AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0903550


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0903550 MtrunA17_Chr6g0451941 97.351 151 4 0 1 151 1 151 7.34e-109 306
Msa0903550 MtrunA17_Chr7g0262351 33.628 113 74 1 25 137 14 125 4.56e-17 72.8
Msa0903550 MtrunA17_Chr8g0364781 34.259 108 69 1 33 138 12 119 1.16e-14 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0903550 AT5G26594.1 31.250 112 77 0 33 144 18 129 8.95e-17 72.4

Find 30 sgRNAs with CRISPR-Local

Find 130 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACCTCGGGTCCATTGATTA+TGG 0.250485 6_2:-764719 None:intergenic
AGCAATGCATTCATTGGATA+TGG 0.328332 6_2:-764544 None:intergenic
GGTCAAAGGTGTTGGGGTGC+TGG 0.364151 6_2:-765404 None:intergenic
CATCATATGCTTGAATCAAT+AGG 0.390164 6_2:+764601 Msa0903550:CDS
CTCTCTCGGGTCAAAGGTGT+TGG 0.401830 6_2:-765412 None:intergenic
TTTGATTTGCCCATAATCAA+TGG 0.409566 6_2:+764709 Msa0903550:CDS
GATCAAAATGTGCAAATGTT+TGG 0.412226 6_2:+765364 Msa0903550:CDS
CACTATGTGCAGGCTCTGTT+CGG 0.424190 6_2:-764627 None:intergenic
TCTCTCGGGTCAAAGGTGTT+GGG 0.429071 6_2:-765411 None:intergenic
ACCTCGGGTCCATTGATTAT+GGG 0.437317 6_2:-764718 None:intergenic
TCTACTAGCAATGCATTCAT+TGG 0.442738 6_2:-764550 None:intergenic
GTGAGGCAGATGCGTGCAAT+GGG 0.459873 6_2:+765301 Msa0903550:CDS
CATATGATGCTCTAAGCGTC+TGG 0.510351 6_2:-764587 None:intergenic
TGATGAACACAAAACTCTCT+CGG 0.519844 6_2:-765426 None:intergenic
ACAAAACTCTCTCGGGTCAA+AGG 0.520328 6_2:-765418 None:intergenic
ATGAATGCATTGCTAGTAGA+TGG 0.520529 6_2:+764553 Msa0903550:CDS
GATGAACACAAAACTCTCTC+GGG 0.532140 6_2:-765425 None:intergenic
CTCTCGGGTCAAAGGTGTTG+GGG 0.537212 6_2:-765410 None:intergenic
GCTTCTTGAGCACTATGTGC+AGG 0.556886 6_2:-764637 None:intergenic
AAGTTGCAATCAACAATGGA+TGG 0.566106 6_2:+764442 None:intergenic
GGGATACAGAGCAAGGTGGT+TGG 0.588650 6_2:+765322 Msa0903550:CDS
GGTGAGGCAGATGCGTGCAA+TGG 0.598157 6_2:+765300 Msa0903550:CDS
ACAATGGATGGAGGAACCAC+AGG 0.607474 6_2:+764454 None:intergenic
ATCTGCATTAGTTTCACATG+CGG 0.612322 6_2:-765462 None:intergenic
TGCAATGGGGATACAGAGCA+AGG 0.629234 6_2:+765315 Msa0903550:CDS
GCCCATAATCAATGGACCCG+AGG 0.655096 6_2:+764717 Msa0903550:CDS
TTGCAATCAACAATGGATGG+AGG 0.668830 6_2:+764445 None:intergenic
GAGGAACCACAGGATATAAG+CGG 0.671047 6_2:+764464 Msa0903550:CDS
TGAGGCAGATGCGTGCAATG+GGG 0.781176 6_2:+765302 Msa0903550:CDS
AATGGGGATACAGAGCAAGG+TGG 0.782718 6_2:+765318 Msa0903550:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAATAAATTTTTGATACCT+CGG - chr6_2:764737-764756 None:intergenic 15.0%
!!! AATATATAAGTAATTTTGTC+CGG - chr6_2:764912-764931 None:intergenic 15.0%
