AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1023190

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1023190 MtrunA17_Chr7g0240771 89.362 94 6 1 1 94 301 390 9.55e-53 169
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 28 sgRNAs with CRISPR-Local

Find 143 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTATATAGTCTTCAAGCTTT+AGG 0.234041 7_1:-50544131 None:intergenic
GTCTTCAAGCTTTAGGTTAA+GGG 0.268229 7_1:-50544124 None:intergenic
TCCACCTCTAATGTTGAAAA+TGG 0.300073 7_1:+50544192 Msa1023190:CDS
AGTCTTCAAGCTTTAGGTTA+AGG 0.313871 7_1:-50544125 None:intergenic
TGCTGCTGGCTGAGGCCTGC+TGG 0.319876 7_1:-50544451 None:intergenic
TTGCTCACTGCTGCTGGCTG+AGG 0.373008 7_1:-50544459 None:intergenic
AATTCATTGCTCACTGCTGC+TGG 0.394423 7_1:-50544465 None:intergenic
CTGTTGCTCCTCCAAGGCAT+AGG 0.402791 7_1:+50544385 Msa1023190:CDS
GCAGCAGCAACAATACCAGC+AGG 0.436574 7_1:+50544436 Msa1023190:CDS
TGTTGCTCCTCCAAGGCATA+GGG 0.447970 7_1:+50544386 Msa1023190:CDS
AGGGGATTTGATGTAACAAA+AGG 0.449526 7_1:+50544592 Msa1023190:three_prime_UTR
AAAGCTTGAAGACTATATAG+TGG 0.470534 7_1:+50544134 Msa1023190:CDS
ACATTATTACCCCTATGCCT+TGG 0.482077 7_1:-50544396 None:intergenic
TTATTACCCCTATGCCTTGG+AGG 0.498317 7_1:-50544393 None:intergenic
ATGATGAAAATGATATGAAA+TGG 0.513671 7_1:+50544521 Msa1023190:three_prime_UTR
AAATGGTCCTTTGATTTGCT+TGG 0.515224 7_1:+50544538 Msa1023190:three_prime_UTR
TGTAGCTTGTGCAACTGCAT+TGG 0.518913 7_1:+50544080 Msa1023190:intron
TAGCTGCTGTTGCTCCTCCA+AGG 0.520474 7_1:+50544379 Msa1023190:CDS
AAGCTTGAAGACTATATAGT+GGG 0.550779 7_1:+50544135 Msa1023190:CDS
TGCATTGGTTCCAGCTAGAG+TGG 0.566049 7_1:+50544095 Msa1023190:CDS
AATTCAAGCTTCCACAGGAG+TGG 0.580658 7_1:+50544484 Msa1023190:CDS
CAATGAATTCAAGCTTCCAC+AGG 0.583392 7_1:+50544479 Msa1023190:CDS
AATGCTACCAAGCAAATCAA+AGG 0.589835 7_1:-50544545 None:intergenic
CATCAGTACGTCCACTCCTG+TGG 0.602987 7_1:-50544495 None:intergenic
GATGCAAGTGTTGTTGCGGC+TGG 0.606152 7_1:-50544161 None:intergenic
AAACGATGCAAGTGTTGTTG+CGG 0.650274 7_1:-50544165 None:intergenic
GTTGCTCCTCCAAGGCATAG+GGG 0.664201 7_1:+50544387 Msa1023190:CDS
AGCTTGAAGACTATATAGTG+GGG 0.692039 7_1:+50544136 Msa1023190:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAATAAATACAGTTTATAA+GGG - chr7_1:50544289-50544308 None:intergenic 10.0%
!! ATAAATAAATACAGTTTATA+AGG - chr7_1:50544290-50544309 None:intergenic 10.0%
!! TAAACTGTATTTATTTATTT+CGG + chr7_1:50544292-50544311 Msa1023190:intron 10.0%
!! TAAATAAATACAGTTTATAA+GGG - chr7_1:50544289-50544308 None:intergenic 10.0%
