AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0845130

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0845130 MtrunA17_Chr5g0416431 98.925 93 1 0 1 93 1 93 7.68e-61 180
Msa0845130 MtrunA17_Chr8g0362131 79.762 84 16 1 10 93 10 92 1.71e-42 134
Msa0845130 MtrunA17_Chr7g0217141 72.826 92 24 1 1 92 1 91 8.00e-41 129
Msa0845130 MtrunA17_Chr6g0453041 69.737 76 23 0 17 92 15 90 3.68e-34 112
Msa0845130 MtrunA17_Chr3g0093001 74.026 77 18 1 17 93 17 91 3.81e-34 112
Msa0845130 MtrunA17_Chr7g0237771 45.946 74 40 0 8 81 3 76 9.86e-12 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0845130 AT1G26945.1 83.784 74 12 0 19 92 19 92 3.26e-39 125
Msa0845130 AT3G28857.1 64.894 94 30 2 1 93 1 92 3.87e-36 118
Msa0845130 AT3G47710.1 69.149 94 25 3 1 93 1 91 3.62e-35 115
Msa0845130 AT5G15160.1 73.333 75 19 1 19 92 18 92 3.39e-32 108
Msa0845130 AT1G74500.1 72.727 77 18 2 17 92 17 91 3.08e-31 105
Msa0845130 AT5G39860.1 65.385 78 26 1 17 93 15 92 1.80e-30 103

Find 47 sgRNAs with CRISPR-Local

Find 124 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATGATAATAAAATTAAATT+TGG 0.194346 5_4:+23886444 None:intergenic
GCTAGACATTGTTATAATTA+AGG 0.199410 5_4:+23886200 None:intergenic
TATCTGTGTAGGGTTTAATT+TGG 0.245749 5_4:-23885397 Msa0845130:three_prime_UTR
TGACCGATTGTCACAACTTT+TGG 0.275530 5_4:-23885570 Msa0845130:CDS
GAGCGGCTAGCGCGAAGTTC+GGG 0.276939 5_4:+23886087 None:intergenic
TTCTATAGCTATAAATAAAA+TGG 0.297131 5_4:-23885245 None:intergenic
GTGCTCAAGCAGCTATTATT+AGG 0.330670 5_4:-23885529 Msa0845130:CDS
GGAGCGGCTAGCGCGAAGTT+CGG 0.362273 5_4:+23886086 None:intergenic
GAAGTTATGTGAAATGAGTA+TGG 0.366690 5_4:+23886349 None:intergenic
GTTATTCTCTTATCTGTGTA+GGG 0.379197 5_4:-23885407 Msa0845130:three_prime_UTR
CTTATAGGTTTCAGCTACTA+AGG 0.382941 5_4:-23885651 Msa0845130:intron
TGTTATTCTCTTATCTGTGT+AGG 0.387894 5_4:-23885408 Msa0845130:three_prime_UTR
AGAGGAACCACCGGATTGTC+TGG 0.389390 5_4:+23886164 None:intergenic
GGGGATAAGTTGTTGTAACT+TGG 0.418381 5_4:+23886107 None:intergenic
GGAGGAGAGTGAAGAGGAGT+GGG 0.429020 5_4:+23886470 None:intergenic
GGTTTGTAGACCAAGGCAAA+AGG 0.461588 5_4:-23885376 Msa0845130:three_prime_UTR
AGAGAGGAAATGAGGTTGGT+TGG 0.463003 5_4:+23886297 None:intergenic
AAATAAACAAAGAGAAAGAG+AGG 0.468720 5_4:+23886281 None:intergenic
GATAATAAAATTAAATTTGG+AGG 0.476768 5_4:+23886447 None:intergenic
AGAAAGAGAGGAAATGAGGT+TGG 0.479603 5_4:+23886293 None:intergenic
GGTTGGTTGGTTGTCAGAGA+AGG 0.483101 5_4:+23886310 None:intergenic
ATAATAAAATTAAATTTGGA+GGG 0.484167 5_4:+23886448 None:intergenic
