AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene83609

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83609.t1 MTR_2g103820 62.000 50 19 0 41 90 24 73 1.71e-13 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 35 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGTTTGTTGCTTCTGCTTA+TGG 0.167276 2.2:+1531377 MS.gene83609:CDS
AGCATACCCTCTATGGAAAA+TGG 0.193414 2.2:+1530949 MS.gene83609:CDS
CAATAGTCCATTCATCCTTT+TGG 0.207992 2.2:-1531289 None:intergenic
TGCAATTCCCATTTCTTCTT+AGG 0.233686 2.2:-1531485 None:intergenic
TCTAAGAAATTATGTCTATT+AGG 0.248117 2.2:+1530534 None:intergenic
TTCAAGTTTCTTACTATTGC+AGG 0.278520 2.2:-1530653 None:intergenic
GAATCCAAGCATACCCTCTA+TGG 0.309434 2.2:+1530942 MS.gene83609:CDS
AGATGAGGAAATTCTCAAAA+AGG 0.353004 2.2:+1531337 MS.gene83609:CDS
TGCAAGTACTGCATGAAGTA+TGG 0.359830 2.2:+1531504 MS.gene83609:CDS
CTCCTTAGTTTGATGTTATG+AGG 0.361414 2.2:+1531252 MS.gene83609:intron
ATATGGATCCTAAGAAGAAA+TGG 0.387085 2.2:+1531477 MS.gene83609:CDS
ATCATTATGATGAGAAGAAA+GGG 0.396325 2.2:+1531438 MS.gene83609:CDS
CTTGGATTCAGTAGACTCAT+TGG 0.408460 2.2:-1530928 None:intergenic
TTTGAGAATTTCCTCATCTT+CGG 0.410560 2.2:-1531333 None:intergenic
CACTAGCAGGGTGTGTCTTA+AGG 0.411819 2.2:+1530977 MS.gene83609:CDS
GGGAAAGGAAATGCAACATA+TGG 0.432000 2.2:+1531460 MS.gene83609:CDS
TATCATTATGATGAGAAGAA+AGG 0.461921 2.2:+1531437 MS.gene83609:CDS
CTGCATGAAGTATGGACATA+AGG 0.464768 2.2:+1531512 MS.gene83609:CDS
GCATACCCTCTATGGAAAAT+GGG 0.470893 2.2:+1530950 MS.gene83609:CDS
GAAAATGGGAAGACACTAGC+AGG 0.482307 2.2:+1530964 MS.gene83609:CDS
TATGGATCCTAAGAAGAAAT+GGG 0.504397 2.2:+1531478 MS.gene83609:CDS
TGATGACTGGAAAGATACTC+TGG 0.505483 2.2:+1530842 MS.gene83609:CDS
ACAATACCCAAAAGGATGAA+TGG 0.508332 2.2:+1531282 MS.gene83609:CDS
ATTCAGTAGACTCATTGGTA+AGG 0.536630 2.2:-1530923 None:intergenic
GATTGTCTTAGTATGATGAC+TGG 0.559196 2.2:+1530829 MS.gene83609:intron
GACTTCTTACAATACCCAAA+AGG 0.567602 2.2:+1531274 MS.gene83609:CDS
GACTCATTGGTAAGGGCAGT+AGG 0.581845 2.2:-1530915 None:intergenic
AAAAGACAATGGAGAAAAGG+TGG 0.583354 2.2:+1530701 MS.gene83609:CDS
TTCAGTAGACTCATTGGTAA+GGG 0.583995 2.2:-1530922 None:intergenic
TGATATAGTTACCGAAGATG+AGG 0.593197 2.2:+1531322 MS.gene83609:CDS
TGCTTCTGCTTATGGCACAA+AGG 0.606548 2.2:+1531385 MS.gene83609:CDS
CATTATGATGAGAAGAAAGG+GGG 0.619177 2.2:+1531440 MS.gene83609:CDS
AAGAAACTTGAAAACTAGAG+AGG 0.619289 2.2:+1530664 MS.gene83609:CDS
TCATTATGATGAGAAGAAAG+GGG 0.626507 2.2:+1531439 MS.gene83609:CDS
