AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene053084

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053084.t1 MTR_6g004420 97.633 169 3 1 1 169 1 168 1.27e-117 330
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053084.t1 AT3G27520 43.011 186 84 3 5 168 13 198 3.94e-43 142

Find 25 sgRNAs with CRISPR-Local

Find 94 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTCGATTCCTTCTACTTC+TGG 0.230489 6.2:+474839 MS.gene053084:CDS
TTCGGCTACGTCGCATAAAT+TGG 0.237128 6.2:-476360 None:intergenic
TTCTCTAGCGCGTTCTGATC+TGG 0.317517 6.2:-474659 None:intergenic
AAGCTCCCATTCGTCGTCTT+CGG 0.371753 6.2:-474561 None:intergenic
CTTTGTTTGATCTACCAATC+TGG 0.375451 6.2:+476420 MS.gene053084:CDS
GGCGCTGTTGAGGAGGGTTC+CGG 0.396139 6.2:-474638 None:intergenic
AGAAAGCTGCAATGCACTTA+AGG 0.416394 6.2:-474771 None:intergenic
TCTTGATGATCTTCTCTCTC+AGG 0.421372 6.2:+474880 MS.gene053084:CDS
TTGTTTAGAACACATTGCTT+CGG 0.440413 6.2:-476378 None:intergenic
GGAATCCGAAGACGACGAAT+GGG 0.447320 6.2:+474556 MS.gene053084:CDS
AAACTTGCAGGTGGAAGCTC+AGG 0.449746 6.2:+476316 MS.gene053084:intron
TCAGCAGATCCAGAAGTAGA+AGG 0.457904 6.2:-474848 None:intergenic
CTGATCTGGCGCTGTTGAGG+AGG 0.476115 6.2:-474645 None:intergenic
AGTTGAGACGACGGCGTTTG+CGG 0.478873 6.2:-474613 None:intergenic
TGGAATCCGAAGACGACGAA+TGG 0.496694 6.2:+474555 MS.gene053084:CDS
GCTTAAATCCAAGTATGAAA+AGG 0.514430 6.2:+474718 MS.gene053084:CDS
ATGAAAAGGAAATTGTTCAG+TGG 0.519688 6.2:+474732 MS.gene053084:CDS
TGATCTGGCGCTGTTGAGGA+GGG 0.521322 6.2:-474644 None:intergenic
GTTCTGATCTGGCGCTGTTG+AGG 0.533842 6.2:-474648 None:intergenic
TGAAAAGGAAATTGTTCAGT+GGG 0.537819 6.2:+474733 MS.gene053084:CDS
AACGCTTGCATTAGCTCAAG+TGG 0.538919 6.2:-476449 None:intergenic
TCAAGTGGTGTAGACCAGAT+TGG 0.583060 6.2:-476434 None:intergenic
ACGCCGTCGTCTCAACTCAC+CGG 0.630008 6.2:+474619 MS.gene053084:CDS
TGGGAGCTTTGCTATGACGA+CGG 0.651451 6.2:+474575 MS.gene053084:CDS
GTTCCGGTGAGTTGAGACGA+CGG 0.727268 6.2:-474622 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATTAATAAATATTTATGG+TGG + chr6.2:475503-475522 MS.gene053084:intron 10.0%
!! AAATAAAGTTTGAAAATTTG+AGG + chr6.2:475024-475043 MS.gene053084:intron 15.0%
!! AGTCTTCTAATTTAATAAAT+TGG + chr6.2:475281-475300 MS.gene053084:intron 15.0%
!! GTCTTCTAATTTAATAAATT+GGG + chr6.2:475282-475301 MS.gene053084:intron 15.0%