!! ATAAATAAATACAGTTTATA+AGG - chr7_1:50544290-50544309 None:intergenic 10.0%
!! TAAACTGTATTTATTTATTT+CGG + chr7_1:50544292-50544311 Msa1023190:intron 10.0%
!! AAATTATTAAATATCACAAC+CGG - chr7_1:50543992-50544011 None:intergenic 15.0%
!! AAACTGTATTTATTTATTTC+GGG + chr7_1:50544293-50544312 Msa1023190:intron 15.0%
!! AAATTATTAAATATCACAAC+CGG - chr7_1:50543992-50544011 None:intergenic 15.0%
!! AAACTGTATTTATTTATTTC+GGG + chr7_1:50544293-50544312 Msa1023190:intron 15.0%
!! AAAATTAACATCATCATCAT+GGG - chr7_1:50543725-50543744 None:intergenic 20.0%
!!! AATGTTTTAATGCATTTAAG+AGG + chr7_1:50543797-50543816 Msa1023190:intron 20.0%
!!! ATGTTTTAATGCATTTAAGA+GGG + chr7_1:50543798-50543817 Msa1023190:intron 20.0%
!!! TTTAAAATGTTACAACACAA+TGG + chr7_1:50543847-50543866 Msa1023190:intron 20.0%
!! AACTGTATTTATTTATTTCG+GGG + chr7_1:50544294-50544313 Msa1023190:intron 20.0%
!!! TATTAAATCTTTGACTTTTG+TGG + chr7_1:50544348-50544367 Msa1023190:intron 20.0%
!! ATGATGAAAATGATATGAAA+TGG + chr7_1:50544521-50544540 Msa1023190:three_prime_UTR 20.0%
!!! AGTTTTATAGAAGAAACAAT+AGG + chr7_1:50544620-50544639 Msa1023190:three_prime_UTR 20.0%
!! AAAATTAACATCATCATCAT+GGG - chr7_1:50543725-50543744 None:intergenic 20.0%
!!! AATGTTTTAATGCATTTAAG+AGG + chr7_1:50543797-50543816 Msa1023190:intron 20.0%
!!! ATGTTTTAATGCATTTAAGA+GGG + chr7_1:50543798-50543817 Msa1023190:intron 20.0%
!!! TTTAAAATGTTACAACACAA+TGG + chr7_1:50543847-50543866 Msa1023190:intron 20.0%
!! AACTGTATTTATTTATTTCG+GGG + chr7_1:50544294-50544313 Msa1023190:intron 20.0%
!!! TATTAAATCTTTGACTTTTG+TGG + chr7_1:50544348-50544367 Msa1023190:intron 20.0%
!! ATGATGAAAATGATATGAAA+TGG + chr7_1:50544521-50544540 Msa1023190:three_prime_UTR 20.0%
!!! AGTTTTATAGAAGAAACAAT+AGG + chr7_1:50544620-50544639 Msa1023190:three_prime_UTR 20.0%
! GAAAAAAAAAAGTAATCACC+TGG - chr7_1:50543703-50543722 None:intergenic 25.0%
! CAAAATTAACATCATCATCA+TGG - chr7_1:50543726-50543745 None:intergenic 25.0%
!!! TTTTAATTGTTTTGGATGTG+TGG + chr7_1:50543965-50543984 Msa1023190:intron 25.0%
! CTACAATCACACAAAAAAAT+TGG - chr7_1:50544065-50544084 None:intergenic 25.0%
! ACTGTATTTATTTATTTCGG+GGG + chr7_1:50544295-50544314 Msa1023190:intron 25.0%
!!! AAGAAACAATAGGTCTTTTT+TGG + chr7_1:50544630-50544649 Msa1023190:three_prime_UTR 25.0%
! GAAAAAAAAAAGTAATCACC+TGG - chr7_1:50543703-50543722 None:intergenic 25.0%
! CAAAATTAACATCATCATCA+TGG - chr7_1:50543726-50543745 None:intergenic 25.0%
