AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene09971

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene09971.t1 MTR_2g035730 63.063 111 12 2 1 111 1 82 3.22e-38 125
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCGGCTTCCTGGGCTTCT+TGG 0.176884 5.2:+4837432 None:intergenic
GCTATCATCCTTCGGCTTCC+TGG 0.179821 5.2:+4837423 None:intergenic
TCTGGAAGAACATCATAATT+TGG 0.181172 5.2:+4837603 None:intergenic
TTCCTGGGCTTCTTGGCTTT+TGG 0.290426 5.2:+4837439 None:intergenic
GCCACGAGACTGTGCTGTTT+CGG 0.316421 5.2:-4837706 MS.gene09971:CDS
TCACTCTTCTTGCCGGTTAT+CGG 0.339241 5.2:-4837570 MS.gene09971:CDS
TTAACTATGTGAGGGATAAC+TGG 0.365336 5.2:-4837668 MS.gene09971:CDS
TTCTCATTTCTTGATGCATC+AGG 0.365722 5.2:+4837543 None:intergenic
AAGAGTGATTGTGATGCTTC+TGG 0.369536 5.2:+4837585 None:intergenic
ATCACAATCACTCTTCTTGC+CGG 0.370709 5.2:-4837577 MS.gene09971:CDS
GAAGGTGCAAGAAGAAGAAA+AGG 0.370973 5.2:-4837486 MS.gene09971:CDS
CTATCATCCTTCGGCTTCCT+GGG 0.424580 5.2:+4837424 None:intergenic
TATTGATAAACCTATGTCTC+GGG 0.452192 5.2:+4837640 None:intergenic
GCATCAGGCTGACCGATAAC+CGG 0.466669 5.2:+4837558 None:intergenic
GTCTCGTGGCTGAAAGGGCA+AGG 0.467952 5.2:+4837719 None:intergenic
GGTCGTGATCCAGCTATGAT+AGG 0.473752 5.2:-4837756 MS.gene09971:CDS
CTCCAAAAGCCAAGAAGCCC+AGG 0.474778 5.2:-4837441 MS.gene09971:CDS
TCTGCACTTCCTATCATAGC+TGG 0.492222 5.2:+4837747 None:intergenic
GCACAGTCTCGTGGCTGAAA+GGG 0.494388 5.2:+4837714 None:intergenic
TTATCCCTCACATAGTTAAA+CGG 0.497017 5.2:+4837672 None:intergenic
AGCACAGTCTCGTGGCTGAA+AGG 0.500951 5.2:+4837713 None:intergenic
GAAACACTGCTATCATCCTT+CGG 0.515544 5.2:+4837415 None:intergenic
ATATTGATAAACCTATGTCT+CGG 0.524517 5.2:+4837639 None:intergenic
GCTATGATAGGAAGTGCAGA+TGG 0.538135 5.2:-4837744 MS.gene09971:CDS
ACTGGATGACCCCGAGACAT+AGG 0.551501 5.2:-4837650 MS.gene09971:CDS
GTTTCACGATCATTCATGGC+GGG 0.552327 5.2:+4837795 None:intergenic
CAAGAAGCCCAGGAAGCCGA+AGG 0.555978 5.2:-4837431 MS.gene09971:CDS
CTACTCCGTTTAACTATGTG+AGG 0.583386 5.2:-4837677 MS.gene09971:CDS
TGAAGGATTGAGTGTCAAGA+AGG 0.583448 5.2:-4837508 MS.gene09971:CDS
GGATTGAGTGTCAAGAAGGA+AGG 0.603585 5.2:-4837504 MS.gene09971:CDS
TCTCGTGGCTGAAAGGGCAA+GGG 0.616671 5.2:+4837720 None:intergenic
TCCGAAACAGCACAGTCTCG+TGG 0.624687 5.2:+4837705 None:intergenic
CTATGATAGGAAGTGCAGAT+GGG 0.640456 5.2:-4837743 MS.gene09971:CDS
GAGAATGTGGAGAATGCTGA+AGG 0.641502 5.2:-4837525 MS.gene09971:CDS
TGCATCAAGAAATGAGAATG+TGG 0.643643 5.2:-4837538 MS.gene09971:CDS
TACTCCGTTTAACTATGTGA+GGG 0.653092 5.2:-4837676 MS.gene09971:CDS
ATTGATAAACCTATGTCTCG+GGG 0.666123 5.2:+4837641 None:intergenic
TGTTTCACGATCATTCATGG+CGG 0.677866 5.2:+4837794 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATATTGATAAACCTATGTCT+CGG + chr5.2:4837566-4837585 None:intergenic 25.0%
!!! GAAACAAAACCATTTTTTTC+TGG - chr5.2:4837425-4837444 MS.gene09971:CDS 25.0%
TATTGATAAACCTATGTCTC+GGG + chr5.2:4837565-4837584 None:intergenic 30.0%
TCTGGAAGAACATCATAATT+TGG + chr5.2:4837602-4837621 None:intergenic 30.0%
TTATCCCTCACATAGTTAAA+CGG + chr5.2:4837533-4837552 None:intergenic 30.0%
