AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene04750

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene04750.t1 MTR_8g103265 95.376 173 8 0 1 173 1 173 3.72e-121 339
MS.gene04750.t1 MTR_8g103265 95.322 171 8 0 3 173 52 222 3.48e-119 336
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene04750.t1 AT4G01790 48.936 141 60 1 1 141 38 166 1.32e-43 142

Find 39 sgRNAs with CRISPR-Local

Find 96 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCCATTGCTGTTGGAATTA+AGG 0.157846 4.2:+2273685 MS.gene04750:CDS
TTTCACTGACTGCAGGTTAA+AGG 0.230538 4.2:+2274194 MS.gene04750:intron
TATTATCCTTAACAAATATC+AGG 0.234820 4.2:-2273619 None:intergenic
GACAAAGCATCTTCAAAGTT+TGG 0.272288 4.2:+2273577 MS.gene04750:CDS
TGCAGCAACAATTTGCTATT+GGG 0.276797 4.2:+2272985 MS.gene04750:intron
TTGCAGCAACAATTTGCTAT+TGG 0.304157 4.2:+2272984 MS.gene04750:intron
GTTCTTTGCCAGAAAAGATA+TGG 0.347038 4.2:+2272853 MS.gene04750:CDS
AAAGAAGGTTCTTTGAGATT+AGG 0.350873 4.2:+2273641 MS.gene04750:CDS
ACAAAGTTTCCCTGTTTGTC+AGG 0.362507 4.2:-2274320 None:intergenic
AACACCTTCAGTTAAACTTC+AGG 0.377815 4.2:+2273103 MS.gene04750:CDS
CCAGCTGAATTTGATTCATC+AGG 0.390898 4.2:-2274275 None:intergenic
TGTTCCCCTGATATTTGTTA+AGG 0.407666 4.2:+2273613 MS.gene04750:CDS
TTTGTTAAGGATAATAAAGA+AGG 0.432172 4.2:+2273626 MS.gene04750:CDS
GAATCAGCAAGGCATTTAGA+TGG 0.437664 4.2:+2272828 MS.gene04750:CDS
AACCGGTTATTCCGATGAGC+AGG 0.471864 4.2:+2272799 None:intergenic
TTATGATTGCTTGTGACTGA+TGG 0.485746 4.2:-2273080 None:intergenic
ATTATCCTTAACAAATATCA+GGG 0.488976 4.2:-2273618 None:intergenic
TTGAAAACTGCCATTGCTGT+TGG 0.496333 4.2:+2273677 MS.gene04750:CDS
CAAAGTTTCCCTGTTTGTCA+GGG 0.499070 4.2:-2274319 None:intergenic
TTCAAAGTTTGGCTTCATCA+AGG 0.506495 4.2:+2273588 MS.gene04750:CDS
TATGATTGCTTGTGACTGAT+GGG 0.507385 4.2:-2273079 None:intergenic
CCTGATGAATCAAATTCAGC+TGG 0.516597 4.2:+2274275 MS.gene04750:CDS
GCAGCAACAATTTGCTATTG+GGG 0.528210 4.2:+2272986 MS.gene04750:intron
AACCATGTGCAGAGTTTGAA+AGG 0.539889 4.2:+2273042 MS.gene04750:CDS
GACCTTTCAAACTCTGCACA+TGG 0.559436 4.2:-2273044 None:intergenic
CGGTTATTCCGATGAGCAGG+GGG 0.559631 4.2:+2272802 None:intergenic
GCCAGAAAAGATATGGACAA+AGG 0.562195 4.2:+2272860 MS.gene04750:CDS
CGCTATTAATAAAATTGTCG+AGG 0.562774 4.2:+2274220 MS.gene04750:CDS
CACATGGTTTCATACGCTCT+AGG 0.578288 4.2:-2273028 None:intergenic
AACCTTAATTCCAACAGCAA+TGG 0.585166 4.2:-2273687 None:intergenic
ACCGGTTATTCCGATGAGCA+GGG 0.585921 4.2:+2272800 None:intergenic
TCAACCTGAAGTTTAACTGA+AGG 0.601860 4.2:-2273107 None:intergenic
TTTCAACACCCTGACAAACA+GGG 0.614691 4.2:+2274311 MS.gene04750:CDS
