AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0503020

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0503020 MtrunA17_Chr1g0207551 33.571 140 80 2 16 142 74 213 5.24e-20 85.1
Msa0503020 MtrunA17_Chr2g0329031 34.532 139 73 4 16 142 54 186 1.86e-16 74.7
Msa0503020 MtrunA17_Chr2g0296781 31.579 133 78 3 23 142 42 174 3.89e-14 68.2
Msa0503020 MtrunA17_Chr3g0080351 30.556 144 71 4 16 142 116 247 8.30e-13 64.3
Msa0503020 MtrunA17_Chr5g0448761 31.034 116 66 3 38 140 129 243 3.40e-12 62.8
Msa0503020 MtrunA17_Chr2g0287651 27.027 111 68 2 43 140 147 257 6.77e-12 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0503020 AT4G15090.1 34.266 143 78 3 16 142 91 233 6.80e-23 93.6
Msa0503020 AT4G15090.5 34.266 143 78 3 16 142 91 233 6.80e-23 93.6
Msa0503020 AT4G15090.3 34.266 143 78 3 16 142 91 233 6.80e-23 93.6
Msa0503020 AT4G15090.2 34.266 143 78 3 16 142 91 233 6.80e-23 93.6
Msa0503020 AT4G15090.4 34.266 143 78 3 16 142 91 233 6.80e-23 93.6
Msa0503020 AT1G76320.1 35.036 137 72 4 16 140 37 168 1.00e-16 75.9
Msa0503020 AT1G76320.4 35.036 137 72 4 16 140 37 168 1.00e-16 75.9
Msa0503020 AT1G76320.2 35.036 137 72 4 16 140 37 168 1.01e-16 75.9
Msa0503020 AT1G76320.3 35.036 137 72 4 16 140 37 168 1.06e-16 75.9
Msa0503020 AT3G22170.2 29.577 142 72 4 16 140 110 240 3.75e-14 68.6
Msa0503020 AT3G22170.1 29.577 142 72 4 16 140 110 240 3.75e-14 68.6
Msa0503020 AT4G38180.1 30.189 106 62 1 38 131 142 247 6.49e-13 65.1

