AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0271530


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0271530 MtrunA17_Chr2g0278341 96.907 97 3 0 1 97 1 97 4.34e-63 191
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0271530 AT1G25260.1 69.072 97 30 0 1 97 1 97 4.76e-44 144

Find 11 sgRNAs with CRISPR-Local

Find 17 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTTTGTTTCTCTTAGATTT+TGG 0.161156 2_3:-2943565 None:intergenic
ATTCGAAATTGAAAGAGTTT+AGG 0.242754 2_3:+2943804 Msa0271530:CDS
CTTTGAAACTTTGTGAAGAT+TGG 0.248050 2_3:-2943918 None:intergenic
TTCGAAATTGAAAGAGTTTA+GGG 0.248422 2_3:+2943805 Msa0271530:CDS
CACAAAGAATTGATAATTAA+TGG 0.257611 2_3:+2943719 Msa0271530:CDS
TTTGAAACTTTGTGAAGATT+GGG 0.382034 2_3:-2943917 None:intergenic
AAAGTAATGCAAGTTGCTAT+TGG 0.403753 2_3:+2943869 Msa0271530:CDS
CAATCTTCACAAAGTTTCAA+AGG 0.483461 2_3:+2943919 Msa0271530:CDS
AAAATTTCACAGTCACATTG+AGG 0.502429 2_3:+2943512 Msa0271530:five_prime_UTR
AAATTTCACAGTCACATTGA+GGG 0.552927 2_3:+2943513 Msa0271530:five_prime_UTR
AAATCTAAGAGAAACAAACA+AGG 0.734245 2_3:+2943568 Msa0271530:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTGTTTTATTTTTTTGTTG+TGG + chr2_3:2943971-2943990 Msa0271530:CDS 15.0%
!!! CACAAAGAATTGATAATTAA+TGG + chr2_3:2943719-2943738 Msa0271530:CDS 20.0%
!!! TGTTTGTTTCTCTTAGATTT+TGG - chr2_3:2943568-2943587 None:intergenic 25.0%
! AAATCTAAGAGAAACAAACA+AGG + chr2_3:2943568-2943587 Msa0271530:CDS 25.0%
! ATTCGAAATTGAAAGAGTTT+AGG + chr2_3:2943804-2943823 Msa0271530:CDS 25.0%
! TTCGAAATTGAAAGAGTTTA+GGG + chr2_3:2943805-2943824 Msa0271530:CDS 25.0%
!! TTTGAAACTTTGTGAAGATT+GGG - chr2_3:2943920-2943939 None:intergenic 25.0%
AAAATTTCACAGTCACATTG+AGG + chr2_3:2943512-2943531 Msa0271530:five_prime_UTR 30.0%
AAATTTCACAGTCACATTGA+GGG + chr2_3:2943513-2943532 Msa0271530:five_prime_UTR 30.0%
!! GATTTTGGCATTTTGAACTA+TGG - chr2_3:2943553-2943572 None:intergenic 30.0%
CTTTCAAAGACAACGAAAAA+AGG + chr2_3:2943689-2943708 Msa0271530:CDS 30.0%
!!! TCAAGTAGCAAGTTTTTTCT+TGG + chr2_3:2943839-2943858 Msa0271530:CDS 30.0%
AAAGTAATGCAAGTTGCTAT+TGG + chr2_3:2943869-2943888 Msa0271530:CDS 30.0%
!! CTTTGAAACTTTGTGAAGAT+TGG - chr2_3:2943921-2943940 None:intergenic 30.0%
CAATCTTCACAAAGTTTCAA+AGG + chr2_3:2943919-2943938 Msa0271530:CDS 30.0%
! TTTGGCATTTTGAACTATGG+AGG - chr2_3:2943550-2943569 None:intergenic 35.0%
AAGACAACGAAAAAAGGAAG+AGG + chr2_3:2943695-2943714 Msa0271530:CDS 35.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 2943503 2944018 2943503 ID=Msa0271530;Name=Msa0271530
chr2_3 mRNA 2943503 2944018 2943503 ID=Msa0271530-mRNA-1;Parent=Msa0271530;Name=Msa0271530-mRNA-1;_AED=0.03;_eAED=0.03;_QI=59|1|0.5|1|1|1|2|0|120
chr2_3 exon 2943503 2943589 2943503 ID=Msa0271530-mRNA-1:exon:1404;Parent=Msa0271530-mRNA-1
chr2_3 exon 2943684 2944018 2943684 ID=Msa0271530-mRNA-1:exon:1405;Parent=Msa0271530-mRNA-1
chr2_3 five_prime_UTR 2943503 2943561 2943503 ID=Msa0271530-mRNA-1:five_prime_utr;Parent=Msa0271530-mRNA-1
chr2_3 CDS 2943562 2943589 2943562 ID=Msa0271530-mRNA-1:cds;Parent=Msa0271530-mRNA-1
chr2_3 CDS 2943684 2944018 2943684 ID=Msa0271530-mRNA-1:cds;Parent=Msa0271530-mRNA-1
Gene Sequence

>Msa0271530

ATGCCAAAATCTAAGAGAAACAAACAAGTTACACTTTCAAAGACAACGAAAAAAGGAAGAGGTCACAAAGAATTGATAATTAATGGAATAAGAGACGCAGCTGAAAAATACAGTTCAATTTACGTTTTCAATTTTCAGAATATGAGAAATTCGAAATTGAAAGAGTTTAGGGAACAATTACAATCAAGTAGCAAGTTTTTTCTTGGATCTAACAAAGTAATGCAAGTTGCTATTGGTCGTTCTGCTTCTGATGAAATCAAACCCAATCTTCACAAAGTTTCAAAGGTTGTTTTGTCTTGCAATATCGTTCTGTTTTTTGTTTTATTTTTTTGTTGTGGATTAGAAAAATGTGATTTTGATTAG

Protein sequence

>Msa0271530

MPKSKRNKQVTLSKTTKKGRGHKELIINGIRDAAEKYSSIYVFNFQNMRNSKLKEFREQLQSSSKFFLGSNKVMQVAIGRSASDEIKPNLHKVSKVVLSCNIVLFFVLFFCCGLEKCDFD*