AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene09882


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene09882.t1 MTR_7g099390 96.403 139 4 1 1 139 1 138 5.11e-94 268
MS.gene09882.t1 MTR_1g069235 57.971 138 47 3 11 138 11 147 4.83e-34 116
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene09882.t1 AT2G20260 52.667 150 48 3 6 139 3 145 1.56e-38 127
MS.gene09882.t1 AT4G28750 66.355 107 25 1 43 138 35 141 4.24e-32 111

Find 30 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTCACCTAATAATGTTTC+AGG 0.245319 7.3:+13022959 MS.gene09882:CDS
CCAATTCTAGACTTGTTGTT+AGG 0.258382 7.3:+13023050 MS.gene09882:CDS
ACACACCTTAGCACCTCTTT+TGG 0.283501 7.3:-13023149 None:intergenic
TTGTTGAATCTTACCACAAC+TGG 0.285947 7.3:-13023732 None:intergenic
ACAACTGGGTAGCGAGTATT+AGG 0.348189 7.3:-13023717 None:intergenic
AACATAGCATCAGCAGCTTC+AGG 0.370983 7.3:+13022929 MS.gene09882:CDS
TCCTACTGGTTCAATGGTAT+TGG 0.371489 7.3:+13023577 MS.gene09882:CDS
GTGTTGCCTGAAACATTATT+AGG 0.375498 7.3:-13022965 None:intergenic
CCTAACAACAAGTCTAGAAT+TGG 0.406311 7.3:-13023050 None:intergenic
ATCAACAAACAACTATGCTT+TGG 0.412222 7.3:+13023773 MS.gene09882:CDS
TTGGTGTTCTTTGTAGTAGT+AGG 0.427451 7.3:-13023031 None:intergenic
CTGGTTCAATGGTATTGGTT+CGG 0.430132 7.3:+13023582 MS.gene09882:CDS
TTCGGTTGTTGCTGTTGATC+AGG 0.443107 7.3:+13023600 MS.gene09882:CDS
CTATGCTTTGGATGAGATTG+AGG 0.451083 7.3:+13023785 MS.gene09882:CDS
CAATTCTAGACTTGTTGTTA+GGG 0.467358 7.3:+13023051 MS.gene09882:CDS
AAAGAATCCTACTGGTTCAA+TGG 0.482430 7.3:+13023571 MS.gene09882:CDS
TGGTGTTCTTTGTAGTAGTA+GGG 0.490325 7.3:-13023030 None:intergenic
TTCTTAGAAAAGAATCCTAC+TGG 0.502179 7.3:+13023563 MS.gene09882:CDS
GCTGCAACACCAACTGTTGA+AGG 0.512678 7.3:+13023088 MS.gene09882:CDS
CCACCAATTGGTCCCAAAAG+AGG 0.526898 7.3:+13023136 MS.gene09882:CDS
ACATAGCATCAGCAGCTTCA+GGG 0.527887 7.3:+13022930 MS.gene09882:CDS
ACTTGTTGTTAGGGCATCTG+AGG 0.546313 7.3:+13023060 MS.gene09882:CDS
TGGTCCCAAAAGAGGTGCTA+AGG 0.552862 7.3:+13023144 MS.gene09882:CDS
TGTTGTTAGGGCATCTGAGG+AGG 0.552889 7.3:+13023063 MS.gene09882:CDS
GCTGCCTCACCTTCAACAGT+TGG 0.556449 7.3:-13023097 None:intergenic
TAATACTCGCTACCCAGTTG+TGG 0.602018 7.3:+13023719 MS.gene09882:CDS
TGTTGAATCTTACCACAACT+GGG 0.616418 7.3:-13023731 None:intergenic
AACACCAACTGTTGAAGGTG+AGG 0.628187 7.3:+13023093 MS.gene09882:CDS
ATTAGCATCTAGAATGAACA+TGG 0.637216 7.3:+13023000 MS.gene09882:CDS
ACCAATACCATTGAACCAGT+AGG 0.690175 7.3:-13023578 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTAAAGTATACTTTCATA+CGG - chr7.3:13023214-13023233 None:intergenic 15.0%
!!! CTAAGTTTTATTTATTTTGT+TGG + chr7.3:13023520-13023539 MS.gene09882:intron 15.0%
!!! GTAGTTTTTTTTTAGAAATA+TGG + chr7.3:13023235-13023254 MS.gene09882:intron 15.0%
