AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0152500


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0152500 MtrunA17_Chr1g0161551 92.857 84 5 1 1 84 1 83 2.95e-50 154
Msa0152500 MtrunA17_Chr6g0479181 41.228 114 63 2 9 122 53 162 3.21e-23 89.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0152500 AT1G14760.2 42.157 102 54 3 22 119 32 132 1.44e-19 78.6
Msa0152500 AT1G70510.1 36.792 106 59 2 22 122 68 170 6.75e-12 61.2
Msa0152500 AT1G23380.1 34.906 106 61 2 22 122 84 186 2.31e-11 59.7

Find 19 sgRNAs with CRISPR-Local

Find 126 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGATGGAGGGTAAAGAAAT+TGG 0.288718 1_4:+15188113 None:intergenic
GTTTGGACTAGTTGTTGTTT+TGG 0.335695 1_4:-15188801 None:intergenic
CCATCCTTTGTTTGAAGCAT+TGG 0.359729 1_4:+15188202 Msa0152500:CDS
TGATCAAGCTCTGAATTGTT+TGG 0.360004 1_4:-15188818 None:intergenic
TTCAGAGCTTGATCACTTCA+TGG 0.367274 1_4:+15188826 Msa0152500:CDS
AAGTGATGCATGGAAGAAAT+TGG 0.438853 1_4:+15188766 Msa0152500:CDS
GTCTCACATCAATTGTTTGA+AGG 0.470627 1_4:+15188229 Msa0152500:CDS
TATATTCAACTGCAGGAACT+TGG 0.501461 1_4:+15190076 Msa0152500:CDS
GTTCATCAATCACGTCTTTG+AGG 0.505826 1_4:-15190018 None:intergenic
AAAAGAAAGTGAAAATGAAG+AGG 0.568561 1_4:+15188157 Msa0152500:CDS
CCAATGCTTCAAACAAAGGA+TGG 0.572089 1_4:-15188202 None:intergenic
TTGATATAACAAGTGATGCA+TGG 0.576358 1_4:+15188756 Msa0152500:CDS
GGAAAGGGAAGTGATGATGT+AGG 0.576930 1_4:+15188134 Msa0152500:CDS
TGCTACGTATATTCAACTGC+AGG 0.578517 1_4:+15190069 Msa0152500:CDS
TCAACCAATGCTTCAAACAA+AGG 0.579326 1_4:-15188206 None:intergenic
GAGGGTAAAGAAATTGGAAA+GGG 0.582588 1_4:+15188119 Msa0152500:CDS
GGAGGGTAAAGAAATTGGAA+AGG 0.606364 1_4:+15188118 Msa0152500:CDS
TATTTCTTAGGTCGGATCTG+AGG 0.611391 1_4:+15188721 Msa0152500:intron
CAACTGCAGGAACTTGGTGA+AGG 0.630993 1_4:+15190082 Msa0152500:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAATATAGTGTATAATTA+TGG + chr1_4:15188376-15188395 Msa0152500:intron 10.0%
!! ATATTAATATATACACAAAA+AGG + chr1_4:15188453-15188472 Msa0152500:intron 10.0%
!! TATTAATATATACACAAAAA+GGG + chr1_4:15188454-15188473 Msa0152500:intron 10.0%
!! ATAGATATATAAATTCTTTA+CGG + chr1_4:15189052-15189071 Msa0152500:intron 10.0%
!! AAATAATAATCTATAAAAGA+TGG - chr1_4:15189590-15189609 None:intergenic 10.0%
!! AAATAATAATCTATAAAAGA+TGG - chr1_4:15189590-15189609 None:intergenic 10.0%
!! AATAATATAGTGTATAATTA+TGG + chr1_4:15188376-15188395 Msa0152500:intron 10.0%
!! ATATTAATATATACACAAAA+AGG + chr1_4:15188453-15188472 Msa0152500:intron 10.0%
!! TATTAATATATACACAAAAA+GGG + chr1_4:15188454-15188473 Msa0152500:intron 10.0%