CTGAATTTGATTCATCAGGT+CGG 0.627196 4.2:-2274271 None:intergenic
CCGGTTATTCCGATGAGCAG+GGG 0.633897 4.2:+2272801 None:intergenic
TTATCCTTAACAAATATCAG+GGG 0.650486 4.2:-2273617 None:intergenic
GATTGCTTGTGACTGATGGG+AGG 0.673407 4.2:-2273076 None:intergenic
CTTCTGACTGTAGCTCACGA+TGG 0.681030 4.2:+2273552 MS.gene04750:CDS
GGTTATTCCGATGAGCAGGG+GGG 0.754880 4.2:+2272803 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATTTTTGTAAATTATTTC+GGG + chr4.2:2273852-2273871 MS.gene04750:intron 10.0%
!! AAACTAGTTATTTATTACCA+AGG - chr4.2:2273403-2273422 None:intergenic 20.0%
!! ACTTAGGTAAAAGTAATATA+TGG + chr4.2:2273430-2273449 MS.gene04750:intron 20.0%
!! ATATTAAAAATAGAGTAAGC+TGG - chr4.2:2273222-2273241 None:intergenic 20.0%
!! ATTATCCTTAACAAATATCA+GGG - chr4.2:2273621-2273640 None:intergenic 20.0%
!! TATTATCCTTAACAAATATC+AGG - chr4.2:2273622-2273641 None:intergenic 20.0%
!! TTTGTTAAGGATAATAAAGA+AGG + chr4.2:2273626-2273645 MS.gene04750:CDS 20.0%
!!! ATTTTATTTTATGATGATGC+AGG + chr4.2:2273517-2273536 MS.gene04750:intron 20.0%
!!! CATTCATATGTTTTATAGTT+AGG - chr4.2:2272906-2272925 None:intergenic 20.0%
!!! TTAATATTTCTACCTTTACA+TGG + chr4.2:2273235-2273254 MS.gene04750:intron 20.0%
!!! TTTCTTTTATTCTGATATGA+AGG + chr4.2:2273130-2273149 MS.gene04750:intron 20.0%
! AAACTGATATATAGAAATGC+AGG - chr4.2:2273953-2273972 None:intergenic 25.0%
! CACAAGATATATATTCTGTT+TGG + chr4.2:2273724-2273743 MS.gene04750:intron 25.0%
! CAGATCTTATTAGCAAAATA+AGG - chr4.2:2273976-2273995 None:intergenic 25.0%
! GAATGAATTTAGCAATATGT+AGG + chr4.2:2272921-2272940 MS.gene04750:intron 25.0%
! TAGTTAGGAAAATCAAGTTA+AGG - chr4.2:2272891-2272910 None:intergenic 25.0%
! TGATTGTGATATTGAAAACT+AGG - chr4.2:2273912-2273931 None:intergenic 25.0%
! TTATCCTTAACAAATATCAG+GGG - chr4.2:2273620-2273639 None:intergenic 25.0%
!! AACTAGTTTATTCTGTACTT+AGG + chr4.2:2273414-2273433 MS.gene04750:intron 25.0%
!! GTGAATATATTTTCTCTTCA+AGG - chr4.2:2273497-2273516 None:intergenic 25.0%
!!! ATAACCTTCTAAAGCTATTT+TGG + chr4.2:2274132-2274151 MS.gene04750:intron 25.0%
AAAAGCCTAACTATAACTAC+CGG - chr4.2:2273280-2273299 None:intergenic 30.0%
ATAGTCATATAACGTTTACC+TGG + chr4.2:2272952-2272971 MS.gene04750:intron 30.0%
CAGAATATATATCTTGTGTG+AGG - chr4.2:2273722-2273741 None:intergenic 30.0%
CGCTATTAATAAAATTGTCG+AGG + chr4.2:2274220-2274239 MS.gene04750:CDS 30.0%
GACACATTAAACTCAAGAAA+TGG - chr4.2:2274016-2274035 None:intergenic 30.0%
TGAAAACTAGGATTCATCAA+GGG - chr4.2:2273900-2273919 None:intergenic 30.0%
TTAAAAATAGAGTAAGCTGG+AGG - chr4.2:2273219-2273238 None:intergenic 30.0%