!!! TTTTTTAGAAATATGGAATT+GGG + chr7.3:13023242-13023261 MS.gene09882:intron 15.0%
!!! TTTTTTTAGAAATATGGAAT+TGG + chr7.3:13023241-13023260 MS.gene09882:intron 15.0%
!! AATTTCCAAATTACAAACTA+GGG - chr7.3:13023306-13023325 None:intergenic 20.0%
!! ATTATAAACTGATAGTAACT+TGG + chr7.3:13023447-13023466 MS.gene09882:intron 20.0%
!! ATTCTTACTAGAAAAAACTA+AGG - chr7.3:13023278-13023297 None:intergenic 20.0%
!! TTCTTACTAGAAAAAACTAA+GGG - chr7.3:13023277-13023296 None:intergenic 20.0%
!!! GTTTTTTCTAGTAAGAATTA+CGG + chr7.3:13023280-13023299 MS.gene09882:intron 20.0%
!!! TGTTTTTCCTACTAAATTAT+TGG - chr7.3:13023488-13023507 None:intergenic 20.0%
! CAATTTCCAAATTACAAACT+AGG - chr7.3:13023307-13023326 None:intergenic 25.0%
! TTCATACGGCATAATTTATT+TGG - chr7.3:13023200-13023219 None:intergenic 25.0%
! TTGTCAACCAATAATTTAGT+AGG + chr7.3:13023478-13023497 MS.gene09882:intron 25.0%
!! CTAGTTTGTAATTTGGAAAT+TGG + chr7.3:13023305-13023324 MS.gene09882:intron 25.0%
ATCAACAAACAACTATGCTT+TGG + chr7.3:13023773-13023792 MS.gene09882:CDS 30.0%
ATCCTACACAACACAATAAA+AGG - chr7.3:13023697-13023716 None:intergenic 30.0%
CTACTTCAAAATCAATCATG+TGG + chr7.3:13023635-13023654 MS.gene09882:intron 30.0%
GAAATATGGAATTGGGAAAA+TGG + chr7.3:13023249-13023268 MS.gene09882:intron 30.0%
TTCTTAGAAAAGAATCCTAC+TGG + chr7.3:13023563-13023582 MS.gene09882:CDS 30.0%
TTGTCACCTAATAATGTTTC+AGG + chr7.3:13022959-13022978 MS.gene09882:CDS 30.0%
! ATTAGCATCTAGAATGAACA+TGG + chr7.3:13023000-13023019 MS.gene09882:CDS 30.0%
! TTCCTTTTATTGTGTTGTGT+AGG + chr7.3:13023692-13023711 MS.gene09882:intron 30.0%
!! CAATTCTAGACTTGTTGTTA+GGG + chr7.3:13023051-13023070 MS.gene09882:CDS 30.0%
!!! CACATGATTGATTTTGAAGT+AGG - chr7.3:13023637-13023656 None:intergenic 30.0%
!!! TTTTGTTGGTTCTACTTAAC+AGG + chr7.3:13023534-13023553 MS.gene09882:intron 30.0%
GTGTTGCCTGAAACATTATT+AGG - chr7.3:13022968-13022987 None:intergenic 35.0%
TGGTGTTCTTTGTAGTAGTA+GGG - chr7.3:13023033-13023052 None:intergenic 35.0%
TGTTGAATCTTACCACAACT+GGG - chr7.3:13023734-13023753 None:intergenic 35.0%
TTGTTGAATCTTACCACAAC+TGG - chr7.3:13023735-13023754 None:intergenic 35.0%
! CCTAACAACAAGTCTAGAAT+TGG - chr7.3:13023053-13023072 None:intergenic 35.0%
! TGGTTCTACTTAACAGGTTA+AGG + chr7.3:13023540-13023559 MS.gene09882:intron 35.0%
! TTGGTGTTCTTTGTAGTAGT+AGG - chr7.3:13023034-13023053 None:intergenic 35.0%
!! AAAGAATCCTACTGGTTCAA+TGG + chr7.3:13023571-13023590 MS.gene09882:CDS 35.0%
!! CCAATTCTAGACTTGTTGTT+AGG + chr7.3:13023050-13023069 MS.gene09882:CDS 35.0%
ACCAATACCATTGAACCAGT+AGG - chr7.3:13023581-13023600 None:intergenic 40.0%
! CTATGCTTTGGATGAGATTG+AGG + chr7.3:13023785-13023804 MS.gene09882:CDS 40.0%