Find 29 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATAAATTGCAATGGAAAA+TGG 0.239631 3_4:+45896316 Msa0503020:CDS
GAGACTTATTGATTCTTCTA+TGG 0.270224 3_4:-45896407 None:intergenic
GGCCATTGTGGCGAAAATTT+TGG 0.314750 3_4:-45896475 None:intergenic
TTCATACCCTCCATGTTGTT+TGG 0.327554 3_4:-45896496 None:intergenic
CTCTTTATGCTAAATCTGTT+GGG 0.330055 3_4:+45896177 Msa0503020:CDS
TCTCTTTATGCTAAATCTGT+TGG 0.349983 3_4:+45896176 Msa0503020:CDS
TATGCTAAATCTGTTGGGTT+TGG 0.363737 3_4:+45896182 Msa0503020:CDS
TCTTATGCTTGCACAAGATA+TGG 0.382444 3_4:+45896219 Msa0503020:CDS
TTGAAACTTTAGAACATGTT+GGG 0.425181 3_4:+45896442 Msa0503020:CDS
GGAAAATAATGTGCATATGT+TGG 0.461584 3_4:-45896381 None:intergenic
ATTGAAACTTTAGAACATGT+TGG 0.475539 3_4:+45896441 Msa0503020:CDS
TAACCCACATCCTTGTTTGA+AGG 0.485538 3_4:+45896266 Msa0503020:CDS
CGCATCAAAATAAATTGCAA+TGG 0.515633 3_4:+45896309 Msa0503020:CDS
TCTACCTTCAAACAAGGATG+TGG 0.522851 3_4:-45896270 None:intergenic
GGGAGATGCAACATCAATGT+TGG 0.546622 3_4:+45896587 Msa0503020:CDS
TTATTGATTCTTCTATGGCA+AGG 0.552372 3_4:-45896402 None:intergenic
CGTCGTTTGACATTAGAGTC+GGG 0.556413 3_4:+45896567 Msa0503020:CDS
TCCATGTTGTTTGGCCATTG+TGG 0.559258 3_4:-45896487 None:intergenic
TCGTCGTTTGACATTAGAGT+CGG 0.559689 3_4:+45896566 Msa0503020:CDS
TTGTTTGAAGGTAGATTGTG+AGG 0.582052 3_4:+45896278 Msa0503020:CDS
GCCACAATGGCCAAACAACA+TGG 0.584490 3_4:+45896486 Msa0503020:CDS
TGAAACTTTAGAACATGTTG+GGG 0.588710 3_4:+45896443 Msa0503020:CDS
CTACCTTCAAACAAGGATGT+GGG 0.609045 3_4:-45896269 None:intergenic
CATGGAGGGTATGAAAACAT+TGG 0.636187 3_4:+45896504 Msa0503020:CDS
AGGATGTGGGTTATGTGCGG+TGG 0.667999 3_4:-45896256 None:intergenic
TCACAATCTACCTTCAAACA+AGG 0.682122 3_4:-45896276 None:intergenic
CAATGGCCAAACAACATGGA+GGG 0.684081 3_4:+45896490 Msa0503020:CDS
ACAATGGCCAAACAACATGG+AGG 0.716314 3_4:+45896489 Msa0503020:CDS
ACAAGGATGTGGGTTATGTG+CGG 0.747780 3_4:-45896259 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAAATTGCAATGGAAAA+TGG + chr3_4:45896316-45896335 Msa0503020:CDS 20.0%
!!! ATTGAAACTTTAGAACATGT+TGG + chr3_4:45896441-45896460 Msa0503020:CDS 25.0%
!!! TTGAAACTTTAGAACATGTT+GGG + chr3_4:45896442-45896461 Msa0503020:CDS 25.0%
TCTCTTTATGCTAAATCTGT+TGG + chr3_4:45896176-45896195 Msa0503020:CDS 30.0%
CTCTTTATGCTAAATCTGTT+GGG + chr3_4:45896177-45896196 Msa0503020:CDS 30.0%
!!! ATTTATTTTGATGCGTAAGC+TGG - chr3_4:45896304-45896323 None:intergenic 30.0%
CGCATCAAAATAAATTGCAA+TGG + chr3_4:45896309-45896328 Msa0503020:CDS 30.0%
CATTAAAGATCACAATCATG+AGG + chr3_4:45896353-45896372 Msa0503020:intron 30.0%
GGAAAATAATGTGCATATGT+TGG - chr3_4:45896384-45896403 None:intergenic 30.0%
!! TTATTGATTCTTCTATGGCA+AGG - chr3_4:45896405-45896424 None:intergenic 30.0%
!! GAGACTTATTGATTCTTCTA+TGG - chr3_4:45896410-45896429 None:intergenic 30.0%
!! TGAAACTTTAGAACATGTTG+GGG + chr3_4:45896443-45896462 Msa0503020:CDS 30.0%
TATGCTAAATCTGTTGGGTT+TGG + chr3_4:45896182-45896201 Msa0503020:CDS 35.0%
TCTTATGCTTGCACAAGATA+TGG + chr3_4:45896219-45896238 Msa0503020:CDS 35.0%
TCACAATCTACCTTCAAACA+AGG - chr3_4:45896279-45896298 None:intergenic 35.0%
TTGTTTGAAGGTAGATTGTG+AGG + chr3_4:45896278-45896297 Msa0503020:CDS 35.0%
! AACCAAAATTTTCGCCACAA+TGG + chr3_4:45896473-45896492 Msa0503020:CDS 35.0%
! TAACCCACATCCTTGTTTGA+AGG + chr3_4:45896266-45896285 Msa0503020:CDS 40.0%
CTACCTTCAAACAAGGATGT+GGG - chr3_4:45896272-45896291 None:intergenic 40.0%
TCTACCTTCAAACAAGGATG+TGG - chr3_4:45896273-45896292 None:intergenic 40.0%
TTCATACCCTCCATGTTGTT+TGG - chr3_4:45896499-45896518 None:intergenic 40.0%
! CATGGAGGGTATGAAAACAT+TGG + chr3_4:45896504-45896523 Msa0503020:CDS 40.0%
TCGTCGTTTGACATTAGAGT+CGG + chr3_4:45896566-45896585 Msa0503020:CDS 40.0%
! ACAAGGATGTGGGTTATGTG+CGG - chr3_4:45896262-45896281 None:intergenic 45.0%
! GGCCATTGTGGCGAAAATTT+TGG - chr3_4:45896478-45896497 None:intergenic 45.0%
! TCCATGTTGTTTGGCCATTG+TGG - chr3_4:45896490-45896509 None:intergenic 45.0%
ACAATGGCCAAACAACATGG+AGG + chr3_4:45896489-45896508 Msa0503020:CDS 45.0%
CAATGGCCAAACAACATGGA+GGG + chr3_4:45896490-45896509 Msa0503020:CDS 45.0%
CGTCGTTTGACATTAGAGTC+GGG + chr3_4:45896567-45896586 Msa0503020:CDS 45.0%
GGGAGATGCAACATCAATGT+TGG + chr3_4:45896587-45896606 Msa0503020:CDS 45.0%
GCCACAATGGCCAAACAACA+TGG + chr3_4:45896486-45896505 Msa0503020:CDS 50.0%
! AGGATGTGGGTTATGTGCGG+TGG - chr3_4:45896259-45896278 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 45896159 45896617 45896159 ID=Msa0503020;Name=Msa0503020
chr3_4 mRNA 45896159 45896617 45896159 ID=Msa0503020-mRNA-1;Parent=Msa0503020;Name=Msa0503020-mRNA-1;_AED=0.12;_eAED=0.23;_QI=0|0|0|1|0|0|2|0|142
chr3_4 exon 45896159 45896341 45896159 ID=Msa0503020-mRNA-1:exon:9829;Parent=Msa0503020-mRNA-1
chr3_4 exon 45896375 45896617 45896375 ID=Msa0503020-mRNA-1:exon:9830;Parent=Msa0503020-mRNA-1
chr3_4 CDS 45896159 45896341 45896159 ID=Msa0503020-mRNA-1:cds;Parent=Msa0503020-mRNA-1
chr3_4 CDS 45896375 45896617 45896375 ID=Msa0503020-mRNA-1:cds;Parent=Msa0503020-mRNA-1
Gene Sequence