AAAGAGAAAGAGAGGAAATG+AGG 0.488212 5_4:+23886289 None:intergenic
AAGAGAGAAATAAATAAAAG+TGG 0.494133 5_4:+23886393 None:intergenic
AATAGCTGCTTGAGCACTGT+TGG 0.496664 5_4:+23885535 None:intergenic
TGTTATAATTAAGGAGGTAG+TGG 0.505098 5_4:+23886209 None:intergenic
TAAAATTAAATTTGGAGGGG+AGG 0.505190 5_4:+23886452 None:intergenic
TGTGAAATGAGTATGGAGTA+AGG 0.505231 5_4:+23886356 None:intergenic
AAGCCAAAAGTTGTGACAAT+CGG 0.524888 5_4:+23885567 None:intergenic
GTTTGTAGACCAAGGCAAAA+GGG 0.528021 5_4:-23885375 Msa0845130:three_prime_UTR
AAAATTAAACTAATTAATCA+AGG 0.530033 5_4:+23885327 None:intergenic
AGATCTCGTTCCAGACAATC+CGG 0.532260 5_4:-23886174 Msa0845130:CDS
GGGAGGAGAGTGAAGAGGAG+TGG 0.537209 5_4:+23886469 None:intergenic
TGGAGGGGAGGAGAGTGAAG+AGG 0.555226 5_4:+23886464 None:intergenic
GTGAAATGAGTATGGAGTAA+GGG 0.559416 5_4:+23886357 None:intergenic
GTTGAATTGTTGAATTGAAG+AGG 0.578890 5_4:+23886492 None:intergenic
TTAATTTGGTTTGTAGACCA+AGG 0.581266 5_4:-23885383 Msa0845130:three_prime_UTR
TAATAAAATTAAATTTGGAG+GGG 0.593264 5_4:+23886449 None:intergenic
AAATAAATACCTTGTTGGAG+CGG 0.605762 5_4:+23886070 None:intergenic
AGACATTGTTATAATTAAGG+AGG 0.612299 5_4:+23886203 None:intergenic
TCGCGCTAGCCGCTCCAACA+AGG 0.613710 5_4:-23886079 Msa0845130:intron
AGTGATCTCAGAGGAACCAC+CGG 0.628272 5_4:+23886155 None:intergenic
AGCGGCTAGCGCGAAGTTCG+GGG 0.650397 5_4:+23886088 None:intergenic
AATTAATCAAGGACTAACAA+AGG 0.658512 5_4:+23885338 None:intergenic
AATAACAATAAAGTGAGACA+AGG 0.708908 5_4:+23885424 None:intergenic
TCTCGTTCCAGACAATCCGG+TGG 0.728257 5_4:-23886171 Msa0845130:CDS
TTGAGCATCAGTGATCTCAG+AGG 0.728981 5_4:+23886146 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATAAAATTAAATTTGGA+GGG + chr5_4:23885300-23885319 None:intergenic 10.0%
!! AAAATTAAACTAATTAATCA+AGG + chr5_4:23886421-23886440 None:intergenic 10.0%
!! ATAATAAAATTAAATTTGGA+GGG + chr5_4:23885300-23885319 None:intergenic 10.0%
!! AAAATTAAACTAATTAATCA+AGG + chr5_4:23886421-23886440 None:intergenic 10.0%
!! TAATAAAATTAAATTTGGAG+GGG + chr5_4:23885299-23885318 None:intergenic 15.0%
!! GATAATAAAATTAAATTTGG+AGG + chr5_4:23885301-23885320 None:intergenic 15.0%
!!! TTTATTTTTTATGGTCTTAT+AGG - chr5_4:23886079-23886098 Msa0845130:intron 15.0%
!! TAATAAAATTAAATTTGGAG+GGG + chr5_4:23885299-23885318 None:intergenic 15.0%
!! GATAATAAAATTAAATTTGG+AGG + chr5_4:23885301-23885320 None:intergenic 15.0%
!!! TTTATTTTTTATGGTCTTAT+AGG - chr5_4:23886079-23886098 Msa0845130:intron 15.0%