AAAATGGGAAGACACTAGCA+GGG 0.713007 2.2:+1530965 MS.gene83609:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CATAATGATATTTTCTTTTA+TGG - chr2.2:1531427-1531446 None:intergenic 15.0%
!! ATATAAGCTTAAAAAGACAA+TGG + chr2.2:1530690-1530709 MS.gene83609:CDS 20.0%
!! TGGTGAACTTATAAAATAAT+TGG + chr2.2:1531191-1531210 MS.gene83609:intron 20.0%
!!! ATCAAACTTCACATAATTTT+TGG - chr2.2:1531060-1531079 None:intergenic 20.0%
!!! TTGTCTTTTTAAGCTTATAT+TGG - chr2.2:1530690-1530709 None:intergenic 20.0%
! ATCATTATGATGAGAAGAAA+GGG + chr2.2:1531438-1531457 MS.gene83609:CDS 25.0%
! TATCATTATGATGAGAAGAA+AGG + chr2.2:1531437-1531456 MS.gene83609:CDS 25.0%
! TTAAAAAGACAATGGAGAAA+AGG + chr2.2:1530698-1530717 MS.gene83609:CDS 25.0%
! TTAGAATTTGCCAATATTGT+TGG + chr2.2:1530803-1530822 MS.gene83609:intron 25.0%
!! TTTTGGCATTTTCATTTTGT+GGG - chr2.2:1531043-1531062 None:intergenic 25.0%
!!! TTTTTGGCATTTTCATTTTG+TGG - chr2.2:1531044-1531063 None:intergenic 25.0%
AAGAAACTTGAAAACTAGAG+AGG + chr2.2:1530664-1530683 MS.gene83609:CDS 30.0%
AATACTGCTAGACAAAGTAA+AGG - chr2.2:1530774-1530793 None:intergenic 30.0%
AGATGAGGAAATTCTCAAAA+AGG + chr2.2:1531337-1531356 MS.gene83609:CDS 30.0%
ATATGGATCCTAAGAAGAAA+TGG + chr2.2:1531477-1531496 MS.gene83609:CDS 30.0%
CAACAAATACTCACATTTCT+TGG - chr2.2:1531111-1531130 None:intergenic 30.0%
GACAATCATACCAACAATAT+TGG - chr2.2:1530816-1530835 None:intergenic 30.0%
TATGGATCCTAAGAAGAAAT+GGG + chr2.2:1531478-1531497 MS.gene83609:CDS 30.0%
TCATTATGATGAGAAGAAAG+GGG + chr2.2:1531439-1531458 MS.gene83609:CDS 30.0%
TTTGACAAGACAAAGTATGA+TGG + chr2.2:1531134-1531153 MS.gene83609:intron 30.0%
TTTGAGAATTTCCTCATCTT+CGG - chr2.2:1531336-1531355 None:intergenic 30.0%
! AATAGTCCATTCATCCTTTT+GGG - chr2.2:1531291-1531310 None:intergenic 30.0%
! TTCAAGTTTCTTACTATTGC+AGG - chr2.2:1530656-1530675 None:intergenic 30.0%
AAAAGACAATGGAGAAAAGG+TGG + chr2.2:1530701-1530720 MS.gene83609:CDS 35.0%
ACAATACCCAAAAGGATGAA+TGG + chr2.2:1531282-1531301 MS.gene83609:CDS 35.0%
ATTCAGTAGACTCATTGGTA+AGG - chr2.2:1530926-1530945 None:intergenic 35.0%
CATTATGATGAGAAGAAAGG+GGG + chr2.2:1531440-1531459 MS.gene83609:CDS 35.0%
CTCATAACATCAAACTAAGG+AGG - chr2.2:1531254-1531273 None:intergenic 35.0%
GACTTCTTACAATACCCAAA+AGG + chr2.2:1531274-1531293 MS.gene83609:CDS 35.0%
GATTGTCTTAGTATGATGAC+TGG + chr2.2:1530829-1530848 MS.gene83609:intron 35.0%
GTCCTCATAACATCAAACTA+AGG - chr2.2:1531257-1531276 None:intergenic 35.0%