!!! TTTTAATTGTTTTGGATGTG+TGG + chr7_1:50543965-50543984 Msa1023190:intron 25.0%
! CTACAATCACACAAAAAAAT+TGG - chr7_1:50544065-50544084 None:intergenic 25.0%
! ACTGTATTTATTTATTTCGG+GGG + chr7_1:50544295-50544314 Msa1023190:intron 25.0%
!!! AAGAAACAATAGGTCTTTTT+TGG + chr7_1:50544630-50544649 Msa1023190:three_prime_UTR 25.0%
!!! TGTACGTTTTTTTGCGTTTT+TGG + chr7_1:50543770-50543789 Msa1023190:intron 30.0%
! TTTTAATGCATTTAAGAGGG+TGG + chr7_1:50543801-50543820 Msa1023190:intron 30.0%
CTAAGTCATAAACGAAAAAC+GGG - chr7_1:50543915-50543934 None:intergenic 30.0%
CCTAAGTCATAAACGAAAAA+CGG - chr7_1:50543916-50543935 None:intergenic 30.0%
! TTAATGTACGTTTTTGCTAC+TGG + chr7_1:50543942-50543961 Msa1023190:intron 30.0%
!!! GCTACTGGTTTTAATTGTTT+TGG + chr7_1:50543957-50543976 Msa1023190:intron 30.0%
CTATATAGTCTTCAAGCTTT+AGG - chr7_1:50544134-50544153 None:intergenic 30.0%
AAAGCTTGAAGACTATATAG+TGG + chr7_1:50544134-50544153 Msa1023190:CDS 30.0%
AAGCTTGAAGACTATATAGT+GGG + chr7_1:50544135-50544154 Msa1023190:CDS 30.0%
! AGTACCATTTTCAACATTAG+AGG - chr7_1:50544199-50544218 None:intergenic 30.0%
GGGGGTTTATTTAATCAAAA+GGG + chr7_1:50544313-50544332 Msa1023190:intron 30.0%
GGGGTTTATTTAATCAAAAG+GGG + chr7_1:50544314-50544333 Msa1023190:intron 30.0%
GGGTTTATTTAATCAAAAGG+GGG + chr7_1:50544315-50544334 Msa1023190:intron 30.0%
GGTTTATTTAATCAAAAGGG+GGG + chr7_1:50544316-50544335 Msa1023190:intron 30.0%
!! ATTTGCTTGGTAGCATTTTA+AGG + chr7_1:50544551-50544570 Msa1023190:three_prime_UTR 30.0%
!! TTTGCTTGGTAGCATTTTAA+GGG + chr7_1:50544552-50544571 Msa1023190:three_prime_UTR 30.0%
!!! TCTTTTTTGGATGAAGATGT+AGG + chr7_1:50544643-50544662 Msa1023190:three_prime_UTR 30.0%
!!! TGTACGTTTTTTTGCGTTTT+TGG + chr7_1:50543770-50543789 Msa1023190:intron 30.0%
! TTTTAATGCATTTAAGAGGG+TGG + chr7_1:50543801-50543820 Msa1023190:intron 30.0%
CTAAGTCATAAACGAAAAAC+GGG - chr7_1:50543915-50543934 None:intergenic 30.0%
CCTAAGTCATAAACGAAAAA+CGG - chr7_1:50543916-50543935 None:intergenic 30.0%
! TTAATGTACGTTTTTGCTAC+TGG + chr7_1:50543942-50543961 Msa1023190:intron 30.0%
!!! GCTACTGGTTTTAATTGTTT+TGG + chr7_1:50543957-50543976 Msa1023190:intron 30.0%
CTATATAGTCTTCAAGCTTT+AGG - chr7_1:50544134-50544153 None:intergenic 30.0%
AAAGCTTGAAGACTATATAG+TGG + chr7_1:50544134-50544153 Msa1023190:CDS 30.0%
AAGCTTGAAGACTATATAGT+GGG + chr7_1:50544135-50544154 Msa1023190:CDS 30.0%
! AGTACCATTTTCAACATTAG+AGG - chr7_1:50544199-50544218 None:intergenic 30.0%
GGGGGTTTATTTAATCAAAA+GGG + chr7_1:50544313-50544332 Msa1023190:intron 30.0%