!!! TGTTTGAATTTTTCATTTTT+TGG + chr6.2:475314-475333 MS.gene053084:intron 15.0%
!!! TTGAAAGAAATTTTGTTTTT+GGG + chr6.2:474926-474945 MS.gene053084:intron 15.0%
!!! TTTGAAAGAAATTTTGTTTT+TGG + chr6.2:474925-474944 MS.gene053084:intron 15.0%
!! AAAACATTTGTCATACATTA+TGG + chr6.2:475900-475919 MS.gene053084:intron 20.0%
!! AATTTAATAAATTGGGACTT+AGG + chr6.2:475289-475308 MS.gene053084:intron 20.0%
! ACAAGTCTATAACTTTACAA+AGG - chr6.2:476221-476240 None:intergenic 25.0%
! ATGAGCTTAATTATTATGCA+TGG + chr6.2:475596-475615 MS.gene053084:intron 25.0%
! TAAATATTTATGGTGGTTTC+TGG + chr6.2:475510-475529 MS.gene053084:intron 25.0%
! TCTTTCAAAATTACGAAGAA+TGG - chr6.2:474914-474933 None:intergenic 25.0%
! TTTGTCATACATTATGGATT+TGG + chr6.2:475906-475925 MS.gene053084:intron 25.0%
!! AACAATTTCCTTTTCATACT+TGG - chr6.2:474729-474748 None:intergenic 25.0%
!!! GTTTTTGGGTATTGATAAAT+GGG + chr6.2:474940-474959 MS.gene053084:intron 25.0%
!!! TATTTTGAGAAATGATGAGT+AGG + chr6.2:476102-476121 MS.gene053084:intron 25.0%
!!! TGTTTTTGGGTATTGATAAA+TGG + chr6.2:474939-474958 MS.gene053084:intron 25.0%
AAAACATTCACCATGTCTTA+TGG + chr6.2:475639-475658 MS.gene053084:intron 30.0%
AATTAAGTAGCCATTATCTC+TGG + chr6.2:476184-476203 MS.gene053084:intron 30.0%
ACTATCAGATCTCAAATCAA+CGG + chr6.2:475748-475767 MS.gene053084:intron 30.0%
ATCAAGACCAAAATCGATAA+AGG - chr6.2:474991-475010 None:intergenic 30.0%
ATGAAAAGGAAATTGTTCAG+TGG + chr6.2:474732-474751 MS.gene053084:CDS 30.0%
ATTACATAGTTCTCAACCAT+CGG - chr6.2:475724-475743 None:intergenic 30.0%
GCTTAAATCCAAGTATGAAA+AGG + chr6.2:474718-474737 MS.gene053084:CDS 30.0%
TAATCCAAATCCATAAGACA+TGG - chr6.2:475652-475671 None:intergenic 30.0%
TCAAGACCAAAATCGATAAA+GGG - chr6.2:474990-475009 None:intergenic 30.0%
TGAAAAGGAAATTGTTCAGT+GGG + chr6.2:474733-474752 MS.gene053084:CDS 30.0%
TTTAGTATTCTCAAACTTGC+AGG + chr6.2:476304-476323 MS.gene053084:intron 30.0%
TTTGTGTAAATTCACTGCTT+AGG + chr6.2:475248-475267 MS.gene053084:intron 30.0%
! AATTTGAGGTTATTGTGAAC+TGG + chr6.2:475038-475057 MS.gene053084:intron 30.0%
! ATAGATTGCGTCAATTTTGT+TGG + chr6.2:475201-475220 MS.gene053084:intron 30.0%
! ATTTGAGGTTATTGTGAACT+GGG + chr6.2:475039-475058 MS.gene053084:intron 30.0%
! CATTATGGATTTGGATTAGA+CGG + chr6.2:475915-475934 MS.gene053084:intron 30.0%
! TTGTTTAGAACACATTGCTT+CGG - chr6.2:476381-476400 None:intergenic 30.0%
