AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1467000


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1467000 MtrunA17_Chr2g0331561 94.340 53 3 0 1 53 1 53 1.23e-25 96.7
Msa1467000 MtrunA17_Chr2g0301161 76.744 43 10 0 1 43 1 43 5.17e-15 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1467000 AT1G79830.4 62.000 50 19 0 1 50 1 50 6.01e-14 63.9
Msa1467000 AT1G79830.5 62.000 50 19 0 1 50 1 50 9.51e-14 63.5
Msa1467000 AT1G79830.2 62.000 50 19 0 1 50 1 50 9.89e-14 63.2
Msa1467000 AT1G79830.3 62.000 50 19 0 1 50 1 50 9.89e-14 63.2
Msa1467000 AT1G79830.1 62.000 50 19 0 1 50 1 50 9.89e-14 63.2

Find 18 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTGTTAAATAAGATGAATT+AGG 0.210453 tig0049551:+678 Msa1467000:intergenic
ATGAAATGAATCATTGAAAA+TGG 0.231756 tig0049551:+616 Msa1467000:intergenic
ATTACCTTGTTGATTATTAC+TGG 0.242314 tig0049551:+158 Msa1467000:intergenic
TTCACAGCTCCCGCCAAATC+AGG 0.315462 tig0049551:+258 Msa1467000:intergenic
TGAATCATACGCATTCATTA+AGG 0.339601 tig0049551:-542 Msa1467000:intron
TTAGATCATGGTTATTGAAA+TGG 0.350049 tig0049551:+574 Msa1467000:intergenic
GTGTTAAATAAGATGAATTA+GGG 0.364954 tig0049551:+679 Msa1467000:intergenic
AGAAAGAATTAGAATAGCGT+TGG 0.422935 tig0049551:-800 Msa1467000:five_prime_UTR
GGGGAACTTCCCTGATTTGG+CGG 0.444852 tig0049551:-268 Msa1467000:CDS
GGGAACTTCCCTGATTTGGC+GGG 0.477952 tig0049551:-267 Msa1467000:CDS
ATTCTTTCTTTCTCACACCT+TGG 0.489528 tig0049551:+814 Msa1467000:intergenic
TCAGTGAGGAATTTAGATCA+TGG 0.525640 tig0049551:+562 Msa1467000:intergenic
ATGAATTAGGGTTACGTGTG+CGG 0.549567 tig0049551:+691 Msa1467000:intergenic
AAGTGAGAAAGCGGGAATGG+AGG 0.555691 tig0049551:+727 Msa1467000:intergenic
TCACAGCTCCCGCCAAATCA+GGG 0.577196 tig0049551:+259 Msa1467000:intergenic
GAATCCAGTAATAATCAACA+AGG 0.674976 tig0049551:-162 Msa1467000:CDS
CAACGTTTCACTCATCACCA+AGG 0.727363 tig0049551:-831 None:intergenic
TGAATGCGTATGATTCAGTG+AGG 0.740431 tig0049551:+548 Msa1466980:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATGAATATGAATTGAATT+AGG + tig0049551:501-520 Msa1467000:intergenic 15.0%
!!! AACTGTTTTTTAAATTTTTG+TGG - tig0049551:572-591 Msa1467000:five_prime_UTR 15.0%
!!! ATTGAATTTGATTGTATTTT+AGG - tig0049551:602-621 Msa1467000:five_prime_UTR 15.0%
!!! TTGAATTTGATTGTATTTTA+GGG - tig0049551:603-622 Msa1467000:five_prime_UTR 15.0%
!! GTGTTAAATAAGATGAATTA+GGG + tig0049551:308-327 Msa1467000:intergenic 20.0%
!! ACAAAAAATAAGAAGATTGT+CGG + tig0049551:348-367 Msa1467000:intergenic 20.0%
!! ATGAAATGAATCATTGAAAA+TGG + tig0049551:371-390 Msa1467000:intergenic 20.0%
!!! TAAAACATTAAATCTGAAAC+CGG + tig0049551:541-560 Msa1467000:intergenic 20.0%
!!! TGAATTTGATTGTATTTTAG+GGG - tig0049551:604-623 Msa1467000:five_prime_UTR 20.0%
! CGTGTTAAATAAGATGAATT+AGG + tig0049551:309-328 Msa1467000:intergenic 25.0%
! TTAGATCATGGTTATTGAAA+TGG + tig0049551:413-432 Msa1467000:intergenic 25.0%
!!! AGGATTAAAGTTTTGAGTTT+TGG - tig0049551:643-662 Msa1467000:five_prime_UTR 25.0%
!!! AAAGTTTTGAGTTTTGGAAT+TGG - tig0049551:649-668 Msa1467000:five_prime_UTR 25.0%
AGAAAGAATTAGAATAGCGT+TGG - tig0049551:184-203 Msa1467000:CDS 30.0%