!! ATAGATATATAAATTCTTTA+CGG + chr1_4:15189052-15189071 Msa0152500:intron 10.0%
!! AAATAATAATCTATAAAAGA+TGG - chr1_4:15189590-15189609 None:intergenic 10.0%
!! AAATAATAATCTATAAAAGA+TGG - chr1_4:15189590-15189609 None:intergenic 10.0%
!! ACAACTTAAATTTATTTAAG+AGG + chr1_4:15188275-15188294 Msa0152500:intron 15.0%
!! GTATTACATACATTAATTAA+TGG + chr1_4:15188848-15188867 Msa0152500:intron 15.0%
!!! TTGTTACTTAGTAATTAATT+TGG - chr1_4:15189089-15189108 None:intergenic 15.0%
!!! TTACTAAGTAACAATTTTTA+TGG + chr1_4:15189095-15189114 Msa0152500:intron 15.0%
!! ACAACTTAAATTTATTTAAG+AGG + chr1_4:15188275-15188294 Msa0152500:intron 15.0%
!! GTATTACATACATTAATTAA+TGG + chr1_4:15188848-15188867 Msa0152500:intron 15.0%
!!! TTGTTACTTAGTAATTAATT+TGG - chr1_4:15189089-15189108 None:intergenic 15.0%
!!! TTACTAAGTAACAATTTTTA+TGG + chr1_4:15189095-15189114 Msa0152500:intron 15.0%
!! TAATTATGGAAAGATAGTTT+AGG + chr1_4:15188390-15188409 Msa0152500:intron 20.0%
!!! TCTTTTTTGCAAAAGAAAAA+TGG + chr1_4:15188637-15188656 Msa0152500:intron 20.0%
!!! AAGAAAAATGGATTAATCAA+AGG + chr1_4:15188649-15188668 Msa0152500:intron 20.0%
!!! AGTAATTAATTTGGATGTTT+TGG - chr1_4:15189080-15189099 None:intergenic 20.0%
!! AATCATATTATATGTGAACT+AGG - chr1_4:15189957-15189976 None:intergenic 20.0%
!! TATGATTCATTTATGTACAT+AGG + chr1_4:15189970-15189989 Msa0152500:intron 20.0%
!! TAATTATGGAAAGATAGTTT+AGG + chr1_4:15188390-15188409 Msa0152500:intron 20.0%
!!! TCTTTTTTGCAAAAGAAAAA+TGG + chr1_4:15188637-15188656 Msa0152500:intron 20.0%
!!! AAGAAAAATGGATTAATCAA+AGG + chr1_4:15188649-15188668 Msa0152500:intron 20.0%
!!! AGTAATTAATTTGGATGTTT+TGG - chr1_4:15189080-15189099 None:intergenic 20.0%
!! AATCATATTATATGTGAACT+AGG - chr1_4:15189957-15189976 None:intergenic 20.0%
!! TATGATTCATTTATGTACAT+AGG + chr1_4:15189970-15189989 Msa0152500:intron 20.0%
! AAAAGAAAGTGAAAATGAAG+AGG + chr1_4:15188157-15188176 Msa0152500:CDS 25.0%
! TAATTTCATTCCATACATGT+TGG - chr1_4:15188681-15188700 None:intergenic 25.0%
!! TCTTCATTCCTTTATTTCTT+AGG + chr1_4:15188709-15188728 Msa0152500:intron 25.0%
! CATACATTAATTAATGGTCA+TGG + chr1_4:15188854-15188873 Msa0152500:intron 25.0%
! TGTGTGTAAAATAGATATTG+TGG + chr1_4:15189008-15189027 Msa0152500:intron 25.0%
! TCATGAAAGTTGTCTATTAA+TGG + chr1_4:15189273-15189292 Msa0152500:intron 25.0%
!!! ACGTAAATTGAAAGTTTTGA+AGG - chr1_4:15189342-15189361 None:intergenic 25.0%
! GTAACTAAAACTTGTCATTA+TGG - chr1_4:15189367-15189386 None:intergenic 25.0%
!!! TTTTTAAGCAAGCATAAACT+AGG + chr1_4:15189851-15189870 Msa0152500:intron 25.0%
! AAAAGAAAGTGAAAATGAAG+AGG + chr1_4:15188157-15188176 Msa0152500:CDS 25.0%