! TACGGCCCTAGTTTGTAATT+TGG + chr7.3:13023298-13023317 MS.gene09882:intron 40.0%
!! CTGGTTCAATGGTATTGGTT+CGG + chr7.3:13023582-13023601 MS.gene09882:CDS 40.0%
!! TCCTACTGGTTCAATGGTAT+TGG + chr7.3:13023577-13023596 MS.gene09882:CDS 40.0%
AAAATCAAGCCCCCACCAAT+TGG + chr7.3:13023124-13023143 MS.gene09882:CDS 45.0%
AACACCAACTGTTGAAGGTG+AGG + chr7.3:13023093-13023112 MS.gene09882:CDS 45.0%
AACATAGCATCAGCAGCTTC+AGG + chr7.3:13022929-13022948 MS.gene09882:CDS 45.0%
ACAACTGGGTAGCGAGTATT+AGG - chr7.3:13023720-13023739 None:intergenic 45.0%
ACATAGCATCAGCAGCTTCA+GGG + chr7.3:13022930-13022949 MS.gene09882:CDS 45.0%
TAATACTCGCTACCCAGTTG+TGG + chr7.3:13023719-13023738 MS.gene09882:CDS 45.0%
! ACACACCTTAGCACCTCTTT+TGG - chr7.3:13023152-13023171 None:intergenic 45.0%
! ATTGGTGGGGGCTTGATTTT+TGG - chr7.3:13023124-13023143 None:intergenic 45.0%
! CACACCTTAGCACCTCTTTT+GGG - chr7.3:13023151-13023170 None:intergenic 45.0%
! TTCGGTTGTTGCTGTTGATC+AGG + chr7.3:13023600-13023619 MS.gene09882:CDS 45.0%
!! ACTTGTTGTTAGGGCATCTG+AGG + chr7.3:13023060-13023079 MS.gene09882:CDS 45.0%
!!! CTCTTTTGGGACCAATTGGT+GGG - chr7.3:13023138-13023157 None:intergenic 45.0%
!!! TCTTTTGGGACCAATTGGTG+GGG - chr7.3:13023137-13023156 None:intergenic 45.0%
!! AATTATCATATAAATTAAAA+AGG - chr7.3:13023351-13023370 None:intergenic 5.0%
!! ATTATCATATAAATTAAAAA+GGG - chr7.3:13023350-13023369 None:intergenic 5.0%
CCACCAATTGGTCCCAAAAG+AGG + chr7.3:13023136-13023155 MS.gene09882:CDS 50.0%
GCTGCAACACCAACTGTTGA+AGG + chr7.3:13023088-13023107 MS.gene09882:CDS 50.0%
! TGTTGTTAGGGCATCTGAGG+AGG + chr7.3:13023063-13023082 MS.gene09882:CDS 50.0%
!! TGGTCCCAAAAGAGGTGCTA+AGG + chr7.3:13023144-13023163 MS.gene09882:CDS 50.0%
!!! CCTCTTTTGGGACCAATTGG+TGG - chr7.3:13023139-13023158 None:intergenic 50.0%
!!! CTTTTGGGACCAATTGGTGG+GGG - chr7.3:13023136-13023155 None:intergenic 50.0%
!!! GCACCTCTTTTGGGACCAAT+TGG - chr7.3:13023142-13023161 None:intergenic 50.0%
GCTGCCTCACCTTCAACAGT+TGG - chr7.3:13023100-13023119 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 13022917 13023818 13022917 ID=MS.gene09882
chr7.3 mRNA 13022917 13023818 13022917 ID=MS.gene09882.t1;Parent=MS.gene09882
chr7.3 exon 13022917 13023165 13022917 ID=MS.gene09882.t1.exon1;Parent=MS.gene09882.t1
chr7.3 CDS 13022917 13023165 13022917 ID=cds.MS.gene09882.t1;Parent=MS.gene09882.t1
chr7.3 exon 13023556 13023621 13023556 ID=MS.gene09882.t1.exon2;Parent=MS.gene09882.t1
chr7.3 CDS 13023556 13023621 13023556 ID=cds.MS.gene09882.t1;Parent=MS.gene09882.t1
chr7.3 exon 13023714 13023818 13023714 ID=MS.gene09882.t1.exon3;Parent=MS.gene09882.t1
chr7.3 CDS 13023714 13023818 13023714 ID=cds.MS.gene09882.t1;Parent=MS.gene09882.t1
Gene Sequence