!! ATTACTTATATATTAATCAC+TGG + chr6_2:764918-764937 Msa0903550:intron 15.0%
!!! TAAATAAATTTTTGATACCT+CGG - chr6_2:764737-764756 None:intergenic 15.0%
!!! AATATATAAGTAATTTTGTC+CGG - chr6_2:764912-764931 None:intergenic 15.0%
!! ATTACTTATATATTAATCAC+TGG + chr6_2:764918-764937 Msa0903550:intron 15.0%
!!! AAATAAATTTTTGATACCTC+GGG - chr6_2:764736-764755 None:intergenic 20.0%
!!! AAACTAGTTAGTTTAAAATG+TGG - chr6_2:764793-764812 None:intergenic 20.0%
!!! ATATATAAGTAATTTTGTCC+GGG - chr6_2:764911-764930 None:intergenic 20.0%
!! TAAAATTGACAACTCATTTA+TGG - chr6_2:765210-765229 None:intergenic 20.0%
!!! AAATAAATTTTTGATACCTC+GGG - chr6_2:764736-764755 None:intergenic 20.0%
!!! AAACTAGTTAGTTTAAAATG+TGG - chr6_2:764793-764812 None:intergenic 20.0%
!!! ATATATAAGTAATTTTGTCC+GGG - chr6_2:764911-764930 None:intergenic 20.0%
!! TAAAATTGACAACTCATTTA+TGG - chr6_2:765210-765229 None:intergenic 20.0%
! CAGTTAATCTCATATTTAGA+CGG + chr6_2:764839-764858 Msa0903550:intron 25.0%
! ACTTATATATTAATCACTGG+CGG + chr6_2:764921-764940 Msa0903550:intron 25.0%
! TAAGATGAATTCTTATCAAC+TGG + chr6_2:764991-765010 Msa0903550:intron 25.0%
!!! GGATCTATTTTGATCATATA+TGG - chr6_2:765048-765067 None:intergenic 25.0%
!!! TTCCTAATTACTTTTGTAGT+TGG + chr6_2:765279-765298 Msa0903550:intron 25.0%
! CAGTTAATCTCATATTTAGA+CGG + chr6_2:764839-764858 Msa0903550:intron 25.0%
! ACTTATATATTAATCACTGG+CGG + chr6_2:764921-764940 Msa0903550:intron 25.0%
! TAAGATGAATTCTTATCAAC+TGG + chr6_2:764991-765010 Msa0903550:intron 25.0%
!!! GGATCTATTTTGATCATATA+TGG - chr6_2:765048-765067 None:intergenic 25.0%
!!! TTCCTAATTACTTTTGTAGT+TGG + chr6_2:765279-765298 Msa0903550:intron 25.0%
CATCATATGCTTGAATCAAT+AGG + chr6_2:764601-764620 Msa0903550:CDS 30.0%
!! TTTGATTTGCCCATAATCAA+TGG + chr6_2:764709-764728 Msa0903550:CDS 30.0%
TTAATCTCATATTTAGACGG+TGG + chr6_2:764842-764861 Msa0903550:intron 30.0%
TAATCTCATATTTAGACGGT+GGG + chr6_2:764843-764862 Msa0903550:intron 30.0%
!!! TCAACTGGACTATTTTTTGT+TGG + chr6_2:765006-765025 Msa0903550:intron 30.0%
ATCCTTTGTCATCAACTTTA+TGG + chr6_2:765064-765083 Msa0903550:intron 30.0%
!! TACCATAAAGTTGATGACAA+AGG - chr6_2:765069-765088 None:intergenic 30.0%
ATTTATGGACTTGGATTTGA+CGG - chr6_2:765195-765214 None:intergenic 30.0%
CACCAACTACAAAAGTAATT+AGG - chr6_2:765284-765303 None:intergenic 30.0%
!! AATTACTTTTGTAGTTGGTG+AGG + chr6_2:765284-765303 Msa0903550:intron 30.0%
GATCAAAATGTGCAAATGTT+TGG + chr6_2:765364-765383 Msa0903550:CDS 30.0%
CATCATATGCTTGAATCAAT+AGG + chr6_2:764601-764620 Msa0903550:CDS 30.0%
!! TTTGATTTGCCCATAATCAA+TGG + chr6_2:764709-764728 Msa0903550:CDS 30.0%
TTAATCTCATATTTAGACGG+TGG + chr6_2:764842-764861 Msa0903550:intron 30.0%
