AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene05491


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene05491.t1 MTR_6g085000 100.000 191 0 0 1 191 1 191 4.48e-139 385
MS.gene05491.t1 MTR_6g021670 99.476 191 1 0 1 191 1 191 7.51e-139 385
MS.gene05491.t1 MTR_8g087480 65.909 44 7 1 145 188 51 86 1.77e-12 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene05491.t1 AT1G48830 81.152 191 36 0 1 191 1 191 2.55e-116 328
MS.gene05491.t1 AT1G48830 81.152 191 36 0 1 191 1 191 2.55e-116 328
MS.gene05491.t1 AT3G02560 80.628 191 37 0 1 191 1 191 8.53e-114 322
MS.gene05491.t1 AT3G02560 80.628 191 37 0 1 191 1 191 8.53e-114 322
MS.gene05491.t1 AT3G02560 80.628 191 37 0 1 191 1 191 8.53e-114 322
MS.gene05491.t1 AT5G16130 81.383 188 35 0 1 188 1 188 2.24e-113 321

Find 51 sgRNAs with CRISPR-Local

Find 87 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACAGCCAAGTTGATGTTTC+TGG 0.170905 6.2:+84065417 MS.gene05491:intron
TCAGTATTGTTTCTCTCCTT+TGG 0.234939 6.2:-84066406 None:intergenic
CAGTATTGTTTCTCTCCTTT+GGG 0.277926 6.2:-84066405 None:intergenic
AGAATCTAGGCCTCAGTAAC+AGG 0.289126 6.2:-84066496 None:intergenic
ATAGTTTACCTTCATGATCT+TGG 0.292174 6.2:-84066187 None:intergenic
AAATTCACGTCAGGCTCGTT+AGG 0.322256 6.2:+84065496 MS.gene05491:CDS
GGATCCATCAATTCTGTATC+TGG 0.328918 6.2:-84066166 None:intergenic
TGAGCAGCAGAGCCTTTCTT+TGG 0.360132 6.2:-84066057 None:intergenic
CGTACCAGATACAGAATTGA+TGG 0.382090 6.2:+84066162 MS.gene05491:CDS
GTTGCAGGCTCTGTTTGATC+TGG 0.398358 6.2:+84065260 MS.gene05491:intron
TCGTGAAAATGTTTACTTCA+AGG 0.415835 6.2:+84065081 None:intergenic
CGCTGAGCCTACTGAATTTG+AGG 0.426295 6.2:+84065127 MS.gene05491:CDS
GCAGCAGAGCCTTTCTTTGG+TGG 0.437765 6.2:-84066054 None:intergenic
ATTTGAGGAGTCAGTTGGAC+AGG 0.472058 6.2:+84065142 MS.gene05491:CDS
TCCTCAATCTGTAGGGGACA+TGG 0.482798 6.2:-84065461 None:intergenic
TGGTGGCCTGACGATTCTCC+TGG 0.483590 6.2:-84066037 None:intergenic
GTTTCCGCAAAATTCACGTC+AGG 0.487674 6.2:+84065487 MS.gene05491:CDS
GTTTGAGTACCCTGTTACTG+AGG 0.503056 6.2:+84066486 MS.gene05491:CDS
CGTGGACAGCAGTGAGTGTA+CGG 0.505350 6.2:-84066092 None:intergenic
TTCTGGCAACCGCAAGGCTG+TGG 0.507229 6.2:+84065434 MS.gene05491:CDS
GTGTTGCCTGCTGAGATTGT+TGG 0.507352 6.2:+84066135 MS.gene05491:CDS