AAATGTGAAACTGCATGTTG+CGG + chr6.2:476053-476072 MS.gene053084:intron 35.0%
ACTTTACAAAGGATGTTCCA+AGG - chr6.2:476210-476229 None:intergenic 35.0%
GTTGTTTACCACTTTGTCTA+TGG - chr6.2:475341-475360 None:intergenic 35.0%
TCTCAGCCATCAATTCAAAT+CGG - chr6.2:475976-475995 None:intergenic 35.0%
TCTTCCAATTCTAAACACTC+CGG - chr6.2:475468-475487 None:intergenic 35.0%
TTCACCATGTCTTATGGATT+TGG + chr6.2:475645-475664 MS.gene053084:intron 35.0%
TTTAGCTAGACTTTACAGAC+CGG + chr6.2:475446-475465 MS.gene053084:intron 35.0%
! CTTTGTTTGATCTACCAATC+TGG + chr6.2:476420-476439 MS.gene053084:CDS 35.0%
! TTCTGTGTTTCTGTTGATGT+TGG + chr6.2:475115-475134 MS.gene053084:intron 35.0%
! TTTGAATTGATGGCTGAGAT+CGG + chr6.2:475977-475996 MS.gene053084:intron 35.0%
!! TTTCAAGCTTTAAGCGATCT+TGG - chr6.2:475774-475793 None:intergenic 35.0%
!! TTTTTGGTCCATAGACAAAG+TGG + chr6.2:475330-475349 MS.gene053084:intron 35.0%
!!! GCGTCAATTTTGTTGGTTTT+AGG + chr6.2:475208-475227 MS.gene053084:intron 35.0%
!!! TAGCTACCCTTTATCGATTT+TGG + chr6.2:474981-475000 MS.gene053084:intron 35.0%
ACCACAATGTCGAAATTGCT+AGG - chr6.2:475423-475442 None:intergenic 40.0%
ACCTAGCAATTTCGACATTG+TGG + chr6.2:475419-475438 MS.gene053084:intron 40.0%
AGAAAGCTGCAATGCACTTA+AGG - chr6.2:474774-474793 None:intergenic 40.0%
AGCCATCAATTCAAATCGGA+AGG - chr6.2:475972-475991 None:intergenic 40.0%
AGTATTCTCAAACTTGCAGG+TGG + chr6.2:476307-476326 MS.gene053084:intron 40.0%
GATATGTGTGTGAGTTTCAG+TGG - chr6.2:475370-475389 None:intergenic 40.0%
GCAGTGAATTTACACAAACC+AGG - chr6.2:475246-475265 None:intergenic 40.0%
GCCATCAATTCAAATCGGAA+GGG - chr6.2:475971-475990 None:intergenic 40.0%
TATCTTGACCGCAGTTACTT+TGG - chr6.2:475804-475823 None:intergenic 40.0%
TGAAACTCACACACATATCC+CGG + chr6.2:475371-475390 MS.gene053084:intron 40.0%
! TCTTGATGATCTTCTCTCTC+AGG + chr6.2:474880-474899 MS.gene053084:CDS 40.0%
! TTTAGGTTCAGCTGTAAACC+TGG + chr6.2:475225-475244 MS.gene053084:intron 40.0%
!! TTGTCGATTCCTTCTACTTC+TGG + chr6.2:474839-474858 MS.gene053084:CDS 40.0%
AACGCTTGCATTAGCTCAAG+TGG - chr6.2:476452-476471 None:intergenic 45.0%
ACTGTGTGCCAAAGTAACTG+CGG + chr6.2:475793-475812 MS.gene053084:intron 45.0%
CTAGGTTAGACACCTTGACT+CGG - chr6.2:475405-475424 None:intergenic 45.0%
TAGGTTAGACACCTTGACTC+GGG - chr6.2:475404-475423 None:intergenic 45.0%
TCAAGTGGTGTAGACCAGAT+TGG - chr6.2:476437-476456 None:intergenic 45.0%