TAATCTCATATTTAGACGGT+GGG + chr6_2:764843-764862 Msa0903550:intron 30.0%
!!! TCAACTGGACTATTTTTTGT+TGG + chr6_2:765006-765025 Msa0903550:intron 30.0%
ATCCTTTGTCATCAACTTTA+TGG + chr6_2:765064-765083 Msa0903550:intron 30.0%
!! TACCATAAAGTTGATGACAA+AGG - chr6_2:765069-765088 None:intergenic 30.0%
ATTTATGGACTTGGATTTGA+CGG - chr6_2:765195-765214 None:intergenic 30.0%
CACCAACTACAAAAGTAATT+AGG - chr6_2:765284-765303 None:intergenic 30.0%
!! AATTACTTTTGTAGTTGGTG+AGG + chr6_2:765284-765303 Msa0903550:intron 30.0%
GATCAAAATGTGCAAATGTT+TGG + chr6_2:765364-765383 Msa0903550:CDS 30.0%
!!! ATCCACATTTTTTTCTCCTC+TGG - chr6_2:764499-764518 None:intergenic 35.0%
AGCAATGCATTCATTGGATA+TGG - chr6_2:764547-764566 None:intergenic 35.0%
TCTACTAGCAATGCATTCAT+TGG - chr6_2:764553-764572 None:intergenic 35.0%
ATGAATGCATTGCTAGTAGA+TGG + chr6_2:764553-764572 Msa0903550:CDS 35.0%
TCTCACGTATTTCTTTGTTC+TGG - chr6_2:764881-764900 None:intergenic 35.0%
TATCTCATAGCTGAACTATC+TGG - chr6_2:765101-765120 None:intergenic 35.0%
AATCAAACAACCTCACTTGA+TGG + chr6_2:765139-765158 Msa0903550:intron 35.0%
TGACAACTCATTTATGGACT+TGG - chr6_2:765204-765223 None:intergenic 35.0%
TGATGAACACAAAACTCTCT+CGG - chr6_2:765429-765448 None:intergenic 35.0%
!! AGAGTTTTGTGTTCATCACT+GGG + chr6_2:765431-765450 Msa0903550:CDS 35.0%
!!! ATCCACATTTTTTTCTCCTC+TGG - chr6_2:764499-764518 None:intergenic 35.0%
AGCAATGCATTCATTGGATA+TGG - chr6_2:764547-764566 None:intergenic 35.0%
TCTACTAGCAATGCATTCAT+TGG - chr6_2:764553-764572 None:intergenic 35.0%
ATGAATGCATTGCTAGTAGA+TGG + chr6_2:764553-764572 Msa0903550:CDS 35.0%
TCTCACGTATTTCTTTGTTC+TGG - chr6_2:764881-764900 None:intergenic 35.0%
TATCTCATAGCTGAACTATC+TGG - chr6_2:765101-765120 None:intergenic 35.0%
AATCAAACAACCTCACTTGA+TGG + chr6_2:765139-765158 Msa0903550:intron 35.0%
TGACAACTCATTTATGGACT+TGG - chr6_2:765204-765223 None:intergenic 35.0%
TGATGAACACAAAACTCTCT+CGG - chr6_2:765429-765448 None:intergenic 35.0%
!! AGAGTTTTGTGTTCATCACT+GGG + chr6_2:765431-765450 Msa0903550:CDS 35.0%
!! TTTTTGCCGCTTATATCCTG+TGG - chr6_2:764473-764492 None:intergenic 40.0%
AGCCAGAGGAGAAAAAAATG+TGG + chr6_2:764494-764513 Msa0903550:CDS 40.0%
! GCGATGCAAATTTTGTTGAC+TGG + chr6_2:764658-764677 Msa0903550:CDS 40.0%
ATATTTAGACGGTGGGTCTT+TGG + chr6_2:764850-764869 Msa0903550:intron 40.0%
TATTTAGACGGTGGGTCTTT+GGG + chr6_2:764851-764870 Msa0903550:intron 40.0%
GATGAACACAAAACTCTCTC+GGG - chr6_2:765428-765447 None:intergenic 40.0%
!! GAGAGTTTTGTGTTCATCAC+TGG + chr6_2:765430-765449 Msa0903550:CDS 40.0%
!! TTTTTGCCGCTTATATCCTG+TGG - chr6_2:764473-764492 None:intergenic 40.0%
