AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene85759

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene85759.t1 MTR_3g073080 90.909 33 3 0 1 33 472 504 1.48e-16 72.8
MS.gene85759.t1 MTR_3g073080 90.909 33 3 0 1 33 208 240 2.10e-16 72.4
MS.gene85759.t1 MTR_3g073080 90.909 33 3 0 1 33 4 36 2.96e-16 72.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 18 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTACCCTATGCACACATAAT+TGG 0.211435 1.2:-32888323 MS.gene85759:CDS
GAGGCTCTTCAACTACATTT+AGG 0.281000 1.2:-32886971 None:intergenic
TCTGCATCTGCCTCCGGCAT+TGG 0.339714 1.2:+32888282 None:intergenic
CTGCATCTGCCTCCGGCATT+GGG 0.356862 1.2:+32888283 None:intergenic
ATGCACACATAATTGGGATA+TGG 0.373855 1.2:-32888316 MS.gene85759:CDS
ATATATCTGACTGCACAAAT+AGG 0.395800 1.2:+32887004 None:intergenic
TACCCTATGCACACATAATT+GGG 0.416917 1.2:-32888322 MS.gene85759:CDS
TTATTGTCTGCATCTGCCTC+CGG 0.449792 1.2:+32888276 None:intergenic
ATCCCAATTATGTGTGCATA+GGG 0.512882 1.2:+32888320 None:intergenic
TATCCCAATTATGTGTGCAT+AGG 0.526401 1.2:+32888319 None:intergenic
GGTACAATCAGCTGTAGCCT+TGG 0.538349 1.2:+32888341 None:intergenic
TAGGATCCATGCACTTCTAT+CGG 0.546454 1.2:+32887023 None:intergenic
GCCTCCGGCATTGGGAAGAG+TGG 0.566459 1.2:+32888291 None:intergenic
CAGATATATCTATTGTAATG+AGG 0.568090 1.2:-32886990 MS.gene85759:CDS
GGAACCACTCTTCCCAATGC+CGG 0.571157 1.2:-32888295 MS.gene85759:CDS
ACCACTCTTCCCAATGCCGG+AGG 0.658673 1.2:-32888292 MS.gene85759:CDS
AGTTTATACGACGTATACAC+AGG 0.665776 1.2:-32887048 MS.gene85759:CDS
CAGGTGCCGATAGAAGTGCA+TGG 0.677112 1.2:-32887029 MS.gene85759:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAATCAAAACTATTTAATAT+TGG + chr1.2:32887259-32887278 None:intergenic 15.0%
!! TATAATTGAGTATCATTGAA+AGG - chr1.2:32888244-32888263 MS.gene85759:intron 20.0%
!! TATTAATTGACATCAGTTAA+AGG + chr1.2:32887426-32887445 None:intergenic 20.0%
!!! ATGGTTTTTAAAATCTTTAG+TGG - chr1.2:32887351-32887370 MS.gene85759:intron 20.0%
!!! ATTTTAAAAACCATACTCTT+TGG + chr1.2:32887345-32887364 None:intergenic 20.0%
!!! TTCATACTTATAATTTGCAA+TGG - chr1.2:32887598-32887617 MS.gene85759:intron 20.0%
!!! TTTTAAAAACCATACTCTTT+GGG + chr1.2:32887344-32887363 None:intergenic 20.0%
! AAATGCTAAATTTCTTGTAG+TGG + chr1.2:32887671-32887690 None:intergenic 25.0%
! AAGAATAAGCCTATTAATGA+AGG + chr1.2:32888093-32888112 None:intergenic 25.0%
! ATATTTGTAGTTATGCATTC+TGG - chr1.2:32887443-32887462 MS.gene85759:intron 25.0%
! CAGATATATCTATTGTAATG+AGG - chr1.2:32888330-32888349 MS.gene85759:CDS 25.0%
! TAGCATTATCCTTCATTAAT+AGG - chr1.2:32888081-32888100 MS.gene85759:intron 25.0%