!! TTTTGTTTCACGATCATTCA+TGG + chr5.2:4837414-4837433 None:intergenic 30.0%
ATTGATAAACCTATGTCTCG+GGG + chr5.2:4837564-4837583 None:intergenic 35.0%
TACTCCGTTTAACTATGTGA+GGG - chr5.2:4837526-4837545 MS.gene09971:CDS 35.0%
TGCATCAAGAAATGAGAATG+TGG - chr5.2:4837664-4837683 MS.gene09971:CDS 35.0%
TTAACTATGTGAGGGATAAC+TGG - chr5.2:4837534-4837553 MS.gene09971:CDS 35.0%
TTCTCATTTCTTGATGCATC+AGG + chr5.2:4837662-4837681 None:intergenic 35.0%
AAGAGTGATTGTGATGCTTC+TGG + chr5.2:4837620-4837639 None:intergenic 40.0%
ATCACAATCACTCTTCTTGC+CGG - chr5.2:4837625-4837644 MS.gene09971:CDS 40.0%
CTACTCCGTTTAACTATGTG+AGG - chr5.2:4837525-4837544 MS.gene09971:CDS 40.0%
GAAACACTGCTATCATCCTT+CGG + chr5.2:4837790-4837809 None:intergenic 40.0%
GGATCACGACCAGAAAAAAA+TGG + chr5.2:4837437-4837456 None:intergenic 40.0%
TGAAGGATTGAGTGTCAAGA+AGG - chr5.2:4837694-4837713 MS.gene09971:CDS 40.0%
TGTTTCACGATCATTCATGG+CGG + chr5.2:4837411-4837430 None:intergenic 40.0%
! CTATGATAGGAAGTGCAGAT+GGG - chr5.2:4837459-4837478 MS.gene09971:CDS 40.0%
! GAAGGTGCAAGAAGAAGAAA+AGG - chr5.2:4837716-4837735 MS.gene09971:CDS 40.0%
GAGAATGTGGAGAATGCTGA+AGG - chr5.2:4837677-4837696 MS.gene09971:CDS 45.0%
GGATTGAGTGTCAAGAAGGA+AGG - chr5.2:4837698-4837717 MS.gene09971:CDS 45.0%
GTTTCACGATCATTCATGGC+GGG + chr5.2:4837410-4837429 None:intergenic 45.0%
TCTGCACTTCCTATCATAGC+TGG + chr5.2:4837458-4837477 None:intergenic 45.0%
! GCTATGATAGGAAGTGCAGA+TGG - chr5.2:4837458-4837477 MS.gene09971:CDS 45.0%
! TCACTCTTCTTGCCGGTTAT+CGG - chr5.2:4837632-4837651 MS.gene09971:CDS 45.0%
CTATCATCCTTCGGCTTCCT+GGG + chr5.2:4837781-4837800 None:intergenic 50.0%
GGTCGTGATCCAGCTATGAT+AGG - chr5.2:4837446-4837465 MS.gene09971:CDS 50.0%
!! TTCCTGGGCTTCTTGGCTTT+TGG + chr5.2:4837766-4837785 None:intergenic 50.0%
ACTGGATGACCCCGAGACAT+AGG - chr5.2:4837552-4837571 MS.gene09971:CDS 55.0%
AGCACAGTCTCGTGGCTGAA+AGG + chr5.2:4837492-4837511 None:intergenic 55.0%
CTCCAAAAGCCAAGAAGCCC+AGG - chr5.2:4837761-4837780 MS.gene09971:CDS 55.0%
GCACAGTCTCGTGGCTGAAA+GGG + chr5.2:4837491-4837510 None:intergenic 55.0%
GCATCAGGCTGACCGATAAC+CGG + chr5.2:4837647-4837666 None:intergenic 55.0%
GCTATCATCCTTCGGCTTCC+TGG + chr5.2:4837782-4837801 None:intergenic 55.0%
TCCGAAACAGCACAGTCTCG+TGG + chr5.2:4837500-4837519 None:intergenic 55.0%
TCTCGTGGCTGAAAGGGCAA+GGG + chr5.2:4837485-4837504 None:intergenic 55.0%
!! GCCACGAGACTGTGCTGTTT+CGG - chr5.2:4837496-4837515 MS.gene09971:CDS 55.0%
!! GGGCTTCTTGGCTTTTGGAG+TGG + chr5.2:4837761-4837780 None:intergenic 55.0%
CAAGAAGCCCAGGAAGCCGA+AGG - chr5.2:4837771-4837790 MS.gene09971:CDS 60.0%
CTTCGGCTTCCTGGGCTTCT+TGG + chr5.2:4837773-4837792 None:intergenic 60.0%
GTCTCGTGGCTGAAAGGGCA+AGG + chr5.2:4837486-4837505 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 4837404 4837820 4837404 ID=MS.gene09971
chr5.2 mRNA 4837404 4837820 4837404 ID=MS.gene09971.t1;Parent=MS.gene09971
chr5.2 exon 4837404 4837820 4837404 ID=MS.gene09971.t1.exon1;Parent=MS.gene09971.t1
chr5.2 CDS 4837404 4837820 4837404 ID=cds.MS.gene09971.t1;Parent=MS.gene09971.t1
Gene Sequence

