AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene43830

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene43830.t1 MTR_4g123470 86.364 154 21 0 11 164 72 225 8.57e-99 284
MS.gene43830.t1 MTR_7g113060 84.211 38 6 0 126 163 3 40 6.99e-17 74.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 37 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGTTCCTATCGTTGGATA+TGG 0.258835 5.2:+59875263 MS.gene43830:CDS
CACAGTGCATGTACAAAATC+AGG 0.330296 5.2:+59874837 MS.gene43830:CDS
TAGGGACTACCTCATACTTT+TGG 0.338565 5.2:+59875396 MS.gene43830:intron
AATCGTGATGTTTCACTCTA+AGG 0.342040 5.2:-59875425 None:intergenic
CATAAGGTCCCCACAACATT+AGG 0.363936 5.2:-59875449 None:intergenic
TCCGAACATCACATTTGGTA+TGG 0.409212 5.2:-59875511 None:intergenic
CGATTGTTCTATGAGTTTAG+TGG 0.421818 5.2:+59875107 MS.gene43830:CDS
ATCTACTTCCACCAAGGTAC+TGG 0.428620 5.2:-59875148 None:intergenic
ACCTTTGAAGTTCCTATCGT+TGG 0.439777 5.2:+59875257 MS.gene43830:CDS
TTGTGCTGCCAATGGTATTG+AGG 0.463000 5.2:+59875551 MS.gene43830:CDS
TGCCACACTCATGGAATGAT+AGG 0.466864 5.2:-59875219 None:intergenic
CCCATACCAAATGTGATGTT+CGG 0.470215 5.2:+59875510 MS.gene43830:CDS
GTCATGTGTTTATTAACGCT+TGG 0.474103 5.2:-59875634 None:intergenic
CCAAATGTGATGTTCGGAAA+AGG 0.475440 5.2:+59875516 MS.gene43830:CDS
AAACGATGCTGCCACACTCA+TGG 0.481669 5.2:-59875228 None:intergenic
CCGAACATCACATTTGGTAT+GGG 0.484360 5.2:-59875510 None:intergenic
GGCCGTTGTTGACAGATGGT+TGG 0.487397 5.2:+59875075 MS.gene43830:intron
AGGAATTTGCCAAAAGTATG+AGG 0.497368 5.2:-59875405 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.501205 5.2:+59875552 MS.gene43830:CDS
ATTATTGCTTTCCAGTACCT+TGG 0.503165 5.2:+59875137 MS.gene43830:CDS
ATCACGATTACCTAATGTTG+TGG 0.515574 5.2:+59875439 MS.gene43830:CDS
TCACGATTACCTAATGTTGT+GGG 0.516456 5.2:+59875440 MS.gene43830:CDS
ACAGGAATGATATTGTCATA+AGG 0.528831 5.2:-59875465 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.541156 5.2:-59875483 None:intergenic
ATTGCTTTCCAGTACCTTGG+TGG 0.549152 5.2:+59875140 MS.gene43830:CDS
TTTCAAGTGCAAGTGCGTCA+TGG 0.567746 5.2:+59875590 MS.gene43830:CDS
GTCTCCGCCCTCAATACCAT+TGG 0.581950 5.2:-59875559 None:intergenic
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 5.2:+59875520 MS.gene43830:CDS
TCCAACGATAGGAACTTCAA+AGG 0.611311 5.2:-59875258 None:intergenic
GTCGATCCATATCCAACGAT+AGG 0.629633 5.2:-59875269 None:intergenic
ACCCTATCATTCCATGAGTG+TGG 0.630625 5.2:+59875217 MS.gene43830:CDS
GCCACACTCATGGAATGATA+GGG 0.640732 5.2:-59875218 None:intergenic
CACGATTACCTAATGTTGTG+GGG 0.648368 5.2:+59875441 MS.gene43830:CDS
ACACTCATGGAATGATAGGG+TGG 0.656827 5.2:-59875215 None:intergenic
TTTGAAATCTACTTCCACCA+AGG 0.681040 5.2:-59875154 None:intergenic
TGGATCGACGATATCACCGA+AGG 0.688446 5.2:+59875283 MS.gene43830:CDS
GCTGCCAATGGTATTGAGGG+CGG 0.739556 5.2:+59875555 MS.gene43830:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTTTTTTTTCTTTTTTTT+AGG + chr5.2:59875377-59875396 MS.gene43830:intron 10.0%
!!! GTTTTTTTTTCTTTTTTTTA+GGG + chr5.2:59875378-59875397 MS.gene43830:intron 10.0%
!! TTCTATTTAAATAAGATGAA+CGG + chr5.2:59874887-59874906 MS.gene43830:intron 15.0%
!! AAAAAACAATAAACAACCTT+CGG - chr5.2:59875302-59875321 None:intergenic 20.0%
! AAGTTTACGGAATAAGTTTA+CGG - chr5.2:59874916-59874935 None:intergenic 25.0%
ACAGGAATGATATTGTCATA+AGG - chr5.2:59875468-59875487 None:intergenic 30.0%
AGTTAGGCAGAAAAAGTTTA+CGG - chr5.2:59874929-59874948 None:intergenic 30.0%
TGTTCAACAAATCAGTTAGT+CGG + chr5.2:59875054-59875073 MS.gene43830:intron 30.0%
!! ACTTTTTCTGCCTAACTTAT+AGG + chr5.2:59874932-59874951 MS.gene43830:intron 30.0%
AATCGTGATGTTTCACTCTA+AGG - chr5.2:59875428-59875447 None:intergenic 35.0%
ATCACGATTACCTAATGTTG+TGG + chr5.2:59875439-59875458 MS.gene43830:CDS 35.0%
ATTATTGCTTTCCAGTACCT+TGG + chr5.2:59875137-59875156 MS.gene43830:CDS 35.0%
CGATTGTTCTATGAGTTTAG+TGG + chr5.2:59875107-59875126 MS.gene43830:CDS 35.0%
