AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene32924

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 52 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTATGTCTTCACAAGCTTT+AGG 0.218586 3.1:-81078450 MS.gene32924:CDS
ATTTCTTGTTGATGCTTTGT+AGG 0.248605 3.1:+81078393 None:intergenic
GATAATTCATCATTTCTTAA+AGG 0.258078 3.1:+81080061 None:intergenic
CTTTCAAGCTTCTTCCTTGA+TGG 0.269680 3.1:+81078203 None:intergenic
ACATTCGACTTGTCTACTAT+TGG 0.276222 3.1:+81078255 None:intergenic
TTATGTCTTCACAAGCTTTA+GGG 0.298843 3.1:-81078449 MS.gene32924:CDS
TTATCATCAAATGGGTCATT+AGG 0.302998 3.1:-81080043 MS.gene32924:CDS
CTCACCGATGATTCGATTTA+CGG 0.303465 3.1:-81078717 MS.gene32924:CDS
GTTCTAATGTTGCATCTAAC+TGG 0.314264 3.1:-81079961 MS.gene32924:CDS
CATTCGACTTGTCTACTATT+GGG 0.338002 3.1:+81078256 None:intergenic
AAACAAGTTCACTATCAAAA+TGG 0.341580 3.1:-81080100 MS.gene32924:CDS
AACGAAGAGATTGAAATTAG+AGG 0.372610 3.1:-81078903 MS.gene32924:CDS
ATCCTTAGGAGGACACAAAA+AGG 0.374040 3.1:-81078610 MS.gene32924:CDS
AATGATGAATTATCATCAAA+TGG 0.381464 3.1:-81080052 MS.gene32924:CDS
CGAATTATCGGTGAGATTGA+TGG 0.404763 3.1:+81078551 None:intergenic
CATAGTAATCATCATGCATA+TGG 0.409756 3.1:-81079932 MS.gene32924:CDS
CGACCCACGAATCGAATTAT+CGG 0.427366 3.1:+81078539 None:intergenic
AACAATACTACTAATATTGT+TGG 0.430734 3.1:-81079986 MS.gene32924:CDS
AAATACCTTGATGTTTCTGC+TGG 0.436996 3.1:+81079871 None:intergenic
GGGGAGATACGTCTTCATTA+TGG 0.444725 3.1:-81078869 MS.gene32924:CDS
TCACCGATGATTCGATTTAC+GGG 0.450292 3.1:-81078716 MS.gene32924:CDS
GACGCAAGAAAATGTATTTG+AGG 0.462564 3.1:+81078488 None:intergenic
GAAATAGAAGCACATGATAG+AGG 0.472787 3.1:+81078822 None:intergenic
ATGATGAATTATCATCAAAT+GGG 0.500216 3.1:-81080051 MS.gene32924:CDS
TCGCTTATCATCACTTGTTG+AGG 0.515757 3.1:+81080016 None:intergenic
CGATAATTCGATTCGTGGGT+CGG 0.519440 3.1:-81078538 MS.gene32924:CDS
TACTCTTCACGATCCTTAGG+AGG 0.520807 3.1:-81078621 MS.gene32924:CDS
AATACTACTAATATTGTTGG+TGG 0.531727 3.1:-81079983 MS.gene32924:CDS
GTGAAGAGTAAAACTCTCTC+CGG 0.531973 3.1:+81078634 None:intergenic
CTCACCGATAATTCGATTCG+TGG 0.537516 3.1:-81078543 MS.gene32924:CDS
TCGGTGAGATTAACGAAAAG+AGG 0.543222 3.1:+81078732 None:intergenic
TAATTTCATCATAAGACCCT+CGG 0.547601 3.1:+81078329 None:intergenic
AATTAGAGGATCAAATGCAA+GGG 0.558949 3.1:-81078889 MS.gene32924:CDS
TCGGTGAGATTGATGGAAAG+AGG 0.566132 3.1:+81078558 None:intergenic
CGAGACCAGCAGAAACATCA+AGG 0.569455 3.1:-81079876 MS.gene32924:intron
CTTATGATGAAATTAGAAGA+TGG 0.574093 3.1:-81078321 MS.gene32924:CDS
TGATCATCATCTTACCATCA+AGG 0.576493 3.1:-81078217 MS.gene32924:CDS