!! AAGAGAGAAATAAATAAAAG+TGG + chr5_4:23885355-23885374 None:intergenic 20.0%
!! TAGAAAAATAAATACCTTGT+TGG + chr5_4:23885683-23885702 None:intergenic 20.0%
!! AAGAGAGAAATAAATAAAAG+TGG + chr5_4:23885355-23885374 None:intergenic 20.0%
!! TAGAAAAATAAATACCTTGT+TGG + chr5_4:23885683-23885702 None:intergenic 20.0%
!!! TGTTTTTTGTAATGTTGCTA+AGG + chr5_4:23885327-23885346 None:intergenic 25.0%
! AAATAAACAAAGAGAAAGAG+AGG + chr5_4:23885467-23885486 None:intergenic 25.0%
! AGACATTGTTATAATTAAGG+AGG + chr5_4:23885545-23885564 None:intergenic 25.0%
! GCTAGACATTGTTATAATTA+AGG + chr5_4:23885548-23885567 None:intergenic 25.0%
! AATAACAATAAAGTGAGACA+AGG + chr5_4:23886324-23886343 None:intergenic 25.0%
! AATTAATCAAGGACTAACAA+AGG + chr5_4:23886410-23886429 None:intergenic 25.0%
!!! TGTTTTTTGTAATGTTGCTA+AGG + chr5_4:23885327-23885346 None:intergenic 25.0%
! AAATAAACAAAGAGAAAGAG+AGG + chr5_4:23885467-23885486 None:intergenic 25.0%
! AGACATTGTTATAATTAAGG+AGG + chr5_4:23885545-23885564 None:intergenic 25.0%
! GCTAGACATTGTTATAATTA+AGG + chr5_4:23885548-23885567 None:intergenic 25.0%
! AATAACAATAAAGTGAGACA+AGG + chr5_4:23886324-23886343 None:intergenic 25.0%
! AATTAATCAAGGACTAACAA+AGG + chr5_4:23886410-23886429 None:intergenic 25.0%
GTTGAATTGTTGAATTGAAG+AGG + chr5_4:23885256-23885275 None:intergenic 30.0%
TAAAATTAAATTTGGAGGGG+AGG + chr5_4:23885296-23885315 None:intergenic 30.0%
GAAGTTATGTGAAATGAGTA+TGG + chr5_4:23885399-23885418 None:intergenic 30.0%
TGTTATAATTAAGGAGGTAG+TGG + chr5_4:23885539-23885558 None:intergenic 30.0%
AAATAAATACCTTGTTGGAG+CGG + chr5_4:23885678-23885697 None:intergenic 30.0%
ACAATACAATACACAAGTTG+TGG + chr5_4:23885940-23885959 None:intergenic 30.0%
CATAAAAAACTTGCATAGAG+AGG - chr5_4:23886139-23886158 Msa0845130:CDS 30.0%
TGTTATTCTCTTATCTGTGT+AGG - chr5_4:23886337-23886356 Msa0845130:five_prime_UTR 30.0%
GTTATTCTCTTATCTGTGTA+GGG - chr5_4:23886338-23886357 Msa0845130:five_prime_UTR 30.0%
TATCTGTGTAGGGTTTAATT+TGG - chr5_4:23886348-23886367 Msa0845130:five_prime_UTR 30.0%
!! TTAATTTGGTTTGTAGACCA+AGG - chr5_4:23886362-23886381 Msa0845130:five_prime_UTR 30.0%
GTTGAATTGTTGAATTGAAG+AGG + chr5_4:23885256-23885275 None:intergenic 30.0%
TAAAATTAAATTTGGAGGGG+AGG + chr5_4:23885296-23885315 None:intergenic 30.0%
GAAGTTATGTGAAATGAGTA+TGG + chr5_4:23885399-23885418 None:intergenic 30.0%
TGTTATAATTAAGGAGGTAG+TGG + chr5_4:23885539-23885558 None:intergenic 30.0%
AAATAAATACCTTGTTGGAG+CGG + chr5_4:23885678-23885697 None:intergenic 30.0%
ACAATACAATACACAAGTTG+TGG + chr5_4:23885940-23885959 None:intergenic 30.0%