TTCTTGAGTTTAATGTGTCA+TGG + chr4.2:2274017-2274036 MS.gene04750:intron 30.0%
TTGAAAACTAGGATTCATCA+AGG - chr4.2:2273901-2273920 None:intergenic 30.0%
! AACTCCTAGTATAATTTGCA+GGG - chr4.2:2273322-2273341 None:intergenic 30.0%
! ACTAACTGTGTTTGAAATTG+TGG - chr4.2:2273377-2273396 None:intergenic 30.0%
!! AAAGAAGGTTCTTTGAGATT+AGG + chr4.2:2273641-2273660 MS.gene04750:CDS 30.0%
!! GAAACCAAAATAGCTTTAGA+AGG - chr4.2:2274139-2274158 None:intergenic 30.0%
AAATGCAGGATTGAAAAGCA+AGG - chr4.2:2273939-2273958 None:intergenic 35.0%
AACACCTTCAGTTAAACTTC+AGG + chr4.2:2273103-2273122 MS.gene04750:CDS 35.0%
AACCTTAATTCCAACAGCAA+TGG - chr4.2:2273690-2273709 None:intergenic 35.0%
AACTATAACTACCGGTACAT+GGG - chr4.2:2273272-2273291 None:intergenic 35.0%
AAGTAATATATGGCTGCTTC+TGG + chr4.2:2273440-2273459 MS.gene04750:intron 35.0%
AATAGCAAATTGTTGCTGCA+AGG - chr4.2:2272985-2273004 None:intergenic 35.0%
AATGCAGGATTGAAAAGCAA+GGG - chr4.2:2273938-2273957 None:intergenic 35.0%
AATTGTGGATGCGAAAACAA+TGG - chr4.2:2273362-2273381 None:intergenic 35.0%
CTGAATTTGATTCATCAGGT+CGG - chr4.2:2274274-2274293 None:intergenic 35.0%
GTTCTTTGCCAGAAAAGATA+TGG + chr4.2:2272853-2272872 MS.gene04750:CDS 35.0%
TAACTATAACTACCGGTACA+TGG - chr4.2:2273273-2273292 None:intergenic 35.0%
TATGATTGCTTGTGACTGAT+GGG - chr4.2:2273082-2273101 None:intergenic 35.0%
TCAACCTGAAGTTTAACTGA+AGG - chr4.2:2273110-2273129 None:intergenic 35.0%
TGATCCCTGCAAATTATACT+AGG + chr4.2:2273315-2273334 MS.gene04750:intron 35.0%
TTATGATTGCTTGTGACTGA+TGG - chr4.2:2273083-2273102 None:intergenic 35.0%
TTCATCAAGGGAAGCTATTA+TGG - chr4.2:2273888-2273907 None:intergenic 35.0%
TTGGAATTAAGGTTAGATCC+TGG + chr4.2:2273696-2273715 MS.gene04750:intron 35.0%
! ACCTTTGTCCATATCTTTTC+TGG - chr4.2:2272864-2272883 None:intergenic 35.0%
! ATGTACCGGTAGTTATAGTT+AGG + chr4.2:2273272-2273291 MS.gene04750:intron 35.0%
! CAACTCCTAGTATAATTTGC+AGG - chr4.2:2273323-2273342 None:intergenic 35.0%
! GACAAAGCATCTTCAAAGTT+TGG + chr4.2:2273577-2273596 MS.gene04750:CDS 35.0%
! GTATTTGAAGCACCATGTAA+AGG - chr4.2:2273250-2273269 None:intergenic 35.0%
! TGTTCCCCTGATATTTGTTA+AGG + chr4.2:2273613-2273632 MS.gene04750:CDS 35.0%
! TTCAAAGTTTGGCTTCATCA+AGG + chr4.2:2273588-2273607 MS.gene04750:CDS 35.0%
!! AGAAGAATTCAAGAGTGTCA+TGG + chr4.2:2274042-2274061 MS.gene04750:intron 35.0%
!! TGCAGCAACAATTTGCTATT+GGG + chr4.2:2272985-2273004 MS.gene04750:intron 35.0%
!! TTGCAGCAACAATTTGCTAT+TGG + chr4.2:2272984-2273003 MS.gene04750:intron 35.0%
!!! CAAACACAGTTAGTTTTCCT+TGG + chr4.2:2273383-2273402 MS.gene04750:intron 35.0%