AGCCAGAGGAGAAAAAAATG+TGG + chr6_2:764494-764513 Msa0903550:CDS 40.0%
! GCGATGCAAATTTTGTTGAC+TGG + chr6_2:764658-764677 Msa0903550:CDS 40.0%
ATATTTAGACGGTGGGTCTT+TGG + chr6_2:764850-764869 Msa0903550:intron 40.0%
TATTTAGACGGTGGGTCTTT+GGG + chr6_2:764851-764870 Msa0903550:intron 40.0%
GATGAACACAAAACTCTCTC+GGG - chr6_2:765428-765447 None:intergenic 40.0%
!! GAGAGTTTTGTGTTCATCAC+TGG + chr6_2:765430-765449 Msa0903550:CDS 40.0%
GAGGAACCACAGGATATAAG+CGG + chr6_2:764464-764483 Msa0903550:CDS 45.0%
TAAGCGGCAAAAAAAGCCAG+AGG + chr6_2:764480-764499 Msa0903550:CDS 45.0%
! CATATGATGCTCTAAGCGTC+TGG - chr6_2:764590-764609 None:intergenic 45.0%
! ACCTCGGGTCCATTGATTAT+GGG - chr6_2:764721-764740 None:intergenic 45.0%
! TACCTCGGGTCCATTGATTA+TGG - chr6_2:764722-764741 None:intergenic 45.0%
AATACGTGAGACTCAGATCC+CGG + chr6_2:764890-764909 Msa0903550:intron 45.0%
GTGAGTATGAAACCCATCGT+CGG - chr6_2:764957-764976 None:intergenic 45.0%
! CAAGTTGACTCCATCAAGTG+AGG - chr6_2:765152-765171 None:intergenic 45.0%
ACAAAACTCTCTCGGGTCAA+AGG - chr6_2:765421-765440 None:intergenic 45.0%
GAGGAACCACAGGATATAAG+CGG + chr6_2:764464-764483 Msa0903550:CDS 45.0%
TAAGCGGCAAAAAAAGCCAG+AGG + chr6_2:764480-764499 Msa0903550:CDS 45.0%
! CATATGATGCTCTAAGCGTC+TGG - chr6_2:764590-764609 None:intergenic 45.0%
! ACCTCGGGTCCATTGATTAT+GGG - chr6_2:764721-764740 None:intergenic 45.0%
! TACCTCGGGTCCATTGATTA+TGG - chr6_2:764722-764741 None:intergenic 45.0%
AATACGTGAGACTCAGATCC+CGG + chr6_2:764890-764909 Msa0903550:intron 45.0%
GTGAGTATGAAACCCATCGT+CGG - chr6_2:764957-764976 None:intergenic 45.0%
! CAAGTTGACTCCATCAAGTG+AGG - chr6_2:765152-765171 None:intergenic 45.0%
ACAAAACTCTCTCGGGTCAA+AGG - chr6_2:765421-765440 None:intergenic 45.0%
CACTATGTGCAGGCTCTGTT+CGG - chr6_2:764630-764649 None:intergenic 50.0%
GCTTCTTGAGCACTATGTGC+AGG - chr6_2:764640-764659 None:intergenic 50.0%
GGTATCCTCATACCGACGAT+GGG + chr6_2:764942-764961 Msa0903550:intron 50.0%
TGAAACCCATCGTCGGTATG+AGG - chr6_2:764950-764969 None:intergenic 50.0%
TGCAATGGGGATACAGAGCA+AGG + chr6_2:765315-765334 Msa0903550:CDS 50.0%
AATGGGGATACAGAGCAAGG+TGG + chr6_2:765318-765337 Msa0903550:CDS 50.0%
!! TCTCTCGGGTCAAAGGTGTT+GGG - chr6_2:765414-765433 None:intergenic 50.0%
CACTATGTGCAGGCTCTGTT+CGG - chr6_2:764630-764649 None:intergenic 50.0%
GCTTCTTGAGCACTATGTGC+AGG - chr6_2:764640-764659 None:intergenic 50.0%
GGTATCCTCATACCGACGAT+GGG + chr6_2:764942-764961 Msa0903550:intron 50.0%
TGAAACCCATCGTCGGTATG+AGG - chr6_2:764950-764969 None:intergenic 50.0%
TGCAATGGGGATACAGAGCA+AGG + chr6_2:765315-765334 Msa0903550:CDS 50.0%
AATGGGGATACAGAGCAAGG+TGG + chr6_2:765318-765337 Msa0903550:CDS 50.0%