ATCGTCAGGCCACCAAAGAA+AGG 0.508890 6.2:+84066045 MS.gene05491:CDS
TTGCCACCAGGAGAATCGTC+AGG 0.510117 6.2:+84066031 MS.gene05491:CDS
GAAGAAAATCAGCAAGGACA+AGG 0.510615 6.2:+84065103 MS.gene05491:CDS
GAAACCCTTCCTCAATCTGT+AGG 0.511555 6.2:-84065469 None:intergenic
TCCATGTCCCCTACAGATTG+AGG 0.519730 6.2:+84065460 MS.gene05491:CDS
GCAGTTTACAGGAAACTCTC+AGG 0.525392 6.2:+84066451 MS.gene05491:CDS
AAACCCTTCCTCAATCTGTA+GGG 0.532886 6.2:-84065468 None:intergenic
AATTCACGTCAGGCTCGTTA+GGG 0.538364 6.2:+84065497 MS.gene05491:CDS
ACTGAATTTGAGGAGTCAGT+TGG 0.548538 6.2:+84065137 MS.gene05491:CDS
CGTTTGCCAACAATCTCAGC+AGG 0.559003 6.2:-84066141 None:intergenic
TGTCCCCTACAGATTGAGGA+AGG 0.573232 6.2:+84065464 MS.gene05491:CDS
ATGTAATCCTCATTGCCACC+AGG 0.584954 6.2:+84066019 MS.gene05491:CDS
CGATTCTCCTGGTGGCAATG+AGG 0.590532 6.2:-84066026 None:intergenic
AAGAAAATCAGCAAGGACAA+GGG 0.599976 6.2:+84065104 MS.gene05491:CDS
TGATGTTTCTGGCAACCGCA+AGG 0.602547 6.2:+84065428 MS.gene05491:CDS
GGTTGCCAGAAACATCAACT+TGG 0.607356 6.2:-84065422 None:intergenic
TGAGAAGAAATTCAGCGGAA+AGG 0.621961 6.2:+84065524 MS.gene05491:CDS
ACTGACTCCTCAAATTCAGT+AGG 0.622702 6.2:-84065134 None:intergenic
TGATGGATCCAAGATCATGA+AGG 0.639271 6.2:+84066179 MS.gene05491:CDS
GTCCCCTACAGATTGAGGAA+GGG 0.640329 6.2:+84065465 MS.gene05491:CDS
AACCCTTCCTCAATCTGTAG+GGG 0.640960 6.2:-84065467 None:intergenic
TGTCCACGAGGCAATGCTCG+AGG 0.642990 6.2:+84066107 MS.gene05491:CDS
TTCAAGGAAGAAAATCAGCA+AGG 0.648771 6.2:+84065097 MS.gene05491:CDS
GCAGTGAGTGTACGGCTGCG+TGG 0.657285 6.2:-84066084 None:intergenic
TACACTCACTGCTGTCCACG+AGG 0.659160 6.2:+84066095 MS.gene05491:CDS
TGGCCTGACGATTCTCCTGG+TGG 0.662830 6.2:-84066034 None:intergenic
GAATCTAGGCCTCAGTAACA+GGG 0.677360 6.2:-84066495 None:intergenic
CATCCTCGAGCATTGCCTCG+TGG 0.690997 6.2:-84066110 None:intergenic
CATGGATAACCACAGCCTTG+CGG 0.691240 6.2:-84065443 None:intergenic
GAGCTTGAGAAGAAATTCAG+CGG 0.694607 6.2:+84065519 MS.gene05491:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAATAAGAAATAATGTTAA+TGG + chr6.2:84066346-84066365 MS.gene05491:intron 15.0%
!! ATTAGTATACAATAAAGTTA+AGG - chr6.2:84065981-84066000 None:intergenic 15.0%
!! AAATTGGAACAAAAAATTGT+CGG - chr6.2:84065621-84065640 None:intergenic 20.0%
!! AGAATAAAGTTCTTGAAATA+AGG - chr6.2:84065670-84065689 None:intergenic 20.0%