TGAATCATACGCATTCATTA+AGG - tig0049551:442-461 Msa1467000:intron 30.0%
GTTTAATGCGAAAAATGCAT+GGG - tig0049551:695-714 Msa1467000:five_prime_UTR 30.0%
TTTAATGCGAAAAATGCATG+GGG - tig0049551:696-715 Msa1467000:five_prime_UTR 30.0%
!! AAGAATTTTGATACTGCTCT+TGG - tig0049551:780-799 Msa1467000:five_prime_UTR 30.0%
GAATCCAGTAATAATCAACA+AGG - tig0049551:822-841 Msa1467000:five_prime_UTR 30.0%
ATTCTTTCTTTCTCACACCT+TGG + tig0049551:173-192 Msa1460150:intergenic 35.0%
CTCTGCAAAAACAAAGATGA+TGG + tig0049551:223-242 Msa1467000:intergenic 35.0%
TGAGAGAAAAAGTGAGAAAG+CGG + tig0049551:269-288 Msa1467000:intergenic 35.0%
TCAGTGAGGAATTTAGATCA+TGG + tig0049551:425-444 Msa1467000:intergenic 35.0%
GGTTTAATGCGAAAAATGCA+TGG - tig0049551:694-713 Msa1467000:five_prime_UTR 35.0%
TTAATGCGAAAAATGCATGG+GGG - tig0049551:697-716 Msa1467000:five_prime_UTR 35.0%
!!! CTTGGTTTTGAAGAGAAAGA+TGG - tig0049551:798-817 Msa1467000:five_prime_UTR 35.0%
AAAAAGTGAGAAAGCGGGAA+TGG + tig0049551:263-282 Msa1467000:intergenic 40.0%
GAGAGAAAAAGTGAGAAAGC+GGG + tig0049551:268-287 Msa1467000:intergenic 40.0%
ATGAATTAGGGTTACGTGTG+CGG + tig0049551:296-315 Msa1467000:intergenic 40.0%
TGAATGCGTATGATTCAGTG+AGG + tig0049551:439-458 Msa1467000:intergenic 40.0%
!! TTCCTCTGCATTGATTGATC+CGG - tig0049551:519-538 Msa1467000:intron 40.0%
!!! GAGTTTTGGAATTGGTGTGT+AGG - tig0049551:657-676 Msa1467000:five_prime_UTR 40.0%
!!! TTGGTGTGTAGGTTTTGAGA+TGG - tig0049551:668-687 Msa1467000:five_prime_UTR 40.0%
AACCGGATCAATCAATGCAG+AGG + tig0049551:524-543 Msa1467000:intergenic 45.0%
GGGGATCTGAAAATTGTGTG+AGG - tig0049551:623-642 Msa1467000:five_prime_UTR 45.0%
!!! GTGTAGGTTTTGAGATGGCA+TGG - tig0049551:673-692 Msa1467000:five_prime_UTR 45.0%
AAGTGAGAAAGCGGGAATGG+AGG + tig0049551:260-279 Msa1467000:intergenic 50.0%
ATGGGGGAACTTCCCTGATT+TGG - tig0049551:713-732 Msa1467000:five_prime_UTR 50.0%
!! GGGGAACTTCCCTGATTTGG+CGG - tig0049551:716-735 Msa1467000:five_prime_UTR 55.0%
!! GGGAACTTCCCTGATTTGGC+GGG - tig0049551:717-736 Msa1467000:five_prime_UTR 55.0%
TCACAGCTCCCGCCAAATCA+GGG + tig0049551:728-747 Msa1467000:intergenic 55.0%
TTCACAGCTCCCGCCAAATC+AGG + tig0049551:729-748 Msa1467000:intergenic 55.0%
Chromosome Type Strat End Strand Name
tig0049551 gene 161 845 161 ID=Msa1467000;Name=Msa1467000
tig0049551 mRNA 161 845 161 ID=Msa1467000-mRNA-1;Parent=Msa1467000;Name=Msa1467000-mRNA-1;_AED=0.00;_eAED=0.00;_QI=311|1|1|1|0|0.5|2|0|53
tig0049551 exon 161 327 161 ID=Msa1467000-mRNA-1:exon:25181;Parent=Msa1467000-mRNA-1
tig0049551 exon 543 845 543 ID=Msa1467000-mRNA-1:exon:25180;Parent=Msa1467000-mRNA-1
tig0049551 five_prime_UTR 543 845 543 ID=Msa1467000-mRNA-1:five_prime_utr;Parent=Msa1467000-mRNA-1
tig0049551 five_prime_UTR 320 327 320 ID=Msa1467000-mRNA-1:five_prime_utr;Parent=Msa1467000-mRNA-1
tig0049551 CDS 161 319 161 ID=Msa1467000-mRNA-1:cds;Parent=Msa1467000-mRNA-1
Gene Sequence

>Msa1467000

ATGGCATGGTTTAATGCGAAAAATGCATGGGGGAACTTCCCTGATTTGGCGGGAGCTGTGAATAAGCTTCAAGAGAGTGTCAAGAGTATTGAGAAGAATTTTGATACTGCTCTTGGTTTTGAAGAGAAAGATGGTGAATCCAGTAATAATCAACAAGGT

Protein sequence

>Msa1467000

MAWFNAKNAWGNFPDLAGAVNKLQESVKSIEKNFDTALGFEEKDGESSNNQQG