GGGGTTTATTTAATCAAAAG+GGG + chr7_1:50544314-50544333 Msa1023190:intron 30.0%
GGGTTTATTTAATCAAAAGG+GGG + chr7_1:50544315-50544334 Msa1023190:intron 30.0%
GGTTTATTTAATCAAAAGGG+GGG + chr7_1:50544316-50544335 Msa1023190:intron 30.0%
!! ATTTGCTTGGTAGCATTTTA+AGG + chr7_1:50544551-50544570 Msa1023190:three_prime_UTR 30.0%
!! TTTGCTTGGTAGCATTTTAA+GGG + chr7_1:50544552-50544571 Msa1023190:three_prime_UTR 30.0%
!! CCGTTTTTCGTTTATGACTT+AGG + chr7_1:50543913-50543932 Msa1023190:intron 35.0%
!! GTCTTCAAGCTTTAGGTTAA+GGG - chr7_1:50544127-50544146 None:intergenic 35.0%
!! AGTCTTCAAGCTTTAGGTTA+AGG - chr7_1:50544128-50544147 None:intergenic 35.0%
AGCTTGAAGACTATATAGTG+GGG + chr7_1:50544136-50544155 Msa1023190:CDS 35.0%
TCCACCTCTAATGTTGAAAA+TGG + chr7_1:50544192-50544211 Msa1023190:CDS 35.0%
! ACCATTTTCAACATTAGAGG+TGG - chr7_1:50544196-50544215 None:intergenic 35.0%
CGGGGGTTTATTTAATCAAA+AGG + chr7_1:50544312-50544331 Msa1023190:intron 35.0%
!! AAATGGTCCTTTGATTTGCT+TGG + chr7_1:50544538-50544557 Msa1023190:three_prime_UTR 35.0%
AATGCTACCAAGCAAATCAA+AGG - chr7_1:50544548-50544567 None:intergenic 35.0%
!! TGGTAGCATTTTAAGGGATT+TGG + chr7_1:50544558-50544577 Msa1023190:three_prime_UTR 35.0%
!! GGTAGCATTTTAAGGGATTT+GGG + chr7_1:50544559-50544578 Msa1023190:three_prime_UTR 35.0%
!! GTAGCATTTTAAGGGATTTG+GGG + chr7_1:50544560-50544579 Msa1023190:three_prime_UTR 35.0%
!! TAGCATTTTAAGGGATTTGG+GGG + chr7_1:50544561-50544580 Msa1023190:three_prime_UTR 35.0%
AGGGGATTTGATGTAACAAA+AGG + chr7_1:50544592-50544611 Msa1023190:three_prime_UTR 35.0%
!! CCGTTTTTCGTTTATGACTT+AGG + chr7_1:50543913-50543932 Msa1023190:intron 35.0%
!! GTCTTCAAGCTTTAGGTTAA+GGG - chr7_1:50544127-50544146 None:intergenic 35.0%
!! AGTCTTCAAGCTTTAGGTTA+AGG - chr7_1:50544128-50544147 None:intergenic 35.0%
AGCTTGAAGACTATATAGTG+GGG + chr7_1:50544136-50544155 Msa1023190:CDS 35.0%
TCCACCTCTAATGTTGAAAA+TGG + chr7_1:50544192-50544211 Msa1023190:CDS 35.0%
! ACCATTTTCAACATTAGAGG+TGG - chr7_1:50544196-50544215 None:intergenic 35.0%
CGGGGGTTTATTTAATCAAA+AGG + chr7_1:50544312-50544331 Msa1023190:intron 35.0%
!! AAATGGTCCTTTGATTTGCT+TGG + chr7_1:50544538-50544557 Msa1023190:three_prime_UTR 35.0%
AATGCTACCAAGCAAATCAA+AGG - chr7_1:50544548-50544567 None:intergenic 35.0%
!! TGGTAGCATTTTAAGGGATT+TGG + chr7_1:50544558-50544577 Msa1023190:three_prime_UTR 35.0%
!! GGTAGCATTTTAAGGGATTT+GGG + chr7_1:50544559-50544578 Msa1023190:three_prime_UTR 35.0%
!! GTAGCATTTTAAGGGATTTG+GGG + chr7_1:50544560-50544579 Msa1023190:three_prime_UTR 35.0%