!! TTAAAGCAATTTAAAAACCA+AGG - chr6.2:84065705-84065724 None:intergenic 20.0%
!!! AGGTTATATATTGATTACTA+CGG + chr6.2:84065162-84065181 MS.gene05491:intron 20.0%
!!! ATTTTTTAAGGCTAATGTTA+TGG - chr6.2:84065932-84065951 None:intergenic 20.0%
!!! GATGTATTTGTTTTAAGTTT+TGG - chr6.2:84066252-84066271 None:intergenic 20.0%
!!! TGTGAGAAAACAATTTTTTA+AGG - chr6.2:84065944-84065963 None:intergenic 20.0%
! CTGTAAAACTGAAATTAATC+AGG + chr6.2:84065756-84065775 MS.gene05491:intron 25.0%
! TAATGTTAATGGAATTCTTG+TGG + chr6.2:84066357-84066376 MS.gene05491:intron 25.0%
!!! TTGTTTTAAGTTTTGGTTGA+TGG - chr6.2:84066245-84066264 None:intergenic 25.0%
ACACAAAACAGGAAGTTATT+TGG - chr6.2:84066221-84066240 None:intergenic 30.0%
ATAGTTTACCTTCATGATCT+TGG - chr6.2:84066190-84066209 None:intergenic 30.0%
CAAATTCTTTAGTGTACGTT+TGG - chr6.2:84065903-84065922 None:intergenic 30.0%
GACAGAATCGTAATAAAAGA+TGG - chr6.2:84065596-84065615 None:intergenic 30.0%
GATTACATCCTACAAGTTAA+AGG - chr6.2:84066007-84066026 None:intergenic 30.0%
TTAGAAAGAATAACTGGCAA+AGG - chr6.2:84065568-84065587 None:intergenic 30.0%
! AAACATTTTCTGCAGTTTAC+AGG + chr6.2:84066440-84066459 MS.gene05491:CDS 30.0%
! TCTGTGTATATAGGTGTTTT+TGG + chr6.2:84066381-84066400 MS.gene05491:intron 30.0%
!! CTAATGAACCTTTAACTTGT+AGG + chr6.2:84065996-84066015 MS.gene05491:intron 30.0%
!! GTTATTTTGCAAAATCACTC+TGG + chr6.2:84066274-84066293 MS.gene05491:intron 30.0%
!!! TGTTTTGAATTTGTTGTTGC+AGG + chr6.2:84065245-84065264 MS.gene05491:intron 30.0%
AACTGAAATTAATCAGGCTG+CGG + chr6.2:84065762-84065781 MS.gene05491:intron 35.0%
AAGAAAATCAGCAAGGACAA+GGG + chr6.2:84065104-84065123 MS.gene05491:CDS 35.0%
CGAGTAGAAGACAAAGAAAT+TGG - chr6.2:84065637-84065656 None:intergenic 35.0%
GTCTAAGCATGTGTTTGATT+TGG + chr6.2:84065784-84065803 MS.gene05491:intron 35.0%
GTGCAGTTAGAAAGAATAAC+TGG - chr6.2:84065574-84065593 None:intergenic 35.0%
GTGTAAGGATGTGTTCTTTA+TGG + chr6.2:84065339-84065358 MS.gene05491:intron 35.0%
TACATCAATTCTGCAGTGTA+AGG + chr6.2:84065324-84065343 MS.gene05491:intron 35.0%
TCTTTAGTGTACGTTTGGTT+TGG - chr6.2:84065898-84065917 None:intergenic 35.0%
TTCAAGGAAGAAAATCAGCA+AGG + chr6.2:84065097-84065116 MS.gene05491:CDS 35.0%
! ATTCTGTTTTGCATTCTCCT+TGG + chr6.2:84065685-84065704 MS.gene05491:intron 35.0%
