCTTCAACTT+AGG + chr4.2:28605452-28605471 MS.gene74462:intron 30.0%
! AAGTCATAAAAGTGCAATTG+AGG - chr4.2:28605412-28605431 None:intergenic 30.0%
! TCATTATAGTTGCACTGTTT+TGG + chr4.2:28605510-28605529 MS.gene74462:intron 30.0%
AAAGTTAGTTCAGAGAGATG+TGG + chr4.2:28605883-28605902 MS.gene74462:CDS 35.0%
AAGTTAGTTCAGAGAGATGT+GGG + chr4.2:28605884-28605903 MS.gene74462:CDS 35.0%
CAAGTGCGGAATATAAACAT+TGG + chr4.2:28605555-28605574 MS.gene74462:CDS 35.0%
TTATTATGGGTTTGTGACTG+CGG + chr4.2:28605361-28605380 MS.gene74462:intron 35.0%
TTGCTTTCCAAGTACTTGAT+TGG + chr4.2:28605744-28605763 MS.gene74462:CDS 35.0%
!!! TTTGGTTTTGTACAGTTTCG+CGG + chr4.2:28605528-28605547 MS.gene74462:intron 35.0%
ATAAACATTGGAGGTGGTCT+GGG + chr4.2:28605567-28605586 MS.gene74462:CDS 40.0%
ATGCTCTTCAGCGTATTCAT+GGG + chr4.2:28605622-28605641 MS.gene74462:CDS 40.0%
CGGAATATAAACATTGGAGG+TGG + chr4.2:28605561-28605580 MS.gene74462:CDS 40.0%
GTGAGATTCCAGATAACAAG+CGG + chr4.2:28605592-28605611 MS.gene74462:CDS 40.0%
GTGCGGAATATAAACATTGG+AGG + chr4.2:28605558-28605577 MS.gene74462:CDS 40.0%
TATAAACATTGGAGGTGGTC+TGG + chr4.2:28605566-28605585 MS.gene74462:CDS 40.0%
TATGCTCTTCAGCGTATTCA+TGG + chr4.2:28605621-28605640 MS.gene74462:CDS 40.0%
TGGGTATTCAATGCTACAGA+GGG + chr4.2:28605915-28605934 MS.gene74462:CDS 40.0%
TTATGACTTTGCGTGGTGTA+GGG + chr4.2:28605423-28605442 MS.gene74462:intron 40.0%
TTTATGACTTTGCGTGGTGT+AGG + chr4.2:28605422-28605441 MS.gene74462:intron 40.0%
! CAATGTGATGAGCTTTTCCA+CGG - chr4.2:28605653-28605672 None:intergenic 40.0%
! TGCACTTTTATGACTTTGCG+TGG + chr4.2:28605416-28605435 MS.gene74462:intron 40.0%
AGGAGGACTATGCGTACTTA+CGG + chr4.2:28605998-28606017 MS.gene74462:CDS 45.0%
ATGCCGATAGTTTACCCTGT+CGG + chr4.2:28605945-28605964 MS.gene74462:CDS 45.0%
CATCACATTGTGTGTGAGCT+TGG + chr4.2:28605663-28605682 MS.gene74462:CDS 45.0%
CTTCAGCGTATTCATGGGAT+TGG + chr4.2:28605627-28605646 MS.gene74462:CDS 45.0%
GTGGGTATTCAATGCTACAG+AGG + chr4.2:28605914-28605933 MS.gene74462:CDS 45.0%
TAGTTCAGAGAGATGTGGGA+AGG + chr4.2:28605888-28605907 MS.gene74462:CDS 45.0%
TTCAATGCTACAGAGGGATC+AGG + chr4.2:28605921-28605940 MS.gene74462:CDS 45.0%
! TCACGGATAAGTTTTGCCGA+AGG - chr4.2:28605327-28605346 None:intergenic 45.0%
!! TACTCAAGCCGCTTGTTATC+TGG - chr4.2:28605603-28605622 None:intergenic 45.0%
AGGACTATGCGTACTTACGG+AGG + chr4.2:28606001-28606020 MS.gene74462:CDS 50.0%
ATACAAATGCCCGCACTAGG+AGG + chr4.2:28605981-28606000 MS.gene74462:CDS 50.0%
CCAATATAGCTGCCTGCCTT+CGG + chr4.2:28605308-28605327 MS.gene74462:CDS 50.0%
CTCATACAAATGCCCGCACT+AGG + chr4.2:28605978-28605997 MS.gene74462:CDS 50.0%
TACGCATAGTCCTCCTAGTG+CGG - chr4.2:28605994-28606013 None:intergenic 50.0%
TCAGAGAGATGTGGGAAGGT+TGG + chr4.2:28605892-28605911 MS.gene74462:CDS 50.0%
TCCCCGACAGGGTAAACTAT+CGG - chr4.2:28605951-28605970 None:intergenic 50.0%
TGCCGATAGTTTACCCTGTC+GGG + chr4.2:28605946-28605965 MS.gene74462:CDS 50.0%
! AGAGATGTGGGAAGGTTGGT+GGG + chr4.2:28605896-28605915 MS.gene74462:CDS 50.0%
! GGATAAGTTTTGCCGAAGGC+AGG - chr4.2:28605323-28605342 None:intergenic 50.0%
AACATTGGAGGTGGTCTGGG+AGG + chr4.2:28605570-28605589 MS.gene74462:CDS 55.0%
ACGCATAGTCCTCCTAGTGC+GGG - chr4.2:28605993-28606012 None:intergenic 55.0%
AGTTTCGCGGTGTGCAAGTG+CGG + chr4.2:28605541-28605560 MS.gene74462:intron 55.0%
ATGAGTTCGTTGTCCCCGAC+AGG - chr4.2:28605963-28605982 None:intergenic 55.0%
CCGAAGGCAGGCAGCTATAT+TGG - chr4.2:28605311-28605330 None:intergenic 55.0%
GAGAGATGTGGGAAGGTTGG+TGG + chr4.2:28605895-28605914 MS.gene74462:CDS 55.0%
GCCGATAGTTTACCCTGTCG+GGG + chr4.2:28605947-28605966 MS.gene74462:CDS 55.0%
TGAGTTCGTTGTCCCCGACA+GGG - chr4.2:28605962-28605981 None:intergenic 55.0%
!! CGTATTCATGGGATTGGCCG+TGG + chr4.2:28605633-28605652 MS.gene74462:CDS 55.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 28605283 28606033 28605283 ID=MS.gene74462
chr4.2 mRNA 28605283 28606033 28605283 ID=MS.gene74462.t1;Parent=MS.gene74462
chr4.2 exon 28605283 28605342 28605283 ID=MS.gene74462.t1.exon1;Parent=MS.gene74462.t1
chr4.2 CDS 28605283 28605342 28605283 ID=cds.MS.gene74462.t1;Parent=MS.gene74462.t1
chr4.2 exon 28605543 28605776 28605543 ID=MS.gene74462.t1.exon2;Parent=MS.gene74462.t1
chr4.2 CDS 28605543 28605776 28605543 ID=cds.MS.gene74462.t1;Parent=MS.gene74462.t1
chr4.2 exon 28605881 28606033 28605881 ID=MS.gene74462.t1.exon3;Parent=MS.gene74462.t1
chr4.2 CDS 28605881 28606033 28605881 ID=cds.MS.gene74462.t1;Parent=MS.gene74462.t1
Gene Sequence