! TATCTCTGTAATAGAAACAA+AGG + chr1.2:32887307-32887326 None:intergenic 25.0%
! TATTTGTAGTTATGCATTCT+GGG - chr1.2:32887444-32887463 MS.gene85759:intron 25.0%
! TTTAAAAACCATACTCTTTG+GGG + chr1.2:32887343-32887362 None:intergenic 25.0%
!! GTAATTTTCAACACACTATT+TGG - chr1.2:32887958-32887977 MS.gene85759:intron 25.0%
!! GTTATAATGAGATCTGTTTT+TGG - chr1.2:32888006-32888025 MS.gene85759:intron 25.0%
!!! TAGTTTTGATTCAATTGAGA+CGG - chr1.2:32887267-32887286 MS.gene85759:intron 25.0%
!!! TTATTAGTTTGTGAACTTCA+GGG - chr1.2:32887117-32887136 MS.gene85759:intron 25.0%
!!! TTTATTAGTTTGTGAACTTC+AGG - chr1.2:32887116-32887135 MS.gene85759:intron 25.0%
AATTGACATCAGTTAAAGGA+AGG + chr1.2:32887422-32887441 None:intergenic 30.0%
AGAATGTGTTCAATGTTTGA+TGG - chr1.2:32887560-32887579 MS.gene85759:intron 30.0%
ATATACTCCAGTAAAAGAAC+TGG + chr1.2:32887195-32887214 None:intergenic 30.0%
ATATATCTGACTGCACAAAT+AGG + chr1.2:32888319-32888338 None:intergenic 30.0%
TATACTCCAGTAAAAGAACT+GGG + chr1.2:32887194-32887213 None:intergenic 30.0%
TTGCAGATAATTCATATCGT+TGG - chr1.2:32887810-32887829 MS.gene85759:intron 30.0%
! AAGAAATTTAGCATTTTGCC+CGG - chr1.2:32887675-32887694 MS.gene85759:intron 30.0%
! AATATTTTCCCCAAAGAGTA+TGG - chr1.2:32887332-32887351 MS.gene85759:intron 30.0%
!! TATTAGTTTGTGAACTTCAG+GGG - chr1.2:32887118-32887137 MS.gene85759:intron 30.0%
!! TTTCTGTTTTAGGCAATGTT+TGG - chr1.2:32887699-32887718 MS.gene85759:intron 30.0%
!!! ATAATGAGATCTGTTTTTGG+AGG - chr1.2:32888009-32888028 MS.gene85759:intron 30.0%
!!! TCTGTTTTTGGAGGTTTAAA+TGG - chr1.2:32888018-32888037 MS.gene85759:intron 30.0%
AAGAGAGTGACATGTCAATT+CGG + chr1.2:32887098-32887117 None:intergenic 35.0%
ACTTTCAGTGTATTGAGTCT+AGG - chr1.2:32887881-32887900 MS.gene85759:intron 35.0%
AGTTTATACGACGTATACAC+AGG - chr1.2:32888272-32888291 MS.gene85759:intron 35.0%
ATACTCCAGTAAAAGAACTG+GGG + chr1.2:32887193-32887212 None:intergenic 35.0%
ATCCCAATTATGTGTGCATA+GGG + chr1.2:32887003-32887022 None:intergenic 35.0%
ATGCACACATAATTGGGATA+TGG - chr1.2:32887004-32887023 MS.gene85759:CDS 35.0%
ATGCAGTATGCTTCAATTCT+TGG - chr1.2:32888150-32888169 MS.gene85759:intron 35.0%
ATGTAGAGCTTCAAGAAGAA+AGG + chr1.2:32887511-32887530 None:intergenic 35.0%
GGGGATAATTGAACACTATT+TGG + chr1.2:32887490-32887509 None:intergenic 35.0%
TACCCTATGCACACATAATT+GGG - chr1.2:32886998-32887017 MS.gene85759:CDS 35.0%
TAGACTCAATACACTGAAAG+TGG + chr1.2:32887882-32887901 None:intergenic 35.0%
TATCCCAATTATGTGTGCAT+AGG + chr1.2:32887004-32887023 None:intergenic 35.0%
