AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1400690


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1400690 MtrunA17_Chr7g0262501 99.074 108 0 1 1 108 1 107 9.39e-74 214
Msa1400690 MtrunA17_Chr1g0183081 92.784 97 7 0 3 99 7 103 8.28e-65 191
Msa1400690 MtrunA17_Chr1g0188281 56.842 95 41 0 1 95 38 132 6.34e-38 124
Msa1400690 MtrunA17_Chr6g0476661 55.789 95 42 0 1 95 4 98 1.22e-37 122
Msa1400690 MtrunA17_Chr6g0476721 47.674 86 45 0 7 92 40 125 7.11e-25 90.9
Msa1400690 MtrunA17_Chr5g0394191 44.706 85 47 0 7 91 9 93 6.13e-23 85.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1400690 AT3G04300.1 67.368 95 31 0 5 99 1 95 6.44e-46 143
Msa1400690 AT4G28703.1 63.366 101 28 1 6 97 7 107 2.27e-41 132
Msa1400690 AT4G10300.1 61.538 91 35 0 5 95 44 134 9.30e-40 129
Msa1400690 AT4G10280.1 36.559 93 56 1 7 96 48 140 7.32e-18 73.9
Msa1400690 AT4G10290.1 34.343 99 62 1 7 102 20 118 2.64e-13 61.6