! CAGTATTGTTTCTCTCCTTT+GGG - chr6.2:84066408-84066427 None:intergenic 35.0%
! TCAGTATTGTTTCTCTCCTT+TGG - chr6.2:84066409-84066428 None:intergenic 35.0%
! TCTTGTGGTTCTGTGTATAT+AGG + chr6.2:84066372-84066391 MS.gene05491:intron 35.0%
AAACCCTTCCTCAATCTGTA+GGG - chr6.2:84065471-84065490 None:intergenic 40.0%
ACTGAATTTGAGGAGTCAGT+TGG + chr6.2:84065137-84065156 MS.gene05491:CDS 40.0%
CGTACCAGATACAGAATTGA+TGG + chr6.2:84066162-84066181 MS.gene05491:CDS 40.0%
GAAGAAAATCAGCAAGGACA+AGG + chr6.2:84065103-84065122 MS.gene05491:CDS 40.0%
GAGCTTGAGAAGAAATTCAG+CGG + chr6.2:84065519-84065538 MS.gene05491:CDS 40.0%
GGATCCATCAATTCTGTATC+TGG - chr6.2:84066169-84066188 None:intergenic 40.0%
TGAGAAGAAATTCAGCGGAA+AGG + chr6.2:84065524-84065543 MS.gene05491:CDS 40.0%
! ACTGACTCCTCAAATTCAGT+AGG - chr6.2:84065137-84065156 None:intergenic 40.0%
! TGATGGATCCAAGATCATGA+AGG + chr6.2:84066179-84066198 MS.gene05491:CDS 40.0%
!! TACAGCCAAGTTGATGTTTC+TGG + chr6.2:84065417-84065436 MS.gene05491:intron 40.0%
!! TGGTTGATGGAACACAAAAC+AGG - chr6.2:84066232-84066251 None:intergenic 40.0%
!!! ATAGGTGTTTTTGGACCCAA+AGG + chr6.2:84066390-84066409 MS.gene05491:intron 40.0%
AAATTCACGTCAGGCTCGTT+AGG + chr6.2:84065496-84065515 MS.gene05491:CDS 45.0%
AACCCTTCCTCAATCTGTAG+GGG - chr6.2:84065470-84065489 None:intergenic 45.0%
AATTCACGTCAGGCTCGTTA+GGG + chr6.2:84065497-84065516 MS.gene05491:CDS 45.0%
ATGCATGCCTTGTAATCGTG+TGG + chr6.2:84065855-84065874 MS.gene05491:intron 45.0%
ATGTAATCCTCATTGCCACC+AGG + chr6.2:84066019-84066038 MS.gene05491:CDS 45.0%
ATTTGAGGAGTCAGTTGGAC+AGG + chr6.2:84065142-84065161 MS.gene05491:CDS 45.0%
GAAACCCTTCCTCAATCTGT+AGG - chr6.2:84065472-84065491 None:intergenic 45.0%
GCAGTTTACAGGAAACTCTC+AGG + chr6.2:84066451-84066470 MS.gene05491:CDS 45.0%
GGTTGCCAGAAACATCAACT+TGG - chr6.2:84065425-84065444 None:intergenic 45.0%
GTTTCCGCAAAATTCACGTC+AGG + chr6.2:84065487-84065506 MS.gene05491:CDS 45.0%
GTTTGAGTACCCTGTTACTG+AGG + chr6.2:84066486-84066505 MS.gene05491:CDS 45.0%
TGCATGCCTTGTAATCGTGT+GGG + chr6.2:84065856-84065875 MS.gene05491:intron 45.0%
! ACGGACTATTGTTGTTGCTG+TGG + chr6.2:84065181-84065200 MS.gene05491:intron 45.0%
!! TCAGCTCACTTTTGAGCTCA+TGG - chr6.2:84065296-84065315 None:intergenic 45.0%
ATCGTCAGGCCACCAAAGAA+AGG + chr6.2:84066045-84066064 MS.gene05491:CDS 50.0%