! TAATTTCATTCCATACATGT+TGG - chr1_4:15188681-15188700 None:intergenic 25.0%
!! TCTTCATTCCTTTATTTCTT+AGG + chr1_4:15188709-15188728 Msa0152500:intron 25.0%
! CATACATTAATTAATGGTCA+TGG + chr1_4:15188854-15188873 Msa0152500:intron 25.0%
! TGTGTGTAAAATAGATATTG+TGG + chr1_4:15189008-15189027 Msa0152500:intron 25.0%
! TCATGAAAGTTGTCTATTAA+TGG + chr1_4:15189273-15189292 Msa0152500:intron 25.0%
!!! ACGTAAATTGAAAGTTTTGA+AGG - chr1_4:15189342-15189361 None:intergenic 25.0%
! GTAACTAAAACTTGTCATTA+TGG - chr1_4:15189367-15189386 None:intergenic 25.0%
!!! TTTTTAAGCAAGCATAAACT+AGG + chr1_4:15189851-15189870 Msa0152500:intron 25.0%
TGTAAGTAATGTATTCCTCA+TGG - chr1_4:15188426-15188445 None:intergenic 30.0%
AGGGTAAAAAAGACAACAAA+AGG + chr1_4:15188473-15188492 Msa0152500:intron 30.0%
GGGTAAAAAAGACAACAAAA+GGG + chr1_4:15188474-15188493 Msa0152500:intron 30.0%
AAGGATATATCCAACATGTA+TGG + chr1_4:15188668-15188687 Msa0152500:intron 30.0%
! CATTCCTTTATTTCTTAGGT+CGG + chr1_4:15188713-15188732 Msa0152500:intron 30.0%
TTGATATAACAAGTGATGCA+TGG + chr1_4:15188756-15188775 Msa0152500:CDS 30.0%
! AATCAAATTTGTTCGCTCAA+TGG + chr1_4:15188960-15188979 Msa0152500:intron 30.0%
GTCAAAAAGTTGTTGCAAAA+TGG - chr1_4:15189155-15189174 None:intergenic 30.0%
! AAAGCTTTTGCTTCTTTTGT+TGG - chr1_4:15190043-15190062 None:intergenic 30.0%
TGTAAGTAATGTATTCCTCA+TGG - chr1_4:15188426-15188445 None:intergenic 30.0%
AGGGTAAAAAAGACAACAAA+AGG + chr1_4:15188473-15188492 Msa0152500:intron 30.0%
GGGTAAAAAAGACAACAAAA+GGG + chr1_4:15188474-15188493 Msa0152500:intron 30.0%
AAGGATATATCCAACATGTA+TGG + chr1_4:15188668-15188687 Msa0152500:intron 30.0%
! CATTCCTTTATTTCTTAGGT+CGG + chr1_4:15188713-15188732 Msa0152500:intron 30.0%
TTGATATAACAAGTGATGCA+TGG + chr1_4:15188756-15188775 Msa0152500:CDS 30.0%
! AATCAAATTTGTTCGCTCAA+TGG + chr1_4:15188960-15188979 Msa0152500:intron 30.0%
GTCAAAAAGTTGTTGCAAAA+TGG - chr1_4:15189155-15189174 None:intergenic 30.0%
! AAAGCTTTTGCTTCTTTTGT+TGG - chr1_4:15190043-15190062 None:intergenic 30.0%
GAGGGTAAAGAAATTGGAAA+GGG + chr1_4:15188119-15188138 Msa0152500:CDS 35.0%
TCAACCAATGCTTCAAACAA+AGG - chr1_4:15188209-15188228 None:intergenic 35.0%
GTCTCACATCAATTGTTTGA+AGG + chr1_4:15188229-15188248 Msa0152500:CDS 35.0%
AGATCCGACCTAAGAAATAA+AGG - chr1_4:15188720-15188739 None:intergenic 35.0%
AAGTGATGCATGGAAGAAAT+TGG + chr1_4:15188766-15188785 Msa0152500:CDS 35.0%
!!! GTTTGGACTAGTTGTTGTTT+TGG - chr1_4:15188804-15188823 None:intergenic 35.0%
!! TGATCAAGCTCTGAATTGTT+TGG - chr1_4:15188821-15188840 None:intergenic 35.0%
!!! TACATAGGAAGCATTTTGCA+TGG + chr1_4:15189985-15190004 Msa0152500:intron 35.0%