TCACGATTACCTAATGTTGT+GGG + chr5.2:59875440-59875459 MS.gene43830:CDS 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr5.2:59875486-59875505 None:intergenic 35.0%
! AGGAATTTGCCAAAAGTATG+AGG - chr5.2:59875408-59875427 None:intergenic 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr5.2:59875157-59875176 None:intergenic 35.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr5.2:59875520-59875539 MS.gene43830:CDS 40.0%
CACAGTGCATGTACAAAATC+AGG + chr5.2:59874837-59874856 MS.gene43830:CDS 40.0%
CACGATTACCTAATGTTGTG+GGG + chr5.2:59875441-59875460 MS.gene43830:CDS 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr5.2:59875516-59875535 MS.gene43830:CDS 40.0%
CCCATACCAAATGTGATGTT+CGG + chr5.2:59875510-59875529 MS.gene43830:CDS 40.0%
CCGAACATCACATTTGGTAT+GGG - chr5.2:59875513-59875532 None:intergenic 40.0%
CTGCCTAACTTATAGGATGT+CGG + chr5.2:59874939-59874958 MS.gene43830:intron 40.0%
GAAGTTCCTATCGTTGGATA+TGG + chr5.2:59875263-59875282 MS.gene43830:CDS 40.0%
TCCAACGATAGGAACTTCAA+AGG - chr5.2:59875261-59875280 None:intergenic 40.0%
TCCGAACATCACATTTGGTA+TGG - chr5.2:59875514-59875533 None:intergenic 40.0%
TCTCCGACATCCTATAAGTT+AGG - chr5.2:59874945-59874964 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr5.2:59875519-59875538 None:intergenic 40.0%
! TAGGGACTACCTCATACTTT+TGG + chr5.2:59875396-59875415 MS.gene43830:intron 40.0%
!! ACCTTTGAAGTTCCTATCGT+TGG + chr5.2:59875257-59875276 MS.gene43830:CDS 40.0%
ACACTCATGGAATGATAGGG+TGG - chr5.2:59875218-59875237 None:intergenic 45.0%
ACCCTATCATTCCATGAGTG+TGG + chr5.2:59875217-59875236 MS.gene43830:CDS 45.0%
ATCTACTTCCACCAAGGTAC+TGG - chr5.2:59875151-59875170 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG + chr5.2:59875140-59875159 MS.gene43830:CDS 45.0%
CATAAGGTCCCCACAACATT+AGG - chr5.2:59875452-59875471 None:intergenic 45.0%
CTCCAACCATCTGTCAACAA+CGG - chr5.2:59875080-59875099 None:intergenic 45.0%
GCCACACTCATGGAATGATA+GGG - chr5.2:59875221-59875240 None:intergenic 45.0%
GTCGATCCATATCCAACGAT+AGG - chr5.2:59875272-59875291 None:intergenic 45.0%
TCTAGCAAGTGACATTGCTC+TGG - chr5.2:59875008-59875027 None:intergenic 45.0%
TGCCACACTCATGGAATGAT+AGG - chr5.2:59875222-59875241 None:intergenic 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr5.2:59875551-59875570 MS.gene43830:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + chr5.2:59875543-59875562 MS.gene43830:CDS 45.0%
! GAGCAATGTCACTTGCTAGA+TGG + chr5.2:59875008-59875027 MS.gene43830:intron 45.0%
! GTCACTTGCTAGATGGTGAT+GGG + chr5.2:59875015-59875034 MS.gene43830:intron 45.0%
! TGTCACTTGCTAGATGGTGA+TGG + chr5.2:59875014-59875033 MS.gene43830:intron 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr5.2:59875552-59875571 MS.gene43830:CDS 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG + chr5.2:59875590-59875609 MS.gene43830:CDS 45.0%
AAACGATGCTGCCACACTCA+TGG - chr5.2:59875231-59875250 None:intergenic 50.0%
TGGATCGACGATATCACCGA+AGG + chr5.2:59875283-59875302 MS.gene43830:CDS 50.0%
AGTCGGCCGTTGTTGACAGA+TGG + chr5.2:59875071-59875090 MS.gene43830:intron 55.0%
GGCCGTTGTTGACAGATGGT+TGG + chr5.2:59875075-59875094 MS.gene43830:intron 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr5.2:59875562-59875581 None:intergenic 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr5.2:59875555-59875574 MS.gene43830:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 59874825 59875644 59874825 ID=MS.gene43830
chr5.2 mRNA 59874825 59875644 59874825 ID=MS.gene43830.t1;Parent=MS.gene43830
chr5.2 exon 59874825 59874858 59874825 ID=MS.gene43830.t1.exon1;Parent=MS.gene43830.t1
chr5.2 CDS 59874825 59874858 59874825 ID=cds.MS.gene43830.t1;Parent=MS.gene43830.t1
chr5.2 exon 59875090 59875304 59875090 ID=MS.gene43830.t1.exon2;Parent=MS.gene43830.t1
chr5.2 CDS 59875090 59875304 59875090 ID=cds.MS.gene43830.t1;Parent=MS.gene43830.t1
chr5.2 exon 59875399 59875644 59875399 ID=MS.gene43830.t1.exon3;Parent=MS.gene43830.t1
chr5.2 CDS 59875399 59875644 59875399 ID=cds.MS.gene43830.t1;Parent=MS.gene43830.t1
Gene Sequence