!! TCTCTCGGGTCAAAGGTGTT+GGG - chr6_2:765414-765433 None:intergenic 50.0%
GCCCATAATCAATGGACCCG+AGG + chr6_2:764717-764736 Msa0903550:CDS 55.0%
CGGTATCCTCATACCGACGA+TGG + chr6_2:764941-764960 Msa0903550:intron 55.0%
GTGAGGCAGATGCGTGCAAT+GGG + chr6_2:765301-765320 Msa0903550:CDS 55.0%
TGAGGCAGATGCGTGCAATG+GGG + chr6_2:765302-765321 Msa0903550:CDS 55.0%
GGGATACAGAGCAAGGTGGT+TGG + chr6_2:765322-765341 Msa0903550:CDS 55.0%
!! CTCTCGGGTCAAAGGTGTTG+GGG - chr6_2:765413-765432 None:intergenic 55.0%
! CTCTCTCGGGTCAAAGGTGT+TGG - chr6_2:765415-765434 None:intergenic 55.0%
GCCCATAATCAATGGACCCG+AGG + chr6_2:764717-764736 Msa0903550:CDS 55.0%
CGGTATCCTCATACCGACGA+TGG + chr6_2:764941-764960 Msa0903550:intron 55.0%
GTGAGGCAGATGCGTGCAAT+GGG + chr6_2:765301-765320 Msa0903550:CDS 55.0%
TGAGGCAGATGCGTGCAATG+GGG + chr6_2:765302-765321 Msa0903550:CDS 55.0%
GGGATACAGAGCAAGGTGGT+TGG + chr6_2:765322-765341 Msa0903550:CDS 55.0%
!! CTCTCGGGTCAAAGGTGTTG+GGG - chr6_2:765413-765432 None:intergenic 55.0%
! CTCTCTCGGGTCAAAGGTGT+TGG - chr6_2:765415-765434 None:intergenic 55.0%
GGTGAGGCAGATGCGTGCAA+TGG + chr6_2:765300-765319 Msa0903550:CDS 60.0%
!! GGTCAAAGGTGTTGGGGTGC+TGG - chr6_2:765407-765426 None:intergenic 60.0%
GGTGAGGCAGATGCGTGCAA+TGG + chr6_2:765300-765319 Msa0903550:CDS 60.0%
!! GGTCAAAGGTGTTGGGGTGC+TGG - chr6_2:765407-765426 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 764457 765471 764457 ID=Msa0903550;Name=Msa0903550
chr6_2 mRNA 764457 765471 764457 ID=Msa0903550-mRNA-1;Parent=Msa0903550;Name=Msa0903550-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|0|0|1|1|1|2|0|151
chr6_2 exon 764457 764738 764457 ID=Msa0903550-mRNA-1:exon:302;Parent=Msa0903550-mRNA-1
chr6_2 exon 765298 765471 765298 ID=Msa0903550-mRNA-1:exon:303;Parent=Msa0903550-mRNA-1
chr6_2 CDS 764457 764738 764457 ID=Msa0903550-mRNA-1:cds;Parent=Msa0903550-mRNA-1
chr6_2 CDS 765298 765471 765298 ID=Msa0903550-mRNA-1:cds;Parent=Msa0903550-mRNA-1
Gene Sequence

>Msa0903550

ATGGATGGAGGAACCACAGGATATAAGCGGCAAAAAAAGCCAGAGGAGAAAAAAATGTGGATCAAAAAGCGTGAATTGTATGACACTCCATATCCAATGAATGCATTGCTAGTAGATGGTGTGACTGCAACCAGACGCTTAGAGCATCATATGCTTGAATCAATAGGCATCCGAACAGAGCCTGCACATAGTGCTCAAGAAGCGATGCAAATTTTGTTGACTGGTGTCAAATTTGACTTCATATTTGTTGATTTTGATTTGCCCATAATCAATGGACCCGAGTTGGTGAGGCAGATGCGTGCAATGGGGATACAGAGCAAGGTGGTTGGTATGTTAACAAACTTCAATGATCAAAATGTGCAAATGTTTGGAGAAGCAAGAGCTAATGCCAGCACCCCAACACCTTTGACCCGAGAGAGTTTTGTGTTCATCACTGGGATCTTGCGCCGCATGTGA

Protein sequence

>Msa0903550

MDGGTTGYKRQKKPEEKKMWIKKRELYDTPYPMNALLVDGVTATRRLEHHMLESIGIRTEPAHSAQEAMQILLTGVKFDFIFVDFDLPIINGPELVRQMRAMGIQSKVVGMLTNFNDQNVQMFGEARANASTPTPLTRESFVFITGILRRM*