TATATTCAACTGCAGGAACT+TGG + chr1_4:15190076-15190095 Msa0152500:CDS 35.0%
GAGGGTAAAGAAATTGGAAA+GGG + chr1_4:15188119-15188138 Msa0152500:CDS 35.0%
TCAACCAATGCTTCAAACAA+AGG - chr1_4:15188209-15188228 None:intergenic 35.0%
GTCTCACATCAATTGTTTGA+AGG + chr1_4:15188229-15188248 Msa0152500:CDS 35.0%
AGATCCGACCTAAGAAATAA+AGG - chr1_4:15188720-15188739 None:intergenic 35.0%
AAGTGATGCATGGAAGAAAT+TGG + chr1_4:15188766-15188785 Msa0152500:CDS 35.0%
!!! GTTTGGACTAGTTGTTGTTT+TGG - chr1_4:15188804-15188823 None:intergenic 35.0%
!! TGATCAAGCTCTGAATTGTT+TGG - chr1_4:15188821-15188840 None:intergenic 35.0%
!!! TACATAGGAAGCATTTTGCA+TGG + chr1_4:15189985-15190004 Msa0152500:intron 35.0%
TATATTCAACTGCAGGAACT+TGG + chr1_4:15190076-15190095 Msa0152500:CDS 35.0%
GGAGGGTAAAGAAATTGGAA+AGG + chr1_4:15188118-15188137 Msa0152500:CDS 40.0%
CCAATGCTTCAAACAAAGGA+TGG - chr1_4:15188205-15188224 None:intergenic 40.0%
! CCATCCTTTGTTTGAAGCAT+TGG + chr1_4:15188202-15188221 Msa0152500:CDS 40.0%
! GGAAAGATAGTTTAGGACCA+CGG + chr1_4:15188397-15188416 Msa0152500:intron 40.0%
TATTTCTTAGGTCGGATCTG+AGG + chr1_4:15188721-15188740 Msa0152500:intron 40.0%
TTCAGAGCTTGATCACTTCA+TGG + chr1_4:15188826-15188845 Msa0152500:CDS 40.0%
!! GTACGTATGGTTTTGCATGT+GGG - chr1_4:15189405-15189424 None:intergenic 40.0%
AATACGTTGTGACGTACGTA+TGG - chr1_4:15189418-15189437 None:intergenic 40.0%
AATACGTTGTGACGTACGTA+TGG - chr1_4:15189418-15189437 None:intergenic 40.0%
GTTCATCAATCACGTCTTTG+AGG - chr1_4:15190021-15190040 None:intergenic 40.0%
TGCTACGTATATTCAACTGC+AGG + chr1_4:15190069-15190088 Msa0152500:CDS 40.0%
GGAGGGTAAAGAAATTGGAA+AGG + chr1_4:15188118-15188137 Msa0152500:CDS 40.0%
CCAATGCTTCAAACAAAGGA+TGG - chr1_4:15188205-15188224 None:intergenic 40.0%
! CCATCCTTTGTTTGAAGCAT+TGG + chr1_4:15188202-15188221 Msa0152500:CDS 40.0%
! GGAAAGATAGTTTAGGACCA+CGG + chr1_4:15188397-15188416 Msa0152500:intron 40.0%
TATTTCTTAGGTCGGATCTG+AGG + chr1_4:15188721-15188740 Msa0152500:intron 40.0%
TTCAGAGCTTGATCACTTCA+TGG + chr1_4:15188826-15188845 Msa0152500:CDS 40.0%
!! GTACGTATGGTTTTGCATGT+GGG - chr1_4:15189405-15189424 None:intergenic 40.0%
AATACGTTGTGACGTACGTA+TGG - chr1_4:15189418-15189437 None:intergenic 40.0%
AATACGTTGTGACGTACGTA+TGG - chr1_4:15189418-15189437 None:intergenic 40.0%
GTTCATCAATCACGTCTTTG+AGG - chr1_4:15190021-15190040 None:intergenic 40.0%
TGCTACGTATATTCAACTGC+AGG + chr1_4:15190069-15190088 Msa0152500:CDS 40.0%
! GGAAAGGGAAGTGATGATGT+AGG + chr1_4:15188134-15188153 Msa0152500:CDS 45.0%
!! TGGTTTTGCATGTGGGTTGA+GGG - chr1_4:15189398-15189417 None:intergenic 45.0%