TATGTCTTCACAAGCTTTAG+GGG 0.577249 3.1:-81078448 MS.gene32924:CDS
ATGAAATTAGAAGATGGTGT+TGG 0.580707 3.1:-81078315 MS.gene32924:CDS
TCGAATGTGGTTGGCAGACG+TGG 0.583035 3.1:-81078240 MS.gene32924:CDS
GTAGACAAGTCGAATGTGGT+TGG 0.590394 3.1:-81078249 MS.gene32924:CDS
AAATTAGAGGATCAAATGCA+AGG 0.596143 3.1:-81078890 MS.gene32924:CDS
CGACCCGTAAATCGAATCAT+CGG 0.620370 3.1:+81078713 None:intergenic
TCACCGATAATTCGATTCGT+GGG 0.623824 3.1:-81078542 MS.gene32924:CDS
ATGTCTTCACAAGCTTTAGG+GGG 0.627825 3.1:-81078447 MS.gene32924:CDS
CTTGCATGTAAAAGTCTCTG+AGG 0.631561 3.1:+81078662 None:intergenic
ATTGATCGATTGAAGACCGA+GGG 0.641525 3.1:-81078345 MS.gene32924:CDS
AATAGTAGACAAGTCGAATG+TGG 0.644495 3.1:-81078253 MS.gene32924:CDS
ATTAGAGGATCAAATGCAAG+GGG 0.648497 3.1:-81078888 MS.gene32924:CDS
TATTTGTGTAGAAAACACGT+TGG 0.679210 3.1:-81078926 MS.gene32924:intron
ATTATGGTCTAATGTTCGCG+AGG 0.681107 3.1:-81078853 MS.gene32924:CDS
TATTGATCGATTGAAGACCG+AGG 0.703035 3.1:-81078346 MS.gene32924:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTTATTTAAAAAAAAA+AGG - chr3.1:81078546-81078565 MS.gene32924:CDS 0.0%
!!! TTTTTTTTAAATAAAAAAAA+AGG + chr3.1:81078545-81078564 None:intergenic 0.0%
!! ATTGCTATAAAAGATATATA+CGG - chr3.1:81078785-81078804 MS.gene32924:CDS 15.0%
!!! AAATCATTAAAAAAAAGTGT+AGG + chr3.1:81079379-81079398 None:intergenic 15.0%
!!! AATGGAAAACTTAATTTTTT+CGG + chr3.1:81079249-81079268 None:intergenic 15.0%
!! AACAATACTACTAATATTGT+TGG - chr3.1:81078371-81078390 MS.gene32924:CDS 20.0%
!! AATGATGAATTATCATCAAA+TGG - chr3.1:81078305-81078324 MS.gene32924:CDS 20.0%
!! ATGATGAATTATCATCAAAT+GGG - chr3.1:81078306-81078325 MS.gene32924:CDS 20.0%
!! GATAATTCATCATTTCTTAA+AGG + chr3.1:81078299-81078318 None:intergenic 20.0%
!!! ACAATTACATTTTGTATGTT+TGG + chr3.1:81079054-81079073 None:intergenic 20.0%
!!! CGTGTTATTTACAATTTTAA+CGG - chr3.1:81078512-81078531 MS.gene32924:CDS 20.0%
!!! TTCAAAAATATATTTTCACC+CGG + chr3.1:81079168-81079187 None:intergenic 20.0%
! AAACAAGTTCACTATCAAAA+TGG - chr3.1:81078257-81078276 MS.gene32924:CDS 25.0%
! AATACTACTAATATTGTTGG+TGG - chr3.1:81078374-81078393 MS.gene32924:CDS 25.0%
! CTTATGATGAAATTAGAAGA+TGG - chr3.1:81080036-81080055 MS.gene32924:CDS 25.0%
!!! ATTTTTTCGGTCAAGATAAA+CGG + chr3.1:81079236-81079255 None:intergenic 25.0%
AAATTAGAGGATCAAATGCA+AGG - chr3.1:81079467-81079486 MS.gene32924:intron 30.0%
AACAATAATCATAACGACGA+AGG + chr3.1:81079284-81079303 None:intergenic 30.0%
AACGAAGAGATTGAAATTAG+AGG - chr3.1:81079454-81079473 MS.gene32924:intron 30.0%
AAGCAACATAAGCAGTTAAA+TGG + chr3.1:81079202-81079221 None:intergenic 30.0%