>MS.gene09882

ATGGCTAGTTGCAACATAGCATCAGCAGCTTCAGGGTTTGTGTTGTCACCTAATAATGTTTCAGGCAACACAAACACTAATTTATTAGCATCTAGAATGAACATGGTGATGTACCCTACTACTACAAAGAACACCAATTCTAGACTTGTTGTTAGGGCATCTGAGGAGGCTGCTGCAACACCAACTGTTGAAGGTGAGGCAGCTCCAAAAATCAAGCCCCCACCAATTGGTCCCAAAAGAGGTGCTAAGGTGTGTTATATTTTGTGTCATCTATACACTTCCAAATAAATTATGCCGTATGAAAGTATACTTTAATTTGTAGTTTTTTTTTAGAAATATGGAATTGGGAAAATGGTTCCCTTAGTTTTTTCTAGTAAGAATTACGGCCCTAGTTTGTAATTTGGAAATTGGAATCACATTTTATGTCACACCCTTTTTAATTTATATGATAATTGTAAGTTTAAGTATGCAAAAATATTTTTATACAAATAAGTATAGCACTAAAATCATGCAATTGTTTTGAAACTTCGATTATAAACTGATAGTAACTTGGAATTTGTGTTGTCAACCAATAATTTAGTAGGAAAAACATTTTTTCTTCTTCTAAGTTTTATTTATTTTGTTGGTTCTACTTAACAGGTTAAGGTTCTTAGAAAAGAATCCTACTGGTTCAATGGTATTGGTTCGGTTGTTGCTGTTGATCAGGTTAGTTTCTCTCCTACTTCAAAATCAATCATGTGGATTTTGATCTCTTTGTAAGTTTCACTAAATTAATTTCCTTTTATTGTGTTGTGTAGGATCCTAATACTCGCTACCCAGTTGTGGTAAGATTCAACAAAGTTAACTATGCAAATGTATCAACAAACAACTATGCTTTGGATGAGATTGAGGAAGTCAAATGA

Protein sequence

>MS.gene09882.t1

MASCNIASAASGFVLSPNNVSGNTNTNLLASRMNMVMYPTTTKNTNSRLVVRASEEAAATPTVEGEAAPKIKPPPIGPKRGAKVKVLRKESYWFNGIGSVVAVDQDPNTRYPVVVRFNKVNYANVSTNNYALDEIEEVK