CATAAAAAACTTGCATAGAG+AGG - chr5_4:23886139-23886158 Msa0845130:CDS 30.0%
TGTTATTCTCTTATCTGTGT+AGG - chr5_4:23886337-23886356 Msa0845130:five_prime_UTR 30.0%
GTTATTCTCTTATCTGTGTA+GGG - chr5_4:23886338-23886357 Msa0845130:five_prime_UTR 30.0%
TATCTGTGTAGGGTTTAATT+TGG - chr5_4:23886348-23886367 Msa0845130:five_prime_UTR 30.0%
!! TTAATTTGGTTTGTAGACCA+AGG - chr5_4:23886362-23886381 Msa0845130:five_prime_UTR 30.0%
GTGAAATGAGTATGGAGTAA+GGG + chr5_4:23885391-23885410 None:intergenic 35.0%
TGTGAAATGAGTATGGAGTA+AGG + chr5_4:23885392-23885411 None:intergenic 35.0%
AAAGAGAAAGAGAGGAAATG+AGG + chr5_4:23885459-23885478 None:intergenic 35.0%
! ATTTGTGAGAGTGTGTATGA+AGG + chr5_4:23885802-23885821 None:intergenic 35.0%
GATACAATGCACATATTGTG+TGG - chr5_4:23885857-23885876 Msa0845130:intron 35.0%
!! TGTGTGGACATTGTTAGTTT+TGG - chr5_4:23885873-23885892 Msa0845130:intron 35.0%
CTTATAGGTTTCAGCTACTA+AGG - chr5_4:23886094-23886113 Msa0845130:CDS 35.0%
AAGCCAAAAGTTGTGACAAT+CGG + chr5_4:23886181-23886200 None:intergenic 35.0%
GTGAAATGAGTATGGAGTAA+GGG + chr5_4:23885391-23885410 None:intergenic 35.0%
TGTGAAATGAGTATGGAGTA+AGG + chr5_4:23885392-23885411 None:intergenic 35.0%
AAAGAGAAAGAGAGGAAATG+AGG + chr5_4:23885459-23885478 None:intergenic 35.0%
! ATTTGTGAGAGTGTGTATGA+AGG + chr5_4:23885802-23885821 None:intergenic 35.0%
GATACAATGCACATATTGTG+TGG - chr5_4:23885857-23885876 Msa0845130:intron 35.0%
!! TGTGTGGACATTGTTAGTTT+TGG - chr5_4:23885873-23885892 Msa0845130:intron 35.0%
CTTATAGGTTTCAGCTACTA+AGG - chr5_4:23886094-23886113 Msa0845130:CDS 35.0%
AAGCCAAAAGTTGTGACAAT+CGG + chr5_4:23886181-23886200 None:intergenic 35.0%
AGAAAGAGAGGAAATGAGGT+TGG + chr5_4:23885455-23885474 None:intergenic 40.0%
GGGGATAAGTTGTTGTAACT+TGG + chr5_4:23885641-23885660 None:intergenic 40.0%
GTGCATGTGAATGATGACTT+GGG + chr5_4:23885826-23885845 None:intergenic 40.0%
TGTGCATGTGAATGATGACT+TGG + chr5_4:23885827-23885846 None:intergenic 40.0%
CAAGTTGTGGCAAAGAATTG+AGG + chr5_4:23885927-23885946 None:intergenic 40.0%
! TGACCGATTGTCACAACTTT+TGG - chr5_4:23886175-23886194 Msa0845130:CDS 40.0%
GTGCTCAAGCAGCTATTATT+AGG - chr5_4:23886216-23886235 Msa0845130:five_prime_UTR 40.0%
GTTTGTAGACCAAGGCAAAA+GGG - chr5_4:23886370-23886389 Msa0845130:five_prime_UTR 40.0%
! TATAGTAAGCCCTTTTGCCT+TGG + chr5_4:23886382-23886401 None:intergenic 40.0%
AGAAAGAGAGGAAATGAGGT+TGG + chr5_4:23885455-23885474 None:intergenic 40.0%
GGGGATAAGTTGTTGTAACT+TGG + chr5_4:23885641-23885660 None:intergenic 40.0%