TAAGGTCATAGGTTACACTA+TGG + chr2.2:1530995-1531014 MS.gene83609:intron 35.0%
TGATATAGTTACCGAAGATG+AGG + chr2.2:1531322-1531341 MS.gene83609:CDS 35.0%
TGCAATTCCCATTTCTTCTT+AGG - chr2.2:1531488-1531507 None:intergenic 35.0%
TTCAGTAGACTCATTGGTAA+GGG - chr2.2:1530925-1530944 None:intergenic 35.0%
! ACAAAGTATGATGGTGTTAG+CGG + chr2.2:1531143-1531162 MS.gene83609:intron 35.0%
! ACCCGGTTTAGCAAAATTTT+CGG - chr2.2:1530728-1530747 None:intergenic 35.0%
! ACCGAAAATTTTGCTAAACC+GGG + chr2.2:1530724-1530743 MS.gene83609:CDS 35.0%
! CAATAGTCCATTCATCCTTT+TGG - chr2.2:1531292-1531311 None:intergenic 35.0%
! CTCCTTAGTTTGATGTTATG+AGG + chr2.2:1531252-1531271 MS.gene83609:intron 35.0%
! GACCGAAAATTTTGCTAAAC+CGG + chr2.2:1530723-1530742 MS.gene83609:CDS 35.0%
!! ATTTCTTGGCTTTGTCAAAG+TGG - chr2.2:1531097-1531116 None:intergenic 35.0%
!! TTTCTTGGCTTTGTCAAAGT+GGG - chr2.2:1531096-1531115 None:intergenic 35.0%
AAAATGGGAAGACACTAGCA+GGG + chr2.2:1530965-1530984 MS.gene83609:CDS 40.0%
AACATCAAACTAAGGAGGCA+AGG - chr2.2:1531249-1531268 None:intergenic 40.0%
ACACTATGGAGAAGTCCATT+AGG + chr2.2:1531009-1531028 MS.gene83609:intron 40.0%
AGCATACCCTCTATGGAAAA+TGG + chr2.2:1530949-1530968 MS.gene83609:CDS 40.0%
CTTGGATTCAGTAGACTCAT+TGG - chr2.2:1530931-1530950 None:intergenic 40.0%
GCATACCCTCTATGGAAAAT+GGG + chr2.2:1530950-1530969 MS.gene83609:CDS 40.0%
GGGAAAGGAAATGCAACATA+TGG + chr2.2:1531460-1531479 MS.gene83609:CDS 40.0%
TGATGACTGGAAAGATACTC+TGG + chr2.2:1530842-1530861 MS.gene83609:CDS 40.0%
! GTCTTCCCATTTTCCATAGA+GGG - chr2.2:1530958-1530977 None:intergenic 40.0%
! TGCAAGTACTGCATGAAGTA+TGG + chr2.2:1531504-1531523 MS.gene83609:CDS 40.0%
! TGTCTTCCCATTTTCCATAG+AGG - chr2.2:1530959-1530978 None:intergenic 40.0%
!! CAGTTTGTTGCTTCTGCTTA+TGG + chr2.2:1531377-1531396 MS.gene83609:CDS 40.0%
!! TTTTCCATAGAGGGTATGCT+TGG - chr2.2:1530949-1530968 None:intergenic 40.0%
AGGGTGTGTCTTAAGGTCAT+AGG + chr2.2:1530984-1531003 MS.gene83609:intron 45.0%
AGTGTAAAGAACAGCGTACC+CGG - chr2.2:1530745-1530764 None:intergenic 45.0%
GAAAATGGGAAGACACTAGC+AGG + chr2.2:1530964-1530983 MS.gene83609:CDS 45.0%
GAATCCAAGCATACCCTCTA+TGG + chr2.2:1530942-1530961 MS.gene83609:CDS 45.0%
TGATGAGAAGAAAGGGGGAA+AGG + chr2.2:1531445-1531464 MS.gene83609:CDS 45.0%
TGCTTCTGCTTATGGCACAA+AGG + chr2.2:1531385-1531404 MS.gene83609:CDS 45.0%
TTGTGGGATGCTTTGCCTAA+TGG - chr2.2:1531027-1531046 None:intergenic 45.0%
! GCGAGAGCATATCATGATGT+TGG + chr2.2:1531171-1531190 MS.gene83609:intron 45.0%
!! AATTCTTTAAATAAAATAAA+AGG - chr2.2:1530608-1530627 None:intergenic 5.0%