AACCATGTGCAGAGTTTGAA+AGG + chr4.2:2273042-2273061 MS.gene04750:CDS 40.0%
AAGCCATGGTCAAATAACAC+GGG - chr4.2:2274101-2274120 None:intergenic 40.0%
ACAAAGTTTCCCTGTTTGTC+AGG - chr4.2:2274323-2274342 None:intergenic 40.0%
CAAAGTTTCCCTGTTTGTCA+GGG - chr4.2:2274322-2274341 None:intergenic 40.0%
CAAGCCATGGTCAAATAACA+CGG - chr4.2:2274102-2274121 None:intergenic 40.0%
CATATAACGTTTACCTGGAC+TGG + chr4.2:2272957-2272976 MS.gene04750:intron 40.0%
CCAGCTGAATTTGATTCATC+AGG - chr4.2:2274278-2274297 None:intergenic 40.0%
CCTGATGAATCAAATTCAGC+TGG + chr4.2:2274275-2274294 MS.gene04750:CDS 40.0%
GAACTAGTAACAACAGGTAC+AGG - chr4.2:2273179-2273198 None:intergenic 40.0%
GAAGAATTCAAGAGTCCAAC+AGG + chr4.2:2274068-2274087 MS.gene04750:intron 40.0%
GCCAGAAAAGATATGGACAA+AGG + chr4.2:2272860-2272879 MS.gene04750:CDS 40.0%
TATAGTGACATCTCAAGCCA+TGG - chr4.2:2274115-2274134 None:intergenic 40.0%
TATATATCTTGTGTGAGGCC+AGG - chr4.2:2273717-2273736 None:intergenic 40.0%
TGCGATGAACTAGTAACAAC+AGG - chr4.2:2273185-2273204 None:intergenic 40.0%
TGCTTCAAATACCCATGTAC+CGG + chr4.2:2273258-2273277 MS.gene04750:intron 40.0%
TTGAAAACTGCCATTGCTGT+TGG + chr4.2:2273677-2273696 MS.gene04750:CDS 40.0%
TTTCAACACCCTGACAAACA+GGG + chr4.2:2274311-2274330 MS.gene04750:CDS 40.0%
! GAATCAGCAAGGCATTTAGA+TGG + chr4.2:2272828-2272847 MS.gene04750:CDS 40.0%
! GTTTATCTTTCACTGACTGC+AGG + chr4.2:2274187-2274206 MS.gene04750:intron 40.0%
! TGCCATTGCTGTTGGAATTA+AGG + chr4.2:2273685-2273704 MS.gene04750:CDS 40.0%
! TTTCACTGACTGCAGGTTAA+AGG + chr4.2:2274194-2274213 MS.gene04750:intron 40.0%
! TTTTCAACACCCTGACAAAC+AGG + chr4.2:2274310-2274329 MS.gene04750:CDS 40.0%
!! GCAGCAACAATTTGCTATTG+GGG + chr4.2:2272986-2273005 MS.gene04750:intron 40.0%
ATATATGGCTGCTTCTGGTG+TGG + chr4.2:2273445-2273464 MS.gene04750:intron 45.0%
CACATGGTTTCATACGCTCT+AGG - chr4.2:2273031-2273050 None:intergenic 45.0%
GACCTTTCAAACTCTGCACA+TGG - chr4.2:2273047-2273066 None:intergenic 45.0%
TATATGGCTGCTTCTGGTGT+GGG + chr4.2:2273446-2273465 MS.gene04750:intron 45.0%
!! GAACCCGTGTTATTTGACCA+TGG + chr4.2:2274095-2274114 MS.gene04750:intron 45.0%
!!! TTTATTTTTGTAAATTATTT+CGG + chr4.2:2273851-2273870 MS.gene04750:intron 5.0%
CTTCTGACTGTAGCTCACGA+TGG + chr4.2:2273552-2273571 MS.gene04750:CDS 50.0%
GATTGCTTGTGACTGATGGG+AGG - chr4.2:2273079-2273098 None:intergenic 50.0%
AACACGGGTTCGTTGCCTGT+TGG - chr4.2:2274086-2274105 None:intergenic 55.0%
TTGCTGCAAGGTTCCAGTCC+AGG - chr4.2:2272973-2272992 None:intergenic 55.0%
GCAGGGGGGTTGAATCAGCA+AGG + chr4.2:2272817-2272836 MS.gene04750:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 2272813 2274358 2272813 ID=MS.gene04750