!! TAGCATTTTAAGGGATTTGG+GGG + chr7_1:50544561-50544580 Msa1023190:three_prime_UTR 35.0%
AGGGGATTTGATGTAACAAA+AGG + chr7_1:50544592-50544611 Msa1023190:three_prime_UTR 35.0%
!!! ATTGTTTTGGATGTGTGGAC+CGG + chr7_1:50543970-50543989 Msa1023190:intron 40.0%
! AAACGATGCAAGTGTTGTTG+CGG - chr7_1:50544168-50544187 None:intergenic 40.0%
ACATTATTACCCCTATGCCT+TGG - chr7_1:50544399-50544418 None:intergenic 40.0%
CAATGAATTCAAGCTTCCAC+AGG + chr7_1:50544479-50544498 Msa1023190:CDS 40.0%
!!! GGATTTGGGGGAGTATTTTA+GGG + chr7_1:50544573-50544592 Msa1023190:three_prime_UTR 40.0%
!!! GATTTGGGGGAGTATTTTAG+GGG + chr7_1:50544574-50544593 Msa1023190:three_prime_UTR 40.0%
!!! ATTGTTTTGGATGTGTGGAC+CGG + chr7_1:50543970-50543989 Msa1023190:intron 40.0%
! AAACGATGCAAGTGTTGTTG+CGG - chr7_1:50544168-50544187 None:intergenic 40.0%
ACATTATTACCCCTATGCCT+TGG - chr7_1:50544399-50544418 None:intergenic 40.0%
CAATGAATTCAAGCTTCCAC+AGG + chr7_1:50544479-50544498 Msa1023190:CDS 40.0%
!!! GGATTTGGGGGAGTATTTTA+GGG + chr7_1:50544573-50544592 Msa1023190:three_prime_UTR 40.0%
!!! GATTTGGGGGAGTATTTTAG+GGG + chr7_1:50544574-50544593 Msa1023190:three_prime_UTR 40.0%
! TGTAGCTTGTGCAACTGCAT+TGG + chr7_1:50544080-50544099 Msa1023190:intron 45.0%
TTATTACCCCTATGCCTTGG+AGG - chr7_1:50544396-50544415 None:intergenic 45.0%
AATTCATTGCTCACTGCTGC+TGG - chr7_1:50544468-50544487 None:intergenic 45.0%
AATTCAAGCTTCCACAGGAG+TGG + chr7_1:50544484-50544503 Msa1023190:CDS 45.0%
!!! GGGATTTGGGGGAGTATTTT+AGG + chr7_1:50544572-50544591 Msa1023190:three_prime_UTR 45.0%
! TGTAGCTTGTGCAACTGCAT+TGG + chr7_1:50544080-50544099 Msa1023190:intron 45.0%
TTATTACCCCTATGCCTTGG+AGG - chr7_1:50544396-50544415 None:intergenic 45.0%
AATTCATTGCTCACTGCTGC+TGG - chr7_1:50544468-50544487 None:intergenic 45.0%
AATTCAAGCTTCCACAGGAG+TGG + chr7_1:50544484-50544503 Msa1023190:CDS 45.0%
!!! GGGATTTGGGGGAGTATTTT+AGG + chr7_1:50544572-50544591 Msa1023190:three_prime_UTR 45.0%
!! TGCATTGGTTCCAGCTAGAG+TGG + chr7_1:50544095-50544114 Msa1023190:CDS 50.0%
TGTTGCTCCTCCAAGGCATA+GGG + chr7_1:50544386-50544405 Msa1023190:CDS 50.0%
!! TGCATTGGTTCCAGCTAGAG+TGG + chr7_1:50544095-50544114 Msa1023190:CDS 50.0%
TGTTGCTCCTCCAAGGCATA+GGG + chr7_1:50544386-50544405 Msa1023190:CDS 50.0%
! GATGCAAGTGTTGTTGCGGC+TGG - chr7_1:50544164-50544183 None:intergenic 55.0%
TAGCTGCTGTTGCTCCTCCA+AGG + chr7_1:50544379-50544398 Msa1023190:CDS 55.0%
CTGTTGCTCCTCCAAGGCAT+AGG + chr7_1:50544385-50544404 Msa1023190:CDS 55.0%