>MS.gene09971

ATGCCCGCCATGAATGATCGTGAAACAAAACCATTTTTTTCTGGTCGTGATCCAGCTATGATAGGAAGTGCAGATGGGCCCTTGCCCTTTCAGCCACGAGACTGTGCTGTTTCGGAGTCTGCTACTCCGTTTAACTATGTGAGGGATAACTGGATGACCCCGAGACATAGGTTTATCAATATGCAGCTGACAAATCCAAATTATGATGTTCTTCCAGAAGCATCACAATCACTCTTCTTGCCGGTTATCGGTCAGCCTGATGCATCAAGAAATGAGAATGTGGAGAATGCTGAAGGATTGAGTGTCAAGAAGGAAGGTGCAAGAAGAAGAAAAGGAAGTCTAAGAGTGCTGTTACCACTCCAAAAGCCAAGAAGCCCAGGAAGCCGAAGGATGATAGCAGTGTTTCACTATGTATAA
Protein sequence

>MS.gene09971.t1

MPAMNDRETKPFFSGRDPAMIGSADGPLPFQPRDCAVSESATPFNYVRDNWMTPRHRFINMQLTNPNYDVLPEASQSLFLPVIGQPDASRNENVENAEGLSVKKEGARRRKGSLRVLLPLQKPRSPGSRRMIAVFHYV