>MS.gene74462

ATGTTTGGCTCTGCTGGAATGTTTTCCAATATAGCTGCCTGCCTTCGGCAAAACTTATCCGTGAGTTTTCTCTTTTCATTATTATGGGTTTGTGACTGCGGTCCTTTTTTGTTTTAGAACATTATGCCTCAATTGCACTTTTATGACTTTGCGTGGTGTAGGGTTTTGTTTCTTTCTTAGCTTCAACTTAGGGATTAATGCATCTCCGCATGCTTTGCAATTAAAAATCATTATAGTTGCACTGTTTTGGTTTTGTACAGTTTCGCGGTGTGCAAGTGCGGAATATAAACATTGGAGGTGGTCTGGGAGGTGAGATTCCAGATAACAAGCGGCTTGAGTATGCTCTTCAGCGTATTCATGGGATTGGCCGTGGAAAAGCTCATCACATTGTGTGTGAGCTTGGAGTTGAGAACAAATATGTGAAGGACCTAAGCAAAAGAGAACTATATTCTCTTCGCGAATTGCTTTCCAAGTACTTGATTGGAAATGATTTGGTATTCTCATCTTCTTTACATTTTGATTTTGCACCTTTTCTATTTTTGTTCCATAATATAATGTATAATGTCTGAGATTGTTTTGTTTTTTCTTTTTCTTTCAGAAAAAGTTAGTTCAGAGAGATGTGGGAAGGTTGGTGGGTATTCAATGCTACAGAGGGATCAGGCATGCCGATAGTTTACCCTGTCGGGGACAACGAACTCATACAAATGCCCGCACTAGGAGGACTATGCGTACTTACGGAGGTTCAAGATAA
Protein sequence

>MS.gene74462.t1

MFGSAGMFSNIAACLRQNLSFRGVQVRNINIGGGLGGEIPDNKRLEYALQRIHGIGRGKAHHIVCELGVENKYVKDLSKRELYSLRELLSKYLIGNDLKKLVQRDVGRLVGIQCYRGIRHADSLPCRGQRTHTNARTRRTMRTYGGSR