CATGGATAACCACAGCCTTG+CGG - chr6.2:84065446-84065465 None:intergenic 50.0%
CGCTGAGCCTACTGAATTTG+AGG + chr6.2:84065127-84065146 MS.gene05491:CDS 50.0%
CGTTTGCCAACAATCTCAGC+AGG - chr6.2:84066144-84066163 None:intergenic 50.0%
CTGCAACCCACACGATTACA+AGG - chr6.2:84065865-84065884 None:intergenic 50.0%
GTCCCCTACAGATTGAGGAA+GGG + chr6.2:84065465-84065484 MS.gene05491:CDS 50.0%
GTGTTGCCTGCTGAGATTGT+TGG + chr6.2:84066135-84066154 MS.gene05491:CDS 50.0%
GTTGCAGGCTCTGTTTGATC+TGG + chr6.2:84065260-84065279 MS.gene05491:intron 50.0%
TCCATGTCCCCTACAGATTG+AGG + chr6.2:84065460-84065479 MS.gene05491:CDS 50.0%
TCCTCAATCTGTAGGGGACA+TGG - chr6.2:84065464-84065483 None:intergenic 50.0%
TGAGCAGCAGAGCCTTTCTT+TGG - chr6.2:84066060-84066079 None:intergenic 50.0%
TGTCCCCTACAGATTGAGGA+AGG + chr6.2:84065464-84065483 MS.gene05491:CDS 50.0%
! CGAGCCTGACGTGAATTTTG+CGG - chr6.2:84065494-84065513 None:intergenic 50.0%
!! TGATGTTTCTGGCAACCGCA+AGG + chr6.2:84065428-84065447 MS.gene05491:CDS 50.0%
CGATTCTCCTGGTGGCAATG+AGG - chr6.2:84066029-84066048 None:intergenic 55.0%
CGTGGACAGCAGTGAGTGTA+CGG - chr6.2:84066095-84066114 None:intergenic 55.0%
GCAGCAGAGCCTTTCTTTGG+TGG - chr6.2:84066057-84066076 None:intergenic 55.0%
TACACTCACTGCTGTCCACG+AGG + chr6.2:84066095-84066114 MS.gene05491:CDS 55.0%
TTGCCACCAGGAGAATCGTC+AGG + chr6.2:84066031-84066050 MS.gene05491:CDS 55.0%
TGGCCTGACGATTCTCCTGG+TGG - chr6.2:84066037-84066056 None:intergenic 60.0%
TGGTGGCCTGACGATTCTCC+TGG - chr6.2:84066040-84066059 None:intergenic 60.0%
TGTCCACGAGGCAATGCTCG+AGG + chr6.2:84066107-84066126 MS.gene05491:CDS 60.0%
TTCTGGCAACCGCAAGGCTG+TGG + chr6.2:84065434-84065453 MS.gene05491:CDS 60.0%
! CATCCTCGAGCATTGCCTCG+TGG - chr6.2:84066113-84066132 None:intergenic 60.0%
GCAGTGAGTGTACGGCTGCG+TGG - chr6.2:84066087-84066106 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 84065089 84066513 84065089 ID=MS.gene05491
chr6.2 mRNA 84065089 84066513 84065089 ID=MS.gene05491.t1;Parent=MS.gene05491
chr6.2 exon 84065089 84065163 84065089 ID=MS.gene05491.t1.exon1;Parent=MS.gene05491.t1
chr6.2 CDS 84065089 84065163 84065089 ID=cds.MS.gene05491.t1;Parent=MS.gene05491.t1
chr6.2 exon 84065267 84065340 84065267 ID=MS.gene05491.t1.exon2;Parent=MS.gene05491.t1