TGTAGAGCTTCAAGAAGAAA+GGG + chr1.2:32887510-32887529 None:intergenic 35.0%
TGTTTGGTATCTATTGCTGT+TGG - chr1.2:32887715-32887734 MS.gene85759:intron 35.0%
! AGAAATTTAGCATTTTGCCC+GGG - chr1.2:32887676-32887695 MS.gene85759:intron 35.0%
! GCAATTTTGGATTTTGCAGA+AGG - chr1.2:32887743-32887762 MS.gene85759:intron 35.0%
!! AAAAGTGCAAGCTTTTCATC+TGG + chr1.2:32887791-32887810 None:intergenic 35.0%
ACACGTGAGATTTATGCAAC+TGG + chr1.2:32887912-32887931 None:intergenic 40.0%
AGTTATGCATTCTGGGTGTT+TGG - chr1.2:32887451-32887470 MS.gene85759:intron 40.0%
ATTGCCTAAAACAGAAACCC+GGG + chr1.2:32887696-32887715 None:intergenic 40.0%
CATTGCCTAAAACAGAAACC+CGG + chr1.2:32887697-32887716 None:intergenic 40.0%
GCCTAAGAGTTATTGGAGTA+AGG - chr1.2:32887765-32887784 MS.gene85759:intron 40.0%
GCCTTACTCCAATAACTCTT+AGG + chr1.2:32887769-32887788 None:intergenic 40.0%
GTACCCTATGCACACATAAT+TGG - chr1.2:32886997-32887016 MS.gene85759:CDS 40.0%
GTACGCATGTAAGAAGCTAT+AGG - chr1.2:32887219-32887238 MS.gene85759:CDS 40.0%
GTAGAGCTTCAAGAAGAAAG+GGG + chr1.2:32887509-32887528 None:intergenic 40.0%
TACTCCAGTAAAAGAACTGG+GGG + chr1.2:32887192-32887211 None:intergenic 40.0%
TAGGATCCATGCACTTCTAT+CGG + chr1.2:32888300-32888319 None:intergenic 40.0%
TCATCCAAAAGCTTGTGCAA+AGG + chr1.2:32887984-32888003 None:intergenic 40.0%
TGCATAAATCTCACGTGTGA+AGG - chr1.2:32887914-32887933 MS.gene85759:intron 40.0%
TTGATTCAATTGAGACGGTC+TGG - chr1.2:32887272-32887291 MS.gene85759:intron 40.0%
!! GGAGGTTTAAATGGTTTGCT+TGG - chr1.2:32888027-32888046 MS.gene85759:intron 40.0%
GCAGAAGGCCTAAGAGTTAT+TGG - chr1.2:32887758-32887777 MS.gene85759:intron 45.0%
GTGACATGTCAATTCGGAGA+AGG + chr1.2:32887092-32887111 None:intergenic 45.0%
TTATTGTCTGCATCTGCCTC+CGG + chr1.2:32887047-32887066 None:intergenic 45.0%
! GTATCTATTGCTGTTGGAGC+AGG - chr1.2:32887721-32887740 MS.gene85759:intron 45.0%
! TTTGCCCGGGTTTCTGTTTT+AGG - chr1.2:32887689-32887708 MS.gene85759:intron 45.0%
!! TTGGCCTTTGCACAAGCTTT+TGG - chr1.2:32887977-32887996 MS.gene85759:intron 45.0%
CCAGTAAAAGAACTGGGGGA+AGG + chr1.2:32887188-32887207 None:intergenic 50.0%
GGTACAATCAGCTGTAGCCT+TGG + chr1.2:32886982-32887001 None:intergenic 50.0%
TCAATTGAGACGGTCTGGAG+TGG - chr1.2:32887277-32887296 MS.gene85759:intron 50.0%
! CCTTCCCCCAGTTCTTTTAC+TGG - chr1.2:32887185-32887204 MS.gene85759:intron 50.0%
! CGTTGGCTAGTTGCAGATCA+AGG - chr1.2:32887827-32887846 MS.gene85759:intron 50.0%
! GCTGTTGGAGCAGGCAATTT+TGG - chr1.2:32887730-32887749 MS.gene85759:intron 50.0%
GGAACCACTCTTCCCAATGC+CGG - chr1.2:32887025-32887044 MS.gene85759:CDS 55.0%
!! CAGGTGCCGATAGAAGTGCA+TGG - chr1.2:32888291-32888310 MS.gene85759:CDS 55.0%