GTTGCTCCTCCAAGGCATAG+GGG + chr7_1:50544387-50544406 Msa1023190:CDS 55.0%
GCAGCAGCAACAATACCAGC+AGG + chr7_1:50544436-50544455 Msa1023190:CDS 55.0%
CATCAGTACGTCCACTCCTG+TGG - chr7_1:50544498-50544517 None:intergenic 55.0%
! GATGCAAGTGTTGTTGCGGC+TGG - chr7_1:50544164-50544183 None:intergenic 55.0%
TAGCTGCTGTTGCTCCTCCA+AGG + chr7_1:50544379-50544398 Msa1023190:CDS 55.0%
CTGTTGCTCCTCCAAGGCAT+AGG + chr7_1:50544385-50544404 Msa1023190:CDS 55.0%
GTTGCTCCTCCAAGGCATAG+GGG + chr7_1:50544387-50544406 Msa1023190:CDS 55.0%
GCAGCAGCAACAATACCAGC+AGG + chr7_1:50544436-50544455 Msa1023190:CDS 55.0%
CATCAGTACGTCCACTCCTG+TGG - chr7_1:50544498-50544517 None:intergenic 55.0%
! TTGCTCACTGCTGCTGGCTG+AGG - chr7_1:50544462-50544481 None:intergenic 60.0%
! TTGCTCACTGCTGCTGGCTG+AGG - chr7_1:50544462-50544481 None:intergenic 60.0%
AGGGCATGCGCCACTCTAGC+TGG - chr7_1:50544108-50544127 None:intergenic 65.0%
AGGGCATGCGCCACTCTAGC+TGG - chr7_1:50544108-50544127 None:intergenic 65.0%
! TGCTGCTGGCTGAGGCCTGC+TGG - chr7_1:50544454-50544473 None:intergenic 70.0%
! TGCTGCTGGCTGAGGCCTGC+TGG - chr7_1:50544454-50544473 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 50543685 50544665 50543685 ID=Msa1023190;Name=Msa1023190
chr7_1 mRNA 50543685 50544665 50543685 ID=Msa1023190-mRNA-1;Parent=Msa1023190;Name=Msa1023190-mRNA-1;_AED=0.04;_eAED=0.04;_QI=0|1|0.66|1|0.5|0.66|3|150|94
chr7_1 exon 50543685 50543703 50543685 ID=Msa1023190-mRNA-1:exon:9908;Parent=Msa1023190-mRNA-1
chr7_1 exon 50544085 50544213 50544085 ID=Msa1023190-mRNA-1:exon:9909;Parent=Msa1023190-mRNA-1
chr7_1 exon 50544379 50544665 50544379 ID=Msa1023190-mRNA-1:exon:9910;Parent=Msa1023190-mRNA-1
chr7_1 CDS 50543685 50543703 50543685 ID=Msa1023190-mRNA-1:cds;Parent=Msa1023190-mRNA-1
chr7_1 CDS 50544085 50544213 50544085 ID=Msa1023190-mRNA-1:cds;Parent=Msa1023190-mRNA-1
chr7_1 CDS 50544379 50544515 50544379 ID=Msa1023190-mRNA-1:cds;Parent=Msa1023190-mRNA-1
chr7_1 three_prime_UTR 50544516 50544665 50544516 ID=Msa1023190-mRNA-1:three_prime_utr;Parent=Msa1023190-mRNA-1
Gene Sequence

>Msa1023190

AATTCAACAAAAAAACCAGCTTGTGCAACTGCATTGGTTCCAGCTAGAGTGGCGCATGCCCTTAACCTAAAGCTTGAAGACTATATAGTGGGGTGCCAGCCGCAACAACACTTGCATCGTTTTAATTCCACCTCTAATGTTGAAAATGTAGCTGCTGTTGCTCCTCCAAGGCATAGGGGTAATAATGTCAATTCACAAAAGAAGCGCAGCAGCAACAATACCAGCAGGCCTCAGCCAGCAGCAGTGAGCAATGAATTCAAGCTTCCACAGGAGTGGACGTACTGA
Protein sequence

>Msa1023190

NSTKKPACATALVPARVAHALNLKLEDYIVGCQPQQHLHRFNSTSNVENVAAVAPPRHRGNNVNSQKKRSSNNTSRPQPAAVSNEFKLPQEWTY*