GTGCATGTGAATGATGACTT+GGG + chr5_4:23885826-23885845 None:intergenic 40.0%
TGTGCATGTGAATGATGACT+TGG + chr5_4:23885827-23885846 None:intergenic 40.0%
CAAGTTGTGGCAAAGAATTG+AGG + chr5_4:23885927-23885946 None:intergenic 40.0%
! TGACCGATTGTCACAACTTT+TGG - chr5_4:23886175-23886194 Msa0845130:CDS 40.0%
GTGCTCAAGCAGCTATTATT+AGG - chr5_4:23886216-23886235 Msa0845130:five_prime_UTR 40.0%
GTTTGTAGACCAAGGCAAAA+GGG - chr5_4:23886370-23886389 Msa0845130:five_prime_UTR 40.0%
! TATAGTAAGCCCTTTTGCCT+TGG + chr5_4:23886382-23886401 None:intergenic 40.0%
! AGAGAGGAAATGAGGTTGGT+TGG + chr5_4:23885451-23885470 None:intergenic 45.0%
AGATCTCGTTCCAGACAATC+CGG - chr5_4:23885571-23885590 Msa0845130:CDS 45.0%
TTGAGCATCAGTGATCTCAG+AGG + chr5_4:23885602-23885621 None:intergenic 45.0%
AGCTAGTTGCAACATGCAAG+TGG - chr5_4:23886001-23886020 Msa0845130:intron 45.0%
GCTAGTTGCAACATGCAAGT+GGG - chr5_4:23886002-23886021 Msa0845130:intron 45.0%
! AATAGCTGCTTGAGCACTGT+TGG + chr5_4:23886213-23886232 None:intergenic 45.0%
GGTTTGTAGACCAAGGCAAA+AGG - chr5_4:23886369-23886388 Msa0845130:five_prime_UTR 45.0%
! AGAGAGGAAATGAGGTTGGT+TGG + chr5_4:23885451-23885470 None:intergenic 45.0%
AGATCTCGTTCCAGACAATC+CGG - chr5_4:23885571-23885590 Msa0845130:CDS 45.0%
TTGAGCATCAGTGATCTCAG+AGG + chr5_4:23885602-23885621 None:intergenic 45.0%
AGCTAGTTGCAACATGCAAG+TGG - chr5_4:23886001-23886020 Msa0845130:intron 45.0%
GCTAGTTGCAACATGCAAGT+GGG - chr5_4:23886002-23886021 Msa0845130:intron 45.0%
! AATAGCTGCTTGAGCACTGT+TGG + chr5_4:23886213-23886232 None:intergenic 45.0%
GGTTTGTAGACCAAGGCAAA+AGG - chr5_4:23886369-23886388 Msa0845130:five_prime_UTR 45.0%
!! TATGATAATAAAATTAAATT+TGG + chr5_4:23885304-23885323 None:intergenic 5.0%
!!! GTAATATTTTTTATTTTTTA+TGG - chr5_4:23886070-23886089 Msa0845130:intron 5.0%
!! TATGATAATAAAATTAAATT+TGG + chr5_4:23885304-23885323 None:intergenic 5.0%
!!! GTAATATTTTTTATTTTTTA+TGG - chr5_4:23886070-23886089 Msa0845130:intron 5.0%
! GGTTGGTTGGTTGTCAGAGA+AGG + chr5_4:23885438-23885457 None:intergenic 50.0%
AGTGATCTCAGAGGAACCAC+CGG + chr5_4:23885593-23885612 None:intergenic 50.0%
AGTTGCAACATGCAAGTGGG+TGG - chr5_4:23886005-23886024 Msa0845130:intron 50.0%
! GGTTGGTTGGTTGTCAGAGA+AGG + chr5_4:23885438-23885457 None:intergenic 50.0%
AGTGATCTCAGAGGAACCAC+CGG + chr5_4:23885593-23885612 None:intergenic 50.0%
AGTTGCAACATGCAAGTGGG+TGG - chr5_4:23886005-23886024 Msa0845130:intron 50.0%
GGAGGAGAGTGAAGAGGAGT+GGG + chr5_4:23885278-23885297 None:intergenic 55.0%
TCTCGTTCCAGACAATCCGG+TGG - chr5_4:23885574-23885593 Msa0845130:CDS 55.0%