ACCACTCTTCCCAATGCCGG+AGG - chr1.2:32887028-32887047 MS.gene85759:CDS 60.0%
CTGCATCTGCCTCCGGCATT+GGG + chr1.2:32887040-32887059 None:intergenic 60.0%
TCTGCATCTGCCTCCGGCAT+TGG + chr1.2:32887041-32887060 None:intergenic 60.0%
! GCCTCCGGCATTGGGAAGAG+TGG + chr1.2:32887032-32887051 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 32886972 32888370 32886972 ID=MS.gene85759
chr1.2 mRNA 32886972 32888370 32886972 ID=MS.gene85759.t1;Parent=MS.gene85759
chr1.2 exon 32888273 32888370 32888273 ID=MS.gene85759.t1.exon1;Parent=MS.gene85759.t1
chr1.2 CDS 32888273 32888370 32888273 ID=cds.MS.gene85759.t1;Parent=MS.gene85759.t1
chr1.2 exon 32887188 32887239 32887188 ID=MS.gene85759.t1.exon2;Parent=MS.gene85759.t1
chr1.2 CDS 32887188 32887239 32887188 ID=cds.MS.gene85759.t1;Parent=MS.gene85759.t1
chr1.2 exon 32886972 32887076 32886972 ID=MS.gene85759.t1.exon3;Parent=MS.gene85759.t1
chr1.2 CDS 32886972 32887076 32886972 ID=cds.MS.gene85759.t1;Parent=MS.gene85759.t1
Gene Sequence

>MS.gene85759

ATGATCACCAAGGCTACAGCTGATTGTACCCTATGCACACATAATTGGGATATGGAACCACTCTTCCCAATGCCGGAGGCAGATGCAGACAATAAAGAGTAAGTTGTTTCTTGTTTACCTTCTCCGAATTGACATGTCACTCTCTTTATTAGTTTGTGAACTTCAGGGGCTTATGATTTTCACTGATCTTCAAGATTTGATCAATGTAGTGTTCCTTCCCCCAGTTCTTTTACTGGAGTATATATAAGTACGCATGTAAGAAGCTATAGGATTTTAGATGTTATCCAATATTAAATAGTTTTGATTCAATTGAGACGGTCTGGAGTGGCTCACCTTTGTTTCTATTACAGAGATACTATTAATATTTTCCCCAAAGAGTATGGTTTTTAAAATCTTTAGTGGTGCAAAGCACTTGTAGTTATACATAAATTTGCAAAGTATTTGTATCCTTCCTTTAACTGATGTCAATTAATATTTGTAGTTATGCATTCTGGGTGTTTGGACAAACAATCTTTCCAAATAGTGTTCAATTATCCCCTTTCTTCTTGAAGCTCTACATAGACATGACAAGATTTGTATATGTATATGAGAATGTGTTCAATGTTTGATGGTGAATAACAAATGATTTCATACTTATAATTTGCAATGGAAAGAAACTAGTGAGTTTCTATGTGTTGAGTGTGTTGAACTGTTAAACCACTACAAGAAATTTAGCATTTTGCCCGGGTTTCTGTTTTAGGCAATGTTTGGTATCTATTGCTGTTGGAGCAGGCAATTTTGGATTTTGCAGAAGGCCTAAGAGTTATTGGAGTAAGGCCAGATGAAAAGCTTGCACTTTTTGCAGATAATTCATATCGTTGGCTAGTTGCAGATCAAGGTGTGTCAATCTCTTTTTTCTTTATCTTTTCCACTTTCAGTGTATTGAGTCTAGGAATTGCCAGTTGCATAAATCTCACGTGTGAAGGAAGTGTAATTTTACTATCAGTGTAATTTTCAACACACTATTTGGCCTTTGCACAAGCTTTTGGATGACTGTTATAATGAGATCTGTTTTTGGAGGTTTAAATGGTTTGCTTGGACTAATGAATGTATCACTCAAAACACTATACTAGCATTATCCTTCATTAATAGGCTTATTCTTCTGAAATCTGCAGAGAAGAATACTTGTGATATGTCTGATGCAGTATGCTTCAATTCTTGGTCTTTCTAGCATTAGTTTTTCTAGAATGTCTTGTGATTTTTTATTGTATGTTTATACTGTTATTTTTTTTTTATAATTGAGTATCATTGAAAGGTGCATAGTTTATACGACGTATACACAGGTGCCGATAGAAGTGCATGGATCCTATTTGTGCAGTCAGATATATCTATTGTAATGAGGCTCTTCAACTACATTTAG
Protein sequence

>MS.gene85759.t1

MITKATADCTLCTHNWDMEPLFPMPEADADNKELILLKSAEKNTCDMSDAVHSLYDVYTGADRSAWILFVQSDISIVMRLFNYI