!! ATGGTTTTGCATGTGGGTTG+AGG - chr1_4:15189399-15189418 None:intergenic 45.0%
!! CGTACGTATGGTTTTGCATG+TGG - chr1_4:15189406-15189425 None:intergenic 45.0%
! GGAAAGGGAAGTGATGATGT+AGG + chr1_4:15188134-15188153 Msa0152500:CDS 45.0%
!! TGGTTTTGCATGTGGGTTGA+GGG - chr1_4:15189398-15189417 None:intergenic 45.0%
!! ATGGTTTTGCATGTGGGTTG+AGG - chr1_4:15189399-15189418 None:intergenic 45.0%
!! CGTACGTATGGTTTTGCATG+TGG - chr1_4:15189406-15189425 None:intergenic 45.0%
TGTATTCCTCATGGTGACCG+TGG - chr1_4:15188417-15188436 None:intergenic 50.0%
! TTGCATGTGGGTTGAGGGTT+CGG - chr1_4:15189393-15189412 None:intergenic 50.0%
! GACGTACGTATGGTTCTGCT+AGG - chr1_4:15189639-15189658 None:intergenic 50.0%
! CAACTGCAGGAACTTGGTGA+AGG + chr1_4:15190082-15190101 Msa0152500:CDS 50.0%
TGTATTCCTCATGGTGACCG+TGG - chr1_4:15188417-15188436 None:intergenic 50.0%
! TTGCATGTGGGTTGAGGGTT+CGG - chr1_4:15189393-15189412 None:intergenic 50.0%
! GACGTACGTATGGTTCTGCT+AGG - chr1_4:15189639-15189658 None:intergenic 50.0%
! CAACTGCAGGAACTTGGTGA+AGG + chr1_4:15190082-15190101 Msa0152500:CDS 50.0%
TTAGGACCACGGTCACCATG+AGG + chr1_4:15188408-15188427 Msa0152500:intron 55.0%
TTAGGACCACGGTCACCATG+AGG + chr1_4:15188408-15188427 Msa0152500:intron 55.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 15188116 15190114 15188116 ID=Msa0152500;Name=Msa0152500
chr1_4 mRNA 15188116 15190114 15188116 ID=Msa0152500-mRNA-1;Parent=Msa0152500;Name=Msa0152500-mRNA-1;_AED=0.03;_eAED=0.04;_QI=0|0|0|1|1|1|3|0|124
chr1_4 exon 15188116 15188250 15188116 ID=Msa0152500-mRNA-1:exon:5983;Parent=Msa0152500-mRNA-1
chr1_4 exon 15188731 15188847 15188731 ID=Msa0152500-mRNA-1:exon:5984;Parent=Msa0152500-mRNA-1
chr1_4 exon 15189992 15190114 15189992 ID=Msa0152500-mRNA-1:exon:5985;Parent=Msa0152500-mRNA-1
chr1_4 CDS 15188116 15188250 15188116 ID=Msa0152500-mRNA-1:cds;Parent=Msa0152500-mRNA-1
chr1_4 CDS 15188731 15188847 15188731 ID=Msa0152500-mRNA-1:cds;Parent=Msa0152500-mRNA-1
chr1_4 CDS 15189992 15190114 15189992 ID=Msa0152500-mRNA-1:cds;Parent=Msa0152500-mRNA-1
Gene Sequence

>Msa0152500

ATGGAGGGTAAAGAAATTGGAAAGGGAAGTGATGATGTAGGAAAAGAAAGTGAAAATGAAGAGGTTCTAAAGAAGATTATTGCAAGCCATCCTTTGTTTGAAGCATTGGTTGAGTCTCACATCAATTGTTTGAAGGTCGGATCTGAGGATGCAAAAGAGTTTGATATAACAAGTGATGCATGGAAGAAATTGGTCAACACAAAGTCCAAAACAACAACTAGTCCAAACAATTCAGAGCTTGATCACTTCATGGAAGCATTTTGCATGGCACTGAGCAACCTCAAAGACGTGATTGATGAACCAACAAAAGAAGCAAAAGCTTTCATCAATGCTACGTATATTCAACTGCAGGAACTTGGTGAAGGAAATAATTAA

Protein sequence

>Msa0152500

MEGKEIGKGSDDVGKESENEEVLKKIIASHPLFEALVESHINCLKVGSEDAKEFDITSDAWKKLVNTKSKTTTSPNNSELDHFMEAFCMALSNLKDVIDEPTKEAKAFINATYIQLQELGEGNN*