AGAGGAACCACCGGATTGTC+TGG + chr5_4:23885584-23885603 None:intergenic 55.0%
GGAGGAGAGTGAAGAGGAGT+GGG + chr5_4:23885278-23885297 None:intergenic 55.0%
TCTCGTTCCAGACAATCCGG+TGG - chr5_4:23885574-23885593 Msa0845130:CDS 55.0%
AGAGGAACCACCGGATTGTC+TGG + chr5_4:23885584-23885603 None:intergenic 55.0%
GGGAGGAGAGTGAAGAGGAG+TGG + chr5_4:23885279-23885298 None:intergenic 60.0%
TGGAGGGGAGGAGAGTGAAG+AGG + chr5_4:23885284-23885303 None:intergenic 60.0%
GGGAGGAGAGTGAAGAGGAG+TGG + chr5_4:23885279-23885298 None:intergenic 60.0%
TGGAGGGGAGGAGAGTGAAG+AGG + chr5_4:23885284-23885303 None:intergenic 60.0%
AGCGGCTAGCGCGAAGTTCG+GGG + chr5_4:23885660-23885679 None:intergenic 65.0%
GAGCGGCTAGCGCGAAGTTC+GGG + chr5_4:23885661-23885680 None:intergenic 65.0%
GGAGCGGCTAGCGCGAAGTT+CGG + chr5_4:23885662-23885681 None:intergenic 65.0%
TCGCGCTAGCCGCTCCAACA+AGG - chr5_4:23885666-23885685 Msa0845130:intron 65.0%
AGCGGCTAGCGCGAAGTTCG+GGG + chr5_4:23885660-23885679 None:intergenic 65.0%
GAGCGGCTAGCGCGAAGTTC+GGG + chr5_4:23885661-23885680 None:intergenic 65.0%
GGAGCGGCTAGCGCGAAGTT+CGG + chr5_4:23885662-23885681 None:intergenic 65.0%
TCGCGCTAGCCGCTCCAACA+AGG - chr5_4:23885666-23885685 Msa0845130:intron 65.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 23885248 23886519 23885248 ID=Msa0845130;Name=Msa0845130
chr5_4 mRNA 23885248 23886519 23885248 ID=Msa0845130-mRNA-1;Parent=Msa0845130;Name=Msa0845130-mRNA-1;_AED=0.00;_eAED=0.00;_QI=311|1|1|1|1|1|2|266|93
chr5_4 exon 23885248 23885666 23885248 ID=Msa0845130-mRNA-1:exon:9729;Parent=Msa0845130-mRNA-1
chr5_4 exon 23886080 23886519 23886080 ID=Msa0845130-mRNA-1:exon:9728;Parent=Msa0845130-mRNA-1
chr5_4 five_prime_UTR 23886209 23886519 23886209 ID=Msa0845130-mRNA-1:five_prime_utr;Parent=Msa0845130-mRNA-1
chr5_4 CDS 23886080 23886208 23886080 ID=Msa0845130-mRNA-1:cds;Parent=Msa0845130-mRNA-1
chr5_4 CDS 23885514 23885666 23885514 ID=Msa0845130-mRNA-1:cds;Parent=Msa0845130-mRNA-1
chr5_4 three_prime_UTR 23885248 23885513 23885248 ID=Msa0845130-mRNA-1:three_prime_utr;Parent=Msa0845130-mRNA-1
Gene Sequence

>Msa0845130

ATGTCTAGCAGAAGATCTCGTTCCAGACAATCCGGTGGTTCCTCTGAGATCACTGATGCTCAAATCACTGATCTCATTTCCAAGTTACAACAACTTATCCCCGAACTTCGCGCTAGCCGCTCCAACAAGGTTTCAGCTACTAAGGTATTGCAAGAGACTTGCAACTACATAAAAAACTTGCATAGAGAGGTTGATGATTTAAGTGACCGATTGTCACAACTTTTGGCTTCTACAGATTCCAACAGTGCTCAAGCAGCTATTATTAGGAGCTTACTTATGTAA
Protein sequence

>Msa0845130

MSSRRSRSRQSGGSSEITDAQITDLISKLQQLIPELRASRSNKVSATKVLQETCNYIKNLHREVDDLSDRLSQLLASTDSNSAQAAIIRSLLM*