chr4.2 mRNA 2272813 2274358 2272813 ID=MS.gene04750.t1;Parent=MS.gene04750
chr4.2 exon 2272813 2272881 2272813 ID=MS.gene04750.t1.exon1;Parent=MS.gene04750.t1
chr4.2 CDS 2272813 2272881 2272813 ID=cds.MS.gene04750.t1;Parent=MS.gene04750.t1
chr4.2 exon 2272990 2273124 2272990 ID=MS.gene04750.t1.exon2;Parent=MS.gene04750.t1
chr4.2 CDS 2272990 2273124 2272990 ID=cds.MS.gene04750.t1;Parent=MS.gene04750.t1
chr4.2 exon 2273539 2273706 2273539 ID=MS.gene04750.t1.exon3;Parent=MS.gene04750.t1
chr4.2 CDS 2273539 2273706 2273539 ID=cds.MS.gene04750.t1;Parent=MS.gene04750.t1
chr4.2 exon 2274209 2274358 2274209 ID=MS.gene04750.t1.exon4;Parent=MS.gene04750.t1
chr4.2 CDS 2274209 2274358 2274209 ID=cds.MS.gene04750.t1;Parent=MS.gene04750.t1
Gene Sequence

>MS.gene04750

ATGAGCAGGGGGGTTGAATCAGCAAGGCATTTAGATGGAAGTTCTTTGCCAGAAAAGATATGGACAAAGGTTTAACCTTAACTTGATTTTCCTAACTATAAAACATATGAATGAATTTAGCAATATGTAGGAGTCTTGCATAGTCATATAACGTTTACCTGGACTGGAACCTTGCAGCAACAATTTGCTATTGGGGTTAATGACGTAACTCGTGTCCTAGAGCGTATGAAACCATGTGCAGAGTTTGAAAGGTCAGCTCAACTCCTCCCATCAGTCACAAGCAATCATAAAACACCTTCAGTTAAACTTCAGGTTGATTTCTTTTATTCTGATATGAAGGAAATGTAAATTATTTATTTAGTACCTGTACCTGTTGTTACTAGTTCATCGCATCTAATTAAATCCTCCAGCTTACTCTATTTTTAATATTTCTACCTTTACATGGTGCTTCAAATACCCATGTACCGGTAGTTATAGTTAGGCTTTTTGTTCTTGCTGATGCTGATCCCTGCAAATTATACTAGGAGTTGACAGTGTGTATAGAAACCATTGTTTTCGCATCCACAATTTCAAACACAGTTAGTTTTCCTTGGTAATAAATAACTAGTTTATTCTGTACTTAGGTAAAAGTAATATATGGCTGCTTCTGGTGTGGGCGTGTAGCTTTGTTTTATAAGCAAGCCTTGAAGAGAAAATATATTCACATTTTATTTTATGATGATGCAGGCTGTGCTTGTAGCTTCTGACTGTAGCTCACGATGGCTGACAAAGCATCTTCAAAGTTTGGCTTCATCAAGGAGTGTTCCCCTGATATTTGTTAAGGATAATAAAGAAGGTTCTTTGAGATTAGGTGAACTTGTTAAATTGAAAACTGCCATTGCTGTTGGAATTAAGGTTAGATCCTGGCCTCACACAAGATATATATTCTGTTTGGTTTTTAATCATTTTTCGTTTAAAGTGCTCTCATGAAATTATAAAAGAAAGTGATTATTTTATCAAAATAAAATAAGCTAATTCAAACATGTATTTTTTTTTTTTTTTATTTTTGTAAATTATTTCGGGTAACTACATTCCATAATAGCTTCCCTTGATGAATCCTAGTTTTCAATATCACAATCAACTCCCTTGCTTTTCAATCCTGCATTTCTATATATCAGTTTCCTTATTTTGCTAATAAGATCTGCTCAAGAACACTTGACACCATTTCTTGAGTTTAATGTGTCATGGTGAGAAGAATTCAAGAGTGTCATGGTGAGAAGAATTCAAGAGTCCAACAGGCAACGAACCCGTGTTATTTGACCATGGCTTGAGATGTCACTATAACCTTCTAAAGCTATTTTGGTTTCATCTTTCTTTCTTTTTAGATATTGAGTTGTTTATCTTTCACTGACTGCAGGTTAAAGGAAACGCTATTAATAAAATTGTCGAGGATATTATTCAAGTCGATGAATGTAGACTCCGACCTGATGAATCAAATTCAGCTGGAATATTTGACGATTTTCAACACCCTGACAAACAGGGAAACTTTGTCACAGATATAATTTAA
Protein sequence

>MS.gene04750.t1

MSRGVESARHLDGSSLPEKIWTKQQFAIGVNDVTRVLERMKPCAEFERSAQLLPSVTSNHKTPSVKLQAVLVASDCSSRWLTKHLQSLASSRSVPLIFVKDNKEGSLRLGELVKLKTAIAVGIKVKGNAINKIVEDIIQVDECRLRPDESNSAGIFDDFQHPDKQGNFVTDII