CACTAGCAGGGTGTGTCTTA+AGG + chr2.2:1530977-1530996 MS.gene83609:CDS 50.0%
GACTCATTGGTAAGGGCAGT+AGG - chr2.2:1530918-1530937 None:intergenic 50.0%
!! TTGGTGAGAGCACCTTGATC+TGG + chr2.2:1531210-1531229 MS.gene83609:intron 50.0%
ACTAAGGAGGCAAGGACTCG+AGG - chr2.2:1531241-1531260 None:intergenic 55.0%
CTCGAGGACTCTCCAGATCA+AGG - chr2.2:1531225-1531244 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 1530545 1531532 1530545 ID=MS.gene83609
chr2.2 mRNA 1530545 1531532 1530545 ID=MS.gene83609.t1;Parent=MS.gene83609
chr2.2 exon 1530545 1530555 1530545 ID=MS.gene83609.t1.exon1;Parent=MS.gene83609.t1
chr2.2 CDS 1530545 1530555 1530545 ID=cds.MS.gene83609.t1;Parent=MS.gene83609.t1
chr2.2 exon 1530637 1530745 1530637 ID=MS.gene83609.t1.exon2;Parent=MS.gene83609.t1
chr2.2 CDS 1530637 1530745 1530637 ID=cds.MS.gene83609.t1;Parent=MS.gene83609.t1
chr2.2 exon 1530840 1530998 1530840 ID=MS.gene83609.t1.exon3;Parent=MS.gene83609.t1
chr2.2 CDS 1530840 1530998 1530840 ID=cds.MS.gene83609.t1;Parent=MS.gene83609.t1
chr2.2 exon 1531260 1531532 1531260 ID=MS.gene83609.t1.exon4;Parent=MS.gene83609.t1
chr2.2 CDS 1531260 1531532 1531260 ID=cds.MS.gene83609.t1;Parent=MS.gene83609.t1
Gene Sequence

>MS.gene83609

ATGTCTATTAGGTTAGTTTACTTCAAAACATATTTCTAATTTTATCTAGATGTTTGTCATCCTTTTATTTTATTTAAAGAATTCTTGTGTAGTTTTCAAGAGTTAGAACCTGCAATAGTAAGAAACTTGAAAACTAGAGAGGCCAATATAAGCTTAAAAAGACAATGGAGAAAAGGTGGACCGAAAATTTTGCTAAACCGGGTACGCTGTTCTTTACACTATAAAACCTTTACTTTGTCTAGCAGTATTTTTTCGTTGTTAGAATTTGCCAATATTGTTGGTATGATTGTCTTAGTATGATGACTGGAAAGATACTCTGGATCTATTGTTAGCTATTAACAACTTTGATTTAGCTTTAAGAAATGAGAAGCCTACTGCCCTTACCAATGAGTCTACTGAATCCAAGCATACCCTCTATGGAAAATGGGAAGACACTAGCAGGGTGTGTCTTAAGGTCATAGGTTACACTATGGAGAAGTCCATTAGGCAAAGCATCCCACAAAATGAAAATGCCAAAAATTATGTGAAGTTTGATGTTGAAAAGCTCACCCACTTTGACAAAGCCAAGAAATGTGAGTATTTGTTGTTGTTTGACAAGACAAAGTATGATGGTGTTAGCGGTACGTGCGAGAGCATATCATGATGTTGGTGAACTTATAAAATAATTGGTGAGAGCACCTTGATCTGGAGAGTCCTCGAGTCCTTGCCTCCTTAGTTTGATGTTATGAGGACTTCTTACAATACCCAAAAGGATGAATGGACTATTGTTGAGTTGATTGATATAGTTACCGAAGATGAGGAAATTCTCAAAAAGGCTAAATTTCAAAGTGTTCAGTTTGTTGCTTCTGCTTATGGCACAAAGGATGTCAAGAGAAACTACCATAAAAGAAAATATCATTATGATGAGAAGAAAGGGGGAAAGGAAATGCAACATATGGATCCTAAGAAGAAATGGGAATTGCAAGTACTGCATGAAGTATGGACATAA
Protein sequence

>MS.gene83609.t1

MSISFQELEPAIVRNLKTREANISLKRQWRKGGPKILLNRYDDWKDTLDLLLAINNFDLALRNEKPTALTNESTESKHTLYGKWEDTSRVCLKFDVMRTSYNTQKDEWTIVELIDIVTEDEEILKKAKFQSVQFVASAYGTKDVKRNYHKRKYHYDEKKGGKEMQHMDPKKKWELQVLHEVWT