>Msa0503020

ATGCATACTCATTCTACTCTCTTTATGCTAAATCTGTTGGGTTTGGAATTTATTGATGTGTCTTATGCTTGCACAAGATATGGAAAAAAGAGAGCATCCACCGCACATAACCCACATCCTTGTTTGAAGGTAGATTGTGAGGCCAGCTTACGCATCAAAATAAATTGCAATGGAAAATGGATTGTTTTTCCAACATATGCACATTATTTTCCTTGCCATAGAAGAATCAATAAGTCTCAAAAGAACTGTATTGAAACTTTAGAACATGTTGGGGTGAAAACAACCAAAATTTTCGCCACAATGGCCAAACAACATGGAGGGTATGAAAACATTGGCTACTTTGAGAAAGACATTAGAAATCATTTAGATAAAAGTCGTCGTTTGACATTAGAGTCGGGAGATGCAACATCAATGTTGGAGTGTTTT
Protein sequence

>Msa0503020

MHTHSTLFMLNLLGLEFIDVSYACTRYGKKRASTAHNPHPCLKVDCEASLRIKINCNGKWIVFPTYAHYFPCHRRINKSQKNCIETLEHVGVKTTKIFATMAKQHGGYENIGYFEKDIRNHLDKSRRLTLESGDATSMLECF