Find 22 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTCTGAAGCCATGAGGTTT+TGG 0.241413 tig0022476:-8021 None:intergenic
TTACATGCAATGTGGGATTT+TGG 0.280274 tig0022476:-7942 None:intergenic
AATTTCAATTGGTACTTTCC+TGG 0.284978 tig0022476:-8243 None:intergenic
CAAGTACAACTGAGTCCTTT+TGG 0.330475 tig0022476:-8369 None:intergenic
CAAAAGGACTCAGTTGTACT+TGG 0.347089 tig0022476:+8370 Msa1400690:CDS
CTGAGAAGGGTTTCTTTCAA+TGG 0.378765 tig0022476:-8053 None:intergenic
CTTCTGCATCAAATTTCAAT+TGG 0.414470 tig0022476:-8254 None:intergenic
AAAAGATGGGGTTGTTCTCC+AGG 0.417937 tig0022476:+8225 Msa1400690:intron
AAACATGTTATTTATTGAAA+GGG 0.428832 tig0022476:+8277 Msa1400690:CDS
GAAACATGTTATTTATTGAA+AGG 0.444821 tig0022476:+8276 Msa1400690:CDS
AAAGTGAAAGCATACACAAA+AGG 0.467313 tig0022476:+8300 Msa1400690:CDS
TTCTTTCAATGGTGATTCGA+AGG 0.500926 tig0022476:-8042 None:intergenic
CAGCTAAACGTGACTGAGAA+GGG 0.513726 tig0022476:-8066 None:intergenic
GACCTTGTCACCATTCCAAA+AGG 0.519526 tig0022476:+8354 Msa1400690:CDS
AAGTGAAAGCATACACAAAA+GGG 0.539574 tig0022476:+8301 Msa1400690:CDS
GTTCTCTTCCCAAAACCTCA+TGG 0.549774 tig0022476:+8012 Msa1400690:exon
ATTAATAGTAATTAACAAGA+TGG 0.549911 tig0022476:-8462 None:intergenic
CTGAATTGAACATCAAGTGC+TGG 0.553924 tig0022476:+8086 Msa1400690:CDS
TCAGCTAAACGTGACTGAGA+AGG 0.572317 tig0022476:-8067 None:intergenic
AAAAGGACTCAGTTGTACTT+GGG 0.580307 tig0022476:+8371 Msa1400690:CDS
TTATCTCTTCTTCATGTCAG+AGG 0.585717 tig0022476:-8575 None:intergenic
TTCGAAGGTCTGAAGCCATG+AGG 0.682433 tig0022476:-8027 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAACATGTTATTTATTGAAA+GGG + tig0022476:8277-8296 Msa1400690:CDS 15.0%
!! ATTAATAGTAATTAACAAGA+TGG - tig0022476:8465-8484 None:intergenic 15.0%
!! TTAAGAAAGAATACATACTT+GGG - tig0022476:8112-8131 None:intergenic 20.0%
!! ATTAAGAAAGAATACATACT+TGG - tig0022476:8113-8132 None:intergenic 20.0%
!!! TTTTTGCATTAATCTAACAA+AGG + tig0022476:8163-8182 Msa1400690:intron 20.0%
!!! GAAACATGTTATTTATTGAA+AGG + tig0022476:8276-8295 Msa1400690:CDS 20.0%
!!! TTTTTTGTTACATGCAATGT+GGG - tig0022476:7952-7971 None:intergenic 25.0%
!!! TTTTTTTGTTACATGCAATG+TGG - tig0022476:7953-7972 None:intergenic 25.0%
GGGGTGTAAAAATAAAAGAT+GGG + tig0022476:8212-8231 Msa1400690:intron 30.0%
GGGTGTAAAAATAAAAGATG+GGG + tig0022476:8213-8232 Msa1400690:intron 30.0%
AATTTCAATTGGTACTTTCC+TGG - tig0022476:8246-8265 None:intergenic 30.0%
CTTCTGCATCAAATTTCAAT+TGG - tig0022476:8257-8276 None:intergenic 30.0%
! AAAGTGAAAGCATACACAAA+AGG + tig0022476:8300-8319 Msa1400690:CDS 30.0%
! AAGTGAAAGCATACACAAAA+GGG + tig0022476:8301-8320 Msa1400690:CDS 30.0%
! TCATCAGATTTTGTAGAGTT+TGG + tig0022476:8324-8343 Msa1400690:CDS 30.0%
TTCTTTCAATGGTGATTCGA+AGG - tig0022476:8045-8064 None:intergenic 35.0%
!!! GGTCCTTTTGTTTTGTAATG+TGG + tig0022476:8184-8203 Msa1400690:intron 35.0%
CAGCCACATTACAAAACAAA+AGG - tig0022476:8190-8209 None:intergenic 35.0%
!!! TTTGTTTTGTAATGTGGCTG+TGG + tig0022476:8190-8209 Msa1400690:intron 35.0%
!! TTGTTTTGTAATGTGGCTGT+GGG + tig0022476:8191-8210 Msa1400690:intron 35.0%
! GGGGGTGTAAAAATAAAAGA+TGG + tig0022476:8211-8230 Msa1400690:intron 35.0%
AAAAGGACTCAGTTGTACTT+GGG + tig0022476:8371-8390 Msa1400690:CDS 35.0%
CTGAGAAGGGTTTCTTTCAA+TGG - tig0022476:8056-8075 None:intergenic 40.0%
CTGAATTGAACATCAAGTGC+TGG + tig0022476:8086-8105 Msa1400690:CDS 40.0%
! TGTTTTGTAATGTGGCTGTG+GGG + tig0022476:8192-8211 Msa1400690:intron 40.0%
!! GATTTTGTAGAGTTTGGAGC+TGG + tig0022476:8330-8349 Msa1400690:CDS 40.0%
!! ACAACTGAGTCCTTTTGGAA+TGG - tig0022476:8367-8386 None:intergenic 40.0%
! CAAGTACAACTGAGTCCTTT+TGG - tig0022476:8372-8391 None:intergenic 40.0%
CAAAAGGACTCAGTTGTACT+TGG + tig0022476:8370-8389 Msa1400690:CDS 40.0%
GTTCTCTTCCCAAAACCTCA+TGG + tig0022476:8012-8031 Msa1400690:exon 45.0%
!! GTCTGAAGCCATGAGGTTTT+GGG - tig0022476:8023-8042 None:intergenic 45.0%
CAGCTAAACGTGACTGAGAA+GGG - tig0022476:8069-8088 None:intergenic 45.0%
TCAGCTAAACGTGACTGAGA+AGG - tig0022476:8070-8089 None:intergenic 45.0%
! GTTTTGTAATGTGGCTGTGG+GGG + tig0022476:8193-8212 Msa1400690:intron 45.0%
AAAAGATGGGGTTGTTCTCC+AGG + tig0022476:8225-8244 Msa1400690:intron 45.0%
GACCTTGTCACCATTCCAAA+AGG + tig0022476:8354-8373 Msa1400690:CDS 45.0%
!!! GTCCTTTTGGAATGGTGACA+AGG - tig0022476:8359-8378 None:intergenic 45.0%
!! GGTCTGAAGCCATGAGGTTT+TGG - tig0022476:8024-8043 None:intergenic 50.0%
! TTCGAAGGTCTGAAGCCATG+AGG - tig0022476:8030-8049 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0022476 gene 7943 8596 7943 ID=Msa1400690;Name=Msa1400690
tig0022476 mRNA 7943 8596 7943 ID=Msa1400690-mRNA-1;Parent=Msa1400690;Name=Msa1400690-mRNA-1;_AED=0.01;_eAED=0.01;_QI=88|1|1|1|1|1|2|123|108
tig0022476 exon 7943 8113 7943 ID=Msa1400690-mRNA-1:exon:17806;Parent=Msa1400690-mRNA-1
tig0022476 exon 8230 8596 8230 ID=Msa1400690-mRNA-1:exon:17807;Parent=Msa1400690-mRNA-1
tig0022476 five_prime_UTR 7943 8030 7943 ID=Msa1400690-mRNA-1:five_prime_utr;Parent=Msa1400690-mRNA-1
tig0022476 CDS 8031 8113 8031 ID=Msa1400690-mRNA-1:cds;Parent=Msa1400690-mRNA-1
tig0022476 CDS 8230 8473 8230 ID=Msa1400690-mRNA-1:cds;Parent=Msa1400690-mRNA-1
tig0022476 three_prime_UTR 8474 8596 8474 ID=Msa1400690-mRNA-1:three_prime_utr;Parent=Msa1400690-mRNA-1
Gene Sequence

>Msa1400690

ATGGCTTCAGACCTTCGAATCACCATTGAAAGAAACCCTTCTCAGTCACGTTTAGCTGAATTGAACATCAAGTGCTGGCCCAAATGGGGTTGTTCTCCAGGAAAGTACCAATTGAAATTTGATGCAGAAGAAACATGTTATTTATTGAAAGGGAAAGTGAAAGCATACACAAAAGGGTCATCAGATTTTGTAGAGTTTGGAGCTGGAGACCTTGTCACCATTCCAAAAGGACTCAGTTGTACTTGGGATGTTTCTGTAGCTGTTGACAAGTACTACAAATTTGAATCATCTTCTTCTTCATCATCATCATCTTCACCATCTTGTTAA

Protein sequence

>Msa1400690

MASDLRITIERNPSQSRLAELNIKCWPKWGCSPGKYQLKFDAEETCYLLKGKVKAYTKGSSDFVEFGAGDLVTIPKGLSCTWDVSVAVDKYYKFESSSSSSSSSSPSC*