AATGTCAAGTTAAGCAATAG+AGG + chr3.1:81079140-81079159 None:intergenic 30.0%
AATTAGAGGATCAAATGCAA+GGG - chr3.1:81079468-81079487 MS.gene32924:intron 30.0%
ACAATAATCATAACGACGAA+GGG + chr3.1:81079283-81079302 None:intergenic 30.0%
ACTTATTGAACTATGTTCAC+AGG - chr3.1:81078731-81078750 MS.gene32924:CDS 30.0%
ATGAAATTAGAAGATGGTGT+TGG - chr3.1:81080042-81080061 MS.gene32924:CDS 30.0%
ATTTCTTGTTGATGCTTTGT+AGG + chr3.1:81079967-81079986 None:intergenic 30.0%
CATAGTAATCATCATGCATA+TGG - chr3.1:81078425-81078444 MS.gene32924:CDS 30.0%
CTTATTGAACTATGTTCACA+GGG - chr3.1:81078732-81078751 MS.gene32924:CDS 30.0%
TAATTTCATCATAAGACCCT+CGG + chr3.1:81080031-81080050 None:intergenic 30.0%
TATTTGTGTAGAAAACACGT+TGG - chr3.1:81079431-81079450 MS.gene32924:intron 30.0%
TGTAGTGAATAACCTATGAT+CGG + chr3.1:81078667-81078686 None:intergenic 30.0%
TTATCATCAAATGGGTCATT+AGG - chr3.1:81078314-81078333 MS.gene32924:CDS 30.0%
TTATGTCTTCACAAGCTTTA+GGG - chr3.1:81079908-81079927 MS.gene32924:CDS 30.0%
TTTATGTCTTCACAAGCTTT+AGG - chr3.1:81079907-81079926 MS.gene32924:CDS 30.0%
!! ATCGATTTGTCACGTTTAAA+CGG + chr3.1:81078579-81078598 None:intergenic 30.0%
AATAGTAGACAAGTCGAATG+TGG - chr3.1:81080104-81080123 MS.gene32924:CDS 35.0%
AGTGACTTGAGAACAAACAT+TGG - chr3.1:81079081-81079100 MS.gene32924:intron 35.0%
ATTAGAGGATCAAATGCAAG+GGG - chr3.1:81079469-81079488 MS.gene32924:intron 35.0%
GACGCAAGAAAATGTATTTG+AGG + chr3.1:81079872-81079891 None:intergenic 35.0%
GGACACAAAAAGGTTCATAA+AGG - chr3.1:81079757-81079776 MS.gene32924:intron 35.0%
GGACACAAAAAGGTTCATAA+GGG - chr3.1:81079757-81079776 MS.gene32924:intron 35.0%
GTTCTAATGTTGCATCTAAC+TGG - chr3.1:81078396-81078415 MS.gene32924:CDS 35.0%
TGATCATCATCTTACCATCA+AGG - chr3.1:81080140-81080159 MS.gene32924:CDS 35.0%
! AAATACCTTGATGTTTCTGC+TGG + chr3.1:81078489-81078508 None:intergenic 35.0%
! ACATTCGACTTGTCTACTAT+TGG + chr3.1:81080105-81080124 None:intergenic 35.0%
! CATTCGACTTGTCTACTATT+GGG + chr3.1:81080104-81080123 None:intergenic 35.0%
! CTTAACTTGACATTGAAGTC+CGG - chr3.1:81079146-81079165 MS.gene32924:intron 35.0%
! CTTTTACATGCAAGATTTGC+CGG - chr3.1:81079704-81079723 MS.gene32924:intron 35.0%
! CTTTTTCTTTAGCCGATCAT+AGG - chr3.1:81078652-81078671 MS.gene32924:CDS 35.0%
! GAAATAGAAGCACATGATAG+AGG + chr3.1:81079538-81079557 None:intergenic 35.0%
! TATGTCTTCACAAGCTTTAG+GGG - chr3.1:81079909-81079928 MS.gene32924:CDS 35.0%
! TTAACTTGACATTGAAGTCC+GGG - chr3.1:81079147-81079166 MS.gene32924:intron 35.0%
! TTTTACTCTTCACGATCCTT+AGG - chr3.1:81079733-81079752 MS.gene32924:intron 35.0%
ATCCTTAGGAGGACACAAAA+AGG - chr3.1:81079747-81079766 MS.gene32924:intron 40.0%