chr6.2 CDS 84065267 84065340 84065267 ID=cds.MS.gene05491.t1;Parent=MS.gene05491.t1
chr6.2 exon 84065422 84065545 84065422 ID=MS.gene05491.t1.exon3;Parent=MS.gene05491.t1
chr6.2 CDS 84065422 84065545 84065422 ID=cds.MS.gene05491.t1;Parent=MS.gene05491.t1
chr6.2 exon 84066018 84066200 84066018 ID=MS.gene05491.t1.exon4;Parent=MS.gene05491.t1
chr6.2 CDS 84066018 84066200 84066018 ID=cds.MS.gene05491.t1;Parent=MS.gene05491.t1
chr6.2 exon 84066394 84066513 84066394 ID=MS.gene05491.t1.exon5;Parent=MS.gene05491.t1
chr6.2 CDS 84066394 84066513 84066394 ID=cds.MS.gene05491.t1;Parent=MS.gene05491.t1
Gene Sequence

>MS.gene05491

ATGTTTACTTCAAGGAAGAAAATCAGCAAGGACAAGGGCGCTGAGCCTACTGAATTTGAGGAGTCAGTTGGACAGGTTATATATTGATTACTACGGACTATTGTTGTTGCTGTGGTTGCTGATTAGTCTCTATAATTGCAAAATCTAAATCATTATTGTTTTGAATTTGTTGTTGCAGGCTCTGTTTGATCTGGAAAACACTAACCATGAGCTCAAAAGTGAGCTGAAAGATTTATACATCAATTCTGCAGTGTAAGGATGTGTTCTTTATGGTTTGTTTGAAAATACATCTGTTTTCTTCGTCTCATGTCTACTGTTTTCTGTTATCTACAGCCAAGTTGATGTTTCTGGCAACCGCAAGGCTGTGGTTATCCATGTCCCCTACAGATTGAGGAAGGGTTTCCGCAAAATTCACGTCAGGCTCGTTAGGGAGCTTGAGAAGAAATTCAGCGGAAAGGTAATCAAAGTCTTTTATACCTTTGCCAGTTATTCTTTCTAACTGCACCATCTTTTATTACGATTCTGTCTACCGACAATTTTTTGTTCCAATTTCTTTGTCTTCTACTCGTTATTTTTATCCTTATTTCAAGAACTTTATTCTGTTTTGCATTCTCCTTGGTTTTTAAATTGCTTTAATTTATATTTACTTGAGAGTAGTTCTATTCAGCTGTAAAACTGAAATTAATCAGGCTGCGGTCTAAGCATGTGTTTGATTTGGCTTCATAGTTTTCATAATCACTTTGTAGCTTCTCTTTATCACGACAGAATGCATGCCTTGTAATCGTGTGGGTTGCAGTGAAAAGAAGCCAAACCAAACGTACACTAAAGAATTTGATGATACCATAACATTAGCCTTAAAAAATTGTTTTCTCACAGATTTATATGTGATCCTTAACTTTATTGTATACTAATGAACCTTTAACTTGTAGGATGTAATCCTCATTGCCACCAGGAGAATCGTCAGGCCACCAAAGAAAGGCTCTGCTGCTCAGCGTCCACGCAGCCGTACACTCACTGCTGTCCACGAGGCAATGCTCGAGGATGTCGTGTTGCCTGCTGAGATTGTTGGCAAACGTACCAGATACAGAATTGATGGATCCAAGATCATGAAGGTAAACTATTCTAACAGCCAAATAACTTCCTGTTTTGTGTTCCATCAACCAAAACTTAAAACAAATACATCTCGTTATTTTGCAAAATCACTCTGGTGAAATTTATTTACATGATAGTCGTTTTTATTATGCTATAATATTAAAAAGAATAAGAAATAATGTTAATGGAATTCTTGTGGTTCTGTGTATATAGGTGTTTTTGGACCCAAAGGAGAGAAACAATACTGAATACAAGCTCGAAACATTTTCTGCAGTTTACAGGAAACTCTCAGGCAAAGATGTTGTGTTTGAGTACCCTGTTACTGAGGCCTAG

Protein sequence

>MS.gene05491.t1

MFTSRKKISKDKGAEPTEFEESVGQALFDLENTNHELKSELKDLYINSAVQVDVSGNRKAVVIHVPYRLRKGFRKIHVRLVRELEKKFSGKDVILIATRRIVRPPKKGSAAQRPRSRTLTAVHEAMLEDVVLPAEIVGKRTRYRIDGSKIMKVFLDPKERNNTEYKLETFSAVYRKLSGKDVVFEYPVTEA