>MS.gene43830

ATGTTCGTTCTTCACAGTGCATGTACAAAATCAGGTTTGTTTCATTTGATGATTTAATATTTTTCTATTTAAATAAGATGAACGGATTCCGTAAACTTATTCCGTAAACTTTTTCTGCCTAACTTATAGGATGTCGGAGAACTGCAGCTATTCTTCGTTGCTGAATATTTCTACGAGCTACCAGAGCAATGTCACTTGCTAGATGGTGATGGGAATACTCATAACGTCGTGTTCAACAAATCAGTTAGTCGGCCGTTGTTGACAGATGGTTGGAGTGCATTGCGATTGTTCTATGAGTTTAGTGGAAGTAAGATTATTGCTTTCCAGTACCTTGGTGGAAGTAGATTTCAAATCTTTATTTTTGCTCATAACATTACTCTAGCTGATTATCCACCCTATCATTCCATGAGTGTGGCAGCATCGTTTTATTGTACCTTTGAAGTTCCTATCGTTGGATATGGATCGACGATATCACCGAAGGTTGTTTATTGTTTTTTTGTTGCAATTCAATTAGATATATGTTGTAATAAAGTATTTTTGTCTGTCATTAACAGTTTTTTTTTCTTTTTTTTAGGGACTACCTCATACTTTTGGCAAATTCCTTAGAGTGAAACATCACGATTACCTAATGTTGTGGGGACCTTATGACAATATCATTCCTGTGAGACTCAAATATACAGACGAACCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAGTGCGTCATGGACGAAAAATATGTTATCGTATCCAAGCGTTAA
Protein sequence

>MS.gene43830.t1

MFVLHSACTKSDGWSALRLFYEFSGSKIIAFQYLGGSRFQIFIFAHNITLADYPPYHSMSVAASFYCTFEVPIVGYGSTISPKGLPHTFGKFLRVKHHDYLMLWGPYDNIIPVRLKYTDEPIPNVMFGKGWTSFCAANGIEGGDVLIFKCKCVMDEKYVIVSKR