ATTATGGTCTAATGTTCGCG+AGG - chr3.1:81079504-81079523 MS.gene32924:intron 40.0%
ATTGATCGATTGAAGACCGA+GGG - chr3.1:81080012-81080031 MS.gene32924:CDS 40.0%
CGAATTATCGGTGAGATTGA+TGG + chr3.1:81079809-81079828 None:intergenic 40.0%
CTCACCGATGATTCGATTTA+CGG - chr3.1:81079640-81079659 MS.gene32924:intron 40.0%
CTTGCATGTAAAAGTCTCTG+AGG + chr3.1:81079698-81079717 None:intergenic 40.0%
GGGACACAAAAAGGTTCATA+AGG - chr3.1:81079930-81079949 MS.gene32924:CDS 40.0%
GTGAAGAGTAAAACTCTCTC+CGG + chr3.1:81079726-81079745 None:intergenic 40.0%
TATTGATCGATTGAAGACCG+AGG - chr3.1:81080011-81080030 MS.gene32924:CDS 40.0%
TCACCGATGATTCGATTTAC+GGG - chr3.1:81079641-81079660 MS.gene32924:intron 40.0%
TCGGTGAGATTAACGAAAAG+AGG + chr3.1:81079628-81079647 None:intergenic 40.0%
TGCGTACAAGAAAGAGTGAA+TGG + chr3.1:81078918-81078937 None:intergenic 40.0%
! AACCTTTTTGTGTCCTCCTA+AGG + chr3.1:81079752-81079771 None:intergenic 40.0%
! CGAAGGGAGTATGTGATAAA+TGG + chr3.1:81079267-81079286 None:intergenic 40.0%
! TCACCGATAATTCGATTCGT+GGG - chr3.1:81079815-81079834 MS.gene32924:intron 40.0%
! TCGCTTATCATCACTTGTTG+AGG + chr3.1:81078344-81078363 None:intergenic 40.0%
!! ATGTCTTCACAAGCTTTAGG+GGG - chr3.1:81079910-81079929 MS.gene32924:CDS 40.0%
CGACCCACGAATCGAATTAT+CGG + chr3.1:81079821-81079840 None:intergenic 45.0%
CGACCCGTAAATCGAATCAT+CGG + chr3.1:81079647-81079666 None:intergenic 45.0%
GGGGAGATACGTCTTCATTA+TGG - chr3.1:81079488-81079507 MS.gene32924:intron 45.0%
GTAGACAAGTCGAATGTGGT+TGG - chr3.1:81080108-81080127 MS.gene32924:CDS 45.0%
TACTCTTCACGATCCTTAGG+AGG - chr3.1:81079736-81079755 MS.gene32924:intron 45.0%
TCGGTGAGATTGATGGAAAG+AGG + chr3.1:81079802-81079821 None:intergenic 45.0%
! CGATAATTCGATTCGTGGGT+CGG - chr3.1:81079819-81079838 MS.gene32924:intron 45.0%
! CTCACCGATAATTCGATTCG+TGG - chr3.1:81079814-81079833 MS.gene32924:intron 45.0%
!! AGCTTTAGGGGGACACAAAA+AGG - chr3.1:81079921-81079940 MS.gene32924:CDS 45.0%
!!! ATAAATTTTTAAAATTTGAA+AGG + chr3.1:81078988-81079007 None:intergenic 5.0%
!!! CATATATATTTTAATTTTTT+TGG - chr3.1:81078685-81078704 MS.gene32924:CDS 5.0%
CGAGACCAGCAGAAACATCA+AGG - chr3.1:81078481-81078500 MS.gene32924:CDS 50.0%
TCGAATGTGGTTGGCAGACG+TGG - chr3.1:81080117-81080136 MS.gene32924:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 81078206 81080173 81078206 ID=MS.gene32924
chr3.1 mRNA 81078206 81080173 81078206 ID=MS.gene32924.t1;Parent=MS.gene32924
chr3.1 exon 81079877 81080173 81079877 ID=MS.gene32924.t1.exon1;Parent=MS.gene32924.t1
chr3.1 CDS 81079877 81080173 81079877 ID=cds.MS.gene32924.t1;Parent=MS.gene32924.t1