TCAGCAGATCCAGAAGTAGA+AGG - chr6.2:474851-474870 None:intergenic 45.0%
TGTTCCAAGGCCAGAGATAA+TGG - chr6.2:476197-476216 None:intergenic 45.0%
TTCGGCTACGTCGCATAAAT+TGG - chr6.2:476363-476382 None:intergenic 45.0%
! CAGACCGGAGTGTTTAGAAT+TGG + chr6.2:475461-475480 MS.gene053084:intron 45.0%
! GCCCTTCCGATTTGAATTGA+TGG + chr6.2:475967-475986 MS.gene053084:intron 45.0%
!! TCTCAACCATCGGTTCAGAT+CGG - chr6.2:475714-475733 None:intergenic 45.0%
!! GAAATATTAATAAATATTTA+TGG + chr6.2:475500-475519 MS.gene053084:intron 5.0%
AAACTTGCAGGTGGAAGCTC+AGG + chr6.2:476316-476335 MS.gene053084:intron 50.0%
AAGCTCCCATTCGTCGTCTT+CGG - chr6.2:474564-474583 None:intergenic 50.0%
GGAATCCGAAGACGACGAAT+GGG + chr6.2:474556-474575 MS.gene053084:CDS 50.0%
GTAGCCATTATCTCTGGCCT+TGG + chr6.2:476190-476209 MS.gene053084:intron 50.0%
GTGTCACGCTGTTGTTGCAT+TGG + chr6.2:476141-476160 MS.gene053084:intron 50.0%
GTTCAGATCGGACGACAAGA+CGG - chr6.2:475702-475721 None:intergenic 50.0%
TGGAATCCGAAGACGACGAA+TGG + chr6.2:474555-474574 MS.gene053084:CDS 50.0%
TTCTCTAGCGCGTTCTGATC+TGG - chr6.2:474662-474681 None:intergenic 50.0%
! TGGGAGCTTTGCTATGACGA+CGG + chr6.2:474575-474594 MS.gene053084:CDS 50.0%
AGTTGAGACGACGGCGTTTG+CGG - chr6.2:474616-474635 None:intergenic 55.0%
GTTCTGATCTGGCGCTGTTG+AGG - chr6.2:474651-474670 None:intergenic 55.0%
TGATCTGGCGCTGTTGAGGA+GGG - chr6.2:474647-474666 None:intergenic 55.0%
TGTCGTCCGATCTGAACCGA+TGG + chr6.2:475705-475724 MS.gene053084:intron 55.0%
! GTTCCGGTGAGTTGAGACGA+CGG - chr6.2:474625-474644 None:intergenic 55.0%
!! CCTTGACTCGGGTTCGAATC+CGG - chr6.2:475393-475412 None:intergenic 55.0%
!! CTTGACTCGGGTTCGAATCC+GGG - chr6.2:475392-475411 None:intergenic 55.0%
ACGCCGTCGTCTCAACTCAC+CGG + chr6.2:474619-474638 MS.gene053084:CDS 60.0%
CCGGATTCGAACCCGAGTCA+AGG + chr6.2:475390-475409 MS.gene053084:intron 60.0%
CTGATCTGGCGCTGTTGAGG+AGG - chr6.2:474648-474667 None:intergenic 60.0%
GGCGCTGTTGAGGAGGGTTC+CGG - chr6.2:474641-474660 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 474554 476487 474554 ID=MS.gene053084
chr6.2 mRNA 474554 476487 474554 ID=MS.gene053084.t1;Parent=MS.gene053084
chr6.2 exon 474554 474901 474554 ID=MS.gene053084.t1.exon1;Parent=MS.gene053084.t1
chr6.2 CDS 474554 474901 474554 ID=cds.MS.gene053084.t1;Parent=MS.gene053084.t1