chr3.1 exon 81078206 81078937 81078206 ID=MS.gene32924.t1.exon2;Parent=MS.gene32924.t1
chr3.1 CDS 81078206 81078937 81078206 ID=cds.MS.gene32924.t1;Parent=MS.gene32924.t1
Gene Sequence

>MS.gene32924

ATGGTTTATCTTTTTGGAGTTAACATTGACTATCATCACAATCAACAACAAAAACAAGTTCACTATCAAAATGGTACGAGAAACAATGATCCTTTAAGAAATGATGAATTATCATCAAATGGGTCATTAGGATTTCCTCAACAAGTGATGATAAGCGACAACAACAACAATACTACTAATATTGTTGGTGGTTCTAATGTTGCATCTAACTGGTTTGTGCATAGTAATCATCATGCATATGGATCTCTATATTCTTATGTTAGAAACAACTCTCTCGAGACCAGCAGAAACATCAAGGTATTTCAACGTGTTATTTACAATTTTAACGGACAAGTTCCTTTTTTTTTATTTAAAAAAAAAAGGATAAGTTCCGTTTAAACGTGACAAATCGATAATTCTTCTATTATTCACTACATATATATTATCTTATTCATTGATTGTTTCTTCTTTTTCTTTAGCCGATCATAGGTTATTCACTACATATATATTTTAATTTTTTTGGTCAGATTTGAAACATAGATTTTTACTTATTGAACTATGTTCACAGGGACGTGTGTAACTTTTATCATTGTGTTGTTGATTGCTATAAAAGATATATACGGAAACGAAACAAAAAATATAAATATTTATTATATTTTTTGATAAAAAATATAAATGTTTATAGTTACTTTTCTTTATAAAAATCTCATAAATTATTTATTATGTATTTCCATTCACTCTTTCTTGTACGCACTTTCGTTCACTCTTGTAGCTTTGAAATTTTGCTAAAAATTCACTGTCCTTTCAAATTTTAAAAATTTATGAAGTAATAAAATCTTCTGTATTATAAATGCATTGATCAAAATCCAAACATACAAAATGTAATTGTAAAAAACAGTGACTTGAGAACAAACATTGGAAACAAAATTTCTCATGTTTGTTTTTTGACAAGCCTCTATTGCTTAACTTGACATTGAAGTCCGGGTGAAAATATATTTTTGAAGAGTTCATGCTCCATTTAACTGCTTATGTTGCTTACTAAAGTTTTCCGTTTATCTTGACCGAAAAAATTAAGTTTTCCATTTATCACATACTCCCTTCGTCGTTATGATTATTGTTGTTGTTGTCACTTGTCATCATCATTGTTATTAACTTATTATTATCATTATTGTTTATTATTTTTTATGTTCACCTACACTTTTTTTTAATGATTTTAATGTTAATTTATGAATATTATGTATTAATGTATTTGTGTAGAAAACACGTTGGAACGAAGAGATTGAAATTAGAGGATCAAATGCAAGGGGAGATACGTCTTCATTATGGTCTAATGTTCGCGAGGAGCTTATGCCTCTATCATGTGCTTCTATTTCTGCTTGCAGCAACAACAACAACAAGCGAGTAAAAGTTGAACAATGTCAAATTTTAAACATCAAGACGCCTCTTTTCGTTAATCTCACCGATGATTCGATTTACGGGTCGAATATGCAAGAACGTGATTTTTTTGCGACCTCAGAGACTTTTACATGCAAGATTTGCCGGAGAGAGTTTTACTCTTCACGATCCTTAGGAGGACACAAAAAGGTTCATAAAGGTGAGAGCACACTCACAGAGCCTCTTTCCATCAATCTCACCGATAATTCGATTCGTGGGTCGGTGATGCAAGAAGATGATTTATACGCTACCTCAAATACATTTTCTTGCGTCATTTGTAAGAGAAAGTTTATGTCTTCACAAGCTTTAGGGGGACACAAAAAGGTTCATAAGGGTAAGCGTACACCTACAAAGCATCAACAAGAAATACAAGAGACGATAAATTTTTCGTCTATTGATCGATTGAAGACCGAGGGTCTTATGATGAAATTAGAAGATGGTGTTGGAGAGTCTTCTTCTATAAACGTTGATATGAAGTCAAACCCAATAGTAGACAAGTCGAATGTGGTTGGCAGACGTGGTGATCATCATCTTACCATCAAGGAAGAAGCTTGA
Protein sequence

>MS.gene32924.t1

MVYLFGVNIDYHHNQQQKQVHYQNGTRNNDPLRNDELSSNGSLGFPQQVMISDNNNNTTNIVGGSNVASNWFVHSNHHAYGSLYSYVRNNSLETSRNIKKTRWNEEIEIRGSNARGDTSSLWSNVREELMPLSCASISACSNNNNKRVKVEQCQILNIKTPLFVNLTDDSIYGSNMQERDFFATSETFTCKICRREFYSSRSLGGHKKVHKGESTLTEPLSINLTDNSIRGSVMQEDDLYATSNTFSCVICKRKFMSSQALGGHKKVHKGKRTPTKHQQEIQETINFSSIDRLKTEGLMMKLEDGVGESSSINVDMKSNPIVDKSNVVGRRGDHHLTIKEEA