chr6.2 exon 476326 476487 476326 ID=MS.gene053084.t1.exon2;Parent=MS.gene053084.t1
chr6.2 CDS 476326 476487 476326 ID=cds.MS.gene053084.t1;Parent=MS.gene053084.t1
Gene Sequence

>MS.gene053084

ATGGAATCCGAAGACGACGAATGGGAGCTTTGCTATGACGACGGCTTCGTCTACAAACGCCGCAAACGCCGTCGTCTCAACTCACCGGAACCCTCCTCAACAGCGCCAGATCAGAACGCGCTAGAGAAGTTACGAATAGAACGAAAGAAAACGACACTTTTGAAGCTTAAATCCAAGTATGAAAAGGAAATTGTTCAGTGGGAACATTTATCAAACACCTTAAGTGCATTGCAGCTTTCTTCTTCAAATCAGCTTAATGAGCAGCAACAGCAGCAAAATCAAAACTTGTCGATTCCTTCTACTTCTGGATCTGCTGAATCGTCTCTTCTTGATGATCTTCTCTCTCAGGTAACTTCACCATTCTTCGTAATTTTGAAAGAAATTTTGTTTTTGGGTATTGATAAATGGGTTTGAAATTTGTGTTTTTTAGCTACCCTTTATCGATTTTGGTCTTGATTTTGAATAATATGAAATAAAGTTTGAAAATTTGAGGTTATTGTGAACTGGGTCTGAAATTTGCGTTTGTTAGAGTTGTGAAATTCTGACAAAAAAATATGTTTTTTCTGTGTTTCTGTTGATGTTGGAGTTTGAAGTGATTTATGTGAATAATGACATGTATGTATGCTGAAATTTAGTTTACAGTTACTATAGATTGCGTCAATTTTGTTGGTTTTAGGTTCAGCTGTAAACCTGGTTTGTGTAAATTCACTGCTTAGGAAGCATTGTTAGTCTTCTAATTTAATAAATTGGGACTTAGGAATGTTTGAATTTTTCATTTTTTGGTCCATAGACAAAGTGGTAAACAACTATACACCACTGAAACTCACACACATATCCCGGATTCGAACCCGAGTCAAGGTGTCTAACCTAGCAATTTCGACATTGTGGTGAGTTTAGCTAGACTTTACAGACCGGAGTGTTTAGAATTGGAAGAAGTTAGAAGTTAGAAATATTAATAAATATTTATGGTGGTTTCTGGCTTTTATGATTATCTCATGTTATTTCTGTTAGACTCTTAATTGCGTTTATGAGAAATATCAATATGAGCTTAATTATTATGCATGGACTGCGTAAAAAAAATTATAAAAACATTCACCATGTCTTATGGATTTGGATTAGACGCAGTAATTGTGTCATGTAGTATTCCGTCTTGTCGTCCGATCTGAACCGATGGTTGAGAACTATGTAATCTGAACTATCAGATCTCAAATCAACGGCCAAGATCGCTTAAAGCTTGAAACTGTGTGCCAAAGTAACTGCGGTCAAGATAGCTTCTTAGTTCAGTTTATGAAAAATATGAACATGAACTTAATTGTTATGCGTAGTTGTTGTAGAAAAAAATTATAAAAACATTTGTCATACATTATGGATTTGGATTAGACGGAGTAACTGCGTAATGCAGTACTGCATTTTGCCCTTCCGATTTGAATTGATGGCTGAGATCGGTTAACTGTGTAATTTGAACTGTCAGATCTCAATTCAACGAGTAAGATTACTTAAAATGTGAAACTGCATGTTGCGGTATTTGCAACAAAATACTTGTGCAGATATTTTGAGAAATGATGAGTAGGATATGATTGATTGTTTGTGTCACGCTGTTGTTGCATTGGTGTGTATGATGATTAAACTCAATTAAGTAGCCATTATCTCTGGCCTTGGAACATCCTTTGTAAAGTTATAGACTTGTTAATCTAACTGAACTGCATATGTAGTGAATAGTGTTGAATGTTGATGAGTTTGTCACTCTTAATTTAGTATTCTCAAACTTGCAGGTGGAAGCTCAGGAAGCAATCATTCATGATATTTCCAATTTATGCGACGTAGCCGAAGCAATGTGTTCTAAACAAGAAGAACAGTATAAACAATCTTTGTTTGATCTACCAATCTGGTCTACACCACTTGAGCTAATGCAAGCGTTATGCTATGATGATTGA
Protein sequence

>MS.gene053084.t1

MESEDDEWELCYDDGFVYKRRKRRRLNSPEPSSTAPDQNALEKLRIERKKTTLLKLKSKYEKEIVQWEHLSNTLSALQLSSSNQLNEQQQQQNQNLSIPSTSGSAESSLLDDLLSQVEAQEAIIHDISNLCDVAEAMCSKQEEQYKQSLFDLPIWSTPLELMQALCYDD